Lineage-specific partitions in archaeal transcription

Coulson, Richard M. R.; Touboul, Nathalie; Ouzounis, Christos  A.

doi:https://doi.org/10.1155/2006/629868

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Research Article | Open Access

Volume 2 | Article ID 629868 | https://doi.org/10.1155/2006/629868

Lineage-specific partitions in archaeal transcription

Richard M. R. Coulson,¹Nathalie Touboul,²and Christos A. Ouzounis³

Received13 Sept 2006

Accepted23 Oct 2006

Abstract

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.

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Copyright © 2006 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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