Literature DB >> 32284602

Computational design of anti-CRISPR proteins with improved inhibition potency.

Jan Mathony1,2, Zander Harteveld3,4, Carolin Schmelas5,6, Julius Upmeier Zu Belzen1,2,7, Sabine Aschenbrenner1,2,8, Wei Sun9,10, Mareike D Hoffmann1,8, Christina Stengl1, Andreas Scheck3,4, Sandrine Georgeon3,4, Stéphane Rosset3,4, Yanli Wang9,10, Dirk Grimm5,6,11, Roland Eils2,7, Bruno E Correia12,13, Dominik Niopek14,15.   

Abstract

Anti-CRISPR (Acr) proteins are powerful tools to control CRISPR-Cas technologies. However, the available Acr repertoire is limited to naturally occurring variants. Here, we applied structure-based design on AcrIIC1, a broad-spectrum CRISPR-Cas9 inhibitor, to improve its efficacy on different targets. We first show that inserting exogenous protein domains into a selected AcrIIC1 surface site dramatically enhances inhibition of Neisseria meningitidis (Nme)Cas9. Then, applying structure-guided design to the Cas9-binding surface, we converted AcrIIC1 into AcrIIC1X, a potent inhibitor of the Staphylococcus aureus (Sau)Cas9, an orthologue widely applied for in vivo genome editing. Finally, to demonstrate the utility of AcrIIC1X for genome engineering applications, we implemented a hepatocyte-specific SauCas9 ON-switch by placing AcrIIC1X expression under regulation of microRNA-122. Our work introduces designer Acrs as important biotechnological tools and provides an innovative strategy to safeguard CRISPR technologies.

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Year:  2020        PMID: 32284602     DOI: 10.1038/s41589-020-0518-9

Source DB:  PubMed          Journal:  Nat Chem Biol        ISSN: 1552-4450            Impact factor:   15.040


  42 in total

1.  Engineered anti-CRISPR proteins for optogenetic control of CRISPR-Cas9.

Authors:  Felix Bubeck; Mareike D Hoffmann; Zander Harteveld; Sabine Aschenbrenner; Andreas Bietz; Max C Waldhauer; Kathleen Börner; Julia Fakhiri; Carolin Schmelas; Laura Dietz; Dirk Grimm; Bruno E Correia; Roland Eils; Dominik Niopek
Journal:  Nat Methods       Date:  2018-10-30       Impact factor: 28.547

2.  A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity.

Authors:  Martin Jinek; Krzysztof Chylinski; Ines Fonfara; Michael Hauer; Jennifer A Doudna; Emmanuelle Charpentier
Journal:  Science       Date:  2012-06-28       Impact factor: 47.728

3.  Multiplex genome engineering using CRISPR/Cas systems.

Authors:  Le Cong; F Ann Ran; David Cox; Shuailiang Lin; Robert Barretto; Naomi Habib; Patrick D Hsu; Xuebing Wu; Wenyan Jiang; Luciano A Marraffini; Feng Zhang
Journal:  Science       Date:  2013-01-03       Impact factor: 47.728

4.  RNA-guided human genome engineering via Cas9.

Authors:  Prashant Mali; Luhan Yang; Kevin M Esvelt; John Aach; Marc Guell; James E DiCarlo; Julie E Norville; George M Church
Journal:  Science       Date:  2013-01-03       Impact factor: 47.728

5.  Multiple mechanisms for CRISPR-Cas inhibition by anti-CRISPR proteins.

Authors:  Joseph Bondy-Denomy; Bianca Garcia; Scott Strum; Mingjian Du; MaryClare F Rollins; Yurima Hidalgo-Reyes; Blake Wiedenheft; Karen L Maxwell; Alan R Davidson
Journal:  Nature       Date:  2015-09-23       Impact factor: 49.962

