A compendium of DNA-binding specificities of transcription factors in Pseudomonas syringae
Ligang Fan, Tingting Wang, Canfeng Hua, Wenju Sun, Xiaoyu Li, Lucas Grunwald, Jingui Liu, Nan Wu, Xiaolong Shao, Yimeng Yin, Jian Yan, Xin Deng
Abstract
Pseudomonas syringae is a Gram-negative and model pathogenic bacterium that causes plant diseases worldwide. Here, we set out to identify binding motifs for all 301 annotated transcription factors (TFs) of P. syringae using HT-SELEX. We successfully identify binding motifs for 100 TFs. We map functional interactions between the TFs and their targets in virulence-associated pathways, and validate many of these interactions and functions using additional methods such as ChIP-seq, electrophoretic mobility shift assay (EMSA), RT-qPCR, and reporter assays. Our work identifies 25 virulence-associated master regulators, 14 of which had not been characterized as TFs before.