Global Genome Mining in Fungi for Natural Product Discovery

Genome mining has been proven invaluable for discovering natural products, yet a significant challenge remains in selectively extracting biosynthetic gene clusters (BGCs) for untapped natural products from the vast array of available genome sequences. To overcome this challenge, we developed a fungal genome mining tool, FunBGCeX, which targets BGCs encoding enzymes lacking a detectable protein domain (i.e., “domainless” enzymes) that are often overlooked by existing bioinformatic tools. Using the genome mining tool, we scanned approximately 2,000 fungal genomes for BGCs encoding a homologue of Pyr4-family terpene cyclases, which are representative examples of apparently domainless enzymes, leading to the discovery of a number of BGCs with unique features. Further characterization of selected BGCs led to the discovery of the first fungal onoceroid triterpenoids and unprecedented onoceroid synthases. Moreover, our global genome mining uncovered unusual biosynthetic mechanisms underlying the formation of phthalide– and hydroquinone–drimane hybrids. These findings collectively demonstrate the utility of our genome mining approach in unveiling previously undescribed forms of biosynthetic pathways and natural product scaffolds. We believe that our genome mining strategy can be broadly applied to the discovery of unexploited fungal natural products with novel scaffolds.