PhyloNaP: a tool for phylogeny-based function prediction of enzymes involved in biosynthesis of natural products

Introduction: The rise of antibiotic resistance underscores the urgent need for novel antibiotics derived from natural products (NPs). Genome mining has revealed diverse biosynthetic gene clusters (BGCs) that encode these compounds. Accurate structural knowledge of NPs is essential for extraction and other experimental procedures; however, structure prediction is challenging due to limited functional annotations for tailoring enzymes in NP biosynthesis.

Goals: This project aims to develop PhyloNaP, a database and tool for the functional annotation of enzymes involved in NP biosynthesis, with the focus on tailoring enzymes using phylogenetic analysis. By consolidating fragmented phylogenetic and functional data, PhyloNaP enables more accurate NP structure predictions, ultimately aiding in the discovery of new antibiotics and other therapeutics.

Materials & Methods: PhyloNaP integrates functional annotations from literature and public repositories such as MiBiG, SwissProt, and AntiSMASHdb. The database stores phylogenetic trees, sequence alignments, and functional annotations gathered from publications and generated specifically for this project. Currently, PhyloNaP includes enzyme families like methyltransferases, P450s, and halogenases, with each tree annotated with experimentally validated data on substrates and products.

Results: Using PhyloNaP, researchers can explore annotated enzymes, classify new enzymes, and position them within existing phylogenetic trees. This mapping allows users to examine the functional characteristics of closely related enzymes. PhyloNaP also demonstrate substrate features and potential modification sites, enhancing the reliability of NP structure predictions. Additionally, PhyloNaP incorporates information on the taxonomy of the enzyme"s source organism and the main characteristics of its BGC, with links to corresponding NPs in the MiBIG database.

Summary: PhyloNaP fills a critical gap in NP research by providing a centralized repository of annotated phylogenetic data. Researchers are encouraged to contribute new trees, thereby enriching this shared resource and increasing its utility across the scientific community. By integrating both phylogenetic and functional data, PhyloNaP has the potential to accelerate the discovery of valuable natural products.

Acknowledgment: This project has received funding from the European Union"s Horizon Europe program under the Marie Skłodowska-Curie grant agreement No 101072485.