THE PROKARYOTES Systematics Focus on animals and plants

  • Slides: 42
Download presentation
THE PROKARYOTES

THE PROKARYOTES

Systematics • Focus on animals and plants – History limited to 20% of evolutionary

Systematics • Focus on animals and plants – History limited to 20% of evolutionary time • How to classify prokaryotes? Limited in morphological characters

Carl Richard Woese 1928 -2012, USA; Developed system based on 16 S r. RNA

Carl Richard Woese 1928 -2012, USA; Developed system based on 16 S r. RNA in 1977

Carl Woese and George Fox

Carl Woese and George Fox

r. RNA Emile Zuckerkandl (1922 -2013); Austria & USA. Molecular biology and molecular clock

r. RNA Emile Zuckerkandl (1922 -2013); Austria & USA. Molecular biology and molecular clock Linus Carl Pauling (1901 -1994) USA Founder of fields like quantum chemistry and molecular biology Suggested that a tree of life might be generated by comparing sequences of biopolymers like RNA Zuckerkandl and Pauling

Flow of information in a cell, the central dogma of molecular biology…

Flow of information in a cell, the central dogma of molecular biology…

 • When DNA is transcribed, the result is an RNA molecule DNA molecule

• When DNA is transcribed, the result is an RNA molecule DNA molecule Gene 1 Gene 2 Gene 3 DNA strand Transcription RNA Translation Codon Polypeptide Amino acid Figure 10. 10

 • When DNA is transcribed, the result is an RNA molecule DNA molecule

• When DNA is transcribed, the result is an RNA molecule DNA molecule Gene 1 Gene 2 Gene 3 • RNA is then translated into a sequence of amino acids DNA strand Transcription RNA Translation Codon Polypeptide Amino acid Figure 10. 10

Ribosomal Function A typical prokaryotic cell may have 10, 000+ ribosomes

Ribosomal Function A typical prokaryotic cell may have 10, 000+ ribosomes

Where does r. RNA enter the picture?

Where does r. RNA enter the picture?

Ribosomal Structure Two subunits

Ribosomal Structure Two subunits

Ribosomal subunits= r. RNA molecules + proteins

Ribosomal subunits= r. RNA molecules + proteins

Prokaryotes Eukaryotes

Prokaryotes Eukaryotes

A modification of Woese from Brock et al. (1994).

A modification of Woese from Brock et al. (1994).

The system we propose here will repair the damage that has been the unavoidable

The system we propose here will repair the damage that has been the unavoidable consequence of constructing taxonomic systems in ignorance of the likely course of microbial evolution, and on the basis of flawed premises (that life is dichotomously organized; that negative characteristics can define meaningful taxonomies). - Carl R. Woese, Otto Kandler, and Mark L. Wheelis. 1990. Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proceedings of the National Academy of Sciences. USA. 87: 4576 -4579.

Two different supertrees generated by ML methods for complete genomes of 45 taxa. Daubin

Two different supertrees generated by ML methods for complete genomes of 45 taxa. Daubin et al. 2002

Ciniglia et al. 2004

Ciniglia et al. 2004

Lang et al. 2013 Using 24 genes and 3000 taxa

Lang et al. 2013 Using 24 genes and 3000 taxa

Gram Stain and Structure

Gram Stain and Structure

Eubacteria • >9 Kingdoms • Same type of ribosomes • Polysaccharide of outer wall

Eubacteria • >9 Kingdoms • Same type of ribosomes • Polysaccharide of outer wall made of murein • Most groups involved in global nutrient cycling • Many of economic importance • Disease • Other functions (e. g. antibiotic producers)

Proteobacteria • Disparate functional groups joined by molecular sequences • Likely the source of

Proteobacteria • Disparate functional groups joined by molecular sequences • Likely the source of mitochondria

Alphaproteobacteria • Rikettsias (typhus Rocky Mtn spotted fever • Rhizobias (N-fixing bacteria) • Likely

Alphaproteobacteria • Rikettsias (typhus Rocky Mtn spotted fever • Rhizobias (N-fixing bacteria) • Likely the ancestor of mitochondria was from this group

Gammaproteobacteria • Usually small rods or cocci • Causative agents of Bubonic Plague, Tularemia,

Gammaproteobacteria • Usually small rods or cocci • Causative agents of Bubonic Plague, Tularemia, Legioner’s Disease, Cholera • Includes Escherichia coli

