A compendium of DNA-binding specificities of transcription factors in Pseudomonas syringae.
Ligang FanTingting WangCanfeng HuaWenju SunXiaoyu LiLucas GrunwaldJingui LiuNan WuXiaolong ShaoYimeng YinJian YanXin DengPublished in: Nature communications (2020)
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.
Keyphrases
- dna binding
- transcription factor
- biofilm formation
- gram negative
- high throughput
- pseudomonas aeruginosa
- multidrug resistant
- escherichia coli
- staphylococcus aureus
- genome wide
- antimicrobial resistance
- candida albicans
- single cell
- crispr cas
- plant growth
- genome wide identification
- rna seq
- circulating tumor cells
- gene expression
- binding protein