1. Genetics and Genomics
  2. Microbiology and Infectious Disease
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An atlas of the binding specificities of transcription factors in Pseudomonas aeruginosa directs prediction of novel regulators in virulence

  1. Tingting Wang
  2. Wenju Sun
  3. Ligang Fan
  4. Canfeng Hua
  5. Nan Wu
  6. Shaorong Fan
  7. Jilin Zhang
  8. Xin Deng  Is a corresponding author
  9. Jian Yan  Is a corresponding author
  1. City University of Hong Kong, Hong Kong
  2. Northwest University, China
  3. Karolinska Institute, Sweden
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Cite this article as: eLife 2021;10:e61885 doi: 10.7554/eLife.61885

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.

Article and author information

Author details

  1. Tingting Wang

    Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong
    Competing interests
    The authors declare that no competing interests exist.
  2. Wenju Sun

    School of Medicine, Northwest University, Xi'an, China
    Competing interests
    The authors declare that no competing interests exist.
  3. Ligang Fan

    Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong
    Competing interests
    The authors declare that no competing interests exist.
  4. Canfeng Hua

    Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong
    Competing interests
    The authors declare that no competing interests exist.
  5. Nan Wu

    School of Medicine, Northwest University, Xi'an, China
    Competing interests
    The authors declare that no competing interests exist.
  6. Shaorong Fan

    School of Medicine, Northwest University, Xi'an, China
    Competing interests
    The authors declare that no competing interests exist.
  7. Jilin Zhang

    Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
    Competing interests
    The authors declare that no competing interests exist.
  8. Xin Deng

    Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, Hong Kong
    For correspondence
    xindeng@cityu.edu.hk
    Competing interests
    The authors declare that no competing interests exist.
  9. Jian Yan

    Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong
    For correspondence
    jian.yan@cityu.edu.hk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1267-2870

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.

Reviewing Editor

  1. Christina L Stallings, Washington University School of Medicine, United States

Publication history

  1. Received: August 7, 2020
  2. Accepted: March 26, 2021
  3. Accepted Manuscript published: March 29, 2021 (version 1)

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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