Prokaryotes Chapter 28

Prokaryotic Diversity Oldest, structurally simplest, and most abundant forms of life Abundant for over a billion years before eukaryotes 90 and 99% unknown and undescribed Fall into 2 domains –Bacteria (also called Eubacteria) –Archaea (formerly called Archaebacteria) Many archaeans are extremophiles 2

Unicellularity –Most are single-celled –May stick together to form associations and biofilms Cell size –Size varies tremendously –Most are less than 1  m in diameter Nucleoid –Chromosome is single circular double-stranded DNA –Found in the nucleoid region of cell –Often have plasmids Cell division and genetic recombination –Most divide by binary fission –exchange genetic material extensively 3

Genetic recombination –Occurs through horizontal gene transfer –NOT a form of reproduction Internal compartmentalization –No membrane-bounded organelles –No internal compartment –Ribosomes differ from eukaryotic form Flagella –Simple in structure –Different from eukaryotic flagella Metabolic diversity –Oxygenic and anoxygenic photosynthesis –Chemolithotrophic 4

They differ in four key areas: –Plasma membranes –Cell walls –DNA replication –Gene expression 5 Bacteria and archaea differ fundamentally

Plasma membranes –Plasma membranes of archaea differ from bacteria and eukaryotes Archaean membrane lipids composed of glycerol linked to hydrocarbon chains by ether linkages Ester linkages in bacteria and eukaryotes 6 Bacteria and archaea differ fundamentally

Cell walls –Both kinds of prokaryotes typically have cell walls covering the plasma membrane Archeae cell walls lack peptidoglycan Bacteria cell walls have peptidoglycan, but a variety of proteins and carbohydrates 7

Gene expression –Gene expression differs between archaea and bacteria Archaea have more than one RNA polymerase These enzymes closely resemble the eukaryotic RNA polymerase Translation machinery is more similar to that of eukaryotes 8

9 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Common ancestor Domain Bacteria Domain Archaea Domain Eukarya The three-domain system of phylogeny originated by Carl Woese Tree is based on rRNA sequences.

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. CrenarchaeotaEuryarchaeotaAquificaeThermotogaeChloroflexi Thermophiles Bacteria Archaea BacilliClostridiumActinobacteria Gram-positive bacteria High G/CLow G/C (Firmicutes) EuryarchaeotaAquificaeBacilliActinobacteriaSpirochaetes µm Archaea differ greatly from bacteria. Although both are prokaryotes, archaeal cell walls lack peptidoglycan; plasma membranes are made of different kinds of lipids than bacterial plasma membranes; RNA and ribosomal proteins are more like eukaryotes than bacteria. Mostly anaerobic. Examples include Methanococcus, Thermoproteus, Halobacterium. The Aquificae represent the deepest or oldest branch of bacteria. Aquifex pyrophilus is a rod- shaped hyper- thermophile with a temperature optimum at 85°C; a chemo- autotroph, it oxidizes hydrogen or sulfur. Several other related phyla are also thermophiles. Gram-positive bacteria. Largely solitary; many form endospores. Responsible for many significant human diseases, including anthrax (Bacillus anthracis); botulism (Clostridium botulinum); and other common diseases (staphylococcus, streptococcus). Some gram-positive bacteria form branching filaments and some produce spores; often mistaken for fungi. Produce many commonly used antibiotics, including streptomycin and tetracycline. One of the most common types of soil bacteria; also common in dental plaque. Streptomyces, Actinomyces. Long, coil-shaped cells that stain gram- negative. Common in aquatic environments. Rotation of internal filaments produces a corkscrew movement. Some spirochetes such as Treponema pallidum (syphilis) and Borrelia burgdorferi (Lyme disease) are significant human pathogens µm 1 µm µm22.15 µm Deinococcus- Thermus a: © SPL/Photo Researchers, Inc.; b; © Dr. R. Rachel and Prof. Dr. K. O. Stetten, University of Regensburg, Lehrstuhl fuer Mikrobiologie, Regensburg, Germany; c: © Andrew Syred/SPL/Photo Researchers, Inc.; d: © Microfiield Scientific Ltd/SPL/Photo Researchers, Inc.; e: © Alfred Paseika/SPL/Photo Researchers, Inc. 10

11 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. f: © Dr. Robert Calentine/Visuals Unlimited; g: © Science VU/S. Watson/Visuals Unlimited; h: © Dennis Kunkel Microscopy, Inc.; i: © Prof. Dr. Hans Reichenbach, Helmholtz Centre for Infection Research, Braunschweig Cyanobacteria Chlorobi BetaGammaDelta ProteobacteriaPhotosynthetic Spirochaetes CyanobacteriaBetaGammaDelta µm µm 750 µm Cyanobacteria are a form of photosynthetic bacterium common in both marine and freshwater environ- ments. Deeply pigmented; often responsible for “blooms” in polluted waters. Both colonial and solitary forms are common. Some filamentous forms have cells specialized for nitrogen fixation. A nutritionally diverse group that includes soil bacteria like the lithotroph Nitrosomonas that recycle nitrogen within ecosystems by oxidizing the ammonium ion (NH 4 + ). Other members are heterotrophs and photoheterotrophs. Gammas are a diverse group including photosynthetic sulfur bacteria, pathogens, like Legionella, and the enteric bacteria that inhabit animal intestines. Enterics include Escherichia coli, Salmonella (food poisoning), and Vibrio cholerae (cholera). Pseudomonas are a common form of soil bacteria, responsible for many plant diseases, and are important opportunistic pathogens. The cells of myxobacteria exhibit gliding motility by secreting slimy polysaccharides over which masses of cells glide; when the soil dries out, cells aggregate to form upright multicellular colonies called fruiting bodies. Other delta bacteria are solitary predators that attack other bacteria (Bdellovibrio) and bacteria used in bioremediation (Geobacter). Epsilon– Helicobacter Alpha– Rickettsia

