• Comparative sequence analysis of 16S RNA molecules has elucidated that life on Earth is of 3 primary lineages (referred to as domains):
• (i) Eukarya
• (ii) Bacteria
• (iii)Archaea
• Kingdom Crenarchaeota: mainly hyperthermophiles
• Kingdom Euryarchaeota: methanogens, halophiles, Thermoplasma  & Archaeoglobus
• Kingdom Korarchaeota: based on 16S rRNA sequences from uncultured microbes from terrestrial hot springs

Structural distinction between the domains

• Cell Walls
• Bacterial = peptidoglycan
• Archaeal = pseudopeptidoglycan, or protein only
• Eukaryal = plants (polysaccharide), animals (none), fungi (chitin)
 
• Cell Membranes
• Bacterial and eucaryal lipids = straight chain fatty acids linked to glycerol molecules by ester linkages
• Archael lipids = branched chain hydrocarbons linked to glycerol molecules by ether linkages - fatty acid components are not found in archeal lipids

Molecular Biology comparisons

• Genome organisation
• Similar to bacteria
• Chromosome is a single, circular DNA molecule
• Extrachromosomal elements (eg plasmids) are found in archaea
• Genomic resistance to thermal denaturation & genomic structural intergrity in extreme thermophiles is related to:
• high intracellular salt concentrations (solutes)
• DNA binding proteins (aka Histone-like proteins similar to Eucarya):
• MC1 : Methanosarcinaceae
• HMf: Methanobacteriales
• share amino acid homology to Eucaryal Histone proteins
• organization of DNA in chromatin-like structure
• histone + Eucarya DNA = negative supercoiling & nucleosome
• HMf + Archaea DNA = positive supercoiling
• HTa: Thermoplasma
• HTa-like: Sulfolobus

• DNA Replication
• Archael DNA polymerases have been identified with primary protein sequences resembling polymerases from eukaryotes, eukaryal viruses and E.coli
• Some posses 3'-5' exonuclease (or proofreading) activity
• A Halobacterium halobium polymerase / primase has been identified with reverse transcriptase activity
• Topoisomerases, gyrase and restriction endonucleases have also been identified in Archaea
 
• Transcription
• Archael RNA polymerases are complex, consisting of up tp 14 subunits (c.f. 4 in E.coli)
• Comparative sequence homology of genes encoding subunits suggests that the polymerase is more closely related to eukaryal polymerases than bacterial
• Unlike, E.coli RNA polymerase, Archael RNA polymerases are unable to initiate transcription in vitro; This is also seen in eukaryotes where general transcription factors are required for initiation
• Archael promoters have an A-T rich sequence at -32 to -25 bp upstream of the transcriptional start: the consensus sequence resembles a eukaryotic TATA box
 
• Gene Organisation
• Primary sequence of archael proteins more often resemble eukaryotic homologues than bacterial ones
• Functionally related genes are often organised in operon like structures
• Introns have been found in archael 23S and 16S rRNA and tRNA genes
• Varying arrangements of genes can be seen in Archaea
• Methyl coenzyme M reductase, RNAP and bacterio-opsin genes are good examples
 
• Translation
• Translation signals resemble those found in bacteria (i.e. there are short regions of complementarity between the 5' end of the mRNA and the 3' end of the 16S rRNA)
 
• Cloning and Expression
• Cloning usually follows protein-purification using standard molecular biology techniques
• Expression in heterologous hosts may be complcated by the altered environment in which expression is occuring and differences in translation and post-translational mechanisms

References:

• Madigan, M.T., Martinko, J.M. and Parker, J. Brock, Biology of Microorganisms, Prentice Hall, 8th Edition, 1997

 
• M.Ciaramella et al, Molecular biology of extremophiles, World Journal of Microbiology and Biotechnology, Vol 11, pp 71-84, 1995

 
• Danson et al., Archaebacteria, Biochemistry and Biotechnology, London: Biochemical Society, 1992

 
• Brown, J.W. et al, Gene Structure, Organisation and Expression in Archaebacteria. CRC Critical Reviews in Microbiology, Vol 16, No. 4, 1989