Breaking the Silence: New Strategies for Discovering Novel Natural Products

Microorganisms are a major source of new therapeutic agents. My group has been developing new genomics-driven, synthetic biology-enabled strategies to discover and produce novel natural products from sequenced genomes and metagenomes. One strategy is to refactor target cryptic gene clusters in heterologous hosts. As proof of concept, we used this strategy to awaken the silent polyketide spectinabilin pathway from Streptomyces spectabilis in Streptomyces lividans and activate a cryptic pathway containing a polyketide synthase-non-ribosomal peptide synthetases from Streptomyces grieseus in Streptomyces lividans, which led to the discovery of two novel tetramic acid natural products that have never been reported in literature. To increase the throughput, we are establishing a fully integrated robotic system to automate all the steps in gene cluster refactoring and product detection. A second strategy is to activate the target cryptic gene clusters in their native hosts by knocking-in strong promoters upstream of the target cryptic gene clusters using a CRISPR/Cas9 system. We successfully activated more than 10 cryptic gene clusters from five different Streptomyces and uncovered a number of novel natural products. A third strategy is to express the uncharacterized biosynthetic gene clusters in heterologous hosts using a direct cloning method based on artificial restriction enzymes.