Systematic deletion of Salmonella small RNA genes identifies CyaR, a conserved CRP-dependent riboregulator of OmpX synthesis

Post-transcriptional repression of porin synthesis has emerged as a major function of Hfq-dependent, small non-coding RNAs (sRNAs). Many enterobacteria express OmpX-like porins, a family of outer membrane proteins whose physiological roles and structural properties have been studied intensively. While regulatory sRNAs have been identified for most major and many minor porins of Salmonella and Escherichia coli, a post-transcriptional regulator of OmpX levels has never been found. Here, we have taken a 'reverse target search' approach by systematic inactivation of Salmonella sRNA genes, and screening 35 sRNA deletion strains for effects on OmpX synthesis. We have identified the Hfq-dependent CyaR (formerly RyeE) sRNA as an ompX repressor. Global transcriptomic profiling following induction of CyaR expression suggests that ompX mRNA is the primary target of this sRNA under standard growth conditions. The results of phylogenetic and mutational analyses suggest that a conserved RNA hairpin of CyaR, featuring a C-rich apical loop, acts to sequester the Shine-Dalgarno sequence of ompX mRNA and to inhibit translational initiation. We have also discovered that cyaR expression is tightly controlled by the cyclic AMP receptor protein, CRP. This represents a new link between porin repression and nutrient availability that is likely to be widely conserved among enterobacteria.