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Sporulation is the last-ditch response to starvation; it is suppressed until alternative responses prove inadequate.
Learning Objectives
• Explain sporulation in Bacillus
Key Points
• B. subtilis can divide symmetrically to make two daughter cells (binary fission), or asymmetrically, producing a single endospore that is resistant to environmental factors such as heat, desiccation, radiation, and chemical insult which can persist in the environment for long periods of time.
• The process of endospore formation has profound morphological and physiological consequences: radical post-replicative remodelling of two progeny cells, accompanied eventually by cessation of metabolic activity in one daughter cell (the spore ) and death by lysis of the other (the ‘mother cell’).
• Sporulation in B. subtilis is induced by starvation; the sporulation developmental program is not initiated immediately when growth slows due to nutrient limitation.
Key Terms
• endospore: A dormant, tough, and non-reproductive structure produced by certain bacteria from the Firmicute phylum.
• sporulation: The process of a bacterium becoming a spore.
Bacillus subtilis is a rod-shaped, Gram-postive bacteria that is naturally found in soil and vegetation. It is known for its ability to form a small, tough, protective, and metabolically dormant endospore. B. subtilis can divide symmetrically to make two daughter cells (binary fission), or asymmetrically, producing a single endospore that is resistant to environmental factors such as heat, desiccation, radiation, and chemical insult which can persist in the environment for long periods of time. The endospore is formed at times of nutritional stress, allowing the organism to persist in the environment until conditions become favourable. The process of endospore formation has profound morphological and physiological consequences: radical post-replicative remodeling of two progeny cells, accompanied eventually by cessation of metabolic activity in one daughter cell (the spore) and death by lysis of the other (the ‘mother cell’).
Although sporulation inB. subtilis is induced by starvation, the sporulation developmental program is not initiated immediately when growth slows due to nutrient limitation. A variety of alternative responses can occur:
• The activation of flagellar motility to seek new food sources by chemotaxis
• The production of antibiotics to destroy competing soil microbes
• The secretion of hydrolytic enzymes to scavenge extracellular proteins and polysaccharides, or the induction of ‘competence’ for uptake of exogenous DNA for consumption, with the occasional side-effect that new genetic information is stably integrated.
Sporulation is a last-ditch response to starvation, and it is suppressed until alternative responses prove inadequate. Even then, certain conditions must be met, such as chromosome integrity, the state of chromosomal replication, and the functioning of the Krebs cycle.
Sporulation requires a great deal of time and energy, and it is essentially irreversible, making it crucial for a cell to monitor its surroundings efficiently and ensure that sporulation is embarked upon at only the most appropriate times. The wrong decision can be catastrophic: a vegetative cell will die if the conditions are too harsh, while bacteria-forming spores in an environment which is conducive to vegetative growth will be outcompeted. In short, initiation of sporulation is a very tightly regulated network with numerous checkpoints for efficient control.
Two transcriptional regulators, σH and Spo0A, play key roles in initiation of sporulation. Several additional proteins participate, mainly by controlling the accumulated concentration of Spo0A~P. Spo0A lies at the end of a series of inter-protein phosphotransfer reactions, Kin–Spo0F–Spo0B–Spo0A, termed as a ‘phosphorelay’. | textbooks/bio/Microbiology/Microbiology_(Boundless)/07%3A_Microbial_Genetics/7.20%3A_Developmental_Regulation/7.20A%3A__Sporulation_in_Bacillus.txt |
A Caulobacter is used for studying the regulation of the cell cycle, asymmetric cell division, and cellular differentiation.
LEARNING OBJECTIVES
Explain how caulobacter serve as a model organism
Key Points
• The Caulobacter cell cycle regulatory system controls many modular subsystems that organize the progression of cell growth and reproduction.
• The central feature of the cell cycle regulation is a cyclical genetic circuit—a cell cycle engine –- that is centered around the successive interactions of four master regulatory proteins: DnaA, GcrA, CtrA, and CcrM.
• The interactions of four master regulatory proteins: DnaA, GcrA, CtrA, and CcrM directly control the timing of expression of over 200 genes. The four master regulatory proteins are synthesized and then eliminated from the cell one after the other over the course of the cell cycle.
Key Terms
• senescence: Ceasing to divide by mitosis because of shortening of telomeres or excessive DNA damage.
• differentiation: In cellular differentiation, a less specialized cell becomes a more specialized cell.
• modular: Consisting of separate modules; especially where each module performs or fulfills some specified function and could be replaced by a similar module for the same function, independently of the other modules.
Caulobacter crescentus is a Gram-negative, oligotrophic bacterium widely distributed in fresh water lakes and streams. Caulobacter is an important model organism for studying the regulation of the cell cycle, asymmetric cell division, and cellular differentiation. Caulobacter daughter cells have two very different forms. One daughter is a mobile “swarmer” cell that has a single flagellum at one cell pole that provides swimming motility for chemotaxis. The other daughter, called the “stalked” cell has a tubular stalk structure protruding from one pole that has an adhesive holdfast material on its end, with which the stalked cell can adhere to surfaces. Swarmer cells differentiate into stalked cells after a short period of motility. Chromosome replication and cell division only occurs in the stalked cell stage. Its name is due to the fact that it forms a crescent shape; crescentin is a protein that imparts this shape.
In the laboratory, researchers distinguish between C. crescentusstrain CB15 (the strain originally isolated from a freshwater lake) and NA1000 (the primary experimental strain). In strain NA1000, which was derived from CB15 in the 1970’s, the stalked and predivisional cells can be physically separated in the laboratory from new swarmer cells, while cell types from strain CB15 cannot be physically separated. The isolated swarmer cells can then be grown as a synchronized cell culture. Detailed study of the molecular development of these cells as they progress through the cell cycle has enabled researchers to understand Caulobacter cell cycle regulation in great detail. Due to this capacity to be physically synchronized, strain NA1000 has become the predominant experimental Caulobacter strain throughout the world. Additional phenotypic differences between the two strains have subsequently accumulated due to selective pressures on the NA1000 strain in the laboratory environment. The genetic basis of the phenotypic differences between the two strains results from coding, regulatory, and insertion/deletion polymorphisms at five chromosomal loci. “C. Crescentus” is synonymous with “Caulobacter Vibrioides. ”
The Caulobacter cell cycle regulatory system controls many modular subsystems that organize the progression of cell growth and reproduction. A control system constructed using biochemical and genetic logic circuitry organizes the timing of initiation of each of these subsystems. The central feature of the cell cycle regulation is a cyclical genetic circuit—a cell cycle engine –- that is centered around the successive interactions of four master regulatory proteins: DnaA, GcrA, CtrA, and CcrM. These four proteins directly control the timing of expression of over 200 genes. The four master regulatory proteins are synthesized and then eliminated from the cell one after the other over the course of the cell cycle. Several additional cell signaling pathways are also essential to the proper functioning of this cell cycle engine.
The principal role of these signaling pathways is to ensure reliable production and elimination of the CtrA protein from the cell at just the right times in the cell cycle. An essential feature of the Caulobacter cell cycle is that the chromosome is replicated once and only once per cell cycle. This is in contrast to the E. coli cell cycle where there can be overlapping rounds of chromosome replication simultaneously underway. The opposing roles of the Caulobacter DnaA and CtrA proteins are essential to the tight control of Caulobacter chromosome replication. The DnaA protein acts at the origin of replication to initiate the replication of the chromosome. The CtrA protein, in contrast, acts to block initiation of replication, so it must be removed from the cell before chromosome replication can begin. Multiple additional regulatory pathways integral to cell cycle regulation and involving both phospho signaling pathways and regulated control of protein proteolysis act to assure that DnaA and CtrA are present in the cell exactly when they are needed.
Caulobacter was the first asymmetric bacterium shown to age. Reproductive senescence was measured as the decline in the number of progeny produced over time. A similar phenomenon has since been described in the bacterium Escherichia coli, which gives rise to morphologically similar daughter cells.
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Chemotaxis is the phenomenon whereby bacterial cells direct their movements according to certain chemicals in their environment.
LEARNING OBJECTIVES
Explain how chemotaxis works in bacteria that have flagella
Key Points
• Chemoattractants and chemorepellents are inorganic or organic substances possessing chemotaxis -inducer effect in motile cells.
• Some bacteria, such as E. coli, have several flagella that can rotate to facilitate chemotaxis.
• The overall movement of a bacterium is the result of alternating tumble and swim phases.
Key Terms
• chemotaxis: Chemotaxis is the phenomenon whereby somatic cells, bacteria, and other single-cell or multicellular organisms direct their movements in response to certain chemicals in their environment.
• flagella: A flagellum is a lash-like appendage that protrudes from the cell body of certain prokaryotic and eukaryotic cells.
• movement: Physical motion between points in space.
Chemotaxis is the phenomenon whereby somatic cells, bacteria, and other single-cell or multicellular organisms direct their movements according to certain chemicals in their environment. This is important for bacteria to find food (for example, glucose) by swimming towards the highest concentration of food molecules, or to flee from poisons (for example, phenol).
Positive chemotaxis occurs if the movement is toward a higher concentration of the chemical in question. Conversely, negative chemotaxis occurs if the movement is in the opposite direction.
Chemoattractants and chemorepellents are inorganic or organic substances possessing chemotaxis-inducer effect in motile cells. Effects of chemoattractants are elicited via described or hypothetic chemotaxis receptors; the chemoattractant moiety of a ligand is target cell specific and concentration dependent. Most frequently investigated chemoattractants are formyl peptides and chemokines. Responses to chemorepellents result in axial swimming and they are considered a basic motile phenomena in bacteria. The most frequently investigated chemorepellents are inorganic salts, amino acids and some chemokines.
Some bacteria, such as E. coli, have several flagella per cell (4–10 typically). These can rotate in two ways:
1. Counter-clockwise rotation – aligns the flagella into a single rotating bundle, causing the bacterium to swim in a straight line.
2. Clockwise rotation – breaks the flagella bundle apart such that each flagellum points in a different direction, causing the bacterium to tumble in place.
The directions of rotation are given for an observer outside the cell looking down the flagella toward the cell.
Overall movements in bacterium
This is the result of alternating tumble and swim phases. If one watches a bacterium swimming in a uniform environment, its movement will look like a random walk with relatively straight swims interrupted by random tumbles that reorient it. Bacteria such as E. coli are unable to choose the direction in which they swim, and are unable to swim in a straight line for more than a few seconds due to rotational diffusion: they “forget” the direction in which they are going. By repeatedly evaluating their course, and adjusting if they are moving in the wrong direction, bacteria can direct their motion to find favorable locations with high concentrations of attractants (usually food) and avoid repellents (usually poisons).
In the presence of a chemical gradient bacteria will chemotax, or direct their overall motion based on the gradient. If the bacterium senses that it is moving in the correct direction (toward attractant/away from repellent), it will keep swimming in a straight line for a longer time before tumbling. If it is moving in the wrong direction, it will tumble sooner and try a new direction at random. In other words, bacteria like E. coli use temporal sensing to decide whether their situation is improving or not. In this way, it finds the location with the highest concentration of attractant (usually the source) quite well. Even under very high concentrations, it can still distinguish very small differences in concentration. Fleeing from a repellent works with the same efficiency.
Purposeful random walk
This is a result of simply choosing between two methods of random movement; namely tumbling and straight swimming. In fact, chemotactic responses such as forgetting direction and choosing movements resemble the decision-making abilities of higher life-forms with brains that process sensory data.
The helical nature of the individual flagellar filament is critical for this movement to occur. As such, the protein that makes up the flagellar filament, flagellin, is quite similar among all flagellated bacteria. Vertebrates seem to have taken advantage of this fact by possessing an immune receptor (TLR5) designed to recognize this conserved protein.
As in many instances in biology, there are bacteria that do not follow this rule. Many bacteria, such as Vibrio, are monoflagellated and have a single flagellum at one pole of the cell. Their method of chemotaxis is different. Others possess a single flagellum that is kept inside the cell wall. These bacteria move by spinning the whole cell, which is shaped like a corkscrew.
Signal transduction in bacteria
The proteins CheW and CheA bind to the receptor. The activation of the receptor by an external stimulus causes autophosphorylation in the histidine kinase, CheA, at a single highly-conserved histidine residue. CheA in turn transfers phosphoryl groups to conserved aspartate residues in the response regulators CheB and CheY [note: CheA is a histidine kinase and it does not actively transfer the phosphoryl group. The response regulator CheB takes the phosphoryl group from CheA]. This mechanism of signal transduction is called a two-component system and is a common form of signal transduction in bacteria.
CheY induces tumbling by interacting with the flagellar switch protein FliM, inducing a change from counter-clockwise to clockwise rotation of the flagellum. Change in the rotation state of a single flagellum can disrupt the entire flagella bundle and cause a tumble. | textbooks/bio/Microbiology/Microbiology_(Boundless)/07%3A_Microbial_Genetics/7.21%3A_Sensing_and_Signal_Transduction/7.21A%3A__Chemotaxis.txt |
Two-component systems couple mechanism to allow organisms to sense and respond to changes in many different environmental conditions.
LEARNING OBJECTIVES
Describe the structure and function of a bacterial two-component regulatory system
Key Points
• Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions.
• Signal transduction can occur through the transfer of phosphoryl groups from adenosine triphosphate ( ATP ) to a specific histidine residue in the histidine kinases (HK).
• A variant of the two-component system is the phospho-relay system.
Key Terms
• Two-component systems: Two-component systems serve as a basic stimulus-response coupling mechanism to allow organisms to sense and respond to changes in many different environmental conditions. They typically consist of a membrane-bound histidine kinase that senses a specific environmental stimulus and a corresponding response regulator that mediates the cellular response, mostly through differential expression of target genes.
• Signal transduction: Signal transduction occurs when an extracellular signaling molecule activates a cell surface receptor. In turn, this receptor alters intracellular molecules creating a response.
• histidine kinase: Histidine Kinases (HK) are multifunctional, typically transmembrane, proteins of the transferase class that play a role in signal transduction across the cellular membrane.
Two-Component Systems
In molecular biology, two-component systems serve as a basic stimulus-response coupling mechanism allowing organisms to sense and respond to changes in many different environmental conditions. They typically consist of a membrane -bound histidine kinase that senses a specific environmental stimulus and a corresponding response regulator that mediates the cellular response. Two component signaling systems are widely occurring in prokaryotes whereas only a few two-component systems have been identified in eukaryotic organisms.
Signal transduction occurs through the transfer of phosphoryl groups from adenosine triphosphate (ATP) to a specific histidine residue in the histidine kinases (HK). This is an autophosphorylation reaction. Subsequently the histidine kinase catalyzes the transfer of the phosphate group on the phosphorylated histidine residues to an aspartic acid residue on the response regulator (RR). Phosphorylation causes the response regulator’s conformation to change, usually activating an attached output domain, which then leads to the stimulation (or repression) of expression of target genes. The level of phosphorylation of the response regulator controls its activity. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK.
Two-component signal transduction systems enable bacteria to sense, respond and adapt to a wide range of environments, stressors and growth conditions. Some bacteria can contain as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk. These pathways have been adapted to respond to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, temperature, chemoattractants, pH and more. In E. coli the EnvZ/OmpR osmoregulation system controls the differential expression of the outer membrane porin proteins OmpF and OmpC. The KdpD sensor kinase proteins regulate the kdpFABC operon responsible for potassium transport in bacteria including E. coli and Clostridium acetobutylicum. The N-terminal domain of this protein forms part of the cytoplasmic region of the protein, which may be the sensor domain responsible for sensing turgor pressure.
System Variants
A variant of the two-component system is the phospho-relay system. Here a hybrid HK autophosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response.
Signal transducing histidine kinases are the key elements in two-component signal transduction systems. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation, and CheA, which plays a central role in the chemotaxis system. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes ) the phosphotransfer from aspartyl phosphate back to ADP or to water. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily.
HKs can be roughly divided into two classes: orthodox and hybrid kinases. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain.
The Hpr Serine/threonine kinase PtsK is the sensor in a multicomponent phosphorelay system in control of carbon catabolic repression in bacteria. This kinase is unusual in that it recognizes the tertiary structure of its target and is a member of a novel family unrelated to any previously described protein phosphorylating enzymes. X-ray analysis of the full-length crystalline enzyme from Staphylococcus xylosus at a resolution of 1.95 A shows the enzyme to consist of two clearly separated domains that are assembled in a hexameric structure resembling a three-bladed propeller. The blades are formed by two N-terminal domains each, and the compact central hub assembles the C-terminal kinase domains. | textbooks/bio/Microbiology/Microbiology_(Boundless)/07%3A_Microbial_Genetics/7.21%3A_Sensing_and_Signal_Transduction/7.21B%3A__Two-Component_Regulatory_Systems.txt |
Quorum sensing is a system of stimulus and response correlated to population density.
LEARNING OBJECTIVES
Explain the mechanism of quorum sensing in bacteria
Key Points
• Some of the best-known examples of quorum sensing come from studies of bacteria.
• Bacteria use quorum sensing to coordinate certain behaviors based on the local density of the bacterial population.
• Bacteria that use quorum sensing constitutively produce and secrete certain signaling molecules (called autoinducers or pheromones).
Key Terms
• quorum sensing: Quorum sensing is a system of stimulus and response correlated to population density. Many species of bacteria use quorum sensing to coordinate gene expression according to the density of their local population.
• density: A measure of the amount of matter contained by a given volume.
• population: A collection of organisms of a particular species, sharing a particular characteristic of interest, most often that of living in a given area.
Quorum sensing is a system of stimulus and response correlated to population density. Many species of bacteria use quorum sensing to coordinate gene expression according to the density of their local population. In similar fashion, some social insects use quorum sensing to determine where to nest. In addition to its function in biological systems, quorum sensing has several useful applications for computing and robotics.
Quorum sensing can function as a decision-making process in any decentralized system, as long as individual components have: (a) a means of assessing the number of other components they interact with and (b) a standard response once a threshold number of components is detected.
Quorum sensing may be achieved by degrading the signalling molecule. Using a KG medium, quorum quenching bacteria can be readily isolated from various environments including that which has previously been considered as unculturable. Recently, a well-studied quorum quenching bacterium has been isolated and its AHL degradation kinetic has been studied by using rapid resolution liquid chromatography (RRLC).
Some of the best-known examples of quorum sensing come from studies of bacteria. Bacteria use quorum sensing to coordinate certain behaviors based on the local density of the bacterial population. Quorum sensing can occur within a single bacterial species as well as between diverse species, and can regulate a host of different processes, in essence, serving as a simple communication network. A variety of different molecules can be used as signals. Common classes of signaling molecules are oligopeptides in Gram-positive bacteria, N-Acyl Homoserine Lactones (AHL) in Gram-negative bacteria, and a family of autoinducers known as autoinducer-2 (AI-2) in both Gram-negative and Gram-positive bacteria.
Bacteria that use quorum sensing constitutively produce and secrete certain signaling molecules (called autoinducers or pheromones). These bacteria also have a receptor that can specifically detect the signaling molecule (inducer). When the inducer binds the receptor, it activates transcription of certain genes, including those for inducer synthesis. There is a low likelihood of a bacterium detecting its own secreted inducer. Thus, in order for gene transcription to be activated, the cell must encounter signaling molecules secreted by other cells in its environment. When only a few other bacteria of the same kind are in the vicinity, diffusion reduces the concentration of the inducer in the surrounding medium to almost zero, so the bacteria produce little inducer. However, as the population grows, the concentration of the inducer passes a threshold, causing more inducer to be synthesized. This forms a positive feedback loop, and the receptor becomes fully activated. Activation of the receptor induces the up-regulation of other specific genes, causing all of the cells to begin transcription at approximately the same time. This coordinated behavior of bacterial cells can be useful in a variety of situations. For instance, the bioluminescent luciferase produced by Vibriofischeri would not be visible if it were produced by a single cell. By using quorum sensing to limit the production of luciferase to situations when cell populations are large, V. fischeri cells are able to avoid wasting energy on the production of useless product.
Three-dimensional structures of proteins involved in quorum sensing were first published in 2001, when the crystal structures of three LuxS orthologs were determined by X-ray crystallography. In 2002, the crystal structure of the receptor LuxP of Vibrio harveyi with its inducer AI-2 (which is one of the few biomolecules containing boron) bound to it was also determined. Many bacterial species, including E. coli, an enteric bacterium and model organism for Gram-negative bacteria, produce AI-2. A comparative genomic and phylogenetic analysis of 138 genomes of bacteria, archaea, and eukaryotes found that “the LuxS enzyme required for AI-2 synthesis is widespread in bacteria, while the periplasmic binding protein LuxP is present only in Vibrio strains,” leading to the conclusion that either “other organisms may use components different from the AI-2 signal transduction system of Vibrio strains to sense the signal of AI-2 or they do not have such a quorum sensing system at all. ” Certain bacteria can produce enzymes called lactonases that can target and inactivate AHLs. | textbooks/bio/Microbiology/Microbiology_(Boundless)/07%3A_Microbial_Genetics/7.21%3A_Sensing_and_Signal_Transduction/7.21C%3A_Quorum_Sensing.txt |
Transcription and translation in archaea resemble these processes in eukaryotes more than in bacteria.
LEARNING OBJECTIVES
Compare the archaea with bacteria and eukaryotes in terms of their general mechanisms of gene expression
Key Points
• The proteins that archaea, bacteria and eukaryotes share form a common core of cell function, relating mostly to transcription, translation, and nucleotide metabolism.
• The archaean RNA polymerase and ribosomes are very close to their equivalents in eukaryotes.
• However, other archaean transcription factors are closer to those found in bacteria.
Key Terms
• archaea: a taxonomic domain of single-celled organisms lacking nuclei that are fundamentally different from bacteria.
• transcription: Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes.
• eukaryotes: A eukaryote is an organism whose cells contain complex structures enclosed within membranes. Eukaryotes may more formally be referred to as the taxon Eukarya or Eukaryota. The defining membrane-bound structure that sets eukaryotic cells apart from prokaryotic cells is the nucleus, or nuclear envelope, within which the genetic material is carried.
The Archaea constitute a domain of single-celled microorganisms. These microbes have no cell nucleus or any other membrane-bound organelles within their cells.
Archaea are genetically distinct from bacteria and eukaryotes, with up to 15% of the proteins encoded by any one archaeal genome being unique to the domain, even though most of these unique genes have no known function. Of the remainder of the unique proteins that have an identified function, most belong to the Euryarchaea and are involved in methanogenesis. The proteins that archaea, bacteria and eukaryotes share form a common core of cell function, relating mostly to transcription, translation, and nucleotide metabolism. Other characteristic archaean features are the organization of genes of related function—such as enzymes that catalyze steps in the same metabolic pathway into novel operons, and large differences in tRNA genes and their aminoacyl tRNA synthetases.
Transcription and translation in archaea resemble these processes in eukaryotes more than in bacteria, with the archaean RNA polymerase and ribosomes being very close to their equivalents in eukaryotes. Although archaea only have one type of RNA polymerase, its structure and function in transcription seems to be close to that of the eukaryotic RNA polymerase II, with similar protein assemblies (the general transcription factors) directing the binding of the RNA polymerase to a gene’s promoter. However, other archaean transcription factors are closer to those found in bacteria. Post-transcriptional modification is simpler than in eukaryotes, since most archaean genes lack introns, although there are many introns in their transfer RNA and ribosomal RNA genes, and introns may occur in a few protein-encoding genes.
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Learning Objectives
• Define the transcriptome
The transcriptome is the set of all RNA molecules, including mRNA, rRNA, tRNA, and other non-coding RNA produced in one or a population of cells. The term can be applied to the total set of transcripts in a given organism, or to the specific subset of transcripts present in a particular cell type. Unlike the genome, which is roughly fixed for a given cell line (excluding mutations), the transcriptome can vary with external environmental conditions. Because it includes all mRNA transcripts in the cell, the transcriptome reflects the genes that are being actively expressed at any given time, with the exception of mRNA degradation phenomena such as transcriptional attenuation.
Analysis of the Transcriptome
The study of transcriptomics, also referred to as expression profiling, examines the expression level of mRNAs in a given cell population, often using high-throughput techniques based on DNA microarray technology. A number of organism-specific transcriptome databases have been constructed and annotated to aid in the identification of genes that are differentially expressed in distinct cell populations.
DNA microarrays can provide a genome-wide method for comparison of the abundance of DNAs in the same samples.The DNA in spots can only be PCR products specific for individual genes. A DNA copy of RNA is made using the enzyme reverse transcriptase. Sequencing is now being used instead of gene arrays to quantify DNA levels, at least semi-quantitatively.
The transcriptomes of stem cells and cancer cells are of particular interest to researchers who seek to understand the processes of cellular differentiation and carcinogenesis. Analysis of the transcriptomes of human oocytes and embryos is used to understand the molecular mechanisms and signaling pathways controlling early embryonic development, and could theoretically be a powerful tool in making proper embryo selection during in vitro fertilization.
Key Points
• Unlike the genome, which is roughly fixed for a given cell line (excluding mutations), the transcriptome can vary with external environmental conditions.
• The transcriptome reflects the genes that are being actively expressed at any given time.
• DNA microarrays can provide a method for comparing on a genome-wide basis the abundance of DNAs in a specific sample.
Key Terms
• transcriptome: The complete set of messenger RNA molecules (transcripts) produced in a cell or a population of cells.
• DNA microarray: a collection of microscopic DNA spots attached to a solid surface forming an array; used to measure the expression levels of large numbers of genes simultaneously
• PCR: polymerase chain reaction
7.22B: Proteomics
Learning Objectives
• Summarize the purpose of, and methods used for, proteomics
Proteomics is the large-scale study of proteins, particularly their structures and functions. The proteome is the entire complement of proteins, including the modifications made to a particular set of proteins, produced by an organism or system. This will vary with time and distinct requirements, or stresses, that a cell or organism undergoes.
While proteomics generally refers to the large-scale experimental analysis of proteins, it is often specifically used for protein purification and mass spectrometry. After genomics and transcriptomics, proteomics is considered the next step in the study of biological systems. It is much more complicated than genomics mostly because while an organism’s genome is more or less constant, the proteome differs from cell to cell and from time to time. This is because distinct genes are expressed in distinct cell types. This means that even the basic set of proteins which are produced in a cell needs to be determined. In the past, this was done by mRNA analysis, but this was found not to correlate with protein content. It is now known that mRNA is not always translated into protein. The amount of protein produced for a given amount of mRNA depends on the gene it is transcribed from and the current physiological state of the cell.
Proteomics confirms the presence of the protein and provides a direct measure of the quantity present. Not only does the translation from mRNA cause differences, but many proteins are also subjected to a wide variety of chemical modifications after translation which are critical to the protein’s function such as phosphorylation, ubiquitination, methylation, acetylation, glycosylation, oxidation, and nitrosylation. Some proteins undergo ALL of these modifications, often in time-dependent combinations, aptly illustrating the potential complexity one has to deal with when studying protein structure and function.
Proteomics typically gives us a better understanding of an organism than genomics. First, the level of transcription of a gene gives only a rough estimate of its level of expression into a protein. An mRNA produced in abundance may be degraded rapidly or translated inefficiently, resulting in a small amount of protein. Second, as mentioned above many proteins experience post-translational modifications that profoundly affect their activities. For example, some proteins are not active until they become phosphorylated. Third, many transcripts give rise to more than one protein through alternative splicing or alternative post-translational modifications. Fourth, many proteins form complexes with other proteins or RNA molecules. They only function in the presence of these other molecules. Finally, protein degradation rate plays an important role in protein content.
One way in which a particular protein can be studied is to develop an antibody which is specific to that modification. For example, there are antibodies that only recognize certain proteins when they are tyrosine-phosphorylated, known as phospho-specific antibodies. There are also antibodies specific to other modifications. These can be used to determine the set of proteins that have undergone the modification of interest. For more quantitative determinations of protein amounts, techniques such as ELISAs can be used.
Most proteins function in collaboration with other proteins. One goal of proteomics is to identify which proteins interact. This is especially useful in determining potential partners in cell signaling cascades. Several methods are available to probe protein–protein interactions. The traditional method is yeast two-hybrid analysis. New methods include protein microarrays, immunoaffinity, and chromatography followed by mass spectrometry, dual polarisation interferometry, Microscale Thermophoresis, and experimental methods such as phage display and computational methods.
One of the most promising developments to come from the study of human genes and proteins has been the identification of potential new drugs for the treatment of disease. This relies on genome and proteome information to identify proteins associated with a disease, which computer software can then use as targets for new drugs. For example, if a certain protein is implicated in a disease, its 3-D structure provides the information to design drugs to interfere with the action of the protein. A molecule that fits the active site of an enzyme, but cannot be released by the enzyme, will inactivate the enzyme. Understanding the proteome, the structure and function of each protein and the complexities of protein–protein interactions will be critical for developing the most effective diagnostic techniques and disease treatments in the future. Moreover, an interesting use of proteomics is using specific protein biomarkers to diagnose disease. A number of techniques allow testing for proteins produced during a particular disease, which helps to diagnose the disease quickly.
Key Points
• The proteome is the entire complement of proteins, including the modifications made to a particular set of proteins, produced by an organism or system.
• The proteome varies with time and distinct requirements, or stresses, that a cell or organism undergoes.
• Proteomics typically gives us a better understanding of an organism than genomics.
Key Terms
• proteomics: The branch of molecular biology that studies the set of proteins expressed by the genome of an organism.
• genomics: The study of the complete genome of an organism.
• mass spectrometry: An analytical technique that measures the mass/charge ratio of the ions formed when a molecule or atom is ionized, vaporized, and introduced into a vacuum. Mass spectrometry may also involve breaking molecules into fragments – thus enabling its structure to be determined. | textbooks/bio/Microbiology/Microbiology_(Boundless)/07%3A_Microbial_Genetics/7.22%3A_Genomics_and_Proteomics/7.22A%3A_Microarrays_and_the_Transcriptome.txt |
Learning Objectives
• Review metabolomics
Metabolomics is the scientific study of chemical processes involving metabolites. The metabolome represents the collection of all metabolites, which are the end products of cellular processes, in a biological cell, tissue, organ, or organism. Thus, while mRNA gene expression data and proteomic analyses do not tell the whole story of what might be happening in a cell, metabolic profiling can give an instantaneous snapshot of the physiology of that cell. One of the challenges of systems biology and functional genomics is to integrate proteomic, transcriptomic, and metabolomic information to give a more complete picture of living organisms.
History and Development
The idea that biological fluids reflect the health of an individual has existed for a long time. The term “metabolic profile” was introduced by Horning, et al. in 1971, after they demonstrated that gas chromatography- mass spectrometry (GC-MS; ) could be used to measure compounds present in human urine and tissue extracts. GC-MS is a method that combines the features of gas-liquid chromatography and mass spectrometry to identify different substances within a test sample. Concurrently, NMR spectroscopy, which was discovered in the 1940s, was also undergoing rapid advances. In 1974, Seeley et al. demonstrated the utility of using NMR to detect metabolites in unmodified biological samples. This first study on muscle tissue highlighted the value of NMR, in that it was determined that 90% of cellular ATP is complexed with magnesium. As sensitivity has improved with the evolution of higher magnetic field strengths and magic-angle spinning, NMR continues to be a leading analytical tool to investigate metabolism.
In 2005, the first metabolomics web database for characterizing human metabolites, METLIN, was developed in the Siuzdak laboratory at The Scripps Research Institute. METLIN contained over 10,000 metabolites and tandem mass spectral data. On January 23, 2007, the Human Metabolome Project, led by Dr. David Wishart of the University of Alberta, Canada, completed the first draft of the human metabolome, consisting of a database of approximately 2500 metabolites, 1200 drugs and 3500 food components.
As late as mid-2010, metabolomics was still considered an “emerging field”. Further, it was noted that further progress in the field was in large part the result of addressing otherwise “irresolvable technical challenges” through technical evolution of mass spectrometry instrumentation. The word was coined in analogy with transcriptomics and proteomics. Like the transcriptome and the proteome, the metabolome is dynamic, changing from second to second. Although the metabolome can be defined readily enough, it is not currently possible to analyse the entire range of metabolites by a single analytical method.
Metabolites are the intermediates and products of metabolism. Within the context of metabolomics, a metabolite is usually defined as any molecule less than 1 kDa in size. However, there are exceptions to this, depending on the sample and detection method. Macromolecules such as lipoproteins and albumin are reliably detected in NMR-based metabolomics studies of blood plasma. In plant-based metabolomics, it is common to refer to “primary metabolites,” which are directly involved in growth, development and reproduction, and “secondary metabolites,” which are indirectly involved in growth, development and reproduction. In contrast, in human-based metabolomics it is more common to describe metabolites as being either endogenous (produced by the host organism) or exogenous. The metabolome forms a large network of metabolic reactions, where outputs from one enzymatic chemical reaction are inputs to other chemical reactions. Such systems have been described as hypercycles.
Separation methods: Gas chromatography, especially when interfaced with mass spectrometry (GC-MS), is one of the most widely used and powerful methods. It offers very high chromatographic resolution, but requires chemical derivatization for many biomolecules: only volatile chemicals can be analysed without derivatization.
Detection methods: Mass spectrometry (MS) is used to identify and to quantify metabolites after separation. Surface-based mass analysis has seen a resurgence in the past decade, with new MS technologies focused on increasing sensitivity, minimizing background, and reducing sample preparation.
Statistical methods: The data generated in metabolomics usually consist of measurements performed on subjects under various conditions. These measurements may be digitized spectra, or a list of metabolite levels. In its simplest form this generates a matrix with rows corresponding to subjects and columns corresponding to metabolite levels.
Key applications
• Toxicity assessment/toxicology. Metabolic profiling, especially of urine or blood plasma samples, can be used to detect the physiological changes caused by toxic insult of a chemical or mixture of chemicals. This is of particular relevance to pharmaceutical companies wanting to test the toxicity of potential drug candidates.
• Functional genomics. Metabolomics can be an excellent tool for determining the phenotype caused by a genetic manipulation, such as gene deletion or insertion. Sometimes this can be a sufficient goal in itself—for instance, to detect any phenotypic changes in a genetically-modified plant intended for human or animal consumption. More exciting is the prospect of predicting the function of unknown genes by comparison with the metabolic perturbations caused by deletion/insertion of known genes.
Key Points
• The metabolome represents the collection of all metabolites in a biological cell, tissue, organ or organism, which are the end products of cellular processes.
• Metabolites are the intermediates and products of metabolism.
• The metabolome forms a large network of metabolic reactions, where outputs from one enzymatic chemical reaction are inputs to other chemical reactions.
• NMR and Mass Spectroscopy are the most widely used techniques to identify metabolites.
Key Terms
• metabolomics: The study of the range of metabolites present in a person’s body at normal times, and when suffering from specific diseases; may be useful as a diagnostic tool
• mass spectrometry: An analytical technique that measures the mass/charge ratio of the ions formed when a molecule or atom is ionized, vaporized, and introduced into a vacuum. Mass spectrometry may also involve breaking molecules into fragments – thus enabling its structure to be determined.
• metabolite: Any substance produced by, or taking part in, a metabolic reaction.
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Biotechnology is the use of biological techniques and engineered organisms to make products or plants and animals that have desired traits.
Learning Objectives
• Describe the historical development of biotechnology
Key Points
• For thousands of years, humankind has used biotechnology in agriculture, food production, and medicine.
• In the late 20th and early 21st century, biotechnology has expanded to include new and diverse sciences such as genomics, recombinant gene technologies, applied immunology, and development of pharmaceutical therapies and diganostic tests.
• Biotechnology has applications in four major industrial areas, including health care (medical), crop production and agriculture, non food (industrial) uses of crops and other products (e.g. biodegradable plastics, vegetable oil, biofuels), and environmental uses.
Key Terms
• nanotechnology: the science and technology of creating nanoparticles and of manufacturing machines which have sizes within the range of nanometres
People have used biotechnology processes, such as selectively breeding animals and fermentation, for thousands of years. Late 19th and early 20thcentury discoveries of how microorganisms carry out commercially useful processes and how they cause disease led to the commercial production of vaccines and antibiotics. Improved methods for animal breeding have also resulted from these efforts. Scientists in the San Francisco Bay Area took a giant step forward with the discovery and development of recombinant DNA techniques in the 1970s. The field of biotechnology continues to accelerate with new discoveries and new applications expected to benefit the economy throughout the 21st century.
In its broadest definition, biotechnology is the application of biological techniques and engineered organisms to make products or modify plants and animals to carry desired traits. This definition also extends to the use of various human cells and other body parts to produce desirable products. Bioindustry refers to the cluster of companies that produce engineered biological products and their supporting businesses. Biotechnology refers to the use of the biological sciences (such as gene manipulation), often in combination with other sciences (such as materials sciences, nanotechnology, and computer software), to discover, evaluate and develop products for bioindustry. Biotechnology products have made it easier to detect and diagnose illnesses. Many of these new techniques are easier to use and some, such as pregnancy testing, can even be used at home. More than 400 clinical diagnostic devices using biotechnology products are in use today. The most important are screening techniques to protect the blood supply against contamination by AIDS and the hepatitis B and C viruses.
7.23B: Applications of Genetic Engineering
Genetic engineering means the manipulation of organisms to make useful products and it has broad applications.
Learning Objectives
• Describe the major applications of genetic engineering
Key Points
• Genetic engineering has applications in medicine, research, industry and agriculture and can be used on a wide range of plants, animals and microorganisms.
• In medicine, genetic engineering has been used to mass-produce insulin, human growth hormones, follistim (for treating infertility), human albumin, monoclonal antibodies, antihemophilic factors, vaccines, and many other drugs.
• In research, organisms are genetically engineered to discover the functions of certain genes.
• Industrial applications include transforming microorganisms such as bacteria or yeast, or insect mammalian cells with a gene coding for a useful protein. Mass quantities of the protein can be produced by growing the transformed organism in bioreactors using fermentation, then purifying the protein.
• Genetic engineering is also used in agriculture to create genetically-modified crops or genetically-modified organisms.
Key Terms
• biotechnology: The use of living organisms (especially microorganisms) in industrial, agricultural, medical, and other technological applications.
• cloning: The production of a cloned embryo by transplanting the nucleus of a somatic cell into an ovum.
Genetic engineering, also called genetic modification, is the direct manipulation of an organism’s genome using biotechnology.
New DNA may be inserted in the host genome by first isolating and copying the genetic material of interest, using molecular-cloning methods to generate a DNA sequence; or by synthesizing the DNA, and then inserting this construct into the host organism. Genes may be removed, or “knocked out”, using a nuclease.
Gene targeting is a different technique that uses homologous recombination to change an endogenous gene, and can be used to delete a gene, remove exons, add a gene, or introduce point mutations. Genetic engineering has applications in medicine, research, industry and agriculture and can be used on a wide range of plants, animals and microorganisms.
Genetic engineering has produced a variety of drugs and hormones for medical use. For example, one of its earliest uses in pharmaceuticals was gene splicing to manufacture large amounts of insulin, made using cells of E. coli bacteria. Interferon, which is used to eliminate certain viruses and kill cancer cells, also is a product of genetic engineering, as are tissue plasminogen activator and urokinase, which are used to dissolve blood clots.
Another byproduct is a type of human growth hormone; it’s used to treat dwarfism and is produced through genetically-engineered bacteria and yeasts. The evolving field of gene therapy involves manipulating human genes to treat or cure genetic diseases and disorders. Modified plasmids or viruses often are the messengers to deliver genetic material to the body’s cells, resulting in the production of substances that should correct the illness. Sometimes cells are genetically altered inside the body; other times scientists modify them in the laboratory and return them to the patient’s body.
Since the 1990s, gene therapy has been used in clinical trials to treat diseases and conditions such as AIDS, cystic fibrosis, cancer, and high cholesterol. Drawbacks of gene therapy are that sometimes the person’s immune system destroys the cells that have been genetically altered, and also that it is hard to get the genetic material into enough cells to have the desired effect. | textbooks/bio/Microbiology/Microbiology_(Boundless)/07%3A_Microbial_Genetics/7.23%3A_Genetic_Engineering_Products/7.23A%3A__Overview_of_Biotechnology.txt |
Many practical applications of recombinant DNA are found in human and veterinary medicine, in agriculture, and in bioengineering.
Learning Objectives
• Describe the advances made possible by recombinant DNA technology
Key Points
• Recombinant DNA (rDNA) is widely used in biotechnology, medicine and research. Proteins and other products that result from the use of rDNA technology are found in essentially every western pharmacy, doctor’s or veterinarian’s office, medical testing laboratory, and biological research laboratory.
• Organisms that have been manipulated using recombinant DNA technology, and products derived from those organisms have found their way into many farms, supermarkets, home medicine cabinets, and even pet shops.
• Biochemical products of recombinant DNA technology in medicine and research include: human recombinant insulin, growth hormone, blood clotting factors, hepatitis B vaccine, and diagnosis of HIV infection.
• Biochemical products of recombinant DNA technology in agriculture include: golden rice, herbicide-resistant crops, and insect-resistant crops.
Key Terms
• retinoblastoma: A malignant tumour of the retina; a hereditary condition found mostly in children.
• neurofibromatosis: A genetic disorder characterized by the presence of multiple neurofibromas under the skin
• cystic fibrosis: An inherited condition in which the exocrine glands produce abnormally viscous mucus, causing chronic respiratory and digestive problems.
• recombinant DNA technology: the process of taking a gene from one organism and inserting it into the DNA of another
Recombinant DNA technology is the latest biochemical analysis that came about to satisfy the need for specific DNA segments. In this process, surrounding DNA from an existing cell is clipped in the desired amount of segments so that it can be copied millions of times.
Recombinant DNA technology engineers microbial cells for producing foreign proteins, and its success solely depends on the precise reading of equivalent genes made with the help of bacterial cell machinery. This process has been responsible for fueling many advances related to modern molecular biology. The last two decades of cloned-DNA sequence studies have revealed detailed knowledge about gene structure as well as its organization. It has provided hints to regulatory pathways with the aid of which gene expression in myriad cell types is controlled by the cells, especially in those organisms having body plan with basic vertebrae structure.
Recombinant DNA technology, apart from being an important tool of scientific research, has also played a vital role in the diagnosis and treatment of various diseases, especially those belonging to genetic disorders.
Some of the recent advances made possible by recombinant DNA technology are:
1. Isolating proteins in large quantities: many recombinant products are now available, including follicle stimulating hormone (FSH), Follistim AQ vial, growth hormone, insulin and some other proteins.
2. Making possible mutation identification: due to this technology, people can be easily tested for mutated protein presence that can lead to breast cancer, neurofibromatosis, and retinoblastoma.
3. Hereditary diseases carrier diagnosis: tests now available to determine if a person is carrying the gene for cystic fibrosis, the Tay-Sachs diseases, Huntington’s disease or Duchenne muscular dystrophy.
4. Gene transfer from one organism to other: the advanced gene therapy can benefit people with cystic fibrosis, vascular disease, rheumatoid arthritis and specific types of cancers.
7.23D: Mammalian Gene Expression in Bacteria
Bacterial genetics can be manipulated to allow for mammalian gene expression systems established in bacteria.
Learning Objectives
• Describe the sequence of events in a genetically engineered expression system
Key Points
• Recently improved methods of DNA chemical synthesis, combined with recombinant DNA technology, permit the design and relatively rapid synthesis of modest-sized genes that can be incorporated into prokaryotic cells for gene expression using genetic engineering.
• The feasibility of this general approach was first demonstrated by the synthesis and expression of the mammalian peptide somatostatin in Escherichia coli.
• Mammalian gene expression can be achieved in many expression hosts by utilizing the host’s naturally occurring machinery.
Key Terms
• ribozyme: A fragment of RNA that can act as an enzyme.
• plasmid: A circle of double-stranded DNA that is separate from the chromosomes, which is found in bacteria and protozoa.
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins and are produced after the process of translation. An expression system that is categorized as a genetic engineering product is a system specifically designed for the production of a gene product of choice. This is normally a protein, although may also be RNA, such as tRNA or a ribozyme.
The genetically engineered expression system contains the appropriate DNA sequence for the gene of choice which is engineered into a plasmid that is introduced into a bacteria host. The molecular machinery that is required to transcribe the DNA is derived from the innate and naturally occurring machinery in the host. The DNA is then transcribed into mRNA and then translated into protein products.
In a genetically engineered system, this entire process of gene expression may be induced depending on the plasmid used. In the broadest sense, mammalian gene expression includes every living cell but the term is more normally used to refer to expression as a laboratory tool. An expression system is therefore often artificial in some manner. Viruses and bacteria are an excellent example of expression systems.
The oldest and most widely used expression systems are cell-based. Expression is often done to a very high level and therefore referred to as overexpression. There are many ways to introduce foreign DNA to a cell for expression, and there are many different host cells which may be used for expression. Each expression system also has distinct advantages and liabilities.
Expression systems are normally referred to by the host and the DNA source or the delivery mechanism for the genetic material. For example, common bacterial hosts are E.coli and B. subtilis. With E. coli, DNA is normally introduced in a plasmid expression vector. The techniques for overexpression in E. coli work by increasing the number of copies of the gene or increasing the binding strength of the promoter region so as to assist transcription. | textbooks/bio/Microbiology/Microbiology_(Boundless)/07%3A_Microbial_Genetics/7.23%3A_Genetic_Engineering_Products/7.23C%3A__Biochemical_Products_of_Recombinant_DNA_Technology.txt |
Genetic engineering enables scientists to create plants, animals, and microorganisms by manipulating genes.
Learning Objectives
• Explain the advantages and disadvantages of producing genetically engineered proteins in bacteria
Key Points
• Systems used for mass production of recombinant human proteins include bacteria, viruses, mammalian cells, animals, and plants.
• Most processes come with advantages and disadvantages, mostly low cost. However, mammalian proteins and products produced in animals bare ethical issues.
• A large number of mammalian proteins are being manufactured by pharmaceutical companies for use in the treatment of human diseases.
Key Terms
• bioreactors: A device that supports a biologically active environment.
The first successful products of genetic engineering were protein drugs like insulin, which is used to treat diabetes, and growth hormone somatotropin. These proteins are made in large quantities by genetically engineered bacteria or yeast in large “bioreactors. ” Some drugs are also made in transgenic plants, such as tobacco. Other human proteins that are used as drugs require biological modifications that only the cells of mammals, such as cows, goats, and sheep, can provide. For these drugs, production in transgenic animals is a good option. Using farm animals for drug production has many advantages because they are reproducible, have flexible production, are easily maintained, and have a great delivery method (e.g. milk).
Recombinant DNA technology not only allows therapeutic proteins to be produced on a large scale but using the same methodology protein molecules may be purposefully engineered. Genetic modifications introduced to a protein have many advantages over chemical modifications. Genetically engineered entities are biocompatible and biodegradable. The changes are introduced in 100% of the molecules with the exclusion of rare errors in gene transcription or translation. The preparations do not contain residual amounts of harsh chemicals used in the conjugation process. Bacterial expression systems, due to their simplicity, are often not able to produce a recombinant human protein identical to the naturally occurring wild type. Bacteria did not develop sophisticated mechanisms for performing post-translational modifications that are present in higher organisms. As a consequence, an increasing number of protein therapeutics is expressed in mammalian cells. However the low cost and simplicity of cultivating bacteria is an unbeatable advantage over any other expression system and therefore E. coli is always a preferable choice both on a lab scale and in industry.
Many mammalian proteins are produced by genetic engineering. These include, in particular, an assortment of hormones and proteins for blood clotting and other blood processes. For example, tissue plasminogen activator (TPA) is a blood protein that scavenges and dissolves blood clots that may form in the final stages of the healing process. TPA is primarily used in heart patients or others suffering from poor circulation to prevent the development of clots that can be life-threatening. Heart disease is a leading cause of death in many developed countries, especially in the United States, so microbially produced TPA is in high demand. In contrast to TPA, the blood clotting factors VII, VIII, and IX are critically important for the formation of blood clots. Hemophiliacs suffer from a deficiency of one or more clotting factors and can therefore be treated with microbially produced clotting factors. In the past hemophiliacs have been treated with clotting factor extracts from pooled human blood, some of which was contaminated with viruses such as HIV and hepatitis C, putting hemophiliacs at high risk for contracting these diseases. Recombinant clotting factors have eliminated this problem.
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Genetic engineering can be used to manufacture new vaccines.
Learning Objectives
• Evaluate genetically engineered vaccines
Key Points
• All vaccines are genetically modified in a way. A gene may be programmed to produce an antiviral protein in a bacterial cell. Once sealed into the DNA, the bacteria is now effectively re-programmed to replicate this new antiviral protein.
• Recombinant engineered vaccines are being extensively explored, especially to eradicate infectious diseases, allergies, and cancers.
• Protocols for genetically engineered vaccines raise issues on their efficacy and overall benefit.
Key Terms
• FDA: Food and Drug Administration, an agency of the United States Department of Health and Human Services.
• vaccine: a substance given to stimulate the body’s production of antibodies and provide immunity against a disease, prepared from the agent that causes the disease, or a synthetic substitute.
• genetic engineering: The deliberate modification of the genetic structure of an organism. The term genetic modification is used as a synonym.
Genetic engineering, also called genetic modification, is the direct manipulation of an organism ‘s genome using biotechnology. New DNA may be inserted in the host genome by first isolating and copying the genetic material of interest using molecular cloning methods to generate a DNA sequence, or by synthesizing the DNA and then inserting this construct into the host organism. Genes may be removed, or “knocked out,” using a nuclease. Gene targeting is a different technique that uses homologous recombination to change an endogenous gene, and can be used to delete a gene, remove exons, add a gene, or introduce point mutations.
Genetic engineering alters the genetic makeup of an organism using techniques that remove heritable material, or that introduce DNA prepared outside the organism either directly into the host or into a cell that is then fused or hybridized with the host. This involves using recombinant nucleic acid (DNA or RNA) techniques to form new combinations of heritable genetic material, followed by the incorporation of that material either indirectly through a vector system or directly through micro-injection, macro-injection and micro-encapsulation techniques.
In medicine, genetic engineering has been used to mass-produce insulin, human growth hormones, follistim (for treating infertility), human albumin, monoclonal antibodies, antihemophilic factors, vaccines,and many other drugs. Vaccination generally involves injecting weak live, killed, or inactivated forms of viruses or their toxins into the person being immunized. Genetically engineered viruses are being developed that can still confer immunity, but lack the infectious sequences. Mouse hybridomas, cells fused together to create monoclonal antibodies have been humanised through genetic engineering to create human monoclonal antibodies.
The process of genetic engineering involves splicing an area of a chromosome, a gene, that controls a certain characteristic of the body. The enzyme endonuclease is used to split a DNA sequence and to split the gene from the rest of the chromosome. For example, this gene may be programmed to produce an antiviral protein. This gene is removed and can be placed into another organism. For example, it can be placed into a bacteria, where it is sealed into the DNA chain using ligase. When the chromosome is once again sealed, the bacteria is now effectively re-programmed to replicate this new antiviral protein. The bacteria can continue to live a healthy life, though genetic engineering and human intervention has actively manipulated what the bacteria actually is.
Despite the early success demonstrated with the hepatitis B vaccine, no other recombinant engineered vaccine has been approved for use in humans. It is unlikely that a recombinant vaccine will be developed to replace an existing licensed human vaccine with a proven record of safety and efficacy. This is due to the economic reality of making vaccines for human use. Genetically engineered subunit vaccines are more costly to manufacture than conventional vaccines, since the antigen must be purified to a higher standard than was demanded of older, conventional vaccines. Each vaccine must also be subjected to extensive testing and review by the FDA, as it would be considered a new product. This is costly to a company in terms of both time and money and is unnecessary if a licensed product is already on the market. Although recombinant subunit vaccines hold great promise, they do present some potential limitations.
In addition to being less reactogenic, recombinant subunit vaccines have a tendency to be less immunogenic than their conventional counterparts. This can be attributed to these vaccines being held to a higher degree of purity than was traditionally done for an earlier generation of licensed subunit vaccines. Ironically, the contaminants often found in conventional subunit vaccines may have aided in the inflammatory process, which is essential for initiating a vigorous immune response. This potential problem may be overcome by employing one of the many new types of adjuvants that are becoming available for use in humans. Recombinant subunit vaccines may also suffer from being too well-defined, because they are composed of a single antigen. In contrast, conventional vaccines contain trace amounts of other antigens that may aid in conferring an immunity to infectious agents that is more solid than could be provided by a monovalent vaccine. This problem can be minimized, where necessary, by creating recombinant vaccines that are composed of multiple antigens from the same pathogen.
7.24B: Genetic Engineering in Animals
The purpose of genetic engineering in animals is to create animals with special characteristics.
Learning Objectives
• Justify genetic engineering in animals
Key Points
• Genetic engineering of animals involves manipulating or modifying the genetic code of selected animals to alter their characteristics and to introduce certain desired traits.
• The genetic engineering in animals has increased significantly in recent years, and the use of this technology brings with it ethical issues, some of which relate to animal welfare.
• Biomedical applications of genetically engineered animals are numerous, and include understanding of gene function, modeling of human disease to either understand disease mechanisms or to aid drug development, and xenotransplantation.
Key Terms
• ecosystem: The interconnectedness of plants, animals, and microbes with each other and their environment.
• Patents: A form of intellectual property.
Scientists are now capable of creating new species of animals by taking genetic material from one, or more, plants or animals, and genetically engineering them into the genes of another animal. This allows scientists to create animals that are completely foreign to the earth and specifically tailored to possess only the traits that humans desire in animals. This means that science can engineer farm animals to grow faster, have healthier meat and flesh, and be less able to feel the pain and suffering often associated with the conditions present in modern factory farms.
Genetically engineered animals are also created to help medical researchers in their quest to find cures for genetic disease, like breast cancer. Finally, endangered animal species can be cloned, thus helping wildlife management in its goals of preserving wild populations of the earth’s biological diversity, and by ensuring that endangered animals’ genetic information will not be lost when the last of the species dies.
This use of modern technology is not without its drawbacks or its critics. By genetically engineering farm and research animals, critics argue, we may be undoing what nature has worked to create over millions of years. Natural animals are specifically adapted to a given environment and when science manipulates the genes of a few species in the ecosystem, the entire balance of the ecosystem might fall completely apart and cause an unknown number of natural animal species to grow extinct.
Others argue that animals should possess, at a bare minimum, the right to be free of genetic manipulation or a reduction in their natural abilities. Despite this debate, the law in both the United States and in Europe, tends to support genetic engineering research and development by allowing genetically engineered animals to be patented. Patents give scientists a monopoly over their genetically engineered animal species, something before unheard of in modern economic systems. Typically, animals could be owned, but never entire species. | textbooks/bio/Microbiology/Microbiology_(Boundless)/07%3A_Microbial_Genetics/7.24%3A_Transgenic_Organisms/7.24A%3A_Genetically_Engineered_Vaccines.txt |
From manipulation of mutant genes to enhanced resistance to disease, biotechnology has allowed advances in medicine.
Learning Objectives
• Give examples of how biotechnology is used in medicine.
Key Points
• The study of pharmacogenomics can result in the development of tailor-made vaccines for people, more accurate means of determining drug dosages, improvements in drug discovery and approval, and the development of safer vaccines.
• Modern biotechnology can be used to manufacture drugs more easily and cheaply, as they can be produced in larger quantities from existing genetic sources.
• Genetic diagnosis involves the process of testing for suspected genetic defects before administering treatment through genetic testing.
• In gene therapy, a good gene is introduced at a random location in the genome to aid the cure of a disease that is caused by a mutated gene.
Key Terms
• gene therapy: any of several therapies involving the insertion of genes into a patient’s cells in order to replace defective ones
• pharmacogenomics: the study of genes that code for enzymes that metabolize drugs, and the design of tailor-made drugs adapted to an individual’s genetic make-up
• immunodeficiency: a depletion in the body’s natural immune system, or in some component of it
Biotechnology in Medicine
It is easy to see how biotechnology can be used for medicinal purposes. Knowledge of the genetic makeup of our species, the genetic basis of heritable diseases, and the invention of technology to manipulate and fix mutant genes provides methods to treat the disease.
Pharmacogenomics is the study of how the genetic inheritance of an individual affects his/her body’s response to drugs. It is a coined word derived from the words “pharmacology” and ” genomics “. It is, therefore, the study of the relationship between pharmaceuticals and genetics. The vision of pharmacogenomics is to be able to design and produce drugs that are adapted to each person’s genetic makeup. Pharmacogenomics results in the following benefits:
1. Development of tailor-made medicines. Using pharmacogenomics, pharmaceutical companies can create drugs based on the proteins, enzymes, and RNA molecules that are associated with specific genes and diseases. These tailor-made drugs promise not only to maximize therapeutic effects, but also to decrease damage to nearby healthy cells.
2. More accurate methods of determining appropriate drug dosages. Knowing a patient’s genetics will enable doctors to determine how well the patient’s body can process and metabolize a medicine. This will maximize the value of the medicine and decrease the likelihood of overdose.
3. Improvements in the drug discovery and approval process. The discovery of potential therapies will be made easier using genome targets. Genes have been associated with numerous diseases and disorders. With modern biotechnology, these genes can be used as targets for the development of effective new therapies, which could significantly shorten the drug discovery process.
4. Better vaccines. Safer vaccines can be designed and produced by organisms transformed by means of genetic engineering. These vaccines will elicit the immune response without the attendant risks of infection. They will be inexpensive, stable, easy to store, and capable of being engineered to carry several strains of pathogen at once.
