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Architecture of genome-wide transcriptional regulatory network reveals dynamic functions and evolutionary trajectories in Pseudomonas syringae
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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 chromatin immunoprecipitation sequencing (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 40,000 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 a 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
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2025-03-31
- Volume
- 13
- ISSN
- 2050-084X (ISSN-L)
- OpenAlex
- W4409071371
- Cited by
- 6
- References
- 85
- Citations by year
- 2026: 1 · 2025: 4
- FWCI
- 2.72
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- creativecommons.org/licenses/by/4.0/ (vor)
- creativecommons.org/licenses/by/4.0/ (am)
- creativecommons.org/licenses/by/4.0/ (tdm)
- Locations
- eLife (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- Funders
- National Natural Science Foundation of China (32172358)
- General Research Funds of Hong Kong (11101722, 11102223, 11102720)
- Shenzhen Science and Technology Fund (JCYJ20210324134000002)
- Theme-based Research Scheme (T11-104/22-R)
- Guangdong Major Project of Basic and Applied Basic Research (2020B0301030005)
- 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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