A conserved small RNA in the RpoS regulon

大肠杆菌中一般应激反应的主要调节因子是核糖核酸聚合酶的σS(Rpos)亚单位，它是另一种西格玛因子调节子相互连接和环境诱导的小非编码RNA(SRNA)调控的一个很好的例子。已经证实，在各种生长和胁迫条件下，rpos mRNA的翻译受到依赖于Hfq的sRNAs的调控。然而，σS是否也通过调节sRNA的诱导在细胞中传递应激信号还不清楚。继我们之前发现的受替代Sigma因子σE或σN控制的sRNA基因之后，我们现在发现了第一个可能受σS调控的sRNA。sdsr是一种与hfq相关的sRNA，在固定相中异常丰富，似乎受到相反编码的srac sRNA的反义调控。基因组的高度保守性和以前的鸟枪法测序证明SDSR是肠道细菌的一种“核心”小RNA，然而它的功能仍然难以捉摸。本项目旨在深入了解SDSR参与σS在大肠杆菌和沙门氏菌中的应激反应和调控的体内靶点和分子机制。我们将使用各种实验方法来确定SDSR表达和基因调控相关的生物学条件，目的是了解SDSR在大型σS网络中的功能。还将讨论srac对SDSR进行反义调控的作用，这可能会在依赖Hfq的sRNA的作用中建立一个新的范式。此外，我们将利用SDSR sRNA的丰度来建立一种通过深度测序来探测体内RNA结构的新方法，并通过滴定sRNA伴侣Hfq的活性来解决该sRNA是否可以间接起全局作用的问题。对SDSR等肠道细菌核心sRNA的研究特别有趣，因为它可能识别超出单个细菌物种的功能和调节原则。

The master regulator of the general stress response in E. coli, the σS (RpoS) subunit of RNA polymerase, is a prime example of the interconnection of alternative sigma factor regulons and the regulation by environmentally induced small noncoding RNAs (sRNAs). It has been well-established that the translation of rpoS mRNA is modulated by Hfq-dependent sRNAs under a variety of growth and stress conditions. However, whether σS also relays stress signals in the cell via the induction of regulatory sRNAs has been unknown. Following our previous discoveries of sRNA genes controlled by the alternative sigma factors, σE or σN, we have now identified SdsR, the first sRNA that might regulated by σS. SdsR is an Hfq-associated sRNA, exceptionally abundant in stationary phase, and seems to be subject to antisense regulation by the oppositely encoded SraC sRNA. A high degree of genomic conservation and its frequent recovery by previous shotgun sequencing identified SdsR as an enterobacterial “core” small RNA, yet its function has remained elusive. This project aims to achieve a thorough understanding of the in vivo targets and molecular mechanisms by which SdsR participates in σS-mediated stress responses and regulation in E. coli and Salmonella. We will use a variety of experimental approaches to determine biological conditions under which SdsR expression and gene regulation is relevant, with the goal of understanding SdsR functions in the large σS network. The effects of putative antisense control of SdsR by SraC will also be addressed, which could establish a new paradigm in the action of Hfq-dependent sRNAs. In addition, we will utilize the abundance of SdsR sRNA to establish a new approach for in vivo RNA structure probing by deep sequencing, and address whether this sRNA can indirectly act as a global by titrating the activity of the sRNA chaperon, Hfq. The study of the enterobacterial core sRNAs such as SdsR is particularly interesting as it might identify functions and regulatory principles that extend beyond individual bacterial species.