RNase III CLASH in MRSA uncovers sRNA regulatory networks coupling metabolism to toxin expression

• Published in: Nature communications Vol. 13; no. 1; pp. 3560 - 20
• Main Authors: McKellar, Stuart W., Ivanova, Ivayla, Arede, Pedro, Zapf, Rachel L., Mercier, Noémie, Chu, Liang-Cui, Mediati, Daniel G., Pickering, Amy C., Briaud, Paul, Foster, Robert G., Kudla, Grzegorz, Fitzgerald, J. Ross, Caldelari, Isabelle, Carroll, Ronan K., Tree, Jai J., Granneman, Sander
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 22.06.2022; Nature Publishing Group; Nature Portfolio
• Subjects: 101/58; 38; 49/23; 49/39; 49/90; 49/91; 631/326/41/1319; 631/45/500; 631/553/1833; 82/29; 82/81; Baits; Biochemistry, Molecular Biology; Crosslinking; Drug resistance; Environmental conditions; Gene Expression Regulation, Bacterial; Gene regulation; Humanities and Social Sciences; Hybrids; Life Sciences; Membranes; Metabolism; Methicillin; Methicillin-Resistant Staphylococcus aureus - genetics; Methicillin-Resistant Staphylococcus aureus - metabolism; Morbidity; multidisciplinary; Multidrug resistance; Post-transcription; Public health; Ribonuclease III; Ribonuclease III - genetics; Ribonuclease III - metabolism; Ribonucleic acid; RNA; RNA, Bacterial - genetics; RNA, Bacterial - metabolism; RNA, Messenger - genetics; RNA, Messenger - metabolism; RNA, Small Untranslated - genetics; RNA, Small Untranslated - metabolism; Science; Science (multidisciplinary); Staphylococcus aureus; Staphylococcus infections; Toxins; Virulence
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-022-31173-y

Methicillin-resistant Staphylococcus aureus (MRSA) is a bacterial pathogen responsible for significant human morbidity and mortality. Post-transcriptional regulation by small RNAs (sRNAs) has emerged as an important mechanism for controlling virulence. However, the functionality of the majority of sRNAs during infection is unknown. To address this, we performed UV cross-linking, ligation, and sequencing of hybrids (CLASH) in MRSA to identify sRNA-RNA interactions under conditions that mimic the host environment. Using a double-stranded endoribonuclease III as bait, we uncovered hundreds of novel sRNA-RNA pairs. Strikingly, our results suggest that the production of small membrane-permeabilizing toxins is under extensive sRNA-mediated regulation and that their expression is intimately connected to metabolism. Additionally, we also uncover an sRNA sponging interaction between RsaE and RsaI. Taken together, we present a comprehensive analysis of sRNA-target interactions in MRSA and provide details on how these contribute to the control of virulence in response to changes in metabolism. Regulatory small RNA (sRNA) interact with mRNAs to regulate their stability, transcription, and translation via diverse mechanisms. Here, McKellar et al. apply RNase IIICLASH of multi-drug resistant Staphylococcus aureus under different culture conditions to link the network of RNA-RNA interactions to environmental conditions and find that the production of small membrane-permeabilizing toxins is strongly regulated by sRNAs.