Anti-CRISPR Proteins

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Anti-CRISPR proteins (also Acr proteins ) are proteins that inhibit an adaptive antiviral mechanism of bacteria and archaea , the CRISPR - Cas .

properties

In the course of the coevolution of bacteria and their viruses , the bacteriophages , defense mechanisms against bacteriophages as well as inhibitors of bacteriophages against bacterial defense mechanisms were developed by bacteria. Various anti-CRISPR proteins have arisen in bacteriophages against CRISPR-Cas. For complete inhibition of CRISPR / Cas there is a threshold level of the dose of anti-CRISPR proteins. Anti-CRISPR proteins tend to occur more frequently in dormant than in virulent phages. Anti-CRISPR proteins inhibit CRISPR-Cas at various binding sites. In some bacteriophages, several anti-CRISPR proteins are produced simultaneously, which inhibit different binding sites. Some anti-CRISPR proteins are encoded by mobile genetic elements .

By 2018, 22 different protein families of anti-CRISPR proteins had been described that show little homology to one another . These 22 protein families can be assigned to two classes. By 2018, anti-CRISPR proteins were used against the Cas proteins of the subgroups IC, ID, IE (anti-CRISPR proteins AcrE1 to AcrE4), IF (anti-CRISPR proteins AcrF1 to AcrF10), II-A, II-C and VA.

The anti-CRISPR proteins AcrE1 to AcrE4, AcrF1 to AcrF10, AcrIIA1 to AcrA5 and AcrIIC1 to AcrIIC3 are short proteins of 52 to 149 amino acids . Presumably, anti-CRISPR proteins are also involved in controlling the recombination of bacterial DNA .

The Anti-CRISPRdb database lists anti-CRISPR proteins.

Mechanisms

The anti-CRISPR proteins AcrF1, AcrF2, AcrF10 and AcrIIA2 inhibit the binding of CRISPR / Cas to the target DNA, while AcrF3 blocks the DNA-binding channel of CRISPR / Cas. AcrIIA4 similar to Protospacer Adjacent Motif and prevents the conformational change of the HNH - protein domain of Cas. AcrIIC1 binds to the HNH domain of Cas and blocks the active site . AcrIIC3 dimerizes Cas9 and prevents DNA binding. The Cas subgroup IF is inhibited by all known anti-CRISPR proteins. Some anti-CRISPR proteins act against several subgroups of Cas proteins.

use

The CRISPR / Cas method is based on the CRISPR-Cas as a biochemical method for genome editing . Therefore, the use of anti-CRISPR proteins for conditional inhibition and thus for temporal, tissue-specific or cell cycle- specific control of the CRISPR-Cas method was proposed. Since CRISPR / Cas cuts DNA as long as it is active, a time limit can also limit unspecific cuts that can lead to undesired mutations .

For example, anti-CRISPR proteins are induced at a desired point in time or fusion proteins of anti-CRISPR proteins with light-controlled proteins are used to control the timing of the method. The combination of light-sensitive proteins with anti-CRISPR proteins enables CRISPR-Cas to be activated only during light irradiation, for example the combination of the anti-CRISPR protein AcrIIA4 (an inhibitor of Cas9 ) with the light-sensitive protein LOV2 from Avena sativa ( oat seeds ).

history

Anti-CRISPR proteins encoded by bacteriophages were first described in 2013.

literature

  • J. Wang, J. Ma, Z. Cheng, X. Meng, L. You, M. Wang, X. Zhang, Y. Wang: A CRISPR evolutionary arms race: structural insights into viral anti-CRISPR / Cas responses. In: Cell research. Volume 26, number 10, 09 2016, pp. 1165–1168, doi : 10.1038 / cr.2016.103 , PMID 27585537 , PMC 5113301 (free full text).

