In silico profiling, docking analysis, and protein interactions of secondary metabolites in Musa spp. Against the SGE1 protein of Fusarium oxysporum f. sp. cubense

IF 2.6 4区生物学 Q2 BIOLOGY

Computational Biology and Chemistry Pub Date : 2024-10-05 DOI:10.1016/j.compbiolchem.2024.108230

Preeti Sonkar , Shalini Purwar , Prachi Bhargva , Ravindra Pratap Singh , Jawaher Alkahtani , Abdulrahman Al-hashimi , Yheni Dwiningsih , Salim Khan

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引用次数: 0

Abstract

Banana Fusarium Wilt (BFW), caused by Fusarium oxysporum f. sp. cubense (Foc), threatens banana crops globally, with the pathogen's virulence partially regulated by the Sge1 transcription factor, which enhances disease severity. Certain Musa species display resistance to Foc, suggesting inherent genetic traits that confer immunity against Sge1Foc. This study utilized bioinformatics tools to investigate the mechanisms underlying this resistance in Musa accuminata subsp. aalaccensis. Through in silico analyses, we explored interactions between Musa spp. and Foc, focusing on the Sge1 protein. Tools such as Anti-SMASH, AutoDockVina 4.0, STRING, and Phoenix facilitated the profiling of secondary metabolites in Musa spp. and the identification of biosynthetic gene clusters involved in defense. Our results indicate that secondary metabolites, including saccharides, terpenes, and polyketides, are crucial to the plant's immune response. Molecular docking studies of selected Musa metabolites, such as 3-Phenylphenol, Catechin, and Epicatechin, revealed 3-Phenylphenol as having the highest binding affinity to the Sge1Foc protein (-6.7 kcal/mol).Further analysis of gene clusters associated with secondary metabolite biosynthesis in Musa spp. identified key domains like Chalcone synthase, Phenylalanine ammonia-lyase, Aminotran 1–2, and CoA-ligase, which are integral to phenylpropanoid production—a critical pathway for secondary metabolites. The study highlights that the phenylpropanoid pathway and secondary metabolite biosynthesis are vital for Musa spp. resistance to Foc. Flavonoids and lignin may inhibit Sge1 protein formation, potentially disrupting Foc's cellular processes. These findings emphasize the role of phenylpropanoid pathways and secondary metabolites in combating BFW and suggest that targeting these pathways could offer innovative strategies for enhancing resistance and controlling BFW in banana crops. This research lays the groundwork for developing sustainable methods to protect banana cultivation and ensure food security.

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针对 Fusarium oxysporum f. sp. cubense 的 SGE1 蛋白的硅学剖析、对接分析以及麝香树次生代谢物与蛋白质的相互作用

由 Fusarium oxysporum f. sp. cubense（Foc）引起的香蕉镰刀菌枯萎病（Banana Fusarium Wilt，BFW）威胁着全球的香蕉作物，病原体的毒力部分受 Sge1 转录因子的调控，而 Sge1 转录因子会增强病害的严重性。某些蕈蚊物种对 Foc 具有抗性，这表明其固有的遗传特性赋予了对 Sge1Foc 的免疫力。本研究利用生物信息学工具研究了茄子亚种（Musa accuminata subsp.通过硅学分析，我们探索了麝香草属植物与 Foc 之间的相互作用，重点是 Sge1 蛋白。Anti-SMASH、AutoDockVina 4.0、STRING 和 Phoenix 等工具有助于分析穆萨属植物的次生代谢物，并确定参与防御的生物合成基因簇。我们的研究结果表明，次生代谢物（包括糖类、萜烯类和多酮类化合物）对植物的免疫反应至关重要。对 3-苯基苯酚、儿茶素和表儿茶素等选定的麝香草代谢物进行的分子对接研究显示，3-苯基苯酚与 Sge1Foc 蛋白的结合亲和力最高（-6.7 kcal/mol）。进一步分析与麝香草次生代谢物生物合成相关的基因簇，发现了查耳酮合成酶、苯丙氨酸氨解酶、氨基曲霉 1-2 和 CoA 连接酶等关键域，它们是苯丙类化合物生产不可或缺的部分--这是次生代谢物的关键途径。该研究强调，苯丙酮途径和次生代谢物的生物合成对麝香草属植物抵抗 Foc 至关重要。类黄酮和木质素可能会抑制 Sge1 蛋白的形成，从而可能破坏 Foc 的细胞过程。这些发现强调了苯丙类途径和次生代谢物在抗BFW中的作用，并表明针对这些途径可提供创新战略，增强香蕉作物的抗性并控制BFW。这项研究为开发保护香蕉种植和确保粮食安全的可持续方法奠定了基础。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Computational Biology and Chemistry 生物-计算机：跨学科应用

CiteScore

6.10

自引率

3.20%

发文量

142

审稿时长

24 days

期刊介绍： Computational Biology and Chemistry publishes original research papers and review articles in all areas of computational life sciences. High quality research contributions with a major computational component in the areas of nucleic acid and protein sequence research, molecular evolution, molecular genetics (functional genomics and proteomics), theory and practice of either biology-specific or chemical-biology-specific modeling, and structural biology of nucleic acids and proteins are particularly welcome. Exceptionally high quality research work in bioinformatics, systems biology, ecology, computational pharmacology, metabolism, biomedical engineering, epidemiology, and statistical genetics will also be considered. Given their inherent uncertainty, protein modeling and molecular docking studies should be thoroughly validated. In the absence of experimental results for validation, the use of molecular dynamics simulations along with detailed free energy calculations, for example, should be used as complementary techniques to support the major conclusions. Submissions of premature modeling exercises without additional biological insights will not be considered. Review articles will generally be commissioned by the editors and should not be submitted to the journal without explicit invitation. However prospective authors are welcome to send a brief (one to three pages) synopsis, which will be evaluated by the editors.