Exploring a general multi-pronged activation strategy for natural product discovery in Actinomycetes
Dillon W. P. Tay, Lee Ling Tan, Elena Heng, Nadiah Zulkarnain, Kuan Chieh Ching, Mario Wibowo, Elaine Jinfeng Chin, Zann Tan, Chung Yan Leong, Veronica Ng, Lay Kien Yang, Deborah Chwee San Seow, Yi Wee Lim, Winston T. H. Koh, Lokanand Koduru, Yoganathan Kanagasundaram, Siew Bee Ng, Yee Hwee Lim, Fong Tian Wong, Yee Hwee Lim, Fong Tian Wong
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.