Accessing the hidden biosynthetic capabilities of fungi

PROJECT SUMMARY Filamentous fungi are a major source of valuable natural products (e.g. antibacterial penicillin, the immunosuppressant cyclosporin, the cholesterol-lowering drug lovastatin, the fungicide azoxystrobin and the pesticide paraherquamide). Yet despite progress in genomic sequencing and the characterization of large numbers of fungal NPs, the identification of small molecules with genuinely new structures and activities has not kept pace with genome sequence. These key gaps are a consequence of current bioinformatic and genome mining procedures which are biased towards locating well-characterized classes of NPs, which follow the assumption that all genes important for synthesis of any particular NP will be clustered and lack consideration of how fungal ecology can inform chemical synthesis. We have addressed these challenges by developing the first genome-mining pipeline capable of identifying the new widespread chemical class of natural products in fungi, the isocyanides and uncovering the unexpected role of copper in regulating both isocyanide synthase (ICS) biosynthetic gene cluster (BGC) expression and compound production. To continue these advances, here we focus on three key areas of investigation including (i) elucidating products of ICS BGCs containing genes encoding unusual enzymatic features unique chemistries and/or target proteins, (ii) examining the hypothesis that isocyanides direct microbiome composition dependent on metal concentrations and (iii) exploring the potential of computational innovation to significantly advance an understanding of the foundations of fungal NP logic. Overall, this work will advance the field of NP discovery in new directions that includes promoting the chemistry and ecology of the poorly understood isocyanide NPs, dissecting consequences of NP elaboration on microbiome composition and aligning molecular and chemical proficiencies with computational innovations for uncharted NP discovery routes. Using molecular, chemical, ecological and computational tools, we are poised to uncover fundamental questions in complex fungal networks governing NP synthesis. Better understanding of these mechanisms is critical to elucidating NP classes with specific biological roles and, ultimately, to provide knowledge to address escalating direct and indirect challenges confronting human health worldwide.