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DNA Research Advance Access originally published online on January 10, 2006
DNA Research 2005 12(5):269-280; doi:10.1093/dnares/dsi016
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© The Author 2006. Kazusa DNA Research Institute
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Genome-Wide Survey of Transcription Factors in Prokaryotes Reveals Many Bacteria-Specific Families Not Found in Archaea

Yoshiaki Minezaki1, Keiichi Homma1,2 and Ken Nishikawa1,*

1Laboratory of Gene-Product Informatics, Center for Information Biology–DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems 1111 Yata, Mishima, Shizuoka, 411-8540 Japan
2Japan Science and Technology Corporation 1–8, Honcho 4-chome, Kawaguchi City, Saitama, 332-0012, Japan

Assignment of all transcription factors (TFs) from genome sequence data is not a straightforward task due to the wide variation in TFs among different species. A DNA binding domain (DBD) and a contiguous non-DBD with a characteristic SCOP or Pfam domain combination are observed in most members of TF families. We found that most of the experimentally verified TFs in prokaryotes are detectable by a combination of SCOP or Pfam domains assigned to DBDs and non-DBDs. Based on this finding, we set up rules to detect TFs and classify them into 52 TF families. Application of the rules to 154 entirely sequenced prokaryotic genomes detected >18 000 TFs classified into families, which have been made publicly available from the ‘GTOP_TF’ database. Despite the rough proportionality of the number of TFs per genome with genome size, species with reduced genomes, i.e. obligatory parasites and symbionts, have only a few if any TFs, reflecting a nearly complete loss. Also the number of TFs is significantly lower in archaea than in bacteria. In addition, all but 1 of the 19 TF families present in archaea is present in bacteria, whereas 33 TF families are found exclusively in bacteria. This observation indicates that a number of new TF families have evolved in bacteria, making the transcription regulatory system more divergent in bacteria than in archaea.

Key words: transcription factor; domain organization; DNA binding; prokaryote; comparative genomics

*To whom correspondence should be addressed. Tel. +81-55-981-6859, Fax. +81-55-981-6889, E-mail: knishika{at}genes.nig.ac.jp

Communicated by Osamu Ohara


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