Prokaryotes PDF

What is a prokaryote? BIOL 108 Winter 2024 © 2024 Neil Harris − Despite their divergence, both domains inherited a simple prokaryotic cell organization from a common ancestor. − Prokaryotic cells differ significantly from eukaryotic cells in several aspects (see Table 27.2):  Prokaryotes are charac...

What is a prokaryote? BIOL 108 Winter 2024 © 2024 Neil Harris − Despite their divergence, both domains inherited a simple prokaryotic cell organization from a common ancestor. − Prokaryotic cells differ significantly from eukaryotic cells in several aspects (see Table 27.2):  Prokaryotes are characterized by their small size (0.5–5 µm) and unicellularity, although some can form colonies. In contrast, eukaryotic cells at typically larger in size (10–100 µm). The compact size of prokaryotic cells supports high rates of metabolism due to shorter diffusional distances, but diffusion also places limits on the size of prokaryotic cells. Prokaryotic cells exhibit a variety of shapes (Fig 27.2).  Unlike eukaryotic cells, prokaryotic cells possess circular genomes that are not enclosed by a nuclear membrane, i.e. lack a nucleus. pro = first/before, karyon = kernel (i.e. nucleus); cf. eu = true  Prokaryotic cells lack membrane-bounded organelles. Prokaryotic cell organization Universal ancestor Earth’s initial life forms were prokaryotes, with the Archaea and Bacteria domains evolving as distinct branches. Eukaryotic cell organization Domain Eukarya Domain Archaea Domain Bacteria Prokaryotes (paraphyletic) Topic 10: Prokaryotes Filamentous cyanobacteria (Anabaena sperica; WC) Fig 27.2 The most common shapes of prokaryotes 1 Structural and functional adaptations contribute to the success of prokaryotes 1. Cell-surface structures − Nearly all prokaryotic cells have a cell wall that provides:  Structural support – maintains cell shape and prevents it from bursting in a hypotonic environment (lower solute concentrations than cell contents).  Protection. BIOL 108 Winter 2024 © 2024 Neil Harris − Bacterial cell walls contain peptidoglycan, a network of sugar polymers cross-linked by short peptides.  Archaea cell walls contain polysaccharides and proteins but lack peptidoglycan.  Eukaryote cell walls are made of cellulose (plants) or chitin (fungi). cell wall 2 Structural and functional adaptations contribute to the success of prokaryotes BIOL 108 Winter 2024 © 2024 Neil Harris 1. Cell-surface structures − Gram stain provides a quick and effective means of distinguishing bacteria based on their cell wall characteristics.  Gram-positive bacteria exhibit simple cell walls characterized by a significant presence of externalfacing peptidoglycan. This thick layer of peptidoglycan contributes to the retention of the crystal violet stain during Gram staining.  Gram-negative bacteria possess thinner layers of peptidoglycan and an additional outer lipopolysaccharide membrane that influences the staining process. The lipopolysaccharide outer membrane adds complexity to the cell structure and serves as a protective barrier. The outer membrane can contain toxins and enhance resistance to certain antibiotics, making Gram-negative bacteria often more pathogenic than their Gram-positive counterparts. Many antibiotics target peptidoglycan and damage bacterial cell walls Fig 27.3 Gram staining 3 Structural and functional adaptations contribute to the success of prokaryotes BIOL 108 Winter 2024 © 2024 Neil Harris 1. Cell-surface structures − Many prokaryotes are surrounded by a sticky polysaccharide or protein layer called a capsule.  Capsules adhere cells to one another and surfaces. Form adhesive biofilms, communities of cells in a slimy extracellular matrix, e.g. dental plaque.  Capsules retain water, protecting the cells against desiccation.  The capsule often allows pathogenic bacteria to evade the host’s immune system, thereby increasing pathogenicity. Capsules can protect prokaryotic cells from engulfment by eukaryotic cells, such as macrophages, helping prokaryotic cells avoid destruction. Fig 27.4 Capsule around Streptococcus bacterium adheres to a tonsil cell in the respiratory tract − Some prokaryotes have fimbriae, hair-like appendages that facilitate cell adhesion to substrates or other cells within a colony. − Distinct from fimbriae, pili (or sex pili) are longer structures that play a role in the exchange of DNA between prokaryotic cells.  