Diverse Mechanisms of CRISPR-Cas9 Inhibition by Type IIC Anti-CRISPR Proteins

被引:78
作者
Zhu, Yalan [1 ,2 ]
Gao, Ang [3 ]
Zhan, Qi [1 ,2 ]
Wang, Yong [1 ]
Feng, Han [1 ]
Liu, Songqing [1 ]
Gao, Guangxia [4 ]
Serganov, Alexander [3 ]
Gao, Pu [1 ]
机构
[1] Chinese Acad Sci, Inst Biophys, Natl Lab Biomacromol, CAS Key Lab Infect & Immun,CAS Ctr Excellence Bio, Beijing 100101, Peoples R China
[2] Univ Chinese Acad Sci, Beijing 100049, Peoples R China
[3] NYU, Sch Med, Dept Biochem & Mol Pharmacol, New York, NY 10016 USA
[4] Chinese Acad Sci, Inst Biophys, CAS Ctr Excellence Biomacromol, CAS Key Lab Infect & Immun, Beijing 100101, Peoples R China
基金
国家重点研发计划; 中国国家自然科学基金;
关键词
VIRAL SUPPRESSORS; CRYSTAL-STRUCTURE; STRUCTURAL BASIS; RNA; CAS; COMPLEX; RECOGNITION;
D O I
10.1016/j.molcel.2019.01.038
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Anti-CRISPR proteins (Acrs) targeting CRISPR-Cas9 systems represent natural "off switches" for Cas9-based applications. Recently, AcrIIC1, AcrIIC2, and AcrIIC3 proteins were found to inhibit Neisseria meningitidis Cas9 (NmeCas9) activity in bacterial and human cells. Here we report biochemical and structural data that suggest molecular mechanisms of AcrIIC2-and AcrIIC3-mediated Cas9 inhibition. AcrIIC2 dimer interacts with the bridge helix of Cas9, interferes with RNA binding, and prevents DNA loading into Cas9. AcrIIC3 blocks the DNA loading step through binding to a non-conserved surface of the HNH domain of Cas9. AcrIIC3 also forms additional interactions with the REC lobe of Cas9 and induces the dimerization of the AcrIIC3-Cas9 complex. While AcrIIC2 targets Cas9 orthologs from different sub-types, albeit with different efficiency, AcrIIC3 specifically inhibits NmeCas9. Structure-guided changes in NmeCas9 orthologs convert them into antiCRISPR-sensitive proteins. Our studies provide insights into anti-CRISPR-mediated suppression mechanisms and guidelines for designing regulatory tools in Cas9-based applications.
引用
收藏
页码:296 / +
页数:21
相关论文
共 44 条
[1]   PHENIX: a comprehensive Python']Python-based system for macromolecular structure solution [J].
Adams, Paul D. ;
Afonine, Pavel V. ;
Bunkoczi, Gabor ;
Chen, Vincent B. ;
Davis, Ian W. ;
Echols, Nathaniel ;
Headd, Jeffrey J. ;
Hung, Li-Wei ;
Kapral, Gary J. ;
Grosse-Kunstleve, Ralf W. ;
McCoy, Airlie J. ;
Moriarty, Nigel W. ;
Oeffner, Robert ;
Read, Randy J. ;
Richardson, David C. ;
Richardson, Jane S. ;
Terwilliger, Thomas C. ;
Zwart, Peter H. .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2010, 66 :213-221
[2]   Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease [J].
Anders, Carolin ;
Niewoehner, Ole ;
Duerst, Alessia ;
Jinek, Martin .
NATURE, 2014, 513 (7519) :569-+
[3]   Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system [J].
Bondy-Denomy, Joe ;
Pawluk, April ;
Maxwell, Karen L. ;
Davidson, Alan R. .
NATURE, 2013, 493 (7432) :429-U181
[4]   Multiple mechanisms for CRISPR-Cas inhibition by anti-CRISPR proteins [J].
Bondy-Denomy, Joseph ;
Garcia, Bianca ;
Strum, Scott ;
Du, Mingjian ;
Rollins, MaryClare F. ;
Hidalgo-Reyes, Yurima ;
Wiedenheft, Blake ;
Maxwell, Karen L. ;
Davidson, Alan R. .
NATURE, 2015, 526 (7571) :136-+
[5]   Bacteriophage Cooperation Suppresses CRISPR-Cas3 and Cas9 Immunity [J].
Borges, Adair L. ;
Zhang, Jenny Y. ;
Rollins, MaryClare F. ;
Osuna, Beatriz A. ;
Wiedenheft, Blake ;
Bondy-Denomy, Joseph .
CELL, 2018, 174 (04) :917-+
[6]   Structure Reveals Mechanisms of Viral Suppressors that Intercept a CRISPR RNA-Guided Surveillance Complex [J].
Chowdhury, Saikat ;
Carter, Joshua ;
Rollins, MaryClare F. ;
Golden, Sarah M. ;
Jackson, Ryan N. ;
Hoffmann, Connor ;
Nosaka, Lyn'Al ;
Bondy-Denomy, Joseph ;
Maxwell, Karen L. ;
Davidson, Alan R. ;
Fischer, Elizabeth R. ;
Lander, Gabriel C. ;
Wiedenheft, Blake .
CELL, 2017, 169 (01) :47-+
[7]   CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III [J].
Deltcheva, Elitza ;
Chylinski, Krzysztof ;
Sharma, Cynthia M. ;
Gonzales, Karine ;
Chao, Yanjie ;
Pirzada, Zaid A. ;
Eckert, Maria R. ;
Vogel, Joerg ;
Charpentier, Emmanuelle .
NATURE, 2011, 471 (7340) :602-+
[8]   Structural basis of CRISPR-SpyCas9 inhibition by an anti-CRISPR protein [J].
Dong, De ;
Guo, Minghui ;
Wang, Sihan ;
Zhu, Yuwei ;
Wang, Shuo ;
Xiong, Zhi ;
Yang, Jianzheng ;
Xu, Zengliang ;
Huang, Zhiwei .
NATURE, 2017, 546 (7658) :436-+
[9]   Systematic discovery of antiphage defense systems in the microbial pangenome [J].
Doron, Shany ;
Melamed, Sarah ;
Ofir, Gal ;
Leavitt, Azita ;
Lopatina, Anna ;
Keren, Mai ;
Amitai, Gil ;
Sorek, Rotem .
SCIENCE, 2018, 359 (6379)
[10]   Features and development of Coot [J].
Emsley, P. ;
Lohkamp, B. ;
Scott, W. G. ;
Cowtan, K. .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2010, 66 :486-501