RsaC sRNA modulates the oxidative stress response of Staphylococcus aureus during manganese starvation

Abstract

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, sodA mRNA was identified as a primary target of RsaC sRNA. SodA is a Mn-dependent superoxide dismutase involved in oxidative stress response. 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. The mature and stable form of RsaC inhibits the synthesis of the Mn-containing enzyme SodA synthesis and favors the oxidative stress response mediated by SodM, an alternative SOD enzyme using either Mn or Fe as co-factor. In addition, other putative targets of RsaC are involved in oxidative stress (ROS and NOS) and metal homeostasis (Fe and Zn). Consequently, RsaC may balance two interconnected defensive responses, i.e. oxidative stress and metal-dependent nutritional immunity.

Grad‐seq in a Gram‐positive bacterium reveals exonucleolytic sRNA activation in competence control

“…Several additional ncRNAs were included for comparison or controls: the functionally related csRNA1, which ended up in cluster 2, probably because its peak in fractions 3–4 was weaker than for the other csRNAs (Fig EV4G); riboswitch‐derived F20 from cluster 2; F41 sRNA from cluster 3, which also clearly peaks in the LMW fractions; and tmRNA, which is known to bind the SmpB protein (Fig B). For unclear reasons, attempts to use the MS2 aptamer, which successfully captured RBPs and RNA–RNA interactions from Salmonella , E. coli, and Staphylococcus aureus lysates (Said et al , ; Corcoran et al , ; Lalaouna et al , , ; Smirnov et al , ; Tomasini et al , ), failed. While we did recover the MS2‐tagged RNAs after incubation with lysates, no protein co‐purified at all.…”

The power of cooperation: Experimental and computational approaches in the functional characterization of bacterial sRNAs

“…In the following, we exemplify how the results of MAPS, RIL‐seq, and CopraRNA for the E. coli sRNA RyhB, and MAPS and CopraRNA for the S. aureus sRNA RsaA can be integrated, to test this assumption. Of note, S. aureus is the only Gram‐positive bacterium for which the full targetome of a specific sRNA was defined (Bronesky et al, ; Lalaouna et al, ; Rochat et al, ; Tomasini et al, ).…”

“…These sRNAs are very heterogeneous in length, sequence composition, and secondary structure. They can originate from their own genes or may be processed from the 5′ or 3′ UTRs of protein‐coding genes (Chao et al, ; Lalaouna et al, ). Some sRNAs, such as ArcZ in Escherichia coli (Mandin & Gottesman, ) or RprA in Salmonella enterica (Papenfort, Espinosa, Casadesus, & Vogel, ) are even further processed by RNase E, which resulted in different sRNA fragments.…”

“…These sRNAs are very heterogeneous in length, sequence composition, and secondary structure. They can originate from their own genes or may be processed from the 5′ or 3′ UTRs of protein-coding genes (Chao et al, 2017;Lalaouna et al, 2019).…”

“…Of note, S. aureus is the only Gram-positive bacterium for which the full targetome of a specific sRNA was defined (Bronesky et al, 2019;Lalaouna et al, 2019;Rochat et al, 2018;Tomasini et al, 2017).…”