Genetic exchange enhances the adaptability and genetic diversity of prokaryotic populations. Fig 27.5 Fimbriae 4 Structural and functional adaptations contribute to the success of prokaryotes BIOL 108 Winter 2024 © 2024 Neil Harris 2. Endospores − Some prokaryotes can produce metabolically inactive endospores, which can endure harsh conditions for extended periods, ranging from decades to even centuries.  Endospores are compact, rounded, dormant cells that develop within certain prokaryotes when environmental conditions become unfavourable.  Endospore formation is triggered by various environmental stressors, such as elevated temperatures or nutrient scarcity.  Endospores possess a tough protective coat that confers resistance to UV light, chemicals, heat, high salt concentrations, and extreme pH levels.  Once formed, endospores enter a state of dormancy and remain inert until environmental conditions become conducive to growth. This adaptive strategy ensures the survival of prokaryotic organisms through periods of adversity, contributing to their long-term persistence in diverse and fluctuating environments. Fig 27.6 Bacillus anthracis (anthrax) endospore 5 Structural and functional adaptations contribute to the success of prokaryotes 3. Motility − Approximately half of all prokaryotes possess the ability to move actively (motile). − Motile prokaryotes typically achieve movement through flagella, whip-like appendages either distributed across the cell surface or concentrated at one or both ends of the cell.  Flagella can move some species up to 50 ‘body’ lengths per second.  The flagella in bacteria, archaea, and eukaryotes are constructed from distinct proteins, suggesting independent evolutionary origins for these motility structures. BIOL 108 Winter 2024 © 2024 Neil Harris − In heterogeneous environments, many prokaryotes exhibit taxes (singular = taxis), which is the ability to move in response to a specific stimulus.  Movement can involve either moving toward or away from a stimulus, e.g. positive phototaxis is the movement towards light. Helicobacter pylori with multiple flagella (WC) Positive chemotaxis: Escherichia coli cluster around pipette with glucose 6 Structural and functional adaptations contribute to the success of prokaryotes BIOL 108 Winter 2024 © 2024 Neil Harris 4. Simple internal organization and DNA − Prokaryotic cells are characterized by a straightforward internal structure without complex compartmentalization. − Prokaryotes lack membrane-enclosed organelles, including a distinct nucleus, mitochondria, or chloroplasts − Some prokaryotes exhibit specialized membranes that fulfill specific metabolic functions. Fig 27.8 Specialized membranes of prokaryotes  These membranes are typically infoldings of the plasma membrane, such as observed in cyanobacteria, where thylakoid membranes embed photosynthetic pigments for the light-dependent reactions of photosynthesis. 7 Structural and functional adaptations contribute to the success of prokaryotes BIOL 108 Winter 2024 © 2024 Neil Harris 4. Simple internal organization and DNA − Prokaryotes have small genomes consisting of a single circular chromosome.  The chromosome is not surrounded by a membrane (no nucleus).  Instead, the chromosome condenses within an irregularly shaped region known as the nucleoid. − Some species of bacteria also have smaller circular DNA molecules called plasmids.  Plasmids are compact rings of DNA containing a limited number of ‘extra’ genes, providing prokaryotes with additional genetic versatility. Fig 27.9 A prokaryotic chromosome and plasmids 8 Structural and functional adaptations contribute to the success of prokaryotes BIOL 108 Winter 2024 © 2024 Neil Harris 5. Reproduction − Prokaryotes reproduce quickly by binary fission, with the ability to divide every 1-3 hours.  The speed of binary fission depends on the environment, e.g. E. coli divide every 12–24 hours in the gut, but under ideal conditions, this can occur as frequently as once every 20 minutes. − Since prokaryotes are unicellular, binary fission is asexual reproduction, generating genetically identical copies of cells. − Rapid prokaryote reproduction is facilitated by the combination of small cell sizes, uncomplicated genomes, and the efficiency of binary fission.  