Mechanism of CsrA-Mediated Global Control

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DESCRIPTION (provided by applicant): Insight into posttranscriptional regulatory mechanisms and global regulatory circuitry will be sought through the study of the carbon storage regulatory system (Csr) of Escherichia coli. Csr includes: CsrA, an RNA binding protein that regulates translation and/or the stability of a large number of target mRNAs; CsrB and CsrC, noncoding sRNAs that use molecular mimicry to sequester and antagonize CsrA; BarA-UvrY, a two- component signal transduction system that activates transcription of csrB and csrC; and CsrD, a protein that specifically targets CsrB and CsrC RNAs for degradation by RNase E. In E. coli, CsrA regulates metabolism, motility, and multicellular behavior on a broad scale. Our recently published RNA-seq studies identified 712 different RNAs that bind to CsrA, including mRNAs for >40 regulatory factors. Our published and preliminary findings further reveal that Csr is reciprocally linked to a number of other global regulatory circuits, implying tht Csr affects bacterial physiology on a global scale. We hypothesize that this complex circuitry allows Csr to reinforce the transcriptional effects of stress response systems at a posttranscriptional level. The specific aims of this proposal are: 1) Identify reciprocal regulatoy interactions of Csr with other global regulatory systems and elucidate novel CsrA-mediated regulatory mechanisms, which have come to light from the results of genetic screens and RNA-seq studies. We will focus on CsrA-mediated regulation of two stress-response sigma factors (¿S and ¿E), and two ribonucleases that participate in bulk mRNA turnover (RNase E and PNPase). 2) Define the CsrB/C RNA turnover pathway, focusing on the mechanism by which CsrD promotes RNase E-dependent cleavage. Of particular interest, our preliminary results indicate that CsrD specifically couples CsrB synthesis with targeted turnover by RNase E, suggesting that the influence of RNA synthesis on RNA decay may be an underappreciated feature of RNA biology. 3) Determine the molecular mechanisms by which DeaD, a DEAD-box RNA helicase, positively regulates CsrB/C RNA levels. Our preliminary results indicate that DeaD directly affects expression of the response regulator UvrY, which is required for csrB/C transcription. Our results further suggest that DeaD unwinds a secondary structure that inhibits translation of uvrY. Thus, these studies will determine the mechanism of an important regulatory influence on the Csr system and provide fundamental insight into the role of DeaD helicase in translation. The long-range objectives of these studies are to fully understand the regulatory components, genetic circuitry, molecular mechanisms, and biological functions of the Csr system, thereby defining basic principles that underpin a regulatory super-network. Highly conserved regulatory systems homologous to Csr control the expression of virulence factors and/or transmission traits in numerous human, animal, and plant pathogens, responsible for diverse infections. Thus, these studies will provide fundamental understanding of the regulation of bacterial metabolism and pathogenesis and may suggest novel therapeutic and/or vaccine strategies.