Methylation Dynamics in Helicobacter pylori: Exploring Acidic Stress Effects on Epigenetic Acclimation.

Helicobacter pylori is the only known bacterium classified as a Class I carcinogen and infects over 50% of the global population. Although most infections are asymptomatic, 10–15% progress to gastric cancer or peptic ulcers, reflecting significant strain-strain variability as well as host variability. H. pylori exhibits an unusually high number of restriction-modification (R-M) systems relative to its small genome, contributing to a dynamic methylome increasingly implicated in bacterial gene regulation. In this study, we analyzed the methylomes of two mutant strains of H. pylori 26695, each under neutral (pH 7) and acidic (pH 5) growth conditions. We identified one hypomethylated region of 21kBp with 21 annotated genes across all four methylomes analyzed. Notably, over 660 protein coding regions and 12 different promoters displayed differential methylation between pH conditions, involved in the expression of several known virulence factors. The vacA gene, encoding the Vacuolating Cytotoxin A, exhibited eight differentially methylated positions between pH 7 and pH 5 within the H. pylori 26695 control mutant methylome, potentially contributing to its previously documented 32-fold down regulation of mRNA in acidic environments. Methylation changes were also enriched among genes encoding cell envelope proteins, specifically within flagellar associated coding regions and within the genes sabA and babA. Together, these results highlight a remarkable plasticity of the H. pylori methylome and suggest that dynamic DNA methylation, responsive to environmental pH both dependent upon and independent of the ArsRS two-component system, serves as an important layer of gene regulation in acclimation to hostile gastric environments.