High-throughput screen reveals sRNAs regulating crRNA biogenesis by targeting CRISPR leader to repress Rho termination

Ping Lin, Qinqin Pu, Qun Wu, Chuanmin Zhou, Biao Wang, Jacob Schettler, Zhihan Wang, Shugang Qin, Pan Gao, Rongpeng Li, Guoping Li, Zhenyu Cheng, Lefu Lan (), Jianxin Jiang () and Min Wu ()
Additional contact information
Ping Lin: Institute of Surgery Research, Daping Hospital, Army Medical University
Qinqin Pu: University of North Dakota
Qun Wu: University of North Dakota
Chuanmin Zhou: University of North Dakota
Biao Wang: University of North Dakota
Jacob Schettler: University of North Dakota
Zhihan Wang: University of North Dakota
Shugang Qin: University of North Dakota
Pan Gao: University of North Dakota
Rongpeng Li: Jiangsu Normal University
Guoping Li: Southwestern Medical University, Pulmonary and Allergy Institute, Affiliated Hospital
Zhenyu Cheng: Dalhousie University
Lefu Lan: Chinese Academy of Sciences
Jianxin Jiang: Institute of Surgery Research, Daping Hospital, Army Medical University
Min Wu: University of North Dakota

Nature Communications, 2019, vol. 10, issue 1, 1-12

Abstract: Abstract Discovery of CRISPR-Cas systems is one of paramount importance in the field of microbiology. Currently, how CRISPR-Cas systems are finely regulated remains to be defined. Here we use small regulatory RNA (sRNA) library to screen sRNAs targeting type I-F CRISPR-Cas system through proximity ligation by T4 RNA ligase and find 34 sRNAs linking to CRISPR loci. Among 34 sRNAs for potential regulators of CRISPR, sRNA pant463 and PhrS enhance CRISPR loci transcription, while pant391 represses their transcription. We identify PhrS as a regulator of CRISPR-Cas by binding CRISPR leaders to suppress Rho-dependent transcription termination. PhrS-mediated anti-termination facilitates CRISPR locus transcription to generate CRISPR RNA (crRNA) and subsequently promotes CRISPR-Cas adaptive immunity against bacteriophage invasion. Furthermore, this also exists in type I-C/-E CRISPR-Cas, suggesting general regulatory mechanisms in bacteria kingdom. Our findings identify sRNAs as important regulators of CRISPR-Cas, extending roles of sRNAs in controlling bacterial physiology by promoting CRISPR-Cas adaptation priming.

Date: 2019
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DOI: 10.1038/s41467-019-11695-8

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