Deciphering the mechanisms of fungal mycoparasitism by functional genomics-driven approaches

背景。植物病原真菌的生物防治通常是从生物防治剂（BCA）或真菌寄生虫的角度来考虑，而不是从病原体的角度来考虑。就像支寄生虫利用多种机制控制真菌病原体一样，病原体也有多种反应来抵抗它们的攻击。我的研究项目旨在了解控制这些相互作用的分子和生化过程。需要考虑的因素包括霉菌感染所需的基因和涉及的关键代谢物和代谢途径，真菌病原体防御所需的基因和代谢物，以及两个微生物伴侣信号网络的调节机制。这些过程将在由两个真菌伙伴组成的病理系统中进行研究：分枝寄生虫秀丽隐杆线虫和植物病原体索拉根丝核菌。秀丽线虫作为一种分枝寄生虫的成功，是由于它拥有一套酶，可以降解茄状芽孢杆菌的细胞壁，以及一些基因和蛋白质，这些基因和蛋白质有助于它以其他方式攻击病原体。最近的研究表明，索拉尼真菌通过过度表达编码活性氧酶的基因来应对秀丽隐杆线虫的攻击，从而减少氧化应激和有毒代谢物的产生。科学的方法。目的是阐明参与寄生相互作用的两个伙伴之间的生物学过程。更广泛的目标是通过提供所涉及的潜在生物学过程的全景视图，特别是从植物病原体的角度，更好地了解真菌的相互作用。我将通过以下方式实现这些目标：(I)利用高通量蛋白质组学和代谢组学技术对茄茄霉在菌寄生条件下的全球蛋白质组学和代谢组学进行比较；（ii）使用有针对性的内部真菌文库和分析标准以及生物计算工具鉴定假定的蛋白质功能和标志性代谢物；（iii）基于已识别的生物标志物代谢物构建代谢组学网络。（iv）通过使用先进的统计软件和生物信息学工具识别代谢组学和蛋白质组学数据集之间的联合系统变异，实现代谢组学和蛋白质组学之间的调节联系；（vi）体外测试鉴定鉴定的代谢产物生物标志物，这些生物标志物在索拉尼真菌防御秀丽隐杆线虫中发挥作用。新颖性和预期意义。关于病原体对生物防治剂耐药性的实验数据数量有限，因此很难就生物防治系统的稳定性或相反的侵蚀性得出合理的结论。我的假设是，对应对拮抗剂攻击的病原体自卫机制进行更深入的研究，将有助于更好地理解这种相互作用，从而更有可能提供一种新的方法，以提高基于生物的植物疾病控制策略的持久性，并对转基因（微生物或植物）的部署产生影响。蛋白质组学和代谢组学与数据挖掘工具的结合将为生物防治的基础和应用研究提供重要信息。它还将为表达谱提供基础，这将使识别参与特定生理过程的蛋白质和代谢物成为可能。本计划将资助培养组学、生物信息学和分子植物病理学方面的5名研究生、2名本科生和1名PDF，并提供在生物技术和医疗市场力量中高度需要的新一代HQP培训。

BACKGROUND. Biological control of plant pathogenic fungi is usually considered from the perspective of the biocontrol agent (BCA) or a fungal parasite rather than that of the pathogen. Just as mycoparasites use a diverse arsenal of mechanisms to dominate fungal pathogens, pathogens also have diverse responses to counteract their attack. My research program is aimed at understanding the molecular and biochemical processes governing these interactions. Factors that need to be considered include the mycoparasite’s genes required for infection and the key metabolites and metabolic pathways involved, the fungal pathogen’s defense genes and metabolites required for defense, as well as the mechanisms by which both microbial partners’ signaling networks are regulated. These processes will be studied in a pathosystem composed of two fungal partners: the mycoparasite Stachybotrys elegans and the plant pathogen, Rhizoctonia solani. The success of S. elegans as a mycoparasite is due to its possession of a suite of enzymes that degrade the cell walls of R. solani, and to genes and proteins that facilitate its attack on the pathogen in other ways. Recent studies have shown that R. solani responds to S. elegans attack by over-expressing genes encoding for enzymes that quench reactive oxygen, thereby reducing oxidative stress as well as the production of toxic metabolites. SCIENTIFIC APPROACH. The aim is to elucidate the biological processes involved in parasitic interactions between both partners. The broader aim is to better understand mycoparasitic interactions in general by providing a panoramic view of the underlying biological processes involved, particularly from the plant pathogen’s point of view. I will accomplish these goals by: (i) global proteomic and metabolomic comparisons of R. solani under mycoparasitic conditions using high throughput proteomics and metabolomics; (ii) Identification of putative protein functions and of signatory metabolites using targeted in-house fungal libraries and analytical standards along with bio-computational tools; (iii) constructing metabolomics networks based on identified biomarkers metabolites. (iv) achieving regulatory links between the metabolome and proteome via the identification of the joint systematic variation across metabolomics and proteomics datasets using advanced statistical software and bioinformatics tools; (vi) in-vitro testing of identified metabolite biomarkers that play a role in R. solani defence against S. elegans. NOVELTY AND EXPECTED SIGNIFICANCE. The limited amount of experimental data on resistance of pathogens to biological control agents makes it difficult to draw sound conclusions on the stability or conversely, erosion of biological control systems. My hypothesis is that more intensive study of the pathogen self-defense mechanisms for coping with antagonist’s assault will lead to a better understanding of this interaction, and thus will be more likely to provide a novel approach to improving the durability of biologically-based plant disease control strategies and has implications for the deployment of transgenes (microorganisms or plants). The integration of proteomics and metabolomics in conjunction with data mining tools will provide important information for use in fundamental and applied research on biocontrol. It will also provide a base for expression profiling, which will enable the identification of proteins and metabolites involved in specific physiological processes. This proposal will support training of 5 graduate students, two undergraduates students, and a PDF in ‘omics’ disciplines, bioinformatics and molecular plant pathology as well as providing training of new generation of HQP that are highly sought in the biotechnological and medical market force.