Pro-CRISPR PcrIIC1-associated Cas9 system for enhanced bacterial immunity

Shouyue Zhang, Ao Sun, Jing-Mei Qian, Shuo Lin, Wenjing Xing, Yun Yang, Han-Zhou Zhu, Xin-Yi Zhou, Yan-Shuo Guo, Yun Liu, Yu Meng, Shu-Lin Jin, Wenhao Song, Cheng-Ping Li, Zhaofu Li, Shuai Jin, Jian-Hua Wang, Meng-Qiu Dong, Caixia Gao, Chunlai Chen (), Yang Bai () and Jun-Jie Gogo Liu ()
Additional contact information
Shouyue Zhang: Tsinghua University
Ao Sun: Tsinghua University
Jing-Mei Qian: Chinese Academy of Sciences
Shuo Lin: Tsinghua University
Wenjing Xing: Tsinghua University
Yun Yang: Tsinghua University
Han-Zhou Zhu: Tsinghua University
Xin-Yi Zhou: Chinese Academy of Sciences
Yan-Shuo Guo: Chinese Academy of Sciences
Yun Liu: Tsinghua University
Yu Meng: Tsinghua University
Shu-Lin Jin: Tsinghua University
Wenhao Song: Tsinghua University
Cheng-Ping Li: Tsinghua University
Zhaofu Li: Tsinghua University
Shuai Jin: Tsinghua University
Jian-Hua Wang: National Institute of Biological Sciences
Meng-Qiu Dong: National Institute of Biological Sciences
Caixia Gao: University of Chinese Academy of Sciences
Chunlai Chen: Tsinghua University
Yang Bai: Chinese Academy of Sciences
Jun-Jie Gogo Liu: Tsinghua University

Nature, 2024, vol. 630, issue 8016, 484-492

Abstract: Abstract The CRISPR system is an adaptive immune system found in prokaryotes that defends host cells against the invasion of foreign DNA1. As part of the ongoing struggle between phages and the bacterial immune system, the CRISPR system has evolved into various types, each with distinct functionalities2. Type II Cas9 is the most extensively studied of these systems and has diverse subtypes. It remains uncertain whether members of this family can evolve additional mechanisms to counter viral invasions3,4. Here we identify 2,062 complete Cas9 loci, predict the structures of their associated proteins and reveal three structural growth trajectories for type II-C Cas9. We found that novel associated genes (NAGs) tended to be present within the loci of larger II-C Cas9s. Further investigation revealed that CbCas9 from Chryseobacterium species contains a novel β-REC2 domain, and forms a heterotetrameric complex with an NAG-encoded CRISPR–Cas-system-promoting (pro-CRISPR) protein of II-C Cas9 (PcrIIC1). The CbCas9–PcrIIC1 complex exhibits enhanced DNA binding and cleavage activity, broader compatibility for protospacer adjacent motif sequences, increased tolerance for mismatches and improved anti-phage immunity, compared with stand-alone CbCas9. Overall, our work sheds light on the diversity and ‘growth evolutionary’ trajectories of II-C Cas9 proteins at the structural level, and identifies many NAGs—such as PcrIIC1, which serves as a pro-CRISPR factor to enhance CRISPR-mediated immunity.

Date: 2024
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DOI: 10.1038/s41586-024-07486-x

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