Comprehensive curation and analysis of fungal biosynthetic gene clusters of published natural products

Abstract

Microorganisms produce a wide range of natural products (NPs) with clinically and agriculturally relevant biological activities. In bacteria and fungi, genes encoding successive steps in a biosynthetic pathway tend to be clustered on the chromosome as biosynthetic gene clusters (BGCs). Historically, “activity-guided” approaches to NP discovery have focused on bioactivity screening of NPs produced by culturable microbes. In contrast, recent “genome mining” approaches first identify candidate BGCs, express these biosynthetic genes using synthetic biology methods, and finally test for the production of NPs. Fungal genome mining efforts and the exploration of novel sequence and NP space are limited, however, by the lack of a comprehensive catalog of BGCs encoding experimentally-validated products. In this study, we generated a comprehensive reference set of fungal NPs whose biosynthetic gene clusters are described in the published literature. To generate this dataset, we first identified NCBI records that included both a peer-reviewed article and an associated nucleotide record. We filtered these records by text and homology criteria to identify putative NP-related articles and BGCs. Next, we manually curated the resulting articles, chemical structures, and protein sequences. The resulting catalog contains 197 unique NP compounds covering several major classes of fungal NPs, including polyketides, non-ribosomal peptides, terpenoids, and alkaloids. The distribution of articles published per compound shows a bias towards the study of certain popular compounds, such as the aflatoxins. Phylogenetic analysis of biosynthetic genes suggests that much chemical and enzymatic diversity remains to be discovered in fungi. Our catalog was incorporated into the recently launched Minimum Information about Biosynthetic Gene cluster (MIBiG) repository to create the largest known set of fungal BGCs and associated NPs, a resource that we anticipate will guide future genome mining and synthetic biology efforts toward discovering novel fungal enzymes and metabolites.

Predominately Uncultured Microbes as Sources of Bioactive Agents

“…These include, but are not limited to: discussion of eliciting secondary metabolism in actinomycetes (Seyedsayamdost et al, 2012; Abdelmohsen et al, 2015; Rutledge and Challis, 2015); methodologies for determining the compounds expressed (Adnani et al, 2014; Luzzatto-Knaan et al, 2015; Medema and Fischbach, 2015; Mohimani and Pevzner, 2016); analyses of the biosynthetic clusters identified in fungi to published natural product structures (Li et al, 2016b); small-scale plate-based techniques for fungal co-culture (Bertrand et al, 2014); on-demand production of secondary metabolites (Bode et al, 2015); mixed culture of endophytes (Chagas et al, 2013); metabolomics in induced cultures (Derewacz et al, 2015; van der Lee and Medema, 2016; Zhang et al, 2016a,b; Ziemert et al, 2016); use of synthetic biological techniques to further expand the chemical biodiversity discovered (Smanski et al, 2016); and a recent review of the array of approaches to study such cryptic cluster expression by Zarins-Tutt et al (2016).…”

Metabolomics‐based chemotaxonomy of root endophytic fungi for natural products discovery

“…However, the establishment of functional links between natural products and ecology is difficult, and largely hindered by the low annotation yields. A comprehensive identification of compounds will likely further such inferences, by allowing comparisons among structural similarities in entire metabolomes and their correlation with phylogenetic and ecological resemblance among their producing fungi (Li et al ., ).…”

Six Key Traits of Fungi: Their Evolutionary Origins and Genetic Bases

“…Only a small proportion of the adaptive biological functions of SMs are characterized (it is sometimes argued that most have no current functions [95]), but a subset of these is known to have important ecological roles (96). As with plants, the most obvious roles for SMs are defense and competition (Fig.…”