A small RNA guides a post-transcriptional regulatory protein to its target

RNA-binding proteins are central to post-transcriptional regulation and are generally thought to recognize their target RNAs through direct binding. Here, we uncover a previously unrecognized mechanism in which a small RNA (sRNA) guides a protein regulator to specific target mRNAs, enabling programmable post-transcriptional control. By mapping in pathogenic Escherichia coli the RNA interactome of CsrA, a global post-transcriptional regulator, we identify [~]800 ternary complexes in which CsrA simultaneously binds an sRNA and an mRNA. Focusing on one class of these complexes, we show that PasE, a newly discovered sRNA, directs CsrA to virulence-associated mRNAs that are otherwise not targeted by CsrA, resulting in their repression. Altering the PasE seed sequence redirects CsrA to selected mRNAs, establishing a modular RNA-guided platform for gene regulation. Together, our findings reveal a new and likely widespread mechanism of bacterial post-transcriptional regulation and provide a framework for a new type of RNA-based synthetic regulation. HighlightsO_LIThe PasE sRNA can direct the CsrA post-transcriptional regulator to target mRNAs that are otherwise not targeted by CsrA. C_LIO_LIThe CsrA-PasE complex controls the virulence of enteropathogenic E. coli. C_LIO_LIThe PasE seed can be synthetically reprogrammed to direct CsrA to new target mRNAs. C_LIO_LIHundreds of additional sRNA-CsrA-mRNA regulatory complexes are formed in pathogenic E. coli. C_LI