Mining for a new class of fungal natural products: The evolution, diversity, and distribution of isocyanide synthase biosynthetic gene clusters

Authors: NICKLES, GRANT - University Of Wisconsin; OESTEREICHER, BRANDON - University Of Wisconsin; KELLER, NANCY - University Of Wisconsin; Drott, Milton

Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/6/2023
Publication Date: 7/10/2023
Citation: Nickles, G.R., Oestereicher, B., Keller, N.P., Drott, M.T. 2023. Mining for a new class of fungal natural products: The evolution, diversity, and distribution of isocyanide synthase biosynthetic gene clusters. Nucleic Acids Research. 51(14):7220-7235. https://doi.org/10.1093/nar/gkad573.
DOI: https://doi.org/10.1093/nar/gkad573

Interpretive Summary: Isocyanides (also called isonitriles) are a chemical class of compound that are produced by bacteria and fungi. These compounds have unique chemical properties that explain the ecology of organisms, including plant-pathogens like Fusarium sp., and that have been harnessed for anthropocentric aims. However, only a handful of isocyanide genes have ever been characterized, slowing research into this important group of compounds. Here we developed a bioinformatic pipeline that can identify the genes that biosynthesize isocyanide compounds from genome sequence data. We identify 3,800 isocyanide biosynthetic gene clusters in 3,300 genomes that we map across the fungal kingdom. We detail evolutionary and ecological associations of these genes and map them onto the fungal kingdom in ways that will facilitate and help guide research into this new class of compound. Our results will enable efforts to harness their unique chemical properties and better understand how they are involved in microbial competition and pathogenesis.

Technical Abstract: The products of non-canonical isocyanide synthase (ICS) biosynthetic gene clusters (BGCs) have strong bioactivities that mediate pathogenesis, microbial competition, metal-homeostasis through metal-associated chemistry. We sought to enable research into this class of compound by characterizing the biosynthetic potential and evolutionary history of these genes across the fungal kingdom. We developed the first genome-mining pipeline to identify ICS BGCs, locating 3,800 ICS BGCs in 3,300 genomes. Genes in these clusters share promoter motifs and are maintained in contiguous groupings by natural selection. ICS BGCs are not evenly distributed across Fungi, evidence of gene-family expansions in several Ascomycete families. We show that the dit1/dit2 gene cluster family (GCF), which was thought to only exist in yeast, is present in nearly 30% of all Ascomycetes, including many filamentous fungi. The evolutionary history of the dit GCF is marked by deep divergences and phylogenetic incompatibilities that raise questions about convergent evolution and suggest selection or ancient horizontal gene transfers has shaped the evolution of this cluster in some yeast and dimorphic fungi. Our results create a roadmap for future research into ICS BGCs. We developed a website (www.isocyanides.fungi.wisc.edu) that facilitates exploration, filtering, and downloading of all ICS BGCs and GCFs identified within this study.