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

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 functi...

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Autores principales: Fan, Ligang, Wang, Tingting, Hua, Canfeng, Sun, Wenju, Li, Xiaoyu, Grunwald, Lucas, Liu, Jingui, Wu, Nan, Shao, Xiaolong, Yin, Yimeng, Yan, Jian, Deng, Xin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2020
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7532196/
https://www.ncbi.nlm.nih.gov/pubmed/33009392
http://dx.doi.org/10.1038/s41467-020-18744-7
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author Fan, Ligang
Wang, Tingting
Hua, Canfeng
Sun, Wenju
Li, Xiaoyu
Grunwald, Lucas
Liu, Jingui
Wu, Nan
Shao, Xiaolong
Yin, Yimeng
Yan, Jian
Deng, Xin
author_facet Fan, Ligang
Wang, Tingting
Hua, Canfeng
Sun, Wenju
Li, Xiaoyu
Grunwald, Lucas
Liu, Jingui
Wu, Nan
Shao, Xiaolong
Yin, Yimeng
Yan, Jian
Deng, Xin
author_sort Fan, Ligang
collection PubMed
description 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.
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spelling pubmed-75321962020-10-19 A compendium of DNA-binding specificities of transcription factors in Pseudomonas syringae Fan, Ligang Wang, Tingting Hua, Canfeng Sun, Wenju Li, Xiaoyu Grunwald, Lucas Liu, Jingui Wu, Nan Shao, Xiaolong Yin, Yimeng Yan, Jian Deng, Xin Nat Commun Article 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. Nature Publishing Group UK 2020-10-02 /pmc/articles/PMC7532196/ /pubmed/33009392 http://dx.doi.org/10.1038/s41467-020-18744-7 Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Fan, Ligang
Wang, Tingting
Hua, Canfeng
Sun, Wenju
Li, Xiaoyu
Grunwald, Lucas
Liu, Jingui
Wu, Nan
Shao, Xiaolong
Yin, Yimeng
Yan, Jian
Deng, Xin
A compendium of DNA-binding specificities of transcription factors in Pseudomonas syringae
title A compendium of DNA-binding specificities of transcription factors in Pseudomonas syringae
title_full A compendium of DNA-binding specificities of transcription factors in Pseudomonas syringae
title_fullStr A compendium of DNA-binding specificities of transcription factors in Pseudomonas syringae
title_full_unstemmed A compendium of DNA-binding specificities of transcription factors in Pseudomonas syringae
title_short A compendium of DNA-binding specificities of transcription factors in Pseudomonas syringae
title_sort compendium of dna-binding specificities of transcription factors in pseudomonas syringae
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7532196/
https://www.ncbi.nlm.nih.gov/pubmed/33009392
http://dx.doi.org/10.1038/s41467-020-18744-7
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