Bacterial mRNA have short half-lives which allows rapid changes to the transcriptome. The processing of an mRNA may be directed, enhanced, or inhibited by direct base-pairing with regulatory non-coding RNA (ncRNA), which have emerged as ubiquitous gene regulators. Regulatory ncRNA can be generated from a variety of sources including released or independently transcribed from the untranslated regions (UTRs) of mRNAs and internal fragments of CDSs. We have recently used the RNA proximity-dependant ligation technique CLASH and MS2-affinity purification coupled with RNA-seq (MAPS) to capture and confirm RNA-RNA interactions in the Gram-positive MRSA. Surprisingly, we found that many mRNA-mRNA interactions were recovered, highlighting for the first time the extensive use of regulatory mRNAs (entire mRNA transcripts) and not just ncRNAs to coordinate gene expression. We found that a novel mRNA (vigR) functions as a regulatory ‘hub’ required for MRSA pathogenesis and vancomycin tolerance. We confirm direct mRNA-mRNA interactions between vigR and two target mRNAs involved in cell wall biogenesis, the autolysin isaA and the desuccinylase dapE that is required for lysine and peptidoglycan precursor biosynthesis. These findings underscore the complexity and importance of regulatory mRNA-mRNA interactions in coordinating bacterial gene expression.