DNA adenine methylation influences gene expression and biofilm formation in Streptococcus mutans

Streptococcus mutans, a key oral pathogen, utilizes quorum sensing to regulate biofilm formation-a major virulence factor in the development of dental caries (tooth decay). Our recent research uncovered a complex interplay between the CSP-ComDE quorum sensing pathway and the Type II DpnII restriction-modification (R-M) system in S. mutans. The DpnII R-M system methylates adenine at 5'-GATC-3' sites and cleaves unmethylated DNA, significantly influencing foreign DNA acquisition and gene expression. In this study, we investigated the impact of a ΔRM mutant, which lacks adenine methylation, on biofilm formation. The ΔRM mutant formed fragile biofilms that easily detach from surfaces, with significantly reduced exopolysaccharide content and increased extracellular DNA, which appears to be associated with membrane vesicle production rather than cell lysis. RNA-seq analysis revealed only few differentially expressed genes directly involved in biofilm formation, such as gtfC, suggesting that the biofilm defect may result from indirect effects or alternative regulatory mechanisms. Notably, the downregulation of mutanobactin-related genes and upregulation of genes involved in de novo purine nucleotide biosynthesis point to novel pathways influenced by DNA methylation. These findings contribute to a deeper understanding of the multifactorial nature of biofilm formation and the role of epigenetic modifications in microbial behavior.

This study highlights the critical role of DNA methylation in regulating biofilm formation and virulence in Streptococcus mutans. By examining the interplay between adenine methylation, extracellular DNA (eDNA), membrane vesicles (MVs), and glucan production, we provide new insights into the complex biology of biofilm development. Our findings challenge traditional views by emphasizing the importance of MVs and eDNA in maintaining biofilm integrity. Understanding these epigenetics modifications not only advances our knowledge of microbial regulation but also identifies novel targets for antimicrobial therapy. Since adenine methylation is rare or absent in mammalian cells, targeting this modification presents a promising strategy to disrupt biofilm formation and combat bacterial infections. The insights gained from this study may inform the development of innovative approaches to manage biofilm-associated infections and improve oral health outcomes.