ArchaeaArchaea

ExtremophilesExtremophiles

Evolutionarily PrimitiveEvolutionarily Primitive

Formerly known as Formerly known as ArchaeabacteriaArchaeabacteria

HistoryHistory Originally grouped with BacteriaOriginally grouped with Bacteria

Recognized in 1977Recognized in 1977 Carl Woese and George FoxCarl Woese and George Fox 16S rRNA sequencing16S rRNA sequencing

Greek Greek archaeaarchaea “ancient” “ancient”

Common ancestor thought to be a simplistic Common ancestor thought to be a simplistic prokarya with poorly organized genetic material prokarya with poorly organized genetic material

Thought to be involved in evolution of Eukarya-Thought to be involved in evolution of Eukarya-not acceptednot accepted

MorphologyMorphology Spherical, rod-shaped, spiral, lobed, Spherical, rod-shaped, spiral, lobed,

filamentous, or rectangularfilamentous, or rectangular

MorphologyMorphology

0.1-15 microns0.1-15 microns Single circular chromosomeSingle circular chromosome Single cell membraneSingle cell membrane FlagellaFlagella No organellesNo organelles

EcologyEcology Extremophiles (coined 1974)Extremophiles (coined 1974)

Thermophiles (up to 113C)Thermophiles (up to 113C) Black smokersBlack smokers GeysersGeysers

PsycrophilesPsycrophiles Acidophiles and AlkaliphilesAcidophiles and Alkaliphiles HalophilesHalophiles Some combine extremes, ie Some combine extremes, ie PicrophilusPicrophilus (~60C (~60C

and 0.5pH)and 0.5pH) MethanogensMethanogens

Often found in the guts of ruminants, termites Often found in the guts of ruminants, termites and even humansand even humans

Found in all known environmentsFound in all known environments

Adaptations to ExtremesAdaptations to Extremes

In extreme pH must avoid hydrolysis of In extreme pH must avoid hydrolysis of proteins-achieved by changing internal pHproteins-achieved by changing internal pH Anaerobes do not maintain stasis, while Anaerobes do not maintain stasis, while

aerobes doaerobes do Specific enzymes are active at optimal pHSpecific enzymes are active at optimal pH Structure of cell membrane stabilized in Structure of cell membrane stabilized in

high temperature environments by:high temperature environments by: Allows for formation of carbon rings which Allows for formation of carbon rings which

increases stabilityincreases stability Ether linkage is less reactive than ester linkageEther linkage is less reactive than ester linkage Tetraether moleculesTetraether molecules

Can form monolayers (Sulfolobus and Thermoplasma)Can form monolayers (Sulfolobus and Thermoplasma)

Adaptations to ExtremesAdaptations to Extremes

Protection of genetic materialProtection of genetic material High salt concentrations in cytoplasmHigh salt concentrations in cytoplasm DNA binding proteins similar to eukaryotic DNA binding proteins similar to eukaryotic

histoneshistones Share amino acid homologyShare amino acid homology MC1-MC1-MethanosarcinaceaeMethanosarcinaceae HMf-HMf-MethanobacterialesMethanobacteriales

Organizes DNA in sturctures similar to chromatinOrganizes DNA in sturctures similar to chromatin Allows for positive supercoilingAllows for positive supercoiling Eukarya have negative supercoiling (nucleosome)Eukarya have negative supercoiling (nucleosome)

HTa-HTa-ThermoplasmaThermoplasma HTa (like)-HTa (like)-SulfolobusSulfolobus

EvolutionEvolution

Primitive formPrimitive form Related to EukaryaRelated to Eukarya

tRNAtRNA RibosomesRibosomes TATA binding proteins and TFIIB (transcription)TATA binding proteins and TFIIB (transcription) Similar initiation and elongation factors for Similar initiation and elongation factors for

translationtranslation Similarities to bacterial genetic materialSimilarities to bacterial genetic material

EvolutionEvolution

PhylaPhyla

Based on rRNA sequencesBased on rRNA sequences Originally two groupsOriginally two groups Currently three recognizedCurrently three recognized

