NORMAL GENOMIC

• Koonin EV, Mushegian AR, Galperin MY, Walker DR
• Comparison of archaeal and bacterial genomes: computer analysis of proteinsequences predicts novel functions and suggests a chimeric origin for thearchaea.
• Mol Microbiol. 1997; 25: 619-37
• Display abstract

• Protein sequences encoded in three complete bacterial genomes, those ofHaemophilus influenzae, Mycoplasma genitalium and Synechocystis sp., andthe first available archaeal genome sequence, that of Methanococcusjannaschii, were analysed using the BLAST2 algorithm and methods for aminoacid motif detection. Between 75% and 90% of the predicted proteinsencoded in each of the bacterial genomes and 73% of the M. jannaschiiproteins showed significant sequence similarity to proteins from otherspecies. The fraction of bacterial and archaeal proteins containingregions conserved over long phylogenetic distances is nearly the same andclose to 70%. Functions of 70-85% of the bacterial proteins and about 70%of the archaeal proteins were predicted with varying precision. Thiscontrasts with the previous report that more than half of the archaealproteins have no homologues and shows that, with more sensitive methodsand detailed analysis of conserved motifs, archaeal genomes become asamenable to meaningful interpretation by computer as bacterial genomes.The analysis of conserved motifs resulted in the prediction of a number ofpreviously undetected functions of bacterial and archaeal proteins and inthe identification of novel protein families. In spite of the generallyhigh conservation of protein sequences, orthologues of 25% or less of theM. jannaschii genes were detected in each individual completely sequencedgenome, supporting the uniqueness of archaea as a distinct domain of life.About 53% of the M. jannaschii proteins belong to families of paralogues,a fraction similar to that in bacteria with larger genomes, such asSynechocystis sp. and Escherichia coli, but higher than that in H.influenzae, which has approximately the same number of genes as M.jannaschii. Certain groups of proteins, e.g. molecular chaperones and DNArepair enzymes, thought to be ubiquitous and represented in the minimalgene set derived by bacterial genome comparison, are missing in M.jannaschii, indicating massive non-orthologous displacement of genesresponsible for essential functions. An unexpectedly large fraction of theM. jannaschii gene products, 44%, shows significantly higher similarity tobacterial than to eukaryotic proteins, compared with 13% that haveeukaryotic proteins as their closest homologues (the rest of the proteinsshow approximately the same level of similarity to bacterial andeukaryotic homologues or have no homologues). Proteins involved intranslation, transcription, replication and protein secretion are mostclosely related to eukaryotic proteins, whereas metabolic enzymes,metabolite uptake systems, enzymes for cell wall biosynthesis and manyuncharacterized proteins appear to be 'bacterial'. A similar prevalence ofproteins of apparent bacterial origin was observed among the currentlyavailable sequences from the distantly related archaeal genus, Sulfolobus.It is likely that the evolution of archaea included at least one majormerger between ancestral cells from the bacterial lineage and the lineageleading to the eukaryotic nucleocytoplasm.