Chen Fang, Sun Yue, Huang Jiadai, Li Tianmin, Lu Beifang, He Zhe, Li Jingwei, Wang Tianqi, Hu Haiyan, Deng Xin
Department of Biomedicine, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, 999077, China.
School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, 999077, China.
Nucleic Acids Res. 2025 Jun 6;53(11). doi: 10.1093/nar/gkaf493.
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.
丁香假单胞菌是一种极具破坏性的植物细菌病原体，在全球农业中会引发严重病害并导致重大产量损失，它具有涉及许多转录因子（TFs）的复杂调控系统。尽管赖斯盒式转录调控因子（LTTR）蛋白家族是一组参与多种生理功能的知名转录因子，但LTTRs在丁香假单胞菌中的作用仍 largely未知。在本研究中，我们对一个赖斯盒式转录因子PSPPH4638进行了表征，并将其命名为毒力和代谢调节因子VimR。使用染色质免疫沉淀测序对VimR进行全基因组鉴定，结果显示基因组中有1032个结合位点，其中85%位于基因间区域。转录组分析表明，在King's B培养基（KB）和基本培养基（MM）中，分别有454个和82个基因因ΔvimR而表达发生改变。联合分析表明，在KB中99个基因直接受VimR影响。VimR被鉴定为III型分泌系统、氧化应激反应以及三羧酸循环等关键代谢途径的抑制因子。此外，我们发现VimR正向参与VI型分泌系统以及丙氨酸、天冬氨酸和谷氨酸代谢。进一步验证表明，VimR广泛存在于假单胞菌中，在不同的丁香假单胞菌菌株中具有相似的结合能力，在铜绿假单胞菌中具有相似的调控功能。综上所述，我们的研究结果鉴定出了一个保守的主转录因子，它可调节假单胞菌中的III型分泌系统、VI型分泌系统以及多种代谢途径。