CrenarchaeotaCrenarchaeota EuryarchaeotaEuryarchaeota KorarchaeotaKorarchaeota

CrenarchaeotaCrenarchaeota Rod, spherical, filamentous, and oddly shaped cellsRod, spherical, filamentous, and oddly shaped cells Organotrophic and lithotrophicOrganotrophic and lithotrophic Most are anaerobesMost are anaerobes Lack histone like proteinsLack histone like proteins Some sulfur dependent (as electron acceptor or Some sulfur dependent (as electron acceptor or

donor)donor) Thermophiles (82-110 Celcius; up to 113C known)Thermophiles (82-110 Celcius; up to 113C known) ThermoacidophilesThermoacidophiles PsycrophilesPsycrophiles

Discovered when lipids of composition similar to other Discovered when lipids of composition similar to other archaea were found in ocean waterarchaea were found in ocean water

Could be a major contributor to global carbon fixationCould be a major contributor to global carbon fixation GeneraGenera

SulfolobusSulfolobus, , DesulfurococcusDesulfurococcus, , PyrodictiumPyrodictium, , ThermoproteusThermoproteus, , ThermofilumThermofilum

EuryarchaeotaEuryarchaeota

Broad ecological rangeBroad ecological range Thermophilic aerobes and anaerobesThermophilic aerobes and anaerobes

PyrococcusPyrococcus and and ThermococcusThermococcus S-metabolizers S-metabolizers Extreme ThermophilicExtreme Thermophilic Sulfate reducing archaeaSulfate reducing archaea ThermoplasmsThermoplasms HalobacteriaHalobacteria MethanogensMethanogens

EuryarchaeotaEuryarchaeota Extreme Thermophilic S-metabolizersExtreme Thermophilic S-metabolizers

Thermococci (anaerobic)Thermococci (anaerobic) Reduce sulfur to sulfideReduce sulfur to sulfide FlagellatedFlagellated (80-100 Celcius)(80-100 Celcius)

ArchaeoglobiArchaeoglobi Sulfate reducing archaeaSulfate reducing archaea

Sulfate, sulfite, thyosulfate into sulfideSulfate, sulfite, thyosulfate into sulfide ThermophilicThermophilic

Including marine thermal ventsIncluding marine thermal vents Has cell wall with glycoprotein subunitsHas cell wall with glycoprotein subunits Gram negativeGram negative

EuryarchaeotaEuryarchaeota

ThermoplasmsThermoplasms Thermoacidophiles that lack cell wallsThermoacidophiles that lack cell walls

Cell membrane strengthened by various Cell membrane strengthened by various proteinsproteins

55-59 Celcius at pH 1-255-59 Celcius at pH 1-2 May be aerobicMay be aerobic May be flagellatedMay be flagellated Mine refuse pilesMine refuse piles

EuryarchaeotaEuryarchaeota

HalobacteriaHalobacteria HalobacteriumHalobacterium and and HaloferaxHaloferax Dependent on high salt concentrationsDependent on high salt concentrations AerobicAerobic Some flagellatedSome flagellated Chemoherterotrophs with respiratory Chemoherterotrophs with respiratory

metabolismmetabolism Some use light to form ATP (not Some use light to form ATP (not

photosynthesis-no chlorophyl)photosynthesis-no chlorophyl) Rhodopsin (4 types)Rhodopsin (4 types)

EuryarchaeotaEuryarchaeota

MethanogensMethanogens MethanosarcinaMethanosarcina Themophilic varietes (84-110 Celcius) including Themophilic varietes (84-110 Celcius) including

MethanobacteriumMethanobacterium, , MethanococcusMethanococcus, , MethanothermusMethanothermus

AnaerobicsAnaerobics Convert carbon dioxide, hydrogen gas, menthanol, Convert carbon dioxide, hydrogen gas, menthanol,

acetate to methane (and carbon dioxide) for energyacetate to methane (and carbon dioxide) for energy AutotrophicAutotrophic Survive in conditions similar to those of a young Survive in conditions similar to those of a young

EarthEarth

KorarchaeotaKorarchaeota

Recently discovered in terrestrial geysersRecently discovered in terrestrial geysers YellowstoneYellowstone

Separation supported by 16S rRNA Separation supported by 16S rRNA sequencingsequencing

Evolutionary divergence from within Evolutionary divergence from within Crenarchaeota or from before divergence Crenarchaeota or from before divergence of Crenarchaeota and Euryarchaeotaof Crenarchaeota and Euryarchaeota

