Finding Diamonds in the Rough: Resistance-Gene-Directed Discovery of Fungal Natural Products
Bioactive natural products have evolved to inhibit specific cellular targets and have served as lead molecules for health and agricultural applications for the last century. The post-genomics era has brought a renaissance in natural product discovery using synthetic biology tools. However, compared to traditional bioactivity-guided approaches, genome mining of natural products with specific and potent biological activities remains challenging. Here we proposed a resistance gene directed strategy to discover new natural products of desired bioactivity from genomic data. Our approach is based on the co-clustering of a self-resistance gene in the natural product biosynthetic gene cluster, which serves as a window to potential biological activity of the encoded compound. To demonstrate the feasibility, we first successfully located and verified the biosynthetic gene cluster of a glyceraldehyde-3-phosphate dehydrogenase inhibitor heptelidic acid by using a resistance gene. We showed the glyceraldehyde-3-phosphate dehydrogenase homolog hepG, co-localized with biosynthetic genes, is able to confer self-resistance to the producing organism using in vitro biochemical analysis. Next we present the discovery and validation of a highly potent herbicide lead that targets a critical metabolic enzyme that is required for plant survival. We queried dihydroxyacid dehydratase in the branched-chain amino acid biosynthetic pathway in plants, which is often targeted for herbicide development. We also showed that the fungal sesquiterpenoid aspterric acid discovered using this method is a submicromolar inhibitor of DHAD and is effective as an herbicide in spray applications. The self-resistance gene astD was validated to be insensitive to aspterric acid and was deployed as a transgene in the establishment of plants that are resistant to aspterric acid. This herbicide-resistance gene combination complements urgent efforts in overcoming weed resistance. Our discovery demonstrates the potential of using a resistance-gene directed approach in the mining of bioactive natural products.