Architecture of the genome-wide transcriptional regulatory network reveals the dynamic biological functions and divergent evolutionary trajectory in Pseudomonas syringae
The model Gram-negative plant pathogen Pseudomonas syringae utilizes hundreds of transcription factors (TFs) to manipulate its functional processes, including virulence and metabolic pathways to control its infection to host plants. Although the molecular mechanisms of regulators have been studied for decades, the comprehensive understanding throughout the genome-wide TFs in P. syringae remains uncertain. Here, we set out to investigate the binding characteristics of 170 of all 301 annotated TFs using ChIP-seq. To further explore and delineate the physiological and pathogenic roles of TFs in P. syringae, we integrated both the 118 different position weight matrix (PWM) motifs of 100 TFs analyzed by HT-SELEX previously and more than 26000 direct interactions of 170 TFs here, mapped the hierarchical regulatory network not only between TFs but also within TFs and target genes. We next investigated the co-association statistics across the 26000 interactions and identified the high co_x0002_association scores of bottom TFs in the hierarchical network. The evolution analysis revealed the functional variability of TFs between different pathovars of P. syringae. Topological modularity network of all ChIPed TFs and their targets exhibited the various biological functions. Overall, our work provided the global transcriptional regulatory network of genome-wide TFs in P. syringae, including 35 virulence_x0002_associated and metabolic TFs, which promoted the development of effective treatment and prevention strategies for the related infectious diseases. Overall design: Chromatin immunoprecipitation sequencing (ChIP-seq) for 170 transcription factors in Pseudomonas syringae 1448A The name of each sample consists of three parts: one is the strain label, the second is the locus_tag of TF, and the last -number represents the biological replicate.  For example, PSPPH_0001-1 indicates the first biological replicate of TF 0001 in the PSPPH strain (1448A). Control samples are EV/HACK labelled.