Genome-wide distribution and putative regulatory roles of G-quadruplex motifs in oral bacteria

Introduction G-quadruplexes (G4s) are non-canonical DNA secondary structures with established regulatory roles in eukaryotes, yet their prevalence, distribution, and functional significance in bacteria remain poorly understood. Methods We conducted a comprehensive survey of G4 motifs across 381 reference genomes representing 150 genera of oral bacteria. Computational prediction was used to identify G4 motifs and characterize their genomic distribution, GC-content dependence, and functional associations. Additionally, comparative analysis of orthologous promoters across 35 genera was performed to investigate the evolutionary conservation and turnover of promoter-associated G4 motifs. Results We identified 48,234 G4 motifs and found that their genomic density increased exponentially with GC content. G4 motifs were enriched in promoter regions relative to genome-wide expectations and preferentially associated with genes involved in signal transduction, virulence, transcriptional regulation, and transport. Comparative analysis revealed that promoter-associated G4s were shared among congeneric species more frequently than expected by chance, but their sharing declined sharply with increasing phylogenetic distance. Moreover, G4-forming sequences showed no greater conservation than other G-rich sequences within the same promoters, suggesting rapid evolutionary turnover. Discussion These findings demonstrate that G4 motifs are non-randomly distributed across oral bacterial genomes and exhibit evolutionary patterns consistent with inheritance and rapid turnover. The enrichment of G4s in promoters of functionally relevant genes highlights candidate loci for future experimental investigation of G4-mediated transcriptional regulation in oral bacteria.