Linking fungal secondary metabolites and their biosynthetic gene clusters

Fungi are well recognized for their ability to produce a variety of secondary metabolites, which offer opportunities to produce food additives, colorants, cosmetics, enzymes, and biopesticides. However, some fungal metabolites can generate serious health hazards and enormous economic losses, the mycotoxins [1].

An early assessment of the strains’ metabolite production potential is a growing concern in industrial and academic biotechnology, aiming to avoid safety hazards and save time and money during product development. This is especially important for start-up companies developing novel fungal fermented foods since even strains generally recognized as safe (GRAS), such as Aspergillus niger and A. oryzae, out of the well-established conditions of their intended use, could potentially produce mycotoxins.

Dereplication and the application of metabolomic high-throughput techniques, including mass networking tools, enable the rapid identification of compounds in complex samples [2]. However, metabolomic approaches only reflect chemical production under the specific tested conditions.

Genome mining approaches, on the other hand, enable the identification of biosynthetic gene clusters (BGCs) responsible for forming a particular molecule in an organism, giving an estimation of its production capabilities [3]. However, there is a mismatch between the number of predicted metabolites, known molecules, and molecules linking to their respective BGC, even for the most well-studied fungal species [4].

Therefore, to contribute to the easy assessment of fungal strains, new BGCs still need to be identified. This work uses a synergistic approach combining metabolomics, genome mining, and molecular biology tools to accomplish this task. Using genome mining approaches and retrobiosynthesis analysis, high-quality sequences of Aspergillus strains from the section Nigri allowed us to establish potential BGCs responsible for the biosynthesis of the detected compounds by untargeted analysis. Additionally, targeted detection methods were developed by liquid chromatography coupled to high-resolution mass spectrometry (MS), which will enable the fast dereplication of the target compounds during the forthcoming knock-out experiments.