Genome-wide survey of transcription factors in prokaryotes reveals many bacteria-specific families not found in Archaea
Genome-wide survey of transcription factors in prokaryotes reveals many bacteria-specific families not found in Archaea
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DOI：
10.1093/dnares/dsi016
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发表时间：
2005-10-31
期刊：
影响因子：
4.1
通讯作者：
Nishikawa, Ken
中科院分区：
文献类型：
--
作者：
Minezaki, Yoshiaki;Homma, Keiichi;Nishikawa, Ken
从基因组序列数据中分配所有转录因子（TF）并不是一项简单的任务，因为不同物种之间的TF差异很大。在TF家族的大多数成员中观察到DNA结合结构域（DBD）和具有特征性SCOP或Pfam结构域组合的连续非DBD。我们发现，大多数实验验证的TF在原核生物中是可检测的SCOP或Pfam域分配给DBDs和非DBDs的组合。基于这一发现，我们建立了规则来检测TF，并将其分为52个TF家族。应用该规则对154个完全测序的原核生物基因组检测到> 18 000个TF，这些TF被分类到家族中，这些TF已经从'GTOP_TF'数据库中公开提供。尽管每个基因组的TF数量与基因组大小大致成比例，但基因组减少的物种，即专性寄生虫和共生体，只有很少的TF，如果有的话，反映了几乎完全的损失。此外，TF的数量在古细菌中显著低于细菌。此外，除了我的19个TF家族存在于古细菌中存在于细菌中，而33 TF家族被发现专门在细菌中。这一观察结果表明，一些新的TF家族已经在细菌中进化，使得细菌中的转录调控系统比古细菌中的更加多样化。
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 I 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.