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Archaea, 2:117–125
© 2006 Heron Publishing—Victoria, Canada
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Lineage-specific partitions in archaeal transcription

Richard M. R. Coulson (1, 2), Nathalie Touboul (3) and Christos A. Ouzounis (4)

1. Microarray Group, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U.K. / 2. Corresponding author ([email protected]) / 3. ALCIMED, 84 boulevard Vivier Merle, 69 485 Lyon Cedex 03, France / 4. Computational Genomics Unit, Institute of Agrobiotechnology, Center for Research and Technology Hellas, Thessalonica GR-57001, Greece / Received September 13, 2006; accepted October 23, 2006; published online November 20, 2006


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.

Keywords: genome profiling, protein families, sequence clustering, transcription-associated proteins.

ISSN 1472-3654 (Online) ISSN 1472-3646 (Print) Copyright © 2002–2007 Heron Publishing