Regulatory RNA Ern0160 controls Enterococcus faecium virulence through direct modulation of expression of LysM domain-containing proteins

Background Enterococcus faecium is a commensal of the human gut microbiota that can become an opportunistic pathogen, particularly in immunocompromised individuals. Small RNAs (sRNA) are thought to contribute to this shift by enabling rapid bacterial adaptation to environmental changes. Despite this, knowledge of sRNA in E. faecium remains limited. Ern0160, in particular, has attracted interest for its involvement in antibiotic and biocide responses, as well as its role in intestinal colonization in a murine model. Results In this study, we investigated the functions of Ern0160 in E. faecium Aus0004 reference strain and sought to identify its mRNA targets. Transcriptomic and in silico analyses revealed potential regulatory targets, including two homologous genes encoding LysM-containing domain proteins (EFAU004_01059 and EFAU004_01150), both associated with enterococcal pathogenicity. Experimental validation confirmed that increased expression of Ern0160 led to repression of these genes. We further demonstrated direct and specific interactions between Ern0160 and the two homologous target mRNAs. Functional assays in the Galleria mellonella larvae infection model showed that deletion of Ern0160 resulted in increased host mortality, whereas deletion of its targets genes resulted in decreased mortality. These results are consistent with previous findings linking these genes to E. faecium virulence in murine model of systemic and urinary tract infections. Conclusions Our findings suggest that Ern0160 contributes to a regulatory network that modulates E. faecium colonization and infection by targeting genes involved in antimicrobial response and virulence. This study highlights the potential of regulatory RNAs such as Ern0160 to shape the pathogenic behavior of a multi-drug resistant and clinically significant bacterium.