Archaea

NANOARCHAEOTA

Four phyla in Archaea� Euryarchaeota:

� Methano-producing and extreme halophiles

� Thermoplasma: acidophilic, thermophilic, cell wall-less

� Crenarchaeota: Hyperthermophilic Archaea: Thermoproteus, � Hyperthermophilic Archaea: Thermoproteus, Pyrolobus, and Pyrodictium

� Cold-adapted Archaea

� Korarchaeota: hyperthermophiles

� Nanoarchaeota: single species (Nanoarchaeum), a parasite of another archaeon, Ignicoccus

Basic Archae Morphology

A: A coccus with many flagella at one end (Methanococcus janaschii)B: A lobed coccus no flagella (Methanosarcina barkeri) C: A bacillus no flagella (Methanothermus fervidus)D: An elongate bacillus form (Methanobacterium thermoautotrophicum)

A B C D

Characteristics of Archaea

� Cell walls

� Lack peptidoglycan (like Eukarya)

� Peptidoglycan analog (pseudopeptidoglycan)

� Polysaccharide

� Protein

� Glycoprotein

� S-layer

Consisting of alternating residues of β-(1,3) linkedN-acetyltalosaminuronic acid (NAT) and N-Acetylglucosamine(NAG)

Peptidoglycan vs pseudopeptidoglycan

Peptidoglycan vs pseudopeptidoglycan

L-alanin

L- lysine

L-glutamate

D-glutamic acid

L- lysine or DAP

D-alanine

L-glutamate

G GT

L-alanine

D-glutamic acid

G GM

ArchaeArchaeArchaeArchaeaaaa BacteriumBacteriumBacteriumBacterium

A. Schematic representation of a cross-section of the cell envelope of Sulfolobus solfataricusshowing the cytoplasmic membrane, with membrane-spanning tetraether lipids and an S-layer composed of two proteins a surface-covering protein (red oval) and a membrane-anchoring protein (yellow oblong). B. Schematic representation of a cell envelope of an archaeon that stains positive with the Gram stain and that contains a pseudomurein layer in addition to the S-layer. The cytoplasmic membrane is composed of diether lipids.


� Membrane

HyperthermophilicArchaea

Exception ......

Bacteria: membrane contains ether-linked lipids:

� Thermophilic sulfate-reducing bacterium

Thermodesulfobacterium

� A few of sulfate-reducing bacteria

� Propionibacterium species


� Membrane

� Lipid monolayer (stable at harsk condition)

� Stable at high temperature (less denaturation)

� Ether-linked


� RNA polymerase


� Feature of protein synthesis

� Ribosome: 70S ( ~ bacteria)

� Initiator tRNA carries unmodified methionine


� Feature of protein synthesis

� Diphteria toxin inhibits protein synthesis of Archaea

(~ Eukarya) but not Bacteria

� Antibiotics that inhibits protein synthesis in Bacteria

do not affect in Archaea

Summary of major differential featuresCharacteristics Bacteria Archaea Eukarya

Prokaryotic structure √ √ ×

Circular DNA √ √ ×

Histone protein × √ √

Nucleus × × √

Cell wall (muramic acid) √ × ×Cell wall (muramic acid) √ × ×

Membrane lipids Esther Ether Esther

Ribosomes 70S 70S 80S

Initiator tRNA fMet Met Met

Introns × × √

Operons √ √ ×

Capping and polyA mRNA × × √

Plasmids √ √ Rare

Summary of major differential features

Characteristics Bacteria Archaea Eukarya

Ribosome sensitivity to DT × √ √

RNA polymerase One Several Three

Subunits of RNA polymerase 4 8-12 12-14

Transcription factors × √ √Transcription factors × √ √

Promotor structure -10 and -35 TATA box TATA box

Sensitivity to chloramphenicol,

streptomycin, kanamycin

√ × ×

Phylum Euryarchaeota� Extremely Halophilic Archaea

� Halobacterium, Haloferax, Natronobacterium

Hypersaline environment

� Requires high concentration of salt: 2-4 M of NaCl� Some can grow at 5 M (32%, limit f NaCl saturation)� Water balance; compatible solute (an organic or

inorganic substance accumulated in the cytoplasm of a halophilic organism in order to maintain osmotic pressure), in this case, pumping ion K+

Phylum Euryarchaeota� Extremely Halophilic Archaea

� Cell wall: � Glycoprotein:

