Small regulatory RNAs modulate lactococcal susceptibility to cell wall-targeting antimicrobials

The contribution of small RNAs to the regulation of cell wall defence mechanisms-crucial for protecting bacteria from environmental insults-remains poorly understood in Lactococcus cremoris, a model organism for studying lactic acid bacteria. Characterization of the profiles of 193 putative small regulatory RNAs (sRNAs), including 131 newly identified in this study, revealed altered expression of 20 and 25 sRNAs following treatment with cell wall-targeting antimicrobials, lysozyme and penicillin G, respectively. Further analysis and genome-wide functional screening identified four sRNAs that affected lysozyme response in opposite directions: elevated levels of sLLM1042+, sLLM2-, and sLLM1993+ were associated with increased resistance, whereas sLLM461+ with decreased resistance. Moreover, elevated expression of sLLM2-, sLLM1042+, or both promoted sensitivity to penicillin G and certain abiotic stresses, and exerted pleiotropic effects on gene regulation at both RNA and protein levels, suggesting broader regulatory impacts. Notably, the sLLM2- mediated decrease in four putative tellurium resistance proteins resulted in increased sensitivity to tellurite stress. As sLLM2- mutations, altering lysozyme and penicillin responses, also reduced alanine racemase Alr expression, we suggest that sRNA upregulation modulates D-alanine levels, thereby affecting lipoteichoic acid modification or peptidoglycan synthesis. Our findings support a contribution of sRNAs to LAB responses to cell wall-targeting antimicrobials.