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

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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.