Unique characteristics of Unique characteristics of ArchaeaArchaea

Cell membraneCell membrane Single layerSingle layer Pseudopeptidoglycan or proteinPseudopeptidoglycan or protein L-glycerol (stereoisomer)L-glycerol (stereoisomer) Ether linkage (C-20 diether lipids)Ether linkage (C-20 diether lipids) Some tetraether molecules (C-40 tetraether Some tetraether molecules (C-40 tetraether

lipids)lipids) Branching hydrophobic side chainBranching hydrophobic side chain

Carbon ring formationCarbon ring formation Resistant to lysozyme and beta-lactam antibioticsResistant to lysozyme and beta-lactam antibiotics

Flagella have unique composition and Flagella have unique composition and developmentdevelopment

Cell MembraneCell Membrane

Unique CharacteristicsUnique Characteristics

Metabolic differencesMetabolic differences ADP dependent kinase (not ATP)ADP dependent kinase (not ATP) Pyrophosphate-linked kinases (not Pyrophosphate-linked kinases (not

pyrophosphate dependent pyrophosphate dependent phosphofructokinases)phosphofructokinases)

Organotrophs, autotrophs, and an unusual Organotrophs, autotrophs, and an unusual form of photosynthesisform of photosynthesis

No Archaea uses the full respiration or No Archaea uses the full respiration or photosynthetic cycles, but instead employs photosynthetic cycles, but instead employs many of the steps individuallymany of the steps individually

Methanogens and some extreme thermophiles Methanogens and some extreme thermophiles use glycogen instead of glucoseuse glycogen instead of glucose

Unique CharacteristicsUnique Characteristics

Intracellular bodiesIntracellular bodies rRNA (16S) sequencerRNA (16S) sequence tRNAtRNA PlasmidsPlasmids Lack of organelles (similar to bacteria)Lack of organelles (similar to bacteria)

Unique CharacteristicsUnique Characteristics

Genetic MaterialGenetic Material Resistance to denaturation by heat seen in Resistance to denaturation by heat seen in

thermophilesthermophiles Similar structure to bacteriaSimilar structure to bacteria Some sequencing has revealed sections of DNA Some sequencing has revealed sections of DNA

that are shared with bacteria (gene sharing that are shared with bacteria (gene sharing between bacteria and archaea?)between bacteria and archaea?)

Primary protein sequence is similar to EukaryaPrimary protein sequence is similar to Eukarya Genes with similar functions organized Genes with similar functions organized

together (similar to operons)together (similar to operons) Introns are found in rRNA and tRNA genesIntrons are found in rRNA and tRNA genes

Unique CharacteristicsUnique Characteristics

ReplicationReplication DNA Polymerase similar to that of DNA Polymerase similar to that of

eukaryotes, eukaryal virueseukaryotes, eukaryal virues andand E. coli E. coli 3’-5’ exonuclease (proofreading)3’-5’ exonuclease (proofreading) Restriction endonucleaseRestriction endonuclease TopoisomeraseTopoisomerase

GyraseGyrase Halobacterium halobiumHalobacterium halobium has reverse has reverse

transcriptasetranscriptase

Unique CharacteristicsUnique Characteristics

TranscriptionTranscription RNA polymerase has up to 14 subunits (RNA polymerase has up to 14 subunits (E. E.

colicoli has only 4) and is similar to eukaryotes has only 4) and is similar to eukaryotes Requires general transcription factors to Requires general transcription factors to

initiate (like eukarya)initiate (like eukarya) Promoters have an A-T rich sequence Promoters have an A-T rich sequence

similar to eukarya TATA boxsimilar to eukarya TATA box Translation Translation

Signals similar to bacteriaSignals similar to bacteria

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

SourcesSources

Brown, J. R. and Doolittle, W. F. 1997. ArchaeaBrown, J. R. and Doolittle, W. F. 1997. Archaea and the Prokaryote-to-Eukaryote Transition. and the Prokaryote-to-Eukaryote Transition. Microbiology and Molecular Biology Reviews. 61 Microbiology and Molecular Biology Reviews. 61 (4): 456-502.(4): 456-502.

Griffith University-http://trishul.sci.gu.edu.au/Griffith University-http://trishul.sci.gu.edu.au/ Kevbrin, V. V., Romanek, C. S., Wiegel, J. Kevbrin, V. V., Romanek, C. S., Wiegel, J.

Alkalithermophiles: A Double Challenge from Alkalithermophiles: A Double Challenge from Extreme Environments.Extreme Environments.

Microbiology 6Microbiology 6thth ed. ed. University of California Berkley-University of California Berkley-

www.ucmp.berkeley.edu/archaea/archaea.htmlwww.ucmp.berkeley.edu/archaea/archaea.html