Activating natural product synthesis using CRISPR interference and activation systems in Streptomyces

The rise of antibiotic-resistant bacteria represents a major threat to global health, creating an urgent need to discover new antibiotics. Natural products derived from the genus Streptomyces represent a rich and diverse repertoire of chemical molecules from which new antibiotics are likely to be found. However, a major challenge is that the biosynthetic gene clusters (BGCs) responsible for natural product synthesis are often poorly expressed under laboratory culturing conditions, thus preventing the isolation and screening of novel chemicals. To address this, we describe a novel approach to activate silent BGCs through rewiring endogenous regulation using synthetic gene regulators based upon CRISPR-Cas. First, we refine CRISPR interference (CRISPRi) and create CRISPR activation (CRISPRa) systems that allow for highly programmable and effective gene repression and activation in Streptomyces. We then harness these tools to activate a silent BGC by perturbing its endogenous regulatory network. Together, this work advances the synthetic regulatory toolbox for Streptomyces and facilitates the programmable activation of silent BGCs for novel chemical discovery.

Automated summary

The rise of antibiotic-resistant bacteria is a major threat to global health, necessitating the discovery of new antibiotics. Natural products derived from Streptomyces offer a diverse pool of chemical molecules for potential antibiotic discovery. However, the poor expression of biosynthetic gene clusters (BGCs) responsible for natural product synthesis under laboratory conditions poses a challenge for isolating and screening novel chemicals. This study presents a novel approach using synthetic gene regulators based on CRISPR-Cas to activate silent BGCs by rewiring endogenous regulation. These tools enable programmable activation of silent BGCs and advance the synthetic regulatory toolbox for Streptomyces, facilitating the discovery of new chemical compounds.