Modern biotechnology can be used to manufacture existing drugs more easily and cheaply. The first genetically-engineered products were medicines designed to combat human diseases. In 1978, Genentech joined a gene for insulin with a plasmid vector and put the resulting gene into a bacterium called Escherichia coli. Insulin, widely used for the treatment of diabetes, was previously extracted from sheep and pigs. It was very expensive and often elicited unwanted allergic responses. The resulting genetically-engineered bacterium enabled the production of vast quantities of human insulin at low cost. Since then, modern biotechnology has made it possible to produce more easily and cheaply the human growth hormone, clotting factors for hemophiliacs, fertility drugs, erythropoietin, and other drugs. Genomic knowledge of the genes involved in diseases, disease pathways, and drug-response sites are expected to lead to the discovery of thousands more new targets.
Genetic Diagnosis and Gene Therapy
The process of testing for suspected genetic defects before administering treatment is called genetic diagnosis by genetic testing. Depending on the inheritance patterns of a disease-causing gene, family members are advised to undergo genetic testing. Treatment plans are based on the findings of genetic tests that determine the type of cancer. If the cancer is caused by inherited gene mutations, other female relatives are also advised to undergo genetic testing and periodic screening for breast cancer. Genetic testing is also offered for fetuses to determine the presence or absence of disease-causing genes in families with specific, debilitating diseases.
Genetic testing involves the direct examination of the DNA molecule itself. A scientist scans a patient’s DNA sample for mutated sequences. There are two major types of gene tests. In the first type, a researcher may design short pieces of DNA whose sequences are complementary to the mutated sequences. These probes will seek their complement among the base pairs of an individual’s genome. If the mutated sequence is present in the patient’s genome, the probe will bind to it and flag the mutation. In the second type, a researcher may conduct the gene test by comparing the sequence of DNA bases in a patient’s gene to a normal version of the gene.
Gene therapy is a genetic engineering technique used to cure disease. In its simplest form, it involves the introduction of a good gene at a random location in the genome to aid the cure of a disease that is caused by a mutated gene. The good gene is usually introduced into diseased cells as part of a vector transmitted by a virus that can infect the host cell and deliver the foreign DNA. More advanced forms of gene therapy try to correct the mutation at the original site in the genome, such as is the case with treatment of severe combined immunodeficiency (SCID).
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Transposons allow genes to be transferred to a host organism’s chromosome, interrupting or modifying the function of a gene.
Learning Objectives
• Describe the utility of experimentally introduced Transposons
Key Points
• Transposons contain signals to truncate expression of an interrupted gene, thus inactivating it.
• Transposons are widely used tools in biology, frequently utilized for insertion mutagenesis, large-scale gene disruption studies, and gene tagging.
• Transposon-mediated gene disruption experiments and promoter traps rely on promiscuous, undirected, and pseudo-random insertion of the transposon.
Key Terms
• transposable: Able to be transposed (in any sense).
• plasmid: A circle of double-stranded DNA that is separate from the chromosomes, which is found in bacteria and protozoa.
A transposable element (TE) is a DNA sequence that can change its relative position (self-transpose) within the genome of a single cell. The mechanism of transposition can be either “copy and paste” or “cut and paste. ” Transposition can create phenotypically significant mutations and alter the cell’s genome size. Barbara McClintock’s discovery of these jumping genes early in her career earned her a Nobel prize in 1983.
Transposons in bacteria usually carry an additional gene for function other than transposition—often for antibiotic resistance. In bacteria, transposons can jump from chromosomal DNA to plasmid DNA and back, allowing for the transfer and permanent addition of genes such as those encoding antibiotic resistance (multi-antibiotic resistant bacterial strains can be generated in this way). When the transposable elements lack additional genes, they are known as insertion sequences. Transposons are semi-parasitic DNA sequences that can replicate and spread through the host ‘s genome. They can be harnessed as a genetic tool for analysis of gene and protein function. The use of transposons is well-developed in Drosophila (in which P elements are most commonly used) and in Thale cress (Arabidopsis thaliana) and bacteria such as Escherichia coli (E. coli ).
Synthetic DNA transposon system are constructed to introduce precisely defined DNA sequences into the chromosomes of vertebrate animals for the purposes of introducing new traits and to discover new genes and their functions (e.g. by establishing a loss-of-function phenotype or gene inactivation). Transposition is a precise process in which a defined DNA segment is excised from one DNA molecule and moved to another site in the same or different DNA molecule or genome.
Insertional inactivation is a technique used in recombinant DNA engineering where a plasmid (such as pBR322) is used to disable the expression of a gene. A gene is inactivated by inserting a fragment of DNA into the middle of its coding sequence. Any future products from the inactivated gene will not work because of the extra codes added to it. An example is the use of pBR322, which has genes that respectively encode polypeptides that confer resistance to ampicillin and tetracyclin antibiotics. As a result, when a genetic region is interrupted by integration of pBR322, the gene function is lost but new gene function (resistance to specific antibiotics) is gained. An alternative strategy for insertional mutagenesis has been used in vertebrate animals to find genes that cause cancer. In this case a transposon, e.g. Sleeping Beauty, is designed to interrupt a gene in such a way that it causes maximal genetic havoc. Specifically, the transposon contains signals to truncate expression of an interrupted gene at the site of the insertion and then restart expression of a second truncated gene. This method has been used to identify oncogenes. | textbooks/bio/Microbiology/Microbiology_(Boundless)/07%3A_Microbial_Genetics/7.25%3A_Molecular_Techniques/7.25A%3A__Inactivating_and_Marking_Target_Genes_with_Transposons.txt |
An insertion site is the position at which a transposable genetic element is integrated.
Learning Objectives
• Discuss the uses of sequencing insertions sites
Key Points
• Several methods exist to analyze insertion sequences, including inverse polymerase chain reaction. The inverse PCR involves a series of restriction digests and ligation, resulting in a looped fragment that can be primed for PCR from a single section of known sequence.
• The amplified product can then be sequenced and compared with DNA databases to locate the sequence which has been disrupted.
• Other techniques include Southern hybridization and modifications of the PCR protocol.
Key Terms
• transposons: A segment of DNA that can move to a different position within a genome.
An insertion sequence (also known as an IS, an insertion sequence element, or an IS element) is a short DNA sequence that acts as a simple transposable element.
Insertion sequences have two major characteristics: they are small relative to other transposable elements (generally around 700 to 2500 bp in length) and only code for proteins implicated in the transposition activity (they are thus different from other transposons, which also carry accessory genes such as antibiotic-resistance genes).
These proteins are usually the transposase which catalyse the enzymatic reaction allowing the IS to move, and also one regulatory protein which either stimulates or inhibits the transposition activity. The coding region in an insertion sequence is usually flanked by inverted repeats. For example, the well-known IS911 (1250 bp) is flanked by two 36bp inverted repeat extremities and the coding region has two genes partially overlapping orfA and orfAB, coding the transposase (OrfAB) and a regulatory protein (OrfA).
A particular insertion sequence may be named according to the form ISn, where n is a number (e.g. IS1, IS2, IS3, IS10, IS50, IS911, IS26, etc.); this is not the only naming scheme used, however. Although insertion sequences are usually discussed in the context of prokaryotic genomes, certain eukaryotic DNA sequences belonging to the family of Tc1/mariner transposable elements may be considered to be insertion sequences.
In addition to occurring autonomously, insertion sequences may also occur as parts of composite transposons; in a composite transposon, two insertion sequences flank one or more accessory genes, such as an antibiotic-resistance gene (e.g. Tn10, Tn5). Nevertheless, there exist another sort of transposons, called unit transposons, that do not carry insertion sequences at their extremities (e.g. Tn7). A complex transposon does not rely on flanking insertion sequences for resolvase. The resolvase is part of the tns genome and cuts at flanking inverted repeats.
Although several methods are available for locating ISs in microbial genomes, they are either labor intensive or inefficient. These include Southern hybridization, inverse Polymerase Chain Reaction (iPCR), and most recently, vectorette PCR to identify and map the genomic positions of the insertion sequences.
Southern hybridization is rather time-consuming and requires additional procedures for localizing ISs. Inverse PCR, a commonly-used PCR method for recovering unknown flanking sequences of a known target sequence, uses a library of circularized chromosomal DNA fragments as a template and two outward primers located in each end of the known fragment for amplification. However, when a target sequence has multiple genomic locations, the variously-sized DNA circles formed are difficult to amplify simultaneously. Also, the length of each restriction DNA fragment containing a target sequence must be determined by Southern hybridization followed by sub-genomic fractioning before intramolecular ligation and PCR amplification. These difficulties render Southern hybridization and iPCR impractical as techniques for quickly surveying repetitive elements in genomes.
Vectorette PCR (vPCR) is another method used to amplify unknown sequences flanking a characterized DNA fragment. It involves cutting genomic DNAs with a restriction enzyme, ligating vectorettes to the ends, and amplifying the flanking sequences of a known sequence using primers derived from the known sequence along with a vectorette primer.
7.25C: Northern Blots
Northern blots allow investigators to determine messenger RNA molecular weight and sample content.
Learning Objectives
• Evaluate the applications of Northern Blots
Key Points
• RNA (either total RNA or just mRNA) is separated by gel electrophoresis, usually an agarose gel. Because there are so many different RNA molecules on the gel, it usually appears as a smear rather than discrete bands.
• The RNA is transfered to a sheet of special blotting paper called nitrocellulose, though other types of paper, or membranes, can be used. The RNA molecules retain the same pattern of separation they had on the gel.
• The blot is incubated with a probe which is single-stranded DNA. This probe will form base pairs with its complementary RNA sequence and bind to form a double-stranded RNA-DNA molecule. The probe is either radioactive or has an enzyme bound to it.
Key Terms
• hybridization: The act of hybridizing, or the state of being hybridized.
The Northern blot is a technique used in molecular biology research to study gene expression in a sample, through detection of RNA (or isolated messenger RNA ). With Northern blotting it is possible to observe cellular control over structure and function by determining the particular gene expression levels during differentiation, morphogenesis, as well as abnormal or diseased conditions. Northern blotting involves the use of electrophoresis to separate RNA samples by size and detection with a hybridization probe complementary to part of or the entire target sequence.
The term ‘Northern blot’ actually refers specifically to the capillary transfer of RNA from the electrophoresis gel to the blotting membrane. However, the entire process is commonly referred to as Northern blotting. The northern blot technique was developed in 1977 by James Alwine, David Kemp, and George Stark at Stanford University. Northern blotting takes its name from its similarity to the first blotting technique, the Southern blot, named for biologist Edwin Southern. The major difference is that RNA, rather than DNA, is analyzed in the Northern blot.
A general blotting procedure starts with extraction of total RNA from a homogenized tissue sample or from cells. Eukaryotic mRNA can then be isolated through the use of oligo (dT) cellulose chromatography to isolate only those RNAs with a poly(A) tail. RNA samples are then separated by gel electrophoresis. Since the gels are fragile and the probes are unable to enter the matrix, the RNA samples, now separated by size, are transferred to a nylon membrane through a capillary or vacuum blotting system. | textbooks/bio/Microbiology/Microbiology_(Boundless)/07%3A_Microbial_Genetics/7.25%3A_Molecular_Techniques/7.25B%3A_DNA_Sequencing_of_Insertion_Sites.txt |
Learning Objectives
• Show the uses of Western Blots
The Western blot (sometimes called the protein immunoblot) is a widely accepted analytical technique used to detect specific proteins in a given sample of tissue homogenate or extract. Western blot samples can be taken from whole tissue or from cell culture. Solid tissues are first broken down mechanically using either a blender (for larger sample volumes), a homogenizer (smaller volumes), or by sonication. Assorted detergents, salts, and buffers may be employed to encourage lysis of cells and to solubilize proteins. The technique uses gel electrophoresis to separate native proteins by 3-D structure or denatured proteins by the length of the polypeptide.
The proteins are then transferred to a membrane (typically nitrocellulose or PVDF), where they are stained with antibodies specific to the target protein. There are now many reagent companies that specialize in providing antibodies (both monoclonal and polyclonal antibodies) against tens of thousands of different proteins belonging to signaling pathways or cell surface receptor antigens, or other cellular or soluble components. Commercial antibodies can be expensive, although the unbound antibody can be reused between experiments. This method is used in the fields of molecular biology, biochemistry, immunogenetics and other molecular biology disciplines. Other related techniques include using antibodies to detect proteins in tissues and cells by immunostaining and enzyme-linked immunosorbent assay (ELISA). This method originated in the laboratory of George Stark at Stanford. The name Western blot was given to the technique by W. Neal Burnette and is a play on the name Southern blot, a technique for DNA detection developed earlier by Edwin Southern. Detection of RNA is termed Northern blot.
Key Points
• After separation by gel electrophoresis using SDS-PAGE, proteins are transfered to a sheet of special blotting paper called nitrocellulose, though other types of paper, or membranes, can be used. The proteins retain the same pattern of separation they had on the gel.
• The blot is incubated with a generic protein (such as milk proteins) to bind to any remaining sticky places on the nitrocellulose. An antibody is then added to the solution which is able to bind to its specific protein. The antibody is conjugated to alkaline phosphatase or horseradish peroxidase.
• The location of the antibody is revealed by incubating it with a colorless substrate that the attached enzyme converts to a colored product that can be seen and photographed.
Key Terms
• electrophoresis: a method for the separation and analysis of large molecules (such as proteins) by migrating a colloidal solution of them through a gel; gel electrophoresis
7.25E: DNA Mobility Shifts
DNA mobility shift assay is a technique for studying gene regulation and determining protein-DNA interactions.
Learning Objectives
• Identify the utility of DNA mobility shift assays
Key Points
• The interaction of proteins with DNA is central to the control of many cellular processes, including DNA replication, recombination and repair, transcription, and viral assembly.
• An advantage of studying protein-DNA interactions by an electrophoretic mobility shift assay is the ability to resolve complexes of different stoichiometry or conformation.
• The source of the DNA-binding protein may be a crude nuclear or whole cell extract, in vitro transcription product, or a purified preparation.
Key Terms
• polyacrylamide: Any of a range of cross-linked polymers of acrylamide; used to form soft gels.
A mobility shift assay is electrophoretic separation of a protein-DNA or protein- RNA mixture on a polyacrylamide or agarose gel for a short period. The speed at which different molecules (and combinations thereof) move through the gel is determined by their size and charge, and to a lesser extent, their shape. The control lane (a DNA probe without protein present) will contain a single band corresponding to the unbound DNA or RNA fragment. However, assuming that the protein is capable of binding to the fragment, the lane with protein present will contain another band that represents the larger, less mobile, complex of nucleic acid probe bound to protein, which is “shifted” up on the gel (since it has moved more slowly).
Under the correct experimental conditions, the interaction between the DNA and protein is stabilized and the ratio of bound to unbound nucleic acid on the gel reflects the fraction of free and bound probe molecules as the binding reaction enters the gel. This stability is in part due to the low ionic strength of the buffer, but also due to a “caging effect”; the protein, surrounded by the gel matrix, is unable to diffuse away from the probe before they recombine. If the starting concentrations of protein and probe are known, and if the stoichiometry of the complex is known, the apparent affinity of the protein for the nucleic acid sequence may be determined. An antibody that recognizes the protein can be added to this mixture to create an even larger complex with a greater shift. This method is referred to as a supershift assay, and is used to unambiguously identify a protein present in the protein-nucleic acid complex. | textbooks/bio/Microbiology/Microbiology_(Boundless)/07%3A_Microbial_Genetics/7.25%3A_Molecular_Techniques/7.25D%3A_Western_Bolts.txt |
Protein tags are peptide sequences genetically grafted onto a recombinant protein.
Learning Objectives
• Indicate the uses of protein affinity tags
Key Points
• Affinity tags are appended to proteins so that they can be purified from their crude biological source using an affinity technique.
• Recombinant proteins that carry small affinity tags are efficiently expressed in bacteria, insect, or mammalian cells.
• After cell lysis and clearing of the lysate, tagged proteins are purified using an immobilized-metal affinity chromatography procedure.
Key Terms
• protein: Proteins are large biological molecules consisting of one or more chains of amino acids.
• affinity: An attractive force between atoms, or groups of atoms, that contributes toward their forming bonds.
• recombinant: This term refers to something formed by combining existing elements in a new combination. Thus, the phrase recombinant DNA refers to an organism created in the lab by adding DNA from another species.
Protein tags are peptide sequences genetically grafted onto a recombinant protein. Often these tags are removable by chemical agents or by enzymatic means, such as proteolysis or intein splicing. Tags are attached to proteins for various purposes.
Affinity tags are appended to proteins so that they can be purified from their crude biological source using an affinity technique. These include chitin binding protein (CBP), maltose binding protein (MBP), and glutathione-S-transferase (GST). The poly (His) tag is a widely-used protein tag; it binds to metal matrices.
Solubilization tags are used, especially for recombinant proteins expressed in chaperone-deficient species such as E. coli, so as to assist in the proper folding in proteins and keep them from precipitating. These include thioredoxin (TRX) and poly (NANP). Some affinity tags have a dual role as a solubilization agent, such as MBP and GST.
Chromatography tags are used to alter chromatographic properties of the protein to afford different resolution across a particular separation technique. These often consist of polyanionic amino acids, such as FLAG-tag.
Epitope tags are short peptide sequences which are chosen because high-affinity antibodies can be reliably produced in many different species. These are usually derived from viral genes, which explain their high immunoreactivity. Epitope tags include V5-tag, c-myc-tag, and HA-tag. These tags are particularly useful for western blotting, immunofluorescence and immunoprecipitation experiments, although they also find use in antibody purification.
Fluorescence tags are used to give visual readout on a protein. GFP and its variants are the most commonly used fluorescence tags. More advanced applications of GFP include using it as a folding reporter (fluorescent if folded, colorless if not).
Protein tags are also useful for specific enzymatic modification (such as biotin ligase tags) and chemical modification (FlAsH) tag. Often tags are combined to produce multifunctional modifications of the protein. However, with the addition of each tag comes the risk that the native function of the protein may be abolished or compromised by interactions with the tag.
Examples of peptide tags include:
• AviTag, a peptide allowing biotinylation by the enzyme BirA and so the protein can be isolated by streptavidin (GLNDIFEAQKIEWHE)
• Calmodulin-tag, a peptide bound by the protein calmodulin (KRRWKKNFIAVSAANRFKKISSSGAL)
• FLAG-tag, a peptide recognized by an antibody (DYKDDDDK)
• HA-tag, a peptide recognized by an antibody (YPYDVPDYA)
• His-tag, 5-10 histidines bound by a nickel or cobalt chelate (HHHHHH)
• Myc-tag, a short peptide recognized by an antibody (EQKLISEEDL)
• S-tag (KETAAAKFERQHMDS)
• SBP-tag, a peptide which binds to streptavidin (MDEKTTGWRGGHVVEGLAGELEQLRARLEHHPQGQREP)
• Softag 1, for mammalian expression (SLAELLNAGLGGS)
• Softag 3, for prokaryotic expression (TQDPSRVG)
• V5 tag, a peptide recognized by an antibody (GKPIPNPLLGLDST)
• Xpress tag (DLYDDDDK)
Examples of protein tags include:
• BCCP (Biotin Carboxyl Carrier Protein), a protein domain recognized by streptavidin
• Glutathione-S-transferase-tag, a protein which binds to immobilized glutathione
• Green fluorescent protein-tag, a protein which is spontaneously fluorescent and can be bound by nanobodies
• Maltose binding protein-tag, a protein which binds to amylose agarose
• Nus-tag
• Strep-tag, a peptide which binds to streptavidin or the modified streptavidin called streptactin (Strep-tag II: WSHPQFEK)
• Thioredoxin-tag
7.25G: Primer Extension Analysis
Primer extension is used to map the 5′ ends of DNA or RNA fragments.
LEARNING OBJECTIVES
Outline primer extension analysis
Key Points
• Primer extension assay is done by annealing a specific oligonucleotide primer to a position downstream of that 5′ end.
• The primer is radiolabelled, usually at its 5′ end. This is extended with reverse transcriptase, which can copy either an RNA or a DNA template, making a fragment that ends at the 5′ end of the template molecule.
• Primer extension analysis includes selection and preparation of a labeled primer complementary to the RNA transcript of interest; hybridization of the primer to a region of the RNA under study; extension from the primer by an RNA-dependent DNA polymerase to synthesize a cDNA strand.
• Analysis of primer extension of the extended cDNA products is done on denaturing polyacrylaminde gels and autoradiography.
Key Terms
• radiolabelled: Tagged with a radiotracer.
• polyacrylamide: Any of a range of cross-linked polymers of acrylamide; used to form soft gels.
Primer Extension Analysis
Primer extension is a technique whereby the 5′ ends of RNA or DNA can be mapped. Primer extension can be used to determine the start site of RNA transcription for a known gene. This technique requires a radiolabelled primer (usually 20 to 50 nucleotides in length) which is complementary to a region near the 3′ end of the gene. The primer is allowed to anneal to the RNA and reverse transcriptase is used to synthesize cDNA from the RNA until it reaches the 5′ end of the RNA. By running the product on a polyacrylamide gel, it is possible to determine the transcriptional start site, as the length of the sequence on the gel represents the distance from the start site to the radiolabelled primer.
Applications of Primer Extension Analysis
Primer extension analysis has three main applications. First, it is used for mapping the 5′ end of transcripts. This allows one to determine the transcription initiation site (assuming the mRNA isn’t further processed), which helps localize promoters or TATA boxes. Second, it can be used to quantify the amount of transcript in an in vitro transcription system.
Third, it can be used to determine the locations of breaks or modified bases in a mixed population of RNA or DNA samples. This is useful in applications like footprinting. Two different methods are used. In one, the modified nucleotide cannot be recognized by the polymerase or reverse transcriptase; in such cases, the chain ends at the site of modification. In the other, the modification is converted in a later step of the analysis to a strand break by chemical treatment. For instance, the sites of modifications by dimethyl sulfate (DMS) can be identified by treating DNA with DMS, exposing the sample to conditions that break the backbone at the site of modification, followed by primer extension. | textbooks/bio/Microbiology/Microbiology_(Boundless)/07%3A_Microbial_Genetics/7.25%3A_Molecular_Techniques/7.25F%3A_Purifying_Proteins_by_Affinity_Tag.txt |
DNA protection or “footprinting” analysis is a powerful technique for identifying the nucleotides involved in a protein-DNA interaction.
LEARNING OBJECTIVES
Illustrate DNA protection analysis
Key Points
• DNA protection analysis is a technique in which a DNA molecule is ‘incubated’ with a protein that binds to a specific site along the double helix.
• The DNA-binding protein complex is then subjected to restriction endonuclease digestion, which reduces the entire DNA to mono- and oligonucleotide fragments, except for the portion of the DNA molecule that was ‘protected’ from digestion by the binding protein.
• Removal of the protein by simple chemical means—e.g., by gel electrophoresis —allows the study of DNA and binding protein interaction.
Key Terms
• electrophoresis: a method for the separation and analysis of large molecules (such as proteins) by migrating a colloidal solution of them through a gel; gel electrophoresis
• polymerase chain reaction: A technique in molecular biology for creating multiple copies of DNA from a sample; used in genetic fingerprinting etc.
DNA protection or footprinting is a technique from molecular biology/biochemistry that detects DNA-protein interaction using the fact that a protein bound to DNA will often protect that DNA from enzymatic cleavage. This makes it possible to locate a protein binding site on a particular DNA molecule. The method uses an enzyme, deoxyribonuclease (DNase, for short) to cut the radioactively end-labeled DNA, followed by gel electrophoresis to detect the resulting cleavage pattern. For example, the DNA fragment of interest may be amplified by polymerase chain reaction, with the result being many DNA molecules with a radioactive label on one end of one strand of each double stranded molecule. Cleavage by DNase will produce fragments, the smaller of which will move further on the electrophoretic gel.
The fragments which are smaller will appear further on the gel than the longer fragments. The gel is then used to expose a special photographic film. The cleavage pattern of the DNA in the absence of a DNA binding protein, typically referred to as free DNA, is compared to the cleavage pattern of DNA in the presence of a DNA binding protein. If the protein binds DNA, the binding site is protected from enzymatic cleavage. This protection will result in a clear area on the gel which is referred to as the “footprint”. By varying the concentration of the DNA-binding protein, the binding affinity of the protein can be estimated according to the minimum concentration of protein at which a footprint is observed. This technique was developed by David Galas and Albert Schmitz at Geneva in 1977.
7.25I: Whole-Genome DNA-Binding Analysis
Whole-genome DNA-binding analysis is a powerful tool for analyzing epigenetic modifications and DNA sequences bound to regulatory proteins.
LEARNING OBJECTIVES
Describe whole-genome DNA-binding analysis
Key Points
• Whole-genome DNA binding analysis, also known as location analysis, utilizes chromatin immunoprecipitation and microarray chip.
• Whole-genome DNA-binding analysis utilizes ChIP-on-chip method. Briefly, protein -DNA complexes are crosslinked, immunoprecipitated, purified, amplified and labeled, and then allowed to hybridize to a variety of high-resolution arrays.
• This technique is a high-throughput (genome-wide) identification and analysis of DNA fragments that are bound by specific proteins such as histones, and transcriptional factors.
Key Terms
• immunoprecipitation: A technique in which an antigen is precipitated from a solution by using an antibody, or a particular use of this technique.
Genomic DNA sequences are being determined at an increasingly rapid pace. This has created a need for more efficient techniques to determine which parts of these sequences are bound in-vivo by the proteins controlling processes; such as gene expression, DNA replication and chromosomal mechanics.
A whole-genome approach was established to identify and characterize such DNA sequences. The method of chromatin immunoprecipitation, combined with microarrays (ChIP-Chip), is a powerful tool for genome-wide analysis of protein binding. It has also become a widely-used method for genome-wide localization of protein-DNA interactions.
The first step in the ChIP-Chip procedure is to fix protein-DNA interactions in living cells by chemical crosslinking. The crosslinker must be small to diffuse fast into the cells. In practice, formaldehyde is used in most ChIP-Chip experiments. After cell lysis, the DNA is fragmented by sonication. This extract is then subjected to immunoprecipitation (IP) with a specific antibody against the protein of interest.
DNA bound by the protein will be coprecipitated and enriched, compared to DNA not bound by the respective protein. To facilitate immunoprecipitation and subsequent washing, antibodies are usually coupled to either agarose- or magnetic beads via protein A or G. After reversion of crosslinking, the DNA is purified by phenol extraction or commercial polymerase chain reaction (PCR) cleanup kits.
Often, an amplification step is included after DNA purification. Two different fluorescence labels are used to label the IP DNA, and a hybridization -control DNA, respectively. Usually, total DNA before IP (input DNA) is used as hybridization control.
The two differentially-labeled DNAs are hybridized to the same microarray and the difference in fluorescence intensity gives a measure of the enrichment.
7.25J: Two-Hybrid Analysis
Learning Objectives
• Design a two-hybrid experiment
Understanding how proteins are physically connected reveals clues about their structure, function, and makes them an ideal target for drug therapy. Several methodologies exist to study the interaction of proteins in vivo. The most widely employed tools are the yeast two-hybrid system. The yeast two-hybrid screening system is an effective and quick tool for the in vivo study of protein–protein interaction both in prokaryotes and eukaryotes. The method consists of splitting a yeast transcription factor into its binding domain and activation domain, fusing the binding domain to one protein of interest (the bait) and the activation domain to another protein of interest (the prey), and reconstituting the activity of the transcription factor by bringing the two domains back into physical proximity. In the absence of an interaction the domains remain distant, preventing a detectable output. If the two proteins do interact the bait recruits the prey to a specific cellular location where it can stimulate a detectable output (e.g., gene activation). This experimental approach measures direct physical interaction between proteins and is called a binary method. Datasets obtained from such tools are further analyzed using computational methods to draw a map of protein connectivity and achieve system level understanding of a microorganism.
One limitation of classic yeast two-hybrid screens is that they are limited to soluble proteins. It is therefore impossible to use them to study the protein–protein interactions between insoluble integral membrane proteins. The split- ubiquitin system provides a method for overcoming this limitation. In the split-ubiquitin system, two integral membrane proteins to be studied are fused to two different ubiquitin moieties: a C-terminal ubiquitin moiety (“Cub”, residues 35–76) and an N-terminal ubiquitin moiety (“Nub”, residues 1–34). These fused proteins are called the bait and prey, respectively. In addition to being fused to an integral membrane protein, the Cub moiety is also fused to a transcription factor (TF) that can be cleaved off by ubiquitin specific proteases. Upon bait–prey interaction, Nub and Cub-moieties assemble, reconstituting the split-ubiquitin. The reconstituted split-ubiquitin molecule is recognized by ubiquitin specific proteases, which cleave off the reporter protein, allowing it to induce the transcription of reporter genes.
Summary
A key part of gene functional analysis and potential drug target discovery is an understanding of how proteins interact within the cell. Commercially available products facilitate the characterization of these interactions in yeast systems. The basic format involves the creation of two hybrid molecules, one in which a “bait” protein is fused with a transcription factor, and one in which a “prey” protein is fused with a related transcription factor. If the bait and prey proteins indeed interact, then the two factors fused to these two proteins are also brought into proximity with each other.
Key Terms
• computational: Of or relating to computation.
• ubiquitin: A small regulatory protein sequence that directs proteins to specific compartments within the cell. Specifically, a ubiquitin tag directs the protein to a proteasome, which destroys and recycles the components.
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Advanced technology enables tracking cells with light by introducing fluorescent or luminescent reporter genes into the cells’ genome.
LEARNING OBJECTIVES
Compare the ways light can used to track cells
Key Points
• The ability of tracking cells with light has revolutionized molecular biology and provided means to study biological processes as they happen.
• The most common tools used to illuminate a cell are fluorescent (GFP) and luminescent (luciferase) reporter genes.
• Reporter genes are introduced into the host ‘s genome and are controlled by the regulatory sequence of the gene under investigation (gene X). Thus when gene X is expressed it will drive along the expression of the reporter gene and the cell will fluoresce or emit light.
• Many laboratory devices are available to visualize illuminated living cells and these range from fluorescence microscopy to more advanced spectroscopy.
Key Terms
• Spectroscopy: use of light, sound or particle emission to study matter. The emissions provide information about the properties of the matter under investigation. The device often used for such analysis is a spectrometer, which records the spectrum of light emitted (or absorbed) by a given material.
• Fluorescence microscopy: optical microscope that uses fluorescence to study properties of substances. A sample is illuminated with light of a wavelength that excites fluorescence in the sample. The fluoresced light, which is usually at a longer wavelength than the illumination, is then imaged through a microscope objective.
Fluorescence and luminescence
Cells undergo many dynamic processes. In order to visualize these processes we need to be able to film cells over time. This can be achieved by using tools to monitor gene expression to track when proteins are made and where they go in the cell. In molecular biology, researchers use a reporter gene that they attach to a regulatory gene of interest. Reporter genes ideally have distinguishable properties that can be easily detected and measured. The most commonly used reporter genes have biofluorescent or bioluminescent characteristics and can be visualized with the aid of microscopy and other non-invasive imaging equipments. Examples of such reporters are the genes encoding for Green Fluorescent Protein (GFP) and luciferase, respectively. The discovery of GFP changed the way we look at cellular life today. GFP was first isolated from the jellyfish (Aequorea victoria) by the Japanese scientist Osuma Shimomura in the early 1960s. It was then cloned and its sequence identified in 1992 by Douglas Prasher. GFP is widely used in research laboratories as a marking tool to illuminate and track genes in fixed or living cells. Luciferase, isolated from fireflies, is an enzyme present in the cells of bioluminescent organisms that catalyzes the oxidation of luciferin and ATP producing light. Luciferase is similarly useful as a biological marker in living cells and organisms.
Transfection of reporter genes into cells
To introduce a reporter gene into an organism, scientists place the reporter gene and the gene of interest in the same DNA construct to be inserted into the cell or organism. For bacteria or prokaryotic cells in culture, this is usually in the form of a circular DNA molecule called a plasmid. It is important to use a reporter gene that is not natively expressed in the cell or organism under study, since the expression of the reporter is being used as a marker for successful uptake of the gene of interest. This gene’s regulatory sequence now controls the production of GFP or luciferase, in addition to the protein of interest. In cells where the gene is expressed, and the tagged proteins are produced, GFP or luciferase are produced at the same time. Thus, only those cells in which the tagged gene is expressed, or the target proteins are produced, will fluoresce when observed under fluorescence microscopy, or bioluminesce (emit light) when luciferin, the substrate for luciferase is added.
Application of GFP in molecular microbiology
GFP has many advantages over conventional reporter genes in that it is highly stable, non-toxic to living cells and organisms, detection tools are non-invasive and the green light is generated without the addition of external cofactors and measured without application of expensive equipment. Various applications of that reporter gene were documented and vary from being able to monitor microorganism ‘s survival in complex biological systems such as activated sludge to biodegradation of chemical compounds in soil. GFP allowed the detection, determination of spatial location and enumeration of bacterial cells from diverse environmental samples such as biofilm and water. GFP as biomarker is also useful in monitoring gene expression and protein localisation in bacterial cells. | textbooks/bio/Microbiology/Microbiology_(Boundless)/07%3A_Microbial_Genetics/7.26%3A_Cell_Physiology_Techniques/7.26.01%3A_7._26B-_Tracking_Cells_with_Light.txt |
Multiplex and real-time PCR are molecular techniques designed to amplify nucleic acid sequences in a quantitative manner.
LEARNING OBJECTIVES
Illustrate the use and method of multiplex and real-time PCR
Key Points
• Real-time PCR is a molecular tool for nucleic acid amplification monitored as the reaction progresses.
• Multiplex PCR technique can use fluorescence to detect, quantitate, and visualize PCR products on a computer monitor by utilizing numerous primer sets.
• Real-time PCR can be a simplex, amplifying one DNA template with one set of primers, or multiplex, amplifying one or more DNA templates with one or more sets of primers in one reaction.
Key Terms
• agarose gel electrophoresis: Method used for the separation of DNA fragments by size.
• oligonucleotide: A strand of nucleic acid that serves as a starting point for DNA synthesis.
Polymerase Chain Reaction (PCR) is a molecular technique commonly used to amplify nucleic acid sequences. The starting material is a messenger RNA (mRNA) of interest that could be obtained from a wide array of sample types and extracted using commercially available kits and reagents. This mRNA is used to synthesize complementary DNA (cDNA) in a reaction catalyzed by the enzyme reverse transcriptase. The importance of this step is it allows converting a labile RNA into its more stable cDNA form that can be stored and used for multiple applications. The resulting cDNA serves as the template for the PCR reaction. The PCR process can be divided into three steps: DNA denaturation where double-stranded DNA (dsDNA) is separated at temperatures above 90°C, oligonucleotide primers annealing at 50–60°C, and primer extension at 70–78°C. A programmable thermal cycler controls the rate of temperature change, the length of the incubation at each temperature, and the number of times each cycle of temperatures is repeated. The final product of the reaction is called amplicon. It is confirmed by agarose gel electrophoresis for qualitative results.
Real-time polymerase chain (RT-PCR) reaction, also called quantitative real-time PCR (qRt-PCR) is used to amplify and quantify targeted DNA molecules. The use of RT-PCR allows for both detection and quantitation of DNA sequences. The quantity can be an absolute number of copies or a relative amount when normalized to DNA input or additional normalizing genes. The procedure for RT-PCR follows the general principles of PCR, but the defining feature is the ability to detect amplified DNA as the reaction progresses in real time.
Real-time PCR can used to amplify low-abundance DNA templates. It is useful in monitoring the accumulating amplicon. Two common methods that are used to product detection in real-time PCR include the use of non-specific flourescent dyes that intercalate with double-stranded DNA or sequence-specific DNA probes that consist of oligonucleotides labeled with a fluorescent reporter (oligoprobes). The fluorescent reporter permits detection after hybridization of the probe with its complementary DNA target. During real-time PCR with oligoprobes, there is a change in signal following direct interaction with the amplicon. The signal is related to the amount of amplicon present during each cycle and will increase as the amount of specific amplicon increases. The detection of amplicon could be visualized on a graph as the amplification progresses. Real-time PCR assays have been extremely useful for studying microbial agents of infectious disease and have proven valuable for basic microbiological research. The ability to amplify templates from a broad selection of specimen has made it an ideal system for application across the various microbiological disciplines.
A new and improved technology called multiplex PCR was introduced to allow the use of one or more primer sets to potentially amplify multiple templates within a single reaction. Up to 20 different reactions can be run simultaneously, therefore lowering the amount of sample used, reducing the reagents consumed, and collecting far more information per reaction, while simplifying data analyses. Multiplex PCR is a challenging application that typically requires more optimization than standard, single amplicon PCR assays. The key to successful multiplex PCR is the ability to define a single set of reaction parameters (reagent concentrations and cycling parameters) that allows for all primers to anneal with high specificity to their target sequences and be extended with the same efficiency. Primer design, as well as the enzyme and buffer system, are critical factors in this challenge. The results from multiplex PCR can be analyzed using gel electrophoresis or using fluorophores for analysis using during the reaction. Ideally, a real-time multiplex PCR should be able to detect, differentiate, and provide a quantitative result for many different targets without a single target influencing the detection of one of the others (cross-talk) and without loss of sensitivity. It is evident that due to the limited number of fluorophoric labels available and the significant overlap in their emission spectra, quantification of multiplex reaction products is often difficult.
Numerous companies have helped overcome this issue by making dyes available that are compatible for use in multiplex PCR. Since its first description in 1988 by Chamberlain et al, this method has been applied in many areas of DNA testing, including analyses of deletions, mutations, and polymorphisms, or quantitative assays and reverse transcription PCR. Typically, it is used for genotyping applications where simultaneous analysis of multiple markers is required, detection of pathogens or genetically modified organisms, or for microsatellite analyses. Multiplex assays can be tedious and time-consuming to establish, requiring lengthy optimization procedures but once optimized numerous high-throughput genomic assays can be achieved at optimum speed. | textbooks/bio/Microbiology/Microbiology_(Boundless)/07%3A_Microbial_Genetics/7.26%3A_Cell_Physiology_Techniques/7.26.02%3A_7._26C-_Multiplex_and_Real-Time_PCR.txt |
Learning Objectives
• Compare techniques used for mapping protein-protein interactions
In living organisms most of the biological functions are mediated by complex multi-component protein machineries and network activities. The protein complexes formed could be stable (proteins interact for a prolonged period of time) or transient (proteins interact for a brief period of time). Molecular studies are necessary to dissect the constituents of these protein complexes and identify the domains through which a protein interacts with another. Understanding how proteins are physically connected reveals clues about their structure and function and makes them an ideal target for drug therapy. Several methodologies exist to study the interaction of proteins in vivo. The most widely employed tools are the yeast two-hybrid system and affinity purification coupled to mass spectrometry. Datasets obtained from such tools are further analyzed using computational methods to draw a map of protein connectivity and achieve system level understanding of a microorganism. The complete map of protein interactions that can occur in a living organism is called the interactome.
The Yeast Two-hybrid System
The yeast two-hybrid screening system is an effective and quick tool for the in vivo study of protein–protein interaction both in prokaryotes and eukaryotes. The method consists of splitting a yeast transcription factor into its binding domain and activation domain, fusing the binding domain to one protein of interest (the bait) and the activation domain to another protein of interest (the prey), and reconstituting the activity of the transcription factor by bringing the two domains back into physical proximity. In the absence of an interaction the domains remain distant, preventing a detectable output. If the two proteins do interact the bait recruits the prey to a specific cellular location where it can stimulate a detectable output (e.g., gene activation). This experimental approach measures direct physical interaction between proteins and is called a binary method.
Affinity Purification Coupled to Mass Spectrometry
Affinity purification of protein complexes coupled to mass spectrometry is carried out as follows: a specific protein (the bait) is manipulated to express an affinity tag. The tag serves as a tool to purify the bait protein and associated proteins by affinity chromatography. Purified protein complexes are then resolved on native gels and discrete protein bands are excised and digested into small peptide fragments by trypsin.
Peptides are identified using mass spectrometry methods. The identity of the protein associated with a given bait protein is determined by comparing its peptide fingerprint against available databases. This method allows for the identification and quantification of direct binding partners and secondary interacting proteins, and assigns them into protein networks. This experimental approach measures physical interactions between groups of proteins without distinguishing whether they are direct or indirect and is termed co-complex method. Results collected from binary and co-complex experiments are documented into a database. There are many databases accessible online that allow for protein clustering by function and nature of interaction and provide a rich framework for biomedical research.
Key Points
• A key question about a protein, in addition to when and where it is expressed, is with which other proteins does it interact?
• Interaction partners are an immediate lead into biological function and can potentially be exploited for therapeutic purposes.
• Creation of a protein–protein interaction map of the cell would be of immense value to understanding the biology of the cell.
• The most common approaches used to identify protein-protein interactions are the yeast two-hybrid system and affinity purification coupled to mass spectrometry.
Key Terms
• Affinity chromatography: Method of separating a biochemical mixture based on highly specific interactions.
• mass spectrometry: Analytical method that allows ionizing molecules and sorting them according to their mass and charge. | textbooks/bio/Microbiology/Microbiology_(Boundless)/07%3A_Microbial_Genetics/7.26%3A_Cell_Physiology_Techniques/7.26A%3A__Mapping_Protein-Protein_Interactions.txt |
Learning Objectives
• Assess the uses of phage display technology
A phage or bacteriophage is a virus capable of infecting a bacterial cell, and may cause lysis to its host cell. Bacteriophages have a specific affinity for bacteria. They are made of an outer protein coat or capsid that encloses the genetic material (which can be RNA or DNA, about 5,000 to 500,000 nucleotides in length). They inject their genetic material into the bacterium following infection. When the strain is virulent, all the synthesis of the host’s DNA, RNA and proteins ceases. The phage genome is then used to direct the synthesis of phage nucleic acids and proteins using the host’s transcriptional and translational apparatus. When the sub-components of the phage are produced, they self-assemble to form new phage particles. The new phages produce lysozyme that ruptures the cell wall of the host, leading to the release of the new phages, each ready to invade other bacterial cells. This inherent property of phages is the basis for the phage display technology.
Phage display technology is the process of inserting new genetic material into a phage gene. The bacteria process the new gene so that a new protein or peptide is made. This protein or peptide is exposed on the phage surface. Phage display begins by inserting a diverse set of genes into the phage genome with each phage receiving a different gene. The modified gene contains an added segment (an antibody, small protein, or peptide), which is to be expressed on the surface of the phage. Each phage receives only one gene, so each expresses a single protein or peptide. A collection of phage displaying a population of related but diverse proteins or peptides is called a library. The related proteins keep most of the physical and chemical properties of their parent protein. The library is then exposed to an immobilized target. It is anticipated that some members of the library will bind to the target through an interaction between the displayed molecule and the target itself. After the phage is given the chance to bind to a target, the immobilized target is washed to remove phage that did not bind. Replicating the bound phage in bacteria increases the amount of phage several million-fold overnight, providing enough material for sequencing. Sequencing of the phage DNA tells the identity of the peptide that binds the target. Phage libraries are screened for binding to synthetic or native targets.
Phage display technology is advantageous in many applications including selection of inhibitors for the active and allosteric sites of enzymes, receptor agonists and antagonists, and G-protein binding modulatory peptides. Phage display is also used in epitope mapping and analysis of protein-protein interactions. The specific molecules isolated from phage libraries can be used in therapeutic target validation, drug design and vaccine development.
Key Points
• A phage, short for bacteriophage, is a virus that reproduces itself in bacteria.
• Phage display technology introduces genes into the phage’s genome which encoded proteins would be presented on the surface of the phage.
• Displayed proteins are tested for binding affinity against target molecules immobilized on a platform.
Key Terms
• lysozyme: enzyme that damages bacterial cell wall.
• sequencing: the process of reading the nucleotide bases in a DNA molecule.
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• Reporter gene. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Reporter_gene. License: CC BY-SA: Attribution-ShareAlike
• Fluorescent microscopy. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Fluorescent_microscopy. License: CC BY-SA: Attribution-ShareAlike
• Fluorescence microscopy. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Fluores...e%20microscopy. License: CC BY-SA: Attribution-ShareAlike
• Spectroscopy. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Spectroscopy. License: CC BY-SA: Attribution-ShareAlike
• File:Two hybrid assay.svg - Wikipedia, the free encyclopedia. Provided by: Wikipedia. Located at: en.Wikipedia.org/w/index.php?...say.svg&page=1. License: CC BY-SA: Attribution-ShareAlike
• Reporter gene. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/File:Reporter_gene.png. License: CC BY-SA: Attribution-ShareAlike
• GFPneuron. Provided by: Wikimedia. Located at: commons.wikimedia.org/wiki/File:GFPneuron.png. License: CC BY: Attribution
• Multiplex polymerase chain reaction. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Multipl...chain_reaction. License: CC BY-SA: Attribution-ShareAlike
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• oligonucleotide. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/oligonucleotide. License: CC BY-SA: Attribution-ShareAlike
• agarose gel electrophoresis. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/agarose...lectrophoresis. License: CC BY-SA: Attribution-ShareAlike
• File:Two hybrid assay.svg - Wikipedia, the free encyclopedia. Provided by: Wikipedia. Located at: en.Wikipedia.org/w/index.php?...say.svg&page=1. License: CC BY-SA: Attribution-ShareAlike
• Reporter gene. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/File:Reporter_gene.png. License: CC BY-SA: Attribution-ShareAlike
• GFPneuron. Provided by: Wikimedia. Located at: commons.wikimedia.org/wiki/File:GFPneuron.png. License: CC BY: Attribution
• G-Storm thermal cycler. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/File:G-...mal_cycler.jpg. License: CC BY-SA: Attribution-ShareAlike
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• lysozyme. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/lysozyme. License: CC BY-SA: Attribution-ShareAlike
• sequencing. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/sequencing. License: CC BY-SA: Attribution-ShareAlike
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• Reporter gene. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/File:Reporter_gene.png. License: CC BY-SA: Attribution-ShareAlike
• GFPneuron. Provided by: Wikimedia. Located at: commons.wikimedia.org/wiki/File:GFPneuron.png. License: CC BY: Attribution
• G-Storm thermal cycler. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/File:G-...mal_cycler.jpg. License: CC BY-SA: Attribution-ShareAlike
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• File:PhageExterior.svg - Wikipedia, the free encyclopedia. Provided by: Wikipedia. Located at: en.Wikipedia.org/w/index.php?...ior.svg&page=1. License: CC BY-SA: Attribution-ShareAlike | textbooks/bio/Microbiology/Microbiology_(Boundless)/07%3A_Microbial_Genetics/7.26%3A_Cell_Physiology_Techniques/7.26D%3A_Phase_Display.txt |
Evidence for evolution has been obtained through fossil records, embryology, geography, and molecular biology.
LEARNING OBJECTIVES
Explain the development of the theory of evolution
Key Points
• Fossils serve to highlight the differences and similarities between current and extinct species, showing the evolution of form over time.
• Similar anatomy across different species highlights their common origin and can be seen in homologous and vestigial structures.
• Embryology provides evidence for evolution since the embryonic forms of divergent groups are extremely similar.
• The natural distribution of species across different continents supports evolution; species that evolved before the breakup of the supercontinent are distributed worldwide, whereas species that evolved more recently are more localized.
• Molecular biology indicates that the molecular basis for life evolved very early and has been maintained with little variation across all life on the planet.
Key Terms
• homologous structure: the traits of organisms that result from sharing a common ancestor; such traits often have similar embryological origins and development
• biogeography: the study of the geographical distribution of living things
• vestigial structure: genetically determined structures or attributes that have apparently lost most or all of their ancestral function in a given species
Evidence of Evolution
The evidence for evolution is compelling and extensive. Looking at every level of organization in living systems, biologists see the signature of past and present evolution. Darwin dedicated a large portion of his book, On the Origin of Species, to identifying patterns in nature that were consistent with evolution. Since Darwin, our understanding has become clearer and broader.
Fossils, Anatomy, and Embryology
Fossils provide solid evidence that organisms from the past are not the same as those found today; they show a progression of evolution. Scientists calculate the age of fossils and categorize them to determine when the organisms lived relative to each other. The resulting fossil record tells the story of the past and shows the evolution of form over millions of years. For example, scientists have recovered highly-detailed records showing the evolution of humans and horses. The whale flipper shares a similar morphology to appendages of birds and mammals, indicating that these species share a common ancestor. Over time, evolution led to changes in the shapes and sizes of these bones in different species, but they have maintained the same overall layout. Scientists call these synonymous parts homologous structures.
Some structures exist in organisms that have no apparent function at all, appearing to be residual parts from a common ancestor. These unused structures (such as wings on flightless birds, leaves on some cacti, and hind leg bones in whales) are vestigial.
Embryology, the study of the development of the anatomy of an organism to its adult form, provides evidence for evolution as embryo formation in widely-divergent groups of organisms tends to be conserved. Structures that are absent in the adults of some groups often appear in their embryonic forms, disappearing by the time the adult or juvenile form is reached. For example, all vertebrate embryos, including humans, exhibit gill slits and tails at some point in their early development. These disappear in the adults of terrestrial groups, but are maintained in adults of aquatic groups, such as fish and some amphibians. Great ape embryos, including humans, have a tail structure during their development that is lost by birth.
Another form of evidence of evolution is the convergence of form in organisms that share similar environments. For example, species of unrelated animals, such as the arctic fox and ptarmigan living in the arctic region, have been selected for seasonal white phenotypes during winter to blend with the snow and ice. These similarities occur not because of common ancestry, but because of similar selection pressures: the benefits of not being seen by predators.
Biogeography
The geographic distribution of organisms on the planet follows patterns that are best explained by evolution in conjunction with the movement of tectonic plates over geological time. Broad groups that evolved before the breakup of the supercontinent Pangaea (about 200 million years ago) are distributed worldwide. Groups that evolved since the breakup appear uniquely in regions of the planet, such as the unique flora and fauna of northern continents that formed from the supercontinent Laurasia compared to that of the southern continents that formed from the supercontinent Gondwana.
The great diversification of marsupials in Australia and the absence of other mammals reflect Australia’s long isolation. Australia has an abundance of endemic species (those found nowhere else) which is typical of islands whose isolation by expanses of water prevents species from migrating. Over time, these species diverge evolutionarily into new species that look very different from their ancestors that may exist on the mainland. The marsupials of Australia, the finches on the Galápagos, and many species on the Hawaiian Islands are all unique to their one point of origin, yet they display distant relationships to ancestral species on mainlands.
Molecular Biology
Like anatomical structures, the structures of the molecules of life reflect descent with modification. Evidence of a common ancestor for all of life is reflected in the universality of DNA as the genetic material, in the near universality of the genetic code, and in the machinery of DNA replication and expression. In general, the relatedness of groups of organisms is reflected in the similarity of their DNA sequences. This is exactly the pattern that would be expected from descent and diversification from a common ancestor.
DNA sequences have also shed light on some of the mechanisms of evolution. For example, it is clear that the evolution of new functions for proteins commonly occurs after gene duplications that allow the free modification of one copy by mutation, selection, or drift (changes in a population ‘s gene pool resulting from chance), while the second copy continues to produce a functional protein.
8.1B: Elements of Life
Key elements were needed for early life to start on earth.
LEARNING OBJECTIVES
Define the key elements of life
Key Points
• While the exact substituents for early life to form are not completely agreed upon, most theories agree that methane, ammonia, water, hydrogen sulfide, carbon dioxide or carbon monoxide, and phosphate were needed in the absence of molecular oxygen and ozone.
• From a soup of the primordial earth it’s debated whether RNA or protein were the first molecules needed to start simple life, as both can catalyze their self-assembly.
• Once simple molecules formed on primordial earth they could then be placed under selective pressure to replicate, starting the evolution of the first life-forms on earth.
Key Terms
• phospholipid: any lipid like lecithin or cephalin consisting of a diglyceride combined with a phosphate group and a simple organic molecule likecholine or ethanolamine; they are important constituents of biological membranes
• ribozyme: A fragment of RNA that can act as an enzyme.
There is no “standard model” of the origin of life. However, most currently accepted models draw at least some elements from the framework laid out by the Oparin-Haldane hypothesis. The Oparin-Haldane hypothesis suggests that the atmosphere of the early Earth may have been chemically reducing in nature, composed primarily of: methane (CH4), ammonia (NH3), water (H2O), hydrogen sulfide (H2S), carbon dioxide (CO2) or carbon monoxide (CO), with phosphate (PO43-), molecular oxygen (O2) and ozone (O3) either rare or absent.
In such a reducing atmosphere, electrical activity can catalyze the creation of certain basic small molecules (monomers) of life, like amino acids. This was demonstrated in the Miller–Urey experiment by Stanley L. Miller and Harold C. Urey in 1953. Phospholipids (of an appropriate length) can form lipid bilayers, a basic component of the cell membrane.
A fundamental question is about the nature of the first self-replicating molecule. Since replication is accomplished in modern cells through the cooperative action of proteins and nucleic acids, the major schools of thought about how the process originated can be broadly classified as “proteins first” and “nucleic acids first. ” The principal thrust of the “nucleic acids first” argument is as follows:
1. The polymerization of nucleotides into random RNA molecules might have resulted in self-replicating ribozymes (RNA world hypothesis).
2. Selection pressures for catalytic efficiency and diversity might have resulted in ribozymes which catalyse peptidyl transfer (hence formation of small proteins), since oligopeptides complex with RNA to form better catalysts. The first ribosome might have been created by this process, resulting in more prevalent protein synthesis.
3. Synthesized proteins might then out-compete ribozymes in catalytic ability, therefore becoming the dominant biopolymer, relegating nucleic acids to their modern use as a carrier of genomic information.
Biologist John Desmond Bernal coined the term biopoiesis for this process,and suggested that there were a number of clearly defined “stages” that could be recognized in explaining the origin of life:
• Stage 1: The origin of biological monomers
• Stage 2: The origin of biological polymers
• Stage 3: The evolution from molecules to cell | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.01%3A_Origins_of_Life/8.1A%3A_Evidence_of_Evolution.txt |
The question of how simple organic molecules formed a protocell is largely unanswered.
LEARNING OBJECTIVES
Outline key questions that are unknown about early life on earth
Key Points
• Theoretical biologists can easily understand how a protocell can give rise to the life we see around us; however the question of how simple organic compounds can become the more complex constituents we see in life is more difficult to explain.
• Several problems exist with current abiogenesis models, including a primordial earth with conditions not inductive to abiogenesis, the lack of a method for simple organic molecules to polymerize, and the mono-chirality of molecules seen in life.
• A recent idea that the early earth was bombarded with complex organic molecules needed for life is gaining credence and may answer many criticisms that are apparent with terrestrial-based abiogenesis models.
Key Terms
• protocell: A self-organized, endogenously ordered, spherical collection of polypeptides proposed as a stepping-stone to the origin of life
• enantiomer: One of a pair of stereoisomers that is the mirror image of the other, but may not be superimposed on this other stereoisomer. Almost always, a pair of enantiomers contain at least one chiral center, and a sample of either enantiomer will be optically active.
There is substantial understanding of how inorganic molecules can give rise to somewhat simple building blocks of life in the process known as abiogenesis. For example, nucleic and amino acids can be made in laboratory simulations of the early earth, but how these acids polymerized to make the long chain needed for life is unknown. On the other hand, once a simple protocell capable of replication forms, upon encountering its specific antigen, evolution then takes it course and the myriad ways in which cells try to survive can be understood. However, the question of how simple organic molecules form a protocell is largely unanswered.
There are a few problems consistently seen in most scenarios of abiogenesis. One such problem involves polymerization. The thermodynamic equilibrium of amino acid versus peptides is in the direction of separate amino acids. However, a force that drives polymerization is missing. The random association of single amino acids into one short protein string of 100 amino acids without some enzymatic help could take an incredible amount of time, longer than the age of the earth. Several mechanisms for such polymerization have been suggested, but the resolution of this problem may well be in the properties of polyphosphates. Polyphosphates are formed by polymerization of ordinary monophosphate ions PO4−3. Polyphosphates cause polymerization of amino acids into peptides. They are also the logical precursors in the synthesis of key biochemical compounds such as ATP. A key issue seems to be that calcium reacts with soluble phosphate to form insoluble calcium phosphate (apatite), so some plausible mechanism must be found to keep calcium ions from causing precipitation of phosphate.
Further, experiments that show how simple organic molecules can form (like the Miller-Urey experiment) depend on the assumption that the early earth was a reducing environment, having little oxygen. However, current scientific consensus describes the primitive atmosphere as either a weakly-reducing or neutral. Such an atmosphere would diminish both the amount and variety of amino acids that could be produced.
One further problem confronting many abiogenesis models is homochirality. Homochirality is the term used to describe all building blocks in living organisms having the same “handedness” (amino acids being left-handed, nucleic acid sugars (ribose and deoxyribose) being right-handed, and chiral phosphoglycerides). Some process in chemical evolution must account for the origin of this phenomenon. Chiral molecules can be synthesized, but in the absence of a chiral source or a chiral catalyst, they are formed in a 50/50 mixture of both enantiomer.
There are many models that are being used to explain these problems and others; one that is quite intriguing is the idea that the early earth was actually bombarded by extraterrestrial organic molecules. It should be clear the term extraterrestrial in these abiogenesis models are not referring to little green men, but rather complex organic molecules, of which the abiogenesis occurred in the more favorable conditions for such reactions in space. For instance, the environment in space is strongly reducing (ie no oxygen), and it has been suggested that meteorites introduced the phosphorus species to earth, which explains the need of monophosphate. Homochirality may also have started in space, as the studies of the amino acids on a meteorite showed L-alanine to be more than twice as frequent as its D form, and L-glutamic acid was more than 3 times prevalent than its D counterpart. While the idea of extraterrestrial abiogenesis once seemed far-fetched, the presence of organic molecules on meteorites (and recently in stars themselves) adds credence to this exciting possibility.
