MS2-affinity purification coupled with RNA sequencing (MAPS) reveals S. aureus RsaC sRNA targetome

The human opportunistic pathogen Staphylococcus aureus produces numerous small regulatory RNAs (sRNAs) for which functions are still poorly understood. Here, we focused on an atypical and large sRNA called RsaC. Its length varies between different isolates due to the presence of repeated sequences at the 5’ end while its 3’ part is structurally independent and highly conserved. Using MS2-affinity purification coupled with RNA sequencing (MAPS) and quantitative differential proteomics, we identified sodA mRNA as a main target of RsaC sRNA. SodA is a Mn-dependent superoxide dismutase involved in oxidative stress response. We demonstrated that in presence of RsaC, S. aureus cells were less resistant to oxidative stress, in relation with lower activity of SodA enzyme. Remarkably, rsaC gene is co-transcribed with the major manganese ABC transporter MntABC and, consequently, RsaC is mainly produced in response to Mn starvation. This 3’UTR-derived sRNA is released from mntABC-RsaC precursor after cleavage by RNase III. By blocking the Mn-containing enzyme SodA synthesis, RsaC favors oxidative stress response mediated by SodM, an alternative SOD enzyme using either Mn or Fe as co-factor. Thus, RsaC may balance two interconnected defensive responses (i.e. against oxidative stress and manganese starvation) when S. aureus faces host immune cells. Affinity purification of in vivo regulatory complexes coupled with high throughput RNA sequencing methodology or MAPS, standing for “MS2 affinity purification coupled with RNA"