Structured Promoter Variability in Epigenetically Regulated Operons Contributes to Surface Adaptation in Salmonella

Bacterial adaptation to dynamic and hostile environments often relies on the ability to modify surface structures, which are subjected to strong selective pressures. While mutations in coding sequences that alter surface structures have long been recognised as key drivers of bacterial adaptation, this study reveals structured promoter variation as a novel additional layer of functional adaptation. Focusing on the opvAB operon in Salmonella, epigenetically regulated by the coordinated action of Dam methylation and OxyR binding, we investigated the evolutionary dynamics and regulatory architecture of its regulatory region. Comparative genomics of Salmonella subspecies revealed striking variability in this regulatory region. Notably, the opvAB promoter exhibited mutations clustering at specific, recurrent positions, suggesting lineage-specific fine-tuning through structured and potentially functional variability, further demonstrated experimentally by phase variation analysis within clonal populations at the single bacterial cell level. Our findings highlight a potentially overlooked evolutionary mechanism by which bacteria can modulate gene expression through a balance between conservation and variability in regulatory elements. This structured promoter variation likely complements genetic and epigenetic strategies, offering a new perspective on how bacterial populations adapt to environmental challenges.