Literature DB >> 28595896

Structural Basis for the Altered PAM Recognition by Engineered CRISPR-Cpf1.

Hiroshi Nishimasu1, Takashi Yamano2, Linyi Gao3, Feng Zhang4, Ryuichiro Ishitani2, Osamu Nureki5.   

Abstract

The RNA-guided Cpf1 nuclease cleaves double-stranded DNA targets complementary to the CRISPR RNA (crRNA), and it has been harnessed for genome editing technologies. Recently, Acidaminococcus sp. BV3L6 (AsCpf1) was engineered to recognize altered DNA sequences as the protospacer adjacent motif (PAM), thereby expanding the target range of Cpf1-mediated genome editing. Whereas wild-type AsCpf1 recognizes the TTTV PAM, the RVR (S542R/K548V/N552R) and RR (S542R/K607R) variants can efficiently recognize the TATV and TYCV PAMs, respectively. However, their PAM recognition mechanisms remained unknown. Here we present the 2.0 Å resolution crystal structures of the RVR and RR variants bound to a crRNA and its target DNA. The structures revealed that the RVR and RR variants primarily recognize the PAM-complementary nucleotides via the substituted residues. Our high-resolution structures delineated the altered PAM recognition mechanisms of the AsCpf1 variants, providing a basis for the further engineering of CRISPR-Cpf1.
Copyright © 2017 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  CRISPR-Cas system; Cas12a; Cpf1; crystal structure; protospacer adjacent motif

Mesh：

Substances：

Year:  2017        PMID： 28595896      PMCID： PMC5957533          DOI： 10.1016/j.molcel.2017.04.019

Source DB:  PubMed          Journal:  Mol Cell        ISSN： 1097-2765            Impact factor:   17.970


  32 in total

1.  Crystal Structure of Staphylococcus aureus Cas9.

Authors:  Hiroshi Nishimasu; Le Cong; Winston X Yan; F Ann Ran; Bernd Zetsche; Yinqing Li; Arisa Kurabayashi; Ryuichiro Ishitani; Feng Zhang; Osamu Nureki
Journal:  Cell       Date:  2015-08-27       Impact factor: 41.582

2.  Structural Basis for the Altered PAM Specificities of Engineered CRISPR-Cas9.

Authors:  Seiichi Hirano; Hiroshi Nishimasu; Ryuichiro Ishitani; Osamu Nureki
Journal:  Mol Cell       Date:  2016-03-17       Impact factor: 17.970

3.  Type V CRISPR-Cas Cpf1 endonuclease employs a unique mechanism for crRNA-mediated target DNA recognition.

Authors:  Pu Gao; Hui Yang; Kanagalaghatta R Rajashankar; Zhiwei Huang; Dinshaw J Patel
Journal:  Cell Res       Date:  2016-07-22       Impact factor: 25.617

4.  Structure and Engineering of Francisella novicida Cas9.

Authors:  Hisato Hirano; Jonathan S Gootenberg; Takuro Horii; Omar O Abudayyeh; Mika Kimura; Patrick D Hsu; Takanori Nakane; Ryuichiro Ishitani; Izuho Hatada; Feng Zhang; Hiroshi Nishimasu; Osamu Nureki
Journal:  Cell       Date:  2016-02-11       Impact factor: 41.582

5.  In vivo high-throughput profiling of CRISPR-Cpf1 activity.

Authors:  Hui K Kim; Myungjae Song; Jinu Lee; A Vipin Menon; Soobin Jung; Young-Mook Kang; Jae W Choi; Euijeon Woo; Hyun C Koh; Jin-Wu Nam; Hyongbum Kim
Journal:  Nat Methods       Date:  2016-12-19       Impact factor: 28.547

6.  Diversity and evolution of class 2 CRISPR-Cas systems.

Authors:  Sergey Shmakov; Aaron Smargon; David Scott; David Cox; Neena Pyzocha; Winston Yan; Omar O Abudayyeh; Jonathan S Gootenberg; Kira S Makarova; Yuri I Wolf; Konstantin Severinov; Feng Zhang; Eugene V Koonin
Journal:  Nat Rev Microbiol       Date:  2017-01-23       Impact factor: 60.633

Review 7.  An updated evolutionary classification of CRISPR-Cas systems.

