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从生防因子或真菌寄生物的角度考虑，而不是病原体的角度。正如真菌寄生虫使用多种机制来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。我的研究计划旨在了解这些相互作用的分子和生物化学过程。需要考虑的因素包括真菌寄生虫感染所需的基因和所涉及的关键代谢物和代谢途径，真菌病原体的防御基因和防御所需的代谢物，以及调节微生物伴侣信号网络的机制。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：真菌寄生虫Stachyboconiaelegans和植物病原体立枯丝核菌。S. elegans作为一种真菌寄生虫是由于它拥有一套酶，降解R. solani，以及以其他方式促进其攻击病原体的基因和蛋白质。最近的研究表明，R. solani对S.秀丽线虫通过过度表达编码酶的基因来攻击，该酶可以淬灭活性氧，从而减少氧化应激以及有毒代谢物的产生。科学的方法。其目的是阐明双方合作伙伴之间的寄生虫相互作用所涉及的生物过程。更广泛的目的是更好地了解真菌寄生虫的相互作用，一般通过提供一个全景的基本生物过程，特别是从植物病原体的角度来看。我将完成这些目标：（i）全球蛋白质组学和代谢组学的比较R。solani在真菌寄生条件下使用高通量蛋白质组学和代谢组学;（ii）使用有针对性的内部真菌文库和分析标准沿着生物计算工具鉴定推定的蛋白质功能和签名代谢物;（iii）基于鉴定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跨代谢组学和蛋白质组学数据集的联合系统变异，实现代谢组和蛋白质组之间的调控联系;（vi）体外测试在R. solani防御S.优雅新奇和预期意义。关于病原体对生物防治剂的抗性的实验数据有限，因此难以得出关于生物防治系统的稳定性或相反的侵蚀性的合理结论。我的假设是，更深入的研究病原体的自我防御机制，以应对拮抗剂的攻击将导致更好地了解这种相互作用，从而将更有可能提供一种新的方法来提高持久性的生物为基础的植物病害控制策略，并有影响的转基因（微生物或植物）的部署。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。它还将为表达谱分析提供基础，这将使参与特定生理过程的蛋白质和代谢物的鉴定成为可能。该提案将支持在“组学”学科、生物信息学和分子植物病理学方面培训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备受追捧的新一代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.