Binary fission is less complicated than cell division (mitosis) in eukaryotes. see Fig 12.12 Chromosome replication and separation occur simultaneously during binary fission When replication is complete, a septum (dividing line) forms, physically separating the cytoplasm of the cells 9 Prokaryote genetic variation Prokaryotes exhibit significant genetic variation, enabling them to adapt to a wide array of environments and respond to ecological challenges. BIOL 108 Winter 2024 © 2024 Neil Harris Three factors contribute to this genetic diversity : − Rapid reproduction − Mutations − Genetic recombination 10 Prokaryote genetic variation 1. Rapid reproduction − Prokaryotes reproduce rapidly, undergoing frequent cell division through binary fission.  This accelerated reproductive cycle contributes to the rapid generation of genetically diverse populations. BIOL 108 Winter 2024 © 2024 Neil Harris 2. Mutations − Binary fission is asexual reproduction, yielding daughter cells that are typically identical, essentially forming clones. − Mutation rates during binary fission are low (low mutation rate per division), but because of the rapidity of binary fission, mutations can rapidly accumulate within a population over time. − The cumulative effect of mutations and rapid reproduction contributes to significant genetic diversity within prokaryotic populations, enabling for rapid evolution (see Fig 27.10).  Prokaryotes are not “primitive” but are highly evolved as shown by their adaptability and evolutionary success in diverse environments. 11 Prokaryote genetic variation 3. Genetic recombination − Prokaryotes engage in genetic recombination, a process where genetic material is exchanged between individual cells.  Genetic recombination contributes to prokaryote genetic diversity. − When genetic recombination occurs between individuals from different species this is called horizontal gene transfer. BIOL 108 Winter 2024 © 2024 Neil Harris − The mechanism of genetic recombination, which includes processes like transformation, transduction, and conjugation, promotes the integration of diverse genetic elements into prokaryotic genomes. 12 Prokaryote genetic recombination BIOL 108 Winter 2024 © 2024 Neil Harris Transformation 1. Transformation involves the absorption and integration of external DNA from the surrounding environment. − This process includes the uptake of DNA fragments or plasmids, often released from dead bacteria. − Certain bacteria have cell-surface proteins that facilitate the recognition and transportation of DNA, particularly from closely related species. 2. Transduction is the transfer of DNA segments between bacteria by bacteriophages, viruses that infect bacteria (Fig 27.11). 13 Prokaryote genetic recombination BIOL 108 Winter 2024 © 2024 Neil Harris 3. Conjugation occurs when genetic material is exchanged between prokaryotic cells through direct physical contact. − A donor cell transfers DNA to a recipient cell.  The donor cell attaches to a recipient by a pilus, and through a pulling mechanism, brings them into close proximity, enabling the transfer of DNA. − The transfer of genetic material during conjugation is unidirectional, occurring exclusively from the pilus-producing donor to the recipient. Donor cell Fig 27.12 Bacterial conjugation  The transferred DNA can recombine with the bacterial chromosome of the recipient cell, increasing genetic diversity within the prokaryotic population. 14 Prokaryote genetic recombination 3. Conjugation occurs when genetic material is exchanged between prokaryotic cells through direct physical contact. − Plasmids are often transferred during conjugation. BIOL 108 Winter 2024 © 2024 Neil Harris − Plasmids frequently contain antibiotic-resistant genes, contributing to the growing prevalence of antibiotic-resistant bacterial strains.  Horizontal gene transfer is one reason why antibiotic resistance can spread so rapidly between bacterial species.  The increased frequency of antibiotic resistance is often facilitated by horizontal gene transfer, which enables the rapid spread of resistance genes between different bacterial species.  Natural selection favours and increases the proportion of bacteria with these resistance genes following exposure of prokaryote cell populations to antibiotics 15 Prokaryote metabolic diversity Prokaryotes are notable for their remarkable metabolic diversity. − Prokaryotes have evolved diverse nutritional and metabolic adaptations, some of which are not found in eukaryotes. − Metabolism is the chemical pathways used by living organisms to build up molecules (anabolism) or to break down molecules to release energy (catabolism). BIOL 108 Winter 2024 © 2024 Neil Harris Prokaryotes can be categorized by how they obtain energy and carbon: − Source of energy:  Phototrophs obtain energy from light (photo = light, troph = nutrition).  