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• homologous structure. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/homologous%20structure. License: CC BY-SA: Attribution-ShareAlike
• biogeography. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/biogeography. License: CC BY-SA: Attribution-ShareAlike
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• phospholipid. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/phospholipid. License: CC BY-SA: Attribution-ShareAlike
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• Ssc2003-06g. Provided by: Wikimedia. Located at: commons.wikimedia.org/wiki/File:Ssc2003-06g.jpg. License: Public Domain: No Known Copyright | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.01%3A_Origins_of_Life/8.1C%3A_Unresolved_Questions_About_the_Origins_of_Life.txt |
Thumbnail: A cladogram linking all major groups of living organisms to the LUCA (the black trunk at the bottom), based on ribosomal RNA sequence data.
08: Microbial Evolution Phylogeny and Diversity
Astrobiology is the study of the origin, evolution, distribution, and future of life in the universe: extraterrestrial life and life on Earth.
8.02: Astrobiology
Learning Objectives
• Discuss the Martian biosphere
Mars is the fourth planet from the Sun and the second smallest planet in the Solar System. The planet can be seen from Earth with the naked eye. Mars has a thin atmosphere and its surface is very similar to the Earth’s moon (craters). Mars has volcanoes, valleys, deserts, and polar ice caps similar to Earth. Additionally, Mars rotates similarly to Earth and has a tilt that produces seasons.
Mars was first observed at close proximity in 1965 by the Mariner 4. This observation began decades of study and speculations about the structure of the surface of Mars. Scientists hypothesize that its surface is covered by liquid water. Scientists are still collecting and analyzing data concerning its surface. The planet is currently host to five functioning spacecraft: three in orbit—the Mars Odyssey, Mars Express, and Mars Reconnaissance Orbiter; and two on the surface—Mars Exploration Rover Opportunity and the Mars Science Laboratory Curiosity.
Biosphere
A biosphere is typically defined as the part of the Earth and its atmosphere capable of supporting life. A biosphere can also be thought of as an global ecological system that incorporates all living beings and their relationships with the lithosphere, hydrosphere, and atmosphere. Currently, a great deal of research is going into developing hypotheses on a Martian biosphere. This research overlaps greatly with Martian terraforming, which explores how humans might manipulate the Martian environment to make it stable for maintaining life. As mentioned above, scientists are still collecting a great deal of data on the structure and functioning of Mars. This is a burgeoning field of research.
Key Points
• Mars has a thin atmosphere and its surface is very similar to the Earth’s moon (craters) and has volcanoes, valleys, deserts, and polar ice caps similar to Earth itself. Mars rotates similarly to Earth and has a tilt that produces seasons.
• Mars was first observed at close proximity in 1965 by the Mariner 4. Scientists hypothesize that the surface of Mars is covered by liquid water.
• Scientists are still collecting and analyzing data concerning the surface of Mars. The planet is currently host to five functioning spacecraft.
• A biosphere is an global ecological system that incorporates all living beings and their relationships with the lithosphere, hydrosphere, and atmosphere. A great deal of research is going into developing hypotheses on Martian biosphere. Results are currently inconclusive.
Key Terms
• Solar System: The Sun and all the heavenly bodies that orbit around it, including the eight planets, their moons, the asteroids, and comets.
• Mars: The fourth planet in the solar system. Symbol:
• planet: A body which orbits the Sun directly and is massive enough to be in hydrostatic equilibrium (effectively meaning a spheroid) and to dominate its orbit. The eight planets in the Solar System are Mercury, Venus, Earth, Mars, Jupiter, Saturn, Uranus, and Neptune. Pluto was considered a planet until 2006 and has now been reclassified as a dwarf planet.
8.2B: Martian Biosignatures
Learning Objectives
• Describe biosignatures
A biosignature is any substance – such as an element, isotope, molecule, or phenomenon – that provides scientific evidence of past or present life. It is important to understand that while the presence of these substances or events could be a result of past or present life, they are not definitive evidence and should not be treated as such. Scientists determine the significance of a biosignature not only by examining the probability of life creating it, but mostly by the improbability of abiotic processes producing it.
Martian Biosignatures
On Earth, normal mammalian functioning has produced a fog of chemicals that is not replicated by any chemical process. This fog is made up of large amounts of oxygen and small amounts of methane. This mixture of gases has also been observed in the atmosphere of the planet Mars. Due to scientific thought that this fog cannot be formed by a chemical process, logic concludes that there must be some source of life on the planet.
Scientists feel it is necessary to explore their hypotheses, so in the 1970s there were two American probes called Viking I and II that were sent to Mars to explore for life. The probes took images of the planet while in orbit and also while actually on the surface of Mars. The Viking landers carried three life-detection experiments that looked for signs of metabolism. Unfortunately, the imaging and life-detection results were inconclusive. There are plans for future missions to Mars, the Mars Science Laboratory and ExoMars, which will not only search for biosignatures but try to detect habitable environments as well.
Key Points
• A biosignature is any substance – such as an element, isotope, molecule, or phenomenon – that provides scientific evidence of past or present life.
• On Earth, normal mammalian functioning has produced a fog of chemicals that is not replicated by any chemical process. This mixture of gases has also been observed in the atmosphere of the planet Mars.
• In the 1970s there were two American probes called Viking I and II that were sent to Mars to explore the planet for life. The Viking landers carried three life-detection experiments that looked for signs of metabolism, but the imaging and life-detection results were inconclusive.
• There are plans for future missions to Mars to search for more evidence of biosignatures and habitable environments for life.
Key Terms
• biosignature: Any measurable phenomenon that indicates the presence of life.
• metabolism: The complete set of chemical reactions that occur in living cells.
• abiotic: Nonliving, inanimate, characterized by the absence of life; of inorganic matter. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.02%3A_Astrobiology/8.2A%3A_Mars_and_a_Biosphere.txt |
Terraforming Mars is the hypothetical idea that Mars could be altered in such a way to sustain human and terrestrial life forms.
LEARNING OBJECTIVES
Describe terraforming
Key Points
• The phrase “terraforming Mars ” refers to the idea that the planet Mars could be altered in such a way that it could sustain human and terrestrial life.
• The impact of terraforming Mars would be that in the face of global calamity, there would be a place outside of our planet that would be a safe haven for mankind.
• At this point, terraforming Mars is still a hypothetical idea.
• Scientists believe that water and oxygen are available on Mars in a form that could be easily manipulated to be usable by human and terrestrial life.
• Three major changes would have to occur for Mars to sustain life. These changes are: building up the pressure in the atmosphere, keeping it warm, and preventing the atmosphere from being lost to outer space.
Key Terms
• Terraform: To transform the atmosphere or biosphere of another planet into one having the characteristics of Earth.
• electrolysis: The chemical change produced by passing an electric current through a conducting solution or a molten salt.
• Magnetosphere: The comet-shaped region around Earth or another planet in which charged particles are trapped or deflected. It is shaped by the solar wind and the planet’s magnetic field.
Terraforming Mars
The phrase “terraforming Mars” refers to the idea that the planet Mars could be altered in a way so that it could sustain human and terrestrial life. For a deeper understanding of the term, “terra” literally means land or Earth, so mankind would essentially be making (or forming) this land to be more like Earth.
Some people might question why exploring this hypothetical situation is important. The impact of terraforming Mars would be that in the face of global calamity, there would be a place outside of our planet that would be a safe haven for mankind. At this point, terraforming Mars is still a hypothetical idea.
The Process of Terraforming
For Mars to be suitable for human and terrestrial life, changes would be needed to be made to its climate, surface, and general properties. Although Mars is most like Earth out of all the planets in our solar system, it is still highly unsuitable for life as we know it. It is even thought that many years ago, Mars had a more suitable living environment with a thicker atmosphere and sufficient water to sustain life.
There are three major changes necessary for Mars to be suitable for life. The first change involves building up the atmosphere. This simply means that the surface pressure of Mars would need to be increased to sustain life. Currently, there is not a solution to this issue. Second, Mars would need to be kept warm. Scientists are focusing the least energy on solving this issue due to the amount of carbon dioxide on the planet. Carbon dioxide is a greenhouse gas which means that once the planet begins to heat, the excess carbon dioxide will probably help keep the heat near the ground. The last change that needs to be made is keeping the atmosphere from being lost to outer space. Solutions to this problem are not well-documented, but some scientists hypothesize that creating a magnetosphere would be helpful in resolving this issue.
It should be noted that water and oxygen supply are not listed in the necessary changes. Scientists have found that large amounts of water can be found below the Martian surface. It is currently mixed with dry ice (or frozen carbon dioxide), but it could be melted to be used as a water source. Additionally, it is hypothesized that through a process called electrolysis, scientists could separate the water molecules into oxygen and hydrogen to supply the planet with the necessary oxygen supply. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.02%3A_Astrobiology/8.2C%3A_Terraforming_Mars.txt |
Learning Objectives
• Describe the evidence for oceans on Europa and the implications for life
Europa, discovered in 1610 by Galileo Galilei, is one of Jupiter’s four moons (called the Galilean moons). Europa is covered by a layer of water/ice. It is fascinating to note that although Europa maintains a constant temperature of around -145 degrees Celsius, the water on its surface is not completely frozen (referred to as liquid water).
Europa has tidal heating that develops from friction due to its eccentric orbit around Jupiter. In other words, in a similar fashion to the tides flowing in and out on Earth due to the moon’s gravitational pull, the tides on Europa are affected due to its orbit around Jupiter and possibly also its orbital resonance with other Galilean moons. The planet ‘s gravitational pull is stronger on the near side than the far, creating tidal bulges that can crack the icy crust’s surface and heat the interior. It has also been proposed that volcanoes deep under the moon’s surface contain hydrothermal vents that heat and maintain the liquid water.
Scientists propose the Europa’s smooth surface, with very few craters, must be the result of ice covering an ocean which evens out the surface. Originally there were hypotheses that the atmosphere burning up or weathering of the craters were the source of Europa’s smooth surface, but these ideas were discarded due to Europa’s thin atmosphere. Additionally, some parts of the moon’s surface shows blocks of ice that are separated but seem to fit together like a puzzle. These icebergs could have been shifted by slushy or liquid water beneath. Ridges in Europa’s landscape suggest existent water seeping up the ice cracks, refreezing, and then forming higher and higher ridges.
Geologists have analyzed images taken from the Voyager and Galileo expeditions and have come up with two possible models for the surface of this moon: the thick-ice model and the thin-ice model. The thick-ice model refers to Europa’s large craters and their surrounding concentric rings. These rings are filled with what appears to be flat, fresh ice. Due to these observations and assumptions, combined with the calculated amount of heat present on the moon’s surface, the outer crust of solid ice would be about 6-19 miles thick and the liquid water underneath would be about 60 miles deep. The thin-ice model, which is not widely supported by scientists, proposes that the icy crust would be only about 660 feet thick. Other scientists suggest that this layer is simply the outermost layer that changes constantly due to Europa’s tides. Currently, there is little evidence to support this model.
Key Points
• Europa is covered by a layer of liquid ice even though it maintains a constant temperature of around -145 degrees Celsius.
• Europ, has tidal heating that develops from friction due to its eccentric orbit around Jupiter and its relationship with Jupiter’s other moons (known as Galilean moons).
• It has also been proposed that volcanoes deep under the moon’s surface contain hydrothermal vents that heat and maintain the liquid water.
• Scientists propose that Europa’s smooth surface, with very few craters, must be the result of ice covering an ocean which evens out the surface.
• Geologists have analyzed images taken from the Voyager and Galileo expeditions and come up with two possible models for the surface of this moon, the thick-ice model and the thin-ice model. The thick-ice model is more widely held by scientists and has more evidence to support it.
• The thick-ice model notes Europa’s craters and their surrounding concentric rings, which suggest the outer crust of ice would be about 6-19 miles thick and the liquid water underneath would be about 60 miles deep. The thin-ice model proposes that the icy crust would be about 660 ft thick.
Key Terms
• Galileo: Galileo was an unmanned NASA spacecraft which studied the planet Jupiter and its moons.
• eccentric: Not at or in the center; not perfectly circular.
• Crater: A hemispherical pit created by the impact of a meteorite or other object.
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Natural selection can only occur in the presence of genetic variation; environmental conditions determine which traits are selected.
Learning Objectives
• Explain why only heritable variation can be acted upon by natural selection
Key Points
• Genetic variation within a population is a result of mutations and sexual reproduction.
• A mutation may be neutral, reduce an organism’s fitness, or increase an organism’s fitness.
• An adaptation is a heritable trait that increases the survival and rate of reproduction of an organism in its present environment.
• Divergent evolution describes the process in which two species evolve in diverse directions from a common point.
• Convergent evolution is the process in which similar traits evolve independently in species that do not share a recent common ancestry.
Key Terms
• adaptation: modification of something or its parts that makes it more fit for existence under the conditions of its current environment
• divergent evolution: the process by which a species with similar traits become groups that are tremendously different from each other over many generations
• convergent evolution: a trait of evolution in which species not of similar recent origin acquire similar properties due to natural selection
Variation
Natural selection can only take place if there is variation, or differences, among individuals in a population. Importantly, these differences must have some genetic basis; otherwise, the selection will not lead to change in the next generation. This is critical because variation among individuals can be caused by non-genetic reasons, such as an individual being taller due to better nutrition rather than different genes.
Genetic diversity within a population comes from two main mechanisms: mutation and sexual reproduction. Mutation, a change in the DNA sequence, is the ultimate source of new alleles, or new genetic variation in any population. The genetic changes caused by mutation can have one of three outcomes:
• Many mutations will have no effect on the fitness of the phenotype; these are called neutral mutations.
• A mutation may affect the phenotype of the organism in a way that gives it reduced fitness (a lower likelihood of survival or fewer offspring).
• A mutation may produce a phenotype with a beneficial effect on fitness. Different mutations will have a range of effects on the fitness of an organism that expresses them in their phenotype, from a small effect to a great effect.
Sexual reproduction also leads to genetic diversity: when two parents reproduce, unique combinations of alleles assemble to produce the unique genotypes and thus phenotypes in each of the offspring. However, sexual reproduction can not lead to new genes, but rather provides a new combination of genes in a given individual.
Adaptations
A heritable trait that aids the survival and reproduction of an organism in its present environment is called an adaptation. Scientists describe groups of organisms becoming adapted to their environment when a change in the range of genetic variation occurs over time that increases or maintains the “fitness” of the population to its environment. The webbed feet of platypuses are an adaptation for swimming. The snow leopards’ thick fur is an adaptation for living in the cold. The cheetahs’ fast speed is an adaptation for catching prey.
Whether or not a trait is favorable depends on the environmental conditions at the time. The same traits are not always selected because environmental conditions can change. For example, consider a species of plant that grew in a moist climate and did not need to conserve water. Large leaves were selected because they allowed the plant to obtain more energy from the sun. Large leaves require more water to maintain than small leaves, and the moist environment provided favorable conditions to support large leaves. After thousands of years, the climate changed and the area no longer had excess water. The direction of natural selection shifted so that plants with small leaves were selected because those populations were able to conserve water to survive the new environmental conditions.
The evolution of species has resulted in enormous variation in form and function. Sometimes, evolution gives rise to groups of organisms that become tremendously different from each other. When two species evolve in diverse directions from a common point, it is called divergent evolution. Such divergent evolution can be seen in the forms of the reproductive organs of flowering plants which share the same basic anatomies; however, they can look very different as a result of selection in different physical environments and adaptation to different kinds of pollinators.
Flowering Plants: Flowering plants evolved from a common ancestor. Notice that the (a) dense blazing star (Liatrus spicata) and the (b) purple coneflower (Echinacea purpurea) vary in appearance, yet both share a similar basic morphology.
In other cases, similar phenotypes evolve independently in distantly-related species. For example, flight has evolved in both bats and insects; they both have structures we refer to as wings, which are adaptations to flight. However, the wings of bats and insects have evolved from very different original structures. This phenomenon is called convergent evolution, where similar traits evolve independently in species that do not share a recent common ancestry. The two species came to the same function, flying, but did so separately from each other.
These physical changes occur over enormous spans of time and help explain how evolution occurs. Natural selection acts on individual organisms, which in turn can shape an entire species. Although natural selection may work in a single generation on an individual, it can take thousands or even millions of years for the genotype of an entire species to evolve. It is over these large time spans that life on earth has changed and continues to change. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.03%3A_Microbial_Phylogeny/8.3A%3A_Processes_and_Patterns_of_Evolution.txt |
Similar traits can be either homologous structures that share an embryonic origin or analogous structures that share a function.
Learning Objectives
• Explain the difference between homologous and analogous structures
Key Points
• Organisms may be very closely related, even though they look quite different, due to a minor genetic change that caused a major morphological difference.
• Unrelated organisms may appear very similar because both organisms developed common adaptations that evolved within similar environmental conditions.
• To determine the phylogeny of an organism, scientists must determine whether a similarity is homologous or analogous.
• The advancement of DNA technology, the area of molecular systematics, describes the use of information on the molecular level, including DNA analysis.
Key Terms
• analogous: when similar similar physical features occur in organisms because of environmental constraints and not due to a close evolutionary relationship
• homologous: when similar physical features and genomes stem from developmental similarities that are based on evolution
• phylogeny: the evolutionary history of an organism
• molecular systematics: molecular phylogenetics is the analysis of hereditary molecular differences, mainly in DNA sequences, to gain information on an organism’s evolutionary relationships
Two Options for Similarities
In general, organisms that share similar physical features and genomes tend to be more closely related than those that do not. Such features that overlap both morphologically (in form) and genetically are referred to as homologous structures; they stem from developmental similarities that are based on evolution. For example, the bones in the wings of bats and birds have homologous structures.
Notice it is not simply a single bone, but rather a grouping of several bones arranged in a similar way. The more complex the feature, the more probable that any overlap is due to a common evolutionary past. Imagine two people from different countries both inventing a car with all the same parts and in exactly the same arrangement without any previous or shared knowledge. That outcome would be highly improbable. However, if two people both invented a hammer, it would be reasonable to conclude that both could have the original idea without the help of the other. The same relationship between complexity and shared evolutionary history is true for homologous structures in organisms.
Misleading Appearances
Some organisms may be very closely related, even though a minor genetic change caused a major morphological difference to make them look quite different. Similarly, unrelated organisms may be distantly related, but appear very similar. This usually happens because both organisms developed common adaptations that evolved within similar environmental conditions. When similar characteristics occur because of environmental constraints and not due to a close evolutionary relationship, it is called an analogy or homoplasy. For example, insects use wings to fly like bats and birds, but the wing structure and embryonic origin is completely different. These are called analogous structures.
Similar traits can be either homologous or analogous. Homologous structures share a similar embryonic origin; analogous organs have a similar function. For example, the bones in the front flipper of a whale are homologous to the bones in the human arm. These structures are not analogous. The wings of a butterfly and the wings of a bird are analogous, but not homologous. Some structures are both analogous and homologous: the wings of a bird and the wings of a bat are both homologous and analogous. Scientists must determine which type of similarity a feature exhibits to decipher the phylogeny of the organisms being studied.
Molecular Comparisons
With the advancement of DNA technology, the area of molecular systematics, which describes the use of information on the molecular level including DNA analysis, has blossomed. New computer programs not only confirm many earlier classified organisms, but also uncover previously-made errors. As with physical characteristics, even the DNA sequence can be tricky to read in some cases. For some situations, two very closely-related organisms can appear unrelated if a mutation occurred that caused a shift in the genetic code. An insertion or deletion mutation would move each nucleotide base over one place, causing two similar codes to appear unrelated.
Sometimes two segments of DNA code in distantly-related organisms randomly share a high percentage of bases in the same locations, causing these organisms to appear closely related when they are not. For both of these situations, computer technologies have been developed to help identify the actual relationships. Ultimately, the coupled use of both morphologic and molecular information is more effective in determining phylogeny. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.03%3A_Microbial_Phylogeny/8.3B%3A_Distinguishing_between_Similar_Traits.txt |
Taxanomic classification divides species in a hierarchical system beginning with a domain and ending with a single species.
Learning Objectives
• Describe how taxonomic classification of organisms is accomplished and detail the levels of taxonomic classification from domain to species
Key Points
• Categories within taxonomic classification are arranged in increasing specificity.
• The most general category in taxonomic classification is domain, which is the point of origin for all species; all species belong to one of these domains: Bacteria, Archaea, and Eukarya.
• Within each of the three domains, we find kingdoms, the second category within taxonomic classification, followed by subsequent categories that include phylum, class, order, family, genus, and species.
• At each classification category, organisms become more similar because they are more closely related.
• As scientific technology advances, changes to the taxonomic classification of many species must be altered as inaccuracies in classifications are discovered and corrected.
Key Terms
• binomial nomenclature: the scientific system of naming each species of organism with a Latinized name in two parts
• taxon: any of the taxonomic categories such as phylum or subspecies
• Linnaeus: Swedish botanist, physician and zoologist who laid the foundations for the modern scheme of nomenclature; known as the “father of modern taxonomy”
The Levels of Classification
Taxonomy (which literally means “arrangement law”) is the science of classifying organisms to construct internationally-shared classification systems with each organism placed into more and more inclusive groupings. Think about how a grocery store is organized. One large space is divided into departments, such as produce, dairy, and meats. Then each department further divides into aisles, then each aisle into categories and brands, and then, finally, a single product. This organization from larger to smaller, more-specific categories is called a hierarchical system.
The taxonomic classification system (also called the Linnaean system after its inventor, Carl Linnaeus, a Swedish botanist, zoologist, and physician) uses a hierarchical model. Moving from the point of origin, the groups become more specific, until one branch ends as a single species. For example, after the common beginning of all life, scientists divide organisms into three large categories called domains: Bacteria, Archaea, and Eukarya. Within each domain is a second category called a kingdom. After kingdoms, the subsequent categories of increasing specificity are: phylum, class, order, family, genus, and species.
The kingdom Animalia stems from the Eukarya domain. The full name of an organism technically has eight terms. For dogs, it is: Eukarya, Animalia, Chordata, Mammalia, Carnivora, Canidae, Canis, and lupus. Notice that each name is capitalized except for species and that genus and species names are italicized. Scientists generally refer to an organism only by its genus and species, which is its two-word scientific name, in what is called binomial nomenclature. Therefore, the scientific name of the dog is Canis lupus. The name at each level is also called a taxon. In other words, dogs are in order Carnivora. Carnivora is the name of the taxon at the order level; Canidae is the taxon at the family level, and so forth. Organisms also have a common name that people typically use; in this case, dog. Note that the dog is additionally a subspecies: the “familiaris” in Canis lupus familiaris. Subspecies are members of the same species that are capable of mating and reproducing viable offspring, but they are considered separate subspecies due to geographic or behavioral isolation or other factors.
Dogs actually share a domain (Eukarya) with the widest diversity of organisms, including plants and butterflies. At each sublevel, the organisms become more similar because they are more closely related. Historically, scientists classified organisms using physical characteristics, but as DNA technology developed, more precise phylogenies have been determined.
Recent genetic analysis and other advancements have found that some earlier phylogenetic classifications do not align with the evolutionary past; therefore, changes and updates must be made as new discoveries occur. Recall that phylogenetic trees are hypotheses and are modified as data becomes available. In addition, classification historically has focused on grouping organisms mainly by shared characteristics and does not necessarily illustrate how the various groups relate to each other from an evolutionary perspective. For example, despite the fact that a hippopotamus resembles a pig more than a whale, the hippopotamus may be the closest living relative to the whale.
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Bacterial taxonomy is the rank-based classification of bacteria.
Learning Objectives
• Outline the factors that play a role in the classification of bacterial taxonomy
Key Points
• Bacterial species differ amongst each other based on several characteristics, allowing for their identification and classification.
• Gram staining results are most commonly used as a classification tool.
• In 1987 Carl Woese divided the Eubacteria into 11 divisions based on 16S ribosomal RNA (SSU) sequences, which with several additions are still used today.
Key Terms
• bacteria: A type, species, or strain of bacterium.
• taxonomy: the academic discipline of defining groups of biological organisms on the basis of shared characteristics and giving names to those groups. Each group is given a rank and groups of a given rank can be aggregated to form a super group of higher rank and thus create a hierarchical classification.
• Gram stain: Gram staining (or Gram’s method) is a method of differentiating bacterial species into two large groups (Gram-positive and Gram-negative).It is based on the chemical and physical properties of their cell walls. Primarily, it detects peptidoglycan, which is present in a thick layer in Gram positive bacteria. A Gram positive results in a purple/blue color while a Gram negative results in a pink/red color.
Taxonomic Systems
Bacterial taxonomy is the rank-based classification of bacteria. In the scientific classification established by Carl von Linné, each distinct species is assigned to a genus using a two-part binary name (for example, Homo sapiens). This distinct species is then in turn placed within a lower level of a hierarchy of ranks. These ranks range in ascending scale from family to suborder, and upward to order, subclass, class, division/phyla, kingdom and domain.
In the currently accepted scientific classification of Life, there are three domains of microorganisms: the Eukaryotes, Bacteria and Archaea, The different disciplines of study refer to them using differing terms to speak of aspects of these domains, however, though they follow similar principles. Thus botany, zoology, mycology, and microbiology use several different conventions when discussing these domains and their subdivisions. In zoology, for example, there are type specimens, whereas in microbiology there are type strains.
Historical Challenges of Classification
Despite there being little agreement on the major subgroups of the Bacteria, gram staining results were commonly used as a classification tool. As an example, Prokaryotes share many common features, such as lack of nuclear membrane, unicellularity, division by binary-fission and generally small size. Until the advent of molecular phylogeny the Kingdom Prokaryotae was divided into four divisions, a classification scheme still formally followed by Bergey’s manual of systematic bacteriology.The various species differ amongst each other based on several characteristics determined by gram staining, which allowed their identification and classification. Major groups of this system include: Gracilicutes (gram negative); Firmacutes (gram positive); Mollicutes (gram variable, e.g. Mycoplasma); and Mendocutes (uneven gram stain, “metlynogenic bacteria” now known as the Archaea).
Molecular Classification
In the Molecular era of classification, Carl Woese, who is regarded as the forerunner of the molecular phylogeny revolution, argued that the bacteria, archaea, and eukaryotes represent separate lines of descent that diverged early on from an ancestral colony of organisms. However, a few biologists argue that the Archaea and Eukaryota arose from a group of bacteria. In any case, it is thought that viruses and archaea began relationships approximately two billion years ago, and that co-evolution may have been occurring between members of these groups. It is possible that the last common ancestor of the bacteria and archaea was a thermophile, which raises the possibility that lower temperatures are “extreme environments” in archaeal terms, and organisms that live in cooler environments appeared only later. Since the Archaea and Bacteria are no more related to each other than they are to eukaryotes, the term prokaryote’s only surviving meaning is “not a eukaryote”, limiting its value.
With improved methodologies it became clear that the methanogenic bacteria were profoundly different and were erroneously believed to be relics of ancient bacteria. Thus, though Woese identified three primary lines of descent the Archaebacteria, the Eubacteria and the Urkaryotes, the latter now represented by the nucleocytoplasmic component of the Eukaryotes. these lineages were formalised into the rank Domain (regio in Latin) which divided Life into 3 domains: the Eukaryota, the Archaea and the Bacteria. This scheme is still followed today.
In 1987 Carl Woese divided the Eubacteria into 11 divisions based on 16S ribosomal RNA (SSU) sequences, which with several additions are still used today. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.04%3A_Classification_of_Microorganisms/8.4A%3A_The_Taxonomic_Scheme.txt |
Diagnosis of infectious disease sometimes involves identifying an infectious agent either directly or indirectly.
Learning Objectives
• Outline the various types of diagnostic methods used to diagnose a microbial infection
Key Points
• Diagnosis of infectious disease is nearly always initiated by medical history and physical examination.
• Culture allows identification of infectious organisms by examining their microscopic features, by detecting the presence of substances produced by pathogens, and by directly identifying an organism by its genotype.
• Diagnostic methods include: Microbial culture, microscopy, biochemical tests and molecular diagnostics.
Key Terms
• Diagnosis: Diagnosis of infectious disease sometimes involves identifying an infectious agent either directly or indirectly. In practice most minor infectious diseases such as warts, cutaneous abscesses, respiratory system infections and diarrheal diseases are diagnosed by their clinical presentation.
• infectious: Infectious diseases, also known as transmissible diseases or communicable diseases, comprise clinically evident illness (i.e., characteristic medical signs and/or symptoms of disease) resulting from the infection, presence, and growth of pathogenic biological agents in an individual host organism.
• pathogens: A pathogen or infectious agent (colloquially known as a germ) is a microorganism (in the widest sense, such as a virus, bacterium, prion, or fungus) that causes disease in its host. The host may be an animal (including humans), a plant, or even another microorganism.
The Challenge of Diagnosis
Diagnosis of infectious disease sometimes involves identifying an infectious agent either directly or indirectly. In practice most minor infectious diseases such as warts, cutaneous abscesses, respiratory system infections and diarrheal diseases are diagnosed by their clinical presentation. Conclusions about the cause of the disease are based upon the likelihood that a patient came in contact with a particular agent, the presence of a microbe in a community, and other epidemiological considerations. Given sufficient effort, all known infectious agents can be specifically identified. The benefits of identification, however, are often greatly outweighed by the cost, as often there is no specific treatment, the cause is obvious, or the outcome of an infection is benign.
Primary and Opportunistic Pathogens
Among the almost infinite varieties of microorganisms, relatively few cause disease in otherwise healthy individuals. Infectious disease results from the interplay between those few pathogens and the defenses of the hosts they infect. The appearance and severity of disease resulting from any pathogen depends upon the ability of that pathogen to damage the host as well as the ability of the host to resist the pathogen. Clinicians therefore classify infectious microorganisms or microbes according to the status of host defenses – either as primary pathogens or as opportunistic pathogens.
An Orderly Process
Diagnosis of infectious disease is nearly always initiated by taking a medical history and performing a physical examination. More detailed identification techniques involve the culture of infectious agents isolated from a patient. Culture allows identification of infectious organisms by examining their microscopic features, by detecting the presence of substances produced by pathogens, and by directly identifying an organism by its genotype. Other techniques, such as X-rays, CAT scans, PET scans or NMR, are used to produce images of internal abnormalities resulting from the growth of an infectious agent. The images are useful in detection of, for example, a bone abscess or a spongiform encephalopathy produced by a prion.
Diagnostic methods include microbial culture, microscopy, biochemical tests and molecular diagnostics:
• Microbiological culture is a principal tool used to diagnose infectious disease. In a microbial culture, a growth medium is provided for a specific agent. A sample taken from potentially diseased tissue or fluid is then tested for the presence of an infectious agent able to grow within that medium.
• Microscopy may be carried out with simple instruments, such as the compound light microscope, or with instruments as complex as an electron microscope. Samples obtained from patients may be viewed directly under the light microscope, and can often rapidly lead to identification. Microscopy is often also used in conjunction with biochemical staining techniques, and can be made exquisitely specific when used in combination with antibody based techniques.
• Biochemical tests used in the identification of infectious agents include the detection of metabolic or enzymatic products characteristic of a particular infectious agent. Since bacteria ferment carbohydrates in patterns characteristic of their genus and species, the detection of fermentation products is commonly used in bacterial identification. Acids, alcohols and gases are usually detected in these tests when bacteria are grown in selective liquid or solid media.
• Molecular diagnostics using technologies based upon the polymerase chain reaction ( PCR ) method will become nearly ubiquitous gold standards of diagnostics of the near future, for several reasons. First, the catalog of infectious agents has grown to the point that virtually all of the significant infectious agents of the human population have been identified. Second, an infectious agent must grow within the human body to cause disease; essentially it must amplify its own nucleic acids in order to cause a disease. This amplification of nucleic acid in infected tissue offers an opportunity to detect the infectious agent by using PCR. Third, the essential tools for directing PCR, primers, are derived from the genomes of infectious agents, and with time those genomes will be known, if they are not already. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.04%3A_Classification_of_Microorganisms/8.4B%3A_The_Diagnostic_Scheme.txt |
The number of species of bacteria and archaea is surprisingly small, despite their early evolution, genetic, and ecological diversity.
Learning Objectives
• Describe the concept of polyphasic species
Key Points
• The differences in species concepts between the Bacteria and macro-organisms, the difficulties in growing/characterising in pure culture (a prerequisite to naming new species, vide supra), and extensive horizontal gene transfer blurring the distinction of species makes differentiation difficult.
• The most commonly accepted definition is the polyphasic species definition, which takes into account both phenotypic and genetic differences.
• A quicker diagnostic threshhold is to separate species as less than 70% DNA -DNA hybridization, which corresponds to less than 97% 16S DNA sequence identity.
Key Terms
• bacteria: Bacteria constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals. Bacteria were among the first life forms to appear on Earth, and are present in most habitats on the planet.
• species: In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring.
• DNA hybridization: Hybridization is the process of establishing a non-covalent, sequence-specific interaction between two or more complementary strands of nucleic acids into a single complex, which in the case of two strands is referred to as a duplex. Oligonucleotides, DNA, or RNA will bind to their complement under normal conditions, so two perfectly complementary strands will bind to each other readily.
Judging Species in an Asexual Context
Bacteria divide asexually and for the most part do not show regionalisms. In other words, “Everything is everywhere. ” Accordingly, the concept of species which works best for animals, becomes entirely a matter of judgement.
The approximately 5000 species of bacteria and archaea constitute a surprisingly small number, considering their relatively early evolution, genetic diversity, and ability to reside in all ecosystems on Earth. The reason for this numerical peculiarity lies in the differences in species concepts between the bacteria and macro-organisms and in the difficulties in growing and characterizing in pure culture (a prerequisite to naming new species, vide supra). In addition, the extensive amount of horizontal gene transfer among microorganisms results in the blurring of the distinctions between species among microorganisms.
The most commonly accepted definition is the polyphasic species definition,which takes into account both phenotypic and genetic differences. However, a quicker diagnostic ad hoc threshhold to separate species is less than 70% DNA-DNA hybridization, which corresponds to less than 97% 16S DNA sequence identity. It has been noted that if this were applied to animal classification the order of Primates would be considered a single species.
The International Journal of Systematic Bacteriology/International Journal of Systematic and Evolutionary Microbiology (IJSB/IJSEM) is a peer-reviewed journal that acts as the official international forum for the publication of new prokaryotic taxa. If a species is published in a different peer review journal, the author can submit a request to IJSEM with the appropriate description. If the information is correct, the new species will be featured in the Validation List of IJSEM. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.04%3A_Classification_of_Microorganisms/8.4C%3A_The_Species_Concept_in_Microbiology.txt |
Nomenclature is the set of rules and conventions that govern the names of taxa.
Learning Objectives
• Recognize the factors involved with general classification and nomenclature used for microorganism classification
Key Points
• The names ( nomenclature ) given to prokaryotes are regulated by the International Code of Nomenclature of Bacteria (Bacteriological Code).
• Classification is the grouping of organisms into progressively more inclusive groups based on phylogeny and phenotype, while nomenclature is the application of formal rules for naming organisms.
• Taxonomic names are written in italics (or underlined when handwritten) with a majuscule first letter, with the exception of epithets for species and subspecies.
Key Terms
• nomenclature: binomial nomenclature (also called binominal nomenclature or binary nomenclature) is a formal system of naming species of living things by giving each a name composed of two parts, both of which use Latin grammatical forms, although they can be based on words from other languages. Such a name is called a binomial name (which may be shortened to just “binomial”), a binomen or a scientific name; more informally it is also called a Latin name.
• prokaryotes: ( /proʊkæri.oʊts/, pro-kah-ree-otes or /proʊkæriəts/, pro-kah-ree-əts) a group of organisms whose cells lack a cell nucleus (karyon), or any other membrane-bound organelles. Most prokaryotes are unicellular organisms, although a few such as myxobacteria have multicellular stages in their life cycles.
• Bacteriological code: The International Code of Nomenclature of Bacteria (ICNB) or Bacteriological Code (BC) governs the scientific names for bacteria, including Archaea. It denotes the rules for naming taxa of bacteria, according to their relative rank. As such it is one of the Nomenclature Codes of biology.
Nomenclature is the set of rules and conventions which govern the names of taxa. It is the application of formal rules for naming organisms. Classification is the grouping of organisms into progressively more inclusive groups based on phylogeny and phenotype. Despite there being no official and complete classification of prokaryotes, the names (nomenclature) given to prokaryotes are regulated by the International Code of Nomenclature of Bacteria (Bacteriological Code), a book which contains general considerations, principles, rules, and various notes and advises in a similar fashion to the nomenclature codes of other groups.
The taxa which have been correctly described are reviewed in Bergey’s manual of Systematic Bacteriology, which aims to aid in the identification of species and is considered the highest authority. An online version of the taxonomic outline of bacteria and archaea is available. Taxonomic names are written in italics (or underlined when handwritten) with a majuscule first letter with the exception of epithets for species and subspecies. Despite it being common in zoology, tautonyms (e.g. Bison bison) are not acceptable and names of taxa used in zoology, botany or mycology cannot be reused for bacteria (Botany and Zoology do share names).
For bacteria, valid names must have a Latin or Neolatin name and can only use basic latin letters (w and j inclusive, see History of the Latin alphabet for these), consequently hyphens, accents and other letters are not accepted and should be translitterated correctly (e.g. ß=ss). Ancient Greek being written in the Greek alphabet, needs to be translitterated into the Latin alphabet.
Many species are named after people, either the discoverer or a famous person in the field of microbiology, for example Salmonella is after D.E. Salmon, who discovered it (albeit as “Bacillus typhi”). For the generic epithet, all names derived from people must be in the female nominative case, either by changing the ending to -a or to the diminutive -ella, depending on the name. For the specific epithet, the names can be converted into either adjectival form (adding -nus (m.), -na (f.), -num (n.) according to the gender of the genus name) or the genitive of the latinised name.
Many species (the specific epithet) are named after the place they are present or found (e.g. Borrelia burgdorferi). Their names are created by forming an adjective by joining the locality’s name with the ending -ensis (m. or f.) or ense (n.) in agreement with the gender of the genus name, unless a classical Latin adjective exists for the place. However, names of places should not be used as nouns in the genitive case.
For the Prokaryotes (Bacteria and Archaea) the rank kingdom is not used (although some authors refer to phyla as kingdoms). If a new or amended species is placed in new ranks, according to Rule 9 of the Bacteriological Code the name is formed by the addition of an appropriate suffix to the stem of the name of the type genus. For subclass and class the reccomendation from is generally followed, resulting in a neutral plural, however a few names do not follow this and instead keep into account Graeco-Latin grammar (e.g. the female plurals Thermotogae, Aquificae, and Chlamydiae, the male plurals Chloroflexi, Bacilli, and Deinococci, and the Greek plurals Spirochaetes, Gemmatimonadetes, and Chrysiogenetes).
Phyla are not covered by the Bacteriological Code, however, the scientific community generally follows the Ncbi and Lpsn taxonomy, where the name of the phylum is generally the plural of the type genus, with the exception of the Firmicutes, Cyanobacteria, and Proteobacteria, whose names do not stem from a genus name. The higher taxa proposed by Cavalier-Smith are generally disregarded by the molecular phylogeny community (vide supra).
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Microorganisms can be classified on the basis of cell structure, cellular metabolism, or on differences in cell components.
Learning Objectives
• Distinguish between phenotypic characteristics for Bacteria, Archaea and Eukaryotes
Key Points
• The relationship between the three domains ( Bacteria, Archaea, and Eukaryota) is of central importance for understanding the origin of life. Most of the metabolic pathways are common between Archaea and Bacteria, while most genes involved in genome expression are common between Archaea and Eukarya.
• Microorganisms are very diverse. They include bacteria, fungi, algae, and protozoa; microscopic plants, and animals. Single-celled microorganisms were the first forms of life to develop on earth, approximately 3 billion–4 billion years ago.
• The Gram stain characterizes bacteria based on the structural characteristics of their cell walls. By combining morphology and Gram-staining, most bacteria can be classified as belonging to one of 4 groups (Gram-positive cocci, Gram-positive bacilli, Gram-negative cocci, and Gram-negative bacilli).
• There are some basic differences between Bacteria, Archaea, and Eukaryotes in cell morphology and structure which aid in phenotypic classification and identification.
Key Terms
• Gram stain: A method of differentiating bacterial species into two large groups (Gram-positive and Gram-negative).
• microorganism: An organism that is too small to be seen by the unaided eye, especially a single-celled organism, such as a bacterium.
• domain: In the three-domain system, one of three taxa at that rank: Bacteria, Archaea, or Eukaryota.
Microorganisms are very diverse. They include bacteria, fungi, algae, and protozoa; microscopic plants (green algae); and animals such as rotifers and planarians. Most microorganisms are unicellular (single-celled), but this is not universal.
Single-celled microorganisms were the first forms of life to develop on earth, approximately 3 billion–4 billion years ago. Further evolution was slow, and for about 3 billion years in the Precambrian eon, all organisms were microscopic. So, for most of the history of life on earth the only forms of life were microorganisms. Bacteria, algae, and fungi have been identified in amber that is 220 million years old, which shows that the morphology of microorganisms has changed little since the Triassic period. When at the end of the 19thcentury information began to accumulate about the diversity within the bacterial world, scientists started to include the bacteria in phylogenetic schemes to explain how life on earth may have developed. Some of the early phylogenetic trees of the prokaryote world were morphology-based. Others were based on the then-current ideas on the presumed conditions on our planet at the time that life first developed.
Microorganisms tend to have a relatively rapid evolution. Most microorganisms can reproduce rapidly, and microbes such as bacteria can also freely exchange genes through conjugation, transformation, and transduction, even between widely-divergent species. This horizontal gene transfer, coupled with a high mutation rate and many other means of genetic variation, allows microorganisms to swiftly evolve (via natural selection) to survive in new environments and respond to environmental stresses.
The relationship between the three domains (Bacteria, Archaea, and Eukaryota) is of central importance for understanding the origin of life. Most of the metabolic pathways, which comprise the majority of an organism’s genes, are common between Archaea and Bacteria, while most genes involved in genome expression are common between Archaea and Eukarya. Within prokaryotes, archaeal cell structure is most similar to that of Gram-positive bacteria.
Phenotypic Methods of Classifying and Identifying Microorganisms
Classification seeks to describe the diversity of bacterial species by naming and grouping organisms based on similarities. Microorganisms can be classified on the basis of cell structure, cellular metabolism, or on differences in cell components such as DNA, fatty acids, pigments, antigens, and quinones.
There are some basic differences between Bacteria, Archaea, and Eukaryotes in cell morphology and structure which aid in phenotypic classification and identification:
• Bacteria: lack membrane -bound organelles and can function and reproduce as individual cells, but often aggregate in multicellular colonies. Their genome is usually a single loop of DNA, although they can also harbor small pieces of DNA called plasmids. These plasmids can be transferred between cells through bacterial conjugation. Bacteria are surrounded by a cell wall, which provides strength and rigidity to their cells.
• Archaea: In the past, the differences between bacteria and archaea were not recognized and archaea were classified with bacteria as part of the kingdom Monera. Archaea are also single-celled organisms that lack nuclei. Archaea in fact differ from bacteria in both their genetics and biochemistry. While bacterial cell membranes are made from phosphoglycerides with ester bonds, archaean membranes are made of ether lipids.
• Eukaryotes: Unlike bacteria and archaea, eukaryotes contain organelles such as the cell nucleus, the Golgi apparatus, and mitochondria in their cells. Like bacteria, plant cells have cell walls and contain organelles such as chloroplasts in addition to the organelles in other eukaryotes.
The Gram stain, developed in 1884 by Hans Christian Gram, characterizes bacteria based on the structural characteristics of their cell walls. The thick layers of peptidoglycan in the “Gram-positive” cell wall stain purple, while the thin “Gram-negative” cell wall appears pink. By combining morphology and Gram-staining, most bacteria can be classified as belonging to one of four groups (Gram-positive cocci, Gram-positive bacilli, Gram-negative cocci, and Gram-negative bacilli). Some organisms are best identified by stains other than the Gram stain, particularly mycobacteria or Nocardia, which show acid-fastness on Ziehl–Neelsen or similar stains. Other organisms may need to be identified by their growth in special media, or by other techniques, such as serology.
While these schemes allowed the identification and classification of bacterial strains, it was unclear whether these differences represented variation between distinct species or between strains of the same species. This uncertainty was due to the lack of distinct structures in most bacteria, as well as lateral gene transfer between unrelated species. Due to lateral gene transfer, some closely related bacteria can have very different morphologies and metabolisms. To overcome this uncertainty, modern bacterial classification emphasizes molecular systematics, using genetic techniques such as guanine cytosine ratio determination, genome-genome hybridization, as well as sequencing genes that have not undergone extensive lateral gene transfer, such as the rRNA gene. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.05%3A_Methods_of_Classifying_and_Identifying_Microorganisms/8.5A%3A__Phenotypic_Analysis.txt |
Prokaryotic organisms were the first living things on earth and still inhabit every environment, no matter how extreme.
Learning Objectives
• Discuss the origins of prokaryotic organisms in terms of the geologic timeline
Key Points
• All living things can be classified into three main groups called domains; these include the Archaea, the Bacteria, and the Eukarya.
• Prokaryotes arose during the Precambrian Period 3.5 to 3.8 billion years ago.
• Prokaryotic organisms can live in every type of environment on Earth, from very hot, to very cold, to super haline, to very acidic.
• The domains Bacteria and Archaea are the ones containing prokaryotic organisms.
• The Archaea are prokaryotes that inhabit extreme environments, such as inside of volcanoes, while Bacteria are more common organisms, such as E. coli.
Key Terms
• prokaryote: an organism whose cell (or cells) are characterized by the absence of a nucleus or any other membrane-bound organelles
• domain: in the three-domain system, the highest rank in the classification of organisms, above kingdom: Bacteria, Archaea, and Eukarya
• archaea: a taxonomic domain of single-celled organisms lacking nuclei, formerly called archaebacteria, but now known to differ fundamentally from bacteria
Evolution of Prokaryotes
In the recent past, scientists grouped living things into five kingdoms (animals, plants, fungi, protists, and prokaryotes) based on several criteria such as: the absence or presence of a nucleus and other membrane-bound organelles, the absence or presence of cell walls, multicellularity, etc. In the late 20th century, the pioneering work of Carl Woese and others compared sequences of small-subunit ribosomal RNA (SSU rRNA) which resulted in a more fundamental way to group organisms on earth. Based on differences in the structure of cell membranes and in rRNA, Woese and his colleagues proposed that all life on earth evolved along three lineages, called domains. The domain Bacteria comprises all organisms in the kingdom Bacteria, the domain Archaea comprises the rest of the prokaryotes, and the domain Eukarya comprises all eukaryotes, including organisms in the kingdoms Animalia, Plantae, Fungi, and Protista.
The current model of the evolution of the first, living organisms is that these were some form of prokaryotes, which may have evolved out of protobionts. In general, the eukaryotes are thought to have evolved later in the history of life. However, some authors have questioned this conclusion, arguing that the current set of prokaryotic species may have evolved from more complex eukaryotic ancestors through a process of simplification. Others have argued that the three domains of life arose simultaneously, from a set of varied cells that formed a single gene pool.
Two of the three domains, Bacteria and Archaea, are prokaryotic. Based on fossil evidence, prokaryotes were the first inhabitants on Earth, appearing 3.5 to 3.8 billion years ago during the Precambrian Period. These organisms are abundant and ubiquitous; that is, they are present everywhere. In addition to inhabiting moderate environments, they are found in extreme conditions: from boiling springs to permanently frozen environments in Antarctica; from salty environments like the Dead Sea to environments under tremendous pressure, such as the depths of the ocean; and from areas without oxygen, such as a waste management plant, to radioactively-contaminated regions, such as Chernobyl. Prokaryotes reside in the human digestive system and on the skin, are responsible for certain illnesses, and serve an important role in the preparation of many foods. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.05%3A_Methods_of_Classifying_and_Identifying_Microorganisms/8.5B%3A_Classification_of_Prokaryotes.txt |
The molecular approach to microbial phylogenetic analysis revolutionized our thinking about evolution in the microbial world.
Learning Objectives
• Outline the approaches to perform phylogenetic analysis
Key Points
• The purpose of phylogenetic analysis is to understand the past evolutionary path of organisms. Due to technological innovation in modern molecular biology and the rapid advancement in computational science, accurate inference of the phylogeny of a gene or organism seems possible in the near future.
• The developing technology of nucleic acid sequencing, together with the recognition that sequences of building blocks in informational macromolecules can be used as ‘molecular clocks’ that contain historical information, led to the development of the three- domain model ( Archaea – Bacteria -Eucaryota).
• As more genome sequences become available, scientists have found that determining these relationships is complicated by the prevalence of lateral gene transfer among archaea and bacteria.
• Even using improved DNA-based identification methods, the total number of bacterial species is not known and cannot even be estimated with any certainty. Currently, there are a little less than 9,300 known species of prokaryotes.
Key Terms
• Lateral gene transfer: Horizontal gene transfer (HGT), also lateral gene transfer (LGT) or transposition refers to the transfer of genetic material between organisms other than vertical gene transfer. Vertical transfer occurs when there is gene exchange from the parental generation to the offspring. LGT is then a mechanism of gene exchange that happens independently of reproduction.
• microbial phylogenetics: The study of the evolutionary relatedness among various groups of microorganisms.
Microbial phylogenetics is the study of the evolutionary relatedness among various groups of microorganisms. The molecular approach to microbial phylogenetic analysis revolutionized our thinking about evolution in the microbial world. The purpose of phylogenetic analysis is to understand the past evolutionary path of organisms. Even though we will never know for certain the true phylogeny of any organism, phylogenetic analysis provides best assumptions, thereby providing a framework for various disciplines in microbiology. Due to the technological innovation of modern molecular biology and the rapid advancement in computational science, accurate inference of the phylogeny of a gene or organism seems possible in the near future.
Gene sequences can be used to reconstruct the bacterial phylogeny. These studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage. The term “bacteria” was traditionally applied to all microscopic, single-cell prokaryotes. However, molecular systematics showed prokaryotic life to consist of two separate domains, originally called Eubacteria and Archaebacteria, but now called Bacteria and Archaea that evolved independently from an ancient common ancestor. The archaea and eukaryotes are more closely related to each other than to the bacteria. Due to the relatively recent introduction of molecular systematics and a rapid increase in the number of genome sequences that are available, bacterial classification remains a changing and expanding field. For example, a few biologists argue that the Archaea and Eukaryotes evolved from Gram-positive bacteria.
While morphological or metabolic differences allowed the identification and classification of bacterial strains, it was unclear whether these differences represented variation between distinct species or between strains of the same species. This uncertainty was due to the lack of distinctive structures in most bacteria, as well as lateral gene transfer between unrelated species. The developing technology of nucleic acid sequencing, together with the recognition that sequences of building blocks in informational macromolecules can be used as ‘molecular clocks’ that contain historical information, led to the development of the three-domain model (Archaea – Bacteria – Eucaryota) in the late 1970’s, primarily based on small subunit ribosomal RNA sequence comparisons pioneered by Carl Woese and George Fox.
As more genome sequences become available, scientists have found that determining these relationships is complicated by the prevalence of lateral gene transfer (LGT) among archaea and bacteria. Due to lateral gene transfer, some closely related bacteria can have very different morphologies and metabolisms. To overcome this uncertainty, modern bacterial classification emphasizes molecular systematics, using genetic techniques such as guanine cytosine ratio determination, genome-genome hybridization, as well as sequencing genes that have not undergone extensive lateral gene transfer, such as the rRNA gene.
As with bacterial classification, identification of microorganisms is increasingly using molecular methods. Diagnostics using such DNA-based tools, such as polymerase chain reaction, are increasingly popular due to their specificity and speed, compared to culture-based methods. However, even using these improved methods, the total number of bacterial species is not known and cannot even be estimated with any certainty. Following present classification, there are a little less than 9,300 known species of prokaryotes, which includes bacteria and archaea. but attempts to estimate the true level of bacterial diversity have ranged from 107 to 109 total species – and even these diverse estimates may be off by many orders of magnitude.
There are four steps in general phylogenetic analysis of molecular sequences: (i) selection of a suitable molecule or molecules (phylogenetic marker), (ii) acquisition of molecular sequences, (iii) multiple sequence alignment (MSA), and (iv) phylogenetic treeing and evaluation.
Multilocus sequence analysis (MLSA) represents the novel standard in microbial molecular systematics. In this context, MLSA is implemented in a relatively straightforward way, consisting essentially in the concatenation of several sequence partitions for the same set of organisms, resulting in a “supermatrix” which is used to infer a phylogeny by means of distance-matrix or optimality criterion-based methods. This approach is expected to have an increased resolving power due to the large number of characters analyzed and a lower sensitivity to the impact of conflicting signals (i.e. phylogenetic incongruence) that result from eventual horizontal gene transfer events. The strategies used to deal with multiple partitions can be grouped in three broad categories: the total evidence, separate analysis, and combination approaches. The concatenation approach that dominates MLSAs in the microbial molecular systematics literature is known to systematists working with plants and animals as the “total molecular evidence” approach. It has been used to solve difficult phylogenetic questions such as the relationships among the major groups of cetaceans, that of microsporidia and fungi, or the phylogeny of major plant lineages. The total molecular evidence approach has been criticized because by directly concatenating all available sequence alignments. The evidence of conflicting phylogenetic signals in the different data partitions is lost along with the possibility to uncover the evolutionary processes that gave rise to such contradictory signals. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.05%3A_Methods_of_Classifying_and_Identifying_Microorganisms/8.5C%3A_Phylogenetic_Analysis.txt |
In medicine, microorganisms are identified by morphology, physiology, and other attributes; in ecology by habitat, energy, and carbon source.
Learning Objectives
• Outline the traits used to classify: bacteria, viruses and microrganisms in ecology
Key Points
• A pathogen causes disease in its host. In medicine, there are several broad types of pathogens: viruses, bacteria, fungi, eukaryotic parasites, and prions.
• When identifying bacteria in the laboratory, the following characteristics are used: Gram staining, shape, presence of a capsule, bonding tendency, motility, respiration, growth medium, and whether it is intra- or extracellular.
• Viruses are mainly classified by phenotypic characteristics, such as morphology, nucleic acid type, mode of replication, host organisms, and the type of disease they cause.
• In ecology, microorganisms are classified by the type of habitat they require, or trophic level, energy source and carbon source.
• Biologists have found that microbial life has an amazing flexibility for surviving in extreme environments that would be completely inhospitable to complex organisms; these are called extremophiles and many kinds exist.
• Different species of microorganisms use a mix of different sources of energy and carbon. These may be alternations between photo- and chemotrophy, between litho- and organotrophy, between auto- and heterotrophy or a combination of them.
Key Terms
• obligate: Able to exist or survive only in a particular environment or by assuming a particular role: an obligate parasite; an obligate anaerobe.
• pathogen: Any organism or substance, especially a microorganism, capable of causing disease, such as bacteria, viruses, protozoa, or fungi. Microorganisms are not considered to be pathogenic until they have reached a population size that is large enough to cause disease.
• extremophile: An organism that lives under extreme conditions of temperature, salinity, and so on. They are commercially important as a source of enzymes that operate under similar conditions.
Classifying microorganisms in medicine
A pathogen (colloquially known as a germ) is an infectious agent that causes disease in its host. In medicine, there are several broad types of pathogens: viruses, bacteria, fungi, eukaryotic parasites, and prions.
BACTERIA
Although most bacteria are harmless, even beneficial, quite a few are pathogenic. Each pathogenic species has a characteristic spectrum of interactions with its human hosts.
Conditionally, pathogenic bacteria are only pathogenic under certain conditions; such as a wound that allows for entry into the blood, or a decrease in immune function. Bacterial infections can also be classified by location in the body, for example, the vagina, lungs, skin, spinal cord and brain, and urinary tract.
When identifying bacteria in the laboratory, the following chatacteristics are used: Gram staining, shape, presence of a capsule, bonding tendency (singly or in pairs), motility, respiration, growth medium, and whether it is intra- or extracellular.
Culture techniques are designed to grow and identify particular bacteria, while restricting the growth of the others in the sample. Often these techniques are designed for specific specimens: for example, a sputum sample will be treated to identify organisms that cause pneumonia. Once a pathogenic organism has been isolated, it can be further characterised by its morphology, growth patterns (aerobic or anaerobic), patterns of hemolysis, and staining.
VIRUSES
Similar to the classification systems used for cellular organisms, virus classification is the subject of ongoing debate due to their pseudo-living nature. Essentially, they are non-living particles with some chemical characteristics similar to those of life; thus, they do not fit neatly into an established biological classification system.
Viruses are mainly classified by phenotypic characteristics,such as:
• morphology
• nucleic acid type
• mode of replication
• host organisms
• type of disease they cause
Currently there are two main schemes used for the classification of viruses: (1) the International Committee on Taxonomy of Viruses (ICTV) system; and (2) the Baltimore classification system, which places viruses into one of seven groups. To date, six orders have been established by the ICTV:
• Caudovirales
• Herpesvirales
• Mononegavirales
• Nidovirales
• Picornavirales
• Tymovirales
These orders span viruses with varying host ranges, only some of which infect human hosts.
Baltimore classification is a system that places viruses into one of seven groups depending on a combination of:
• their nucleic acid (DNA or RNA)
• strandedness (single or double)
• sense
• method of replication
Other classifications are determined by the disease caused by the virus or its morphology, neither of which is satisfactory as different viruses can either cause the same disease or look very similar. In addition, viral structures are often difficult to determine under the microscope. Classifying viruses according to their genome means that those in a given category will all behave in a similar fashion, offering some indication of how to proceed with further research.
