VimR is a conserved master transcription regulator controlling virulence and metabolism in Pseudomonas

Pseudomonas syringae, a highly destructive plant bacterial pathogen causing severe disease and significant yield losses in agriculture globally, has complex regulatory systems involving many transcriptional factors (TFs). Although the LysR-type transcriptional regulator (LTTR) protein family is a well-known group of TFs involved in diverse physiological functions, the roles of LTTRs in P. syringae remain largely unknown. In this study, we characterized a LysR-type TF, PSPPH4638, and designated it as the virulence and metabolism regulator VimR. Genome-wide identification of VimR using chromatin immunoprecipitation sequencing revealed 1032 binding sites in the genome, of which 85% were in intergenic regions. Transcriptomic analysis showed altered expression of 454 and 82 genes in response to ΔvimR in King's B medium (KB) and minimal medium (MM), respectively. Conjoint analysis showed that 99 genes were directly affected by VimR in KB. VimR was identified as a repressor of the type III secretion system, oxidative stress response, and key metabolic pathways such as the tricarboxylic acid cycle. In addition, we found that VimR was positively involved in the type VI secretion system and alanine, aspartate, and glutamate metabolism. Further verification showed that VimR was widely present in Pseudomonas, displaying similar binding capacity in different strains of P. syringae, and similar regulatory functions in Pseudomonas aeruginosa. Taken together, our findings identified a conserved master TF that regulates type III secretion system, type VI secretion system, and multiple metabolic pathways in Pseudomonas.