Chemotrophs obtain energy from chemicals. − Source of carbon:  Autotrophs use simple inorganic molecules (e.g. CO2) as carbon sources to produce complex organic compounds (auto = self).  Heterotrophs require organic substrates to obtain carbon for growth and development (hetero = other). Heterotrophs “eat” organic nutrients. Enzymes digest organic molecules in the external environment; nutrients are absorbed through the cell membrane. 16 Prokaryote nutritional modes BIOL 108 Winter 2024 © 2024 Neil Harris Energy and carbon sources combine to give four major modes of nutrition: − Photoautotrophy, Chemoautotrophy, Photoheterotrophy, Chemoheterotrophy. Table 27.1 Major Nutritional Modes Mode Energy source Carbon source Types of organisms Photoautotroph Light CO2, HCO3−, or related compound Primary producers that support food webs. Includes photosynthetic prokaryotes (e.g. cyanobacteria), plants, and some protists (e.g. algae). Chemoautotroph Inorganic chemicals (e.g. H2S, NH3, or Fe2+) CO2, HCO3−, or related compound Found in many prokaryotes and is unique to prokaryotes, e.g. sulphur-oxidizing prokaryotes of deep-sea hydrothermal vents. Photoheterotroph Light Organic compounds Unique to some groups of aquatic, extremophile prokaryotes. Chemoheterotroph Organic compounds Organic compounds Many prokaryotes, protists, fungi, and animals. Autotroph Heterotroph 17 Prokaryote metabolic diversity BIOL 108 Winter 2024 © 2024 Neil Harris Prokaryotes exhibit diverse metabolism of oxygen (O2) and nitrogen: − Obligate aerobes depend on O2 for cellular respiration. − Obligate anaerobes are inhibited by O2 and resort to fermentation or anaerobic respiration for energy production.  Facultative anaerobes can survive in the presence or absence of O2. − In contrast, eukaryotes predominantly rely on aerobic respiration, with a notable exception found in yeasts (fungi) that can engage in fermentation. − Nitrogen is an essential element for the synthesis of amino acids and nucleic acids in both prokaryotes and eukaryotes.  Eukaryotes obtain nitrogen from a limited range of nitrogen-containing compounds. − Certain prokaryotes, including some bacteria and methanogens (Archaea), play a crucial role in converting atmospheric nitrogen (N2) into ammonia (NH3) through a process known as biological nitrogen fixation.  This process contributes significantly to the nitrogen cycle, making biological nitrogen accessible in ecosystems. 18 Prokaryotes have radiated into a diverse set of lineages BIOL 108 Winter 2024 © 2024 Neil Harris Prokaryotes inhabit all environments known to support life. − Advances in genomics are continually uncovering the previously unknown extent of prokaryotic diversity. Molecular phylogeny studies have delineated two distinct lineages of prokaryotes: − Domain Bacteria (or ‘Eubacteria’, eu = true) − Domain Archaea (arch = ancient or original) Challenges in Tree of Life reconstruction: − Horizontal gene transfer among prokaryotes complicates the clear identification of the root of the tree of life. − Archaea exhibit traits shared with both bacteria and eukaryotes, contributing to the complexity of evolutionary relationships. − The evolutionary origin of eukaryotes from prokaryotic ancestors remains unclear and is an area of ongoing research. − Molecular systematists continue to unravel the phylogeny of prokaryotes, contributing to our understanding of their evolutionary relationships. Fig 27.15 A simplified phylogeny of prokaryotes 19 Domain Bacteria Bacteria include the majority of wellknown prokaryotic species. − Traditionally, bacterial classification relied on characteristics like morphology, physiology, and staining methods such as the Gram stain. − Molecular systematics has revealed previously concealed relationships among bacteria, resulting in the identification of five major bacterial groups (see Fig 27.15).  Diverse nutritional types, including photoautotrophs, chemoautotrophs, and heterotrophs, are distributed across these major bacterial groups; some exhibit anaerobic while others display aerobic metabolism.  There are between 40–80+ recognized bacterial phyla. BIOL 108 Winter 2024 © 2024 Neil Harris − Bacteria exhibit incredible abundance, with a mere handful of soil containing around 10,000 prokaryotic species. − Bacteria live in almost all habitats!  10× more bacterial cells in and on the human body than the number of human cells constituting the human body. − Some bacteria pose a threat as human pathogens, contributing to ~50% of human diseases.  