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PreprintCited by 6Plant Pathogenic Bacteria StudiesBacterial Genetics and BiotechnologyPlant-Microbe Interactions and Immunity

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Architecture of genome-wide transcriptional regulatory network reveals dynamic functions and evolutionary trajectories in Pseudomonas syringae

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Sun, Yue, Li, Jingwei, Huang, Jiadai, Li, Shumin, Li, Youyue, Lu, Beifang, Deng, Xin·2024·eLife
DOI 10.1101/2024.01.18.576191

Preprint — published as 10.7554/elife.96172.3 · Paper page

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Abstract

The model Gram-negative plant pathogen Pseudomonas syringae utilises hundreds of transcription factors (TFs) to regulate its functional processes, including virulence and metabolic pathways that control its ability to infect host plants. Although the molecular mechanisms of regulators have been studied for decades, a comprehensive understanding of genome-wide TFs in Psph 1448A remains limited. Here, we investigated the binding characteristics of 170 of 301 annotated TFs through ChIP-seq. Fifty-four TFs, 62 TFs and 147 TFs were identified in top-level, middle-level and bottom-level, reflecting multiple higher-order network structures and direction of information-flow. More than forty thousand TF-pairs were classified into 13 three-node submodules which revealed the regulatory diversity of TFs in Psph 1448A regulatory network. We found that bottom-level TFs performed high co-associated scores to their target genes. Functional categories of TFs at three levels encompassed various regulatory pathways. Three and 25 master TFs were identified to involve in virulence and metabolic regulation, respectively. Evolutionary analysis and topological modularity network revealed functional variability and various conservation of TFs in P. syringae ( Psph 1448A, Pst DC3000, Pss B728a and Psa C48). Overall, our findings demonstrated the global transcriptional regulatory network of genome-wide TFs in Psph 1448A. This knowledge can advance the development of effective treatment and prevention strategies for related infectious diseases.

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Metadata

Authors
Sun, Y., Li, J., Huang, J., Li, S., Li, Y., Lu, B., & Deng, X.
Affiliations
  • City University of Hong Kong (HK)
  • University of Hong Kong (HK)
Corresponding author
Deng, Xin
ORCID
Venue
eLife
Publisher
openRxiv
Published
2024-01-18
Volume
13
ISSN
2050-084X (ISSN-L)
DOI
10.1101/2024.01.18.576191
OpenAlex
W4409071371
Cited by
6
References
1
Citations by year
2026: 1 · 2025: 4 · 2024: 1
FWCI
2.72
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • eLife (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
Funders
National Natural Science Foundation of China (32172358, 21103018, 31870116, 31670127)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Pathogenic Bacteria Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant-Microbe Interactions and Immunity
Keywords
Pseudomonas syringae, transcriptional regulatory networks, transcription factors, ChIP-seq, virulence regulation, metabolic regulation, master transcription factors, network modularity, plant pathogens

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