6.  Cell-specific CRISPR-Cas9 activation by microRNA-dependent expression of anti-CRISPR proteins.

Authors:  Mareike D Hoffmann; Sabine Aschenbrenner; Stefanie Grosse; Kleopatra Rapti; Claire Domenger; Julia Fakhiri; Manuel Mastel; Kathleen Börner; Roland Eils; Dirk Grimm; Dominik Niopek
Journal:  Nucleic Acids Res       Date:  2019-07-26       Impact factor: 16.971

7.  A new group of phage anti-CRISPR genes inhibits the type I-E CRISPR-Cas system of Pseudomonas aeruginosa.

Authors:  April Pawluk; Joseph Bondy-Denomy; Vivian H W Cheung; Karen L Maxwell; Alan R Davidson
Journal:  mBio       Date:  2014-04-15       Impact factor: 7.867

8.  Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system.

Authors:  Joe Bondy-Denomy; April Pawluk; Karen L Maxwell; Alan R Davidson
Journal:  Nature       Date:  2012-12-16       Impact factor: 49.962

9.  Gene drive inhibition by the anti-CRISPR proteins AcrIIA2 and AcrIIA4 in Saccharomyces cerevisiae.

Authors:  Erianna M Basgall; Samantha C Goetting; Megan E Goeckel; Rachael M Giersch; Emily Roggenkamp; Madison N Schrock; Megan Halloran; Gregory C Finnigan
Journal:  Microbiology       Date:  2018-02-28       Impact factor: 2.777

10.  Anti-CRISPR-mediated control of gene editing and synthetic circuits in eukaryotic cells.

Authors:  Muneaki Nakamura; Prashanth Srinivasan; Michael Chavez; Matthew A Carter; Antonia A Dominguez; Marie La Russa; Matthew B Lau; Timothy R Abbott; Xiaoshu Xu; Dehua Zhao; Yuchen Gao; Nathan H Kipniss; Christina D Smolke; Joseph Bondy-Denomy; Lei S Qi
Journal:  Nat Commun       Date:  2019-01-14       Impact factor: 14.919

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  6 in total

1.  Listeria Phages Induce Cas9 Degradation to Protect Lysogenic Genomes.

Authors:  Beatriz A Osuna; Shweta Karambelkar; Caroline Mahendra; Kathleen A Christie; Bianca Garcia; Alan R Davidson; Benjamin P Kleinstiver; Samuel Kilcher; Joseph Bondy-Denomy
Journal:  Cell Host Microbe       Date:  2020-04-22       Impact factor: 21.023

Review 2.  Type II anti-CRISPR proteins as a new tool for synthetic biology.

Authors:  Yadan Zhang; Mario Andrea Marchisio
Journal:  RNA Biol       Date:  2020-10-13       Impact factor: 4.652

Review 3.  Base editing: advances and therapeutic opportunities.

Authors:  Elizabeth M Porto; Alexis C Komor; Ian M Slaymaker; Gene W Yeo
Journal:  Nat Rev Drug Discov       Date:  2020-10-19       Impact factor: 112.288

4.  Atomic-scale insights into allosteric inhibition and evolutional rescue mechanism of Streptococcus thermophilus Cas9 by the anti-CRISPR protein AcrIIA6.

Authors:  Xinyi Li; Chengxiang Wang; Ting Peng; Zongtao Chai; Duan Ni; Yaqin Liu; Jian Zhang; Ting Chen; Shaoyong Lu
Journal:  Comput Struct Biotechnol J       Date:  2021-11-16       Impact factor: 7.271

5.  The structure of AcrIE4-F7 reveals a common strategy for dual CRISPR inhibition by targeting PAM recognition sites.

Authors:  Sung-Hyun Hong; Gyujin Lee; Changkon Park; Jasung Koo; Eun-Hee Kim; Euiyoung Bae; Jeong-Yong Suh
Journal:  Nucleic Acids Res       Date:  2022-02-28       Impact factor: 16.971

6.  Inhibition of base editors with anti-deaminases derived from viruses.

Authors:  Zhiquan Liu; Siyu Chen; Liangxue Lai; Zhanjun Li
Journal:  Nat Commun       Date:  2022-02-01       Impact factor: 14.919

  6 in total

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