27 - Bacteria and Archaea Prokaryotic Structural and Functional Adaptations

Basic Characteristics of Prokaryotes

Most are unicellular (some remain attached after cell division) Cells typically .5-5 micrometers in diameter (much smaller than eukaryotes) Well organized - all life's functions in one cell

Cell-Surface Structures Cell wall - protects cell, maintains shape, prevents bursting in hypotonic environments (hypertonic causes plazmolyzation, inhibiting reproduction) Bacterial cell walls contain peptidoglycan (polymer composed of modified sugars crosslinked by short polypeptides)

"molecular fabric" encloses entire bacterium and anchors other molecules that extend from its surface

Archaeal cell walls contain various polysaccharides and proteins, but no peptidoglycan Gram stain - classifies bacterial species into two groups based on cell wall composition

Process: Sample stained with crystal violet dye Sample rinsed with alcohol Sample stained with red dye (like safranin) Gram positive - simpler walls with lots of peptidoglycan, which traps crystal violet in the cytoplasm - masks red safranin, appears purple Gram negative - complex walls with lipopolysaccharides and very little peptidoglycan, so crystal violet is easily rinsed - red safranin shows, appears pink/red Medical applications: Gram negative bacteria - lipopolysaccharides are toxic (cause fever/shock), outer-membrane protects from body's defenses, tend to be more resistant to antibiotics than Gram-positive bacteria Gram positive bacteria - some virulent strains are multi-drug resistant Effectiveness of some antibiotics (penicillin) derives from their ability to inhibit peptidoglycan cross-linking - decreases cell wall functionality Does not harm most human cells (which have no peptidoglycan)

Prokaryote cell wall surrounded by a capsule - sticky layer of polysaccharide or protein which is dense and well defined

Called a slime layer if it is less well organized Enable adherance to their substrate or other individuals in a colony Can protect against dehydration and the host's immune system

Fimbriae - hairlike appendages that allow prokaryotes to stick to substrate or each other (shorter and more numerous than pili)


Motility

Pili (sometimes called sex pili) - appendages that pull two cells together prior to DNA transfer from one cell to the other

Taxis - directed movement toward or away from a stimulus (1/2 of all prokaryotes are capable)

Chemotaxis - changes movement pattern in response to chemicals

Flagella - most common motile element, either scattered over the body or concentrated at one end 1/10 width of eukaryotic flagella; not covered by an extension of membrane Flagella of prokaryotes are different in molecular composition and mechanism of propulsion than eukaryotic flagella Bacterial and archaeal flagella are similar in size and mechanism, but are composed of different proteins Flagella of eukaryotes, bacteria, and archaea are most likely analogous Bacterial flagella probably evolved through exaption (was a secretory system, and other proteins were added over time that made it a flagellum)

Internal Organization - DNA

Prokaryotes lack the complex compartmentalization of eukaryotics Some prokaryotic cells do have specialized membranes that perform metabolic functions Prokaryotic genome is structurally different and usually has much less DNA Genome is usually a circular chromosome with far fewer proteins than eukaryotes Nucleoid - region of the cytoplasm that appears lighter than the surrounding cytoplasm in electron micrographs; contains the chromosomes May also have plasmids - smaller rings of independently replicating DNA; generally carry only a few genes Prokaryotic ribosomes tend to be smaller and differ in protein and RNA content

Reproduction and Adaptation Binary fission - allows prokaryotes to reproduce very quickly in favorable environments Reproduction is limited by nutrient supply, the toxicity of their own metabolic waste, competition from other microorganisms, and consumption by other organisms Key features:

Small Reproduce by binary fission Short generation times Can exist as large populations (in the millions)

Biochemical and/or structural adaptations allow some prokaryotes to withstand harsh environments

Endospores - resistant cells developed by some bacteria when they lack essential nutrients; original cell hides copy of chromosome in endospore, which lies dormant until conditions improve

High generation rate allows fast evolution and adaptation

Genetic Diversity in Prokaryotes

Rapid Reproduction and Mutation

New mutations are rare (and generally occur by errors in DNA replication) but can increase genetic diversity quickly in species with short generation times and large populations Diversity can lead to rapid evolution

Genetic Recombination In eukaryotes, sexual process of meiosis and fertilization foster genetic recombination Prokaryotes use transformation, transduction, and conjugation