Other organisms invariably cause disease in humans, such as obligate intracellular parasites that are able to grow and reproduce only within the cells of other organisms.
CATEGORIES OF MICROORGANISMS IN ECOLOGY
In ecology, microorganisms are classified by the type of habitat they require, or trophic level, energy source and carbon source.
Habitat Type
Biologists have found that microbial life has an amazing flexibility for surviving in extreme environments that would be completely inhospitable to complex organisms. Some even concluded that life may have begun on Earth in hydrothermal vents far under the ocean’s surface.
An extremophile is an organism that thrives in physically or geochemically extreme conditions, detrimental to most life on Earth. Most known extremophiles are microbes. The domain Archaea contains renowned examples, but extremophiles are present in numerous and diverse genetic lineages of both bacteria and archaeans. In contrast, organisms that live in more moderate environments may be termed mesophiles or neutrophiles.
There are many different classes of extremophiles, each corresponding to the way its environmental niche differs from mesophilic conditions. Many extremophiles fall under multiple categories and are termed polyextremophiles. Some examples of types of extremophiles:
• Acidophile: an organism with optimal growth at levels of pH 3 or below
• Xerophile: an organism that can grow in extremely dry, desiccating conditions; exemplified by the soil microbes of the Atacama Desert
• Halophile: an organism requiring at least 0.2M concentrations of salt (NaCl) for growth
• Thermophile: an organism that can thrive at temperatures between 45–122 °C
Trophic level, energy source and carbon source
• Phototrophs: carry out photon capture to acquire energy. They use the energy from light to carry out various cellular metabolic processes. They are not obligatorily photosynthetic. Most of the well-recognized phototrophs are autotrophs, also known as photoautotrophs, and can fix carbon.
• Photoheterotrophs: produce ATP through photophosphorylation but use environmentally-obtained organic compounds to build structures and other bio- molecules.
• Photolithoautotroph: an autotrophic organism that uses light energy, and an inorganic electron donor (e.g., H2O, H2, H2S), and CO2 as its carbon source.
• Chemotrophs: obtain their energy by the oxidation of electron donors in their environments.
• Chemoorganotrophs: organisms which oxidize the chemical bonds in organic compounds as their energy source and attain the carbon molecules they need for cellular function. These oxidized organic compounds include sugars, fats and proteins.
• Chemoorganoheterotrophs (or organotrophs) exploit reduced-carbon compounds as energy sources, such as carbohydrates, fats, and proteins from plants and animals. Chemolithoheterotrophs (or lithotrophic heterotrophs) utilize inorganic substances to produce ATP, including hydrogen sulfide and elemental sulfur.
• Lithoautotroph: derives energy from reduced compounds of mineral origin. May also be referred to as chemolithoautotrophs, reflecting their autotrophic metabolic pathways. Lithoautotrophs are exclusively microbes and most are bacteria. For lithoautotrophic bacteria, only inorganic molecules can be used as energy sources.
• Mixotroph: Can use a mix of different sources of energy and carbon. These may be alternations between photo- and chemotrophy, between litho- and organotrophy, between auto- and heterotrophy or a combination of them. Can be either eukaryotic or prokaryotic.
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Bacteria are a subset of prokaryotes and while very different, they still have some common features.
Learning Objectives
• Identify common bacterial traits
Key Points
• Bacteria vary from species to species, thus assigning many common traits to bacteria is difficult. Bacterial species are typified by their diversity.
• There are three notable common traits of bacteria, 1) lack of membrane-bound organelles, 2) unicellular and 3) small (usually microscopic) size.
• Not all prokaryotes are bacteria, some are archaea, which although they share common physicals features to bacteria, are ancestrally different from bacteria.
Key Terms
• archaea: a taxonomic domain of single-celled organisms lacking nuclei, formerly called archaebacteria but now known to differ fundamentally from bacteria.
• binary fission: a form of asexual reproduction and cell division used by all prokaryotes, (bacteria and archaebacteria)
Bacteria constitute a large domain of prokaryotic microorganisms. Bacteria were among the first life forms to appear on Earth, and are present in most habitats on the planet. Bacteria grow in soil, acidic hot springs, radioactive waste, water, and deep in the Earth’s crust. In addition, they grow in organic matter and the live bodies of plants and animals, providing outstanding examples of mutualism in the digestive tracts of humans, termites, and cockroaches.
But what defines a bacteria? Bacteria as prokaryotes share many common features, such as:
1. A lack of membrane-bound organelles
2. Unicellularity and thus division by binary-fission
3. Generally small size
Bacteria do not tend to have membrane-bound organelles in their cytoplasm and thus contain few large intracellular structures. They consequently lack a true nucleus, mitochondria, chloroplasts, and the other organelles present in eukaryotic cells, such as the Golgi apparatus and endoplasmic reticulum. Bacteria were once seen as simple bags of cytoplasm, but elements such as prokaryotic cytoskeleton, and the localization of proteins to specific locations within the cytoplasm have been found to show levels of complexity. These subcellular compartments have been called “bacterial hyperstructures”.
Unlike in multicellular organisms, increases in cell size (cell growth and reproduction by cell division) are tightly linked in unicellular organisms. Bacteria grow to a fixed size and then reproduce through binary fission, a form of asexual reproduction.
Perhaps the most obvious structural characteristic of bacteria is (with some exceptions) their small size. For example, Escherichia coli cells, an “average” sized bacterium, are about 2 micrometres (μm) long and 0.5 μm in diameter. Small size is extremely important because it allows for a large surface area-to-volume ratio which allows for rapid uptake and intracellular distribution of nutrients and excretion of wastes.
The term “bacteria” was traditionally applied to all microscopic, single-cell prokaryotes, having the similar traits outlined above. However, molecular systematics show prokaryotic life to consist of two separate domains, originally called Eubacteria and Archaebacteria, but now called Bacteria and Archaea that evolved independently from an ancient common ancestor. The archaea and eukaryotes are more closely related to each other than either is to the bacteria. It should be noted that Bacteria and Archaea are similar physically, but have different ancestral origins as determined by DNA of the genomes that encode different prokaryotes. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.06%3A_Bacterial_Diversity/8.6A%3A_Common_Bacterial_Traits.txt |
To classify a species of bacteria, one usually needs to isolate and grow up the species that is to be classified.
Learning Objectives
• Estimate bacterial diversity
Key Points
• Classification is the attempt to identify and group different species of bacteria together by common traits.
• If a bacterium cannot be cultured, it is hard to study it to find commonalities and differences from other species of bacteria.
• Recent advances in molecular technique are allowing uncultured bacteria to be classified.
Key Terms
• viable but nonculturable: Viable but nonculturable (VBNC) bacteria refers to bacteria that are in a state of very low metabolic activity and do not divide, but are alive and have the ability to become culturable once resuscitated.
Describing Diversity
Classification seeks to describe the diversity of bacterial species by naming and grouping organisms based on similarities. Bacteria can be classified on the basis of cell structure, cellular metabolism, or by differences in cell components such as DNA, fatty acids, pigments, antigens, and quinones.
While these schemes previously allowed the identification and classification of bacterial strains, it was long unclear whether these differences represented variation between distinct species or between strains of the same species. This uncertainty resulted from the lack of distinctive structures in most bacteria, as well as lateral gene transfer that occurred between unrelated species. Because of the existence of lateral gene transfer, some closely related bacteria have very different morphologies and metabolisms.
To overcome these uncertainties, modern bacterial classification emphasizes molecular systematics, using genetic techniques such as guanine cytosine ratio determination, genome-genome hybridization, as well as sequencing genes that have not undergone extensive lateral gene transfer, such as the rRNA gene.
Uni-Species Cultures for Identification
While there are several molecular tools that allow us to classify or distinguish different bacterial species, this is predicated on obtaining uni-species cultures of a given bacteria. Culture techniques are designed to promote the growth and identify particular bacteria, while restricting the growth of the other bacteria in the sample. Often these techniques are designed for specific specimens; for example, a sputum sample will be treated to identify organisms that cause pneumonia, while stool specimens are cultured on selective media to identify organisms that cause diarrhoea while preventing growth of non- pathogenic bacteria. Specimens that are normally sterile, such as blood, urine, or spinal fluid, are cultured under conditions designed to grow all possible organisms. Once a pathogenic organism has been isolated, it can be further characterized by its morphology, by growth patterns such as aerobic or anaerobic growth, by patterns of hemolysis and by staining. If a bacteria can not be cultured, classification can prove to be very difficult.
DNA Sequencing
However, recent advances in molecular techniques do allow the sequencing of DNA from bacterial species, without the reliance on a pure culture of that given bacteria. Diagnostics using such DNA-based tools, such as polymerase chain reaction, are increasingly popular due to their specificity and speed, compared to culture-based methods. These methods also allow the detection and identification of “viable but nonculturable” cells that are metabolically active but non-dividing, which can be applied to isolates of bacterial species that cannot be cultured. However, even using these improved methods, the total number of bacterial species is not known and cannot even be estimated with any certainty. Following present classification, there are a little less than 9,300 known species of prokaryotes, which includes bacteria and archaea. Attempts to estimate the true level of bacterial diversity have ranged from 107 to 109 total species – and even these diverse estimates may be off by many orders of magnitude.
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The Proteobacteria are a major group (phylum) of bacteria.
Learning Objectives
• Categorize proteobacteria
Key Points
• Proteobacteria include a wide variety of pathogens, such as Escherichia, Salmonella, Vibrio, Helicobacter, and many other notable genera.
• All proteobacteria are Gram-negative, with an outer membrane mainly composed of lipopolysaccharides.
• The divisions of the proteobacteria include: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Epsilonproteobacteria and Zetaproteobacteria.
Key Terms
• Proteobacteria: The Proteobacteria are a major group (phylum) of bacteria. They include a wide variety of pathogens, such as Escherichia, Salmonella, Vibrio, Helicobacter, and many other notable genera. Others are free-living, and include many of the bacteria responsible for nitrogen fixation.
• pathogens: A pathogen or infectious agent (colloquially known as a germ) is a microorganism (in the widest sense, such as a virus, bacterium, prion, or fungus) that causes disease in its host. The host may be an animal (including humans), a plant, or even another microorganism.
• Gram-negative: Gram-negative bacteria are bacteria that do not retain crystal violet dye in the Gram staining protocol. In a Gram stain test, a counterstain (commonly safranin) is added after the crystal violet, coloring all Gram-negative bacteria with a red or pink color.
The Proteobacteria are a major group (phylum) of bacteria. They include a wide variety of pathogens, such as Escherichia, Salmonella, Vibrio, Helicobacter, and many other notable genera. Others are free-living, and include many of the bacteria responsible for nitrogen fixation.
In 1987, Carl Woese established this grouping, and informally called it the “purple bacteria and their relatives”. Because of the great diversity of forms found in this group, the Proteobacteria are named after Proteus, a Greek god of the sea, capable of assuming many different shapes, and it is therefore not named after the genus Proteus.
All proteobacteria are Gram-negative, with an outer membrane mainly composed of lipopolysaccharides. Many move about using flagella, but some are nonmotile or rely on bacterial gliding. The last include the myxobacteria, a unique group of bacteria that can aggregate to form multicellular fruiting bodies. There is also a wide variety in the types of metabolism. Most members are facultatively or obligately anaerobic, chemoautotrophs, and heterotrophic, but there are numerous exceptions. A variety of genera, which are not closely related to each other, convert energy from light through photosynthesis. These are called purple bacteria, referring to their mostly reddish pigmentation.
The group is defined primarily in terms of ribosomal RNA (rRNA) sequences. The Proteobacteria are divided into six sections, referred to by the Greek letters alpha through zeta, again based on rRNA sequences. These are often treated as classes. The alpha, beta, delta, epsilon sections are monophyletic, but the Gammaproteobacteria due to the Acidithiobacillus genus is paraphyletic to Betaproteobacteria, according to multigenome alignment studies, which if done correctly are more precise than 16S (note that Mariprofundus ferrooxydans sole member of the Zetaproteobacteria was previously misclassified on NCBI taxonomy). Acidithiobacillus contains 5 species and the sole genus in its order Acidithiobacillales.
The divisions of the proteobacteria were once regarded as subclasses (e.g. α-subclass of the Proteobacteria), but are now regarded as classes (e.g. the Alphaproteobacteria). These classes include: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Epsilonproteobacteria and Zetaproteobacteria. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.07%3A_Proteobacteria/8.7A%3A_Overview_of_Proteobacteria.txt |
Learning Objectives
• Describe the Alphaproteobacteria class of Proteobacteria
Alphaproteobacteria is a class of Proteobacteria. Like all Proteobacteria, they are Gram-negative. The Alphaproteobacteria comprise most phototrophic genera, but also several genera metabolising C1-compounds (e.g., Methylobacterium spp.), symbionts of plants (e.g., Rhizobium spp.) and animals, and a group of pathogens, the Rickettsiaceae. In addition, the precursors of the mitochondria of eukaryotic cells are thought to have originated from Rickettsia spp. (See endosymbiotic theory.). Because of their symbiotic properties, scientists often use Alphaproteobacteria of the genus Agrobacterium to transfer foreign DNA into plant genomes, and they also have many other biotechnological properties. Aerobic anoxygenic phototrophic bacteria are alphaproteobacteria, widely distributed marine plankton that may constitute over 10% of the open ocean microbial community.
The Class Alphaproteobacteria comprises ten orders (viz. Magnetococcales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales, Caulobacterales, Kiloniellales, Kordiimonadales, Parvularculales and Sneathiellales).
Comparative analyses of the sequenced genomes have also led to discovery of many conserved indels in widely distributed proteins and whole proteins (i.e. signature proteins) that are distinctive characteristics of either all Alphaproteobacteria, or their different main orders (viz. Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales and Caulobacterales) and families (viz. Rickettsiaceae, Anaplasmataceae, Rhodospirillaceae, Acetobacteraceae, Bradyrhiozobiaceae, Brucellaceae and Bartonellaceae).
These molecular signatures provide novel means for the circumscription of these taxonomic groups and for identification/assignment of new species into these groups. Phylogenetic analyses and conserved indels in large numbers of other proteins provide evidence that Alphaproteobacteria have branched off later than most other phyla and Classes of Bacteria with the exception of Betaproteobacteria and Gammaproteobacteria.
The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Center for Biotechnology Information (NCBI) and the phylogeny is based on 16S rRNA-based LTP release 106 by ‘The All-Species Living Tree’ Project.
Key Points
• The Class Alphaproteobacteria comprises ten orders (viz. Magnetococcales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales, Caulobacterales, Kiloniellales, Kordiimonadales, Parvularculales and Sneathiellales).
• The Alphaproteobacteria comprise most phototrophic genera, but also several genera metabolising C1-compounds (e.g., Methylobacterium spp.), symbionts of plants (e.g., Rhizobium spp.) and animals, and a group of pathogens, the Rickettsiaceae.
• Scientists often use Alphaproteobacteria of the genus Agrobacterium to transfer foreign DNA into plant genomes.
Key Terms
• Alphaproteobacteria: Alphaproteobacteria is a class of Proteobacteria that are Gram-negative.
• phototroph: An organism that carries out photon capture to acquire energy. They use the energy from light to carry out various cellular metabolic processes.
• C1-compounds: chemical compounds containing only one carbon atom, for example, methanol.
8.7C: Betaproteobacteria
Learning Objectives
• Evaluate the importance of Betaproteobacteria
Betaproteobacteria is a class of Proteobacteria that are all Gram-negative. The Betaproteobacteria consist of several groups of aerobic or facultative bacteria that are often highly versatile in their degradation capacities, but also contain chemolithotrophic genera (e.g., the ammonia-oxidising genus Nitrosomonas) and some phototrophs (members of the genera Rhodocyclus and Rubrivivax).
Nitrosomonas is a genus comprising rod shaped chemoautotrophic bacteria. This rare bacteria oxidizes ammonia into nitrite as a metabolic process. Nitrosomonas are useful in treatment of industrial and sewage waste and in the process of bioremediation. They play an important role in the nitrogen cycle by increasing the availability of nitrogen to plants while limiting carbon dioxide fixation.
Betaproteobacteria play a role in nitrogen fixation in various types of plants, oxidizing ammonium to produce nitrite- an important chemical for plant function. Many of them are found in environmental samples, such as waste water or soil. Pathogenic species within this class are the Neisseriaceae (gonorrhea and meningitis) and species of the genus Burkholderia.
Burkholderia is a genus of proteobacteria probably best known for its pathogenic members: Burkholderia mallei, responsible for glanders, a disease that occurs mostly in horses and related animals; Burkholderia pseudomallei, causative agent of melioidosis; and Burkholderia cepacia, an important pathogen of pulmonary infections in people with cystic fibrosis (CF). The Burkholderia (previously part of Pseudomonas) genus name refers to a group of virtually ubiquitous gram-negative, motile, obligately aerobic rod-shaped bacteria including both animal/human (see above) and plant pathogens as well as some environmentally important species.
The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Center for Biotechnology Information (NCBI) and the phylogeny is based on 16S rRNA-based LTP release 106 by ‘The All-Species Living Tree’ Project.
Key Points
• The Betaproteobacteria consist of several groups of aerobic or facultative bacteria that are often highly versatile in their degradation capacities.
• The Betaproteobacteria contain chemolithotrophic genera (e.g., the ammonia-oxidising genus Nitrosomonas) and some phototrophs (members of the genera Rhodocyclus and Rubrivivax).
• Betaproteobacteria play a role in nitrogen fixation in various types of plants, oxidizing ammonium to produce nitrite- an important chemical for plant function.
Key Terms
• Betaproteobacteria: Betaproteobacteria is a class of Proteobacteria. Betaproteobacteria are, like all Proteobacteria, Gram-negative.
• glanders: An infectious disease of horses, mules and donkeys caused by the bacterium Burkholderia, one species of which may be transmitted to humans.
• melioidosis: An infectious disease caused by a Gram-negative bacterium, Burkholderia pseudomallei, found in soil and water. It is endemic in Southeast Asia and northern Australia. Symptoms may include pain in chest, bones, or joints; cough; skin infections, lung nodules and pneumonia. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.07%3A_Proteobacteria/8.7B%3A_Alphaproteobacteria.txt |
Learning Objectives
• Compare the two main groups of morphologically unusual proteobacteria
Two main groups of morphologically unusual proteobacteria include spirillum and prosthecate bacteria. Spirillum in microbiology refers to a bacterium with a cell body that twists like a spiral. It is a genus comprising elongated forms with clusters of flagellae at both poles. Spirillium usually live in stagnant water rich in organic matter. They are twisted and aerobic, and are highly flexible, like a spring.
Prosthecate bacteria are a non-phylogenetically related group of Gram-negative bacteria that possess appendages, termed prosthecae. These cellular appendages are neither pili nor flagella, as they are extensions of the cellular membrane and contain cytosol. Prosthecates are generally chemoorganotrophic aerobes that can grow in nutrient-poor habitats, being able to survive at nutrient levels on the order of parts-per-million – for which reason they are often found in aquatic habitats. These bacteria will attach to surfaces with their prosthecae, allowing a greater surface area with which to take up nutrients (and release waste products). Some prosthecates will grow in nutrient-poor soils as aerobic heterotrophs.
Caulobacter: An Important Model Organism
One notable group of prosthecates is the genus Caulobacter crescentus, a Gram-negative, oligotrophic bacterium widely distributed in fresh water lakes and streams. Caulobacter is an important model organism for studying the regulation of the cell cycle, asymmetric cell division, and cellular differentiation. Caulobacter daughter cells have two very different forms. One daughter is a mobile “swarmer” cell that has a single flagellum at one cell pole that provides swimming motility for chemotaxis. The other daughter, called the “stalked” cell, has a tubular stalk structure protruding from one pole that has an adhesive holdfast material on its end, with which the stalked cell can adhere to surfaces. Swarmer cells differentiate into stalked cells after a short period of motility. Chromosome replication and cell division only occurs in the stalked cell stage. The second word of its name (crescentus) refers to the fact that it forms a crescent shape; crescentin is a protein that imparts this shape.
Key Points
• Spirillum in microbiology refers to a bacterium with a cell body that twists like a spiral.
• Prosthecate bacteria are a non-phylogenetically related group of Gram-negative bacteria that possess appendages, termed prosthecae.
• Caulobacter is an important model organism for studying the regulation of the cell cycle, asymmetric cell division, and cellular differentiation.
Key Terms
• spirillum: Any of various aerobic bacteria of the genus Spirillum, having an elongated spiral form and bearing a tuft of flagella.
• morphologically: In biology, morphology is a branch of bioscience dealing with the study of the form and structure of organisms and their specific structural features.
• prosthecate: Prosthecate bacteria are a non-phylogenetically related group of Gram-negative bacteria that possess appendages, termed prosthecae. These cellular appendages are neither pili nor flagella, as they are extensions of the cellular membrane and contain cytosol. One notable group of prosthecates is the genus Caulobacter.
8.7E: Gammaproteobacteria
Learning Objectives
• Classify Gammaproteobacteria
Gammaproteobacteria is a class of several medically, ecologically and scientifically important groups of bacteria, such as the Enterobacteriaceae ( Escherichia coli ), Vibrionaceae and Pseudomonadaceae. Like all Proteobacteria, the Gammaproteobacteria are Gram-negative.
The Gammaproteobacteria comprise several medically and scientifically important groups of bacteria, such as the Enterobacteriaceae, Vibrionaceae and Pseudomonadaceae. A number of important pathogens belongs to this class, e.g. Salmonella spp. (enteritis and typhoid fever), Yersinia pestis (plague), Vibrio cholerae (cholera), Pseudomonas aeruginosa (lung infections in hospitalized or cystic fibrosis patients), and Escherichia coli (food poisoning).
The Enterobacteriaceae is a large family of Gram-negative bacteria that includes, along with many harmless symbionts, many of the more familiar pathogens, such as Salmonella, Escherichia coli, Yersinia pestis, Klebsiella and Shigella. Other disease-causing bacteria in this family include Proteus, Enterobacter, Serratia, and Citrobacter. This family is the only representative in the order Enterobacteriales of the class Gammaproteobacteria in the phylum Proteobacteria. Phylogenetically, in the Enterobacteriales, several peptidoglycan-less insect endosymbionts form a sister clade to the Enterobacteriaceae, but since they are not validly described, this group is not officially a taxon; examples of these species are Sodalis, Buchnera, Wigglesworthia, Baumannia and Blochmannia. Members of the Enterobacteriaceae can be trivially referred to as enterobacteria, as several members live in the intestines of animals. In fact, the etymology of the family is enterobacterium with the suffix to designate a family (aceae) — not after the genus Enterobacter (which would be “Enterobacteraceae”)— and the type genus is Escherichia.
Members of Chromatium are photosynthetic and oxidize hydrogen sulfide instead of water, producing sulfur as excrement. Some Gammaproteobacteria are methane oxidizers, and many of them are in symbiosis with geothermic ocean vent dwelling animals.
Key Points
• Gammaproteobacteria include an exceeding number of important pathogens, e.g. Salmonella, Yersinia, Vibrio, Pseudomonas aeruginosa.
• Like all Proteobacteria, the Gammaproteobacteria are Gram-negative.
• Some Gammaproteobacteria are methane oxidizers, and many of them are in symbiosis with geothermic ocean vent dwelling animals.
Key Terms
• symbiosis: A close, prolonged association between two or more organisms of different species, regardless of benefit to the members.
• pathogens: A pathogen or infectious agent (colloquially known as a germ) is a microorganism (in the widest sense, such as a virus, bacterium, prion, or fungus) that causes disease in its host. The host may be an animal (including humans), a plant, or even another microorganism.
• Gammaproteobacteria: Gammaproteobacteria is a class of several medically, ecologically and scientifically important groups of bacteria, such as the Enterobacteriaceae (Escherichia coli), Vibrionaceae and Pseudomonadaceae. Like all Proteobacteria, the Gammaproteobacteria are Gram-negative.
8.7F: Deltaproteobacteria
Deltaproteobacteria is a class of Proteobacteria that are Gram-negative.
Learning Objectives
• Review the Deltaproteobacteria class of Proteobacteria
Key Points
• The Deltaproteobacteria comprise a branch of predominantly aerobic genera.
• Deltaproteobacteria include the fruiting-body-forming Myxobacteria which release myxospores in unfavorable environments.
• Deltaproteobacteria include a branch of strictly anaerobic genera, which contains most of the known sulfate- (Desulfovibrio, Desulfobacter, Desulfococcus, Desulfonema, etc. ) and sulfur-reducing bacteria (e.g. Desulfuromonas spp. ).
Key Terms
• aerobic: Living or occurring only in the presence of oxygen.
• Deltaproteobacteria: Deltaproteobacteria is a class of Proteobacteria. All species of this group are, like all Proteobacteria, Gram-negative.
• Gram-negative: Gram-negative bacteria are bacteria that do not retain crystal violet dye in the Gram staining protocol. In a Gram stain test, a counterstain (commonly safranin) is added after the crystal violet, coloring all Gram-negative bacteria with a red or pink color.
Deltaproteobacteria is a class of Proteobacteria. All species of this group are, like all Proteobacteria, Gram-negative.
The Deltaproteobacteria comprise a branch of predominantly aerobic genera, the fruiting-body-forming Myxobacteria that release myxospores in unfavorable environments. It is a branch of strictly anaerobic genera, which contains most of the known sulfate- (Desulfovibrio, Desulfobacter, Desulfococcus, Desulfonema, etc. ) and sulfur-reducing bacteria (e.g. Desulfuromonas spp.) alongside several other anaerobic bacteria with different physiology (e.g. ferric iron-reducing Geobacter spp. and syntrophic Pelobacter and Syntrophus spp.). A pathogenic intracellular Deltaproteobacteria has recently been identified.
The myxobacteria (“slime bacteria”) are a group of bacteria that predominantly live in the soil and feed on insoluble organic substances. The myxobacteria have very large genomes, relative to other bacteria, e.g. 9–10 million nucleotides. Sorangium cellulosum has the largest known (as of 2008) bacterial genome, at 13.0 million nucleotides. Myxobacteria are included among the delta group of proteobacteria, a large taxon of Gram-negative forms.
Myxobacteria can move actively by gliding. They typically travel in swarms (also known as wolf packs), containing many cells kept together by intercellular molecular signals. Individuals benefit from aggregation as it allows accumulation of extracellular enzymes which are used to digest food. This in turn increases feeding efficiency. Myxobacteria produce a number of biomedically and industrially useful chemicals, such as antibiotics. They export those chemicals outside of the cell.
The currently accepted taxonomy is based on the List of Prokaryotic Names with Standing in Nomenclature (LPSN) and National Center for Biotechnology Information (NCBI) and the phylogeny is based on 16S rRNA-based LTP release 106 by ‘The All-Species Living Tree’ Project. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.07%3A_Proteobacteria/8.7D%3A_Morphologically_Unusual_Proteobacteria.txt |
Learning Objectives
• Identify the characteristics of Epsilonproteobacteria
Epsilonproteobacteria is a class of Proteobacteria. All species of this class are, like all Proteobacteria, Gram-negative.
The Epsilonproteobacteria consist of few known genera, mainly the curved to spirilloid Wolinella spp., Helicobacter spp., and Campylobacter spp. Most of the known species inhabit the digestive tract of animals and serve as symbionts (Wolinella spp. in cows) or pathogens (Helicobacter spp. in the stomach, Campylobacter spp. in the duodenum).
There have also been numerous environmental sequences of Epsilonproteobacteria recovered from hydrothermal vents and cold seep habitats. A member of the class Epsilonproteobacteria occurs as an endosymbiont in the large gills of the deep water sea snail Alviniconcha hessleri. Often the epsilonproteobacteria living in hydrothermal deep sea-vents exhibit chemolithotrophic features, and they are able to meet their energy needs by reducing or oxidixing chemical compounds.
Helicobacter
Helicobacter is a genus of Gram-negative bacteria possessing a characteristic helix shape. They were initially considered to be members of the Campylobacter genus, but since 1989 they have been grouped in their own genus. The Helicobacter genus belongs to the class Epsilonproteobacteria, order Campylobacterales, family Helicobacteraceae and already has more than 35 species.
Some species have been found living in the lining of the upper gastrointestinal tract, as well as the liver of mammals and some birds. The most widely known species of the genus is H. pylori which infects up to 50% of the human population. Some strains of this bacterium are pathogenic to humans as it is strongly associated with peptic ulcers, chronic gastritis, duodenitis, and stomach cancer. It also serves as the type species of the genus.
Key Points
• The Epsilonproteobacteria consist of few known genera, mainly the curved to spirilloid Wolinella spp., Helicobacter spp., and Campylobacter spp.
• Most of the known species inhabit the digestive tract of animals and serve as symbionts (Wolinella spp. in cows) or pathogens (Helicobacter spp. in the stomach, Campylobacter spp. in the duodenum).
• There have also been numerous environmental sequences of Epsilonproteobacteria recovered from hydrothermal vents and cold seep habitats.
Key Terms
• Gram-negative: Gram-negative bacteria are bacteria that do not retain crystal violet dye in the Gram staining protocol. In a Gram stain test, a counterstain (commonly safranin) is added after the crystal violet, coloring all Gram-negative bacteria with a red or pink color.
• symbionts: Symbiosis is close and often long-term interaction between two or more different biological species.
• Epsilonproteobacteria: Epsilonproteobacteria is a class of Proteobacteria. All species of this class are, like all Proteobacteria, gram-negative.
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Actinobacteria are Gram-positive bacteria with high guanine and cytosine content in their DNA and can be terrestrial or aquatic.
Learning Objectives
• Discuss the characteristics associated with Actinobacteria
Key Points
• Actinobacteria include some of the most common soil life, freshwater life, and marine life, playing an important role in the decomposition of organic materials, such as cellulose and chitin, and thereby playing a vital part in organic matter turnover and carbon cycle.
• Actinobacteria are well-known as secondary metabolite producers and are hence of high pharmacological and commercial interest, since they can produce antibiotics like actinomycin.
• Actinobacteria are responsible for the peculiar odor emanating from the soil after rain (petrichor), mainly in warmer climates.
Key Terms
• actinomycin: Any of a class of toxic polypeptide antibiotics found in soil bacteria of genus Streptomyces.
• actinobacteria: A group of Gram-positive bacteria with high guanine and cytosine content in their DNA
Actinobacteria is one of the dominant phyla of bacteria. They are Gram-positive bacteria with high guanine and cytosine content in their DNA and can be terrestrial or aquatic. Analysis of glutamine synthetase sequence has been suggested for their phylogenetic analysis.
Actinobacteria include some of the most common soil life, freshwater life, and marine life, playing an important role in the decomposition of organic materials, such as cellulose and chitin; thereby playing a vital part in organic matter turnover and carbon cycle. This replenishes the supply of nutrients in the soil and is an important part of humus formation.
Other Actinobacteria inhabit plants and animals, including a few pathogens, such as Mycobacterium, Corynebacterium, Nocardia, Rhodococcus, and a few species of Streptomyces.
Actinobacteria are well-known as secondary metabolite producers and are hence of high pharmacological and commercial interest. In 1940 Selman Waksman discovered that the soil bacteria he was studying made actinomycin, a discovery for which he received a Nobel Prize. Since then, hundreds of naturally-occurring antibiotics have been discovered in these terrestrial microorganisms, especially from the genus Streptomyces.
Some Actinobacteria form branching filaments, which somewhat resemble the mycelia of the unrelated fungi, among which they were originally classified under the older name Actinomycetes. Most members are aerobic, but a few, such as Actinomyces israelii, can grow under anaerobic conditions. Unlike the Firmicutes, the other main group of Gram-positive bacteria, they have DNA with a high GC-content, and some Actinomycetes species produce external spores.
Some types of Actinobacteria are responsible for the peculiar odor emanating from the soil after rain (petrichor), mainly in warmer climates. The chemical that produces this odor is known as Geosmin. Most Actinobacteria of medical or economic significance are in subclass Actinobacteridae, order Actinomycetales. While many of these cause disease in humans, Streptomyces is notable as a source of antibiotics.
8.8B: Non-Spore-Forming Firmicutes
The Firmicutes are a phylum of bacteria, most of which have Gram-positive cell wall structure and some of which do not produce spores.
Learning Objectives
• Discuss the role of non-spore forming Firmicutes in industrial applications, specifically lactic acid bacteria (LAB)
Key Points
• Many Firmicutes produce endospores, which are resistant to desiccation and can survive extreme conditions.
• The lactic acid bacteria (LAB) comprise a class of Firmicutes that are Gram-positive, low-GC, acid-tolerant, generally non-sporulating, and non-respiring.
• The lactic acid bacteria (LAB) are rod-shaped bacilli or cocci characterized by an increased tolerance to a lower pH range.
• LAB are amongst the most important groups of microorganisms used in the food industry and are the most common microbes employed as probiotics.
Key Terms
• endospore: A dormant, tough, and non-reproductive structure produced by certain bacteria from the Firmicute phylum.
• probiotic: Describing any dietary supplement that contains live bacteria for therapeutic purposes.
• organoleptic: Of or pertaining to the sensory properties of a particular food or chemical: its taste, color, odor and feel.
Firmicutes
From Latin: firmus, strong; cutis, skin; referring to the cell wall. These are a phylum of bacteria, most of which have Gram-positive cell wall structure. A few, however, such as Megasphaera, Pectinatus, Selenomonas and Zymophilus, have a porous pseudo-outer-membrane that causes them to stain Gram-negative.
Scientists once classified the Firmicutes to include all Gram-positive bacteria, but have recently defined them to be of a core group of related forms called the low-G+C group, in contrast to the Actinobacteria.
They have round cells, called cocci (singular, coccus), or rod-like forms (bacillus). Many Firmicutes produce endospores, which are resistant to desiccation and can survive extreme conditions. They are found in various environments, and the group includes some notable pathogens. Those in one family, the heliobacteria, produce energy through photosynthesis. Firmicutes play an important role in beer, wine, and cider spoilage.The group is typically divided into the Clostridia, which are anaerobic, the Bacilli, which are obligate or facultative aerobes, and the Mollicutes.
LACTIC ACID BACTERIA (LAB)
These comprise a class of Firmicutes and are Gram-positive, low-GC, acid-tolerant, generally non-sporulating, non-respiring rod or cocci that are associated by their common metabolic and physiological characteristics.
These bacteria, usually found in decomposing plants and lactic products, produce lactic acid as the major metabolic end-product of carbohydrate fermentation. This trait has, throughout history, linked LAB with food fermentations as acidification inhibits the growth of spoilage agents. Proteinaceous bacteriocins are produced by several LAB strains and provide an additional hurdle for spoilage and pathogenic microorganisms.
Furthermore, lactic acid and other metabolic products contribute to the organoleptic and textural profile of a food item. The industrial importance of the LAB is further evinced by their generally recognized as safe (GRAS) status, due to their ubiquitous appearance in food and their contribution to the healthy microflora of human mucosal surfaces, particularly the gastrointestinal tract.
The lactic acid bacteria (LAB) are rod-shaped bacilli or cocci, characterized by an increased tolerance to a lower pH range. This aspect partially enables LAB to outcompete other bacteria in natural fermentation, as they can withstand the increased acidity from organic acid production (e.g., lactic acid).
LAB PATHWAYS
LAB are amongst the most important groups of microorganisms used in the food industry. Two main hexose fermentation pathways are used to classify LAB genera. Under conditions of excess glucose and limited oxygen, homolactic LAB catabolize one mole of glucose in the Embden-Meyerhof-Parnas pathway to yield two moles of pyruvate. Intracellular redox balance is maintained through the oxidation of NADH, concomitant with pyruvate reduction to lactic acid. This process yields two moles of ATP per mole of glucose consumed.
Representative homolactic LAB genera include Lactococcus, Enterococcus and Streptococcus. Heterofermentative LAB in turn use the pentose phosphate pathway, alternatively referred to as the pentose phosphoketolase pathway. One mole of glucose-6-phosphate is initially dehydrogenated to 6-phosphogluconate and subsequently decarboxylated to yield one mole of CO2. The resulting pentose-5-phosphate is cleaved into one mole glyceraldehyde phosphate (GAP) and one mole acetyl phosphate. GAP is further metabolized to lactate as in homofermentation, with the acetyl phosphate reduced to ethanol via acetyl-CoA and acetaldehyde intermediates.
In theory, end-products (including ATP) are produced in equimolar quantities from the catabolism of one mole of glucose. Obligate heterofermentative LAB include Leuconostoc, Oenococcus and Weissella.
PROBIOTICS
Strains of LAB are the most common microbes employed as probiotics. Most strains belong to the genus Lactobacillus.
Probiotics have been evaluated in research studies in animals and humans with respect to antibiotic-associated diarrhea, travelers’ diarrhea, pediatric diarrhea, inflammatory bowel disease, and irritable bowel syndrome (IBS).
In the future, probiotics will possibly be used for different gastrointestinal diseases, vaginosis, or as delivery systems for vaccines, immunoglobulins, and other therapies. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.08%3A_Gram-Positive_Bacteria_and_Actinobacteria/8.8A%3A_Overview_of_Gram-Positive_Bacteria_and_Actinobacteria.txt |
Learning Objectives
• Describe the characteristics associated with endospores found in Firmicutes
The Firmicutes (Latin: firmus = strong, and cutis = skin, referring to the cell wall ) are a phylum of bacteria, most of which have Gram-positive cell wall structure. A few, however, such as Megasphaera, Pectinatus, Selenomonas and Zymophilus, have a porous pseudo-outer- membrane that causes them to stain Gram-negative. Scientists once classified the Firmicutes to include all Gram-positive bacteria, but have recently defined them to be of a core group of related forms called the low-G+C group, in contrast to the Actinobacteria. They have round cells, called cocci (singular coccus), or rod-like forms (bacillus).
ENDOSPORES
Many Firmicutes produce endospores, which are resistant to desiccation and can survive extreme conditions. They are found in various environments, and the group includes some notable pathogens. Those in one family, the heliobacteria, produce energy through photosynthesis. Firmicutes play an important role in beer, wine, and cider spoilage. The group is typically divided into the Clostridia, which are anaerobic, the Bacilli, which are obligate or facultative aerobes, and the Mollicutes. On phylogenetic trees, the first two groups show up as paraphyletic or polyphyletic, as do their main genera, Clostridium and Bacillus.
An endospore is a dormant, tough, and non-reproductive structure produced by certain bacteria from the Firmicute phylum. The name “endospore” is suggestive of a spore or seed-like form (endo means within), but it is not a true spore (i.e. not an offspring). It is a stripped-down, dormant form to which the bacterium can reduce itself.
ENDOSPORE FORMATION
This is usually triggered by a lack of nutrients, and normally occurs in Gram-positive bacteria. It occurs when the bacterium divides within its cell wall. One side then engulfs the other. Endospores enable bacteria to lie dormant for extended periods, even centuries. When the environment becomes more favorable, it can reactivate itself to the vegetative state.
The endospore consists of the bacterium’s DNA and part of its cytoplasm, surrounded by a very tough outer coating. They can survive without nutrients and are resistant to ultraviolet radiation, desiccation, high temperature, extreme freezing and chemical disinfectants. They are commonly found in soil and water, where they may survive for long periods of time. Bacteria produce a single endospore internally.
The spore is sometimes surrounded by a thin covering known as the exosporium, which overlies the spore coat, which acts like a sieve that excludes large toxic molecules like lysozyme, is resistant to many toxic molecules and may also contain enzymes that are involved in germination. The cortex lies beneath the spore coat and consists of peptidoglycan.
The core wall lies beneath the cortex and surrounds the protoplast or core of the endospore. The core contains the spore chromosomal DNA which is encased in chromatin-like proteins known as SASPs (small acid-soluble spore proteins), that protect the spore DNA from UV radiation and heat. The core also contains normal cell structures, such as ribosomes and other enzymes, but is not metabolically active. Up to 20% of the dry weight of the endospore consists of calcium dipicolinate within the core, which is thought to stabilize the DNA. Dipicolinic acid could be responsible for the heat-resistance of the spore, and calcium may aid in resistance to heat and oxidizing agents.
ENDOSPORE POSITIONING
The position of the endospore differs among bacterial species and is useful in identification. The main types within the cell are terminal, subterminal, and centrally-placed endospores. Terminal endospores are seen at the poles of cells, whereas central endospores are more or less in the middle. Subterminal endospores are those between these two extremes, usually seen far enough towards the poles but close enough to the center so as not to be considered either terminal or central. Lateral endospores are seen occasionally.
When a bacterium detects environmental conditions are becoming unfavorable it may start the process of endosporulation, which takes about eight hours. The DNA is replicated and a membrane wall, known as a spore septum, begins to form between it and the rest of the cell. The plasma membrane of the cell surrounds this wall and pinches off to leave a double membrane around the DNA, and the developing structure is now known as a forespore. Calcium dipicolinate is incorporated into the forespore during this time.
Next the peptidoglycan cortex forms between the two layers and the bacterium adds a spore coat to the outside of the forespore. Sporulation is now complete, and the mature endospore will be released when the surrounding vegetative cell is degraded.
Key Points
• Firmicutes produce endospores, which are resistant to desiccation and can survive extreme conditions.
• An endospore is a dormant, tough, and non-reproductive structure produced by certain bacteria from the Firmicute phylum.
• The endospore consists of the bacterium’s DNA and part of its cytoplasm, surrounded by a very tough outer coating.
• Endospores can survive without nutrients and they are resistant to ultraviolet radiation, desiccation, high temperature, extreme freezing and chemical disinfectants.
Key Terms
• firmicutes: A phylum of bacteria, most of which have Gram-positive cell wall structure.
• endospore: A dormant, tough, and non-reproductive structure produced by certain bacteria from the Firmicute phylum. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.08%3A_Gram-Positive_Bacteria_and_Actinobacteria/8.8C%3A_Firmicutes.txt |
Actinobacteria are a group of Gram-positive bacteria with high guanine and cytosine content in their DNA.
Learning Objectives
• Outline the characteristics associated with Actinobacteria
Key Points
• Actinobacteria is one of the dominant phyla of the bacteria.
• Actinobacteria include some of the most common soil life, freshwater life, and marine life, playing an important role in decomposition of organic materials, such as cellulose and chitin, and thereby playing a vital part in organic matter turnover and carbon cycle.
• Actinobacteria are well known as secondary metabolite producers and hence of high pharmacological and commercial interest.
• Some types of Actinobacteria are responsible for the peculiar odor emanating from the soil after rain (Petrichor), mainly in warmer climates.
Key Terms
• actinobacteria: A group of Gram-positive bacteria with high guanine and cytosine content in their DNA
• petrichor: The distinctive scent which accompanies the first rain after a long warm dry spell.
• actinomycin: Any of a class of toxic polypeptide antibiotics found in soil bacteria of genus Streptomyces.
Actinobacteria are a group of Gram-positive bacteria with high guanine and cytosine content in their DNA. They can be terrestrial or aquatic. Actinobacteria is one of the dominant phyla of the bacteria. Analysis of glutamine synthetase sequence has been suggested for phylogenetic analysis of Actinobacteria.
Actinobacteria include some of the most common soil life, freshwater life, and marine life, playing an important role in decomposition of organic materials, such as cellulose and chitin, and thereby playing a vital part in organic matter turnover and carbon cycle. This replenishes the supply of nutrients in the soil and is an important part of humus formation. Other Actinobacteria inhabit plants and animals, including a few pathogens, such as Mycobacterium, Corynebacterium, Nocardia, Rhodococcus, and a few species of Streptomyces.
Actinobacteria are well known as secondary metabolite producers and hence of high pharmacological and commercial interest. In 1940 Selman Waksman discovered that the soil bacteria he was studying made actinomycin, a discovery for which he received a Nobel Prize. Since then, hundreds of naturally occurring antibiotics have been discovered in these terrestrial microorganisms, especially from the genus Streptomyces.
Some Actinobacteria form branching filaments, which somewhat resemble the mycelia of the unrelated fungi, among which they were originally classified under the older name Actinomycetes. Most members are aerobic, but a few, such as Actinomyces israelii, can grow under anaerobic conditions. Unlike the Firmicutes, the other main group of Gram-positive bacteria, they have DNA with a high GC-content, and some Actinomycetes species produce external spores. Some types of Actinobacteria are responsible for the peculiar odor emanating from the soil after rain (Petrichor), mainly in warmer climates. The chemical that produces this odour is known as Geosmin. Most Actinobacteria of medical or economic significance are in subclass Actinobacteridae, order Actinomycetales. While many of these cause disease in humans, Streptomyces is notable as a source of antibiotics. Of those Actinobacteria not in Actinomycetales, Gardnerella is one of the most researched. Classification of Gardnerella is controversial, and MeSH catalogues it as both a gram-positive and gram-negative organism.
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Learning Objectives
Describe the characteristics associated with Cyanobacteria including: cell types, forms of motility and metabolic properties
• Explain the following laws within the Ideal Gas Law
Cyanobacteria, also known as blue-green bacteria, blue-green algae, and Cyanophyta, is a phylum of bacteria that obtain their energy through photosynthesis. The ability of cyanobacteria to perform oxygenic photosynthesis is thought to have converted the early reducing atmosphere into an oxidizing one, which dramatically changed the composition of life forms on Earth by stimulating biodiversity and leading to the near-extinction of oxygen-intolerant organisms. According to the endosymbiotic theory, chloroplasts in plants and eukaryotic algae have evolved from cyanobacterial ancestors via endosymbiosis.
DISTRIBUTION AND EFFECT ON ECOSYSTEMS
Cyanobacteria can be found in almost every terrestrial and aquatic habitat. Aquatic cyanobacteria are probably best known for the extensive and visible blooms that can form in both freshwater and the marine environment. These can have the appearance of blue-green paint or scum. The association of toxicity with such blooms has frequently led to the closure of recreational waters when blooms are observed. Cyanobacteria include unicellular and colonial species. Colonies may form filaments, sheets, or even hollow balls. Some filamentous colonies show the ability to differentiate into several different cell types, including:
• Vegetative cells, the normal, photosynthetic cells that are formed under favorable growing conditions.
• Akinetes, the climate-resistant spores that may form when environmental conditions become harsh.
• Thick-walled heterocysts, which contain the enzyme nitrogenase, vital for nitrogen fixation. Heterocysts may also form under the appropriate environmental conditions (anoxic) when fixed nitrogen is scarce.
Heterocyst-forming species are specialized for nitrogen fixation and are able to bind nitrogen gas to ammonia (NH3), nitrites (NO−2) or nitrates (NO−3). These molecules can be absorbed by plants and converted into protein and nucleic acids.
Hormogonia
Many cyanobacteria form motile filaments called hormogonia, that travel from the main biomass to bud and form new colonies elsewhere. The cells in a hormogonium are often thinner than those found in the vegetative state, and the cells on either end of the motile chain may be tapered. To break away from the parent colony, a hormogonium often must tear a weaker filament cell, called a necridium.
CYANOBACTERIUM CELLS AND MOTILITY
Individual cells of a cyanobacterium typically have a thick, gelatinous cell wall. They lack flagella, but hormogonia and some species may move about by gliding along surfaces. Many of the multi-cellular filamentous forms of Oscillatoria are capable of a waving motion; the filament oscillates back and forth. In water columns some cyanobacteria float by forming gas vesicles, like in archaea. These vesicles are not organelles as such. They are not bounded by lipid membranes but by a protein sheath.
PHOTOSYNTHESIS AND OTHER METABOLIC PROCESSES
Cyanobacteria use the energy of sunlight to drive photosynthesis, a process where the energy of light is used to split water molecules into oxygen, protons, and electrons. As with any prokaryotic organism, cyanobacter does not show nuclei nor internal membranes; many cyanobacter species have folds on their external membranes which function in photosynthesis. Cyanobacteria get their color from the bluish pigment phycocyanin, which they use to capture light for photosynthesis.
Photosynthesis in cyanobacteria generally uses water as an electron donor and produces oxygen as a by-product, though some species may also use hydrogen sulfide as occurs among other photosynthetic bacteria. Carbon dioxide is reduced to form carbohydrates via the Calvin cycle. In most forms the photosynthetic machinery is embedded into folds of the cell membrane, called thylakoids.
Because of their ability to fix nitrogen in aerobic conditions they are often found in symbiontic partnerships with a number of other groups of organisms, including but not limited to fungi (lichens), corals, pteridophytes (Azolla), and angiosperms (Gunnera).
Many cyanobacteria are able to reduce ambient levels of nitrogen and carbon dioxide under aerobic conditions, a fact that may be responsible for their evolutionary and ecological success. The water-oxidizing photosynthesis is accomplished by coupling the activity of photosystem (PS) II and I (Z-scheme). In anaerobic conditions, they are also able to use only PS I—cyclic photophosphorylation—with electron donors other than water (for example hydrogen sulfide), in the same way as the purple photosynthetic bacteria.
They also share an archaeal property, the ability to reduce elemental sulfur by anaerobic respiration in the dark. Their photosynthetic electron transport shares the same compartment as the components of respiratory electron transport. Their plasma membrane contains only components of the respiratory chain, while the thylakoid membrane hosts both respiratory and photosynthetic electron transport.
Classification
The cyanobacteria were traditionally classified by morphology into five sections, referred to by the numerals I-V. The first three–Chroococcales, Pleurocapsales, and Oscillatoriales–are not supported by phylogenetic studies. However, the latter two–Nostocales and Stigonematales–are monophyletic, and make up the heterocystous cyanobacteria. Some cyanobacteria produce toxins, called cyanotoxins. This results in algal blooms, which can become harmful to other species including humans if the cyanobacteria involved produce toxins.
Key Points
• Cyanobacteria can be found in almost every terrestrial and aquatic habitat.
• Cyanobacteria include unicellular and colonial species.
• Cyanobacteria use the energy of sunlight to drive photosynthesis, a process where the energy of light is used to split water molecules into oxygen, protons, and electrons.
• Many cyanobacteria are able to reduce nitrogen and carbon dioxide under aerobic conditions, which may be responsible for their evolutionary and ecological success.
Key Terms
• cyanobacteria: Cyanobacteria, also known as blue-green bacteria, blue-green algae, and Cyanophyta, is a phylum of bacteria that obtain their energy through photosynthesis.
• photosynthesis: The process by which plants and other photoautotrophs generate carbohydrates and oxygen from carbon dioxide, water, and light energy in chloroplasts.
• heterocyst: A specialized nitrogen-fixing cell formed by some filamentous cyanobacteria. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.09%3A_Nonproteobacteria_Gram-Negative_Bacteria/8.9A%3A_Cyanobacteria.txt |
Learning Objectives
• Describe the mechanisms that specific bacteria use to undergo anoxygenic photosynthetic bacteria, including: green sulfur and purple sulfur bacteria
Phototrophy is the process by which organisms trap light energy (photons) and store it as chemical energy in the form of ATP and/or reducing power in NADPH. There are two major types of phototrophy: chlorophyll-based chlorophototrophy and rhodopsin-based retinalophototrophy. Chlorophototrophy can further be divided into oxygenic photosynthesis and anoxygenic phototrophy.
Oxygenic and anoxygenic photosynthesizing organisms undergo different reactions, either in the presence of light or with no direct contribution of light to the chemical reaction (colloquially called “light reactions” and “dark reactions”, respectively). Anoxygenic photosynthesis is the phototrophic process where light energy is captured and converted to ATP, without the production of oxygen; water is, therefore, not used as an electron donor. There are several groups of bacteria that undergo anoxygenic photosynthesis: green sulfur bacteria, green and red filamentous anoxygenic phototrophs (FAPs), phototrophic purple bacteria, phototrophic acidobacteria, and phototrophic heliobacteria.
ANOXYGENIC PHOTOTROPHS
Anoxygenic phototrophs have photosynthetic pigments called bacteriochlorophylls; these are similar to chlorophyll found in eukaryotes. Bacteriochlorophyll a and b have wavelengths of maximum absorption at 775 nm and 790 nm, respectively. Unlike oxygenic phototrophs, anoxygenic photosynthesis only functions using either one of two possible types of photosystem. This restricts them to cyclic electron flow; they are therefore unable to produce O2 from the oxidization of H2O.
GREEN SULFUR BACTERIA
The green sulfur bacteria are a family of obligately anaerobic photoautotrophic bacteria most closely related to the distant Bacteroidetes. They are non-motile with the exception of Chloroherpeton thalassium, which may glide. They come in sphere, rods, and spiral forms. Photosynthesis is achieved using bacteriochlorophyll (BChl) c, d, or e, in addition to BChl a and chlorophyll a, in chlorosomes attached to the membrane. The electron transport chain (ETC) of green sulfur bacteria uses the reaction centre bacteriochlorophyll pair, P840. When light is absorbed by the reaction center, P840 enters an excited state with a large negative reduction potential, and so readily donates the electron to bacteriochlorophyll 663 which passes it on down the electron chain. The electron is transferred through a series of electron carriers and complexes until it either returns to P840 or is used to reduce NAD+. If the electron leaves the chain to reduce NAD+, P840 must be reduced for the ETC to function again. The green sulfur bacterias’ small dependence on organic molecule transporters and transcription factors indicates that these organisms are adapted to a narrow range of energy-limited conditions, and fit into an ecology shared with the simpler cyanobacteria,
PURPLE SULFUR BACTERIA
The purple sulfur bacteria are a group of Proteobacteria capable of photosynthesis. They are anaerobic or microaerophilic, and are often found in hot springs or stagnant water. Unlike plants, algae, and cyanobacteria, they do not use water as their reducing agent, and so do not produce oxygen. Instead, they use hydrogen sulfide, which is oxidized to produce granules of elemental sulfur. This in turn may be oxidized to form sulfuric acid.The purple sulfur bacteria are divided into two families: the Chromatiaceae and Ectothiorhodospiraceae, which respectively produce internal and external sulfur granules, and show differences in the structure of their internal membranes.
Purple sulfur bacteria are generally found in illuminated anoxic zones of lakes and other aquatic habitats where hydrogen sulfide accumulates. They are also found in “sulfur springs” where geochemically or biologically produced hydrogen sulfide can trigger the formation of blooms of purple sulfur bacteria. Anoxic conditions are required for photosynthesis; these bacteria cannot thrive in oxygenated environments. The electron transport chain of purple non-sulfur bacteria begins when the reaction center bacteriochlorophyll pair, P870, becomes excited by the absorption of light. Excited P870 will then donate an electron to Bacteriopheophytin, which then passes it on to a series of electron carriers down the electron chain. In the process, it will generate a proton motor force (PMF) which can then be used to synthesize ATP by oxidative phosphorylation. The electron returns to P870 at the end of the chain so it can be used again once light excites the reaction-center.
Key Points
• There are several groups of bacteria that undergo anoxygenic photosynthesis: green sulfur bacteria, green and red filamentous anoxygenic phototrophs (FAPs), phototrophic purple bacteria, phototrophic acidobacteria, and phototrophic heliobacteria.
• Anoxygenic phototrophs have photosynthetic pigments called bacteriochlorophylls similar to chlorophyll found in eukaryotes.
• Green sulfur bacteria are a family of obligately anaerobic photoautotrophic bacteria most closely related to the distant Bacteroidetes which are adapted to a narrow range of energy-limited conditions, an ecology shared with the simpler cyanobacteria.
• Purple sulfur bacteria are a group of Proteobacteria capable of photosynthesis, anaerobic or microaerophilic, and often found in hot springs or stagnant water.
Key Terms
• anoxygenic: That does not involve the production of oxygen
• photosynthesis: The process by which plants and other photoautotrophs generate carbohydrates and oxygen from carbon dioxide, water, and light energy in chloroplasts.
• photoautotroph: An organism, such as all green plants, that can synthesize its own food from inorganic material using light as a source of energy | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.09%3A_Nonproteobacteria_Gram-Negative_Bacteria/8.9B%3A_Anoxygenic_Photosynthetic_Bacteria.txt |
Learning Objectives
• Describe the characteristics associated with Prochlorophytes, a member of the Picoplankton
Picoplankton is the fraction of plankton, composed by cells between 0.2 and 2 μm, that is either photosynthetic (photosynthetic picoplankton; ) or heterotrophic (heterotrophic picoplankton). Some species are also mixotrophic. Picoplankton are responsible for the majority of the primary productivity in oligotrophic gyres, and are different from nanoplankton and microplankton. Because they are small, they have a greater surface-to-volume ratio, which enables them to obtain scarce nutrients in these ecosystems.
Prochlorophyta are a photosynthetic prokaryote member of the phytoplankton group Picoplankton. These oligotrophic organisms are abundant in nutrient-poor tropical waters and use a unique photosynthetic pigment, divinyl-chlorophyll, to absorb light and acquire energy. These organisms lack red and blue Phycobilin pigments and have staked thylakoids, both of which make them different from Cyanophyta ( Cyanobacteria ). Prochlorophyta were initially discovered in 1975 near the Great Barrier Reef and off the coast of Mexico. The following year, Ralph A. Lewin, of the Scripps Institution of Oceanography, assigned them as a new algal sub-class.
In addition to Prochlorophyta, other phytoplankton that lack Phycobilin pigments were later found in freshwater lakes in the Netherlands, by Tineke Burger-Wiersma. These organisms were termed Prochlorothrix. In 1986, Prochlorococcus was discovered by Sallie W. Chisholm and his colleagues. These organisms might be responsible for a significant portion of the global primary production.
