GSE158830
RNase III-CLASH of multi-drug resistant Staphylococcus aureus reveals a regulatory mRNA 3'UTR required for intermediate vancomycin resistance
Treatment of methicillin-resistant Staphylococcus aureus (MRSA) infections is dependant on the efficacy of last-line antibiotics like vancomycin. Vancomycin treatment failure is most commonly linked to the emergence of vancomycin-intermediate resistance in clincal isolates (termed VISA). These isolates have not acquired resistance genes but appear to accumulate a heterogenous collection of single nucleotide polymerisms that collectively alter the physiology of the cell to increase vancomycin tolerance. Cell wall thickening is common among VISA isolates and is thought to decrease vancomycin permeability. Changes in regulatory sRNA expression have been correlated with antibiotic stress responses in VISA isolates however the functions of the vast majority of these RNA regulators is unknown. Here we have used the endoribonuclease RNase III to capture RNA-RNA interactions using an RNA proximity-dependant ligation technique termed CLASH. RNase III-CLASH uncovered hundreds of sRNA-mRNA interactions in vivo allowing functional characterisation of many sRNAs for the first time. Surprisingly, we find that an mRNA encoding an unusually long 3'UTR (here termed vigR) functions as a regulatory 'hub' within our RNA-RNA interaction network. We demonstrate vigR promotes expression of the cell wall lytic transglycosylase encoded by isaA through a direct mRNA-mRNA interaction. Further, we find that the vigR mRNA 3'UTR is required for cell wall thickening and that deletion of the vigR 3'UTR re-sensitises VISA to vancomycin. Our results demonstrate the utility of RNase III-CLASH for identifying new regulatory RNA functions and indicate that S. aureus may use mRNA-mRNA interactions to co-ordinate gene expression much more widely than previously appreciated. Overall design: This series consists of four different  sequencing datasets: 1. RNase III-CLASH (RNA proximity-dependant ligation) data from S. aureus JKD6009, 2. dRNA-seq mapping of RNA 5' end,  3. Term-seq mapping of RNA 3' ends, and 4. Total RNA-sequencing data Please note that the following update has been made on Jan 2022: GSM4811620-GSM4811625 raw data files have been replaced (the submitters found that the strains used to generate these FASTQ files had a number of SNPs that might affect the data and generated new sequencing data from re-generated strains). The previous 'd275v_WTv_DESeq2.xls' was replaced with '2021.03.16_MUTvsWT.DEseq2_combined_output.xlsx' Three additional samples were included