A conserved small RNA in the RpoS regulon

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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.