The antivirulent Staphylococcal sRNA SprC regulates CzrB efflux pump to adapt its response to Zinc toxicity

Bacterial regulatory RNAs (sRNAs) are important players to control gene expression. In S. aureus, SprC is an antivirulent trans-acting sRNA known to base-pair with the major autolysin atl mRNA, preventing its translation. Using MS2-affinity purification coupled with RNA sequencing (MAPS), we looked for its sRNA-RNA interactome and identified fourteen novel mRNA targets. In vitro biochemical investigations revealed that SprC binds two of them, czrB and deoD, and uses a single accessible region to regulate its targets, including Atl translation. Unlike Atl regulation, the characterization of the SprC-czrB interaction pinpointed a destabilization of czrAB co-transcript,leading to a decrease of the mRNA level that impaired CzrB Zinc efflux pump expression. On a physiological stand-point, we showed that SprC expression is detrimental to combat against Zinc toxicity. In addition, phagocyctosis assays revealed a significant, but moderate, increase of czrB mRNA level in a sprC-deleted mutant, indicating a functional link between SprC and czrB upon internalization in macrophages, and suggesting a role in resistance to both oxidative and Zinc burst. Altogether, our data uncover a novel pathway in which SprC is implicated, highlighting the multiple strategies employed by S. aureus to balance virulence using an RNA regulator.