Transformation - genotype (and possibly phenotype) of a prokaryotic cell one altered by the uptake of foreign DNA from the surroundings Many bacteria have cell-surface DNA-recognizing proteins Transduction - phages carry prokaryotic genes from one host cell to another Phage infects donor cell Phage DNA replicates; phage proteins halt host cell's protein synthesis and host cell's DNA may be fragmented New phages assemble, perhaps carrying host cell alleles in a phage capsid Phage carrying donor allele infects recipient cell; recombination between donor and recipient DNA occurs Genotype of resulting recombinant cell differs from donor and recipient Conjugation - DNA is transferred between two prokaryotic cells (usually of the same species) that one temporarily joined In bacteria, DNA transfer is always one way In E. coli (best understood): Pilus of the donor cell attaches to recipient cell Pilus retracts, pulling the cells together Possible formation of "mating bridge" - DNA is transferred Ability to form pili and donate DNA due to the F (fertility) factor (piece of DNA) + F plasmid - F factor in plasmid form; F cells have F plasmid and donates DNA to F cells (which lack the F factor); if F plasmid + copy is transferred, F cell becomes an F cell Hfr (high frequency recombination) cell - F factor is built into

chromosome, so chromosomal genes may be transferred + Hfr cell acts like F cell

When chromosomal DNA from an Hfr cell enters an F cell, homologous regions of Hfr and F chromosomes may align
- DNA can be exchanged

R plasmids - carry antibiotic-resistant genes

Antibiotics kill many, but not all, bacteria Natural selection supports proliferation of bacteria with R plasmids Many can also form pili and enable conjugation Any are multi-antibiotic resistant

Nutritional and Metabolic Adaptations

Trophic Types

Mode

Phototrophs - obtain energy from light Chemotrophs - obtain energy from chemicals Autotrophs - need only CO2 in some form as a carbon source Heterotrophs - require at least 1 organic nutrient (ex: glucose) Combinations lead to 4 major nutritional modes Energy source Light Inorganic chemicals Light Carbon source Type of organism

Photoautotroph Chemoautotroph

Photosynthetic prokaryotes CO2, HCO3 , etc Some prokaryotes CO2, HCO3 , etc
Organic compounds Organic compounds Some aquatic and salt-loving prokaryotes Many prokaryotes

Photoheterotroph

Chemoheterotroph Organic compounds Oxygen and Metabolism

Obligate aerobes - must use O2 for cellular respiration Obligate anaerobes - poisoned by oxygen

Some live exclusively by fermentation Anaerobic respiration - substances other than oxygen act as oxidizing agents in ETCs

Facultative anaerobes - use oxygen when present but carry out fermentation or

anaerobic respiration in an anaerobic environment Nitrogen Metabolism

N is essential for the production of amino acids and nucleic acids Nitrogen fixation - bacteria convert atmospheric nitrogen to ammonia

Some cyanobacteria and some methanogens (archaea) are very good - selfsufficient Important to other organisms (plants, particularly)

Metabolic Cooperation Cells work together to perform metabolic functions not otherwise possible; generally takes place in specialized cells of a filament Cyanobacteria Anabaena: some photosynthesize, others fix nitrogen

Heterocysts - fix nitrogen; surrounded by thickened cell wall to protect from oxygen Intercellular connections transfer fixed nitrogen and carbohydrates Cells secrete signaling molecules to recruit other cells Cells produce proteins and polysaccharides that let them stick to substrate and each other Channels allow transport of nutrients and waste

Biofilms - surface coating prokaryotic colonies that often exhibit cooperation

Molecular Systematics Genetic diversity of prokaryotes is immense Entire prokaryotic genomes can be obtained from environmental samples using
metagenomics

Horizontal gene transfer is significant in prokaryotic evolution

Comparing the Three Domains of Life Characteristic Nuclear envelope Membrane-enclosed organelles Peptidoglycan in cell wall Membrane lipids + Unbranched HCs Bacteria Archaea Eukarya

Some branched HCs Several kinds

+ +

Unbranched HCs Several kinds

RNA polymerase

One kind

Initiator amino acid for protein synthesis Introns in genes Response to some antibiotics Histones associated with DNA Circular chromosome Growth at >100degrees Celsius Archaea

Formyl-methionine Methionine

Methionine

Very rare Inhibited

Present in some Not inhibited

Present in many Not inhibited + -

In some +

In some

Extremophiles - can survive in extreme environments

Extreme halophiles - live in highly saline environments; some tolerate the salt, others (Halobacterium) require it Extreme thermophiles - thrive in very hot environments

Have adaptations in DNA and proteins that prevent denaturing

Methanogens - release methane as a byproduct of their metabolism Strict anaerobes Live in extreme and moderate environments; swamps, guts of animals Decompose sewage in waste-treatment facilities

