Census of prokaryotic senses.
Census of prokaryotic senses.
复制标题
原核生物感官普查。
DOI：
10.1128/jb.00311-06
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发表时间：
2006
影响因子：
3.2
通讯作者：
Bourret,RobertB
中科院分区：
文献类型：
--
作者：
Bourret,RobertB
The overwhelming majority of life on our planet is microbial, both in terms of phylogenetic diversity (15, 19) and sheer numbers of organisms (25). Virtually every conceivable environmental niche harbors microorganisms capable of growing there. This evolutionary success likely depends in part on signal transduction, the ability to sense changing environmental conditions and then implement appropriate responses. Bacterial, archaeal, and eukaryotic microorganisms utilize two-component regulatory systems for the purpose of signal transduction. In the prototypical case (Fig. 1A), the first component is a sensor kinase, in which detection of environmental stimuli by an input domain is represented by autophosphorylation of a conserved transmitter domain. Phosphoryl groups are then transferred from the sensor kinase to the second component, a response regulator, in which the phosphorylation status of the conserved receiver domain regulates activity of an output domain. In this issue of the Journal of Bacteriology, Michael Galperin describes a census of output domains in response regulators encoded by 200 different prokaryotic species (6). The results give us a much more detailed and comprehensive look at the diversity of responses implemented by two-component regulatory systems than has previously been available. Some history. The existence of two-component regulatory systems was recognized because researchers independently studying a variety of bacterial regulatory networks sequenced the genes they were investigating and deposited the results in appropriate databanks. When a critical mass of relevant sequences was achieved in the mid-1980s, scientists realized that numerous apparently disparate processes were actually different manifestations of the same phenomenon, namely, two-component regulatory systems (12, 18). During the pre-genome sequencing era, our view of the diversity of two-component regulatory systems was strongly biased by the available sample of what people happened to be studying. In 1993, a comprehensive analysis of response regulator sequences contained 79 entries, which could be subdivided into five groups on the basis of their output domains (24). Most (68%) were transcriptional regulators, with 29% of the total in the OmpR class, 23% in the FixJ/NarL class, and 16% in the NtrC class. Response regulators consisting of a receiver domain alone, with no accompanying output domain, comprised a fourth distinct group, with 9% of the total. Finally, the remaining 23% were lumped together in a miscellaneous category that defied any further rational classification. The conclusion, then, was that most response regulators are transcriptional regulators, of which there are three major classes.A postgenomic perspective. Galperin’s analysis (6) is based on more than 4,600 response regulator sequences and is remarkable for both its similarities and differences to the results of smaller surveys. Again, most (66%) response regulator output domains appeared to bind DNA and regulate transcription, and the same three classes predominated—OmpR-like (33%), FixJ/NarL-like (19%), and NtrC-like (9%)—although at somewhat different percentages than indicated by smaller samples. Also as before, a significant fraction (14%) of response regulators contained only a receiver domain. Due to the large sample size, the primary impact of the present study was to reveal the rich diversity among the minority classes. In addition to the three main types of transcriptional regulators, there were response regulators with LytR-like (3%), Fis-like (1%), and AraC-like (1%) DNA-binding output domains. The old “miscellaneous …
