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

Ligang Fan; Tingting Wang; Canfeng Hua; Wenju Sun; Xiaoyu Li; Lucas Grunwald; Jingui Liu; Nan Wu; Xiaolong Shao; Yimeng Yin; Jian Yan; Xin Deng

doi:10.1038/s41467-020-18744-7

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

Ligang Fan, Tingting Wang, Canfeng Hua, Wenju Sun, Xiaoyu Li, Lucas Grunwald, Jingui Liu, Nan Wu, Xiaolong Shao, Yimeng Yin, Jian Yan^*, Xin Deng^*

^*Corresponding author for this work

Department of Biomedical Sciences

Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

25 Citations (Scopus)

64 Downloads (CityUHK Scholars)

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.

Original language	English
Article number	4947
Journal	Nature Communications
Volume	11
Online published	2 Oct 2020
DOIs	https://doi.org/10.1038/s41467-020-18744-7
Publication status	Published - 2020

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This full text is made available under CC-BY 4.0. https://creativecommons.org/licenses/by/4.0/

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title = "A compendium of DNA-binding specificities of transcription factors in Pseudomonas syringae",

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.",

author = "Ligang Fan and Tingting Wang and Canfeng Hua and Wenju Sun and Xiaoyu Li and Lucas Grunwald and Jingui Liu and Nan Wu and Xiaolong Shao and Yimeng Yin and Jian Yan and Xin Deng",

year = "2020",

doi = "10.1038/s41467-020-18744-7",

language = "English",

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journal = "Nature Communications",

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T1 - A compendium of DNA-binding specificities of transcription factors in Pseudomonas syringae

AU - Fan, Ligang

AU - Wang, Tingting

AU - Hua, Canfeng

AU - Sun, Wenju

AU - Li, Xiaoyu

AU - Grunwald, Lucas

AU - Liu, Jingui

AU - Wu, Nan

AU - Shao, Xiaolong

AU - Yin, Yimeng

AU - Yan, Jian

AU - Deng, Xin

PY - 2020

Y1 - 2020

N2 - 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.

AB - 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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U2 - 10.1038/s41467-020-18744-7

DO - 10.1038/s41467-020-18744-7

M3 - RGC 21 - Publication in refereed journal

C2 - 33009392

SN - 2041-1723

VL - 11

JO - Nature Communications

JF - Nature Communications

M1 - 4947

ER -

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

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ECS: Dissect the Molecular Mechanisms of HERV-H Mediated Shaping of Chromatin 3D Structure in Human Pluripotent Stem Cells

GRF: Elucidating Molecular Mechanism and Signaling Pathway of Novel Protease System RhpPC in Regulating Pathogenicity of Pseudomonas Syringae

ITF: Developing Sodium Acetate As Novel Anti-Pseudomonas Syringae Agent

Cite this

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

Abstract

Publisher's Copyright Statement

Access Output

Other Access Options

Permanent Link

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Projects

ECS: Dissect the Molecular Mechanisms of HERV-H Mediated Shaping of Chromatin 3D Structure in Human Pluripotent Stem Cells

GRF: Elucidating Molecular Mechanism and Signaling Pathway of Novel Protease System RhpPC in Regulating Pathogenicity of Pseudomonas Syringae

ITF: Developing Sodium Acetate As Novel Anti-Pseudomonas Syringae Agent

Cite this