NOVEL PROTEIN FAMILIES IN ARCHEAN GENOMES

In a quest for novel functions in archaea, all archaean hypothetical o pen reading frames (ORFs), as annotated in the Swiss-Prot protein sequ ence database, were used to search the latest databases for the identi fication of characterized homologues, Of the 95 hypothetical archaean ORFs, 25 were found to be homologous to another hypothetical archaean ORF, while 36 were homologous to non-archaean proteins, of which as ma ny as 30 were homologous to a characterized protein family, Thus the l evel of sequence similarity in this set reaches 64%, while the level o f function assignment is only 32%, Of the ORFs with predicted function s, 12 homologies are reported here for the first time and represent ni ne new functions and one gene duplication at an acetyl-coA synthetase locus, The novel functions include components of the transcriptional a nd translational apparatus, such as ribosomal proteins, modification e nzymes and a translation initiation factor, In addition, new enzymes a re identified in archaea, such as cobyric acid synthase, dCTP deaminas e and the first archaean homologues of a new subclass of ATP binding p roteins found in fungi, Finally, it is shown that the putative laminin receptor family of eukaryotes and an archaean homologue belong to the previously characterized ribosomal protein family S2 from eubacteria, From the present and previous work, the major implication is that arc haea seem to have a mode of expression of genetic information rather s imilar to eukaryotes, while eubacteria may have proceeded into unique ways of transcription and translation, In addition, with the detection of proteins in various metabolic and genetic processes in archaea, we can further predict the presence of additional proteins involved in t hese processes.