Lineage-specific partitions in archaeal transcription.
The phylogenetic distribution of the components comprising the transcriptional machinery in the crenarchaeal and euryarchaeal lineages of the Archaea was analyzed in a systematic manner by genome-wide profiling of transcription complements in fifteen complete archaeal genome sequences. Initially, a reference set of transcription-associated proteins (TAPs) consisting of sequences functioning in all aspects of the transcriptional process, and originating from the three domains of life, was used to query the genomes. TAP-families were detected by sequence clustering of the TAPs and their archaeal homologues, and through extensive database searching, these families were assigned a function. The phylogenetic origins of archaeal genes matching hidden Markov model profiles of protein domains associated with transcription, and those encoding the TAP-homologues, showed there is extensive lineage-specificity of proteins that function as regulators of transcription: most of these sequences are present solely in the Euryarchaeota, with nearly all of them homologous to bacterial DNA-binding proteins. Strikingly, the hidden Markov model profile searches revealed that archaeal chromatin and histone-modifying enzymes also display extensive taxon-restrictedness, both across and within the two phyla.
Coulson
Richard M R
RM
Microarray Group, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. coulson@ebi.ac.uk
Touboul
Nathalie
N
Ouzounis
Christos A
CA
D001105:Archaea / Q000235:genetics*; D019843:Archaeal Proteins / Q000235:genetics*; D030562:Databases, Protein; D020745:Genome, Archaeal; D008390:Markov Chains; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D014157:Transcription Factors / Q000235:genetics; D014158:Transcription, Genetic
D019843:Archaeal Proteins; D014157:Transcription Factors