� acidic in nature, contains high aspartate and glutamate

� stabilized by ion Na+, required for cell integrity

� Cytoplasm:� Cytoplasm:� Acidic

� High ion K+ is required for enzyme activity

� Low level of hydrophobic amino acids and lysine

� Polar protein tends to be more soluble

� Ribosome requires ion K +

� Cellular components exposed to external environment require ion Na +, whereas internal components require K +

Methane-producing Archaea:

Metahogens

� Genera: Methanobacterium, Methanocaldococcus, Methanosarcina

� Cell wall diversity:� Pseudopeptidoglycan: Methanobacterium

� Methanochondroitin: Methanoarcina

� Protein or glyprotein: Methanocaldococcus

� Obligate anaerobes

� Hyperthermophilic and thermophilic metahogens: Methanocaldococcus jannaschii (85oC), Methanotorris igneus (88oC), Methanosaeta thermophila (60oC)

Thermoplasmatales: Thermoplasma,

Ferroplasma, Picrophilus� Archaea lacking cell walls: Thermoplasma and Ferroplasma� Optimal temperature: 55oC and pH 2� Survive osmotic pressure without cell wall (hot acid

condition):� Thermoplasma: unique cell membrane ~ lipoglycan

(LPS-like material) with mannose ang glucose and (LPS-like material) with mannose ang glucose and glycoprotein

� Thermoplasma DNA is complexed with highly basic DNA-binding protein ~ histone

Thermoplasmatales: Thermoplasma,

Ferroplasma, Picrophilus

� Ferroplasma:

� Strong acidophile, not thermophile

� Oxidizes Fe2+ → Fe3+ to obtain energy (generates

acid)

� Acidic water at pH 0 � Acidic water at pH 0

� Picrophilus:

� Grows at pH -0.06 to 0.7

� Extreme acid tolerance

� Cell wall: S-layer

Hyperthermophilic Euryarchaeota:

Thermococcales and Methanopyrus

� Thermococcus: obligately anaerobic 70-95 oC

� Pyrococcus: 70 – 106 oC

� Methanopyrus: maximal growth temperature 110oC

� Ether-linked lipid (unsaturated) most Archaea: � Ether-linked lipid (unsaturated) most Archaea:

saturated

Phylum Crenarchaeota� All cultured Crenarchaeota:

� hyperthermophiles (> 80 oC)

� Cold-dwelling Crenarchaeota:� < 0 oC (sea ice) and 2 – 4 oC (seawater)

� Hyperthermophiles from terrestrial volcanic � Hyperthermophiles from terrestrial volcanic habitats: Solfobales and Thermoproteales� Sulfolobus: sulfur-rich acidic hot springs (90 oC and

pH 1-5)

� Thermoproteus and Thermofilum: strict anaerobe

� Pyrobaculum: aerobe, optimal growth temperature (100 oC)

Phylum Nanoarchaeota

� Tiny parasitic cells

� Smallest genome of all known prokaryotes

� Nanoarchaeum:

� Replicates only when attached to the surface of

Ignicoccus cellsIgnicoccus cells

� Optimal growth:90 oC

Evolution and life at high temperatures

� Heat stability of biomolecules:

� Protein folding and thermostability:

� Same structure as non-thermophiles

� Thermostability (hold protein each other and prevent

unfloding):

Highly hydrophobic cores� Highly hydrophobic cores

� More ionic interations on the protein surface

� Chaperonins:

� Assist protein to remain in their native state

� Refold partially denatured proteins

� Function only at high temperatures

� Thermosome: Pyrodictium (optimal growth: 110 oC)



� DNA stability at high temperatures: solutes and

reverse gyrase

� Methanopyrus:

� potassium cyclic 2,3-diphosphoglycerate (salt)

� Prevents chemical damage to DNA (depurination or

depyrimidization at high temperature)



� DNA stability at high temperatures: solutes and reverse DNA gyrase (absent < 80 oC)

reverse DNA gyrasereverse DNA gyrase

Stabilize DNA at high temperature

Prevent DNA helix to denaturation



� DNA stability: DNA-binding protein

� Small heat-stable DNA-binding protein (Sac7d) binds minor

groove of DNA (Sulfolobus) and increases its melting

temperature by 40 oC.

� Highly acidic protein (~ histone) binds DNA � Highly acidic protein (~ histone) binds DNA

(Euryarchaeota): complex maintain double-stranded

structure at high temperature

� Lipid stability

� Stability of monomers

� ATP and NAD

Archaea

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