Many bacteria engage in beneficial interactions with humans, as seen in the diverse bacterial communities residing in the human intestines, hosting around 500–1,000 bacterial species. 20 Examples of major bacterial groups BIOL 108 Winter 2024 © 2024 Neil Harris Fig 27.16a Proteobacteria constitute a vast and metabolically diverse group of gram-negative bacteria. − 5 sub-lineages: alpha to epsilon. − Numerous species of alpha (α) proteobacteria maintain close associations with eukaryotic hosts.  e.g. α-proteobacteria Rhizobium resides in root nodules of legumes and fixes atmospheric N2; plants exchange carbohydrates for fixed nitrogen.  It is hypothesized that the mitochondria of eukaryotes evolved from aerobic α-proteobacteria through endosymbiosis. Fig 27.16b Root nodules on alfalfa roots (WC) 21 Examples of major bacterial groups Fig 27.16a BIOL 108 Winter 2024 © 2024 Neil Harris Proteobacteria constitute a vast and metabolically diverse group of gram-negative bacteria. − Gamma and epsilon proteobacteria include pathogens:  Gamma: e.g. Legionella pneumophila causes Legionnaires’ disease, a severe form of pneumonia, Salmonella enterica is responsible for salmonellosis, a foodborne illness, certain strains of Vibrio cholerae cause cholera, a waterborne diseases.  Gamma: while Escherichia coli is commonly found in the intestines of mammals and is generally non-pathogenic, specific strains can cause severe food poisoning in their hosts.  Epsilon: e.g. Helicobacter pylori is known for causing stomach ulcers. Escherichia coli (WC) Fig 27.16f 22 Examples of major bacterial groups BIOL 108 Winter 2024 © 2024 Neil Harris Chlamydias are obligate intracellular parasites that exclusively inhabit animal cells. − Chlamydias are entirely dependent on a host cell for their survival and reproduction, unable to replicate outside their host. − Chlamydia cell walls lack peptidoglycan (stain gram-negative). − Chlamydia trachomatis is a common sexually transmitted infection (STI) in humans. − Chlamydia trachomatis can also cause contagious eye infections that have the potential to lead to blindness in both humans and other animals. Fig 27.16g Koala with chlamydia injections 23 Examples of major bacterial groups BIOL 108 Winter 2024 © 2024 Neil Harris Cyanobacteria are the only prokaryotes that, like plants, generate oxygen through photoautotrophy. − Cyanobacteria are the first organisms known to have produced oxygen, triggering the Great Oxidation Event (“oxygen revolution”) between 2.7 to 2.3 bya. − Gram-negative in structure, cyanobacteria inhabit a diverse array of terrestrial and aquatic habitats. Fig 27.16i  Cyanobacteria are also called ‘blue-green algae’ (cyano = dark blue). − Chloroplasts of eukaryotes are hypothesized to have evolved from cyanobacteria through endosymbiosis. − While the majority of cyanobacteria are harmless, certain species can produce potent toxins that pose a significant health risk if consumed Cyanobacteria bloom (toxics.usgs.gov) Cyanobacteria bloom in the Great Lakes (WC) 24 Examples of major bacterial groups BIOL 108 Winter 2024 © 2024 Neil Harris “Gram-positive” bacteria are a diverse group, known for their positive staining response to the Gram stain. − But the group also includes gramnegative taxa. − Includes essential decomposers found in soil, such as actinomycetes.  These soil-dwelling species are prolific producers of antibiotics, including streptomycin. Fig 27.16j − Gram-positive bacteria also include dangerous pathogens:  Bacillus anthracis is responsible for anthrax, a common disease affecting livestock and, occasionally, humans.  Clostridium botulinum causes botulism, an infrequent yet potentially fatal illness resulting from a neurotoxin produced by the bacterium. Fig 27.6 Bacillus anthracis (anthrax) can enter a dormant endospore state “Botox” (Botulinum neurotoxin) is lethal at high concentrations. Botox is used to create localized flaccid paralysis in cosmetic applications. Clostridium botulinum (nature.com) 25 Domain Archaea  Archaea cell walls lack peptidoglycan, making them unresponsive to antibiotics that typically inhibit bacterial growth. − Archaea often thrive in environments where energy availability for growth is too restricted to support bacteria or eukaryotes.  Some archaea are extremophiles (phil = love, prefer), thriving in extreme environments characterized by conditions such as low pH, high salt, or high temperatures.  