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

• DOI: 10.1093/dnares/dsi016
• Publication Date: 2007-02-23T01:07:21Z
• Authors: Y. Minezaki; K. Homma; K. Nishikawa
• Keywords: Transcription

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 contiguous non-DBD with characteristic SCOP or Pfam combination are observed most members TF families. We found that experimentally verified prokaryotes detectable by domains assigned DBDs non-DBDs. Based on this finding, we set up rules detect classify them into 52 Application 154 entirely sequenced prokaryotic genomes detected >18 000 classified families, which have been made publicly available 'GTOP_TF' database. Despite rough proportionality number per size, species reduced genomes, i.e. obligatory parasites symbionts, only few if any TFs, reflecting nearly complete loss. Also significantly lower archaea than bacteria. In addition, but 1 19 families present bacteria, whereas 33 exclusively This observation indicates new evolved making regulatory system more divergent bacteria archaea.