Prokaryotic Cell Structure 3 basic shapes –Bacillus – Rod-shaped –Coccus – Spherical –Spirillum – Helical-shaped 12 BacillusCoccusSpirillum 3 µm 2 µm 0.5 µm Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. (left): © Dr. Gary Gaugler/SPL/Photo Researchers, Inc.; (middle): © CNRI/Photo Researchers, Inc.; (right): © Dr. Richard Kessel & Dr. Gene Shih/Visuals Unlimited

Cell wall –Peptidoglycan forms a rigid network Maintains shape Withstands hypotonic environments Archaea have a similar molecule –Gram stain Gram-positive bacteria have a thicker peptidoglycan wall and stain a purple color Gram-negative bacteria contain less peptidoglycan and do not retain the purple-colored dye – retain counterstain and look pink 13

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Gram-positiveGram-negativeGram-positiveGram-negativeGram-positiveGram-negativeGram-positiveGram-negative a. b. 10 µm Crystal violet–iodine complex formed inside cells. All one color. Alcohol dehydrates thick PG layer trapping dye complex. Alcohol has minimal effect on thin PG layer. Dark Purple masks the red dye. Red dye stains the colorless cell. Both cell walls affix the dye. 1. Crystal violet is applied. 2. Gram’s iodine is applied. 3. Alcohol wash is applied. 4. Safranin (red dye) is applied. b: © Jack Bostrack/Visuals Unlimited 14 The Gram stain

Endospores –Develop a thick wall around their genome and a small portion of the cytoplasm –When exposed to environmental stress –Highly resistant to environmental stress Especially heat –When conditions improve can germinate and return to normal cell division –Bacteria causing tetanus, botulism, and anthrax 15

Prokaryotic Genetics Prokaryotes do not reproduce sexually 3 types of horizontal gene transfer –Conjugation – cell-to-cell contact –Transduction – by bacteriophages –Transformation – from the environment All 3 processes also observed in archaea 16

Conjugation Plasmids may encode advantageous info –Are not required for normal function In E. coli, conjugation is based on the presence of the F plasmid (fertility factor) –F + cells contain the plasmid –F - cells do not 17 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. a. 2 µm © Dr. Dennis Kunkel/Visuals Unlimited

Transduction Generalized transduction –Virtually any gene can be transferred –Occurs via accidents in the lytic cycle –Viruses package bacterial DNA and transfer it in a subsequent infection Specialized transduction –Occurs via accidents in the lysogenic cycle –Imprecise excision of prophage DNA –Only a few host genes can be transferred 18

19 Infection with Phage Phage adheres to cell.Phage DNA is injected in to cell.Phage DNA is replicated and host DNA is degraded. Phage particles are packaged with DNA and are released. Infection with Transducing Phage Cell contains DNA from donor. Transducing phage adheres to cell. Phage injects a piece of chromosomal DNA. DNA is incorporated by homologous recombination. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Transformation Natural transformation –Occurs in many bacterial species, including Streptococcus which was studied by Griffith –DNA that is released from a dead cell is picked up by another live cell –Encoded by bacterial chromosome Not an accident of plasmid or phage biology 20

Tuberculosis (TB) Scourge for thousands of years Mycobacterium tuberculosis Afflicts the respiratory system Thwarts immune system Easily transferred from person to person through the air Multidrug-resistant (MDR) strains are very alarming 21

Beneficial Prokaryotes Decomposers release a dead organism’s atoms to the environment Fixation –Photosynthesizers fix carbon into sugars Ancient cyanobacteria added oxygen to air –Nitrogen fixers reduce N 2 to NH 3 (ammonia) Anabaena in aquatic environments Rhizobium in soil 22

Symbiosis refers to the ecological relationship between different species that live in direct contact with each other –Mutualism – both parties benefit Nitrogen-fixing bacteria on plant roots Cellulase-producing bacteria in animals –Commensalism – one organism benefits and the other is unaffected –Parasitism – one organism benefits and the other is harmed 23

Bacteria are used in genetic engineering –“Biofactories” that produce various chemicals, including insulin and antibiotics Bacteria are used for bioremediation –Remove pollutants from water, air, and soil –Biostimulation – adds nutrients to encourage growth of naturally occurring microbes Exxon Valdez oil spill 24