Repurposing endogenous type I-E CRISPR-Cas systems for natural product discovery in Streptomyces

Qun Zhou, Yatong Zhao, Changqiang Ke, Haojun Wang, Sheng Gao, Hui Li, Yan Zhang, Yang Ye () and Yunzi Luo ()
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Qun Zhou: School of Chemical Engineering and Technology, Tianjin University
Yatong Zhao: School of Chemical Engineering and Technology, Tianjin University
Changqiang Ke: Chinese Academy of Sciences
Haojun Wang: Sichuan University
Sheng Gao: Sichuan University
Hui Li: Sichuan University
Yan Zhang: School of Chemical Engineering and Technology, Tianjin University
Yang Ye: Chinese Academy of Sciences
Yunzi Luo: School of Chemical Engineering and Technology, Tianjin University

Nature Communications, 2024, vol. 15, issue 1, 1-12

Abstract: Abstract The multifunctional proteins of class 2 CRISPR systems such as Cas9, have been employed to activate cryptic biosynthetic gene clusters (BGCs) in Streptomyces, which represent a large and hidden reservoir of natural products. However, such approaches are not applicable to most Streptomyces strains with reasons to be comprehended. Inspired by the prevalence of the class 1 subtype especially the type I-E CRISPR system in Streptomyces, here we report the development of the type I-E CRISPR system into a series of transcriptional regulation tools. We further demonstrate the effectiveness of such activators in nine phylogenetically distant Streptomyces strains. Using these tools, we successfully activate 13 out of 21 BGCs and lead to the identification and characterization of one polyketide, one Ripp and three alkaloid products. Our work is expected to have a profound impact and to facilitate the discovery of numerous structurally diverse compounds from Streptomyces.

Date: 2024
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DOI: 10.1038/s41467-024-54196-z

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