Ravi Janani, Anantharaman Vivek, Aravind L, Gennaro Maria Laura
Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, 07103, USA.
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20892, USA.
Antonie Van Leeuwenhoek. 2018 May;111(5):753-760. doi: 10.1007/s10482-018-1053-5. Epub 2018 Feb 27.
The phage shock protein (Psp) stress-response system protects bacteria from envelope stress through a cascade of interactions with other proteins and membrane lipids to stabilize the cell membrane. A key component of this multi-gene system is PspA, an effector protein that is found in diverse bacterial phyla, archaea, cyanobacteria, and chloroplasts. Other members of the Psp system include the cognate partners of PspA that are part of known operons: pspF||pspABC in Proteobacteria, liaIHGFSR in Firmicutes, and clgRpspAMN in Actinobacteria. Despite the functional significance of the Psp system, the conservation of PspA and other Psp functions, as well as the various genomic contexts of PspA, remain poorly characterized in Actinobacteria. Here we utilize a computational evolutionary approach to systematically identify the variations of the Psp system in ~450 completed actinobacterial genomes. We first determined the homologs of PspA and its cognate partners (as reported in Escherichia coli, Bacillus subtilis, and Mycobacterium tuberculosis) across Actinobacteria. This survey revealed that PspA and most of its functional partners are prevalent in Actinobacteria. We then found that PspA occurs in four predominant genomic contexts within Actinobacteria, the primary context being the clgRpspAM system previously identified in Mycobacteria. We also constructed a phylogenetic tree of PspA homologs (including paralogs) to trace the conservation and evolution of PspA across Actinobacteria. The genomic context revealed that PspA shows changes in its gene-neighborhood. The presence of multiple PspA contexts or of other known Psp members in genomic neighborhoods that do not carry pspA suggests yet undiscovered functional implications in envelope stress response mechanisms.
噬菌体休克蛋白（Psp）应激反应系统通过与其他蛋白质和膜脂的一系列相互作用来保护细菌免受包膜应激，从而稳定细胞膜。这个多基因系统的一个关键组成部分是PspA，它是一种效应蛋白，存在于多种细菌门类、古细菌、蓝细菌和叶绿体中。Psp系统的其他成员包括作为已知操纵子一部分的PspA的同源伴侣：变形菌门中的pspF||pspABC、厚壁菌门中的liaIHGFSR以及放线菌门中的clgRpspAMN。尽管Psp系统具有重要的功能意义，但在放线菌中，PspA和其他Psp功能的保守性以及PspA的各种基因组背景仍未得到充分表征。在这里，我们利用计算进化方法系统地鉴定了约450个已完成测序的放线菌基因组中Psp系统的变异情况。我们首先确定了放线菌中PspA及其同源伴侣（如在大肠杆菌、枯草芽孢杆菌和结核分枝杆菌中报道的那样）的同源物。这项调查表明，PspA及其大多数功能伴侣在放线菌中普遍存在。然后我们发现，PspA在放线菌中存在于四种主要的基因组背景中，主要背景是先前在分枝杆菌中鉴定出的clgRpspAM系统。我们还构建了PspA同源物（包括旁系同源物）的系统发育树，以追踪PspA在放线菌中的保守性和进化情况。基因组背景显示，PspA在其基因邻域中存在变化。在不携带pspA的基因组邻域中存在多个PspA背景或其他已知的Psp成员，这表明在包膜应激反应机制中可能存在尚未发现的功能含义。
