Non-coding RNA RsaE regulates biofilm thickness, viability and dissemination in methicillin-resistant Staphylococcus aureus

Abstract Methicillin-resistant Staphylococcus aureus (MRSA) is a formidable human pathogen responsible for life-threatening infections worldwide. Central to its pathogenic success is the tightly coordinated regulation of virulence factors, including the phenol soluble modulins (PSM), short amphipathic toxins that drive cytolysis, immune evasion and biofilm maturation. We previously identified the conserved non-coding RNA RsaE as a putative regulator of the psm⍺ operon, but the biological significance of this interaction remained unclear. Here we show that RsaE and endoribonuclease Y jointly regulate psm⍺ transcript abundance at the post-transcriptional and transcriptional levels, the latter primarily through activation of the agr quorum sensing system. We show that the psm⍺ transcript is unusually stable and highly structured, with Shine-Dalgarno sequences of individual toxin-coding sequences differentially accessible, providing a mechanism for translational fine-tuning of individual PSM⍺ peptides. In vitro biofilm analyses revealed that RsaE deletion produces thinner biofilms with reduced extracellular DNA accumulation on the surface and transiently elevated cell viability. Strikingly, in a murine catheter infection model, ΔrsaE biofilms exhibited structural abnormalities and significantly reduced dissemination to kidneys. These findings identify the RsaE non-coding RNA as a key regulator linking central metabolism and quorum sensing to toxin expression, biofilm maturation and infection in MRSA. Author summary Methicillin-resistant Staphylococcus aureus (MRSA) causes severe, often device-associated infections that are hard to treat. A central reason for its success is tight control over toxins such as the ⍺-phenol-soluble modulins (PSM⍺), which help bacteria damage host cells and build/disperse biofilms. Small RNAs (sRNAs) are fast-acting genetic regulators in bacteria, that also regulate toxin production. We show that the conserved sRNA RsaE and the endoribonuclease RNase Y jointly tune the level and lifetime of the psm⍺ RNA transcript, which encodes four PSM⍺ peptides. The psm⍺ RNA is unusually stable and highly structured with its design favouring translation of PSM⍺4 over the other peptides. Removing RsaE or RNase Y increases psm⍺ transcription via the agr quorum-sensing system and further stabilises the psm⍺ RNA. In biofilms, loss of RsaE reduces the thickness and extracellular DNA layer, while increasing early cell viability. In a mouse catheter model, RsaE deletion leads to structurally altered biofilms and reduced early dissemination to kidneys. These results identify RsaE as a key regulator connecting metabolism and quorum sensing to toxin expression, biofilm maturation and disease progression, and point to RNA-centred strategies to regulate MRSA spread from biofilms.