Others inhabit less extreme environments like soils and oceans. Eukaryotic cell organization Domain Eukarya Domain Archaea Domain Bacteria Prokaryotes (paraphyletic) − Archaea and bacteria share a simple prokaryotic cell organization inherited from a common ancestor. Prokaryotic cell organization Universal ancestor Archaea (arch = ancient or original) exhibit characteristics common to both bacteria and eukaryotes (Table 27.2). BIOL 108 Winter 2024 © 2024 Neil Harris − The diversity of Archaea has only recently been fully recognized.  Molecular systematics has revealed numerous new groups of archaea, offering potential insights into the early evolution of life on Earth.  While the textbook describes five taxa (see Fig 27.15), focusing on functional groups provides a more straightforward understanding. 26 Domain Archaea Methanogens thrive in anoxic (low O2) habitats, such as swamps, marshes, and the digestive tracts of animals like ruminants (cattle) and humans. − Methanogens are obligate anaerobes and are poisoned by O2. − Produce methane as a waste metabolite. BIOL 108 Winter 2024 © 2024 Neil Harris Methanobrevibacter smithii is the dominant methane-producing archaeon in the human gut. It has an important role in the digestion of polysaccharides by consuming the end products of bacterial fermentation. Extreme halophiles are found in highly saline environments. − halo = salt, where ‘salt’ is any ionic crystalline compound, not just NaCl. Extreme thermophiles thrive in very hot environments (therm = heat), with some even living in water temperatures exceeding 100°C. − Many of these thermophiles are chemoautotrophs, deriving energy from chemical processes and not relying on sunlight. The colour of salt ponds is due to halophilic archaea Fig 27.17 Extreme thermophiles 27 Prokaryotes play crucial roles in the biosphere BIOL 108 Winter 2024 © 2024 Neil Harris Prokaryote metabolism exerts a profound impact on the biosphere. − Prokaryotes are crucial contributors to oxygen production and nitrogen fixation. Prokaryotes play a major role in the recycling of chemical elements within ecosystems. − Chemoheterotrophic prokaryotes function as decomposers, breaking down deceased organisms and waste products − Chemoheterotroph decomposers enhance the availability of essential nutrients like nitrogen, phosphorus, and potassium, which supports plant growth. Fig 27.18 Impact of bacteria on soil nutrient availability 28 WC Royal Alberta Museum Prokaryote symbiosis BIOL 108 Winter 2024 © 2024 Neil Harris Cyanobacteria symbiosis with tarpaper lichen Prokaryotes frequently form symbiotic relationships. − Symbiosis is a close, long-term ecological relationship between two species, where at least one species benefits.  Symbiosis typically involves a larger host and a smaller symbiont. − Mutualism is a symbiotic relationship in which both species benefit.  Examples include methanogens in the cow’s stomach, intestinal bacteria (Fig 27.20), Rhizobium species in legume roots, and cyanobacteria in lichens. − Commensalism is a symbiotic relationship in which one species benefits, while the other species is unaffected. − Parasitism is a symbiotic relationship in which one species (parasite) benefits at the expense of the other species (host), although the host is not necessarily killed.  Parasites causing diseases are termed pathogens. − Some prokaryotes act as human pathogens, causing diseases, while others interact positively.  The human gut microbiome houses ~5001,000 prokaryote species contributing to human health; many are mutualists, aiding in the breakdown of undigested food in our intestines. Fig 27.20 Bacteria on the colon wall 29 Economic importance of prokaryotes Humans exploit the metabolic and chemical properties of prokaryotes: − Food production, e.g. cheese (Lactococcus) and yogurt (Lactobacillus). − Decomposing prokaryotes.  Prokaryotes are crucial agents in bioremediation, the process of using organisms to eliminate pollutants from the environment.  Prokaryotes are involved in sewage treatment, contributing to the breakdown of organic matter. Fig 27.24 Bioremediation of an oil spill Fig 27.23 Bacteria synthesizing and storing PHA, a component of biodegradable plastics BIOL 108 Winter 2024 © 2024 Neil Harris − Bacteria can be engineered to produce vitamins, antibiotics, hormones, biofuels, and bioplastics. − Prokaryotic research has driven important advances in DNA technology.  E. coli is used in gene cloning through plasmid transformation.  Enzymes extracted from extreme thermophiles, like Thermus aquaticus (“Taq”) found in hot springs, are utilized in PCR to amplify DNA for sequence analysis. Thermus aquaticus (WC) 30