Prochlorophytes are very small microbes generally between 0.2 and 2 µm (Photosynthetic picoplankton). They morphologically resemble Cyanobacteria, formally known as Blue Green Algae. Members of Prochlorophyta have been found as coccoid (spherical) shapes, like Prochlorococcus, and as filaments, like Prochlorothrix.
Key Points
• Picoplankton are responsible for the majority of the primary productivity in oligotrophic gyres, and are different from nanoplankton and microplankton.
• Because they are small, they have a greater surface-to-volume ratio. This enables them to obtain the scarce nutrients in these ecosystems.
• Prochlorophyta are a photosynthetic prokaryote member of the phytoplankton group Picoplankton. They are abundant in nutrient poor tropical waters and use a unique photosynthetic pigment, divinyl-chlorophyll, to absorb light and acquire energy.
Key Terms
• prochlorophyta: a photosynthetic prokaryote member of the phytoplankton group Picoplankton
• picoplankton: plankton composed of cells between 0.2 and 2 micrometers that are either photosynthetic or heterotrophic
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Chlamydiae are a bacterial phylum and class whose members are obligate intracellular pathogens.
Learning Objectives
• Discuss the evidence that supports Chlamydiae as a unique bacterial evolutionary group
Key Points
• Chlamydiae replicate inside the host cells and are termed intracellular.
• Most intracellular chlamydiae are located in an inclusion body or vacuole.
• Chlamydiae is a unique bacterial evolutionary group that separated from other bacteria approximately a billion years ago. It falls into the clade Planctobacteria in the larger clade Gracilicutes.
• Chlamydia infection is a common sexually transmitted infection (STI) in humans caused by the bacterium Chlamydia trachomatis.
Key Terms
• chlamydiae: Chlamydiae is a bacterial phylum and class whose members are obligate intracellular pathogens.
• inclusion body: Inclusion bodies are nuclear or cytoplasmic aggregates of stainable substances, usually proteins.
Chlamydiae are a bacterial phylum and class whose members are obligate intracellular pathogens. Many chlamydiae coexist in an asymptomatic state within specific hosts. It is widely believed that these hosts provide a natural reservoir for these species. All known chlamydiae only grow by infecting eukaryotic host cells. They are as small or smaller than many viruses.
Chlamydiae replicate inside the host cells and are termed intracellular. Most intracellular chlamydiae are located in an inclusion body or vacuole. Outside of cells they survive only as an extracellular infectious form. Chlamydiae can only grow where their host cells grow. Therefore, chlamydiae cannot be propagated in bacterial culture media in the clinical laboratory. Chlamydiae are most successfully isolated while still inside their host cell.
Chlamydiae is a unique bacterial evolutionary group that separated from other bacteria approximately a billion years ago. Cavalier-Smith has postulated that the Chlamydiae fall into the clade Planctobacteria in the larger clade Gracilicutes. The species from this group can be distinguished from all other bacteria by the presence of conserved indels in a number of proteins such as RNA polymerase alpha subunit, Gyrase B, Elongation factor-Tu and Elongation factor-P, and by large numbers of signature proteins that are uniquely present in different chlamydiae species. Reports have varied as to whether Chlamydiae is related to Planctomycetales or Spirochaetes. However, genome sequencing indicates that 11% of the genes in Candidatus Protochlamydia amoebophila UWE25 and 4% in Chlamydiaceae are most similar to chloroplast, plant, and cyanobacterial genes. Phylogeny and shared presence of conserved indels in proteins such as RNA polymerase Beta subunit and lysyl-tRNA synthetase indicate that Verrucomicrobia are the closest free-living relatives of these parasitic organisms.
There are three described species of chlamydiae that commonly infect humans:
1. Chlamydia trachomatis, which causes the eye-disease trachoma and the sexually transmitted infection chlamydia.
2. Chlamydia pneumoniae, which causes a form of pneumonia.
3. Chlamydia psittaci, which causes psittacosis.
Chlamydia infection is a common sexually transmitted infection (STI) in humans caused by the bacterium Chlamydia trachomatis. The term Chlamydia infection can also refer to infection caused by any species belonging to the bacterial family Chlamydiaceae. C. trachomatis is found only in humans. Chlamydia is a major cause of blindness today, especially in developing countries.
Risk factors include a history of chlamydial or other sexually transmitted infection, new or multiple sexual partners, and inconsistent condom use. C. trachomatis infection can be effectively cured with antibiotics once it is detected. Current guidelines recommend: azithromycin, doxycycline, erythromycin, or ofloxacin. Agents recommended for pregnant women include erythromycin or amoxicillin.
8.10B: Planctomycetes
Planctomycetes are a phylum of aquatic bacteria and are found in samples of brackish, marine, and fresh water.
Learning Objectives
• Describe the characteristics associated with Planctomycetes
Key Points
• In structure, the organisms of this group are ovoid and have a holdfast, called the stalk, at the non-reproductive end that helps them to attach to each other during budding.
• The organisms belonging to this group have a glycoprotein rich in glutamate instead of murein in their cell wall.
• The nuclear material in planctomycetes can sometimes be enclosed in a double membrane.
Key Terms
• nucleoid: The irregularly-shaped region within a prokaryote cell where the genetic material is localized.
• operon: A unit of genetic material that functions in a coordinated manner by means of an operator, a promoter, and structural genes that are transcribed together.
• planctomycetes: A phylum of aquatic bacteria that are found in samples of brackish, and marine and fresh water.
• budding: a form of asexual reproduction in which a new organism develops from an outgrowth or bud on another one
Planctomycetes are a phylum of aquatic bacteria. They are found in samples of brackish, marine, and fresh water. They reproduce by budding. In structure, the organisms of this group are ovoid and have a holdfast, called the stalk, at the non-reproductive end that helps them to attach to each other during budding.
The organisms belonging to this group lack murein in their cell wall. Murein is an important heteropolymer present in most bacterial cell walls that serves as a protective component in the cell wall skeleton. Instead, their walls are made up of glycoprotein rich in glutamate. Planctomycetes have internal structures that are more complex than typically expected in prokaryotes. While they do not have a nucleus in the eukaryotic sense, the nuclear material can sometimes be enclosed in a double membrane. In addition to this nucleoid, there are two other membrane-separated compartments; the pirellulosome or riboplasm, which contains the ribosome and related proteins, and the ribosome-free paryphoplasm.
Cavalier-Smith has postulated that the Planctomycetes are within the clade Planctobacteria in the larger clade Gracilicutes. RNA sequencing shows that the planctomycetes are related to the Verrucomicrobia and possibly the Chlamydiae. A number of essential pathways are not organized as operons, which is unusual for bacteria. A number of genes have been found (through sequence comparisons) that are similar to genes found in eukaryotes. One such example is a gene sequence (in Gemmata obscuriglobus) that was found to have significant homology to the integrin alpha-V, a protein that is important in transmembrane signal transduction in eukaryotes. The life cycle of many planctomycetes involves alternation between sessile cells and flagellated swarmer cells. The sessile cells bud to form the flagellated swarmer cells which swim for a while before settling down to attach and begin reproduction. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.10%3A_Irregular_Bacterial_cells/8.10A%3A_Chlamydiae.txt |
Verrucomicrobia is a recently described phylum of bacteria which is part of the PVC superphylum.
Learning Objectives
• Describe the structure of Verrucomicrobia and its placement in the PVC superphylum
Key Points
• The PVC group includes Chlamydiae, Lentisphaerae, Planctomycetes, Verrucomicrobia, Poribacteria and OP3.
• Verrucomicrobia possess a compartmentalised cell plan with a condensed nucleoid and the ribosomes pirellulosome (enclosed by the intracytoplasmic membrane ) and paryphoplasm compartment between the intracytoplasmic membrane and cytoplasmic membrane.
• Evidence suggests that verrucomicrobia are abundant within the environment, and important (especially to soil cultures ).
Key Terms
• verrucomicrobia: Verrucomicrobia is a recently described phylum of bacteria which is part of the PVC superphylum and they possess a compartmentalised cell plan with a condensed nucleoid.
Verrucomicrobia is a recently described phylum of bacteria which is part of the PVC superphylum. The PVC group includes Chlamydiae, Lentisphaerae, Planctomycetes, Verrucomicrobia, Poribacteria and OP3. Support for this superphylum has been found by examining the RNA polymerase protein RpoB.
RpoB is the gene that encodes the β subunit of bacterial RNA polymerase. This protein has a unique 3 amino acid insert in all sequenced Chlamydiae, Lentisphaerae and Verrucomicrobia species. In addition, a conserved protein of unknown function is present in all sequenced species from the phyla Chlamydiae, Lentisphaerae, Planctomycetes and Verrucomicrobia. This protein is absent in the Poribacteria. Study of additional proteins from this proposed superphylum suggests that the Poribacteria may be separate from this clade. The Planctomycetes may be basal to the Chlamydiae-Verrucomicrobia-Lentisphaerae clade.
Like the Planctomycetes species, Verrucomicrobia possess a compartmentalised cell plan with a condensed nucleoid and the ribosomes pirellulosome (enclosed by the intracytoplasmic membrane) and paryphoplasm compartment between the intracytoplasmic membrane and cytoplasmic membrane. Cavalier-Smith has postulated that the Verrucomicrobia belong in the clade Planctobacteria in the larger clade Gracilicutes. 16S rRNA data corroborate that view. In 2008, the whole genome of Methylacidiphilum infernorum (2.3 Mbp) was published. On the single circular chromosome, 2473 predicted proteins were found, 731 of which had no detectable homologs. These analyses also revealed many possible homologs with Proteobacteria.
Evidence suggests that verrucomicrobia are abundant within the environment, and are important especially to soil cultures. Verrucomicrobia have been isolated from fresh water, soil environments and human feces. A number of as-yet uncultivated species have been identified in association with eukaryotic hosts including extrusive explosive ectosymbionts of protists and endosymbionts of nematodes residing in their gametes. While verrucae is another name for the warts often found on the hands and feet, this phylum is so called not because it is a causative agent thereof, but because of its wart-like morphology.
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Bacteroides and Flavobacterium are both Gram-negative bacteria that can be either motile or non-motile.
Learning Objectives
• Describe the role of Bacteroides in the normal flora of the human gastrointestinal tract and the role of Flavobacterium in causing disease in freshwater fish
Key Points
• Bacteroides are characterized by their mutualistic behavior and are typically present in the gastrointestinal tract of mammals to function as normal flora.
• Bacteroides are capable of breaking down and processing large complex molecules within the intestine.
• Flavobacterium are found in both soil and fresh water environments. Pathogenic strains of Flavobacterium can infect fish such as salmonids and trouts.
Key Terms
• mutualistic: Mutually beneficial.
• normal flora: The aggregate of microorganisms that reside on the surface and in deep layers of skin, in the saliva and oral mucosa, in the conjunctiva, and in the gastrointestinal tracts. Also known as human microbiota.
Bacteroides include a specific genus of gram-negative bacillus bacteria. This genus of bacteria is characterized by their sphingolipid based membranes and are typically non-endospore forming and anaerobic. The bacteroides are further characterized as mutualistic and have been identified in the mammalian gastrointestinal system. The ability of the bacteroides to function in an anaerobic environment allow them to reside in the abdominal cavity in aerotolerant conditions. The presence of bacteroides in the normal flora of mammals is indicative of its role in processing complex molecules to simpler ones that can be utilized by the host. The energy sources for the bacteroides are typically derived from the host. The role of bacteroides in the normal flora extends beyond their ability to breakdown larger complex molecules and can display protective function. The bacteroides are able to benefit the host by preventing infection by potential pathogens that may colonize and infect the gut as well. Due to the abundancy of the bacteroides within the gastrointestinal system, bacteroides constitute a significant portion of the fecal bacterial population.
Flavobacterium include a specific genus of gram-negative bacteria that are characterized by their presence in soil and fresh water environments. Flavobacterium can be either non-motile or motile and are rod-shaped. To date, there are 10 established species of flavobacterium and several new proposed species. The flavbacterium are characterized by their ability to cause disease in freshwater fish such as salmon and rainbow trouts. For example, the species Flavobacterium psychrophilum is responsible for causing Bacterial Cold Water Disease (BCWD) on salmonids and Rainbow Trout Fry Disease (RTFS) on rainbow trouts. The species Flavobacterium branchiophilum causes the Bacterial Gill Disease (BGD) on trouts.
8.11B: Acidobacteria
Acidobacteria are a newly formed phylum of bacteria that are physiologically diverse and abundant in soil environments.
Learning Objectives
• Discuss the advantages that Acidobacteria have developed due to their ability to thrive in acidic conditions
Key Points
• Many acidobacteria can be classified as acidophilic organisms because they are able to thrive and reside within highly acidic environments.
• The acidobacteria that are considered to be acidophilic have developed efficient and effective mechanisms to pump out protons to ensure their intracellular environments remains at a neutral pH.
• It is hypothesized that acidobacteria play a major role in the ecosystem based on their abundance in soil.
Key Terms
• acidophilic: Being an acidophile.
Members of Acidobacteria are physiologically diverse. They were first recognized as a novel division in 1997. The members of this phylum are acidophilic, physiologically diverse, and are ubiquitous in soils. The Phylum can be further broken down in Class Acidobacteria with Order Acidobacteriales and Class Solibacteres with Order Solibacterales.
Acidophilic organisms are capable of thriving under highly acidic conditions. The ability to thrive under acidic conditions has promoted the evolution of highly efficient and effective mechanisms that lend them protection in these environments. For example, most acidophiles are able to pump protons out of the intracellular space to maintain a neutral pH within the cytoplasm. The mechanisms used to pump protons out are quick and effective. This is advantageous as the intracellular proteins are not required to develop tolerance against highly acidic conditions. However, not all members of this phylum are considered to be acidophilic.
Since they have only recently been discovered and the large majority have not been cultured, the ecology and metabolism of these bacteria is not well understood. However, these bacteria may be an important contributor to ecosystems, since they are particularly abundant within soils. The first species of this phylum, Acidobacterium capsulatum, was discovered in 1991. Other notable species are Holophaga foetida, Geothrix fermentans, Acanthopleuribacter pedis, and Bryobacter aggregatus.
8.11C: Cytophaga and Relatives
Cytophaga are a type of bacteria characterized as Gram-negative, rod shaped bacteria that utilize a gliding mechanism for locomotion.
Learning Objectives
• Describe the unique form of locomotion for Cytophaga
Key Points
• Cytophaga are commonly associated with infections found on fish as a result of abnormal water temperatures that promote growth.
• Cytophaga columnaris is responsible for columnaris disease in salmonid fish in abnormally high water temperatures and result in lesion and ulcerations on the gill.
• Cytophaga psychrophila is responsible for the cold water disease in trout and results in skin lesions and occurs in subnormal water temperatures.
Key Terms
• myxobacteria: A type of bacteria known as the “slime bacteria” that reside in soil and feed on insoluble organic matter.
• columnaris: A disease characterized by the presence of ulcerations on the skin and the development of fungus-like patches on the gill filaments.
Cytophaga represent gram-negative, gliding, rod-shaped bacteria. The bacterial gliding is a form of locomotion utilized by Cytophaga that allows the bacteria to move under its own power. In this specific type of locomotion, the exact mechanisms are unknown, but it is known that this process does not require a flagella. However, a few mechanisms have been partially identified in certain species that utilize the gliding locomotion and these include the use of a type IV pili, the use of focal adhesion complexes distributed through the body, and the use of a polysaccharide slime that is ejected from one the ends of the body. Gliding can also be found in bacteria that are categorized as cyanobacteria and myxobacteria.
Cytophaga include the following species: Cytophaga columnaris, Cytophaga johnsonae, and Cytophaga psychrophila. The Cytophaga columnaris, also referred to as Flavobacterium columnare or Bacillus columnaris, are responsible for the columnaris disease in salmonid fish. Columnaris disease is characterized by the presence of ulcerations on the skin and the development of fungus-like patches on the gill filaments. This disease is highly contagious and fatal due to the damage of the gills. The Cytophaga johnsonae, or Flavobacterium johnsonae, are associated with false columnaris disease which is similar to columnaris disease and characterized by the presence of damage at the gills. Lastly, the species Cytophaga psychrophila, orFlavobacterium psychrophilum, is responsible for causing bacterial cold water disease (BCWD) in salmonid fish. The disease occurs at subnormal water temperatures and results in lesions on the skin and fins. The Cytophaga species are now referred to as Flavobacterium due to further characterization and change in phylogeny. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.11%3A_Other_Bacterial_Groups/8.11A%3A_Bacteroides_and_Flavobacterium.txt |
Bacteria categorized under the Phylum Bacteroidetes and Phlyum Chlorobi are closely related base on comparative genomic analysis.
Learning Objectives
• Describe the major classes of Bacteroidetes, including: Bacteroidia and Porphyromonas a well as Phlyum Chlorobi
Key Points
• The close relationship between Phylum Bacteroidetes and Phylum Chlorobi are supported by comparative genomic analysis which indicates they are derived from a common ancestor based on unique molecular signatures and common proteins.
• Phylum Bacteroidetes are composed of three large classes of gram-negative bacteria that are rod-shaped, non-spore forming, and present in anaerobic conditions. Bacteroidetes are found in numerous environments ranging from soils, sediments, sea water, and the guts and skin of animals.
• Phylum Chlorobi are composed of green sulfur bacteria that are categorized as photolithotrophic oxidizers of sulfur. Chlorobi species are commonly found in symbiotic relationships with colorless, nonphotosynthetic bacteria.
Key Terms
• photolithotropic: Obtain energy from light and use inorganic electron donors only to fuel biosynthetic reactions.
The Phylum Bacteroidetes are characterized as rod-shaped, gram-negative bacteria that are non-spore forming and are present in anaerobic environments. Bacteroidetes are capable of thriving in numerous environments that include soil, sediments, sea water, and in the guts and on skin of animal hosts. The Bacteroidetes are classified into three large classes which include the Bacteroidia class and the Porphyromonas class. The Bacteroidia class is the most studied and is present in the gastrointestinal system of mammals which allows it to be abundant in the feces. The Porphyromonas class is characterized by their presence in the oral cavity of humans. The bacteria categorized as bacteroidetes are opportunistic and are rarely pathogenic as they constitute part of the normal flora.
The Phylum Chlorobi are characterized by bacteria that are obligately anaerobic photoautotrophic which includes green sulfur bacteria. The green sulfur bacteria are photolithotropic oxidizers of sulfur and utilize a noncyclic electron transport chain. The green sulfur bacteria are closely related to Bacteroidetes and are non-motile and can be found as sphere, rod, or spiral shaped. The most commonly studied model is Chlorobium tepidum which has had its complete genome sequences. Chlorobium species typically exist in symbiotic relationships with a colorless, nonphotosynthetic bacteria.
The Phlyum Chlorobi is often grouped with the Phlyum Bacteroidetes because their branches are very close together in the phylogenetic tree. By utilizing sequencing techniques such as comparative genomic analysis, there have been three proteins which are unique to all members of the Bacteroidetes and Chlorobi phyla but not to other bacteria indicating a conserved protein signature. Further analysis has identified additional molecular signatures that support the close relationship between these two phyla as well indicating a common ancestor.
8.11E: Fusobacteria
Fusobacterium are anaerobic, non-spore forming, gram-negative bacteria that are associated with periodontal disease and Lemierre’s syndrome.
Learning Objectives
• Describe the role of Fusobacterium in Lemierre’s syndrome
Key Points
• Fusobacterium flourish in anaerobic conditions.
• Fucosbacterium necrophorum are responsible for causing Lemierre’s syndrome which is characterized by thrombophlebitis.
• Identification of Fusobacterium within the laboratory is difficult due to their asaccharolytic nature; however, advancements in molecular technology has resulted in identification of numerous species.
Key Terms
• periodontal disease: disease surrounding a tooth
• asaccharolytic: incapable of metabolizing carbohydrates
• septicemia: presence of pathogenic organisms in the bloodstream leading to sepsis
Fusobacteria are a genus of bacteria categorized as gram-negative with similarities to Bacteroides. Fusobacteria are rod-shaped bacilli capable of thriving in anaerobic conditions. However, in contrast to Bacteroides, Fusobacterium have a potent lipopolysaccharide that can function as an endotoxin. The Fusobacterium are associated with infection and disease including periodontal diseases, topical skin ulcers and Lemierres’s syndrome. Fusobacterium are difficult to identify in the laboratory due to their asaccharolytic nature. However, the use of novel molecular biology techniques has allowed for the the identification of new species that are included in Fusobacterium. The diseases attributed to Fusobacterium infection involve symptoms that include tissue necrosis, septicemia, intra-amniotic infections and ulcers.
A specific disease caused by Fusobacteria includes Lemierres’s syndrome. Lemierres’s syndrome is also known as postanginal sepsis and is a form of thrombophlebitis. Thrombophlebitis is inflammation caused by a blood clot. In individuals infected with Fusobacterium necrophorum and additonal Fusobacterium as well, a sore develops in the throat due to infection by a bacterium of the Streptococcus genus. Once this sore develops into a peritonsillar abscess, the pocket is filled with pus and bacteria in close proximity to the tonsils. At this point, bacteria which are capable of thriving in anaerobic conditions, such as Fusobacterium necrophorum can flourish deep in the abscess. At this point, the bacteria are able to pass into the neighboring jugular vein and cause an infected clot to form. The bacteria are then able to circulate throughout the body via the bloodstream and pieces of the blood clot will dissociate from the original site and travel to the lungs. The pieces of the clot will settle in the lungs and block branches of the pulmonary artery, resulting in shortness of breath, chest pain and pneumonia. Fusobacteria are normal flora within the oropharyngeal and can clearly result in disease if conditions are optimal. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.11%3A_Other_Bacterial_Groups/8.11D%3A_Bacteroidetes_and_Chlorobi.txt |
Spirochaetes are characterized by the presence of a double-membrane and long, spiral-shaped cells that are chemoheterotrophic.
Learning Objectives
• Outline the characteristics associated with spirochaetes and the associated diseases
Key Points
• Spirochaetes are chemoheterotrophic in nature and capable of thriving in anaerobic conditions.
• The spirochaetes are categorized by the presence of axial filaments which run lengthwise between the inner and outer membranes in periplasmic space.
• Spirochaetes are capable of causing diseases including leptospirosis, Lyme disease, relapsing fever and syphilis.
Key Terms
• periplasmic: surrounding the plasma of a bacterium
The spirochaetes belong to a phylum of distinctive double-membrane bacteria that are characterized by their long, spiral-shaped cells. The spirochaetes are chemoheterotrophic in nature, free-living and capable of thriving in anaerobic environments. They are often distinguished from other bacterial phyla by the location of their flagella. The flagella, in spirochaetes, runs lengthwise between the inner and outer membranes in the periplasmic space. Often referred to as axial filaments, there is a twisting motion that occurs which allows the spirochaete to move. During reproduction, the spirochaete is capable of undergoing asexual reproduction via binary fission. The binary fission allows for production of two separate spirochaetes.
The spirochaetes can be divided into three families which include: Brachyspiraceae, Leptospiraceae, and Spirochaetaceae. These families are all categorized under a single order, Spirochaetales. There are specific species of spirochaetes that are considered to be pathogenic. Some of the pathogenic species include:
• Leptospira, the cause of leptospirosis – leptospirosis is transmitted to humans from animals and a common form of transmission is by allowing contaminated water to come in contact with unhealed breaks in the skin, eyes and mucous membranes. The water becomes contaminated by coming into contact with the urine of an infected animal.
• Borrelia burgdorferi, Borrelia garinii, Borrelia afzelii, the cause of lyme-disease
• Borrelia recurrentis, the cause of relapsing fever
• Treponema pallidum, subspecies pallidum, the cause of syphilis
• Treponema pallidum, subspecies pertenue, the cause of yaws (tropical infection of the skin, bones and joints)
• Brachyspira pilosicoli and Brachyspira aalborgi, the cause of intestinal spirochetosis
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Along with Thermotogae, members of Aquificae are thermophilic eubacteria.
Learning Objectives
• Differentiate Aquificales from Thermotogae
Key Points
• The phylum Thermotogae is composed of gram-negative staining, anaerobic, mostly thermophilic, and hyperthermophilic bacteria.
• The Aquificae phylum is a diverse collection of bacteria that live in harsh environmental settings. They have been found in hot springs, sulfur pools, and thermal ocean vents.
• A 51 amino acid insertion has been identified in SecA preprotein translocase which is shared by various members of the phylum Aquificae as well as 2 Thermotoga species. The presence of the insertion in the Thermotoga species may be due to a horizontal gene transfer.
• However, a close relationship of the Aquificae to Thermotogae and the deep branching of Aquificae is not supported by phylogenetic studies based upon other gene/ protein sequences and also by conserved signature indels in several highly conserved universal proteins.
Key Terms
• thermophile: An organism — a type of extremophile — that thrives at relatively high temperatures, between 45 and 122 °C (113 and 252 °F). Many thermophiles are archaea. Thermophilic eubacteria are suggested to have been among the earliest bacteria.
• hyperthermophile: An organism that thrives in extremely hot environments— from 60 degrees C (140 degrees F) upwards. An optimal temperature for the existence of hyperthermophiles is above 80°C (176°F). Hyperthermophiles are a subset of extremophiles, micro-organisms within the domain Archaea, although some bacteria are able to tolerate temperatures of around 100°C (212°F), as well.
Along with Thermotogae, members of Aquificae are thermophilic eubacteria (thermophiles).
Aquificales
The Aquificae phylum is a diverse collection of bacteria that live in harsh environmental settings. They have been found in hot springs, sulfur pools, and thermal ocean vents. Members of the genus Aquifex, for example, are productive in water between 85 to 95 °C. They are the dominant members of most terrestrial neutral to alkaline hot springs above 60 degrees Celsius. They are autotrophs, and are the primary carbon fixers in these environments. They are true bacteria (domain bacteria) as opposed to the other inhabitants of extreme environments, the Archaea.
Comparative genomic studies have identified six conserved signature indels (CSIs) that are specific for the species from the phylum Aquificae and provide potential molecular markers for this phylum. Additionally, a 51 amino acid insertion has been identified in SecA preprotein translocase which is shared by various members of the phylum Aquificae as well as two Thermotoga species. The presence of the insertion in the Thermotoga species may be due to a horizontal gene transfer. In the 16S rRNA gene trees, the Aquificae species branch in the proximity of the phylum Thermotogae (another phylum comprising hyperthermophiles) close to the archaeal-bacterial branch point. However, a close relationship of the Aquificae to Thermotogae and the deep branching of Aquificae is not supported by phylogenetic studies based upon other gene/protein sequences and also by conserved signature indels in several highly conserved universal proteins.
Thermotogae
The phylum Thermotogae is composed of gram-negative staining, anaerobic, mostly thermophilic, and hyperthermophilic bacteria. The name of this phylum is derived from the existence of many of these organisms at high temperatures along with the characteristic sheath structure, or “toga,” surrounding the cells of these species. Recently, some Thermotogae existing in mesophilic temperatures have also been identified. Although Thermotogae species exhibit Gram-negative staining, they are bounded by a single unit lipid membrane. Therefore, they are monoderm bacteria. Because of the ability of some Thermotogae species to thrive at high temperatures, they are considered attractive targets for use in industrial processes. The metabolic ability of Thermotogae to utilize different complex-carbohydrates for production of hydrogen gas led to these species being cited as a possible biotechnological source for production of energy alternative to fossil fuels.
This phylum presently consists of a single class (Thermotogae), order (Thermotogales), and family (Thermotogaceae). It contains a total of nine genera (viz. Thermotoga, Petrotoga, Thermosipho, Fervidobacterium, Marinitoga, Kosmotoga, Geotoga, Thermopallium, and Thermococcoides), all of which are currently part of the family Thermotogaceae. In the 16S rRNA trees the Thermotogae have been observed to branch with the Aquificae in close proximity to the archaeal-bacterial branch point. The Thermotogae have also been scrutinized for their supposedly profuse lateral gene transfer (LGT) with Archaeal organisms. However, recent studies based on more robust methodologies suggest that incidence of LGT between Thermotogae and other groups including Archaea is not as high as suggested in earlier studies.
Until recently, no biochemical or molecular markers were known that could distinguish the species from the phylum Thermotogae from all other bacteria. However, a recent comparative genomic study has identified large numbers of conserved signature indels (CSIs) in important proteins that are specific for either all Thermotogae species or a number of its sub-groups. The newly discovered molecular markers provide novel means for identification and circumscription of species from the Thermotogae phylum in molecular terms and for future revisions to the taxonomy of this phylum. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.12%3A_Thermophiles/8.12A%3A_Aquificales_and_Thermotogales.txt |
Learning Objectives
• Compare Deinococcus and Thermus bacteria
DEINOCOCCUS
This is the one genus of three of the Deinococcales group from the Deinococcus-Thermus phylum, and is highly-resistant to environmental hazards. It has several species that are resistant to radiation (they have become famous for their ability to eat nuclear waste and other toxic materials), survive in the vacuum of space, and in extremes of heat and cold. There are 47 species of Deinococcus described according to NCBI on 25 August 2011.
These bacteria have thick cell walls that give them Gram-positive stains, but they include a second membrane and so are closer in structure to those of Gram-negative bacteria. Cavalier-Smith calls this clade Hadobacteria (from Hades, the Greek underworld).
They are also characterized by the presence of the carotenoid pigment Deinoxanthin that give them their pink color, and a high resistance to gamma and UV radiation. They are usually isolated according to these two criteria.
D. RADIODURANS
Deinococcus radiodurans is an extremophilic bacterium, one of the most radioresistant organisms known. It can survive cold, dehydration, vacuum, and acid, and is therefore known as a polyextremophile and has been listed as the world’s toughest bacterium in The Guinness Book of World Records.
D. radiodurans is a rather large, spherical bacterium, with a diameter of 1.5 to 3.5 µm. Four cells normally stick together, forming a tetrad. The bacteria are easily cultured and do not appear to cause disease. Colonies are smooth, convex, and pink to red in color. D. radiodurans does not form endospores and is nonmotile. It is an obligate aerobic chemoorganoheterotroph, i.e., it uses oxygen to derive energy from organic compounds in its environment.
It is often found in habitats rich in organic materials, such as soil, feces, meat, or sewage, but has also been isolated from dried foods, room dust, medical instruments and textiles. It is extremely resistant to ionizing radiation, ultraviolet light, desiccation, and oxidizing and electrophilic agents. Its genome consists of two circular chromosomes, one 2.65 million base pairs long and the other 412 thousand base pairs long, as well as a megaplasmid of 177 thousand base pairs and a plasmid of 46 thousand base pairs. It has about 3,195 genes. In its stationary phase, each bacterial cell contains four copies of this genome; when rapidly multiplying, this increases to eight to 10 copies.
D. radiodurans is capable of withstanding an acute dose of five thousand Gy (five hundred thousand rad) of ionizing radiation with almost no loss of viability, and an acute dose of 15 thousand Gy with 37% viability. A dose of five thousand Gy is estimated to introduce several hundred double-strand breaks (DSBs) into the organism’s DNA (~0.005 DSB/Gy/Mbp (haploid genome)). For comparison, a chest X-ray or Apollo mission involves about one mGy, five Gy can kill a human, two to eight hundred Gy will kill E. coli, and over four thousand Gy will kill the radiation-resistant tardigrade.
Several bacteria of comparable radioresistance are now known, including some species of the genus Chroococcidiopsis (phylum cyanobacteria) and some species of Rubrobacter (phylum actinobacteria); among the archaea, the species Thermococcus gammatolerans shows comparable radioresistance.
D. radiodurans also has a unique ability to repair damaged DNA. It isolates the damaged segments in a controlled area and repairs it. This bacteria can also repair many small fragments from an entire chromosome.
THERMUS
A genus of thermophilic bacteria that can tolerate high temperatures, it is one of several bacteria belonging to the Deinococcus-Thermus group and includes the following three species: T. aquaticus, T. antranikianii, and T. igniterrae. Thermus aquaticus is the source of the heat-resistant enzyme Taq DNA polymerase, one of the most important enzymes in molecular biology because of its use in the polymerase chain reaction (PCR) DNA-amplification technique.
It thrives at 70°C (160°F), but can survive at temperatures of 50°C to 80°C (120°F to 175°F). This bacterium is a chemotroph — it performs chemosynthesis to obtain food. However, since its range of temperature overlaps somewhat with that of the photosynthetic cyanobacteria that share its ideal environment, it is sometimes found living jointly with its neighbors, obtaining energy for growth from their photosynthesis.
Key Points
• The Deinococcales include two families with three genera, Deinococcus and Truepera, the former with several species that are resistant to radiation; they are famous for their ability to eat nuclear waste and other toxic materials, survive in the vacuum of space and in extremes of heat and cold.
• The Thermales include several genera resistant to heat, including Thermus.
• These bacteria have thick cell walls that give them Gram-positive stains, but they include a second membrane and so are closer in structure to those of Gram-negative bacteria.
Key Terms
• radioresistance: Any form of resistance that an organism has to protect itself against the harmful effects of ionizing radiation
• clade: A group of animals or other organisms derived from a common ancestor species.
• polyextremophile: An organism which can tolerate two or more extreme environmental factors.
The Deinococcus-Thermus are a small group of bacteria composed of cocci that are highly-resistant to environmental hazards. There are two main groups: the Deinococcales include two families, with three genera, Deinococcus and Truepera.
The Thermales include several genera resistant to heat (Marinithermus, Meiothermus, Oceanithermus, Thermus, Vulcanithermus).
Though these two groups evolved from a common ancestor, the two mechanisms of resistance appear to be largely independent. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.12%3A_Thermophiles/8.12B%3A_Deinococcus_and_Thermus.txt |
Learning Objectives
• Show the unique features of chloroflexus
As a genus, Chloroflexus spp. are Gram-negative filamentous anoxygenic phototrophic (FAP) organisms that utilize type II photosynthetic reaction centers containing bacteriochlorophyll a similar to the purple bacteria, and light-harvesting chlorosomes containing bacteriochlorophyll c similar to green sulfur bacteria of the Chlorobi. As the name implies, these anoxygenic phototrophs do not produce oxygen as a byproduct of photosynthesis, in contrast to oxygenic phototrophs such as cyanobacteria, algae, and higher plants. While oxygenic phototrophs use water as an electron donor for phototrophy, Chloroflexus uses reduced sulfur compounds such as hydrogen sulfide, thiosulfate, or elemental sulfur. This belies their antiquated name green non-sulfur bacteria. However, Chloroflexus spp. can also utilize hydrogen (H2) as a source of electrons.
Chloroflexus aurantiacus is thought to grow photoheterotrophically in nature, but it has the capability of fixing inorganic carbon through photoautotrophic growth. Instead of using the Calvin-Benson-Bassham Cycle typical of plants, Chloroflexus aurantiacus has been demonstrated to use a novel autotrophic pathway known as the 3-Hydroxypropionate pathway.The complete electron transport chain for Chloroflexus spp. is not yet known. Particularly, Chloroflexus aurantiacus has not been demonstrated to have a cytochrome bc1 complex. It may use different proteins to reduce cytochrome c.
Chloroflexus aurantiacus is a photosynthetic bacterium isolated from hot springs, belonging to the green non-sulfur bacteria. This organism is thermophilic and can grow at temperatures from 35 °C to 70 °C. Chloroflexus aurantiacus can survive in the dark if oxygen is available. When grown in the dark, Chloroflexus aurantiacus has a dark orange color. When grown in sunlight it is dark green. The individual bacteria tend to form filamentous colonies enclosed in sheaths, which are known as trichomes. One of the main reasons for interest in Chloroflexus aurantiacus is in the study of the evolution of photosynthesis.
How did photosynthesis arise in bacteria? The answer to this question is complicated by the fact that there are several types of light-harvesting energy capture systems. Chloroflexus aurantiacus has been of interest in the search for origins of the so-called type II photosynthetic reaction center. One idea is that bacteria with respiratory electron transport evolved photosynthesis by coupling a light-harvesting energy capture system to the pre-existing respiratory electron transport chain. Therefore, rare organisms like Chloroflexus aurantiacus that can survive using either respiration or photosynthesis are of interest in on-going attempts to trace the evolution of photosynthesis.
The Chloroflexi or Chlorobacteria are a phylum of bacteria containing isolates with a diversity of phenotypes including members that are aerobic thermophiles, which use oxygen and grow well in high temperatures, anoxygenic phototrophs, which use light for photosynthesis, and anaerobic halorespirers, which use halogenated organics (such as the toxic chlorinated ethenes and polychlorinated biphenyls) as energy sources. Whereas most bacteria, in terms of diversity, are diderms and stain Gram negative with the exception of the Firmicutes (low CG Gram positives), Actinobacteria (high CG gram positives), and the Deinococcus-Thermus group (Gram positive, but diderms with thick peptidoglycan), the members of the phylum Chloroflexi are monoderms and stain mostly Gram negative.
In 1987, Carl Woese, regarded as the forerunner of the molecular phylogeny revolution, divided Eubacteria into 11 divisions based on 16S ribosomal RNA (SSU) sequences and grouped the genera Chloroflexus, Herpetosiphon, and Thermomicrobium into the “Green non-sulfur bacteria and relatives,” which was temporarily renamed as “Chloroflexi” in Volume One of Bergey’s Manual of Systematic Bacteriology.
Recent phylogenetic analysis of the Chloroflexi has found very weak support for the grouping together of the different classes currently part of the phylum. The six classes that make up the phylum did not consistently form a well-supported monophyletic clade in phylogenetic trees based on concatenated sequences for large datasets of proteins. No conserved signature indels were identified that were uniquely shared by the entire phylum. However, the classes “Chloroflexi” and Thermomicrobia were found to group together consistently by both phylogenetic means and the identification of shared conserved signature indels in the 50S ribosomal protein L19 and the enzyme UDP-glucose 4-epimerase. It has been suggested that the phylum Chloroflexi “sensu stricto” should comprise only the classes Chloroflexi and Thermomicrobia, and the other four classes (“Dehalococcoidetes,” Anaerolineae, Caldilineae, and Ktedonobacteria) may represent one or more independent phyla branching in the neighborhood of the Chloroflexi.
Key Points
• These anoxygenic phototrophs do not produce oxygen as a byproduct of photosynthesis, in contrast to oxygenic phototrophs like cyanobacteria. While oxygenic phototrophs use water as an electron donor for phototrophy, Chloroflexus uses reduced sulfur compounds such as thiosulfate or elemental sulfur.
• The complete electron transport chain for Chloroflexus spp. is not yet known. Particularly, Chloroflexus aurantiacus has not been demonstrated to have a cytochrome bc1 complex, and may use different proteins to reduce cytochrome c.
• The Chloroflexi are a phylum of bacteria containing isolates with a diversity of phenotypes including aerobic thermophiles, which use oxygen and grow well in high temperatures, anoxygenic phototrophs, which use light for photosynthesis, and anaerobic halorespirers, which uses halogenated organics.
• Recent phylogenetic analysis of the Chloroflexi has found very weak support for the grouping together of the different classes currently part of the phylum.
Key Terms
• trichome: Certain (usually filamentous) algae have the terminal cell produced into an elongate “hair-like” structure called a trichome. The same term is applied to such structures in some cyanobacteria.
8.12D: Nitrospirae and Deferribacter
Learning Objectives
• Describe nitrospirae
Nitrospirae is a phylum of bacteria containing only one class: Nitrospira, which itself contains one order: Nitrospirales, and one family: Nitrospiraceae. However, it includes multiple genera, the largest of which is Nitrospira. The first member of this phylum, Nitrospira marina, was discovered in 1986 by Watson et al., isolated from the Gulf of Maine. The second member of this phylum, Thermodesulfovibrio yellowstonii, was discovered in 1994. The third, Nitrospira moscoviensis, was discovered in 1995 from a corroded iron pipe in a Moscow heating system. It is a Gram-negative nitrite-oxidizing organism with a helical to vibroid morphology 0.9-2.2 x 0.2-0.4 micrometers in size.
Some nitrospirae species perform important functions in the Nitrogen Cycle. The Nitrogen Cycle describes the changes in nitrogenous compounds in the environment. Because many of them are toxic, it is important to know something about this cycle. Luckily, these compounds are converted to less and less toxic forms through this Nitrogen Cycle.
To simplify, if you start with your organisms, they release a compound, ammonia, as a waste product or a product of decomposition. Ammonia is both quite toxic and dangerous. By a process known as nitrification, bacteria convert these waste products to less toxic forms. These bacteria live in aerobic conditions and benefit from the presence of oxygen. First the ammonia is converted to nitrites by Nitrosomonas; this compound is still toxic. Next, nitrites are converted to nitrates by Nitrobacter or Nitrospira. Nitrates are much less toxic compared to ammonia and nitrite. In an environment with a healthy colony of these nitrifying bacteria, ammonia and nitrites levels will reach zero.
Deferribacter is a genus in the phylum Deferribacteres (Bacteria).The genus contains 4 species:
• D. abyssi
• D. autotrophicus
• D. desulfuricans
• D. thermophilus
Key Points
• Nitrospirae is a phylum of bacteria. It contains only one class, (Nitrospira), which itself contains one order (Nitrospirales), and one family (Nitrospiraceae). It includes multiple genera, such as Nitrospira, the largest. The first member of this phylum, Nitrospira marina, was discovered in 1985.
• Nitrospira is a genus of bacteria in the phylum Nitrospirae. The second member of this genus was discovered in 1995 from a corroded iron pipe in a Moscow heating system.
• In the nitrogen cycle, nitrites are converted to nitrates by Nitrobacter or Nitrospira.
• Deferribacter is a genus in the phylum Deferribacteres (Bacteria).The genus contains 4 species.
Key Terms
• nitrogen cycle: The natural circulation of nitrogen, in which atmospheric nitrogen is converted to nitrogen oxides by lightning and deposited in the soil by rain where it is assimilated by plants and either eaten by animals (and returned as feces) or decomposed back to elemental nitrogen by bacteria. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.12%3A_Thermophiles/8.12C%3A_Chloroflexus_and_Relatives.txt |
Learning Objectives
• Outline the similarities of Aquifex, Thermocrinis and related bacteria
The Aquificae phylum is a diverse collection of bacteria that live in harsh environmental settings. They have been found in hot springs, sulfur pools, and thermal ocean vents.Members of the genus Aquifex, for example, are productive in water between 85 to 95 °C. They are the dominant members of most terrestrial neutral-to-alkaline hot springs above 60 °C. They are autotrophs, and the primary carbon fixers in these environments. They are true bacteria (domain bacteria).
Comparative genomic studies have identified six conserved signature indels (CSIs) that are specific for the species from the phylum Aquificae and provide potential molecular markers for it. Along with Thermotogae, members of Aquificae are thermophilic eubacteria.
A 51 amino acid insertion has been identified in SecA preprotein translocase which is shared by various members of the phylum Aquificae as well as two Thermotogae species. The presence of the insertion in the Thermotogae species may be due to a horizontal gene transfer. In the 16S rRNA gene trees, the Aquificae species branch in the proximity of the phylum Thermotogae (another phylum comprising hyperthermophilic organisms) close to the archaeal-bacterial branch point. However, a close relationship of the Aquificae to Thermotogae, and the deep branching of Aquificae, is not supported by phylogenetic studies based upon other gene/ protein sequences and also by conserved signature indels in several highly-conserved universal proteins. The Aquificaceae family in the phylum Aquificae contains contains five genera, including Aquifex and Thermocrinis.
Aquifex is a genus of bacteria, one of the few in the phylum Aquificae. The two species generally classified in Aquifex are A. pyrophilus and A. aeolicus. Both are highly thermophilic, growing best in water temperature of 85 °C to 95 °C. Both known species are rod-shaped bacteria with a length of two to six µm and a diameter of around 0.5 µm. They are non-sporeforming, Gram-negative autotrophs. Aquifex means “water-maker” in Latin, and refers to the fact that its method of respiration creates water. They tend to form cell aggregates composed of up to one hundred individual cells. A. pyrophilus can even grow anaerobically by reducing nitrogen instead of oxygen. Like other thermophilic bacteria, Aquifex has important uses in industrial processes.
The genome of A. aeolicus has been successfully mapped. This was made easier by the fact that the length of the genome is only about a third of that for E. coli. Comparison of the A. aeolicus genome to other organisms showed that around 16% of its genes originated from the Archaea domain. Members of this genus are thought to be some of the earliest members of the eubacteria domain. A. aeolicus was discovered north of Sicily, while A. pyrophilus was first found just north of Iceland. A. aeolicus is also known as one of the few bacterial species capable of doing gene silencing.
Key Points
• Along with Thermotogae, members of Aquificae are thermophilic eubacteria. The Aquificaceae family in the phylum Aquificae contains five genera, including Aquifex and Thermocrinis.
• Aquifex is a genus of bacteria, one of the few in the phylum Aquificae. The two species generally classified in Aquifex are A. pyrophilus and A. aeolicus. Both are highly thermophilic, growing best in water temperature of 85 °C to 95 °C.
• The genome of A. aeolicus has been successfully mapped. Comparison of its genome to other organisms showed that around 16% of its genes originated from the Archaea domain. Members of this genus are thought to be some of the earliest members of the eubacteria domain.
Key Terms
• indel: Either an insertion or deletion mutation in the genetic code.
• gene silencing: Any technique or mechanism in which the expression of a gene is prevented.
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Archaea can use a number of different mechanisms to get nutrients and energy.
Learning Objectives
• Discuss archaea energy sources
Key Points
• Lithotrophic archaea use non- organic sources to live.
• Phototrophic archaea use light in a non-photosynthetic fashion to drive ion pumps needed to survive.
• Archaeal energy sources are extremely diverse, including light, metallic ions, and even acidic (pH)-dependent sources.
Key Terms
• autotroph: Any organism that can synthesize its food from inorganic substances, using heat or light as a source of energy.
• calvin cycle: A series of biochemical reactions that take place in the stroma of chloroplasts in photosynthetic organisms.
Archaea exhibit a variety of chemical reactions in their metabolism and use many sources of energy. These reactions are classified into nutritional groups, depending on energy and carbon sources. Some archaea, called lithotrophs, obtain energy from inorganic compounds such as sulfur or ammonia. Other examples include nitrifiers, methanogens, and anaerobic methane oxidizers. In these reactions one compound passes electrons to another in a redox reaction, releasing energy to fuel the cell’s activities. One compound acts as an electron donor and one as an electron acceptor. The energy released generates adenosine triphosphate ( ATP ) through chemiosmosis in the same basic process that happens in the mitochondrion of eukaryotic cells.
Many basic metabolic pathways are shared between all forms of life. For example, archaea use a modified form of glycolysis (the Entner–Doudoroff pathway) and either a complete or partial citric acid cycle. These similarities to other organisms probably reflect both early origins in the history of life and their high level of efficiency.
Some Euryarchaeota are methanogens living in anaerobic environments such as swamps. This form of metabolism evolved early, and it is possible that the first free-living organism was a methanogen. A common reaction in methanogens involves the use of carbon dioxide as an electron acceptor to oxidize hydrogen. Methanogenesis uses a range of coenzymes that are unique to these archaea, such as coenzyme M and methanofuran. Other organic compounds such as alcohols, acetic acid, or formic acid are used as alternative electron acceptors by methanogens. These reactions are common in gut-dwelling archaea. Acetotrophic archaea also break down acetic acid into methane and carbon dioxide directly. These acetotrophs are archaea in the order Methanosarcinales, and are a major part of the communities of microorganisms that produce biogas.
Other archaea, called autotrophs, use CO2 in the atmosphere as a source of carbon, in a process called carbon fixation. This process involves either a highly modified form of the Calvin cycle or a recently discovered metabolic pathway called the 3-hydroxypropionate/4-hydroxybutyrate cycle. In addition, the Crenarchaeota use the reverse Krebs cycle while the Euryarchaeota use the reductive acetyl-CoA pathway. Carbon–fixation is powered by inorganic energy sources.
Phototrophic archaea use sunlight as a source of energy; however, oxygen–generating photosynthesis does not occur in any archaea. Instead, in archaea such as the Halobacteria, light-activated ion pumps generate ion gradients by pumping ions out of the cell across the plasma membrane. The energy stored in these electrochemical gradients is then converted into ATP by ATP synthase. This process is a form of photophosphorylation. The ability of these light-driven pumps to move ions across membranes depends on light-driven changes in the structure of a retinol cofactor buried in the center of the protein.
Besides these, archaeal energy sources are extremely diverse, and range from the oxidation of ammonia by the Nitrosopumilales to the oxidation of hydrogen sulfide or elemental sulfur by species of Sulfolobus, using either oxygen or metal ions as electron acceptors. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.13%3A_Archaeal_Diversity/8.13A%3A_Energy_Conservation_and_Autotrophy_in_Archaea.txt |
Archaea are very different genetically from bacteria and eukaryotes.
Learning Objectives
• Describe the unique features of archaea
Key Points
• Like bacteria and eukaryotes, archaea can be infected by viruses.
• Many unique proteins are encoded by archaea, many of these proteins have unknown functions.
• Introns are more rare than eukaryotic species, and additionally unlike eukaryotes the introns usually do not reside in protein coding genes but rather rRNA and tRNA.
Key Terms
• intron: A portion of a split gene that is included in pre-RNA transcripts but is removed during RNA processing and rapidly degraded.
• ribosome: Small organelles found in all cells; involved in the production of proteins by translating messenger RNA.
• polymerase: Any of various enzymes that catalyze the formation of polymers of DNA or RNA using an existing strand of DNA or RNA as a template.
Archaea usually have a single circular chromosome, the size of which may be as great as 5,751,492 base pairs in Methanosarcina acetivorans, the largest known archaean genome. One-tenth of this size is the tiny 490,885 base-pair genome of Nanoarchaeum equitans, the smallest archaean genome known. It is estimated to contain only 537 protein-encoding genes. Smaller independent pieces of DNA, called plasmids, are also found in archaea. Plasmids may be transferred between cells by physical contact, in a process that may be similar to bacterial conjugation.
Archaea can be infected by double-stranded DNA viruses that are unrelated to any other form of virus and have a variety of unusual shapes, including bottles, hooked rods, or teardrops. These viruses have been studied in most detail in thermophilics, particularly the orders Sulfolobales and Thermoproteales. Two groups of single-stranded DNA viruses that infect archaea have been recently isolated. One group is exemplified by the Halorubrum pleomorphic virus 1 (“Pleolipoviridae”) infecting halophilic archaea and the other one by the Aeropyrum coil-shaped virus (“Spiraviridae”) infecting a hyperthermophilic (optimal growth at 90-95°C) host. Notably, the latter virus has the largest currently reported ssDNA genome. Defenses against these viruses may involve RNA interference from repetitive DNA sequences that are related to the genes of the viruses.
Archaea are genetically distinct from bacteria and eukaryotes, with up to 15% of the proteins encoded by any one archaeal genome being unique to the domain, although most of these unique genes have no known function. Of the remainder of the unique proteins that have an identified function, most belong to the Euryarchaea and are involved in methanogenesis. The proteins that archaea, bacteria, and eukaryotes share form a common core of cell function, relating mostly to transcription, translation, and nucleotide metabolism. Other characteristic archaean features are the organization of genes of related function—such as enzymes that catalyze steps in the same metabolic pathway into novel operons, and large differences in tRNA genes and their aminoacyl tRNA synthetases.
Transcription and translation in archaea resemble these processes in eukaryotes more than in bacteria, with the archaean RNA polymerase and ribosomes being very close to their equivalents in eukaryotes. Although archaea only have one type of RNA polymerase, its structure and function in transcription seems to be close to that of the eukaryotic RNA polymerase II, with similar protein assemblies (the general transcription factors) directing the binding of the RNA polymerase to a gene’s promoter. However, other archaean transcription factors are closer to those found in bacteria. Post-transcriptional modification is simpler than in eukaryotes, since most archaean genes lack introns, although there are many introns in their transfer RNA and ribosomal RNA genes, and introns may occur in a few protein-encoding genes.
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The Crenarchaeota are archaea that have been classified as a phylum of the Archaea domain.
8.14: Crenarchaeota
Crenarchaeota exist in a wide range of habitats and exhibit a great variety of chemical reactions in their metabolism.
Learning Objectives
• Outline the various types of energy metabolism used by Crenarchaeota
Key Points
• The first-discovered archaeans were extremophiles.
• Extremophile archaea are members of four main physiological groups: halophiles, thermophiles, alkaliphiles, and acidophiles.
• Some archaea obtain energy from inorganic compounds such as sulfur or ammonia (they are lithotrophs).
• Other groups of archaea use sunlight as a source of energy (phototrophs) or CO2 in the atmosphere as a source of carbon (autotrophs).
Key Terms
• extremophile: An organism that lives under extreme conditions of temperature, salinity, and so on. They are commercially important as a source of enzymes that operate under similar conditions.
• phototroph: An organism that carries out photon capture to acquire energy. They use the energy from light to carry out various cellular metabolic processes.
• autotroph: Any organism that can synthesize its food from inorganic substances, using heat or light as a source of energy.
The Crenarchaeota are Archaea that have been classified as either a phylum of the Archaea kingdom, or in a kingdom of its own. Archaea exist in a broad range of habitats, and as a major part of global ecosystems, they may contribute up to 20% of earth’s biomass.
The first-discovered archaeans were extremophiles. Indeed, some archaea survive high temperatures, often above 100 °C (212 °F), as found in geysers, black smokers, and oil wells. Other common habitats include very cold habitats and highly saline, acidic, or alkaline water. However, archaea also include mesophiles that grow in mild conditions, in marshland, sewage, the oceans, and soils.
Extremophile archaea are members of four main physiological groups. These are the:
• halophiles
• thermophiles
• alkaliphiles
• acidophiles
These groups are not comprehensive or phylum-specific, nor are they mutually exclusive, since some archaea belong to several groups. Nonetheless, they are a useful starting point for classification Halophiles live in extremely saline environments such as salt lakes. Thermophiles grow best at temperatures above 45 °C (113 °F), in places such as hot springs; hyperthermophilic archaea grow optimally at temperatures greater than 80 °C (176 °F). Other archaea exist in very acidic or alkaline conditions.
Recently, several studies have shown that archae exist not only in mesophilic and thermophilic environments but are also present, sometimes in high numbers, at low temperatures as well, as found in cold oceanic environments.
Chemical reactions and energy sources
Archaea exhibit a great variety of chemical reactions in their metabolism and use many sources of energy. These reactions are classified into nutritional groups, depending on energy and carbon sources.
Some archaea obtain energy from inorganic compounds such as sulfur or ammonia (they are lithotrophs). These include nitrifiers, methanogens and anaerobic methane oxidisers. In these reactions one compound passes electrons to another (in a redox reaction), releasing energy to fuel the cell’s activities. One compound acts as an electron donor and one as an electron acceptor. The energy released generates adenosine triphosphate ( ATP ) through chemiosmosis, in the same basic process that happens in the mitochondrion of eukaryotic cells.
Other groups of archaea use sunlight as a source of energy (phototrophs). However, oxygen–generating photosynthesis does not occur in any of these organisms. Many basic metabolic pathways are shared between all forms of life; for example, archaea use a modified form of glycolysis (the Entner–Doudoroff pathway) and either a complete or partial citric acid cycle. These similarities to other organisms probably reflect both early origins in the history of life and their high level of efficiency.
Some Euryarchaeota are methanogens living in anaerobic environments such as swamps. This form of metabolism evolved early, and it is even possible that the first free-living organism was a methanogen. A common reaction involves the use of carbon dioxide as an electron acceptor to oxidize hydrogen. Methanogenesis involves a range of coenzymes that are unique to these archaea, such as coenzyme M and methanofuran. These reactions are common in gut-dwelling archaea. Acetic acid is also broken down into methane and carbon dioxide directly, by acetotrophic archaea. These acetotrophs are archaea in the order Methanosarcinales, and are a major part of the communities of microorganisms that produce biogas.
Other archaea use CO2 in the atmosphere as a source of carbon, in a process called carbon fixation (they are autotrophs). This process involves either a highly modified form of the Calvin cycle or a recently discovered metabolic pathway called the 3-hydroxypropionate/4-hydroxybutyrate cycle. The Crenarchaeota also use the reverse Krebs cycle while the Euryarchaeota also use the reductive acetyl-CoA pathway. Carbon–fixation is powered by inorganic energy sources. No known archaea carry out photosynthesis.
Archaeal energy sources are extremely diverse, and range from the oxidation of ammonia by the Nitrosopumilales to the oxidation of hydrogen sulfide or elemental sulfur by species of Sulfolobus, using either oxygen or metal ions as electron acceptors.
Phototrophic archaea use light to produce chemical energy in the form of ATP. In the Halobacteria, light-activated ion pumps like bacteriorhodopsin and halorhodopsin generate ion gradients by pumping ions out of the cell across the plasma membrane. The energy stored in these electrochemical gradients is then converted into ATP by ATP synthase (photophosphorylation).
Some marine Crenarchaeota are capable of nitrification, suggesting these organisms may affect the oceanic nitrogen cycle, although these oceanic Crenarchaeota may also use other sources of energy. Vast numbers of archaea are also found in the sediments that cover the sea floor, with these organisms making up the majority of living cells at depths over 1 meter below the ocean bottom.
8.14B: Hyperthermophiles from Terrestrial Volcanic Habitats
A hyperthermophile thrives at relatively high temperatures and can be found in geothermally heated regions of the Earth.
Learning Objectives
• Summarize the traits that define Hyperthermophiles
Key Points
• Unlike other types of bacteria, thermophiles can survive at much hotter temperatures, whereas other bacteria would be damaged or killed if exposed to the same temperatures.
• Thermophiles contain enzymes that can function at high temperatures.
• Hyperthermophiles are particularly extreme thermophiles for which the optimal temperatures are above 80°C, and their membranes and proteins are unusually stable at these extremely high temperatures.
