Exploring a general multi-pronged activation strategy for natural product discovery in Actinomycetes

Abstract

Natural products possess significant therapeutic potential but remain underutilized despite advances in genomics and bioinformatics. While there are approaches to activate and upregulate natural product biosynthesis in both native and heterologous microbial strains, a comprehensive strategy to elicit production of natural products as well as a generalizable and efficient method to interrogate diverse native strains collection, remains lacking. Here, we explore a flexible and robust integrase-mediated multi-pronged activation approach to reliably perturb and globally trigger antibiotics production in actinobacteria. Across 54 actinobacterial strains, our approach yielded 124 distinct activator-strain combinations which consistently outperform wild type. Our approach expands accessible metabolite space by nearly two-fold and increases selected metabolite yields by up to >200-fold, enabling discovery of Gram-negative bioactivity in tetramic acid analogs. We envision these findings as a gateway towards a more streamlined, accelerated, and scalable strategy to unlock the full potential of Nature’s chemical repertoire.

Abstract

A multi-pronged activation approach applied to 54 actinobacterial strains doubles accessible metabolite space and enables discovery of gram-negative bioactivity, offering insights to harness nature’s chemical potential. The approach enhances or triggers natural product production across all 54 native actinobacterial strains, doubling total metabolite production and enabling the discovery of a new tetramic acid analog with gram-negative bioactivity. Insights from this large-scale study could lead to a more streamlined approach to unlock the full potential of nature’s chemical resources.