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

IF 6.4 1区 生物学 Q1 BIOLOGY
eLife Pub Date : 2025-03-31 DOI:10.7554/eLife.96172
Yue Sun, Jingwei Li, Jiadai Huang, Shumin Li, Youyue Li, Beifang Lu, Xin Deng
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引用次数: 0

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.

丁香假单胞菌全基因组转录调控网络结构揭示其动态功能和进化轨迹。
模型革兰氏阴性植物病原体丁香假单胞菌利用数百个转录因子(TFs)来调节其功能过程,包括控制其感染宿主植物能力的毒力和代谢途径。尽管调控因子的分子机制已经研究了几十年,但对Psph 1448A全基因组tf的全面了解仍然有限。在这里,我们通过染色质免疫沉淀测序(ChIP-seq)研究了301个注释tf中的170个的结合特性。顶层、中层和底层分别识别出54个、62个和147个tf,反映了多个高阶网络结构和信息流方向。将40000多个TF对划分为13个3节点子模块,揭示了Psph 1448A调控网络中TF的调控多样性。我们发现,底层tf对其靶基因表现出较高的相关得分。在三个水平上,tf的功能类别包含了不同的调节途径。鉴定出3个和25个主tf分别参与毒力和代谢调节。进化分析和拓扑模块化网络揭示了丁香属(Psph 1448A、Pst DC3000、Pss B728a和Psa C48)中TFs的功能差异和多样性。总的来说,我们的研究结果证明了Psph 1448A中全基因组tf的全球转录调控网络。这些知识可以促进相关传染病的有效治疗和预防策略的发展。
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来源期刊
eLife
eLife BIOLOGY-
CiteScore
12.90
自引率
3.90%
发文量
3122
审稿时长
17 weeks
期刊介绍: eLife is a distinguished, not-for-profit, peer-reviewed open access scientific journal that specializes in the fields of biomedical and life sciences. eLife is known for its selective publication process, which includes a variety of article types such as: Research Articles: Detailed reports of original research findings. Short Reports: Concise presentations of significant findings that do not warrant a full-length research article. Tools and Resources: Descriptions of new tools, technologies, or resources that facilitate scientific research. Research Advances: Brief reports on significant scientific advancements that have immediate implications for the field. Scientific Correspondence: Short communications that comment on or provide additional information related to published articles. Review Articles: Comprehensive overviews of a specific topic or field within the life sciences.
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