Key Terms
• lithotroph: An organism that obtains its energy from inorganic compounds (such as ammonia) via electron transfer.
• thermophile: An organism that lives and thrives at relatively high temperatures; a form of extremophile; many are members of the Archaea.
A thermophile is an organism —a type of extremophile—that thrives at relatively high temperatures, between 45 and 122 °C (113 and 252 °F). Many thermophiles are archaea. Thermophilic eubacteria are suggested to have been among the earliest bacteria. Thermophiles are found in various geothermally heated regions of the Earth, such as the hot springs found in Yellowstone National Park.
Unlike other types of bacteria, thermophiles can survive at much hotter temperatures, whereas other bacteria would be damaged or killed if exposed to the same temperatures. As a prerequisite for their survival, thermophiles contain enzymes that can function at high temperatures. Some of these enzymes are used in molecular biology (for example, heat-stable DNA polymerases for PCR), and in washing agents. Thermophiles are classified into obligate and facultative thermophiles; obligate thermophiles (also called extreme thermophiles) require such high temperatures for growth, whereas facultative thermophiles (also called moderate thermophiles) can thrive at high temperatures, but also at lower temperatures (below 50°C).
Hyperthermophiles are particularly extreme thermophiles for which the optimal temperatures are above 80°C. Thermophiles, meaning “heat-loving,” are organisms with an optimum growth temperature of 50°C or more, a maximum of up to 70°C or more, and a minimum of about 40°C, but these are only approximate. Some extreme thermophiles (hyperthermophiles) require a very high temperature (80°C to 105°C) for growth. Their membranes and proteins are unusually stable at these extremely high temperatures. Thus, many important biotechnological processes use thermophilic enzymes because of their ability to withstand intense heat.
Many of the hyperthermophiles Archea require elemental sulfur for growth. Some are anaerobes that use the sulfur instead of oxygen as an electron acceptor during cellular respiration. Some are lithotrophs that oxidize sulfur to sulfuric acid as an energy source, thus requiring the microorganism to be adapted to very low pH (i.e., it is an acidophile as well as thermophile). These organisms are inhabitants of hot, sulfur-rich environments usually associated with volcanism, such as hot springs, geysers, and fumaroles. In these places, especially in Yellowstone National Park, zonation of microorganisms according to their temperature optima occurs. Often, these organisms are colored due to the presence of photosynthetic pigments. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.14%3A_Crenarchaeota/8.14A%3A_Habitats_and_Energy_Metabolism_of_Crenarchaeota.txt |
Hyperthermophiles live in dark regions of the oceans and use chemosynthesis to produce biomass from single carbon molecules.
Learning Objectives
• Describe the metabolic processes used by hyperthermophiles found in submarine volcanic habitats
Key Points
• Chemosynthesis is the biological conversion of one or more carbon molecules and nutrients into organic matter using the oxidation of inorganic molecules (e.g. hydrogen gas, hydrogen sulfide ) or methane as a source of energy.
• The energy for chemosynthesis can be derived from hydrogen, hydrogen sulfide or ammonia.
• Many chemosynthetic microorganisms are consumed by other organisms in the ocean, and symbiotic associations between chemosynthesizers and respiring heterotrophs are quite common.
Key Terms
• hydrothermal vent: a hot spring, on the floor of the ocean, mostly along the central axes of the mid-ocean ridges, where heated fluids emerge from fissures in the Earth’s crust
• symbiotic: Of a relationship with mutual benefit between two individuals or organisms.
• chemosynthesis: The production of carbohydrates and other compounds from simple compounds such as carbon dioxide, using the oxidation of chemical nutrients as a source of energy rather than sunlight; it is limited to certain bacteria and fungi.
In biochemistry, chemosynthesis is the biological conversion of one or more carbon molecules (usually carbon dioxide or methane) and nutrients into organic matter using the oxidation of inorganic molecules (e.g. hydrogen gas, hydrogen sulfide) or methane as a source of energy. Chemoautotrophs, organisms that obtain carbon through chemosynthesis, are phylogenetically diverse. Groups that include conspicuous or biogeochemically-important taxa include the sulfur-oxidizing gamma and epsilon proteobacteria, the Aquificaeles, the methanogenic archaea and the neutrophilic iron-oxidizing bacteria.
A thermophile is an organism that thrives at relatively high temperatures, between 45 and 122 °C (113 and 252 °F). Thermophiles are found in various geothermally heated regions of the Earth, such as deep sea hydrothermal vents. As a prerequisite for their survival, thermophiles contain enzymes that can function at high temperatures. Some of these enzymes are used in molecular biology (for example, heat-stable DNA polymerases for PCR), and in washing agents.
Thermophiles are classified into obligate and facultative thermophiles: Obligate thermophiles (also called extreme thermophiles) require such high temperatures for growth, whereas facultative thermophiles (also called moderate thermophiles) can thrive at high temperatures, but also at lower temperatures (below 50°C). For example, Venenivibrio stagnispumantis gains energy by oxidizing hydrogen gas.
Many microorganisms in dark regions of the oceans also use chemosynthesis to produce biomass from single carbon molecules. Two categories can be distinguished. In the rare sites at which hydrogen molecules (H2) are available, the energy available from the reaction between CO2 and H2 (leading to production of methane, CH4) can be large enough to drive the production of biomass. Alternatively, in most oceanic environments, energy for chemosynthesis derives from reactions in which substances such as hydrogen sulfide or ammonia are oxidized to produce formaldehyde (which will be used to make carbohydrates) and solid globules of sulfur. This may occur with or without the presence of oxygen. In bacteria that can do this, such as purple sulfur bacteria, yellow globules of sulfur are present and visible in the cytoplasm.
Many chemosynthetic microorganisms are consumed by other organisms in the ocean, and symbiotic associations between chemosynthesizers and respiring heterotrophs are quite common. Large populations of animals can be supported by chemosynthetic secondary production at hydrothermal vents, methane clathrates, cold seeps, whale falls, and isolated cave water. Indeed, it has been hypothesized that chemosynthesis may support life below the surface of Mars, Jupiter’s moon Europa, and other planets. Giant tube worms use bacteria in their trophosome to react hydrogen sulfide with oxygen as a source of energy.
8.14D: Nonthermophilic Crenarchaeota
Nonthermophilic Crenarchaeota can be extreme halophiles living in highly salty environments.
Learning Objectives
• Discuss the characteristics of nonthermophilic crenarchaeota, specifically Halococcus, that allow it to survive in extreme environments
Key Points
• Halococcus is a genus of extreme halophilic archaea.
• Halophiles are found mainly in inland bodies of water with high salinity, where their pigments (from a protein called rhodopsinprotein) tint the sediment bright colors.
• Halococcus and similar halophilic organisms have been utilized economically in the food industry and even in skin-care production.
• Halococcus is able to survive in its high-saline habitat by preventing the dehydration of its cytoplasm using a solute which is either found in their cell structure or is drawn from the external environment.
Key Terms
• halophile: An organism that lives and thrives in an environment of high salinity, often requiring such an environment; a form of extremophile.
Crenarchaeota can be extreme halophiles, and include organisms living in highly salty environments (for example, halococcus).
Halococcus is a genus of extremely halophilic archaea, meaning that they require high salt levels, sometimes as high as 32% NaCl, for optimal growth. Halophiles are found mainly in inland bodies of water with high salinity, where their pigments (from a protein called rhodopsinprotein) tint the sediment bright colors. Rhodopsin protein and other proteins serve to protect Halococcus from the extreme salinities of the environment. Some Halococcus may be located in highly salted soil or foods. Because they can function under such high-salt conditions, Halococcus and similar halophilic organisms have been utilized economically in the food industry and even in skin-care production. Halococcus’ genome has not been sequenced yet, although studies of its 16s rDNA have demonstrated its placement on the phylogenetic tree. Due to the organisms’ potential longevity, Halococcus may be a good candidate for exploring taxonomic similarities to life found in outer space.
Halococcus is able to survive in its high-saline habitat by preventing the dehydration of its cytoplasm. To do this they use a solute, which is either found in their cell structure or is drawn from the external environment. Special chlorine pumps allow the organisms to retain chloride to maintain osmotic balance with the salinity of their habitat. The cells are cocci, 0.6-1.5 micrometres long, with sulfated polysaccharide walls. The cells are organtrophic, using amino acids, organic acids, or carbohydrates for energy. In some cases they are also able to photosynthesize. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.14%3A_Crenarchaeota/8.14C%3A_Hyperthermophiles_from_Submarine_Volcanic_Habitats.txt |
Psychrophiles crenarchaeotes are extremophilic organisms that are capable of growth and reproduction in cold temperatures.
Learning Objectives
• Discuss the specific characteristics associated with psychrophilic crenarchaeotes
Key Points
• Psychrophiles are characterized by lipid cell membranes chemically resistant to the stiffening caused by extreme cold, and often create protein ‘antifreezes’ to keep their internal space liquid and protect their DNA even in temperatures below water’s freezing point.
• Crenarchaea are thought to be very abundant and one of the main contributors to the fixation of carbon.
• Crenarchaeote are abundant in the ocean and some species have a 200 times greater affinity for ammonia than ammonia oxidizing bacteria, leading researchers to challenge the previous belief that ammonia oxidizing bacteria are primarily responsible for nitrification in the ocean.
Key Terms
• crenarchaeota: Archae that have been recently identified to be present in marine environments where they responsible for nitrification.
• psychrophile: An organism that can live and thrive at temperatures much lower than normal; a form of extremophile.
Psychrophiles or cryophiles (adj. cryophilic) are extremophilic organisms that are capable of growth and reproduction in cold temperatures, ranging from −15°C to +10°C. Temperatures as low as −15°C are found in pockets of very salty water (brine) surrounded by sea ice. They can be contrasted with thermophiles, which thrive at unusually hot temperatures. The environments they inhabit are ubiquitous on Earth, as a large fraction of our planetary surface experiences temperatures lower than 15°C. They are present in alpine and arctic soils, high-latitude and deep ocean waters, polar ice, glaciers, and snowfields. Most psychrophiles are bacteria or archaea, and psychrophily is present in widely diverse microbial lineages within those broad groups. Psychrophiles are characterized by lipid cell membranes chemically resistant to the stiffening caused by extreme cold, and often create protein ‘antifreezes’ to keep their internal space liquid and protect their DNA even in temperatures below water’s freezing point.
The Crenarchaeota (Greek for “spring old quality”) (also known as Crenarchaea or eocytes) are Archaea that have been classified as either a phylum of the Archaea kingdom or a kingdom of its own. Initially, the Crenarchaeota were thought to be sulfur-dependent extremophiles but recent studies have identified characteristic Crenarchaeota environmental rRNA indicating the organism may be the most abundant archaea in the marine environment. Originally, they were separated from the other archaea based on rRNA sequences. However, other physiological features, such as lack of histones have supported this division, although some crenarchaea were found to have histones. Until recently all cultured Crenarchaea had been thermophilic or hyperthermophilic organisms, some of which have the ability to grow at up to 113 °C. These organisms stain Gram negative and are morphologically diverse having rod, cocci, filamentous and oddly shaped cells. Beginning in 1992, data were published that reported sequences of genes belonging to the Crenarchaea in marine environments making these bacteria psychrophiles or cryophiles. Since then, analysis of the abundant lipids from the membranes of Crenarchaea taken from the open ocean have been used to determine the concentration of these “low temperature Crenarchaea.” Based on these measurements of their signature lipids, Crenarchaea are thought to be very abundant and one of the main contributors to the fixation of carbon. DNA sequences from Crenarchaea have also been found in soil and freshwater environments, suggesting that this phylum is ubiquitous to most environments.
Nitrification, as stated above, is formally a two-step process; in the first step ammonia is oxidized to nitrite, and in the second step nitrite is oxidized to nitrate. Different microbes are responsible for each step in the marine environment. Several groups of ammonia oxidizing bacteria (AOB) are known in the marine environment, including Nitrosomonas, Nitrospira, and Nitrosococcus. All contain the functional gene ammonia monooxygenase (AMO) which, as its name implies, is responsible for the oxidation of ammonia. More recent metagenomic studies have revealed that some Crenarchaeote Archaea possess AMO. Crenarchaeote are abundant in the ocean and some species have a 200 times greater affinity for ammonia than AOB, leading researchers to challenge the previous belief that AOB are primarily responsible for nitrification in the ocean.
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Diverse Cell Forms of Methanogens
There are over 50 described species of methanogens, sharing over 30 signature proteins.
LEARNING OBJECTIVES
Outline the physical characteristics associated with methanogens
Key Points
• Methanogens are usually either coccoid (spherical) or bacilli (rod shaped).
• Methanogens have a cell wall that is composed of pseudopeptidoglycan, which offers lysozyme resistance.
• There are many diverse strains of methanogens, including M. smithii (found in the human gut), M. kandleri (discovered on the wall of a black smoker), and M acetivorans (found in oil wells, trash dumps, and deep-sea hydrothermal vents ).
Key Terms
• polysaccharide: Complex sugars. A polymer made of many saccharide units linked by glycosidic bonds.
Methanogens belong to the domain archaea, which are distinctly different than bacteria. There are over 50 described species of methanogens, sharing over 30 signature proteins. These species do not form a monophyletic group, but are split into three clades. Therefore, the large numbers of proteins uniquely shared by all methanogens may be due to lateral gene transfers.
Methanogens are usually either coccoid (spherical) or bacilli (rod shaped). The cell walls of of Methanogens, like other Archaea, lack peptidoglycan, a polymer found in the cell walls of the bacteria. Instead, some methanogens have a cell wall that is composed of pseudopeptidoglycan. Pseudopeptidoglycan differs in chemical structure from bacterial peptidoglycan, but resembles eubacterial peptidoglycan in morphology, function, and physical structure. These differences makes these archaea resistant to the enzyme, lysozyme, which only breaks down β (1,4) sugar linkages like those found in peptidoglycan. Those that do not contain pseudopeptidoglycan have at least one paracrystalline array (S-layer) made up of proteins that fit together like a jigsaw puzzle.
There are many diverse strains of methanogens. Methanobrevibacter smithii is the dominant archaeon in the human gut. M. smithii is pivotal in the removal of excess hydrogen from the human gut. They are important for the efficient digestion of polysaccharides, allowing for an increase in the transformation of nutrients into calories.
Methanocaldococcus jannaschii thermophilic methanogen isolated from a hot spring at Woods hole. It was the first archaeon to have its complete genome sequenced, identifying many genes and synthesis pathways unique to the archaea.
Methanopyrus is a genus of methanogens, with a single described species, M. kandleri. M. kandleri is a hyperthermophile, discovered on the wall of a black smoker from the Gulf of California at a depth of 2000 m, at temperatures of 84-110 °C.
Methanosarcina acetivorans is a versatile methane producing microbe which is found in such diverse environments as oil wells, trash dumps, deep-sea hydrothermal vents, and oxygen-depleted sediments beneath kelp beds. Only M. acetivorans and microbes in the genus Methanosarcina use all three known metabolic pathways for methanogenesis.
8.15B: Extremely Halophilic Archaea
Halophiles are extremophiles that thrive in environments with very high concentrations of salt.
Learning Objectives
• Describe the methods employed by halophilic Archaea to prevent water loss
Key Points
• Halophiles can be found anywhere with a salt concentration at least five times greater than that of the ocean.
• Most halophilic organisms cope with the high concentrations of salt by expending energy to exclude salt from their cytoplasm.
• Halophiles prevent this loss of water by increasing the internal osmolarity of the cell by accumulating osmoprotectants or by the selective uptake of potassium ions.
Key Terms
• halotolerance: The adaptation of a living organism to conditions of high salinity (dissolved salt).
• zwitterionic: Pertaining to a neutral molecule containing both positive and negative charge.
• osmoprotectant: Any osmolyte that helps an organism to survive osmotic stress
Halophiles are extremophiles that thrive in environments with very high concentrations of salt. In fact, the very name “halophile” comes from the Greek word for “salt-loving. ” Although some halophilic bacteria and eukaryotes exist, the largest classification of halophiles is in the Archaea domain.
Halophiles can be found anywhere with a salt concentration at least five times greater than that of the ocean. They are categorized as slight, moderate, or extreme halophiles based on the extent of their halotolerance. Halophiles thrive in places such as the Great Salt Lake, Owens Lake in California, evaporation ponds, and the Dead Sea – places that provide an inhospitable environment to most lifeforms.
High salinity represents an extreme environment that relatively few organisms have been able to adapt to and occupy. Most halophilic organisms cope with the high concentrations of salt by expending energy to exclude salt from their cytoplasm to avoid protein aggregation, or “salting out. ” “Normal” organisms would desiccate in these conditions, losing water via osmosis out of the cytoplasm. Halophiles prevent this loss of water by increasing the internal osmolarity of the cell. One way halophilic archaea can increase their internal osmolarity is by accumulating organic compounds – called osmoprotectants – in their cytoplasm. These compatible solutes can be accumulated from the environment or synthesized. The most common compatible solutes are neutral or zwitterionic, and include amino acids, sugars, polyols, betaines and ectoines, as well as derivatives of some of these compounds.
A more radical adaptation to preventing water loss employs the selective influx of potassium (K+) ions into the cytoplasm. In archaea, this adaptation is restricted to the the extremely halophilic family Haloarchaea (often known as Halobacteriaceae). To use this method, the entire intracellular machinery – including enzymes, structural proteins, and charged amino acids that allow the retention of water molecules on their surfaces – must be adapted to high salt levels. In the compatible solute adaptation, little or no adjustment is required of intracellular macromolecules – in fact, the compatible solutes often act as general stress protectants as well as osmoprotectants.
The extremely halophilic Haloarchaea require at least a 2 M salt concentration and are usually found in saturated solutions (about 36% w/v salts). These are the primary inhabitants of salt lakes, inland seas, and evaporating ponds of seawater. The red color of deep salterns is due to the carotenoids (organic pigment) in these archaea. These archaea require salt for growth and they will lyse if they are exposed to less salty environment.
The high concentration of NaCl in halophilic environment limits the availability of oxygen for respiration. Halophiles are chemoheterotrophs, using light for energy and methane as a carbon source under aerobic or anaerobic conditions. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.15%3A_Euryarchaeota/8.15A%3A_Diverse_Cell_Forms_of_Methanogens.txt |
Methanogens are an important group of microoraganisms that produce methane as a metabolic byproduct under anaerobic conditions.
Learning Objectives
• Discuss the characteristics associated with methane-producing archaea
Key Points
• Methanogens are responsible for the methane in the belches of ruminants and in the flatulence in humans.
• Methanogens play a vital ecological role in anaerobic environments by removing excess hydrogen and fermentation products produced by other forms of anaerobic respiration.
• Methanogens play a key role in the remineralization of organic carbon and under the right conditions can form reservoirs of methanogen, a potent greenhouse gas.
Key Terms
• extremophiles: An extremophile (from Latin extremus, meaning “extreme,” and Greek philiā (φ), meaning “love”) is an organism that thrives in physically or geochemically extreme conditions that are detrimental to most life on earth.
Methanogenic archaea, or methanogens, are an important group of microoraganisms that produce methane as a metabolic byproduct under anaerobic conditions. Methanogens belong to the domain archaea, which is distinct from bacteria. Methanogens are commonly found in the guts of animals, deep layers of marine sediment, hydrothermal vents, and wetlands. They are responsible for the methane in the belches of ruminants, as in, the flatulence in humans, and the marsh gas of wetlands. Methanogens should not be confused with methanotrophs, which consume methane rather than produce it.
Methanogens play a vital ecological role in anaerobic environments by removing excess hydrogen and fermentation products produced by other forms of anaerobic respiration. Because of this, methanogens thrive in environments in which all electron acceptors other than CO2 (such as oxygen, nitrate, trivalent iron, and sulfate) have been depleted.
In the human gut, accumulation of hydrogen reduces the efficiency of microbial processes, reducing energy yield. Methanogens such as M. smithii are pivotal in the removal of this excess hydrogen from the gut and may be useful therapeutic targets for reducing energy harvest in obese humans.
In marine sediments, biomethanation is generally confined to where sulfates are depleted, below the top layers. Methanogens play a key role in the remineralization of organic carbon in continental margin sediments and other aquatic sediments with high rates of sedimentation and organic matter. Under the correct temperatures and pressure, biogenic methane can accumulate in massive deposits, which account for significant fractions of organic carbon and key reservoirs of a potent greenhouse gas.
Some methanogens, called extremophiles, can thrive in extreme environments such as hot springs, submarine hydrothermal vents, and hot, dry deserts. Methanogens have been found buried under kilometers of ice in Greenland, as well as in the “solid” rock of the Earth’s crust, kilometers below the surface.
8.15D: Thermoplasmatales Thermocaccales and Methanopyrus
There are many classes in the phylum Euryarchaeota, many of which are extremophiles.
Learning Objectives
• Recognize the characteristics associated with the Euryarchaeota classes of thermophiles: Thermoplasmatales, Thermococcales and Methanopyri
Key Points
• Thermoplasmatales are an order of the class Thermoplasmata. All are acidophiles, growing optimally at pH below 2.
• Another anaerobic Euryarchaeota, often hyperthermophiles, are the Thermococcales of the class Thermocococci.
• Methanopyrus is a genus of methanogen, with a single described species, M. kandleri.
Key Terms
• acidophiles: an organism that thrives under highly acidic conditions (usually at pH 2.0 or below)
• hyperthermophile: An organism that lives and thrives in an extremely hot environment like a deep sea smoker vent; often a member of the Archaea.
There are many classes in the phylum Euryarchaeota, many of which are extremophiles, surviving in extreme conditions that are uninhabitable for most other organisms. Thermoplasmatales, Thermococcales, and Methanopyri are all Euryarchaeota Classes of thermophiles.
Thermoplasmatales are an order of the class Thermoplasmata. All are acidophiles, growing optimally at pH below 2. Picrophilus is currently the most acidophilic of all known organisms growing at a minimum pH of 0.06. Many of these organisms do not contain a cell wall, although this is not true in the case of Picrophilus. Most members of the Thermotoplasmata are thermophilic. A thermophile is an extremophile that thrives at relatively high temperatures, between 45 and 122 °C. Many of them are archaea. Thermophilic eubacteria are suggested to have been among the earliest bacteria. Thermophiles contain enzymes that can function at high temperatures, and can even survive at much higher temperatures, whereas other bacteria would be damaged and sometimes killed if exposed to the same temperatures.
Another anaerobic Euryarchaeota, often hyperthermophiles, are the Thermococcales of the class Thermocococci.
Methanopyrus is a genus of methanogen, with a single described species, Methanopyrus kandleri . It is a hyperthermophile, discovered on the wall of a black smoker from the Gulf of California at a depth of 2000 m, at temperatures of 84-110 °C. Strain 116 was discovered in black smoker fluid of the Kairei hydrothermal field; it can survive and reproduce at 122 °C. It lives in a hydrogen-carbon dioxide rich environment, and like other methanogens reduces the latter to methane. It is placed among the Euryarchaeota, in its own class, Methanopyri. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.15%3A_Euryarchaeota/8.15C%3A_Methane-Producing_Archaea_-_Methanogens.txt |
Archaeoglobus is a genus of Euryarchaeota found in high-temperature oil fields.
Learning Objectives
• Outline the unique traits associated with Archaeoglobus
Key Points
• Archaeoglobus are sulfate-reducing archaea, coupling the reduction of sulfate to sulfide with the oxidation of many different organic carbon sources, including complex polymers.
• Archaeoglobus grow at extremely high temperatures and are found in hydrothermal vents, oil deposits, and hot springs.
• Comparative genomic studies on archaeal genomes provide evidence that members of the genus Archaeoglobus are the closest relatives of methanogenic archaea.
Key Terms
• lithoautotroph: A microbe that takes energy from reduced compounds of minerals.
• heterotroph: An organism that requires an external supply of energy in the form of food as it cannot synthesize its own.
• hyperthermophiles: An organism that thrives in extremely hot environments-from 60 degrees C (140 degrees F) upwards.
Archaeoglobus is a genus of Euryarchaeota found in high-temperature oil fields, where they may contribute to oil field souring. Archaeoglobus are sulfate-reducing archaea, coupling the reduction of sulfate to sulfide with the oxidation of many different organic carbon sources, including complex polymers.
Archaeoglobus grow at extremely high temperatures between 60 and 95 °C, with optimal growth at 83 °C. These hyperthermophiles can be found in hydrothermal vents, oil deposits, and hot springs. They can produce biofilm to form a protective environment when subjected to environmental stresses such as extreme pH or temperature, high concentrations of metal, or the addition of antibiotics, xenobiotics, or oxygen. These archaeons are known to cause the corrosion of iron and steel in oil and gas processing systems by producing iron sulphide. Their bioflims, however, may have industrial or research applications in the detoxification of metal contaminated samples or to gather metals in an economically recoverable form.
Archaeoglobus are lithotrophs, and can be either autotrophic or heterotrophic.The archaeoglobus strain A. lithotrophicus are lithoautotrophs, and derive their energy from hydrogen, sulfate and carbon dioxide. The strain A. profundus are also lithotrophic, but as they require acetate and CO2 for biosynthesis, and are therefore heterotrophs. Archaeoglobus species utilize their environment by acting as scavengers with many potential carbon sources. They can obtain carbon from fatty acids, the degradation of amino acids, aldehydes, organic acids, and possibly carbon monoxide (CO) as well.
Comparative genomic studies on archaeal genomes provide evidence that members of the genus Archaeoglobus are the closest relatives of methanogenic archaea. This is supported by the presence of 10 conserved signature proteins that are uniquely found in all methanogens and Archaeoglobus. Additionally, 18 proteins which are uniquely found in members of Thermococci, Archaeoglobus and methanogens have been identified, suggesting that these three groups of Archaea may have shared a common relative exclusive of other Archaea. However, the possibility that the shared presence of these signature proteins in these archaeal lineages is due to lateral gene transfer cannot be excluded.
The complete genome sequence from Archaeoglobus fulgidus reveals the presence of a complete set of genes for methanogenesis. The function of these genes in A. fulgidus remains unknown, and the lack of the enzyme methyl-CoM reductase does not allow for methanogenesis to occur by a mechanism similar to that found in other methanogens.
The A. fulgidus genome is a circular chromosome of 2,178,000 base pairs, roughly half the size of E. coli. A quarter of the genome encodes preserved proteins whose functions are not yet determined, but are expressed in other archaeons such as Methanococcus jannaschii. Another quarter encodes proteins unique to the archaeal domain. One observation about the genome is that there are many gene duplications and the duplicated proteins are not identical. This suggests metabolic differentiation specifically with respect to the decomposing and recycling carbon pathways through scavenged fatty acids. The duplicated genes also gives the genome a larger genome size than its fellow archaeon M. jannaschii. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.15%3A_Euryarchaeota/8.15E%3A_Archaeoglobus.txt |
Learning Objectives
• Discuss the unique characteristics associated with Nanoarchaeum
Nanoarchaeum equitans is a species of marine Archaea that was discovered in 2002 in a hydrothermal vent off the coast of Iceland on the Kolbeinsey Ridge by Karl Stetter. Strains of this microbe were also found on the Sub-polar Mid Oceanic Ridge and in the Obsidian Pool in Yellowstone National Park. It is a thermophile that grows in temperatures approaching boiling (80 degrees Celsius). Nanoarchaeum grows best in environments with a pH of six, and a salinity concentration of 2%. Nanoarchaeum cannot synthesize lipids but obtains them from its host, Ignicoccus. Nanoarchaeum appears to be an obligatory symbiont of this archaeon Ignicoccus, and must be in contact with it to survive.
Nanoarchaeum cells are only 400 nm in diameter, making it the next smallest known living organism to nanobacteria and nanobes, whose status as living organisms is controversial. Its genome is only 490,885 nucleotides long; the smallest non-viral genome ever sequenced next to that of Candidatus Carsonella ruddii. N. equitans genome consists of a single circular chromosome, and lacks almost all genes required for synthesis of amino acids, nucleotides, cofactors, and lipids, but encodes everything needed for repair and replication. 95% of its DNA encodes for proteins for stable RNA molecules. Nanoarchaeum has small appendages that come out of its circular structure. The cell surface is covered by a thin, lattice-shaped S-layer, which provides structure and protection for the entire cell. Genetically, Nanoarchaeum is peculiar in that its 16S RNA sequence is undetectable by the most common methods.
The sequencing of the Nanoarchaeum genome has revealed a wealth of information about the organism’s biology. The genes for several vital metabolic pathways appear to be missing. Nanoarchaeum cannot synthesize most nucleotides, amino acids, lipids, and cofactors. The cell most likely obtains these biomolecules from Ignicoccus. However, unlike many parasitic microbes, Nanoarchaeum has many DNA repair enzymes, as well as everything necessary to carry out DNA replication, transcription, and translation. This may explain why the genome lacks the large stretches of non-coding DNA characteristic of other parasites. The organism’s ability to produce its own ATP is also in question. Nanoarchaeum lacks the ability to metabolize hydrogen and sulfur for energy, as many thermophiles do. It does have five subunits of an ATP synthase as well as pathways for oxidative deamination. Whether it obtains energy from biological molecules imported from Ignicoccus, or whether it receives ATP directly is currently unknown. The genome and proteome composition of N. equitans are marked with the signatures of dual adaptation – one to high temperature and the other to obligatory parasitism (or symbiosis).
Aciduliprofundum is another genus of the Euryarchaeota, though relatively less is known about it.
Key Points
• Nanoarchaeum grows best in environments with a pH of six and a salinity concentration of 2%.
• Nanoarchaeum cannot synthesize lipids but obtains them from its host, Ignicoccus.
• The genome and proteome composition of N. equitans are marked with the signatures of dual adaptation – one to high temperature and the other to obligatory parasitism.
Key Terms
• nanobes: A tiny filamental structure that may or not be a living organism, and if living, would be the smallest form of life, 1/10 the size of the smallest known bacteria. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.15%3A_Euryarchaeota/8.15F%3A_Nanoarchaeum_and_Aciduliprofundum.txt |
Learning Objectives
• Discuss the characteristics associated with hyperthermophiles
A hyperthermophile is an organism that thrives in extremely hot environments, from 60 degrees C (140 degrees F) and up. Hyperthermophiles are a subset of extremophiles within the domain Archaea. An optimal temperature for the existence of hyperthermophiles is above 80°C (176°F). Some bacteria are even able to tolerate temperatures of around 100°C (212°F). Many hyperthermophiles are also able to withstand other environmental extremes like high acidity or radiation levels.
Hyperthermophiles were first discovered by Thomas D. Brock in hot springs in Yellowstone National Park, Wyoming. Since then, more than 70 species have been discovered. The most hardy hyperthermophiles yet discovered live on the superheated walls of deep-sea hydrothermal vents, requiring temperatures of at least 90°C for survival.
One extraordinary heat-tolerant hyperthermophile is the recently discovered Strain 121, an archaeon living at 121°C in the Pacific Ocean. Strain 121 has been able to double its population during 24 hours in an autoclave at 121°C (hence its name). Strain 121 survived being heated to 130°C for two hours, but was unable to reproduce until it was transferred to fresh growth medium at the relatively cooler temperature of 103°C. The current record growth temperature is 122°C for Methanopyrus kandleri ,an archaeon found in a Central Indian Ridge. Other hyperthermophile archaea include Pyrolobus fumarii, which lives at 113°C in Atlantic hydrothermal vents, and Pyrococcus furiosus, first discovered in Italy near a volcanic vent.
Although no hyperthermophile has yet been discovered living at temperatures above 122°C, their existence is very possible. However, it is thought unlikely that microbes could survive at temperatures above 150°C, as the cohesion of DNA and other vital molecules begins to break down at this point.
There are a number of proposed high temperature adaptions of hyperthermophiles. Early research into hyperthermophiles speculated that their genome could be characterized by high guanine-cytosine content; however, recent studies show that there is no obvious correlation between the GC content of the genome and the optimal environmental growth temperature of the organism. The protein molecules in the hyperthermophiles exhibit hyperthermostability – that is, they can maintain structural stability (and therefore function) at high temperatures. Such proteins are homologous to their functional analogues in organisms which thrive at lower temperatures, but have evolved to exhibit optimal function at much greater temperatures. Most of the low-temperature homologues of the hyperthermostable proteins would be denatured above 60°C. Such hyperthermostable proteins are often commercially important, as chemical reactions proceed faster at high temperatures. The cell membrane of hyperthermophiles contains high levels of saturated fatty acids, which are usually arranged in a C40 monolayer to retain its shape at high temperatures.
Key Points
• Many hyperthermophiles are also able to withstand other environmental extremes like high acidity or radiation levels.
• The current record growth temperature is 122°C for Methanopyrus kandleri.
• Although no hyperthermophile has yet been discovered living at temperatures above 122°C, their existence is very possible.
• It is thought unlikely that microbes could survive at temperatures above 150°C, as the cohesion of DNA and other vital molecules begins to break down at this point.
• The protein molecules in hyperthermophiles exhibit hyperthermostability and can maintain structural stability (and therefore function) to adapt to high temperatures.
Key Terms
• hyperthermophile: An organism that lives and thrives in an extremely hot environment like a deep sea smoker vent; often a member of the Archaea.
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• Methanosarcina acetivorans. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Methanosarcina_acetivorans. License: CC BY-SA: Attribution-ShareAlike
• polysaccharide. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/polysaccharide. License: CC BY-SA: Attribution-ShareAlike
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• Arkea. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/File:Arkea.jpg. License: CC BY-SA: Attribution-ShareAlike | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.15%3A_Euryarchaeota/8.15G%3A_Hyperthermophilic_Archaea_H_and_Microbial_Evolution.txt |
Eukaryotes are very diverse in phylogenic terms, the common feature being a membrane bound nucleus.
Learning Objectives
• Assess the phylogeny of Eukarya
Key Points
• Eukaryotes are broadly determined by the prescence of a membrane bound nucleus, though many eukaryotes have other membrane bound structures.
• The domain of eukarya are broadly grouped into six kingdoms: Excavata, Amoebozoa, Opisthokonta, Rhizaria, Chromalveolata, and Archaeplastida.
• The exact nature of the relationships (i.e. common ancestors) of the the eukarya domain are still debated.
Key Terms
• crown group: In phylogenetics, the crown group of a collection of species consists of the living representatives of the collection together with their ancestors back to their last common ancestor as well as all of that ancestor’s descendants. It is thus a clade, a group consisting of a species and all its descendents.
• cristae: Cristae (singular crista) are the internal compartments formed by the inner membrane of a mitochondrion. They are studded with proteins, including ATP synthase and a variety of cytochromes.
Phylogeny of the Eukarya
A eukaryote is an organism whose cells contain complex structures enclosed within membranes. Eukaryotes may more formally be referred to as the taxon Eukarya or Eukaryota. The defining membrane-bound structure that sets eukaryotic cells apart from prokaryotic cells is the nucleus, or nuclear envelope, within which the genetic material is carried. Most eukaryotic cells also contain other membrane-bound organelles such as mitochondria, chloroplasts, and the Golgi apparatus. All large complex organisms are eukaryotes, including animals, plants, and fungi. The group also includes many unicellular organisms.
rRNA trees constructed during the 1980s and 1990s left most eukaryotes in an unresolved crown group, which was usually divided by the form of the mitochondrial cristae. The few groups that lack mitochondria branched separately, and so the absence was believed to be primitive. But this is now considered an artifact of a divergent evolutionary line, and they are known to have lost them secondarily.
Eukaryotes are split into 6, subdivisions, referred to as kingdoms. They include:
1. Excavata – Various flagellate protozoa
2. Amoebozoa – Most lobose amoeboids and slime moulds
3. Opisthokonta – Animals, fungi, choanoflagellates
4. RhizariaForaminifera – Radiolaria, and various other amoeboid protozoa
5. ChromalveolataStramenopiles (or Heterokonta) – Haptophyta, Cryptophyta (or cryptomonads), and Alveolata
6. Archaeplastida (or Primoplantae) – Land plants, green algae, red algae, and glaucophytes
There is widespread agreement that the Rhizaria belong with the Stramenopiles and the Alveolata, in a clade dubbed the SAR supergroup, so that Rhizara is not one of the main eukaryote groups. The Amoeboza and Opisthokonta are each monophyletic and form a clade, often called the unikonts. There is debate about the true constituents of the animal kingdoms.
Beyond this, there does not appear to be a consensus. It has been estimated that there may be 75 distinct lineages of eukaryotes. Most of these lineages are protists. The known eukaryote genome sizes vary from 8.2 megabases (Mb) in Babesia bovis to 112,000 to 220,050 Mb in the dinoflagellate Prorocentrum micans. This suggests that the genome of the ancestral eukaryote has undergone considerable variation during its evolution. The last common ancestor of all eukaryotes is believed to have been a phagotrophic protist with a nucleus, at least one centriole and cilium, facultatively aerobic mitochondria, sex (meiosis), a dormant cyst with a cell wall of chitin, cellulose, and peroxisomes. Later endosymbiosis led to the spread of plastids in some lineages. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.16%3A_Eukaryotic_Microbial_Diversity/8.16A%3A_Phylogeny_of_the_Eukarya.txt |
Until more recent work, the historical view of eukaryotes has been anthropomorphic.
LEARNING OBJECTIVES
Examine the historical view of eukaryotes
Key Points
• Plants and animals since ancient times have been considered to be related.
• Initially, microscopic organisms were classified into plants or animals.
• Genomic sequencing has reorganized our understanding of life, and how different eukaryotic clades are related.
Key Terms
• kingdom: A rank in the classification of organisms, below domain and above phylum; a taxon at that rank (e.g. the plant kingdom, the animal kingdom).
• clade: A group of animals or other organisms derived from a common ancestor species.
Even back to Antiquity the two clades of animals and plants were recognized. They were given the taxonomic rank of Kingdom (biology) by Linnaeus. Although he included the fungi with plants with some reservations, it was later realized that they are quite distinct and warrant a separate kingdom, the composition of which was not entirely clear until the 1980’s. The various single-cell eukaryotes were originally placed with plants or animals when they became known. The German biologist Georg A. Goldfuss coined the word protozoa in 1830 to refer to organisms such as ciliates and corals. This group was expanded until it encompassed all single-cell eukaryotes. They were given their own kingdom, the Protista, by Ernst Haeckel in 1866.
Biological classification: The hierarchy of biological classification’s eight major taxonomic ranks. A genus contains one or more species. Intermediate minor rankings are not shown.
The eukaryotes came to be composed of four kingdoms: Kingdom Protista, Kingdom Plantae, Kingdom Fungi, and Kingdom Animalia. The protists were understood to be “primitive forms,” and thus an evolutionary grade, united by their primitive unicellular nature. The disentanglement of the deep splits in the tree of life only really got going with DNA sequencing, leading to a system of domains rather than kingdoms as top level rank being put forward by Carl Woese, uniting all the eukaryote kingdoms under the eukaryote domain. As such the tree of life consists of three domains: Archaea, Bacteria, and Eukarya. The arrangement of taxa reflects the fundamental differences in the genomes, a less anthropomorphic “animal-centric” world view. At the same time, work on the protist tree intensified, and is still actively going on today. Several alternative classifications have been forwarded, though there is no consensus in the field.
8.16C: Opisthokonts - Animals and Fungi
Learning Objectives
• Describe Opistkokonts
The opisthokonts, or “fungi/metazoa group”, are a broad group of eukaryotes, including both the animal and fungus kingdoms, together with the eukaryotic microorganisms that are sometimes grouped in the paraphyletic phylum choanozoa (previously assigned to the protist “kingdom”). Both genetic and ultrastructural studies strongly support that opisthokonts form a monophyletic group.
One common characteristic of opisthokonts is that flagellate cells, such as most animal sperm and chytrid spores, propel themselves with a single posterior flagellum. This gives the group its name. In contrast, flagellate cells in other eukaryote groups propel themselves with one or more anterior flagellae. Most fungi do not produce cells with flagellae, but the primitive fungal chytrids do, suggesting that a common ancestor of current fungal species did have a flagellum.
The close relationship between animals and fungi was suggested by Cavalier-Smith in 1987, who used the informal name opisthokonta (the formal name has been used for the chytrids). The discovery was confirmed by later genetic studies. Early phylogenies placed opisthokonts near the plants and other groups that have mitochondria with flat cristae, but this character varies. Cavalier-Smith and Stechmann argue that the uniciliate eukaryotes such as opisthokonts and Amoebozoa, collectively called unikonts, split off from the other biciliate eukaryotes, called bikonts, shortly after they evolved.
Opisthokonts are divided into Holomycota or Nucletmycea (fungi and all organisms more closely related to fungi than to animals) and Holozoa (animals and all organisms more closely related to animals than to fungi); no opisthokonts basal to the Holomycota/Holozoa split have yet been identified.
Key Points
• The unifying feature of opisthokonts is the presence of a flagellum, sometimes only ancestrally or at a specific point in the life cycle.
• Genetic sequencing has confirmed that opisthokonts are genetically related.
• Opisthokonts are split into two groups: holomycota (includes fungi), and holozoa (includes animals).
Key Terms
• monophyletic: Of, pertaining to, or affecting a single phylum (or other taxon) of organisms.
• flagellum: In protists, a long, whiplike membrane-enclosed organelle used for locomotion or feeding. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.16%3A_Eukaryotic_Microbial_Diversity/8.16B%3A_Historical_Overview_of_Eukaryotes.txt |
Genome fusion occurs during endosymbiosis, which is the mechanism proposed as responsible for the first eukaryotic cells.
Learning Objectives
• Describe the genome fusion hypothesis and its relationship to the evolution of eukaryotes
Key Points
• Two symbiotic organisms become endosymbiotic when one species is taken inside the cytoplasm of another species, resulting in genome fusion.
• Genome fusion, by endosymbiosis, between two species, one an Archaea and the other a Bacteria, has been proposed as responsible for the evolution of the first eukaryotic cells.
• Gram-negative bacteria are proposed to result from an endosymbiotic fusion of archaeal and bacterial species through a mechanism that has also been used to explain the double membranes found in mitochondria and chloroplasts.
• The nucleus-first hypothesis proposes the nucleus evolved in prokaryotes first, followed by a later fusion of the new eukaryote with bacteria that became mitochondria.
• The mitochondria-first hypothesis proposes mitochondria were first established in a prokaryotic host, which subsequently acquired a nucleus to become the first eukaryotic cell.
• The eukaryote-first hypothesis proposes prokaryotes actually evolved from eukaryotes by losing genes and complexity.
Key Terms
• genome fusion: a result of endosymbiosis when a genome consists of genes from both the endosymbiont and the host.
• symbiotic: of a relationship with mutual benefit between two individuals or organisms
• endosymbiosis: when one symbiotic species is taken inside the cytoplasm of another symbiotic species and both become endosymbiotic
Genome Fusion and the Evolution of Eukaryotes
Scientists believe the ultimate event in HGT (horizontal gene transfer) occurs through genome fusion between different species when two symbiotic organisms become endosymbiotic. This occurs when one species is taken inside the cytoplasm of another species, which ultimately results in a genome consisting of genes from both the endosymbiont and the host. This mechanism is an aspect of the Endosymbiont Theory, which is accepted by a majority of biologists as the mechanism whereby eukaryotic cells obtained their mitochondria and chloroplasts. However, the role of endosymbiosis in the development of the nucleus is more controversial. Nuclear and mitochondrial DNA are thought to be of different (separate) evolutionary origin, with the mitochondrial DNA being derived from the circular genomes of bacteria that were engulfed by ancient prokaryotic cells. Mitochondrial DNA can be regarded as the smallest chromosome. Interestingly enough, mitochondrial DNA is inherited only from the mother. The mitochondrial DNA degrades in sperm when the sperm degrades in the fertilized egg or, in other instances, when the mitochondria located in the flagellum of the sperm fails to enter the egg.
Within the past decade, the process of genome fusion by endosymbiosis has been proposed to be responsible for the evolution of the first eukaryotic cells. Using DNA analysis and a new mathematical algorithm called conditioned reconstruction (CR), it has been proposed that eukaryotic cells developed from an endosymbiotic gene fusion between two species: one an Archaea and the other a Bacteria. As mentioned, some eukaryotic genes resemble those of Archaea, whereas others resemble those from Bacteria. An endosymbiotic fusion event would clearly explain this observation. On the other hand, this work is new and the CR algorithm is relatively unsubstantiated, which causes many scientists to resist this hypothesis.
Endosymbiosis in eukaryotes: The theory that mitochondria and chloroplasts are endosymbiotic in origin is now widely accepted. More controversial is the proposal that (a) the eukaryotic nucleus resulted from the fusion of archaeal and bacterial genomes; and that (b) Gram-negative bacteria, which have two membranes, resulted from the fusion of Archaea and Gram-positive bacteria, each of which has a single membrane.
More recent work proposes that gram-negative bacteria, which are unique within their domain in that they contain two lipid bilayer membranes, did result from an endosymbiotic fusion of archaeal and bacterial species. The double membrane would be a direct result of endosymbiosis, with the endosymbiont picking up the second membrane from the host as it was internalized. This mechanism has also been used to explain the double membranes found in mitochondria and chloroplasts. A lot of skepticism still surrounds this hypothesis; the ideas are still debated within the biological science community.
There are several other competing hypotheses as to the origin of eukaryotes and the nucleus. One idea about how the eukaryotic nucleus evolved is that prokaryotic cells produced an additional membrane which surrounded the bacterial chromosome. Some bacteria have the DNA enclosed by two membranes; however, there is no evidence of a nucleolus or nuclear pores. Other proteobacteria also have membrane-bound chromosomes. If the eukaryotic nucleus evolved this way, we would expect one of the two types of prokaryotes to be more closely-related to eukaryotes. Another hypothesis, the nucleus-first hypothesis, proposes the nucleus evolved in prokaryotes first, followed by a later fusion of the new eukaryote with bacteria that became mitochondria. The mitochondria-first hypothesis, however, proposes mitochondria were first established in a prokaryotic host, which subsequently acquired a nucleus (by fusion or other mechanisms) to become the first eukaryotic cell. Most interestingly, the eukaryote-first hypothesis proposes prokaryotes actually evolved from eukaryotes by losing genes and complexity. All of these hypotheses are testable. Only time and more experimentation will determine which hypothesis is best supported by data. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.16%3A_Eukaryotic_Microbial_Diversity/8.16D%3A_Endosymbiotic_Theory_and_the_Evolution_of_Eukaryotes.txt |
Protists are an incredibly diverse set of eukaryotes of various sizes, cell structures, metabolisms, and methods of motility.
Learning Objectives
• Describe the metabolism and structure of protists, explaining the structures that provide their motility
Key Points
• Protist cells may contain a single nucleus or many nuclei; they range in size from microscopic to thousands of meters in area.
• Protists may have animal-like cell membranes, plant-like cell walls, or may be covered by a pellicle.
• Some protists are heterotrophs and ingest food by phagocytosis, while other types of protists are photoautotrophs and store energy via photosynthesis.
• Most protists are motile and generate movement with cilia, flagella, or pseudopodia.
Key Terms
• amorphous: lacking a definite form or clear shape
• multinucleate: having more than one nucleus
• pellicle: cuticle, the hard protective outer layer of certain life forms
• taxis: the movement of an organism in response to a stimulus; similar to kinesis, but more direct
• phagocytosis: the process where a cell incorporates a particle by extending pseudopodia and drawing the particle into a vacuole of its cytoplasm
• phagosome: a membrane-bound vacuole within a cell containing foreign material captured by phagocytosis
Cell Structure
The cells of protists are among the most elaborate and diverse of all cells. Most protists are microscopic and unicellular, but some true multicellular forms exist. A few protists live as colonies that behave in some ways as a group of free-living cells and in other ways as a multicellular organism. Still other protists are composed of enormous, multinucleate, single cells that look like amorphous blobs of slime, or in other cases, similar to ferns. Many protist cells are multinucleated; in some species, the nuclei are different sizes and have distinct roles in protist cell function.
Single protist cells range in size from less than a micrometer to thousands of square meters (giant kelp). Animal-like cell membranes or plant-like cell walls envelope protist cells. In other protists, glassy silica-based shells or pellicles of interlocking protein strips encase the cells. The pellicle functions like a flexible coat of armor, preventing the protist from external damage without compromising its range of motion.
Metabolism
Protists exhibit many forms of nutrition and may be aerobic or anaerobic. Protists that store energy by photosynthesis belong to a group of photoautotrophs and are characterized by the presence of chloroplasts. Other protists are heterotrophic and consume organic materials (such as other organisms) to obtain nutrition. Amoebas and some other heterotrophic protist species ingest particles by a process called phagocytosis in which the cell membrane engulfs a food particle and brings it inward, pinching off an intracellular membranous sac, or vesicle, called a food vacuole. The vesicle containing the ingested particle, the phagosome, then fuses with a lysosome containing hydrolytic enzymes to produce a phagolysosome, which breaks down the food particle into small molecules that diffuse into the cytoplasm for use in cellular metabolism. Undigested remains ultimately exit the cell via exocytosis.
Subtypes of heterotrophs, called saprobes, absorb nutrients from dead organisms or their organic wastes. Some protists function as mixotrophs, obtaining nutrition by photoautotrophic or heterotrophic routes, depending on whether sunlight or organic nutrients are available.
Motility
The majority of protists are motile, but different types of protists have evolved varied modes of movement. Protists such as euglena have one or more flagella, which they rotate or whip to generate movement. Paramecia are covered in rows of tiny cilia that they beat to swim through liquids. Other protists, such at amoebae, form cytoplasmic extensions called pseudopodia anywhere on the cell, anchor the pseudopodia to a surface, and pull themselves forward. Some protists can move toward or away from a stimulus; a movement referred to as taxis. Protists accomplish phototaxis, movement toward light, by coupling their locomotion strategy with a light-sensing organ.
8.16F: Newly Discovered Eukaryotes
There are many new species to be discovered, including eukaryotic species.
Learning Objectives
• Recognize Eukaryotic diversity
Key Points
• We know only a fraction of the number of species out there, and most of the attention has been given to large macroscopic species, a true understanding of microscopic eukaryotic life is not known.
• Even though mammals make up a small percentage of the species that are eukaryotes, several new mammalian species have been identified in the last decade.
• As extinction is increasing, we may never know all the eukaryotes that share the world with us.
Key Terms
• extant: Still alive; not extinct.
• metagenomics: The study of genomes recovered from environmental samples; especially the differentiation of genomes from multiple organisms or individuals, either in a symbiotic relationship, or at a crime scene.
According to the Global Taxonomy Initiative and the European Distributed Institute of Taxonomy, the total number of species for some phyla may be much higher than what was known in 2010:10–30 million insects; (of some 0.9 million we know today) 5–10 million bacteria; 1.5 million fungi; of some 0.075 million we know today. The number of microbial species is not reliably known, but the Global Ocean Sampling Expedition dramatically increased the estimates of genetic diversity by identifying an enormous number of new genes from near-surface plankton samples at various marine locations.
From these studies, it is apparent that less than 1% of all species that have been described have been studied beyond simply noting their existence. The vast majority of Earth’s species are microbial. Contemporary biodiversity is “firmly fixated on the visible world”. For example, microbial life is metabolically and environmentally more diverse than multicellular life (e.g., extremophile). On the tree of life, based on analyses of small-subunit ribosomal RNA, visible life consists of barely noticeable twigs. The inverse relationship of size and population recurs higher on the evolutionary ladder.
Due to the advent of mass sequencing tools, thousands of new viral species have been identified in metagenomics studies, while at the same time hundreds of new viral species have been found. On top of that, there have been numerous fungal species identified. However, as suggested above most of the attention is given to large species, which represent a very small portion of the new species identified Even with this in mind, since the beginning of this century, 5 marsupial species, 25 primate, 1 elephant, 1 sloth, 3 rabbit, several rodent species, at least 30 new bat species have been discovered. On top of that several subspecies have been found. Considering how large an elephant is, this should point out how little we know about the numbers of microscopic eukaryotes that are yet to be discovered.
Of course we may never truly identify many eukaryotic species, since the rate of extinction has increased. Many extant species may become extinct before they are described.
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Characteristics of Fungi
Fungi, latin for mushroom, are eukaryotes which are responsible for decomposition and nutrient cycling through the environment.
LEARNING OBJECTIVES
Describe the role of fungi in the ecosystem
Key Points
• Fungi are more closely related to animals than plants.
• Fungi are heterotrophic: they use complex organic compounds as sources of energy and carbon, not photosynthesis.
• Fungi multiply either asexually, sexually, or both.
• The majority of fungi produce spores, which are defined as haploid cells that can undergo mitosis to form multicellular, haploid individuals.
• Fungi interact with other organisms by either forming beneficial or mutualistic associations (mycorrhizae and lichens ) or by causing serious infections.
Key Terms
• mycorrhiza: a symbiotic association between a fungus and the roots of a vascular plant
• spore: a reproductive particle, usually a single cell, released by a fungus, alga, or plant that may germinate into another
• lichen: any of many symbiotic organisms, being associations of fungi and algae; often found as white or yellow patches on old walls, etc.
• Ascomycota: a taxonomic division within the kingdom Fungi; those fungi that produce spores in a microscopic sporangium called an ascus
• heterotrophic: organisms that use complex organic compounds as sources of energy and carbon
Introduction to Fungi
The word fungus comes from the Latin word for mushrooms. Indeed, the familiar mushroom is a reproductive structure used by many types of fungi. However, there are also many fungi species that don’t produce mushrooms at all. Being eukaryotes, a typical fungal cell contains a true nucleus and many membrane-bound organelles. The kingdom Fungi includes an enormous variety of living organisms collectively referred to as Ascomycota, or true Fungi. While scientists have identified about 100,000 species of fungi, this is only a fraction of the 1.5 million species of fungus probably present on earth. Edible mushrooms, yeasts, black mold, and the producer of the antibiotic penicillin, Penicilliumnotatum, are all members of the kingdom Fungi, which belongs to the domain Eukarya.
Fungi, once considered plant-like organisms, are more closely related to animals than plants. Fungi are not capable of photosynthesis: they are heterotrophic because they use complex organic compounds as sources of energy and carbon. Some fungal organisms multiply only asexually, whereas others undergo both asexual reproduction and sexual reproduction with alternation of generations. Most fungi produce a large number of spores, which are haploid cells that can undergo mitosis to form multicellular, haploid individuals. Like bacteria, fungi play an essential role in ecosystems because they are decomposers and participate in the cycling of nutrients by breaking down organic and inorganic materials to simple molecules.
Fungi often interact with other organisms, forming beneficial or mutualistic associations. For example most terrestrial plants form symbiotic relationships with fungi. The roots of the plant connect with the underground parts of the fungus forming mycorrhizae. Through mycorrhizae, the fungus and plant exchange nutrients and water, greatly aiding the survival of both species Alternatively, lichens are an association between a fungus and its photosynthetic partner (usually an alga). Fungi also cause serious infections in plants and animals. For example, Dutch elm disease, which is caused by the fungus Ophiostoma ulmi, is a particularly devastating type of fungal infestation that destroys many native species of elm (Ulmus sp.) by infecting the tree’s vascular system. The elm bark beetle acts as a vector, transmitting the disease from tree to tree. Accidentally introduced in the 1900s, the fungus decimated elm trees across the continent. Many European and Asiatic elms are less susceptible to Dutch elm disease than American elms.
In humans, fungal infections are generally considered challenging to treat. Unlike bacteria, fungi do not respond to traditional antibiotic therapy because they are eukaryotes. Fungal infections may prove deadly for individuals with compromised immune systems.
Fungi have many commercial applications. The food industry uses yeasts in baking, brewing, and cheese and wine making. Many industrial compounds are byproducts of fungal fermentation. Fungi are the source of many commercial enzymes and antibiotics. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.17%3A_Fungi/8.17A%3A_Characteristics_of_Fungi.txt |
From crop and food spoilage to severe infections in animal species, fungal parasites and pathogens are wide spread and difficult to treat.
Learning Objectives
• Give examples of fungi that are plant and animal parasites and pathogens
Key Points
• In plants, fungi can destroy plant tissue directly or through the production of potent toxins, which usually ends in host death and can even lead to ergotism in animals like humans.
• During mycosis, fungi, like dermatophytes, successfully attack hosts directly by colonizing and destroying their tissues.
• Examples of fungal parasites and pathogens in animals that cause mycoses include Batrachochytrium dendrobatidis, Geomyces destructans, and Histoplasma capsulatum.
• Systemic mycoses, such as valley fever, Histoplasmosis, or pulmonary disease, are fungal diseases that spread to internal organs and commonly enter the body through the respiratory system.
• Opportunistic mycoses, fungal infections that are common in all environments, mainly take advantage of individuals who have a compromised immune system, such as AIDS patients.
• Fungi can also cause mycetismus, a disease caused by the ingestion of toxic mushrooms that leads to poisoning.
Key Terms
• mycosis: a fungal disease caused by infection and direct damage
• dermatophyte: a parasitic fungus that secretes extracellular enzymes that break down keratin, causing infections the skin, such as jock itch and athlete’s foot
• aflatoxin: toxic, carcinogenic compounds released by fungi of the genus Aspergillus; contaminate nut and grain harvests
• ergot: any fungus in the genus Claviceps which are parasitic on grasses
Fungal Parasites and Pathogens
The production of sufficient good-quality crops is essential to human existence. Plant diseases have ruined crops, bringing widespread famine. Many plant pathogens are fungi that cause tissue decay and eventual death of the host. In addition to destroying plant tissue directly, some plant pathogens spoil crops by producing potent toxins. Fungi are also responsible for food spoilage and the rotting of stored crops. For example, the fungus Claviceps purpurea causes ergot, a disease of cereal crops (especially of rye). Although the fungus reduces the yield of cereals, the effects of the ergot’s alkaloid toxins on humans and animals are of much greater significance. In animals, the disease is referred to as ergotism. The most common signs and symptoms are convulsions, hallucinations, gangrene, and loss of milk in cattle. The active ingredient of ergot is lysergic acid, which is a precursor of the drug LSD. Smuts, rusts, and powdery or downy mildew are other examples of common fungal pathogens that affect crops.
