Stress-induced DNA methylome plasticity and transcriptional re-programming in Staphylococcus aureus

Staphylococcus aureus , a major human and livestock pathogen, is the second biggest cause of antimicrobial resistance-associated mortality. Although S. aureus transcriptional regulation has been extensively charac-terised, the potential role of DNA methylation in S. aureus transcriptional regulation and stress response re-mains largely undefined. We tackled this gap by combining genome-wide methylation and transcriptomic data acquired before and during exposure of methicillin-resistant Staphylococcus aureus strain USA300 to clinically relevant oxidative, antibiotic and nitrosative stresses. Stress-induced significant DNA methylation changes were far more common in cytosine than adenine, stress-specific, concentrated in gene features, and in many cases occurred alongside transcription changes. Transcription changes reflected metabolic, regula-tory and stress-associated pathway adjustments. We identified twenty-four DNA/RNA methyltransferases; this included four putative novel methyltransferases, three of which were highly prevalent and conserved, evidencing long-term functional relevance. Genome-wide methylation entropy levels were consistent with a finite number of methylation patterns that could correspond to S. aureus subpopulations such as clinically important stress survival subpopulations. Based on combined methylation and transcription change data, moreover, we conjecture that certain methylation change sites are key regulatory nodes. These findings sup-port the principle that DNA methylation is an important component of the regulatory machinery underpin-ning S. aureus adaptability and persistence.