DNA Methylome Regulates Virulence and Metabolism in Pseudomonas syringae

Pseudomonas syringae is a phytopathogenic bacterium that globally inflicts leaf spots and cankers on plants, posing significant challenges for adequate control. Unraveling the DNA methylation patterns within this pathogen can offer novel insights into its pathogenicity mechanisms, thereby facilitating the development of preventive therapeutic approaches. In this study, we conducted single-molecule real-time sequencing (SMRT-seq) to profile the DNA methylation landscape in P. syringae pv. phaseolicola (Psph), Pseudomonas syringae pv. tomato (Pst) and Pseudomonas syringae pv. syringae (Pss). Our investigation profiled comprehensive DNA methylation atlas in three P. syringae strains and identified one type I restriction-modification (R-M) system (HsdMSR), along with its conserved sequence motif associated with N6-methyladenine (6mA) in Psph. Strikingly, about 25%-40% of genes within DNA methylation were conserved in two or three strains, revealing a functional conservation of methylation in P. syringae. Further functional enrichment analysis emphasized the distinctive and similar biological functions among the three species. Subsequent transcriptomic analysis highlighted the involvement of HsdMSR in virulence-related pathways, such as Type III secretion system (T3SS) and biofilm formation in Psph. Notably, the depletion of HsdMSR led to enhanced expression of downstream T3SS genes and alginate biosynthesis proteins. Furthermore, RNA-seq results emphasized its role in modulating metabolic processes by influencing the expression of ribosomal proteins and altering translational efficiency. Further exploration of the mechanisms behind gene transcription regulation suggested that HsdMSR exerts influence on transcriptional processes based on the fully methylated pattern.