IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v11y2020i1d10.1038_s41467-020-18744-7.html
   My bibliography  Save this article

A compendium of DNA-binding specificities of transcription factors in Pseudomonas syringae

Author

Listed:
  • Ligang Fan

    (Northwest University
    City University of Hong Kong, Kowloon Tong)

  • Tingting Wang

    (City University of Hong Kong, Kowloon Tong)

  • Canfeng Hua

    (City University of Hong Kong, Kowloon Tong)

  • Wenju Sun

    (Northwest University)

  • Xiaoyu Li

    (Northwest University)

  • Lucas Grunwald

    (City University of Hong Kong, Kowloon Tong)

  • Jingui Liu

    (City University of Hong Kong, Kowloon Tong)

  • Nan Wu

    (Northwest University)

  • Xiaolong Shao

    (City University of Hong Kong, Kowloon Tong)

  • Yimeng Yin

    (Shanghai Fourth People’s Hospital Affiliated to Tongji University School of Medicine)

  • Jian Yan

    (Northwest University
    City University of Hong Kong, Kowloon Tong)

  • Xin Deng

    (City University of Hong Kong, Kowloon Tong)

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.

Suggested Citation

  • Ligang Fan & Tingting Wang & Canfeng Hua & Wenju Sun & Xiaoyu Li & Lucas Grunwald & Jingui Liu & Nan Wu & Xiaolong Shao & Yimeng Yin & Jian Yan & Xin Deng, 2020. "A compendium of DNA-binding specificities of transcription factors in Pseudomonas syringae," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-18744-7
    DOI: 10.1038/s41467-020-18744-7
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-020-18744-7
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-020-18744-7?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-18744-7. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.