Genome-wide survey of transcription factors in prokaryotes reveals many bacteria-specific families not found in archaea.
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.
Minezaki
Yoshiaki
Y
Laboratory of Gene-Product Informatics, Center for Information Biology-DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems, Yata, Mishima, Shizuoka, Japan.
Homma
Keiichi
K
Nishikawa
Ken
K
D000465:Algorithms; D019843:Archaeal Proteins / Q000235:genetics / Q000378:metabolism*; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D017434:Protein Structure, Tertiary; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*
D019843:Archaeal Proteins; D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D014157:Transcription Factors