A conserved small RNA in the RpoS regulon

E.大肠杆菌是RNA聚合酶的σS（RpoS）亚基，是交替σ因子调节子与环境诱导的小的非编码RNA（sRNA）调控相互连接的主要例子。已经确定的是，在各种生长和应激条件下，rpoS mRNA的翻译受到Hfq依赖性sRNA的调节。然而，σS是否也通过诱导调节性sRNA在细胞中传递应激信号尚不清楚。继我们以前发现由σE或σN控制的sRNA基因之后，我们现在已经鉴定了第一个可能受σS调控的sRNA，即SdsRNA。SdsRNA是一种Hfq相关的sRNA，在稳定期异常丰富，并且似乎受到相反编码的SraC sRNA的反义调控。高度的基因组保守性和以前的鸟枪测序的频繁恢复将SdsRNA鉴定为肠细菌“核心”小RNA，但其功能仍然难以捉摸。本项目旨在深入了解SdsR参与σ S介导的E.大肠杆菌和沙门氏菌。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σS网络中的功能。还将讨论SraC对SdsR的推定反义控制的影响，这可能在Hfq依赖性sRNA的作用中建立新的范例。此外，我们将利用SdsR sRNA的丰度，通过深度测序建立一种体内RNA结构探测的新方法，并通过滴定sRNA伴侣Hfq的活性来解决这种sRNA是否可以间接充当全局。对肠细菌核心sRNA（如SdsR）的研究特别有趣，因为它可能会识别超出单个细菌物种的功能和调控原则。

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.