Aflatoxins are toxic, carcinogenic compounds released by fungi of the genus Aspergillus. Periodically, harvests of nuts and grains are tainted by aflatoxins, leading to massive recall of produce. This sometimes ruins producers and causes food shortages in developing countries.
Animal and Human Parasites and Pathogens
Fungi can affect animals, including humans, in several ways. A mycosis is a fungal disease that results from infection and direct damage. Fungi attack animals directly by colonizing and destroying tissues. Mycotoxicosis is the poisoning of humans (and other animals) by foods contaminated by fungal toxins (mycotoxins). Mycetismus describes the ingestion of preformed toxins in poisonous mushrooms. In addition, individuals who display hypersensitivity to molds and spores develop strong and dangerous allergic reactions. Fungal infections are generally very difficult to treat because, unlike bacteria, fungi are eukaryotes. Antibiotics only target prokaryotic cells, whereas compounds that kill fungi also harm the eukaryotic animal host.
Many fungal infections are superficial; that is, they occur on the animal’s skin. Termed cutaneous (“skin”) mycoses, they can have devastating effects. For example, the decline of the world’s frog population in recent years may be caused by the fungus Batrachochytrium dendrobatidis, which infects the skin of frogs and presumably interferes with gaseous exchange. Similarly, more than a million bats in the United States have been killed by white-nose syndrome, which appears as a white ring around the mouth of the bat. It is caused by the cold-loving fungus Geomyces destructans, which disseminates its deadly spores in caves where bats hibernate. Mycologists are researching the transmission, mechanism, and control of G. destructans to stop its spread.
Fungi that cause the superficial mycoses of the epidermis, hair, and nails rarely spread to the underlying tissue. These fungi are often misnamed “dermatophytes”, from the Greek words dermis meaning skin and phyte meaning plant, although they are not plants. Dermatophytes are also called “ringworms” because of the red ring they cause on skin. They secrete extracellular enzymes that break down keratin (a protein found in hair, skin, and nails), causing conditions such as athlete’s foot and jock itch. These conditions are usually treated with over-the-counter topical creams and powders; they are easily cleared. More persistent superficial mycoses may require prescription oral medications.
Systemic mycoses spread to internal organs, most commonly entering the body through the respiratory system. For example, coccidioidomycosis (valley fever) is commonly found in the southwestern United States where the fungus resides in the dust. Once inhaled, the spores develop in the lungs and cause symptoms similar to those of tuberculosis. Histoplasmosis is caused by the dimorphic fungus Histoplasma capsulatum. It also causes pulmonary infections. In rarer cases, it causes swelling of the membranes of the brain and spinal cord. Treatment of these and many other fungal diseases requires the use of antifungal medications that have serious side effects.
Opportunistic mycoses are fungal infections that are either common in all environments or are part of the normal biota. They mainly affect individuals who have a compromised immune system. Patients in the late stages of AIDS suffer from opportunistic mycoses that can be life threatening. The yeast Candida sp., a common member of the natural biota, can grow unchecked and infect the vagina or mouth (oral thrush) if the pH of the surrounding environment, the person’s immune defenses, or the normal population of bacteria are altered.
Mycetismus can occur when poisonous mushrooms are eaten. It causes a number of human fatalities during mushroom-picking season. Many edible fruiting bodies of fungi resemble highly-poisonous relatives. Amateur mushroom hunters are cautioned to carefully inspect their harvest and avoid eating mushrooms of doubtful origin. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.17%3A_Fungi/8.17B%3A__Fungi_as_Plant_Animal_and_Human_Pathogens.txt |
Fungi are the major decomposers of nature; they break down organic matter which would otherwise not be recycled.
Learning Objectives
• Explain the roles played by fungi in decomposition and recycling
Key Points
• Aiding the survival of species from other kingdoms through the supply of nutrients, fungi play a major role as decomposers and recyclers in the wide variety of habitats in which they exist.
• Fungi provide a vital role in releasing scarce, yet biologically-essential elements, such as nitrogen and phosphorus, from decaying matter.
• Their mode of nutrition, which involves digestion before ingestion, allows fungi to degrade many large and insoluble molecules that would otherwise remain trapped in a habitat.
Key Terms
• decomposer: any organism that feeds off decomposing organic material, especially bacterium or fungi
• exoenzyme: any enzyme, generated by a cell, that functions outside of that cell
• saprobe: an organism that lives off of dead or decaying organic material
Fungi & Their Roles as Decomposers and Recyclers
Fungi play a crucial role in the balance of ecosystems. They colonize most habitats on earth, preferring dark, moist conditions. They can thrive in seemingly-hostile environments, such as the tundra. However, most members of the Kingdom Fungi grow on the forest floor where the dark and damp environment is rich in decaying debris from plants and animals. In these environments, fungi play a major role as decomposers and recyclers, making it possible for members of the other kingdoms to be supplied with nutrients and to live.
The food web would be incomplete without organisms that decompose organic matter. Some elements, such as nitrogen and phosphorus, are required in large quantities by biological systems; yet, they are not abundant in the environment. The action of fungi releases these elements from decaying matter, making them available to other living organisms. Trace elements present in low amounts in many habitats are essential for growth, but would remain tied up in rotting organic matter if fungi and bacteria did not return them to the environment via their metabolic activity.
The ability of fungi to degrade many large and insoluble molecules is due to their mode of nutrition. As seen earlier, digestion precedes ingestion. Fungi produce a variety of exoenzymes to digest nutrients. These enzymes are either released into the substrate or remain bound to the outside of the fungal cell wall. Large molecules are broken down into small molecules, which are transported into the cell by a system of protein carriers embedded in the cell membrane. Because the movement of small molecules and enzymes is dependent on the presence of water, active growth depends on a relatively-high percentage of moisture in the environment.
As saprobes, fungi help maintain a sustainable ecosystem for the animals and plants that share the same habitat. In addition to replenishing the environment with nutrients, fungi interact directly with other organisms in beneficial, but sometimes damaging, ways.
8.17D: Chytridiomycota - The Chytrids
Chytrids are the most primitive group of fungi and the only group that possess gametes with flagella.
Learning Objectives
• Describe the ecology and reproduction of chytrids
Key Points
• The first recognizable chytrids appeared more than 500 million years ago during the late pre-Cambrian period.
• Like protists, chytrids usually live in aquatic environments, but some species live on land.
• Some chytrids are saprobes while others are parasites that may be harmful to amphibians and other animals.
• Chytrids reproduce both sexually and asexually, which leads to the production of zoospores.
• Chytrids have chitin in their cell walls; one unique group also has cellulose along with chitin.
• Chytrids are mostly unicellular, but multicellular organisms do exist.
Key Terms
• chytridiomycete: an organism of the phylum Chytridiomycota
• zoospore: an asexual spore of some algae and fungi
• flagellum: a flagellum is a lash-like appendage that protrudes from the cell body of certain prokaryotic and eukaryotic cells
• coenocytic: a multinucleate cell that can result from multiple nuclear divisions without their accompanying cytokinesis
Chytridiomycota: The Chytrids
The kingdom Fungi contains five major phyla, which were established according to their mode of sexual reproduction or use of molecular data. The Phylum Chytridiomycota (chytrids) is one of the five true phyla of fungi. There is only one class in the Phylum Chytridiomycota, the Chytridiomycetes. The chytrids are the simplest and most primitive Eumycota, or true fungi. The evolutionary record shows that the first, recognizable chytrids appeared during the late pre-Cambrian period, more than 500 million years ago. Like all fungi, chytrids have chitin in their cell walls, but one group of chytrids has both cellulose and chitin in the cell wall. Most chytrids are unicellular; a few form multicellular organisms and hyphae, which have no septa between cells (coenocytic). They reproduce both sexually and asexually; the asexual spores are called diploid zoospores. Their gametes are the only fungal cells known to have a flagellum.
The ecological habitat and cell structure of chytrids have much in common with protists. Chytrids usually live in aquatic environments, although some species live on land. Some species thrive as parasites on plants, insects, or amphibians, while others are saprobes. Some chytrids cause diseases in many species of amphibians, resulting in species decline and extinction. An example of a harmful parasitic chytrid is Batrachochytrium dendrobatidis, which is known to cause skin disease. Another chytrid species, Allomyces, is well characterized as an experimental organism. Its reproductive cycle includes both asexual and sexual phases. Allomyces produces diploid or haploid flagellated zoospores in a sporangium. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.17%3A_Fungi/8.17C%3A_Fungi_Habitat_Decomposition_and_Recycling.txt |
Zygomycota, a small group in the fungi kingdom, can reproduce asexually or sexually, in a process called conjugation.
Learning Objectives
• Describe the ecology and reproduction of Zygomycetes
Key Points
• Most zygomycota are saprobes, while a few species are parasites.
• Zygomycota usually reproduce asexually by producing sporangiospores.
• Zygomycota reproduce sexually when environmental conditions become unfavorable.
• To reproduce sexually, two opposing mating strains must fuse or conjugate, thereby, sharing genetic content and creating zygospores.
• The resulting diploid zygospores remain dormant and protected by thick coats until environmental conditions have improved.
• When conditions become favorable, zygospores undergo meiosis to produce haploid spores, which will eventually grow into a new organism.
Key Terms
• zygomycete: an organism of the phylum Zygomycota
• karyogamy: the fusion of two nuclei within a cell
• zygospore: a spore formed by the union of several zoospores
• conjugation: the temporary fusion of organisms, especially as part of sexual reproduction
Zygomycota: The Conjugated Fungi
The zygomycetes are a relatively small group in the fungi kingdom and belong to the Phylum Zygomycota. They include the familiar bread mold, Rhizopus stolonifer, which rapidly propagates on the surfaces of breads, fruits, and vegetables. They are mostly terrestrial in habitat, living in soil or on plants and animals. Most species are saprobes meaning they live off decaying organic material. Some are parasites of plants, insects, and small animals, while others form symbiotic relationships with plants. Zygomycetes play a considerable commercial role. The metabolic products of other species of Rhizopus are intermediates in the synthesis of semi-synthetic steroid hormones.
Zygomycetes have a thallus of coenocytic hyphae in which the nuclei are haploid when the organism is in the vegetative stage. The fungi usually reproduce asexually by producing sporangiospores. The black tips of bread mold, Rhizopus stolonifer, are the swollen sporangia packed with black spores. When spores land on a suitable substrate, they germinate and produce a new mycelium.
Sexual reproduction starts when conditions become unfavorable. Two opposing mating strains (type + and type –) must be in close proximity for gametangia (singular: gametangium) from the hyphae to be produced and fuse, leading to karyogamy. The developing diploid zygospores have thick coats that protect them from desiccation and other hazards. They may remain dormant until environmental conditions become favorable. When the zygospore germinates, it undergoes meiosis and produces haploid spores, which will, in turn, grow into a new organism. This form of sexual reproduction in fungi is called conjugation (although it differs markedly from conjugation in bacteria and protists), giving rise to the name “conjugated fungi”.
8.17F: Glomeromycota
Learning Objectives
• Describe the ecology and reproduction of Glomeromycetes
In the kingdom Fungi, the Glomeromycota is a newly-established phylum comprised of about 230 species that live in close association with the roots of trees and plants. Fossil records indicate that trees and their root symbionts share a long evolutionary history. It appears that most members of this family form arbuscular mycorrhizae: the hyphae interact with the root cells forming a mutually-beneficial association where the plants supply the carbon source and energy in the form of carbohydrates to the fungus while the fungus supplies essential minerals from the soil to the plant. This association is termed biotrophic. The Glomeromycota species that have arbuscular mycorrhizal are terrestrial and widely distributed in soils worldwide where they form symbioses with the roots of the majority of plant species. They can also be found in wetlands, including salt-marshes, and are associated with epiphytic plants.
The glomeromycetes do not reproduce sexually and cannot survive without the presence of plant roots. They have coenocytic hyphae and reproduce asexually, producing glomerospores. The biochemical and genetic characterization of the Glomeromycota has been hindered by their biotrophic nature, which impedes laboratory culturing. This obstacle was eventually surpassed with the use of root cultures. With the advent of molecular techniques, such as gene sequencing, the phylogenetic classification of Glomeromycota has become clearer. The first mycorrhizal gene to be sequenced was the small-subunit ribosomal RNA (SSU rRNA). This gene is highly conserved and commonly used in phylogenetic studies so it was isolated from spores of each taxonomic group. Using a molecular clock approach based on the substitution rates of SSU sequences, scientists were able to estimate the time of divergence of the fungi. This analysis shows that all glomeromycetes probably descended from a common ancestor 462 and 353 million years ago, making them a monophyletic lineage. A long-held theory is that Glomeromycota were instrumental in the colonization of land by plants.
Key Points
• Most glomeromycetes form arbuscular mycorrhizae, a type of symbiotic relationship between a fungus and plant roots; the plants supply a source of energy to the fungus while the fungus supplies essential minerals to the plant.
• Glomeromycota that have arbuscular mycorrhizal are mostly terrestrial, but can also be found in wetlands.
• The glomeromycetes reproduce asexually by producing glomerospores and cannot survive without the presence of plant roots.
• DNA analysis shows that all glomeromycetes probably descended from a common ancestor 462 and 353 million years ago.
• The classification of fungi as Glomeromycota has been redefined with adoption of molecular techniques.
Key Terms
• biotrophic: describing a parasite that needs its host to stay alive
• arbuscular mycorrhizae: a type of symbiotic relationship between a fungus and the roots of a plant where the plants supply a source of energy to the fungus while the fungus supplies essential minerals to the plant
• glomeromycete: an organism of the phylum Glomeromycota | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.17%3A_Fungi/8.17E%3A_Zygomycota_-_The_Conjugated_Fungi.txt |
Most fungi belong to the Phylum Ascomycota, which uniquely forms of an ascus, a sac-like structure that contains haploid ascospores.
Learning Objectives
• Describe the ecology and the reproduction of Ascomycetes
Key Points
• Ascomycota fungi are the yeasts used in baking, brewing, and wine fermentation, plus delicacies such as truffles and morels.
• Ascomycetes are filamentous and produce hyphae divided by perforated septa.
• Ascomycetes frequently reproduce asexually which leads to the production of conidiophores that release haploid conidiospores.
• Two types of mating strains, a “male” strain which produces an antheridium and a “female” strain which develops an ascogonium, are required for sexual reproduction.
• The antheridium and the ascogonium combine in plasmogamy at the time of fertilization, followed by nuclei fusion in the asci.
• In the ascocarp, a fruiting body, thousands of asci undergo meiosis to generate haploid ascospores ready to be released to the world.
Key Terms
• plasmogamy: stage of sexual reproduction joining the cytoplasm of two parent mycelia without the fusion of nuclei
• Ascomycota: a taxonomic division within the kingdom Fungi; those fungi that produce spores in a microscopic sporangium called an ascus
• ascus: a sac-shaped cell present in ascomycete fungi; it is a reproductive cell in which meiosis and an additional cell division produce eight spores
• ascospore: a sexually-produced spore from the ascus of an Ascomycetes fungus
• conidia: asexual, non-motile spores of a fungus, named after the Greek word for dust, conia; also known as conidiospores and mitospores
• antheridia: a haploid structure or organ producing and containing male gametes (called antherozoids or sperm) present in lower plants like mosses and ferns, primitive vascular psilotophytes, and fungi
• ascogonium: a haploid structure or organ producing and containing female gametes in certain Ascomycota fungi
• ascocarp: the sporocarp of an ascomycete, typically bowl-shaped
• ascomycete: any fungus of the phylum Ascomycota, characterized by the production of a sac, or ascus, which contains non-motile spores
Ascomycota: The Sac Fungi
The majority of known fungi belong to the Phylum Ascomycota, which is characterized by the formation of an ascus (plural, asci), a sac-like structure that contains haploid ascospores. Many ascomycetes are of commercial importance. Some play a beneficial role, such as the yeasts used in baking, brewing, and wine fermentation, plus truffles and morels, which are held as gourmet delicacies. Aspergillus oryzae is used in the fermentation of rice to produce sake. Other ascomycetes parasitize plants and animals, including humans. For example, fungal pneumonia poses a significant threat to AIDS patients who have a compromised immune system. Ascomycetes not only infest and destroy crops directly, they also produce poisonous secondary metabolites that make crops unfit for consumption. Filamentous ascomycetes produce hyphae divided by perforated septa, allowing streaming of cytoplasm from one cell to the other. Conidia and asci, which are used respectively for asexual and sexual reproductions, are usually separated from the vegetative hyphae by blocked (non-perforated) septa.
Asexual reproduction is frequent and involves the production of conidiophores that release haploid conidiospores. Sexual reproduction starts with the development of special hyphae from either one of two types of mating strains. The “male” strain produces an antheridium (plural: antheridia) and the “female” strain develops an ascogonium (plural: ascogonia). At fertilization, the antheridium and the ascogonium combine in plasmogamy without nuclear fusion. Special ascogenous hyphae arise, in which pairs of nuclei migrate: one from the “male” strain and one from the “female” strain. In each ascus, two or more haploid ascospores fuse their nuclei in karyogamy. During sexual reproduction, thousands of asci fill a fruiting body called the ascocarp. The diploid nucleus gives rise to haploid nuclei by meiosis. The ascospores are then released, germinate, and form hyphae that are disseminated in the environment and start new mycelia. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.17%3A_Fungi/8.17G%3A_Ascomycota_-_The_Sac_Fungi.txt |
The basidiomycota are mushroom-producing fungi with developing, club-shaped fruiting bodies called basidia on the gills under its cap.
Learning Objectives
• Describe the ecology and reproduction of the Basidiomycota
Key Points
• The majority of edible fungi belong to the Phylum Basidiomycota.
• The basidiomycota includes shelf fungus, toadstools, and smuts and rusts.
• Unlike most fungi, basidiomycota reproduce sexually as opposed to asexually.
• Two different mating strains are required for the fusion of genetic material in the basidium which is followed by meiosis producing haploid basidiospores.
• Mycelia of different mating strains combine to produce a secondary mycelium that contains haploid basidiospores in what is called the dikaryotic stage, where the fungi remains until a basidiocarp (mushroom) is generated with the developing basidia on the gills under its cap.
Key Terms
• basidiocarp: a fruiting body that protrudes from the ground, known as a mushroom, which has a developing basidia on the gills under its cap
• basidiomycete: a fungus of the phylum Basidiomycota, which produces sexual spores on a basidium
• Basidiomycota: a taxonomic division within the kingdom Fungi: 30,000 species of fungi that produce spores from a basidium
• basidium: a small structure, shaped like a club, found in the Basidiomycota phylum of fungi, that bears four spores at the tips of small projections
• basidiospore: a sexually-reproductive spore produced by fungi of the phylum Basidiomycota
Basidiomycota: The Club Fungi
The fungi in the Phylum Basidiomycota are easily recognizable under a light microscope by their club-shaped fruiting bodies called basidia (singular, basidium), which are the swollen terminal cell of a hypha. The basidia, which are the reproductive organs of these fungi, are often contained within the familiar mushroom, commonly seen in fields after rain, on the supermarket shelves, and growing on your lawn. These mushroom-producing basidiomyces are sometimes referred to as “gill fungi” because of the presence of gill-like structures on the underside of the cap. The “gills” are actually compacted hyphae on which the basidia are borne. This group also includes shelf fungus, which cling to the bark of trees like small shelves. In addition, the basidiomycota includes smuts and rusts, which are important plant pathogens, and toadstools. Most edible fungi belong to the Phylum Basidiomycota; however, some basidiomycetes produce deadly toxins. For example, Cryptococcus neoformans causes severe respiratory illness.
The lifecycle of basidiomycetes includes alternation of generations. Spores are generally produced through sexual reproduction, rather than asexual reproduction. The club-shaped basidium carries spores called basidiospores. In the basidium, nuclei of two different mating strains fuse (karyogamy), giving rise to a diploid zygote that then undergoes meiosis. The haploid nuclei migrate into basidiospores, which germinate and generate monokaryotic hyphae. The mycelium that results is called a primary mycelium. Mycelia of different mating strains can combine and produce a secondary mycelium that contains haploid nuclei of two different mating strains. This is the dikaryotic stage of the basidiomyces lifecyle and it is the dominant stage. Eventually, the secondary mycelium generates a basidiocarp, which is a fruiting body that protrudes from the ground; this is what we think of as a mushroom. The basidiocarp bears the developing basidia on the gills under its cap.
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Protists are eukaryotes that first appeared approximately 2 billion years ago with the rise of atmospheric oxygen levels.
Learning Objectives
• Discuss the origins of eukaryotes in terms of the geologic time line
Key Points
• On a geological time line, protists are among the first organisms that evolved after prokaryotes.
• Today’s eukaryotes evolved from a common ancestor with the following features: a nucleus that divided via mitosis, DNA associated with histones, a cytoskeleton and endomembrane system, the ability to make cilia/flagella.
• Protists vary widely in size, from single cells approximately 10 µm in size to multicellular seaweeds that are visible with the naked eye.
Key Terms
• cyanobacteria: photosynthetic prokaryotic microorganisms, of phylum Cyanobacteria, once known as blue-green algae
• aerobic: living or occurring only in the presence of oxygen
• endomembrane: all the membraneous components inside a eukaryotic cell, including the nuclear envelope, endoplastic reticulum, and Golgi apparatus
Origins of Eukaryotes
Humans have been familiar with macroscopic organisms (organisms big enough to see with the unaided eye) since before there was a written history. It is likely that most cultures distinguished between animals and land plants, but most probably included the macroscopic fungi as plants. Therefore, it became an interesting challenge to deal with the world of microorganisms once microscopes were developed a few centuries ago. Many different naming schemes were used over the last couple of centuries, but it has become the most common practice to refer to eukaryotes that are not land plants, animals, or fungi as protists.
Most protists are microscopic, unicellular organisms that are abundant in soil, freshwater, brackish, and marine environments. They are also common in the digestive tracts of animals and in the vascular tissues of plants. Others invade the cells of other protists, animals, and plants. Not all protists are microscopic. Some have huge, macroscopic cells, such as the plasmodia (giant amoebae) of myxomycete slime molds or the marine green alga Caulerpa, which can have single cells that can be several meters in size. Some protists are multicellular, such as the red, green, and brown seaweeds. It is among the protists that one finds the wealth of ways that organisms can grow. They are among the first organisms to evolve with the rise of eukaryotes.
Eukaryotes in a Geological Time Frame
The oldest fossil evidence of eukaryotes, cells measuring 10 µm or greater, is about 2 billion years old. All fossils older than this appear to be prokaryotes. It is probable that today’s eukaryotes are descended from an ancestor that had a prokaryotic cellular organization. The last common ancestor (LCA) of today’s Eukarya had several characteristics that included: cells with nuclei that divided mitotically and contained linear chromosomes where the DNA was associated with histones; a cytoskeleton and endomembrane system; and the ability to make cilia/flagella during at least part of its life cycle. The LCA was aerobic because it had mitochondria that were the result of an aerobic alpha-proteobacterium that lived inside a host cell. Whether this host had a nucleus at the time of the initial symbiosis remains unknown. The LCA may have had a cell wall for at least part of its life cycle, but more data are needed to confirm this hypothesis. Today’s eukaryotes are very diverse in their shapes, organization, life cycles, and number of cells per individual.
While today’s atmosphere is about one-fifth molecular oxygen (O2), geological evidence shows that it originally lacked O2. Without oxygen, aerobic respiration would not be expected; living things would have relied on fermentation instead. At some point before about 3.5 billion years ago, some prokaryotes evolved the ability to photosynthesize. Cyanobacteria used water as a hydrogen source and released O2 as a waste product. Originally, oxygen-rich environments were probably localized around places where cyanobacteria were active, but by about 2 billion years ago, geological evidence shows that oxygen was building up to higher concentrations in the atmosphere. Oxygen levels similar to today’s levels only arose within the last 700 million years. Recall that the first fossils that we believe to be eukaryotes date to about 2 billion years old, so they appeared as oxygen levels were increasing. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.18%3A_Protists/8.18A%3A_Early_Eukaryotes.txt |
Excavata, defined by a feeding groove that is “excavated” from one side, includes Diplomonads, Parabasalids and Euglenozoans.
Learning Objectives
• Describe characteristics of Excavates, including Diplomonads, Parabasalids and Euglenozoans
Key Points
• Excavata are a supergroup of protists that are defined by an asymmetrical appearance with a feeding groove that is “excavated” from one side; it includes various types of organisms which are parasitic, photosynthetic and heterotrophic predators.
• Excavata includes the protists: Diplomonads, Parabasalids and Euglenozoans.
• Diplomonads are defined by the presence of a nonfunctional, mitochrondrial-remnant organelle called a mitosome.
• Parabasalids are characterized by a semi-functional mitochondria referred to as a hydrogenosome; they are comprised of parasitic protists, such as Trichomonas vaginalis.
• Euglenozoans can be classified as mixotrophs, heterotrophs, autotrophs, and parasites; they are defined by their use of flagella for movement.
Key Terms
• mitosome: an organelle found within certain unicellular eukaryotes which lack mitochondria
• hydrogenosome: a membrane-bound organelle found in ciliates, trichomonads, and fungi which produces molecular hydrogen and ATP
• kinetoplast: a disk-shaped mass of circular DNA inside a large mitochondrion, found specifically in protozoa of the class Kinetoplastea
Excavata
Many of the protist species classified into the supergroup Excavata are asymmetrical, single-celled organisms with a feeding groove “excavated” from one side. This supergroup includes heterotrophic predators, photosynthetic species, and parasites. Its subgroups are the diplomonads, parabasalids, and euglenozoans.
Diplomonads
Among the Excavata are the diplomonads, which include the intestinal parasite, Giardia lamblia. Until recently, these protists were believed to lack mitochondria. Mitochondrial remnant organelles, called mitosomes, have since been identified in diplomonads, but these mitosomes are essentially nonfunctional. Diplomonads exist in anaerobic environments and use alternative pathways, such as glycolysis, to generate energy. Each diplomonad cell has two identical nuclei and uses several flagella for locomotion.
Parabasalids
A second Excavata subgroup, the parabasalids, also exhibits semi-functional mitochondria. In parabasalids, these structures function anaerobically and are called hydrogenosomes because they produce hydrogen gas as a byproduct. Parabasalids move with flagella and membrane rippling. Trichomonas vaginalis, a parabasalid that causes a sexually-transmitted disease in humans, employs these mechanisms to transit through the male and female urogenital tracts. T. vaginalis causes trichomoniasis, which appears in an estimated 180 million cases worldwide each year. Whereas men rarely exhibit symptoms during an infection with this protist, infected women may become more susceptible to secondary infection with human immunodeficiency virus (HIV) or genital wart virus infection, which causes over 90% of cervical cancer. Pregnant women infected with T. vaginalis are at an increased risk of serious complications, such as pre-term delivery.
Euglenozoans
Euglenozoans includes parasites, heterotrophs, autotrophs, and mixotrophs, ranging in size from 10 to 500 µm. Euglenoids move through their aquatic habitats using two long flagella that guide them toward light sources sensed by a primitive ocular organ called an eyespot. The familiar genus, Euglena, encompasses some mixotrophic species that display a photosynthetic capability only when light is present. In the dark, the chloroplasts of Euglena shrink up and temporarily cease functioning; the cells, instead, take up organic nutrients from their environment.
The human parasite, Trypanosoma brucei, belongs to a different subgroup of Euglenozoa, the kinetoplastids. The kinetoplastid subgroup is named after the kinetoplast, a DNA mass carried within the single, oversized mitochondrion possessed by each of these cells. This subgroup includes several parasites, collectively called trypanosomes, which cause devastating human diseases by infecting an insect species during a portion of their life cycle. T. brucei develops in the gut of the tsetse fly after the fly bites an infected human or other mammalian host. The parasite then travels to the insect salivary glands to be transmitted to another human or other mammal when the infected tsetse fly consumes another blood meal. T. brucei is common in central Africa and is the causative agent of African sleeping sickness, a disease associated with severe chronic fatigue and coma; it can be fatal if left untreated. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.18%3A_Protists/8.18B%3A__Excavata.txt |
Alveolates are defined by the presence of an alveolus beneath the cell membrane and include dinoflagellates, apicomplexans and ciliates.
Learning Objectives
• Evaluate traits associated with protists classified as alveolates which include dinoflagellates, apicomplexans, and ciliates
Key Points
• Alveolates are classified under the group Chromalveolata which developed as a result of a secondary endosymbiotic event.
• Dinoflagellates are defined by their flagella structure which lays perpendicular and fits into the cellulose plates of the dinoflagellate, promoting a spinning motion.
• Apicomplexans are defined by the asymmetrical distribution of their microtubules, fibrin, and vacuoles; they include the parasitic protist Plasmodium which causes malaria.
• Ciliates are defined by the presence of cilia (such as the oral groove in the Paramecium), which beat synchronously to aid the organism in locomotion and obtaining nutrients.
• Ciliates are defined by the presence of cilia, which beat synchronously, to aid the organism in locomotion and obtaining nutrients, such as the oral groove in the Paramecium.
Key Terms
• osmoregulation: the homeostatic regulation of osmotic pressure in the body in order to maintain a constant water content
• plastid: any of various organelles found in the cells of plants and algae, often concerned with photosynthesis
• conjugation: the temporary fusion of organisms, especially as part of sexual reproduction
Chromalveolata
Current evidence suggests that species classified as chromalveolates are derived from a common ancestor that engulfed a photosynthetic red algal cell, which itself had already evolved chloroplasts from an endosymbiotic relationship with a photosynthetic prokaryote. Therefore, the ancestor of chromalveolates is believed to have resulted from a secondary endosymbiotic event. However, some chromalveolates appear to have lost red alga-derived plastid organelles or lack plastid genes altogether. Therefore, this supergroup should be considered a hypothesis-based working group that is subject to change and can be subdivided into alveolates and stramenopiles.
Alveolates
A large body of data supports that the alveolates are derived from a shared common ancestor. The alveolates are named for the presence of an alveolus, or membrane-enclosed sac, beneath the cell membrane. The exact function of the alveolus is unknown, but it may be involved in osmoregulation. The alveolates are further categorized into the dinoflagellates, the apicomplexans, and the ciliates.
Dinoflagellates
Dinoflagellates exhibit extensive morphological diversity and can be photosynthetic, heterotrophic, or mixotrophic. Many dinoflagellates are encased in interlocking plates of cellulose with two perpendicular flagella that fit into the grooves between the cellulose plates. One flagellum extends longitudinally and a second encircles the dinoflagellate. Together, the flagella contribute to the characteristic spinning motion of dinoflagellates. These protists exist in freshwater and marine habitats; they are a component of plankton.
Some dinoflagellates generate light, called bioluminescence, when they are jarred or stressed. Large numbers of marine dinoflagellates (billions or trillions of cells per wave) can emit light and cause an entire breaking wave to twinkle or take on a brilliant blue color. For approximately 20 species of marine dinoflagellates, population explosions (called blooms) during the summer months can tint the ocean with a muddy red color. This phenomenon is called a red tide and results from the abundant red pigments present in dinoflagellate plastids. In large quantities, these dinoflagellate species secrete an asphyxiating toxin that can kill fish, birds, and marine mammals. Red tides can be massively detrimental to commercial fisheries; humans who consume these protists may become poisoned.
Apicomplexans
The apicomplexan protists are so named because their microtubules, fibrin, and vacuoles are asymmetrically distributed at one end of the cell in a structure called an apical complex. The apical complex is specialized for entry and infection of host cells. Indeed, all apicomplexans are parasitic. This group includes the genus Plasmodium, which causes malaria in humans. Apicomplexan life cycles are complex, involving multiple hosts and stages of sexual and asexual reproduction.
Ciliates
The ciliates, which include Paramecium and Tetrahymena, are a group of protists 10 to 3,000 micrometers in length that are covered in rows, tufts, or spirals of tiny cilia. By beating their cilia synchronously or in waves, ciliates can coordinate directed movements and ingest food particles. Certain ciliates have fused cilia-based structures that function like paddles, funnels, or fins. Ciliates also are surrounded by a pellicle, providing protection without compromising agility. The genus Parameciumincludes protists that have organized their cilia into a plate-like primitive mouth called an oral groove, which is used to capture and digest bacteria. Food captured in the oral groove enters a food vacuole where it combines with digestive enzymes. Waste particles are expelled by an exocytic vesicle that fuses at a specific region on the cell membrane: the anal pore. In addition to a vacuole-based digestive system, Paramecium also uses contractile vacuoles: osmoregulatory vesicles that fill with water as it enters the cell by osmosis and then contract to squeeze water from the cell.
Paramecium has two nuclei, a macronucleus and a micronucleus, in each cell. The micronucleus is essential for sexual reproduction, whereas the macronucleus directs asexual binary fission and all other biological functions. The process of sexual reproduction in Paramecium underscores the importance of the micronucleus to these protists. Paramecium and most other ciliates reproduce sexually by conjugation. This process begins when two different mating types of Paramecium make physical contact and join with a cytoplasmic bridge. The diploid micronucleus in each cell then undergoes meiosis to produce four haploid micronuclei. Three of these degenerate in each cell, leaving one micronucleus that then undergoes mitosis, generating two haploid micronuclei. The cells each exchange one of these haploid nuclei and move away from each other. A similar process occurs in bacteria that have plasmids. Fusion of the haploid micronuclei generates a completely novel diploid pre-micronucleus in each conjugative cell. This pre-micronucleus undergoes three rounds of mitosis to produce eight copies, while the original macronucleus disintegrates. Four of the eight pre-micronuclei become full-fledged micronuclei, whereas the other four perform multiple rounds of DNA replication and then become new macronuclei. Two cell divisions then yield four new paramecia from each original conjugative cell. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.18%3A_Protists/8.18C%3A_Chromalveolata-_Alveolates.txt |
Stramenophiles include photosynthetic marine algae and heterotrophic protists such as diatoms, brown and golden algae, and oomycetes.
Learning Objectives
• Describe characteristics of the following Stramenophiles: diatoms, brown algae, golden algae, and oomycetes
Key Points
• Stramenophiles, also referred to as heterokonts, are a subclass of chromalveolata, and are identified by the presence of a “hairy” flagellum.
• Diatoms, present in both freshwater and marine plankton, are unicellular photosynthetic protists that are characterized by the presence of a cell wall composed of silicon dioxide that displays intricate patterns.
• Golden algae, present in both freshwater and marine plankton communities, are unicellular photosynthetic protists characterized by the presence of carotenoids (yellow-orange photosynthetic pigments).
• Oomycetes, commonly referred to as water molds, are characterized by their fungus-like morphology, a cellulose-based cell wall, and a filamentous network used for nutrient uptake.
• Oomycetes, commonly referred to as water molds, are characterized by their fungus-like morphology, a cellulose-based cell wall and a filamentous network used for nutrient uptake.
Key Terms
• stipe: the stem of a kelp
• raphe: a ridge or seam on an organ, bodily tissue, or other structure, especially at the join between two halves or sections
• saprobe: an organism that lives off of dead or decaying organic material
Chromalveolates
Current evidence suggests that chromalveolates have an ancestor which resulted from a secondary endosymbiotic event. The species which fall under the classification of chromalveolates have evolved from a common ancestor that engulfed a photosynthetic red algal cell. This red algal cell had previously evolved chloroplasts from an endosymbiotic relationship with a photosynthetic prokaryote. Chromalveolates include very important photosynthetic organisms, such as diatoms, brown algae, and significant disease agents in animals and plants. The chromalveolates can be subdivided into alveolates and stramenopiles.
Stramenopiles
A subgroup of chromalveolates, the stramenopiles, also referred to as heterokonts, includes photosynthetic marine algae and heterotrophic protists. The unifying feature of this group is the presence of a textured, or “hairy,” flagellum. Many stramenopiles also have an additional flagellum that lacks hair-like projections. Members of this subgroup range in size from single-celled diatoms to the massive and multicellular kelp.
Diatoms
The diatoms are unicellular photosynthetic protists that encase themselves in intricately patterned, glassy cell walls composed of silicon dioxide in a matrix of organic particles. These protists are a component of freshwater and marine plankton. Most species of diatoms reproduce asexually, although some instances of sexual reproduction and sporulation also exist. Some diatoms exhibit a slit in their silica shell called a raphe. By expelling a stream of mucopolysaccharides from the raphe, the diatom can attach to surfaces or propel itself in one direction.
During periods of nutrient availability, diatom populations bloom to numbers greater than can be consumed by aquatic organisms. The excess diatoms die and sink to the sea floor where they are not easily reached by saprobes that feed on dead organisms. As a result, the carbon dioxide that the diatoms had consumed and incorporated into their cells during photosynthesis is not returned to the atmosphere. In general, this process by which carbon is transported deep into the ocean is described as the biological carbon pump because carbon is “pumped” to the ocean depths where it is inaccessible to the atmosphere as carbon dioxide. The biological carbon pump is a crucial component of the carbon cycle that helps to maintain lower atmospheric carbon dioxide levels.
Golden Algae
Like diatoms, golden algae are largely unicellular, although some species can form large colonies. Their characteristic gold color results from their extensive use of carotenoids, a group of photosynthetic pigments that are generally yellow or orange in color. Golden algae are found in both freshwater and marine environments, where they form a major part of the plankton community.
Brown Algae
The brown algae are primarily marine, multicellular organisms that are known colloquially as seaweeds. Giant kelps are a type of brown algae. Some brown algae have evolved specialized tissues that resemble terrestrial plants, with root-like holdfasts, stem-like stipes, and leaf-like blades that are capable of photosynthesis. The stipes of giant kelps are enormous, extending in some cases for 60 meters. A variety of algal life cycles exists, but the most complex is alternation of generations in which both haploid and diploid stages involve multicellularity. For instance, compare this life cycle to that of humans. In humans, haploid gametes produced by meiosis (sperm and egg) combine in fertilization to generate a diploid zygote that undergoes many rounds of mitosis to produce a multicellular embryo and then a fetus. However, the individual sperm and egg themselves never become multicellular beings. In the brown algae genus Laminaria, haploid spores develop into multicellular gametophytes, which produce haploid gametes that combine to produce diploid organisms that then become multicellular organisms with a different structure from the haploid form. Terrestrial plants also have evolved alternation of generations.
Oomycetes
The water molds, oomycetes (“egg fungus”), were so-named based on their fungus-like morphology, but molecular data have shown that the water molds are not closely related to fungi. The oomycetes are characterized by a cellulose-based cell wall and an extensive network of filaments that allow for nutrient uptake. As diploid spores, many oomycetes have two oppositely-directed flagella (one hairy and one smooth) for locomotion. The oomycetes are non-photosynthetic and include many saprobes and parasites. The saprobes appear as white fluffy growths on dead organisms. Most oomycetes are aquatic, but some parasitize terrestrial plants. One plant pathogen is Phytophthora infestans, the causative agent of late blight of potatoes, such as occurred in the nineteenth century Irish potato famine. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.18%3A_Protists/8.18D%3A_Chromalveolata-_Stramenopiles.txt |
Rhizaria are a supergroup of protists, typically amoebas, that are characterized by the presence of needle-like pseudopodia.
Learning Objectives
• Describe characteristics associated with Rhizaria
Key Points
• The needle-like pseudopodia are used to carry out a process called cytoplasmic streaming which is a means of locomotion or distributing nutrients and oxygen.
• Two major subclassifications of Rhizaria include Forams and Radiolarians.
• Forams are characterized as unicellular heterotrophic protists that have porous shells, referred to as tests, which can contain photosynthetic algae that the foram can use as a nutrient source.
• Radiolarians are characterized by a glassy silica exterior that displays either bilateral or radial symmetry.
Key Terms
• pseudopodia: temporary projections of eukaryotic cells
• test: the external calciferous shell of a foram
Rhizaria
The Rhizaria supergroup includes many of the amoebas, most of which have threadlike or needle-like pseudopodia. Pseudopodia function to trap and engulf food particles and to direct movement in rhizarian protists. These pseudopods project outward from anywhere on the cell surface and can anchor to a substrate. The protist then transports its cytoplasm into the pseudopod, thereby moving the entire cell. This type of motion, called cytoplasmic streaming, is used by several diverse groups of protists as a means of locomotion or as a method to distribute nutrients and oxygen.
Forams
Foraminiferans, or forams, are unicellular heterotrophic protists, ranging from approximately 20 micrometers to several centimeters in length; they occasionally resemble tiny snails. As a group, the forams exhibit porous shells, called tests, that are built from various organic materials and typically hardened with calcium carbonate. The tests may house photosynthetic algae, which the forams can harvest for nutrition. Foram pseudopodia extend through the pores and allow the forams to move, feed, and gather additional building materials. Foraminiferans are also useful as indicators of pollution and changes in global weather patterns.
The life-cycle involves an alternation between haploid and diploid phases. The haploid phase initially has a single nucleus, and divides to produce gametes with two flagella. The diploid phase is multinucleate, and after meiosis fragments to produce new organisms. The benthic forms has multiple rounds of asexual reproduction between sexual generations.
Radiolarians
A second subtype of Rhizaria, the radiolarians, exhibit intricate exteriors of glassy silica with radial or bilateral symmetry. Radiolarians display needle-like pseudopods that are supported by microtubules which radiate outward from the cell bodies of these protists and function to catch food particles. The shells of dead radiolarians sink to the ocean floor, where they may accumulate in 100 meter-thick depths. Preserved, sedimented radiolarians are very common in the fossil record.
8.18F: Amoebozoa and Opisthokonta
Amoebozoa are a type of protist that is characterized by the presence of pseudopodia which they use for locomotion and feeding.
Learning Objectives
• Describe characteristics of Amoebozoa
Key Points
• Amoebozoa (amoebas) can live in either marine and fresh water or in soil.
• Amoebozoa are characterized by the presence of pseudopodia, which are extensions that can be either tube-like or flat lobes and are used for locomotion and feeding.
• Amooebozoa can be further divided into subclassifications that include slime molds; these can be found as both plasmodial and cellular types.
• Plasmodial slime molds are characterized by the presence of large, multinucleate cells that have the ability to glide along the surface and engulf food particles as they move.
• Cellular molds are characterized by the presence of independent amoeboid cells during times of nutrient abundancy and the development of a cellular mass, called a slug, during times of nutrient depletion.
• Archamoebae, Flabellinea, and Tubulinea are also groups of Amoebozoa; their defining characteristics include: Archamoebae lack mitochondria; Flabellinea flatten during locomotion and lack a shell and flagella; Tubulinea have a rough cylindrical form during locomotion with cylindrical pseudopodia.
Key Terms
• rhizaria: a species-rich supergroup of mostly unicellular eukaryotes that for the most part are amoeboids with filose, reticulose, or microtubule-supported pseudopods
• plasmodium: a mass of cytoplasm, containing many nuclei, created by the aggregation of amoeboid cells of slime molds during their vegetative phase
• sporangia: an enclosure in which spores are formed (also called a fruiting body)
Amoebozoa
Protists are eukaryotic organisms that are classified as unicellular, colonial, or multicellular organisms that do not have specialized tissues. This identifying property sets protists apart from other organisms within the Eukarya domain. The amoebozoans are classified as protists with pseudopodia which are used in locomotion and feeding. Amoebozoans live in marine environments, fresh water, or in soil. In addition to the defining pseudopodia, they also lack a shell and do not have a fixed body. The pseudopodia which are characteristically exhibited include extensions which can be tube-like or flat lobes, rather than the hair-like pseudopodia of rhizarian amoeba. Rhizarian amoeba are amoeboids with filose, reticulose, or microtubule-supported pseudopods and include the groups: Cercozoa, Foraminifera, and Radiolaria and are classified as bikonts. The Amoebozoa include several groups of unicellular amoeba-like organisms that are free-living or parasites that are classified as unikonts. The best known and most well-studied member of this group is the slime mold. Additional members include the Archamoebae, Tubulinea, and Flabellinea.
Slime Molds
A subset of the amoebozoans, the slime molds, has several morphological similarities to fungi that are thought to be the result of convergent evolution. For instance, during times of stress, some slime molds develop into spore -generating fruiting bodies, similar to fungi.
The slime molds are categorized on the basis of their life cycles into plasmodial or cellular types. Plasmodial slime molds are composed of large, multinucleate cells that move along surfaces like an amorphous blob of slime during their feeding stage. Food particles are lifted and engulfed into the slime mold as it glides along. Upon maturation, the plasmodium takes on a net-like appearance with the ability to form fruiting bodies, or sporangia, during times of stress. Haploid spores are produced by meiosis within the sporangia. These spores can be disseminated through the air or water to potentially land in more favorable environments. If this occurs, the spores germinate to form ameboid or flagellate haploid cells that can combine with each other and produce a diploid zygotic slime mold to complete the life cycle.
The cellular slime molds function as independent amoeboid cells when nutrients are abundant. When food is depleted, cellular slime molds pile onto each other into a mass of cells that behaves as a single unit called a slug. Some cells in the slug contribute to a 2–3-millimeter stalk, drying up and dying in the process. Cells atop the stalk form an asexual fruiting body that contains haploid spores. As with plasmodial slime molds, the spores are disseminated and can germinate if they land in a moist environment. One representative genus of the cellular slime molds is Dictyostelium, which commonly exists in the damp soil of forests.
Archamoebae, Flabellinea, and Tubulinea
The Archamoebae are a group of Amoebozoa distinguished by the absence of mitochondria. They include genera that are internal parasites or commensals of animals (Entamoeba and Endolimax). A few species are human pathogens, causing diseases such as amoebic dysentery. The other genera of archamoebae live in freshwater habitats and are unusual among amoebae in possessing flagella. Most have a single nucleus and flagellum, but the giant amoeba, Pelomyxa, has many of each.
The Tubulinea are a major grouping of Amoebozoa, including most of the larger and more familiar amoebae like Amoeba, Arcella, and Difflugia. During locomotion, most Tubulinea have a roughly cylindrical form or produce numerous cylindrical pseudopods. Each cylinder advances by a single central stream of cytoplasm, granular in appearance, and has no subpseudopodia. This distinguishes them from other amoeboid groups, although in some members this is not the normal type of locomotion. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.18%3A_Protists/8.18E%3A_Rhizaria.txt |
Learning Objectives
• Describe the relationship between red algae, green algae, and land plants
Red algae and green algae are included in the supergroup Archaeplastida. It is well documented that land plants evolved from a common ancestor of these protists; their closest relatives are found within this group. Molecular evidence supports that all Archaeplastida are descendants of an endosymbiotic relationship between a heterotrophic protist and a cyanobacterium. The red and green algae include unicellular, multicellular, and colonial forms
Red Algae
Red algae, or rhodophytes, are primarily multicellular, lack flagella, and range in size from microscopic, unicellular protists to large, multicellular forms grouped into the informal seaweed category. The red algae life cycle is an alternation of generations. Some species of red algae contain phycoerythrins, photosynthetic accessory pigments that are red in color and outcompete the green tint of chlorophyll, making these species appear as varying shades of red. Other protists classified as red algae lack phycoerythrins and are parasites. Red algae are common in tropical waters where they have been detected at depths of 260 meters. Other red algae exist in terrestrial or freshwater environments.
Green Algae: Chlorophytes and Charophytes
The most abundant group of algae is the green algae. The green algae exhibit similar features to the land plants, particularly in terms of chloroplast structure. It is well supported that this group of protists share a relatively-recent common ancestors with land plants. The green algae are subdivided into the chlorophytes and the charophytes. The charophytes are the closest-living relatives of land plants, resembling them in morphology and reproductive strategies. Charophytes are common in wet habitats where their presence often signals a healthy ecosystem.
The chlorophytes exhibit great diversity of form and function. Chlorophytes primarily inhabit freshwater and damp soil; they are a common component of plankton. Chlamydomonas is a simple, unicellular chlorophyte with a pear-shaped morphology and two opposing, anterior flagella that guide this protist toward light sensed by its eyespot. More complex chlorophyte species exhibit haploid gametes and spores that resemble Chlamydomonas.
The chlorophyte Volvox is one of only a few examples of a colonial organism, which behaves in some ways like a collection of individual cells, but in other ways like the specialized cells of a multicellular organism. Volvox colonies contain 500 to 60,000 cells, each with two flagella, contained within a hollow, spherical matrix composed of a gelatinous glycoprotein secretion. Individual Volvox cells move in a coordinated fashion and are interconnected by cytoplasmic bridges. Only a few of the cells reproduce to create daughter colonies, an example of basic cell specialization in this organism.
True multicellular organisms, such as the sea lettuce, Ulva, are represented among the chlorophytes. In addition, some chlorophytes exist as large, multinucleate, single cells. Species in the genus Caulerpaexhibit flattened, fern-like foliage and can reach lengths of 3 meters. Caulerpa species undergo nuclear division, but their cells do not complete cytokinesis, remaining instead as massive and elaborate single cells.
Key Points
• Archaeplastida are typically associated with their relationship to land plants; in addition, molecular evidence shows that Archaeplastida evolved from an endosymbiotic relationship between a heterotrophic protist and a cyanobacterium.
• Red algae (rhodophytes), are classified as Archaeplastida and are most often characterized by the presence of the red pigment phycoerythrin; however, there are red algae that lack phycoerythrins and can be classified as parasites.
• Red algae typically exist as multicellular protists that lack flagella; however, they can also exist as unicellular organisms.
• Green algae are the most abundant group of algae and can be further classified as chlorophytes and charophytes.
• Charophytes are the green algae which resemble land plants and are their closest living relative.
• Chlorophytes are the green algae which exhibit a wide range of forms; they can be unicellular, multicellular, or colonial.
Key Terms
• endosymbiotic: that lives within a body or cells of another organism
• plankton: a generic term for all the organisms that float in the sea
8.19B: Protists as Primary Producers Food Sources and Symbionts
Protists function as sources of food for organisms on land and sea.
Learning Objectives
• Give examples of how protists act as primary producers
Key Points
• Photosynthetic protists serve as producers of nutrition for other organisms.
• Protists like zooxanthellae have a symbiotic relationship with coral reefs; the protists act as a food source for coral and the coral provides shelter and compounds for photosynthesis for the protists.
• Protists feed a large portion of the world’s aquatic species and conduct a quarter of the world’s photosynthesis.
• Protists help land-dwelling animals such as cockroaches and termites digest cellulose.
Key Terms
• zooxanthella: an animal of the genus Symbiodinium, a yellow dinoflagellate, notably found in coral reefs
• primary producer: an autotroph organism that produces complex organic matter using photosynthesis or chemosynthesis
Primary Producers/Food Sources
Protists function in various ecological niches. Some protist species are essential components of the food chain and are generators of biomass.
Protists are essential sources of nutrition for many other organisms. In some cases, as in plankton, protists are consumed directly. Alternatively, photosynthetic protists serve as producers of nutrition for other organisms. For instance, photosynthetic dinoflagellates called zooxanthellae use sunlight to fix inorganic carbon. In this symbiotic relationship, these protists provide nutrients for the coral polyps that house them, giving corals a boost of energy to secrete a calcium carbonate skeleton. In turn, the corals provide the protists with a protected environment and the compounds needed for photosynthesis. This type of symbiotic relationship is important in nutrient-poor environments. Without dinoflagellate symbionts, corals lose algal pigments in a process called coral bleaching and they eventually die. This explains why reef-building corals do not reside in waters deeper than 20 meters: insufficient light reaches those depths for dinoflagellates to photosynthesize.
The protists themselves and their products of photosynthesis are essential, directly or indirectly, to the survival of organisms ranging from bacteria to mammals. As primary producers, protists feed a large proportion of the world’s aquatic species. (On land, terrestrial plants serve as primary producers. ) In fact, approximately one-quarter of the world’s photosynthesis is conducted by protists, particularly dinoflagellates, diatoms, and multicellular algae.
Protists do not only create food sources for sea-dwelling organisms. Certain anaerobic parabasalid species exist in the digestive tracts of termites and wood-eating cockroaches where they contribute an essential step in the digestion of cellulose ingested by these insects as they bore through wood.
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Learning Objectives
• Describe the attributes of helminths
Parasitic worms that inhabit the intestinal tract (blood, tissue and organs) of humans are referred to as helminths. They receive nourishment and protection by living within the host where they cause disease. The parasitic intestinal helminths can be divided into three groups which include Nematodes (roundworms), Cestodes (tapeworms), and Trematodes (flukes). Helminths share numerous characteristics that contribute to their parasitic quality including the presence of attachment organs. These attachment organs include bothria (sucking grooves: Cestodes or tapeworms, which may also have a rostellum (crown of thorns with hooks); Old World Hookworms: cutting teeth; New World Hookworms: cutting plate. These attachment organs allow these particular helminths to reside within their human host. It should be noted, however, that blood and tissue roundworms (Nematodes) exist that will not be discussed in this section.
The three commonly studied and well-known groups include the intestinal Nematodes (round worms), tapeworms (Cestodes), and blood, tissue and organ flukes (Trematodes). Intestinal helminths are commonly transmitted through fecally contaminated food and water and these parasites include Ascaris lumbricoides, Trichuris trichiura (whipworm), and Enterobius vermicularis (pinworm).
Hookworms include Ancylostoma duodenale and Necator americanus, whose larvae penetrate the skin after their ova have been passed in human feces. These soil-transmitted helminths are associated with climates that are warm and moist and where sanitation and hygiene are poor. The eggs are passed in the feces of the infected individual, the larvae hatch, contaminate the soil, and can penetrate the skin when contact is made.
Ascaris lumbricoides, the cause of Ascariasis, is a type of soil transmitted helminth. Ascaris, the largest roundworm, lives in the intestine and the eggs are passed in the feces of the infected person. Ascariasis is caused by ingestion of eggs from food and water contaminated with feces from humans infected with Ascaris, and ingestion allows for continuation of the life cycle. Ascariasis may not be symptomatic, but may become symptomatic or fatal if intestinal blockage occurs without surgical intervention.
Hookworms, another type of soil-transmitted helminth, reside in the small intestine and eggs are passed in the feces of the infected individual. The eggs will mature and hatch in the soil and the immature worms (larvae) will penetrate the skin of humans if contact is made. The hookworm is transmitted by exposing bare skin to contaminated soil.
Whipworms (Trichuris trichiura), a type of soil-transmitted helminth, resides in the large intestine and eggs are passed in the feces of the infected individuals. The eggs will mature into an infective form in the soil and transmission occurs by ingestion of eggs in fecally contaminated food and water. Individuals with whipworm may have light or heavy infections. Light infections are usually not significantly symptomatic. However, heavy symptoms include frequent, painful passage of stool that contains mucus, water, and blood.
This summary does not contain an exhaustive compilation of all human parasitic nematodes, but merely a representation of several species.
Key Points
• Helminths can cause disruption of the hosts nutrient absorption by utilizing all nutrients that pass through the intestinal tract.
• There are four major groups of parasitic worms: monogeneans, cestodes (tapeworms), nematodes (roundworms), and trematodes (flukes).
• Helminths are characterized by the presence of attachment organs which include suckers, hooks, lips, teeth, and dentary plates.
Key Terms
• parasitic worm: Parasitic worms are referred to helminths as they live and feed on living hosts. Helminths receive both nourishment and protection by disrupting the hosts ability to absorb nutrients resulting in weakness and disease of the host.
• bothridia: A sucker or attachment organ on a parasitic worm.
• helminth: A parasitic roundworm or flatworm. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.20%3A_Helminths/8.20A%3A_Characteristics_of_Helminths.txt |
Helminths, or parasitic worms, are eukaryotic parasites characterized by their ability to feed and live on living hosts.
Learning Objectives
• Recall the attributes of helminths
Key Points
• The major groups of parasitic helminths include: platyhelminths (flatworms), acanthocephalins (thorny-headed worms) cestodes (tapeworms), trematodes (flukes) and nematodes (roundworms).
• The classification and identification of helminths are dependent on numerous factors including body shape, body cavity, body covering, digestive tubing, sex and type of attachment organs.
• Parasitic worms disrupt the ability of a host to receive and obtain nourishment.
Key Terms
• acetabulum: A large posterior sucker, for example that of leeches.
• tegument: A natural covering of the body or of a bodily organ.
• bothridia: A sucker or attachment organ on a parasitic worm.
Helminthsare large, multicellular organisms that are visible to the eye once in the adult stage of their life cycle. Helminths and multicellular eukaryotes, can either be free-living or parasitic.
In their adult form, helminths are unable to multiply in humans and utilize numerous mechanisms of transmission to ensure reproductive success. These parasites live in and feed on hosts which allow them to obtain nourishment while disrupting the hosts’ nutrient absorption. Parasitic worms are commonly found within the intestine and thus, are called intestinal parasites. They are able to live in both humans and animals.
The major groups of parasitic helminths include:
• platyhelminths (flatworms)
• acanthocephalins (thorny-headed worms)
• cestodes (tapeworms)
• trematodes (flukes)
• nematodes (roundworms).
The classification and identification of helminths are dependent on numerous factors including body shape, body cavity, body covering, digestive tubing, sex and type of attachment organs.
Platyhelminths (flatworms) include both trematodes (flukes) and cestodes (tapeworms). Specifically, tapeworms are characterized using the above criteria and are organized in a segmented plane. They lack a body cavity and have a tegument body covering. Tapeworms lack a digestive tube and are hermaphroditic. They utilize suckers or bothridia, and rostellum with hooks for an attachment organ.