Authors:  Kira S Makarova; Yuri I Wolf; Omer S Alkhnbashi; Fabrizio Costa; Shiraz A Shah; Sita J Saunders; Rodolphe Barrangou; Stan J J Brouns; Emmanuelle Charpentier; Daniel H Haft; Philippe Horvath; Sylvain Moineau; Francisco J M Mojica; Rebecca M Terns; Michael P Terns; Malcolm F White; Alexander F Yakunin; Roger A Garrett; John van der Oost; Rolf Backofen; Eugene V Koonin
Journal:  Nat Rev Microbiol       Date:  2015-09-28       Impact factor: 60.633

8.  How good are my data and what is the resolution?

Authors:  Philip R Evans; Garib N Murshudov
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2013-06-13

9.  In vivo genome editing using Staphylococcus aureus Cas9.

Authors:  F Ann Ran; Le Cong; Winston X Yan; David A Scott; Jonathan S Gootenberg; Andrea J Kriz; Bernd Zetsche; Ophir Shalem; Xuebing Wu; Kira S Makarova; Eugene V Koonin; Phillip A Sharp; Feng Zhang
Journal:  Nature       Date:  2015-04-01       Impact factor: 49.962

10.  RNA-programmed genome editing in human cells.

Authors:  Martin Jinek; Alexandra East; Aaron Cheng; Steven Lin; Enbo Ma; Jennifer Doudna
Journal:  Elife       Date:  2013-01-29       Impact factor: 8.140
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  32 in total

Review 1.  Non-viral delivery systems for CRISPR/Cas9-based genome editing: Challenges and opportunities.

Authors:  Ling Li; Shuo Hu; Xiaoyuan Chen
Journal:  Biomaterials       Date:  2018-04-18       Impact factor: 12.479

2.  HIV-1 Employs Multiple Mechanisms To Resist Cas9/Single Guide RNA Targeting the Viral Primer Binding Site.

Authors:  Zhen Wang; Wenzhou Wang; Ya Cheng Cui; Qinghua Pan; Weijun Zhu; Patrick Gendron; Fei Guo; Shan Cen; Michael Witcher; Chen Liang
Journal:  J Virol       Date:  2018-09-26       Impact factor: 5.103

Review 3.  Class 2 CRISPR-Cas RNA-guided endonucleases: Swiss Army knives of genome editing.

Authors:  Stefano Stella; Pablo Alcón; Guillermo Montoya
Journal:  Nat Struct Mol Biol       Date:  2017-10-16       Impact factor: 15.369

Review 4.  The Conspicuity of CRISPR-Cpf1 System as a Significant Breakthrough in Genome Editing.

Authors:  Hadi Bayat; Mohammad Hossein Modarressi; Azam Rahimpour
Journal:  Curr Microbiol       Date:  2017-11-30       Impact factor: 2.188

5.  Structural Basis for the Canonical and Non-canonical PAM Recognition by CRISPR-Cpf1.

Authors:  Takashi Yamano; Bernd Zetsche; Ryuichiro Ishitani; Feng Zhang; Hiroshi Nishimasu; Osamu Nureki
Journal:  Mol Cell       Date:  2017-08-03       Impact factor: 17.970

6.  Argonaute-based programmable RNase as a tool for cleavage of highly-structured RNA.

Authors:  Daniel M Dayeh; William A Cantara; Jonathan P Kitzrow; Karin Musier-Forsyth; Kotaro Nakanishi
Journal:  Nucleic Acids Res       Date:  2018-09-19       Impact factor: 16.971

7.  Mechanistic Insights into the cis- and trans-Acting DNase Activities of Cas12a.

Authors:  Daan C Swarts; Martin Jinek
Journal:  Mol Cell       Date:  2019-01-10       Impact factor: 17.970

Review 8.  Recent advances in CRISPR technologies for genome editing.

Authors:  Myeonghoon Song; Taeyoung Koo
Journal:  Arch Pharm Res       Date:  2021-06-23       Impact factor: 4.946

9.  Cryo-EM structure of the RNA-guided ribonuclease Cas12g.

Authors:  Zhuang Li; Heng Zhang; Renjian Xiao; Ruijie Han; Leifu Chang
Journal:  Nat Chem Biol       Date:  2021-01-25       Impact factor: 15.040

10.  Mechanisms for target recognition and cleavage by the Cas12i RNA-guided endonuclease.

Authors:  Heng Zhang; Zhuang Li; Renjian Xiao; Leifu Chang
Journal:  Nat Struct Mol Biol       Date:  2020-09-07       Impact factor: 15.369
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