Galperin Michael Y
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
J Bacteriol. 2006 Jun;188(12):4169-82. doi: 10.1128/JB.01887-05.
CheY-like phosphoacceptor (or receiver [REC]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems. In this work, 4,610 response regulators, encoded in complete genomes of 200 bacterial and archaeal species, were identified and classified by their domain architectures. Previously uncharacterized output domains were analyzed and, in some cases, assigned to known domain families. Transcriptional regulators of the OmpR, NarL, and NtrC families were found to comprise almost 60% of all response regulators; transcriptional regulators with other DNA-binding domains (LytTR, AraC, Spo0A, Fis, YcbB, RpoE, and MerR) account for an additional 6%. The remaining one-third is represented by the stand-alone REC domain (approximately 14%) and its combinations with a variety of enzymatic (GGDEF, EAL, HD-GYP, CheB, CheC, PP2C, and HisK), RNA-binding (ANTAR and CsrA), protein- or ligand-binding (PAS, GAF, TPR, CAP_ED, and HPt) domains, or newly described domains of unknown function. The diversity of domain architectures and the abundance of alternative domain combinations suggest that fusions between the REC domain and various output domains is a widespread evolutionary mechanism that allows bacterial cells to regulate transcription, enzyme activity, and/or protein-protein interactions in response to environmental challenges. The complete list of response regulators encoded in each of the 200 analyzed genomes is available online at http://www.ncbi.nlm.nih.gov/Complete_Genomes/RRcensus.html.
类CheY磷酸受体（或接收结构域[REC]）是细菌信号转导系统中多种应答调节蛋白的常见模块。在本研究中，通过结构域结构对200种细菌和古菌完整基因组中编码的4610个应答调节蛋白进行了鉴定和分类。对以前未表征的输出结构域进行了分析，在某些情况下，将其归类到已知的结构域家族。发现OmpR、NarL和NtrC家族的转录调节蛋白几乎占所有应答调节蛋白的60%；具有其他DNA结合结构域（LytTR、AraC、Spo0A、Fis、YcbB、RpoE和MerR）的转录调节蛋白又占6%。其余三分之一由独立的REC结构域（约14%）及其与多种酶结构域（GGDEF、EAL、HD - GYP、CheB、CheC、PP2C和HisK）、RNA结合结构域（ANTAR和CsrA）、蛋白质或配体结合结构域（PAS、GAF、TPR、CAP_ED和HPt）或新描述的未知功能结构域的组合所代表。结构域结构的多样性和替代结构域组合的丰富性表明，REC结构域与各种输出结构域之间的融合是一种广泛存在的进化机制，使细菌细胞能够响应环境挑战来调节转录、酶活性和/或蛋白质 - 蛋白质相互作用。在http://www.ncbi.nlm.nih.gov/Complete_Genomes/RRcensus.html网站上可在线获取这200个分析基因组中每个基因组所编码的应答调节蛋白的完整列表。
