Self-resistance-gene-guided, high-throughput automated genome mining of bioactive natural products from Streptomyces.

Cell systems Pub Date : 2025-03-19 Epub Date: 2025-03-11 DOI:10.1016/j.cels.2025.101237

Yujie Yuan, Chunshuai Huang, Nilmani Singh, Guanhua Xun, Huimin Zhao

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Abstract

Natural products (NPs) from bacteria, fungi, and plants are a vital source of drug leads, with Streptomyces species being particularly significant due to their capability of producing diverse bioactive compounds. Here, we present a fully automated, scalable, high-throughput platform for discovering bioactive NPs in Streptomyces (FAST-NPS). This platform integrates computational biosynthetic gene cluster (BGC) prediction and prioritization guided by self-resistance genes, automated cloning and heterologous expression, high-throughput fermentation, and product extraction. As a proof of concept, we cloned 105 BGCs (10-100 kb) from 11 Streptomyces strains with a 95% success rate. Heterologous expression in Streptomyces lividans TK24 led to the detection of 23 NPs, including 8 with antibacterial or antitumor bioactivities from 5 BGCs. This work highlights the potential of FAST-NPS to accelerate bioactive NP discovery for biomedical and biotechnological applications. A record of this paper's transparent peer review process is included in the supplemental information.

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Cell systems

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