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

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) family proteins are a well-known group of TFs involved in diverse physiological functions, the roles of LTTRs in P. syringae are still largely unknown. In this study, we characterised a LysR-type TF, PSPPH4638, which is a virulence and metabolism regulator (VimR) with multiple functions. Genome-wide identification of VimR using chromatin immunoprecipitation sequencing revealed 1,032 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 vimR deletion in King's B medium (KB) and minimal medium, 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. Taken together, our findings identified a new TF VimR and revealed its important functions in P. syringae. This is the first time to describe a transcription factor that regulates both type III secretion system and type VI secretion system and multiple metabolic pathways in Pseudomonas syringae. Overall design: RNA-seq profiling of P. savastanoi pv. phaseolicola 1448A (Psph) and vimR deletion derivative in KB and MM , and P. aeruginosa PAO1(PAO1) and PA3565 overexpressing derivative in LB