Spirochaetae

Spirochaetae

Spirochaetae • Spiraled with internal flagella • Many are free-living • Causative agents of

Spirochaetae • Spiraled with internal flagella • Many are free-living • Causative agents of Lyme disease, syphilis, yaws, and relapsing fever

Cyanobacteria

Cyanobacteria

Cyanobacteria • Like free-living chloroplast • Group from which chloroplasts appeared • Form filaments,

Cyanobacteria • Like free-living chloroplast • Group from which chloroplasts appeared • Form filaments, colonies • Very large for bacteria • Some produce toxins • Many are nuisance algae in overfertilized waters • Source of most atmospheric oxygen, especially prior to eukaryotes

Firmicutae • Lack second outer membrane of Eubacteria • Gram positive

Firmicutae • Lack second outer membrane of Eubacteria • Gram positive

Aphragmabacteria • Tiny, smallest genome of any nonvirus • No walls • Obligate parasites

Aphragmabacteria • Tiny, smallest genome of any nonvirus • No walls • Obligate parasites • One causes pneumonia; many plant pathogens

Anoxybacteria • Obligate anaerobes • Causative agents of botulism and tetanus • Botox •

Anoxybacteria • Obligate anaerobes • Causative agents of botulism and tetanus • Botox • Common in soil and animal digestive systems

Endosporobacteria • Produce resistant spores • Many major human pathogens, including anthrax, staph (including

Endosporobacteria • Produce resistant spores • Many major human pathogens, including anthrax, staph (including methicillin-resistant Staphylococcus aureus), strep • Includes Lactobacillus

Actinobacteria • Many are slow-growing and funguslike • Antibiotic sources (e. g. streptomycin, actinomycin)

Actinobacteria • Many are slow-growing and funguslike • Antibiotic sources (e. g. streptomycin, actinomycin) • Causative agents of leprosy and tuberculosis; diptheria • Bacteria which cause holes in Swiss cheese • Bifida, a necessary commensal in our lower bowel

Deinococcobacteria • Thermophiles • Deinococcus withstands 6, 000 rads (and up to 1500 megarads)

Deinococcobacteria • Thermophiles • Deinococcus withstands 6, 000 rads (and up to 1500 megarads) • Thermus, found at Yellowstone, enzymes used for PCR

Archaea Differ from the Eubacteria – – Form of ribosomes No murein Different lipids

Archaea Differ from the Eubacteria – – Form of ribosomes No murein Different lipids Different RNA polymerase

Crenarchaea • These are the hyperthermophiles • They tend to inhabit very hot environments

Crenarchaea • These are the hyperthermophiles • They tend to inhabit very hot environments that are rich in sulfur

Euryarchaeota • Halobacteria • Methanobacteria • Thermoplasmobacteria

Euryarchaeota • Halobacteria • Methanobacteria • Thermoplasmobacteria

The Asgardians Prometheoarcheum, a Lokiarchaeota microbe. Zaremba-Niedzwiedzka et al. 2017. Nature. 541: 353 -358.

The Asgardians Prometheoarcheum, a Lokiarchaeota microbe. Zaremba-Niedzwiedzka et al. 2017. Nature. 541: 353 -358.

Seitz et al. 2019

Seitz et al. 2019

Viruses • Non-cellular • Usually nucleic acid and protein • Types – – –

Viruses • Non-cellular • Usually nucleic acid and protein • Types – – – DNA (ss & ds) RNA (ss & ds) DNA RT RNA RT Prions

Some Human Viral Diseases • • • Herpes Smallpox Hepatitis (B, C, D) Yellow

Some Human Viral Diseases • • • Herpes Smallpox Hepatitis (B, C, D) Yellow Fever Dengue fever West Nile HIV Ebola Rabies Chicken Pox /Shingles • • • Rubella (German Measles) Influenza Polio Mumps Measles Epstein-Barr Hemorrhagic fever Rota Rhinovirus Transmissible spongiform encephalopathy (TSE)

Theories on Origin of Viruses • Regressive Hypothesis: cellular parasites of larger cells that

Theories on Origin of Viruses • Regressive Hypothesis: cellular parasites of larger cells that became simplified • Cellular Origin Hypothesis: pieces of living cells that can replicate (e. g. strands of nucleic acids like plasmids or transposons) • Coevolution Hypothesis: evolved together with the first cells as their parasites