Recombinant Environmental Libraries Provide Access to Microbial Diversity for Drug Discovery from Natural Products

TLDR

The study constructed and screened a 5,000‑clone environmental DNA library from uncultivated soil microbes to tap microbial biodiversity for natural‑product drug discovery. The library was characterized for diversity and heterologous gene expression, then screened by PCR for type I polyketide synthase genes and assayed colonies and extracts for novel compound production. The library contained highly diverse, largely uncharacterized microorganisms, yielded new polyketide synthase genes in at least eight clones, and produced heterologous molecules in five clones, demonstrating the feasibility of using uncultivated microbes for drug discovery.

Abstract

ABSTRACT To further explore possible avenues for accessing microbial biodiversity for drug discovery from natural products, we constructed and screened a 5,000-clone “shotgun” environmental DNA library by using an Escherichia coli-Streptomyces lividans shuttle cosmid vector and DNA inserts from microbes derived directly (without cultivation) from soil. The library was analyzed by several means to assess diversity, genetic content, and expression of heterologous genes in both expression hosts. We found that the phylogenetic content of the DNA library was extremely diverse, representing mostly microorganisms that have not been described previously. The library was screened by PCR for sequences similar to parts of type I polyketide synthase genes and tested for the expression of new molecules by screening of live colonies and cell extracts. The results revealed new polyketide synthase genes in at least eight clones. In addition, at least five additional clones were confirmed by high-pressure liquid chromatography analysis and/or biological activity to produce heterologous molecules. These data reinforce the idea that exploiting previously unknown or uncultivated microorganisms for the discovery of novel natural products has potential value and, most importantly, suggest a strategy for developing this technology into a realistic and effective drug discovery tool.