Anti-CRISPR Proteins (Acr Proteins)

Anti-CRISPR Proteins (Acr Proteins)

Anti-CRISPR proteins (Acr), encoded by phages and other mobile genetic elements, interact with CRISPR-Cas systems to inactivate them. While CRISPR-Cas systems have evolved to recognizes and kill viruses, anti-CRISPR proteins have evolved in viruses as a counter-defense. Like CRISPR-Cas, anti-CRISPR proteins have applications in genome editing.

In the evolutionary arms race between phage and bacteria, mutations can allow phages to escape CRISPR-Cas-mediated destruction. However, bacteria are quick to acquire new spacer sequences which allow them to retarget phage mutants. Anti-CRISPR proteins are another defense mechanism for phages to escape destruction from CRISPR-Cas systems. Anti-CRISPR technology has applications in the enhancement of control and precision in gene editing with CRISPR/Cas systems and in augmenting phage therapy approaches to treat bacterial infections.

Anti-CRISPR proteins act by disrupting DNA binding or by inhibiting the cleavage of target sequences.The first anti-CRISPR proteins were identified in 2013 by a research group lead by Alan R. Davidson at University of Toronto . Anti-CRISPR proteins have been identified that target type I and type II CRISPR-Cas systems.Anti-CRISPR proteins that target the CRISPR-Cas9 system, commonly used for genome editing were identified in 2016 and 2017 by Davidson’s group and Joseph Bondy-Denomy’s group at University of California, San Francisco. In genome editing for therapeutic uses, anti-CRISPR proteins may provide a valuable “off switch” for better control of Cas9 activity. Anti-CRISPR proteins have been shown to reduce off-target cutting by CRISPR-Cas9 in human cells.

Anti-CRISPR proteins are discovered using bioinformatics, experimental and metagenomic screening. In addition to being found in phages, Anti-CRISPR proteins are also found in prophages. A prophage is a phage genome integrated into its host genome during what is called the lysogenic cycle. Anti-CRISPR proteins can also be encoded by non-phage elements, mobile genetic elements, including plasmids and integrative and conjugative elements, transposons, integrons and other uncharacterized elements. Researchers at University of California, San Francisco, discovered sequences of anti-CRISPR genes, aacrIIA, in E. faecalis, which frequently spreads antibiotic resistance genes despite having CRISPR-Cas systems. CRISPR-Cas systems are thought to provide a barrier to horozontal gene transfer. Their work demonstrated that AcrIIA proteins through CRISPR-Cas9 inhibition, can enhance the spread of antibiotic resistance plasmids that encode them.

Defense Advanced Research Projects Agency (DARPA) supported two research studies published in Science in 2018 that identified new anti-CRISPR proteins, including one that inhibits CRISPR-Cas12a, which is becoming more popular for genome editing applications. DARPA supported this research because of the potential for anti-CRISPR proteins to be used as a countermeasure against nefarious use of CRISPR.The two research groups are Jennifer Doudna’s at University of California, Berkeley and Bondy-Denomy’s group.Jennifer Doudna previously founded the company Caribou Biosciences which is developing various applications for CRISPR-Cas technology.

The former DuPont subsidiary DuPont Nutrition and Health, at their US and France locations, collaborated with researchers at Université Laval (Canada) in research on anti-CRISPR proteins. In 2018 Université Laval and Dupont Nutrition Bioscences applied for a patent on methods and compositions for use of anti-CRISPR (ACR) proteins in plants. DuPont Nutrition & Health merged with Industrial Biosciences to form DuPont Nutrition & Biosciences in 2019 to form the subsidiary, DuPont Nutrition Biosciences ApS based in Denmark.


May 28, 2020
Anti-CRISPR protein that inhibits Cas13

A phage-encoded anti-CRISPR enables complete evasion of type VI-A CRISPR-Cas immunity

Science 28 May 2020: eabb6151

Corresponding authors: Dinshaw J. Patel2, Luciano A. Marraffini

The Rockefeller University, New York; Memorial Sloan Kettering Cancer Center, New York

April 14, 2020
AcRanker, a machine learning based method to aid direct identification of new potential anti-CRISPRs

Machine learning predicts new anti-CRISPR proteins

Nucleic Acids Research, Volume 48, Issue 9, 21 May 2020, Pages 4698–4708

Corresponding authors: Jennifer A Doudna, Fayyaz ul Amir Afsar Minhas

University of California Berkeley, Berkeley; Pakistan Institute of Engineering and Applied Sciences (PIEAS)

September 6, 2018
Anti-CRISPR proteins reported that inhibit Cas12a

Systematic discovery of natural CRISPR-Cas12a inhibitors

Science 12 Oct 2018: Vol. 362, Issue 6411, pp. 236-239

Corresponding author: Jennifer A. Doudna

University of California, Berkeley

September 6, 2018
Anti-CRISPR proteins reported that inhibit Cas12a

Discovery of widespread type I and type V CRISPR-Cas inhibitors

Science 12 Oct 2018: Vol. 362, Issue 6411, pp. 240-242

Corresponding author: Joseph Bondy-Denomy

University of California, San Francisco

July 25, 2018
Widespread anti-CRISPR proteins in virulent bacteriophages inhibit a range of Cas9 proteins

Nature Communications volume 9, Article number: 2919 (2018)

Corresponding author: Sylvain Moineau

Université Laval, Québec City

July 2017
Anti-CRISPR protein AcrIIA4 demonstrated to reduce Cas9 off-target editing

Disabling Cas9 by an anti-CRISPR DNA mimic

Science Advances 12 Jul 2017: Vol. 3, no. 7, e1701620

Corresponding authors: Jacob E. Corn and Jennifer A. Doudna

University of California, Berkeley

January 2017
Anti-CRIPR proteins found that inhibit Cas9

Inhibition of CRISPR-Cas9 with Bacteriophage Proteins

Rauch et al., 2017, Cell 168, 150–158

Corresponding author: Joseph Bondy-Denomy

University of California, San Francisco

December 2016
Anti-CRISPR proteins found that inhibit Cas9

Naturally Occurring Off-Switches for CRISPR-Cas9

Pawluk et al., 2016, Cell 167, 1829–1838

Corresponding authors: Erik J. Sontheimer, Karen L. Maxwell, and Alan R. Davidson

University of Toronto

December 16, 2012
Anti-CRISPR proteins identified

Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system

Nature. 2013 Jan 17; 493(7432): 429–432

Joe Bondy-Denomy, April Pawluk, Karen L. Maxwell, and Alan R. Davidson

University of Toronto



Further reading


Brigham, Broad Institute researchers ID molecules that rein in CRISPR systems

Karen Zusi


Kill-Switch for CRISPR Could Make Gene-Editing Safer

Elie Dolgin, Nature magazine


January 17, 2020

Systematic discovery of natural CRISPR-Cas12a inhibitors

Kyle E. Watters, Christof Fellmann, Hua B. Bai, Shawn M. Ren, Jennifer A. Doudna


Documentaries, videos and podcasts


Adding this protein to human cells makes CRISPR-Cas9 more specific



Acrigen Biosciences

Co-Founded by Joseph Bondy-Denomy

Berkeley, California

Technologies to improve efficiency and safety of CRISPR-Cas gene editing

Food & Beverage, Health & Bioscience and Pharma Solutions


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