ArticleNature communications2022
RNase III-CLASH of multi-drug resistant Staphylococcus aureus reveals a regulatory mRNA 3'UTR required for intermediate vancomycin resistance.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 43 citations in OpenAlex.
- A Zur-dependent regulatory RNA involved in maintaining zinc homeostasis in Staphylococcus aureus.Nucleic acids research · 2026Article
- Bacterial small regulatory RNAs.Nature reviews. Microbiology · 2026Review
- From environmental signals to adaptive phenotypes: signal-responsive regulation and network logic of bacterial small RNAs.FEMS microbiology reviews · 2026Review
- RefSeq-corrected transcriptomic and RNA-interaction integration maps medium-associated vancomycin response rewiring inFrontiers in microbiology · 2026Article
- An RNA sponge directs the transition from feast to famine in Caulobacter crescentus.Nature communications · 2025Article
- The type 6 secretion system immunity protein RhsFI has been repurposed for small RNA regulation in pathogenic Escherichia coli.Nucleic acids research · 2025Article
- Counteracting methicillin resistant Staphylococcus aureus through novel Citral-Azithromycin combination.Scientific reports · 2025Article
- Exploring the interactome of the Staphylococcus aureus sRNA Srn_9342 identified a complex formation with RNAIII leading to the modulation of δ-hemolysin expression.BMC microbiology · 2025Article
- What makes a small RNA work?Nucleic acids research · 2025Review
- Temperature-dependent regulation of bacterial cell division hydrolases by the coordinated action of a regulatory RNA and the ClpXP protease.Cell surface (Amsterdam, Netherlands) · 2025Article
- GNNs and ensemble models enhance the prediction of new sRNA-mRNA interactions in unseen conditions.BMC bioinformatics · 2025Article
- BacTermFinder: a comprehensive and general bacterial terminator finder using a CNN ensemble.NAR genomics and bioinformatics · 2025Article
- Review
- The antivirulent Staphylococcal sRNA SprC regulates CzrB efflux pump to adapt its response to zinc toxicity.RNA (New York, N.Y.) · 2024Article
- Cooperation of regulatory RNA and the RNA degradosome in transcript surveillance.Nucleic acids research · 2024Article
- The Impact of the Major Endoribonucleases RNase E and RNase III and of the sRNA StsR on Photosynthesis Gene Expression inInternational journal of molecular sciences · 2024Article
- Interplay of two small RNAs fine-tunes hierarchical flagella gene expression in Campylobacter jejuni.Nature communications · 2024Article
- The functional small RNA interactome reveals targets for the vancomycin-responsive sRNA RsaOI in vancomycin-tolerantmSystems · 2024Article
- Comparative proteomic analysis of vancomycin-sensitive and vancomycin-intermediate resistant Staphylococcus aureus.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2024Article
- Defining Bacterial RNA-RNA Interactomes Using CLASH.Methods in molecular biology (Clifton, N.J.) · 2024Article
Corrections and comments
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- Erratum issued
Authors and funding
15 authors at 3 institutions in 2 countries.
Funding
Abstract
Treatment of methicillin-resistant Staphylococcus aureus infections is dependent on the efficacy of last-line antibiotics including vancomycin. Treatment failure is commonly linked to isolates with intermediate vancomycin resistance (termed VISA). These isolates have accumulated point mutations that collectively reduce vancomycin sensitivity, often by thickening the cell wall. Changes in regulatory small RNA expression have been correlated with antibiotic stress in VISA isolates however the functions of most RNA regulators is unknown. Here we capture RNA-RNA interactions associated with RNase III using CLASH. RNase III-CLASH uncovers hundreds of novel RNA-RNA interactions in vivo allowing functional characterisation of many sRNAs for the first time. Surprisingly, many mRNA-mRNA interactions are recovered and we find that an mRNA encoding a long 3' untranslated region (UTR) (termed vigR 3'UTR) functions as a regulatory 'hub' within the RNA-RNA interaction network. We demonstrate that the vigR 3'UTR promotes expression of folD and the cell wall lytic transglycosylase isaA through direct mRNA-mRNA base-pairing. Deletion of the vigR 3'UTR re-sensitised VISA to glycopeptide treatment and both isaA and vigR 3'UTR deletions impact cell wall thickness. Our results demonstrate the utility of RNase III-CLASH and indicate that S. aureus uses mRNA-mRNA interactions to co-ordinate gene expression more widely than previously appreciated.
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