TI Food and Nutrition, P,O,Box 557, 6700AN Wageningen, The Netherlands.
BMC Genomics. 2011 Aug 1;12:385. doi: 10.1186/1471-2164-12-385.
Sigma-54 is a central regulator in many pathogenic bacteria and has been linked to a multitude of cellular processes like nitrogen assimilation and important functional traits such as motility, virulence, and biofilm formation. Until now it has remained obscure whether these phenomena and the control by Sigma-54 share an underlying theme.
We have uncovered the commonality by performing a range of comparative genome analyses. A) The presence of Sigma-54 and its associated activators was determined for all sequenced prokaryotes. We observed a phylum-dependent distribution that is suggestive of an evolutionary relationship between Sigma-54 and lipopolysaccharide and flagellar biosynthesis. B) All Sigma-54 activators were identified and annotated. The relation with phosphotransfer-mediated signaling (TCS and PTS) and the transport and assimilation of carboxylates and nitrogen containing metabolites was substantiated. C) The function annotations, that were represented within the genomic context of all genes encoding Sigma-54, its activators and its promoters, were analyzed for intra-phylum representation and inter-phylum conservation. Promoters were localized using a straightforward scoring strategy that was formulated to identify similar motifs. We found clear highly-represented and conserved genetic associations with genes that concern the transport and biosynthesis of the metabolic intermediates of exopolysaccharides, flagella, lipids, lipopolysaccharides, lipoproteins and peptidoglycan.
Our analyses directly implicate Sigma-54 as a central player in the control over the processes that involve the physical interaction of an organism with its environment like in the colonization of a host (virulence) or the formation of biofilm.
Sigma-54 是许多病原菌中的中央调控因子，与许多细胞过程有关，如氮同化，以及重要的功能特征，如运动性、毒力和生物膜形成。直到现在，Sigma-54 控制的这些现象和功能是否具有共同的主题仍然不清楚。
我们通过一系列比较基因组分析揭示了它们的共性。A）确定了所有已测序原核生物中 Sigma-54 及其相关激活物的存在。我们观察到一种依赖于门的分布，这表明 Sigma-54 与脂多糖和鞭毛生物合成之间存在进化关系。B）鉴定并注释了所有 Sigma-54 激活物。证实了与磷酸转移介导的信号转导（TCS 和 PTS）以及羧酸和含氮代谢物的运输和同化的关系。C）分析了在编码 Sigma-54、其激活物及其启动子的所有基因的基因组背景中表示的功能注释，以分析门内代表性和门间保守性。使用一种简单的评分策略来定位启动子，该策略旨在识别类似的模体。我们发现与涉及代谢中间产物的运输和生物合成的基因之间存在明显的高度代表性和保守的遗传关联，这些代谢中间产物涉及外多糖、鞭毛、脂质、脂多糖、脂蛋白和肽聚糖的生物合成。
我们的分析直接表明 Sigma-54 是控制涉及生物体与其环境物理相互作用的过程的核心参与者，例如在宿主定植（毒力）或生物膜形成过程中。
