A small regulatory RNA alters Staphylococcus aureus virulence by titrating RNAIII activity

Abstract

Staphylococcus aureus is an opportunistic human and animal pathogen with an arsenal of virulence factors that are tightly regulated during bacterial infection. The latter is achieved through a sophisticated network of regulatory proteins and regulatory RNAs. Here, we describe the involvement of a novel prophage-carried small regulatory S. aureus RNA, SprY, in the control of virulence genes. An MS2-affinity purification assay reveals that SprY forms a complex in vivo with RNAIII, a major regulator of S. aureus virulence genes. SprY binds to the 13th stem-loop of RNAIII, a key functional region involved in the repression of multiple mRNA targets. mRNAs encoding the repressor of toxins Rot and the extracellular complement binding protein Ecb are among the targets whose expression is increased by SprY binding to RNAIII. Moreover, SprY decreases S. aureus hemolytic activity and virulence. Our results indicate that SprY titrates RNAIII activity by targeting a specific stem loop. Thus, we demonstrate that a prophage-encoded sRNA reduces the pathogenicity of S. aureus through RNA sponge activity.

RNase III-mediated processing of atrans-acting bacterial sRNA and itscis-encoded antagonist

“…The potential for independent regulation of CJnc180 and CJnc190 makes an antagonistic relationship attractive. The mechanism by which CJnc180 affects CJnc190 appears to be dependent on the stoichiometry of the two sRNAs, as has been previously proposed (Denham, 2020) and recently demonstrated for the RNAIII antagonist SprY (Le Huyen et al, 2021). A similar variation in sponge and sRNA stoichiometry has been reported for the ChiX sRNA and its decoy, the chbBC intergenic region (Figueroa-Bossi et al, 2009;Plumbridge et al, 2014).…”

“…Such RNA antagonists can be derived from diverse cellular transcripts, including mRNAs (UTRs and coding regions) (Adams and Storz, 2020;Adams et al, 2021;Figueroa-Bossi et al, 2009;Miyakoshi et al, 2015b) and tRNAs (Lalaouna et al, 2015), or can be stand-alone sRNAs encoded in the core genome or in prophages (Bronesky et al, 2019;Melamed et al, 2020;Tree et al, 2014). Unbiased global biochemical and genetic screens for sRNA expression and regulation have recently recovered several characterized examples of trans-acting sRNA antagonists in Gram-positive and Gram-negative bacteria (Bronesky et al, 2019;Chen et al, 2021;Durand et al, 2021;Melamed et al, 2020), including those affecting infection phenotypes via antagonism of central sRNA regulators of virulence (Le Huyen et al, 2021). Despite reports of extensive antisense transcription in diverse bacteria and the demonstrated role of asRNAs in control of mRNA translation and stability (Thomason and Storz, 2010), less is known about whether RNAs encoded in cis to other sRNAs can act also as antagonists or how they might affect the biogenesis, stability, or function of their antisense sRNA partners.…”

RNase III-mediated processing of a trans-acting bacterial sRNA and its cis-encoded antagonist

“…The potential for independent regulation of CJnc180 and CJnc190 makes an antagonistic relationship attractive. The mechanism by which CJnc180 affects CJnc190 appears to be dependent on the stoichiometry of the two sRNAs, as has been previously proposed (Denham, 2020) and recently demonstrated for the RNAIII antagonist SprY (Le Huyen et al, 2021). A similar variation in sponge and sRNA stoichiometry has been reported for the ChiX sRNA and its decoy, the chbBC intergenic region (Figueroa-Bossi et al, 2009;Plumbridge et al, 2014).…”

“…Such RNA antagonists can be derived from diverse cellular transcripts, including mRNAs (UTRs and coding regions) ( Adams and Storz, 2020 ; Adams et al, 2021 ; Figueroa-Bossi et al, 2009 ; Miyakoshi et al, 2015b ) and tRNAs ( Lalaouna et al, 2015 ), or can be stand-alone sRNAs encoded in the core genome or in prophages ( Bronesky et al, 2019 ; Melamed et al, 2020 ; Tree et al, 2014 ). Unbiased global biochemical and genetic screens for sRNA expression and regulation have recently recovered several characterized examples of trans -acting sRNA antagonists in Gram-positive and Gram-negative bacteria ( Bronesky et al, 2019 ; Chen et al, 2021 ; Durand et al, 2021 ; Melamed et al, 2020 ), including those affecting infection phenotypes via antagonism of central sRNA regulators of virulence ( Le Huyen et al, 2021 ). Despite reports of extensive antisense transcription in diverse bacteria and the demonstrated role of cis -encoded antisense RNAs (asRNAs) in control of mRNA translation and stability ( Thomason and Storz, 2010 ), less is known about whether RNAs encoded in cis to other sRNAs can act also as antagonists and how they might affect the biogenesis, stability, or function of their antisense sRNA partners.…”

MicroRNAs Encoded by Virus and Small RNAs Encoded by Bacteria Associated with Oncogenic Processes

“…Another way to use this information is to employ small RNAs that regulate genes that favor pathogens in invasion and resistance (Virulence), for example, this can be observed in the work of [113]. This work describes the participation of a S. aureus smallRNA, was used to control virulence genes, and in this work it is shown that an RNA encoded by prophages reduces the pathogenicity of S. aureus through the activity of an RNA sponge [113]. These examples show us that the study and utility of the identification and characterization of sRNAs is expanding and will probably be useful at some point in cancer counting therapies.…”