Euryarchaeota - includes all methanogens, many extreme halophiles, and some extreme thermophiles Crenarchaeota - contains most extreme thermophiles Korarcheota - discovered in a 1996 sample in Yellowstone park Nanoarchaeota - very small; originally found clinging to a crenarchaeote

Bacteria Proteobacteria - all gram-negative, and includes photoautotrophs, chemoautotrophs, and heterotrophs; includes anaerobes and aerobes; 5 recognized subgroups: Alpha proteobacteria - closely associated with eukaryotic hosts: endosymbiotic theory maintains that mitochondria evolved from aerobic alpha proteobacteria Beta proteobacteria - nutritionally diverse group including nitrogen-recycling Nitrosomonas Gamma proteobacteria - include sulfur-producing bacteria, Salmonella, Legionella, Vibrio cholerae, and E. coli Delta proteobacteria - include slime-secreting myxobacteria and offensive bdellovibrios Epsilon proteobacteria - most are pathogenic to humans and other animals; includes Campylobacter (blood poisoning, intestinal inflammation) and

Helicobacter pylori (ulcers)

Chlamydias - can only survive within animal cells; gram-negative, lack peptidoglycan Chlamydia trachomatis - most common cause of blindness; most common STD in the US Spirochetes - helical heterotrophs that travel by rotation; most are free living but some are pathogenic parasites Treponema pallidum - syphilis Borrelia burgdorgeri - Lyme disease Cyanobacteria - photoautotrophs; only prokaryotes with plant-like oxygen-generating photosynthesis Endosymbiotic theory: chloroplasts likely evolved from cyanobacteria Gram-positive bacteria - rival proteobacteria in diversity Actinomycetes - most decompose organic matter in soil (some cause leprosy or TB) Bacillus anthracis - anthrax Clostridium botulinum - botulism Also includes Staphylococcus and Streptococcus Mycoplasmas - very small; only bacteria known to lack cell walls

Prokaryotes and the Biosphere

Chemical Recycling

Decomposers - break down dead organisms and waste products

Chemoheterotrophic prokaryotes and fungi Cyanobacteria - use carbon dioxide to make sugars; produce oxygen Variety of prokaryotes fix atmospheric nitrogen into usable forms

Prokaryotes can convert molecules to forms other organisms can use

Prokaryotes can increase and decrease availability of resources for plant growth (nitrogen, phosphorus, potassium, etc)

Ecological Interactions

Symbiosis - two species live in close contact with each other

Prokaryotes (symbionts) often form symbiotic relationships with larger organisms (hosts)

Mutualism - both species benefit Commensalism - one species benefits, the other is not helped or harmed Parasitism - parasite eats cell contents, tissues, or body fluids of the host

Parasites harm but usually do not kill the host (immediately) Pathogens - parasites that cause disease; many are prokaryotic

Chemoautotrophic bacteria harvest energy from thermal vents to support communities on the ocean floor, where sunlight does not reach

Prokaryotes and Humans

Mutualistic Bacteria

Many kinds live in intestines, helping to digest various foods Bacterium digests food and synthesizes carbohydrates, vitamins, and other nutrients Signals from bacterium activate human genes which build the network of intestinal blood vessels necessary to absorb nutrients Other signals induce production of antimicrobial compounds to kill competitors

Pathogenic Bacteria All known pathogenic prokaryotes are bacteria Some carried by pests (ex: ticks and Lyme disease Usually cause illness by producing poisons

Exotoxins - proteins secreted by certain bacteria and other organisms

Vibrio cholerae secretes exotoxin causing cholera - stimulates intestinal cells to release chloride ions; water follows by osmosis, leading to violent diarrhea and dehydration Clostridium botulinum - secretes exotoxin causing botulism as it ferments in food

Endotoxins - lipopolysaccharide components of the outer membrane of gramnegative bacteria (ex: Salmonella)

Improved sanitation and antibiotics have reduced threat, but antibiotics may also help create super-bacteria Horizontal gene transfer can make normally harmless bacteria into pathogens

O157:H7 - very dangerous strain of E. coli, probably introduced by transduction

Prokaryotes in Research and Technology E. coli used to clone genes Agrobacterium tumefaciens - helps produce transgenic crops PHA (polyhydroxylalkanoate) harvested from bacteria can be used in bioplastics Bioremidiation - use of organisms to remove pollutants from soil, air, or water

Treating sewage, cleaning oil spills, precipitating radioactive material out of groundwater