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

被引：252

作者：

Fan, Ligang ^{[1
,2
]}

Wang, Tingting ^{[2
]}

Hua, Canfeng ^{[2
]}

Sun, Wenju ^{[1
]}

Li, Xiaoyu ^{[1
]}

Grunwald, Lucas ^{[2
]}

Liu, Jingui ^{[2
]}

Wu, Nan ^{[1
]}

Shao, Xiaolong ^{[2
]}

Yin, Yimeng ^{[3
]}

Yan, Jian ^{[1
,2
]}

Deng, Xin ^{[2
]}

机构：

[1] Northwest Univ, Sch Med, Xian 710069, Peoples R China

[2] City Univ Hong Kong, Dept Biomed Sci, Kowloon Tong, Hong Kong, Peoples R China

[3] Tongji Univ, Sch Med, Shanghai Peoples Hosp 4, Translat Res Inst Brain & Brain Like Intelligence, Shanghai 200081, Peoples R China

来源：

NATURE COMMUNICATIONS | 2020年 / 11卷 / 01期

基金：

中国博士后科学基金; 中国国家自然科学基金;

关键词：

PV. TOMATO DC3000; III SECRETION SYSTEM; 2-COMPONENT SYSTEM; RESPONSE REGULATOR; PROTEIN SECRETION; GENOME SEQUENCE; PATHOGEN; GENES; EXPRESSION; VIRULENCE;

D O I：

10.1038/s41467-020-18744-7

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页数：11

共 70 条

[1] Diversity and Complexity in DNA Recognition by Transcription Factors [J].

Badis, Gwenael ;

Berger, Michael F. ;

Philippakis, Anthony A. ;

Talukder, Shaheynoor ;

Gehrke, Andrew R. ;

Jaeger, Savina A. ;

Chan, Esther T. ;

Metzler, Genita ;

Vedenko, Anastasia ;

Chen, Xiaoyu ;

Kuznetsov, Hanna ;

Wang, Chi-Fong ;

Coburn, David ;

Newburger, Daniel E. ;

Morris, Quaid ;

Hughes, Timothy R. ;

Bulyk, Martha L. .

SCIENCE, 2009, 324 (5935) :1720-1723

[2] A Library of Yeast Transcription Factor Motifs Reveals a Widespread Function for Rsc3 in Targeting Nucleosome Exclusion at Promoters [J].

Badis, Gwenael ;

Chan, Esther T. ;

van Bakel, Harm ;

Pena-Castillo, Lourdes ;

Tillo, Desiree ;

Tsui, Kyle ;

Carlson, Clayton D. ;

Gossett, Andrea J. ;

Hasinoff, Michael J. ;

Warren, Christopher L. ;

Gebbia, Marinella ;

Talukder, Shaheynoor ;

Yang, Ally ;

Mnaimneh, Sanie ;

Terterov, Dimitri ;

Coburn, David ;

Yeo, Ai Li ;

Yeo, Zhen Xuan ;

Clarke, Neil D. ;

Lieb, Jason D. ;

Ansari, Aseem Z. ;

Nislow, Corey ;

Hughes, Timothy R. .

MOLECULAR CELL, 2008, 32 (06) :878-887

[3] Phylogenetics of Lophotrochozoan bHLH Genes and the Evolution of Lineage-Specific Gene Duplicates [J].

Bao, Yongbo ;

Xu, Fei ;

Shimeld, Sebastian M. .

GENOME BIOLOGY AND EVOLUTION, 2017, 9 (04) :869-886

[4] Pseudomonas syringae phytotoxins:: Mode of action, regulation, and biosynthesis by peptide and polyketide synthetases [J].

Bender, CL ;

Alarcón-Chaidez, F ;

Gross, DC .

MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS, 1999, 63 (02) :266-+

[5] The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000 [J].

Buell, CR ;

Joardar, V ;

Lindeberg, M ;

Selengut, J ;

Paulsen, IT ;

Gwinn, ML ;

Dodson, RJ ;

Deboy, RT ;

Durkin, AS ;

Kolonay, JF ;

Madupu, R ;

Daugherty, S ;

Brinkac, L ;

Beanan, MJ ;

Haft, DH ;

Nelson, WC ;

Davidsen, T ;

Zafar, N ;

Zhou, LW ;

Liu, J ;

Yuan, QP ;

Khouri, H ;

Fedorova, N ;

Tran, B ;

Russell, D ;

Berry, K ;

Utterback, T ;

Van Aken, SE ;

Feldblyum, TV ;

D'Ascenzo, M ;

Deng, WL ;

Ramos, AR ;

Alfano, JR ;

Cartinhour, S ;

Chatterjee, AK ;

Delaney, TP ;

Lazarowitz, SG ;

Martin, GB ;

Schneider, DJ ;

Tang, XY ;

Bender, CL ;

White, O ;

Fraser, CM ;

Collmer, A .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2003, 100 (18) :10181-10186

[6] GacA directly regulates expression of several virulence genes in Pseudomonas syringae pv. tabaci 11528 [J].

Cha, Ji Young ;

Lee, Dong Gwang ;

Lee, Jun Seung ;

Oh, Jeong-Il ;

Baik, Hyung Suk .

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 2012, 417 (02) :665-672

[7]

Chan Sunny Sun-Kin, 2013, J Stem Cell Res Ther, V3

[8] GacA, the response regulator of a two-component system, acts as a master regulator in Pseudomonas syringae pv. tomato DC3000 by controlling regulatory RNA, transcriptional activators, and alternate sigma factors [J].

Chatterjee, A ;

Cui, YY ;

Yang, HL ;

Collmer, A ;

Alfano, JR ;

Chatterjee, AK .

MOLECULAR PLANT-MICROBE INTERACTIONS, 2003, 16 (12) :1106-1117

[9] Assembly and function of type III secretory systems [J].

Cornelis, GR ;

Van Gijsegem, F .

ANNUAL REVIEW OF MICROBIOLOGY, 2000, 54 :735-774

[10] Molecular mechanisms of two-component system RhpRS regulating type III secretion system in Pseudomonas syringae [J].

Deng, Xin ;

Liang, Haihua ;

Chen, Kai ;

He, Chuan ;

Lan, Lefu ;

Tang, Xiaoyan .

NUCLEIC ACIDS RESEARCH, 2014, 42 (18) :11472-11486

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