The functional small RNA interactome reveals targets for the vancomycin-responsive sRNA RsaOI in vancomycin tolerantStaphylococcus aureus

ABSTRACT RNA-RNA interactome profiling techniques have expanded our understanding of sRNA-mRNA interactions in bacteria. However, determining the function of these interactions for hundreds of sRNA-mRNA pairs is a major challenge. At steady-state, protein and mRNA abundances are often highly correlated and lower than expected protein abundance may indicate translational repression of an mRNA. To specifically identify sRNA-mRNA interactions that regulate mRNA translation, we examined the correlation between gene transcript abundance, ribosome occupancy, and protein levels. We used SOMS to cluster genes with similar transcription and translation patterns and identified a cluster of mRNAs that appeared to be post-transcriptionally repressed. By integrating this clustering analysis with sRNA-mRNA interactome data generated in vancomycin tolerant S. aureus by RNase III-CLASH, we identified sRNAs that may be mediating this translational repression. We have confirmed sRNA-dependant post-transcriptional repression of several mRNAs in this cluster. Two of these interactions are mediated by RsaOI, a sRNA that is highly upregulated by vancomycin treatment. While RsaOI is not essential for vancomycin tolerance, we demonstrate regulation of the phosphocarrier protein HPr and the cell-wall autolysin Atl. These findings suggest that RsaOI may serve as a regulator of carbon metabolism and cell wall turnover during cell wall stress exerted by vancomycin.