Natural products offer unmatched chemical and structural diversity compared to other small-molecule libraries, but traditional natural product discovery programs are not sustainable, demanding too much time, effort, and resources. Here we report a strain prioritization method for natural product discovery. Central to the method is the application of real-time PCR, targeting genes characteristic to the biosynthetic machinery of natural products with distinct scaffolds in a high-throughput format. The practicality and effectiveness of the method were showcased by prioritizing 1911 actinomycete strains for diterpenoid discovery. A total of 488 potential diterpenoid producers were identified, among which six were confirmed as platensimycin and platencin dual producers and one as a viguiepinol and oxaloterpin producer. While the method as described is most appropriate to prioritize strains for discovering specific natural products, variations of this method should be applicable to the discovery of other classes of natural products. Applications of genome sequencing and genome mining to the high-priority strains could essentially eliminate the chance elements from traditional discovery programs and fundamentally change how natural products are discovered.

Significance: There are many differences in the sequences of ketosynthase (KS) domains from the well-studied type I polyketide synthases (PKSs) and the more recently discovered acyltransferase (AT)-less type I PKSs. The AT-less type I PKSs generate polyketides with a high degree of structural diversity, which stems from their evolution by horizontal gene transfer. In comparison, canonical type I PKSs evolve by gene duplication. The seven structures of AT-less type I PKS KSs reveal the molecular details surrounding the evolution of substrate specificity and structural diversity, and their overall differences with canonical type I PKS KSs. Understanding the mechanism of substrate specificity will allow reprogramming of the KS active sites to generate polyketide analogues by PKS and polyketide biosynthetic pathway engineering.

The enediyne natural products have been explored for their phenomenal cytotoxicity. The development of enediynes into anticancer drugs has been successfully achieved through the utilization of polymer- and antibody-drug conjugates (ADCs) as drug delivery systems. An increasing inventory of enediynes would benefit current application of ADCs in many oncology programs. Innovations in expanding the enediyne inventory should take advantage of the current knowledge of enediyne biosynthesis and post-genomics technologies. Bioinformatics analysis of microbial genomes reveals that enediynes are underexplored, in particular from Actinomycetales. This digest highlights the emerging opportunities to explore microbial genomics for the discovery of novel enediyne natural products.