CsrA selectively modulates sRNA-mRNA regulator outcomes

Abstract

Post-transcriptional regulation, by small RNAs (sRNAs) as well as the global Carbon Storage Regulator A (CsrA) protein, play critical roles in bacterial metabolic control and stress responses. The CsrA protein affects selective sRNA-mRNA networks, in addition to regulating transcription factors and sigma factors, providing additional avenues of cross talk between other stress-response regulators. Here, we expand the known set of sRNA-CsrA interactions and study their regulatory effects. <i>In vitro</i> binding assays confirm novel CsrA interactions with ten sRNAs, many of which are previously recognized as key regulatory nodes. Of those 10 sRNA, we identify that McaS, FnrS, SgrS, MicL, and Spot42 interact directly with CsrA <i>in vivo</i>. We find that the presence of CsrA impacts the downstream regulation of mRNA targets of the respective sRNA. <i>In vivo</i> evidence supports enhanced CsrA McaS-<i>csgD</i> mRNA repression and showcases CsrA-dependent repression of the <i>fucP</i> mRNA via the Spot42 sRNA. We additionally identify SgrS and FnrS as potential new sRNA sponges of CsrA. Overall, our results further support the expanding impact of the Csr system on cellular physiology via CsrA impact on the regulatory roles of these sRNAs.