Trematodes are characterized by an unsegmented plane for body shape. They also lack a body cavity and have a tegument for body covering. However, the digestive tube for trematodes ends in the cecum. Trematodes are hermaphroditic and utilize oral suckers, ventral suckers or acetabulum for attachment organs.
Nematodes are characterized by a cylindrical body shape and do indeed have a body cavity. Its body covering is a cuticle and the digestive tube ends in the anus. The sex of nematodes is dioecious (distinct male and female organisms). Lastly, their attachment organs range from lips, teeth, filariform extremities and dentary plates.
8.20C: Distribution and Importance of Parasitic Worms
Parasitic worms, distributed worldwide, are hypothesized to have importance in immune system regulation.
Learning Objectives
• Explain how parasitic worms may be beneficial
Key Points
• Parasitic worms appear to have medicinal properties as well which has opened a new field of research by studying the use of parasitic worms in disease treatment.
• Scientists hypothesize that parasitic worms can be used to combat autoimmune diseases by damping down the immune system of the host by using parasitic worms to active eosinophils and downstream targets.
• Parasitic worms have been linked to a protective role in autoimmune disease development and prevention of metabolic syndrome.
Key Terms
• eosinophils: a type of white blood cell used to fight parasitic infection
Parasitic worms, often the result of horrible illness and disease, appear to have medicinal properties as well. The importance of parasitic worms has come to light in regards to treating various diseases which may benefit from their presence. It is argued that humans have evolved with parasitic worms and there is a mutualistic relationship which mandates the need for parasitic worms to contribute to a healthy immune system. The most common use of parasitic worms for medicinal purposes is in the use against diseases characterized by an overactive immune response. An overactive immune response is often seen in individuals with allergies and hay-fever, specifically in developed countries where parasites have been under strict prevention and control. It is speculated that parasitic worms have the ability to damp down the immune system, which promotes an environment where they can thrive without being attached. In return, the damping down of the immune system is believed to be beneficial, as this may prevent the development of allergies.
An additional study links an increase in metabolic syndrome in the Western world and the success in preventing and eliminating parasites. The study demonstrates that immune system cells, eosinophils, that are present in fat tissue play a role in the prevention of insulin resistance via secretion of interleukin 4. The interleukin 4 is then able to activate macrophages that function in the maintenance of glucose homeostasis. The study showed that parasitic worm infection results in an increase in eosinophils, thus, promoting control of glucose maintenance.
The hypothesis that parasites are necessary for a healthy immune system is currently under investigation and still requires multiple lines of evidence. | textbooks/bio/Microbiology/Microbiology_(Boundless)/08%3A_Microbial_Evolution_Phylogeny_and_Diversity/8.20%3A_Helminths/8.20B%3A_Classification_and_Identification_of_Helminths.txt |
Arthropods are capable of functioning as vectors by transmitting diseases.
Learning Objectives
• Demonstrate how arthropods act as disease vectors
Key Points
• Arthropods will transmit diseases via their ability to function as hematophagous vectors which is characterized as their ability to feed on blood at some or all stages of their life cycles.
• Arthropod vectors include mosquitoes, fleas, sand flies, lice, fleas, ticks and mites.
• Arthropods transmit parasites either by injection into the blood stream of the host directly via their salivary glands, or by forcing parasites into a pool of blood which develops when chewing the skin.
Key Terms
• vector: A carrier of a disease-causing agent.
• hematophagous: feeding on blood
Arthropods are capable of serving as vectors, indicating that they play a major role in disease transmission. Arthropods that serve as vectors include mosquitoes, fleas, sand flies, lice, ticks, and mites. These arthropods are responsible for the transmission of numerous diseases. These types of vectors are considered to be hematophagous. These arthropod vectors are characterized as feeding on blood at some or all stages of their life cycles. The arthropods feed on the blood which typically allows parasites to enter the bloodstream of the host.
The Anopheles mosquito serves as a vector for malaria, filariasis, and arboviruses as well (arthropod-borne-viruses). The Anopheles mosquito inserts its mouthpart under the skin and feeds on the hosts. As the mosquito is feeding on the host blood, the parasites which are carried by the mosquito, are typically located within its salivary glands. The mosquito is able to directly transfer the parasites into the blood stream of the host. Pool feeders, which include both the sand and black fly, responsible for Leishmaniasis and Onchocerciasis diseases, will chew the hosts skin. The chewing action produces a well which promotes the formation of a small pool of blood from which they feed. In the case of sand flies, responsible for Leishmaniasis, the parasites infect the host through the saliva. In the case of black flies, responsible for Onchocerciasis, the parasites are forced out of the insects head into the pool of blood. Tsetse flies are vectors of the human African trypanosomiasis, called “African sleeping sickness”. Additional examples of mosquitoes include the Aedes mosquito which is a vector for avian malaria, dengue fever, and yellow fever.
Fleas are another type of arthropod vector that transmit numerous diseases. The human flea, Pulex irritans, and the Oriental rat flea, Xenopsylla cheopis, are responsible for the transmission of the bubonic plague, murine typhus, and tapeworms.
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• Taenia solium tapeworm scolex with its four suckers and two rows of hooks 5262 lores. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/File:Ta...5262_lores.jpg. License: Public Domain: No Known Copyright
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Thumbnail: This colorized transmission electron microscopic (TEM) image revealed some of the ultrastructural morphology displayed by an Ebola virus virion. (Public Domain; Frederick A. Murphy via CDC).
09: Viruses
Viruses are infectious particles about 100 times smaller than bacteria and can only be observed by electron microscopy.
Learning Objectives
• Describe how viruses were first discovered and how they are detected
Key Points
• Virions, single virus particles, are 20–250 nanometers in diameter.
• In the past, viruses were classified by the type of nucleic acid they contained, DNA or RNA, and whether they had single- or double-stranded nucleic acid.
• Molecular analysis of viral replicative cycles is now more routinely used to classify viruses.
Key Terms
• virus: a submicroscopic infectious organism, now understood to be a non-cellular structure consisting of a core of DNA or RNA surrounded by a protein coat
• virion: a single individual particle of a virus (the viral equivalent of a cell)
Discovery and Detection
Viruses were first discovered after the development of a porcelain filter, called the Chamberland-Pasteur filter, which could remove all bacteria visible in the microscope from any liquid sample. In 1886, Adolph Meyer demonstrated that a disease of tobacco plants, tobacco mosaic disease, could be transferred from a diseased plant to a healthy one via liquid plant extracts. In 1892, Dmitri Ivanowski showed that this disease could be transmitted in this way even after the Chamberland-Pasteur filter had removed all viable bacteria from the extract. Still, it was many years before it was proven that these “filterable” infectious agents were not simply very small bacteria, but were a new type of tiny, disease-causing particle.
Virions, single virus particles, are very small, about 20–250 nanometers in diameter. These individual virus particles are the infectious form of a virus outside the host cell. Unlike bacteria (which are about 100 times larger), we cannot see viruses with a light microscope, with the exception of some large virions of the poxvirus family. It was not until the development of the electron microscope in the late 1930s that scientists got their first good view of the structure of the tobacco mosaic virus (TMV) and other viruses. The surface structure of virions can be observed by both scanning and transmission electron microscopy, whereas the internal structures of the virus can only be observed in images from a transmission electron microscope. The use of these technologies has enabled the discovery of many viruses of all types of living organisms. They were initially grouped by shared morphology. Later, groups of viruses were classified by the type of nucleic acid they contained, DNA or RNA, and whether their nucleic acid was single- or double-stranded. More recently, molecular analysis of viral replicative cycles has further refined their classification.
9.1B: Nature of the Virion
A virion is a complete viral particle consisting of RNA or DNA surrounded by a protein shell, constituting the infective form of a virus.
Learning Objectives
• Illustrate the attributes of a virion
Key Points
• The virion shell or capsid protects the interior core that includes the genome and other proteins. After the virion binds to the surface of a specific host cell, its DNA or RNA is injected into the host cell and viral replication occurs, resulting in the spread of the infection to other host cells.
• A virion is the infectious particle that is designed for transmitting the nucleic acid genome among hosts or host cells.
• Virions are produced in the cytoplasm of complex viral ‘factories,’ the virus.
Key Terms
• capsid: The outer protein shell of a virus.
A virion is an entire virus particle consisting of an outer protein shell called a capsid and an inner core of nucleic acid (either ribonucleic or deoxyribonucleic acid—RNA or DNA). The core confers infectivity, and the capsid provides specificity to the virus. In some virions the capsid is further enveloped by a fatty membrane, in which case the virion can be inactivated by exposure to fat solvents such as ether and chloroform. Many virions are spheroidal—actually icosahedral (the capsid having 20 triangular faces)—with regularly arranged units called capsomeres, two to five or more along each side. The nucleic acid is densely coiled within. Other virions have a capsid consisting of an irregular number of surface spikes, with the nucleic acid loosely coiled within. Virions of most plant viruses are rod-shaped; the capsid is a naked cylinder (lacking a fatty membrane) within which lies a straight or helical rod of nucleic acid.
Virion capsids are formed from identical protein subunits called capsomeres. Viruses can have a lipid “envelope” derived from the host cell membrane. The capsid is made from proteins encoded by the viral genome and its shape serves as the basis for morphological distinction. Virally coded protein subunits will self-assemble to form a capsid, in general requiring the presence of the virus genome. Complex viruses code for proteins that assist in the construction of their capsid. Proteins associated with nucleic acid are known as nucleoproteins, and the association of viral capsid proteins with viral nucleic acid is called a nucleocapsid. The capsid and entire virus structure can be mechanically (physically) probed through atomic force microscopy. | textbooks/bio/Microbiology/Microbiology_(Boundless)/09%3A_Viruses/9.01%3A_Overview_of_Viruses/9.1A%3A_Discovery_and_Detection_of_Viruses.txt |
Learning Objectives
• Generalize the features of viral genomes
Viral diseases have an enormous impact on human health worldwide. Genomic technologies are providing infectious disease researchers an unprecedented capability to study at a genetic level the viruses that cause disease and their interactions with infected hosts. An enormous variety of genomic structures can be seen among viral species; as a group, they contain more structural genomic diversity than plants, animals, archaea, or bacteria. There are millions of different types of viruses, although only about 5,000 of them have been described in detail.
A virus has either DNA or RNA genes and is called a DNA virus or a RNA virus, respectively. The vast majority of viruses have RNA genomes. Plant viruses tend to have single-stranded RNA genomes and bacteriophages tend to have double-stranded DNA genomes. Viral genomes are circular, as in the polyomaviruses, or linear, as in the adenoviruses. The type of nucleic acid is irrelevant to the shape of the genome. Among RNA viruses and certain DNA viruses, the genome is often divided up into separate parts, in which case it is called segmented. For RNA viruses, each segment often codes for only one protein, and they are usually found together in one capsid. However, all segments are not required to be in the same virion for the virus to be infectious, as demonstrated by the brome mosaic virus and several other plant viruses.
A viral genome, irrespective of nucleic acid type, is almost always either single-stranded or double-stranded. Single-stranded genomes consist of an unpaired nucleic acid, analogous to one-half of a ladder split down the middle. Double-stranded genomes consist of two complementary paired nucleic acids, analogous to a ladder. The virus particles of some virus families, such as those belonging to the Hepadnaviridae, contain a genome that is partially double-stranded and partially single-stranded.
Key Points
• In modern molecular biology and genetics, the genome is the entirety of an organism ‘s hereditary information. It is encoded either in DNA or, for many types of virus, in RNA.
• A virus has either DNA or RNA genes and is called a DNA virus or a RNA virus.
• The genome includes both the genes and the non-coding sequences of the DNA/RNA.
Key Terms
• genome: The complete genetic information (either DNA or, in some viruses, RNA) of an organism, typically expressed in the number of basepairs.
9.1D: Host Range
A virus’ host range is the range of cell types and host species a virus is able to infect.
Learning Objectives
• Explain factors that limit viral host range
Key Points
• The host range or host specificity of a parasite is the collection of hosts that an organism can use as a partner.
• The host range is usually a function of an inability of the virus to successfully adsorb and/or enter cells because of an incompatibility between virus capsid proteins (or virus envelope proteins ) and the host receptor molecule.
• The host range is also a function of an incompatibility between the biochemistry of the virus and the biochemistry of the host. For closely related hosts, the biochemical differences can be quite subtle.
Key Terms
• surface receptor: Cell surface receptors (membrane receptors, transmembrane receptors) are specialized integral membrane proteins that take part in communication between the cell and the outside world.
• commensal: A term for a form of symbiosis in which one organism derives a benefit while the other is unaffected
Factors Limiting Viral Infection
A host is an organism that harbors a parasite or a mutual or commensal symbiont, typically providing nourishment and shelter. Resistance to and recovery from viral infections depend on the interactions that occur between the virus and the host. The defenses mounted by the host may act directly on the virus or indirectly on virus replication by altering or killing the infected cell. Non-specific host defenses function early in an encounter with a virus to prevent or limit infection, while the specific host defenses function after infection in recovery to provide immunity for subsequent challenges.
The host defense mechanisms involved in a particular viral infection will vary depending on the virus, dose, and portal of entry. The host has many barriers against infection that are inherent in the organism. These represent the first line of defense, which functions to prevent or limit infection Examples of natural barriers include but are not limited to skin, the expression of surface receptors such as CD4, complement receptors, glycophorin, intercelullar adhesion molecule 1 (ICAM-1), mucus, a ciliated epithelium, low pH, and humoral and cellular components.
The host range of the virus will depend upon the presence of the receptors described above. If a host lacks the receptor for a virus, or if the host cell lacks some component necessary for the replication of a virus, the host will inherently be resistant to that virus. For example, mice lack the receptors for polio viruses and thus are resistant to polio virus. Similarly, humans are inherently resistant to plant and many animal viruses.
9.1E: Viral Size
Most viruses range in size from 5 to 300 nanometers (nm), although some Paramyxoviruses can be up to 14,000 nm long.
Learning Objectives
• Recognize the cause and effect of different sizes of viruses
Key Points
• The size and shape of a virus helps us understand its class and components.
• Viruses also exist in different shapes that include helical, polyhedral, enveloped, and complex.
• Proteins and nucleic acid of viruses determine their size and shape.
Key Terms
• bacteriophage: A virus that specifically infects bacteria.
A virus is an infectious agent of small size and simple composition that can multiply only in living cells of animals, plants, or bacteria. They range in size from about 20 to 400 nanometres in diameter (1 nanometre = 10-9 meters). By contrast, the smallest bacteria are about 400 nanometres in size. A virus consists of a single- or double-stranded nucleic acid and at least one protein surrounded by a protein shell, called a capsid; some viruses also have an outer envelope composed of fatty materials (lipids) and proteins. The nucleic acid carries the virus’s genome —its collection of genes—and may consist of either deoxyribonucleic acid ( DNA ) or ribonucleic acid (RNA). The protein capsid provides protection for the nucleic acid and may contain enzymes that enable the virus to enter its appropriate host cell.
There exists a strong association between viral geometry and features of viral disease outbreaks. The amount and arrangement of the proteins and nucleic acid of viruses determine their size and shape. The protein and nucleic acid constituents have properties unique for each class of virus; when assembled, they determine the size and shape of the virus for that specific class.
Only the largest and most complex viruses can be seen under the light microscope at the highest resolution. Any determination of the size of a virus also must take into account its shape, since different classes of viruses have distinctive shapes. Shapes of viruses are predominantly of two kinds: rods, or filaments, so called because of the linear array of the nucleic acid and the protein subunits; and spheres, which are actually 20-sided (icosahedral) polygons. Most plant viruses are small and are either filaments or polygons, as are many bacterial viruses. The larger and more-complex bacteriophages contain double-stranded DNA as their genetic information and combine both filamentous and polygonal shapes. The classic T4 bacteriophage is composed of a polygonal head, which contains the DNA genome, and a special-function rod-shaped tail of long fibres. Structures such as these are unique to the bacteriophages.
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Viruses of all shapes and sizes consist of a nucleic acid core, an outer protein coating or capsid, and sometimes an outer envelope.
Learning Objectives
• Describe the relationship between the viral genome, capsid, and envelope
Key Points
• Viruses are classified into four groups based on shape: filamentous, isometric (or icosahedral), enveloped, and head and tail.
• Many viruses attach to their host cells to facilitate penetration of the cell membrane, allowing their replication inside the cell.
• Non-enveloped viruses can be more resistant to changes in temperature, pH, and some disinfectants than are enveloped viruses.
• The virus core contains the small single- or double-stranded genome that encodes the proteins that the virus cannot get from the host cell.
Key Terms
• capsid: the outer protein shell of a virus
• envelope: an enclosing structure or cover, such as a membrane
• filamentous: Having the form of threads or filaments
• isometric: of, or being a geometric system of three equal axes lying at right angles to each other (especially in crystallography)
Viral Morphology
Viruses are acellular, meaning they are biological entities that do not have a cellular structure. Therefore, they lack most of the components of cells, such as organelles, ribosomes, and the plasma membrane. A virion consists of a nucleic acid core, an outer protein coating or capsid, and sometimes an outer envelope made of protein and phospholipid membranes derived from the host cell. The capsid is made up of protein subunits called capsomeres. Viruses may also contain additional proteins, such as enzymes. The most obvious difference between members of viral families is their morphology, which is quite diverse. An interesting feature of viral complexity is that host and virion complexity are uncorrelated. Some of the most intricate virion structures are observed in bacteriophages, viruses that infect the simplest living organisms: bacteria.
Morphology
Viruses come in many shapes and sizes, but these are consistent and distinct for each viral family. In general, the shapes of viruses are classified into four groups: filamentous, isometric (or icosahedral), enveloped, and head and tail. Filamentous viruses are long and cylindrical. Many plant viruses are filamentous, including TMV (tobacco mosaic virus). Isometric viruses have shapes that are roughly spherical, such as poliovirus or herpesviruses. Enveloped viruses have membranes surrounding capsids. Animal viruses, such as HIV, are frequently enveloped. Head and tail viruses infect bacteria. They have a head that is similar to icosahedral viruses and a tail shape like filamentous viruses.
Many viruses use some sort of glycoprotein to attach to their host cells via molecules on the cell called viral receptors. For these viruses, attachment is a requirement for later penetration of the cell membrane, allowing them to complete their replication inside the cell. The receptors that viruses use are molecules that are normally found on cell surfaces and have their own physiological functions. Viruses have simply evolved to make use of these molecules for their own replication.
Overall, the shape of the virion and the presence or absence of an envelope tell us little about what disease the virus may cause or what species it might infect, but they are still useful means to begin viral classification. Among the most complex virions known, the T4 bacteriophage, which infects the Escherichia coli bacterium, has a tail structure that the virus uses to attach to host cells and a head structure that houses its DNA. Adenovirus, a non-enveloped animal virus that causes respiratory illnesses in humans, uses glycoprotein spikes protruding from its capsomeres to attach to host cells. Non-enveloped viruses also include those that cause polio (poliovirus), plantar warts (papillomavirus), and hepatitis A (hepatitis A virus).
Enveloped virions like HIV consist of nucleic acid and capsid proteins surrounded by a phospholipid bilayer envelope and its associated proteins. Glycoproteins embedded in the viral envelope are used to attach to host cells. Other envelope proteins include the matrix proteins that stabilize the envelope and often play a role in the assembly of progeny virions. Chicken pox, influenza, and mumps are examples of diseases caused by viruses with envelopes. Because of the fragility of the envelope, non-enveloped viruses are more resistant to changes in temperature, pH, and some disinfectants than are enveloped viruses.
Types of Nucleic Acid
Unlike nearly all living organisms that use DNA as their genetic material, viruses may use either DNA or RNA. The virus core contains the genome or total genetic content of the virus. Viral genomes tend to be small, containing only those genes that encode proteins that the virus cannot obtain from the host cell. This genetic material may be single- or double-stranded. It may also be linear or circular. While most viruses contain a single nucleic acid, others have genomes that have several, called segments.
In DNA viruses, the viral DNA directs the host cell’s replication proteins to synthesize new copies of the viral genome and to transcribe and translate that genome into viral proteins. DNA viruses cause human diseases, such as chickenpox, hepatitis B, and some venereal diseases, like herpes and genital warts.
RNA viruses contain only RNA as their genetic material. To replicate their genomes in the host cell, the RNA viruses encode enzymes that can replicate RNA into DNA, which cannot be done by the host cell. These RNA polymerase enzymes are more likely to make copying errors than DNA polymerases and, therefore, often make mistakes during transcription. For this reason, mutations in RNA viruses occur more frequently than in DNA viruses. This causes them to change and adapt more rapidly to their host. Human diseases caused by RNA viruses include hepatitis C, measles, and rabies. | textbooks/bio/Microbiology/Microbiology_(Boundless)/09%3A_Viruses/9.02%3A_Structure_of_Viruses/9.2A%3A_Viral_Morphology.txt |
Viruses have a variety of shapes and structures.
Learning Objectives
• Distinguish between the 5 main morphological virus types
Key Points
• Viruses are very small and to reliably visualize them, stains and electron microscopy are needed.
• Each virus is a nucleic acid (RNA or DNA) surrounded by a coating, referred to as an envelope or capsid.
• Viruses encode capsid proteins which encase the nucleic acid. Sometimes, viral proteins combine with host proteins to make the envelope.
• The shape of a viral coat has implications on how a virus infects a host.
Key Terms
• capsomere: Any of the individual protein subunits of a viral capsid
• capsid: The outer protein shell of a virus.
• icosahedral: of, relating to, or having the shape of an icosahedron
Viruses display a wide diversity of shapes and sizes, called morphologies. In general, there are five main morphological virus types:
1. Helical – These viruses are composed of a single type of capsomer stacked around a central axis to form a helical structure, which may have a central cavity, or hollow tube.
2. Icosahedral – Most animal viruses are icosahedral or near-spherical with icosahedral symmetry.
3. Prolate – This is an isosahedron elongated along one axis and is a common arrangement of the heads of bacteriophages.
4. Envelope – Some species of virus envelop themselves in a modified form of one of the cell membranes, either the outer membrane surrounding an infected host cell or internal membranes such as nuclear membrane or endoplasmic reticulum, thus gaining an outer lipid bilayer known as a viral envelope.
5. Complex – These viruses possess a capsid that is neither purely helical nor purely icosahedral, and that may possess extra structures such as protein tails or a complex outer wall.
A complete virus particle, known as a virion, consists of nucleic acid surrounded by a protective coat of protein called a capsid. These are formed from identical protein subunits called capsomeres. Viruses can have a lipid “envelope” derived from the host cell membrane. The capsid is made from proteins encoded by the viral genome and its shape serves as the basis for morphological distinction. Virally coded protein subunits will self-assemble to form a capsid, in general requiring the presence of the virus genome. Complex viruses code for proteins that assist in the construction of their capsid. Proteins associated with nucleic acid are known as nucleoproteins, and the association of viral capsid proteins with viral nucleic acid is called a nucleocapsid. The capsid and entire virus structure can be mechanically (physically) probed through atomic force microscopy.
viruses are much smaller than bacteria. Most viruses that have been studied have a diameter between 20 and 300 nanometers. Some filoviruses have a total length of up to 1400 nm; their diameters are only about 80 nm. Most viruses, such as virions, cannot be seen with an optical microscope, so scanning and transmission electron microscopes are used to visualize them.
To increase the contrast between viruses and the background, electron-dense “stains” are used. These are solutions of salts of heavy metals, such as tungsten, that scatter the electrons from regions covered with the stain. When virions are coated with stain (positive staining), fine detail is obscured. Negative staining overcomes this problem by staining the background only.
9.2C: Complex and Asymmetrical Virus Particles
Complex viruses are often asymetrical or symetrical in combination with other structures such as a tail.
Learning Objectives
• Break down the differences between complex and asymmetrical viruses
Key Points
• Viruses can be structurally very different.
• Some complex viruses are large enough to be visible with a light microscope.
• The viruses of archaea are unique compared to other viruses.
Key Terms
• capsid: The outer protein shell of a virus.
• poxvirus: Any of the group of DNA viruses belonging to the family Poxviridae, which cause pox diseases in vertebrates.
Viruses have many structural shapes, often falling into certain categories. While some have symmetrical shapes, viruses with asymmetrical structures are referred to as “complex. ” These viruses possess a capsid that is neither purely helical nor purely icosahedral, and may possess extra structures such as protein tails or a complex outer walls.
Some bacteriophages, such as Enterobacteria phage T4, have a complex structure consisting of an icosahedral head bound to a helical tail, which may have a hexagonal base plate with protruding protein tail fibers. This tail structure acts like a molecular syringe, attaching to the bacterial host and then injecting the viral genome into the cell.
The poxviruses are large, complex viruses that have an unusual morphology. The viral genome is associated with proteins within a central disk structure known as a nucleoid. The nucleoid is surrounded by a membrane and two lateral bodies of unknown function. The virus has an outer envelope with a thick layer of protein studded over its surface. The whole virion is slightly pleiomorphic, ranging from ovoid to brick shape.
Mimivirus is the largest characterized virus, with a capsid diameter of 400 nm. Protein filaments measuring 100 nm project from the surface. The capsid appears hexagonal under an electron microscope, therefore the capsid is probably icosahedral. In 2011, researchers discovered a larger virus on the ocean floor off the coast of Las Cruces, Chile. Provisionally named Megavirus chilensis, it can be seen with a basic optical microscope.
Some viruses that infect archaea have complex structures unrelated to any other form of virus. These include a wide variety of unusual shapes, ranging from spindle-shaped structures, to viruses that resemble hooked rods, teardrops, or even bottles. Other archaeal viruses resemble the tailed bacteriophages, and can have multiple tail structures.
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The International Committee on Taxonomy of Viruses (ICTV) establishes guidelines to maintain viral family uniformity.
Learning Objectives
• Describe the purpose and objectives of the International Committee on Taxonomy of Viruses
Key Points
• Only a small part of the total diversity of viruses has been studied. Analyses of samples from humans found that about 20% of the virus sequences recovered have not been seen before.
• A large majority of sequences of viral samples from the environment, such as from seawater and ocean sediments, are completely novel.
• The general taxonomic structure is as follows: Order (-virales); Family (-viridae); Subfamily (-virinae); Genus (-virus); Species (-virus).
Key Terms
• taxonomy: the academic discipline of defining groups of biological organisms on the basis of shared characteristics and giving names to those groups. Each group is given a rank and groups of a given rank can be aggregated to form a super group of higher rank and thus create a hierarchical classification.
The International Committee on Taxonomy of Viruses (ICTV) is a committee which authorizes and organizes the taxonomic classification of viruses. They have developed a universal taxonomic scheme for viruses and aim to describe all the viruses of living organisms. Members of the committee are considered to be world experts on viruses. The committee formed from and is governed by the Virology Division of the International Union of Microbiological Societies. Detailed work such as delimiting the boundaries of species within a family is typically done by study groups, which consist of experts in the families. The committee also operates an authoritative database (ICTVdB) containing taxonomic information for 1,950 virus species, as of 2005. It is open to the public and is searchable by several different means.
The official objectives of the ICTV are:
1. To develop an internationally agreed upon taxonomy for viruses.
2. To develop internationally agreed upon names for virus taxa, including species and subviral agents.
3. To communicate taxonomic decisions to all users of virus names, in particular the international community of virologists, by publications and via the Internet.
4. To maintain an index of virus names.
5. To maintain an ICTV database on the Internet, that records the data that characterize each named viral taxon, together with the common names of each taxon in all major languages.
Proposals for new names, name changes, and the establishment and taxonomic placement of taxa are handled by the Executive Committee of the ICTV in the form of proposals. All relevant ICTV subcommittees and study groups are consulted prior to a decision being made. The name of a taxon has no status until it has been approved by ICTV, and names will only be accepted if they are linked to approved hierarchical taxa. If no suitable name is proposed for a taxon, the taxon may be approved and the name be left undecided until the adoption of an acceptable international name, when one is proposed to and accepted by ICTV. Names must not convey a meaning for the taxon which would seem to either exclude viruses which are rightfully members of that taxa, exclude members which might one day belong to that taxa, or include viruses which are members of different taxa. | textbooks/bio/Microbiology/Microbiology_(Boundless)/09%3A_Viruses/9.03%3A_Classifying_Viruses/9.3A%3A_The_International_Committee_on_Taxonomy_of_Viruses.txt |
The Baltimore classification groups viruses into families depending on their type of genome.
Learning Objectives
• List the characteristics of viruses that are useful for Baltimore classification
Key Points
• Viral genome ‘s nucleic acid ( DNA or RNA ), strandedness (single-stranded or double-stranded), Sense, and method of replication determine its class.
• Other classifications are determined by the disease caused by the virus or its morphology.
• Viruses can be placed in one of the seven groups.
Key Terms
• genome: The complete genetic information (either DNA or, in some viruses, RNA) of an organism, typically expressed in the number of basepairs.
Virus classification is the process of naming viruses and placing them into a taxonomic system. Much like the classification systems used for cellular organisms, virus classification is the subject of ongoing debate and proposals. This is mainly due to the pseudo-living nature of viruses, which is to say they are non-living particles with some chemical characteristics similar to those of life. As such, they do not fit neatly into the established biological classification system in place for cellular organisms.
Baltimore classification (first defined in 1971) is a classification system that places viruses into one of seven groups depending on a combination of their nucleic acid (DNA or RNA), strandedness (single-stranded or double-stranded), Sense, and method of replication. Named after David Baltimore, a Nobel Prize-winning biologist, these groups are designated by Roman numerals and discriminate viruses depending on their mode of replication and genome type. Other classifications are determined by the disease caused by the virus or its morphology, neither of which are satisfactory due to different viruses either causing the same disease or looking very similar. In addition, viral structures are often difficult to determine under the microscope.
Classifying viruses according to their genome means that those in a given category will all behave in a similar fashion, offering some indication of how to proceed with further research. Viruses can be placed in one of the seven following groups:
1. I: dsDNA viruses (e.g. Adenoviruses, Herpesviruses, Poxviruses)
2. II: ssDNA viruses (+)sense DNA (e.g. Parvoviruses)
3. III: dsRNA viruses (e.g. Reoviruses)
4. IV: (+)ssRNA viruses (+)sense RNA (e.g. Picornaviruses, Togaviruses)
5. V: (−)ssRNA viruses (−)sense RNA (e.g. Orthomyxoviruses, Rhabdoviruses)
6. VI: ssRNA-RT viruses (+)sense RNA with DNA intermediate in life-cycle (e.g. Retroviruses)
7. VII: dsDNA-RT viruses (e.g. Hepadnaviruses)
9.3C: Evolution of Viruses
The evolution of viruses is speculative as they do not fossilize; biochemical and genetic information is used to create virus histories.
Learning Objectives
• Describe the difficulties in determining the origin of viruses
Key Points
• Scientists agree that viruses don’t have a single common ancestor, but have yet to agree on a single hypothesis about virus origins.
• The devolution or the regressive hypothesis suggests that viruses evolved from free-living cells.
• The escapist or the progressive hypothesis suggests that viruses originated from RNA and DNA molecules that escaped from a host cell.
• The self-replicating hypothesis posits a system of self-replication that most probably involves evolution alongside the host cells.
Key Terms
• self-replicating: able to generate a copy of itself
• devolution: degeneration (as opposed to evolution)
Evolution of Viruses
Although biologists have accumulated a significant amount of knowledge about how present-day viruses evolve, much less is known about how viruses originated in the first place. When exploring the evolutionary history of most organisms, scientists can look at fossil records and similar historic evidence. However, viruses do not fossilize, so researchers must conjecture by investigating how today’s viruses evolve and by using biochemical and genetic information to create speculative virus histories.
While most findings agree that viruses don’t have a single common ancestor, scholars have yet to find one hypothesis about virus origins that is fully accepted in the field. One possible hypothesis, called devolution or the regressive hypothesis, proposes to explain the origin of viruses by suggesting that viruses evolved from free-living cells. However, many components of how this process might have occurred are a mystery. A second hypothesis (called escapist or the progressive hypothesis) accounts for viruses having either an RNA or a DNA genome and suggests that viruses originated from RNA and DNA molecules that escaped from a host cell. A third hypothesis posits a system of self-replication similar to that of other self-replicating molecules, probably evolving alongside the cells they rely on as hosts; studies of some plant pathogens support this hypothesis.
As technology advances, scientists may develop and refine further hypotheses to explain the origin of viruses. The emerging field called virus molecular systematics attempts to do just that through comparisons of sequenced genetic material. These researchers hope to one day better understand the origin of viruses, a discovery that could lead to advances in the treatments for the ailments they produce. | textbooks/bio/Microbiology/Microbiology_(Boundless)/09%3A_Viruses/9.03%3A_Classifying_Viruses/9.3B%3A_The_Baltimore_Virus_Classification.txt |
Viruses are obligate intracellular parasites that hijack a host cell’s machinery to replicate, thereby causing disease.
Learning Objectives
• Describe the fundamental characteristics of viruses
Key Points
• Viruses multiply by taking control of the host cell’s genetic material and regulating the synthesis and assembly of new viruses.
• Viruses are able to infect a host cell and cause acute diseases or alter its genetic material to cause chronic diseases such as cancer.
• Most viral infections can resolve in weeks but others are the cause of more serious, debilitating and sometimes fatal diseases.
Key Terms
• vaccination: inoculation with a vaccine in order to protect a particular disease or strain of disease.
• eradication: the act of plucking up by the roots; a rooting out; extirpation; utter destruction.
Viruses are extremely diverse and have evolved to infect nearly all life forms. Amid this diversity, viruses with similar genome organizations exhibit major conserved themes in their replication strategies. Once inside a cell, all viruses must uncoat, replicate, and transcribe their genomes, and then repackage their genomes into viral progeny that are released from cells. RNA viruses in particular must coordinate the switch between plus and minus strand synthesis and between replication and transcription while protecting their genomes from cellular nucleases. Because of the conserved nature of a virus ‘s intracellular life cycle, fundamental advances in our understanding of replication have come from viruses that infect both animal and non-animal hosts.
The devastating effects of viral diseases such as AIDs, smallpox, polio, influenza, diarrhea, and hepatitis are well known, and studies of viral pathogens are easily justified from a world health perspective. Sobering examples of emerging viral diseases have occurred. Among these are the sudden emergence of the coronavirus that causes severe acute respiratory syndrome (SARS), the continued transmission of an avian influenza virus to humans (“bird flu”), and the isolation of poliovirus vaccine -wild type recombinants that have hampered poliovirus eradication efforts. In addition, the threat of bioterrorism became a reality on U.S. soil, creating an obligation for scientists to respond with aggressive countermeasures. Vaccination remains the preferred strategy for controlling viral diseases because the intimate association of viruses with the host cellular machinery complicates the development of safe drugs. However, certain viruses have proven difficult targets for vaccines, and antiviral drugs provide the only option for controlling disease.
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Bacteriophage cultures require host cells in which the virus or phage multiply.
Learning Objectives
• Define the reasons for, and ways to batch culture bacteriophages
Key Points
• A bacteriophage is a type of virus that infects bacteria. It does so by injecting genetic material – either DNA or RNA – which it carries enclosed in an outer protein capsid.
• To enter a host cell, bacteriophages attach to specific receptors on the surface of bacteria, including lipopolysaccharides, teichoic acids, proteins, or even flagella.
• Phage virions do not move independently, they must rely on random encounters with the right receptors when in solution (blood, lymphatic circulation, irrigation, soil water, etc. ).
Key Terms
• bacteriophage: A virus that specifically infects bacteria.
Strategies of Replication
Virus or phage cultures require host cells in which to multiply. For bacteriophages, cultures are grown by infecting bacterial cells. The phage can then be isolated from the resulting plaques in a lawn of bacteria on a plate.
A bacteriophage is any one of a number of viruses that infect bacteria. They do this by injecting genetic material, which they carry enclosed in an outer protein capsid, into a host bacterial cell. The genetic material can be ssRNA, dsRNA, ssDNA, or dsDNA (‘ss-‘ or ‘ds-‘ prefix denotes single-strand or double-strand), along with either circular or linear arrangements.
To enter a host cell, bacteriophages attach to specific receptors on the surface of bacteria, including lipopolysaccharides, teichoic acids, proteins, or even flagella. This specificity means a bacteriophage can infect only those bacteria bearing receptors to which they can bind, which in turn determines the phage’s host range. Host growth conditions also influence the ability of the phage to attach and invade them. As phage virions do not move independently, they must rely on random encounters with the right receptors when in solution within blood, lymphatic circulation, irrigation, soil water, or other environments..
Phages may be released via cell lysis, by extrusion, or, in a few cases, by budding. Lysis, by tailed phages, is achieved by an enzyme called endolysin, which attacks and breaks down the cell wall peptidoglycan. An altogether different phage type, the filamentous phages, make the host cell continually secrete new virus particles. Released virions are described as free, and, unless defective, are capable of infecting a new bacterium. Budding is associated with certain Mycoplasma phages. In contrast to virion release, phages displaying a lysogenic cycle do not kill the host but, rather, become long-term residents as prophage.
9.4B: Tissue Culture of Animal Viruses
Viruses cannot be grown in standard microbiological broths or on agar plates, instead they have be to cultured inside suitable host cells.
Learning Objectives
• Discover the use of, and reasons for, culturing animal viruses in host cells
Key Points
• Tissue culture is a useful method for cultivating clinical samples suspected of harboring a virus. This method helps with the detection, identification, and characterization of viruses in the laboratory.
• Tissue culture of animal viruses involves growing animal cells in flasks using various broth media and then infecting these cells with virus.
• Transfection can be carried out using calcium phosphate, by electroporation, or by mixing a cationic lipid with the material to produce liposomes, which fuse with the cell membrane and deposit their cargo inside.
• Cytopathic effect is a non-lytic damage that viruses cause to cells. These vary in their manifestation and damaging effect.
Key Terms
• cell culture: The complex process by which cells are grown under controlled conditions, generally outside of their natural environment.
• cytopathic effect: Refers to degenerative changes in cells, especially in tissue culture, and may be associated with the multiplication of certain viruses.
Cell culture is the complex process by which cells are grown under controlled conditions, generally outside of their natural environment. In practice, the term “cell culture” now refers to the culturing of cells derived from multi-cellular eukaryotes, especially animal cells. However, there are also cultures of plants, fungi, and microbes, including viruses, bacteria, and protists. The historical development and methods of cell culture are closely interrelated to those of tissue culture and organ culture. Animal cell culture became a common laboratory technique in the mid-1900’s, but the concept of maintaining live cell lines separated from their original tissue source was discovered in the 19th century.
Viruses are obligate intracellular parasites that require living cells in order to replicate. Cultured cells, eggs, and laboratory animals may be used for virus isolation. Although embroyonated eggs and laboratory animals are very useful for the isolation of certain viruses, cell cultures are the sole system for virus isolation in most laboratories. The development of methods for cultivating animal cells has been essential to the progress of animal virology. To prepare cell cultures, tissue fragments are first dissociated, usually with the aid of trypsin or collagenase. The cell suspension is then placed in a flat-bottomed glass or plastic container (petri dish, a flask, a bottle, test tube) together with a suitable liquid medium. e.g. Eagle’s, and an animal serum. After a variable lag, the cells will attach and spread on the bottom of the container and then start dividing, giving rise to a primary culture. Attachment to a solid support is essential for the growth of normal cells.
Cell cultures vary greatly in their susceptibility to different viruses. It is of utmost importance that the most sensitive cell cultures are used for a particular suspected virus. Specimens for cell culture should be transported to the laboratory as soon as possible upon being taken. Swabs should be put in a vial containing virus transport medium. Bodily fluids and tissues should be placed in a sterile container. Upon receipt, the specimen is inoculated into several different types of cell culture depending on the nature of the specimen and the clinical presentation. The maintenance media should be changed after one hour or the next morning. The inoculated tubes should be incubated at 35-37oC in a rotating drum. Rotation is optimal for the isolation of respiratory viruses and result in an earlier appearance of the cytopathic effects (CPE) for many viruses. If stationary tubes are used, it is critical that the culture tubes be positioned so that the cell monolayer is bathed in nutrient medium. | textbooks/bio/Microbiology/Microbiology_(Boundless)/09%3A_Viruses/9.04%3A_Culturing_Viruses/9.4A%3A_Batch_Culture_of_Bacteriophages.txt |
Live animal inoculation is a method used to cultivate viruses.
Learning Objectives
• Describe live animal innoculation
Key Points
• Live inoculation was first used on human volunteers for the study of yellow fever virus.
• Animals of choice for cultivating viruses include monkeys, rabbits, guinea pigs, rats, hamsters, and mice.
• Live animal inoculation requires an experienced personnel to perform various inoculation techniques.
Key Terms
• latent: Existing or present but concealed or inactive.
• oncogenesis: The formation and development of tumors
• inoculation: The introduction of an antigenic substance or vaccine into the body to produce immunity to a specific disease.
Viruses are obligate intracellular parasites and cannot grow on inanimate media. They need living cells for replication, which can be provided by inoculation in live animals among other methods used to culture viruses (cell culture or inoculation of embryonated eggs). Inoculation of human volunteers was the only known method of cultivation of viruses and understanding viral disease. In 1900, Reed and his colleagues used human volunteers for their work on yellow fever. Due to serious risk involved, human volunteers are recruited only when no other method is available and the virus is relatively harmless. Smallpox was likely the first disease people tried to prevent by purposely inoculating themselves with other infections and was the first disease for which a vaccine was produced. Today, studying viruses via the inoculation of humans would require a stringent study of ethical practices by an institutional review board.
In the past few decades, animal inoculation has been employed for virus isolation. The laboratory animals used include monkeys, rabbits, guinea pigs, rats, hamsters, and mice. The choice of animals and route of inoculation (intracerebral, intraperitoneal, subcutaneous, intradermal, or intraocular) depends largely on the type of virus to be isolated. Handling of animals and inoculation into various routes requires special experience and training. In addition to virus isolation, animal inoculation can also be used to observe pathogenesis, immune response, epidemiology, and oncogenesis. Growth of the virus in inoculated animals may be indicated by visible lesions, disease, or death. Sometimes, serial passage into animals may be required to obtain visible evidence of viral growth. Animal inoculation has several disadvantages as immunity may interfere with viral growth, and the animal may harbor latent viruses.
9.4D: Viral Identification
The genetic material within virus particles varies considerably between different types of viruses.
Learning Objectives
• Compare the replication of DNA, RNA, and reverse transcribing viruses
Key Points
• The genome replication of most DNA viruses takes place in the cell’s nucleus.
• RNA viruses can be placed into four different groups depending on their modes of replication.
• Reverse transcribing viruses have ssRNA (Retroviridae, Metaviridae, Pseudoviridae) or dsDNA (Caulimoviridae, and Hepadnaviridae) in their particles.
Key Terms
• genome: The complete genetic information (either DNA or, in some viruses, RNA) of an organism, typically expressed in the number of basepairs.
Replication of Viruses
The genetic material within virus particles and the method by which the material is replicated vary considerably between different types of viruses.
TYPES
DNA viruses: The genome replication of most DNA viruses takes place in the cell’s nucleus. If the cell has the appropriate receptor on its surface, these viruses sometimes enter the cell by direct fusion with the cell membrane (e.g., herpesviruses) or, more usually, by receptor-mediated endocytosis. Most DNA viruses are entirely dependent on the host cell’s DNA and RNA synthesizing machinery and RNA processing machinery; however, viruses with larger genomes may encode much of this machinery themselves. In eukaryotes the viral genome must cross the cell’s nuclear membrane to access this machinery, while in bacteria it need only enter the cell.
RNA viruses: Replication usually takes place in the cytoplasm. RNA viruses can be placed into four different groups, depending on their modes of replication. The polarity of single-stranded RNA viruses largely determines the replicative mechanism, depending on whether or not it can be used directly by ribosomes to make proteins. The other major criterion is whether the genetic material is single-stranded or double-stranded. All RNA viruses use their own RNA replicase enzymes to create copies of their genomes.
Reverse transcribing viruses: These have ssRNA (Retroviridae, Metaviridae, Pseudoviridae) or dsDNA (Caulimoviridae, and Hepadnaviridae) in their particles. Reverse transcribing viruses with RNA genomes (retroviruses), use a DNA intermediate to replicate, whereas those with DNA genomes (pararetroviruses) use an RNA intermediate during genome replication. Both types use a reverse transcriptase, or RNA-dependent DNA polymerase enzyme, to carry out the nucleic acid conversion. Retroviruses integrate the DNA produced by reverse transcription into the host genome as a provirus as a part of the replication process. Pararetroviruses do not, although integrated genome copies, usually of plant pararetroviruses, can give rise to infectious virus. They are susceptible to antiviral drugs that inhibit the reverse transcriptase enzyme, e.g. zidovudine and lamivudine. An example of the first type is HIV, which is a retrovirus. Examples of the second type are the Hepadnaviridae, which includes Hepatitis B virus.
The Baltimore classification developed by David Baltimore is a virus classification system that groups viruses into families, depending on their type of genome (DNA, RNA, single-stranded (ss), double-stranded (ds), etc.) and their method of replication. Classifying viruses according to their genome means that those in a given category will all behave in much the same way, which offers some indication of how to proceed with further research.
In summary:
• I: dsDNA viruses (e.g. Adenoviruses, Herpesviruses, Poxviruses)
• II: ssDNA viruses (+)sense DNA (e.g. Parvoviruses)
• III: dsRNA viruses (e.g. Reoviruses)IV: (+)ssRNA viruses (+)sense RNA (e.g. Picornaviruses, Togaviruses)V: (−)ssRNA viruses (−)sense RNA (e.g. Orthomyxoviruses, Rhabdoviruses)
• VI: ssRNA-RT viruses (+)sense RNA with DNA intermediate in life-cycle (e.g. Retroviruses)
• VII: dsDNA-RT viruses (e.g. Hepadnaviruses)
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Virologists describe the formation of viruses during the infection process in target host cells as viral replication.
Learning Objectives
• Outline the features of viral replication
Key Points
• Viral populations do not grow through cell division, because they are acellular. Instead, they use the machinery and metabolism of a host cell to produce multiple copies of themselves, and they assemble in the cell.
• The life cycle of viruses differs greatly between species but there are six basic stages in the life cycle of viruses: attachment, penetration (viral entry), uncoating, replication, and lysis.
• Some viruses undergo a lysogenic cycle where the viral genome is incorporated by genetic recombination into a specific place in the host’s chromosome.
Key Terms
• lysis: The disintegration or destruction of cells
• leukocyte: A white blood cell.
• uncoating: A process in which the viral capsid of a virus is removed, leading to the release of the viral genomic nucleic acid.
• attachment: specific binding between viral capsid proteins and specific receptors on the host cellular surface
Multiplication Within the Host Cell
Viral replication is the term used indicate the formation of biological viruses during the infection process in the target host cells. Viruses must first penetrate and enter the cell before viral replication can occur. From the perspective of the virus, the purpose of viral replication is to allow reproduction and survival of its kind. By generating abundant copies of its genome and packaging these copies into viruses, the virus is able to continue infecting new hosts.
Replication between viruses is varied and depends on the type of genes involved. Most DNA viruses assemble in the nucleus; most RNA viruses develop solely in cytoplasm. Viral populations do not grow through cell division, because they are acellular. Instead, they hijack the machinery and metabolism of a host cell to produce multiple copies of themselves, and they assemble inside the cell.
The life cycle of viruses differs greatly between species but there are six common basic stages:
Attachment is a specific binding between viral capsid proteins and specific receptors on the host cellular surface. This specificity determines the host range of a virus. For example, HIV can infect only a limited range of human leukocytes. Its surface protein, gp120, specifically interacts only with the CD4 molecule – a chemokine receptor – which is most commonly found on the surface of CD4+ T-Cells. This mechanism has evolved to favor those viruses that infect only cells within which they are capable of replication. Attachment to the receptor can fore the viral envelope protein to undergo either changes that result in the fusion of viral and cellular membranes, or changes of non-enveloped virus surface proteins that allow the virus to enter.
Penetration follows attachment. Virions enter the host cell through receptor-mediated endocytosis or membrane fusion. This is often called viral entry. The infection of plant and fungal cells is different from that of animal cells. Plants have a rigid cell wall made of cellulose, and fungi one of chitin, so most viruses can get inside these cells only after trauma to the cell wall. However, nearly all plant viruses (such as tobacco mosaic virus) can also move directly from cell to cell, in the form of single-stranded nucleoprotein complexes, through pores called plasmodesmata. Bacteria, like plants, have strong cell walls that a virus must breach to infect the cell. However, since bacterial cell walls are much less thick than plant cell walls due to their much smaller size, some viruses have evolved mechanisms that inject their genome into the bacterial cell across the cell wall, while the viral capsid remains outside.
Uncoating is a process in which the viral capsid is removed: This may be by degradation by viral or host enzymes or by simple dissociation. In either case the end-result is the release of the viral genomic nucleic acid.
Replication of viruses depends on the multiplication of the genome. This is accomplished through synthesis of viral messenger RNA (mRNA) from “early” genes (with exceptions for positive sense RNA viruses), viral protein synthesis, possible assembly of viral proteins, then viral genome replication mediated by early or regulatory protein expression. This may be followed, for complex viruses with larger genomes, by one or more further rounds of mRNA synthesis: “late” gene expression is, in general, of structural or virion proteins.
Following the structure-mediated self-assembly of the virus particles, some modification of the proteins often occurs. In viruses such as HIV, this modification (sometimes called maturation) occurs after the virus has been released from the host cell.
Viruses can be released from the host cell by lysis, a process that kills the cell by bursting its membrane and cell wall if present. This is a feature of many bacterial and some animal viruses. Some viruses undergo a lysogenic cycle where the viral genome is incorporated by genetic recombination into a specific place in the host’s chromosome. The viral genome is then known as a provirus or, in the case of bacteriophages a prophage. Whenever the host divides, the viral genome is also replicated. The viral genome is mostly silent within the host; however, at some point the provirus or prophage may give rise to active virus, which may lyse the host cells. Enveloped viruses (e.g., HIV) typically are released from the host cell by budding. During this process the virus acquires its envelope, which is a modified piece of the host’s plasma or other internal membrane. The genetic material within virus particles, and the method by which the material is replicated, varies considerably between different types of viruses. | textbooks/bio/Microbiology/Microbiology_(Boundless)/09%3A_Viruses/9.05%3A_Viral_Replication/9.5A%3A_General_Features_of_Virus_Replication.txt |
Viral infection involves the incorporation of viral DNA into a host cell, replication of that material, and the release of the new viruses.
Learning Objectives
• List the steps of viral replication and explain what occurs at each step
Key Points
• Viral replication involves six steps: attachment, penetration, uncoating, replication, assembly, and release.
• During attachment and penetration, the virus attaches itself to a host cell and injects its genetic material into it.
• During uncoating, replication, and assembly, the viral DNA or RNA incorporates itself into the host cell’s genetic material and induces it to replicate the viral genome.
• During release, the newly-created viruses are released from the host cell, either by causing the cell to break apart, waiting for the cell to die, or by budding off through the cell membrane.
Key Terms
• virion: a single individual particle of a virus (the viral equivalent of a cell)
• glycoprotein: a protein with covalently-bonded carbohydrates
• retrovirus: a virus that has a genome consisting of RNA
Steps of Virus Infections
A virus must use cell processes to replicate. The viral replication cycle can produce dramatic biochemical and structural changes in the host cell, which may cause cell damage. These changes, called cytopathic (causing cell damage) effects, can change cell functions or even destroy the cell. Some infected cells, such as those infected by the common cold virus known as rhinovirus, die through lysis (bursting) or apoptosis (programmed cell death or “cell suicide”), releasing all progeny virions at once. The symptoms of viral diseases result from the immune response to the virus, which attempts to control and eliminate the virus from the body and from cell damage caused by the virus. Many animal viruses, such as HIV (Human Immunodeficiency Virus), leave the infected cells of the immune system by a process known as budding, where virions leave the cell individually. During the budding process, the cell does not undergo lysis and is not immediately killed. However, the damage to the cells that the virus infects may make it impossible for the cells to function normally, even though the cells remain alive for a period of time. Most productive viral infections follow similar steps in the virus replication cycle: attachment, penetration, uncoating, replication, assembly, and release.
Attachment
A virus attaches to a specific receptor site on the host cell membrane through attachment proteins in the capsid or via glycoproteins embedded in the viral envelope. The specificity of this interaction determines the host (and the cells within the host) that can be infected by a particular virus. This can be illustrated by thinking of several keys and several locks where each key will fit only one specific lock.
Entry
The nucleic acid of bacteriophages enters the host cell naked, leaving the capsid outside the cell. Plant and animal viruses can enter through endocytosis, in which the cell membrane surrounds and engulfs the entire virus. Some enveloped viruses enter the cell when the viral envelope fuses directly with the cell membrane. Once inside the cell, the viral capsid is degraded and the viral nucleic acid is released, which then becomes available for replication and transcription.
Replication and Assembly
The replication mechanism depends on the viral genome. DNA viruses usually use host cell proteins and enzymes to make additional DNA that is transcribed to messenger RNA (mRNA), which is then used to direct protein synthesis. RNA viruses usually use the RNA core as a template for synthesis of viral genomic RNA and mRNA. The viral mRNA directs the host cell to synthesize viral enzymes and capsid proteins, and to assemble new virions. Of course, there are exceptions to this pattern. If a host cell does not provide the enzymes necessary for viral replication, viral genes supply the information to direct synthesis of the missing proteins. Retroviruses, such as HIV, have an RNA genome that must be reverse transcribed into DNA, which then is incorporated into the host cell genome.
To convert RNA into DNA, retroviruses must contain genes that encode the virus-specific enzyme reverse transcriptase, which transcribes an RNA template to DNA. Reverse transcription never occurs in uninfected host cells; the needed enzyme, reverse transcriptase, is only derived from the expression of viral genes within the infected host cells. The fact that HIV produces some of its own enzymes not found in the host has allowed researchers to develop drugs that inhibit these enzymes. These drugs, including the reverse transcriptase inhibitor AZT, inhibit HIV replication by reducing the activity of the enzyme without affecting the host’s metabolism. This approach has led to the development of a variety of drugs used to treat HIV and has been effective at reducing the number of infectious virions (copies of viral RNA) in the blood to non-detectable levels in many HIV-infected individuals.
Egress
The last stage of viral replication is the release of the new virions produced in the host organism. They are then able to infect adjacent cells and repeat the replication cycle. As you have learned, some viruses are released when the host cell dies, while other viruses can leave infected cells by budding through the membrane without directly killing the cell. | textbooks/bio/Microbiology/Microbiology_(Boundless)/09%3A_Viruses/9.05%3A_Viral_Replication/9.5B%3A_Steps_of_Virus_Infections.txt |
Host tropism refers to the way in which viruses/pathogens determine which cells become infected by a given pathogen.
Learning Objectives
• Explain viral tropism
Key Points
• Viruses must bind to specific cell surface receptors in order to enter a cell.
• If a cell does not express these receptors then the virus cannot normally infect it.
• In virology, Tissue tropism is the cells and tissues of a host which support growth of a particular virus or bacteria. Some viruses have a broad tissue tropism and can infect many types of cells and tissues. Other viruses may infect primarily a single tissue.
Key Terms
• dendritic cell: Any cell, having branching processes, that forms part of the mammalian immune system.
• macrophage: A white blood cell that phagocytizes necrotic cell debris and foreign material, including viruses, bacteria, and tattoo ink. It presents foreign antigens on MHC II to lymphocytes. Part of the innate immune system.
A tropism is a biological phenomenon, indicating growth or turning movement of a biological organism in response to an environmental stimulus. In tropisms, this response is dependent on the direction of the stimulus (as opposed to nastic movements which are non-directional responses). Viruses and other pathogens also affect what is called “host tropism” or “cell tropism. ” Case tropism refers to the way in which different viruses/pathogens have evolved to preferentially target specific host species or specific cell types within those species.
Host tropism is the name given to a process of tropism that determines which cells can become infected by a given pathogen. Host tropism is determined by the biochemical receptor complexes on cell surfaces that are permissive or non-permissive to the docking or attachment of various viruses.
Various factors determine the ability of a pathogen to infect a particular cell. For example, viruses must bind to specific cell surface receptors to enter a cell. If a cell does not express these receptors then the virus cannot normally infect it. Viral tropism is determined by a combination of susceptibility and permissiveness: a host cell must be both permissive (allow viral entry) and susceptible (possess the receptor complement needed for viral entry) for a virus to establish infection. An example of this is the HIV virus, which exhibits tropism for CD4 related immune cells (e.g. T helper cells, macrophages or dendritic cells). These cells express a CD4 receptor, to which the HIV virus can bind, through the gp120 and gp41 proteins on its surface.
In virology, Tissue tropism is the cells and tissues of a host that support growth of a particular virus or bacteria. Some viruses have a broad tissue tropism and can infect many types of cells and tissues. Other viruses may infect primarily a single tissue.
Factors influencing viral tissue tropism include: 1) the presence of cellular receptors permitting viral entry, 2) availability of transcription factors involved in viral replication, 3) the molecular nature of the viral tropogen, and 4) the cellular receptors are the proteins found on a cell or viral surface.
These receptors are like keys allowing the viral cell to fuse with a cell or attach itself to a cell. The way that these proteins are acquired is through similar process to that of an infection cycle. | textbooks/bio/Microbiology/Microbiology_(Boundless)/09%3A_Viruses/9.05%3A_Viral_Replication/9.5C%3A_Tissue_Tropism_in_Animal_Viruses.txt |
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