Uncovering Small Molecules that Mediate Plant-Fungi Interactions

University Of California-Los Angeles, Los Angeles CA

Investigators

Abstract

The interactions between plants and fungi, both beneficial and deleterious, significantly affect agricultural output, food safety, and bioeconomy. Beneficial fungal-plant interactions can lead to increases in plant robustness and crop yield, while deleterious interactions can lead to devastating plant diseases and tremendous economic loss. Many aspects of these interactions are mediated by small organic molecules known as secondary metabolites produced by the fungi. These molecules can direct impact plant health, effect the symbiotic plant-fungi relationships and control the soil microorganism composition. Despite the importance of these metabolites in mediating plant-fungi interactions, only a limited number of compounds are known. Therefore, a complete understanding of the chemical identities and functions of these molecules is critical to our ability to control the fungal-plant interactions, and to benefit agriculture and plant-based bioeconomy. To do so, the researchers will apply synthetic biology approaches to genetically and chemically catalog the secondary metabolites that can be biosynthesized by different plant-associated fungi. They will then test the biological activities of these compounds directly on model plants grown in the laboratory to assess their functions. If beneficial or deleterious effects on plant are observed, they will perform plant genetic studies to understand the target of the compounds. Successful completion of this project will unveil the multitude of interactions between fungi and plants, provide access to chemicals that can be used to improve plant growth and crop yield, and develop new strategies to overcome the devastating plant diseases caused by pathogenic fungi. It is widely accepted that secondary metabolites are highly important in fungal-plant interactions. However, a very limited number of compounds from fungi has been isolated and characterized. Genome sequences of biocontrol and phytopathogenic fungi have revealed each fungus can encode 50~80 biosynthetic gene clusters (BGCs) that are associated with secondary metabolite biosynthesis, with an overwhelming majority of these (> 90%) remaining uncharacterized with unknown metabolites in laboratory conditions. Transcriptomics data with pathogenic fungi showed numerous BGCs are upregulated during different phases of plant colonization and virulence, yet the metabolites have remained completely unknown. The objectives of this project are to expand the inventory of secondary metabolites from these plant-associated fungi, and to understand their biological roles. Towards these goals, this project will use systems and synthetic biology tools to perform genome mining of the BGCs, and genetic and biochemical approaches to identify the molecular targets of bioactive metabolites. In Objective 1, the researchers will refactor BGCs from the genomes of beneficial fungi such as Trichoderma afroharzianum t-22 and Gliocladium roseum, and produce the compounds in heterologous hosts. Objective 2 will focus on the devastating wheat pathogen Zymoseptoria tritici. The researchers will use bioinformatics and heterologous expression to identify metabolites from BGCs that are elevated during the biotrophic and necrotrophic phases of fungal growth in wheat. In Objective 3, the researchers will analyze the small molecules that exhibit functions on plants for their modes of action using forward genetics in Arabidopsis thaliana. This project represents an important step towards fully mapping the small molecule interactome. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.