Abstract
A high-throughput systematic evolution of ligands by exponential enrichment assay was applied to 371 putative TFs in P. aeruginosa, which resulted in the robust enrichment of 199 sequence motifs describing the binding specificities of 182 TFs. By scanning the genome, we predicted in total 33,709 significant interactions between TFs and their target loci, which were more than 11-fold enriched in the intergenic regions but depleted in the gene body regions. To further explore and delineate the physiological and pathogenic roles of TFs in P. aeruginosa, we constructed regulatory networks for nine major virulence-associated pathways, and found that 51 TFs were potentially significantly associated with these virulence pathways, 32 of which had not been characterized before, and some were even involved in multiple pathways. These results will significantly facilitate future studies on transcriptional regulation in P. aeruginosa and other relevant pathogens, and accelerate to discover effective treatment and prevention strategies for the associated infectious diseases.
Data availability
Sequencing data have been deposited in GEO under accession code GSE151518.
Article and author information
Author details
Funding
National Natural Science Foundation of China (8187364)
- Jian Yan
City University of Hong Kong (7005314)
- Jian Yan
National Natural Science Foundation of China (31900443)
- Wenju Sun
National Natural Science Foundation of China (31870116)
- Xin Deng
Research Grants Council, University Grants Committee (21103018)
- Xin Deng
Research Grants Council, University Grants Committee (21100420)
- Jian Yan
Research Grants Council, University Grants Committee (11101619)
- Xin Deng
China Postdoctoral Science Foundation (2019M663799)
- Wenju Sun
China Postdoctoral Science Foundation (2019M663794)
- Ligang Fan
City University of Hong Kong (9667188)
- Jian Yan
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2021, Wang et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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An atlas of the binding specificities of transcription factors in Pseudomonas aeruginosa directs prediction of novel regulators in virulence
eLife 10:e61885.
https://doi.org/10.7554/eLife.61885
