Insights into the regulation of small RNA expression: SarA represses the expression of two sRNAs in Staphylococcus aureus

Abstract : The opportunistic pathogen Staphylococcus aureus expresses transcription factors (TFs) and regulatory small RNAs (sRNAs) which are essential for bacterial adaptation and infectivity. Until recently, the study of S. aureus sRNA gene expression regulation was under investigated, but it is now an expanding field. Here we address the regulation of Srn 3610 SprC sRNA, an attenuator of S. aureus virulence. We demonstrate that SarA TF represses srn 3610 sprC transcription. DNase I footprinting and deletion analyses show that the SarA binding site on srn 3610 sprC belongs to an essential 22 bpDNA region. Comparative analysis also revealed another possible site, this time in the srn 9340 promoter. SarA specifically binds these two sRNA promoters with high affinity in vitro and also repressestheir transcription in vivo. Chromatin immunoprecipitation (ChIP) assays confirmed SarA attachment to both promoters. ChIP and electrophoretic mobility shift assays targeting sigmaA RNA polymerase subunitor using bacterial RNA polymerase holoenzyme suggestedthat SarA and the sigmaA bind srn 3610 sprC and srn 9340 promoters in a mutually exclusive way. Beyond the mechanistic study of SarA repression of these two sRNAs, this work also suggests that some S. aureus sRNAs belong to the same regulon and act jointly in responding to environmental changes.