@article{35a92ce0ac18483190d473dee062b9ac,
title = "RNase III CLASH in MRSA uncovers sRNA regulatory networks coupling metabolism to toxin expression",
abstract = "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.",
keywords = "Gene Expression Regulation, Bacterial, Methicillin-Resistant Staphylococcus aureus/genetics, RNA, Bacterial/genetics, RNA, Messenger/genetics, RNA, Small Untranslated/genetics, Ribonuclease III/genetics",
author = "McKellar, \{Stuart W\} and Ivayla Ivanova and Pedro Arede and Zapf, \{Rachel L\} and No{\'e}mie Mercier and Liang-Cui Chu and Mediati, \{Daniel G\} and Pickering, \{Amy C\} and Paul Briaud and Robert Foster and Grzegorz Kudla and \{Ross Fitzgerald\}, J and Isabelle Caldelari and Carroll, \{Ronan K\} and Tree, \{Jai J\} and Sander Granneman",
note = "Funding Information: We are grateful to Wei Gao, Tim Stinear and Benjamin Howden for providing the JKD6009 RNase III-HTF strain, Philippe Bouloc for the RsaE over-expression plasmid and Tracy Palmer for the polyclonal EsxA antibody. We would like to thank Pascale Romby and Emma Denham for fruitful discussions and helpful suggestions. We also thank Julia Wong for help with the FACS analyses, Lucas Herrgott for producing recombinant RNase III and Jimi-Carlo Wills and Alexander von Kriegsheim from the proteomics facility at the Institute of Genetics and Molecular Medicine (IGMM) at the University of Edinburgh for performing the mass-spectrometry analyses. Finally, we would like to thank the members of the Granneman lab for critically reading the manuscript. This work was supported by a Medical Research Council Non-Clinical Senior Research Fellowship (MR/R008205/1 to S.G), a Wellcome Trust grant (109093/Z/15/A to S.W.M), a Wellcome Trust Senior Research Fellowship (207507 to G.K), the labEx NetRNA framework (ANR-10-LABX-0036) and the French investment for the future framework (ANR-17-EURE-0023). J.J.T and D.G.M were supported by a grant from the National Health and Medical Research Council Australia (GNT1139313). J.R.F was funded by institute strategic grant funding ISP2: BBS/E/D/20002173 and BBS/E/D/20002174 from the Biotechnology and Biological Sciences Research Council (United Kingdom), SHIELD grant MR/N02995X/1 from the Medical Research Council (United Kingdom) and a Wellcome Trust collaborative award 201531/Z/16/Z. R.K.C and R.L.Z were supported in part by grant AI128376 from the US National Institute of Allergy and Infectious Diseases (to R.K.C.). The proteomics facility at the IGMM is supported by a Wellcome Trust Multiuser Equipment grant (208402/Z/17/Z to Alexander von Kriegsheim). For the purpose of open access, the corresponding author has applied a creative commons attribution (CC BY) licence to any author accepted manuscript version arising. Publisher Copyright: {\textcopyright} 2022, The Author(s).",
year = "2022",
month = jun,
day = "22",
doi = "10.1038/s41467-022-31173-y",
language = "English",
volume = "13",
pages = "1--20",
journal = "Nature Communications",
issn = "2041-1723",
publisher = "Nature Publishing Group",
number = "1",
}