Archaea Extremophiles Evolutionarily Primitive Formerly known as Archaeabacteria

History Originally grouped with Bacteria Recognized in 1977 Carl Woese and George Fox 16S rRNA sequencing Greek archaea “ancient” Common ancestor thought to be a simplistic prokarya with poorly organized genetic material Thought to be involved in evolution of Eukarya-not accepted

Morphology Spherical, rod-shaped, spiral, lobed, filamentous, or rectangular

Morphology 0.1-15 microns Single circular chromosome Single cell membrane Flagella No organelles

Ecology Extremophiles (coined 1974) Methanogens Thermophiles (up to 113C) Black smokers Geysers Psycrophiles Acidophiles and Alkaliphiles Halophiles Some combine extremes, ie Picrophilus (~60C and 0.5pH) Methanogens Often found in the guts of ruminants, termites and even humans Found in all known environments

Adaptations to Extremes In extreme pH must avoid hydrolysis of proteins-achieved by changing internal pH Anaerobes do not maintain stasis, while aerobes do Specific enzymes are active at optimal pH Structure of cell membrane stabilized in high temperature environments by: Allows for formation of carbon rings which increases stability Ether linkage is less reactive than ester linkage Tetraether molecules Can form monolayers (Sulfolobus and Thermoplasma)

Adaptations to Extremes Protection of genetic material High salt concentrations in cytoplasm DNA binding proteins similar to eukaryotic histones Share amino acid homology MC1-Methanosarcinaceae HMf-Methanobacteriales Organizes DNA in sturctures similar to chromatin Allows for positive supercoiling Eukarya have negative supercoiling (nucleosome) HTa-Thermoplasma HTa (like)-Sulfolobus

Evolution Primitive form Related to Eukarya tRNA Ribosomes TATA binding proteins and TFIIB (transcription) Similar initiation and elongation factors for translation Similarities to bacterial genetic material

Evolution

Phyla Based on rRNA sequences Originally two groups Currently three recognized Crenarchaeota Euryarchaeota Korarchaeota

Crenarchaeota Rod, spherical, filamentous, and oddly shaped cells Organotrophic and lithotrophic Most are anaerobes Lack histone like proteins Some sulfur dependent (as electron acceptor or donor) Thermophiles (82-110 Celcius; up to 113C known) Thermoacidophiles Psycrophiles Discovered when lipids of composition similar to other archaea were found in ocean water Could be a major contributor to global carbon fixation Genera Sulfolobus, Desulfurococcus, Pyrodictium, Thermoproteus, Thermofilum

Euryarchaeota Broad ecological range Extreme Thermophilic Thermophilic aerobes and anaerobes Pyrococcus and Thermococcus S-metabolizers Extreme Thermophilic Sulfate reducing archaea Thermoplasms Halobacteria Methanogens

Euryarchaeota Extreme Thermophilic S-metabolizers Archaeoglobi Thermococci (anaerobic) Reduce sulfur to sulfide Flagellated (80-100 Celcius) Archaeoglobi Sulfate reducing archaea Sulfate, sulfite, thyosulfate into sulfide Thermophilic Including marine thermal vents Has cell wall with glycoprotein subunits Gram negative

Euryarchaeota Thermoplasms Thermoacidophiles that lack cell walls Cell membrane strengthened by various proteins 55-59 Celcius at pH 1-2 May be aerobic May be flagellated Mine refuse piles

Euryarchaeota Halobacteria Halobacterium and Haloferax Dependent on high salt concentrations Aerobic Some flagellated Chemoherterotrophs with respiratory metabolism Some use light to form ATP (not photosynthesis-no chlorophyl) Rhodopsin (4 types)

Euryarchaeota Methanogens Methanosarcina Themophilic varietes (84-110 Celcius) including Methanobacterium, Methanococcus, Methanothermus Anaerobics Convert carbon dioxide, hydrogen gas, menthanol, acetate to methane (and carbon dioxide) for energy Autotrophic Survive in conditions similar to those of a young Earth

Korarchaeota Recently discovered in terrestrial geysers Yellowstone Separation supported by 16S rRNA sequencing Evolutionary divergence from within Crenarchaeota or from before divergence of Crenarchaeota and Euryarchaeota

Unique characteristics of Archaea Cell membrane Single layer Pseudopeptidoglycan or protein L-glycerol (stereoisomer) Ether linkage (C-20 diether lipids) Some tetraether molecules (C-40 tetraether lipids) Branching hydrophobic side chain Carbon ring formation Resistant to lysozyme and beta-lactam antibiotics Flagella have unique composition and development

Cell Membrane

Unique Characteristics Metabolic differences ADP dependent kinase (not ATP) Pyrophosphate-linked kinases (not pyrophosphate dependent phosphofructokinases) Organotrophs, autotrophs, and an unusual form of photosynthesis No Archaea uses the full respiration or photosynthetic cycles, but instead employs many of the steps individually Methanogens and some extreme thermophiles use glycogen instead of glucose

Unique Characteristics Intracellular bodies rRNA (16S) sequence tRNA Plasmids Lack of organelles (similar to bacteria)

Unique Characteristics Genetic Material Resistance to denaturation by heat seen in thermophiles Similar structure to bacteria Some sequencing has revealed sections of DNA that are shared with bacteria (gene sharing between bacteria and archaea?) Primary protein sequence is similar to Eukarya Genes with similar functions organized together (similar to operons) Introns are found in rRNA and tRNA genes

Unique Characteristics Replication DNA Polymerase similar to that of eukaryotes, eukaryal virues and E. coli 3’-5’ exonuclease (proofreading) Restriction endonuclease Topoisomerase Gyrase Halobacterium halobium has reverse transcriptase

Unique Characteristics Transcription RNA polymerase has up to 14 subunits (E. coli has only 4) and is similar to eukaryotes Requires general transcription factors to initiate (like eukarya) Promoters have an A-T rich sequence similar to eukarya TATA box Translation Signals similar to bacteria

Ending on a historical note… re-enactment of the separation of archaea from bacteria

Sources Brown, J. R. and Doolittle, W. F. 1997. Archaea and the Prokaryote-to-Eukaryote Transition. Microbiology and Molecular Biology Reviews. 61 (4): 456-502. Griffith University-http://trishul.sci.gu.edu.au/ Kevbrin, V. V., Romanek, C. S., Wiegel, J. Alkalithermophiles: A Double Challenge from Extreme Environments. Microbiology 6th ed. University of California Berkley-www.ucmp.berkeley.edu/archaea/archaea.html