Individual evidence

  1. ↑ a b c K. L. Maxwell: The Anti-CRISPR Story: A Battle for Survival. In: Molecular cell. Volume 68, number 1, October 2017, pp. 8-14, doi : 10.1016 / j.molcel.2017.09.002 , PMID 28985512 .
  2. ^ SY Stanley, KL Maxwell: Phage-Encoded Anti-CRISPR Defenses. In: Annual review of genetics. [Electronic publication before going to press] September 2018, doi : 10.1146 / annurev-genet-120417-031321 , PMID 30208287 .
  3. ↑ a b c d e f g h i j k Y. Zhu, F. Zhang, Z. Huang: Structural insights into the inactivation of CRISPR-Cas systems by diverse anti-CRISPR proteins. In: BMC biology. Volume 16, number 1, March 2018, p. 32, doi : 10.1186 / s12915-018-0504-9 , PMID 29554913 , PMC 5859409 (free full text).
  4. ↑ M. Landsberger, S. Gandon, S. Meaden, C. Rollie, A. Chevallereau, H. Chabas, A. Buckling, ER Westra, S. van Houte: Anti-CRISPR Phages Cooperate to Overcome CRISPR-Cas Immunity. In: Cell . Volume 174, number 4, August 2018, pp. 908–916.e12, doi : 10.1016 / j.cell.2018.05.058 , PMID 30033365 , PMC 6086933 (free full text).
  5. ↑ AP Hynes, GM Rousseau, D. Agudelo, A. Goulet, B. Amigues, J. Loehr, DA Romero, C. Fremaux, P. Horvath, Y. Doyon, C. Cambillau, S. Moineau: Widespread anti-CRISPR proteins in virulent bacteriophages inhibit a range of Cas9 proteins. In: Nature Communications . Volume 9, number 1, July 2018, p. 2919, doi : 10.1038 / s41467-018-05092-w , PMID 30046034 , PMC 6060171 (free full text).
  6. ↑ J. Bondy-Denomy, B. Garcia, S. Strum, M. Du, MF Rollins, Y. Hidalgo-Reyes, B. Wiedenheft, KL Maxwell, AR Davidson: Multiple mechanisms for CRISPR-Cas inhibition by anti-CRISPR proteins . In: Nature . Volume 526, number 7571, October 2015, pp. 136-139, doi : 10.1038 / nature15254 , PMID 26416740 , PMC 4935067 (free full text).
  7. ↑ a b c d e f g h N. D. Marino, JY Zhang, AL Borges, AA Sousa, LM Leon, BJ Rauch, RT Walton, JD Berry, JK Joung, BP Kleinstiver, J. Bondy-Denomy: Discovery of widespread type I. and type V CRISPR-Cas inhibitors. In: Science . Volume 362, number 6411, 10 2018, pp. 240–242, doi : 10.1126 / science.aau5174 , PMID 30190308 .
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  9. ↑ AL Borges, AR Davidson, J. Bondy-Denomy: The Discovery, Mechanisms, and Evolutionary Impact of Anti-CRISPRs. In: Annual review of virology. Volume 4, number 1, 09 2017, pp. 37-59, doi : 10.1146 / annurev-virology-101416-041616 , PMID 28749735 , PMC 6039114 (free full text).
  10. ↑ BJ Rauch, MR Silvis, JF Hultquist, CS Waters, MJ McGregor, NJ Krogan, J. Bondy-Denomy: Inhibition of CRISPR-Cas9 with Bacteriophage Proteins. In: Cell . Volume 168, number 1–2, January 2017, pp. 150–158.e10, doi : 10.1016 / j.cell.2016.12.009 , PMID 28041849 , PMC 5235966 (free full text).
  11. ^ KE Watters, C. Fellmann, HB Bai, SM Ren, JA Doudna: Systematic discovery of natural CRISPR-Cas12a inhibitors. In: Science . Volume 362, number 6411, 10 2018, pp. 236-239, doi : 10.1126 / science.aau5138 , PMID 30190307 , PMC 6185749 (free full text).
  12. ↑ A. Pawluk, RH Staals, C. Taylor, BN Watson, S. Saha, PC Fineran, KL Maxwell, AR Davidson: Inactivation of CRISPR-Cas systems by anti-CRISPR proteins in diverse bacterial species. In: Nature microbiology. Volume 1, number 8, 06 2016, p. 16085, doi : 10.1038 / nmicrobiol.2016.85 , PMID 27573108 .
  13. ^ A. Pawluk, AR Davidson, KL Maxwell: Anti-CRISPR: discovery, mechanism and function. In: Nature reviews. Microbiology. Volume 16, number 1, January 2018, pp. 12-17, doi : 10.1038 / nrmicro.2017.120 , PMID 29062071 .
  14. ↑ C. Dong, GF Hao, HL Hua, S. Liu, AA Labena, G. Chai, J. Huang, N. Rao, FB Guo: Anti-CRISPRdb: a comprehensive online resource for anti-CRISPR proteins. In: Nucleic acids research. Volume 46, D1 January 2018, pp. D393 – D398, doi : 10.1093 / nar / gkx835 , PMID 29036676 , PMC 5753274 (free full text).
  15. ↑ A. Pawluk, RH Staals, C. Taylor, BN Watson, S. Saha, PC Fineran, KL Maxwell, AR Davidson: Inactivation of CRISPR-Cas systems by anti-CRISPR proteins in diverse bacterial species. In: Nature microbiology. Volume 1, number 8, 06 2016, p. 16085, doi : 10.1038 / nmicrobiol.2016.85 , PMID 27573108 .
  16. ↑ LB Harrington, KW Doxzen, E. Ma, JJ Liu, GJ Knott, A. Edraki, B. Garcia, N. Amrani, JS Chen, JC Cofsky, PJ Kranzusch, EJ Sontheimer, AR Davidson, KL Maxwell, JA Doudna: A Broad-Spectrum Inhibitor of CRISPR-Cas9. In: Cell . Volume 170, number 6, September 2017, pp. 1224–1233.e15, doi : 10.1016 / j.cell.2017.07.037 , PMID 28844692 , PMC 5875921 (free full text).
  17. ↑ A. Pawluk, N. Amrani, Y. Zhang, B. Garcia, Y. Hidalgo-Reyes, J. Lee, A. Edraki, M. Shah, EJ Sontheimer, KL Maxwell, AR Davidson: Naturally Occurring Off-Switches for CRISPR-Cas9. In: Cell . Volume 167, number 7, December 2016, pp. 1829–1838.e9, doi : 10.1016 / j.cell.2016.11.017 , PMID 27984730 , PMC 5757841 (free full text).
  18. ↑ a b F. Bubeck, MD Hoffmann, Z. Harteveld, S. Aschenbrenner, A. Bietz, MC Waldhauer, K. Börner, J. Fakhiri, C. Schmelas, L. Dietz, D. Grimm, BE Correia, R. Eils, D. Niopek: Engineered anti-CRISPR proteins for optogenetic control of CRISPR-Cas9. In: Nature methods. Volume 15, Number 11, November 2018, pp. 924-927, doi : 10.1038 / s41592-018-0178-9 , PMID 30377362 .
  19. ↑ J. Bondy-Denomy, A. Pawluk, KL Maxwell, AR Davidson: Bacteriophage genes that inactivate the CRISPR / Cas bacterial immune system. In: Nature . Volume 493, number 7432, January 2013, pp. 429-432, doi : 10.1038 / nature11723 , PMID 23242138 , PMC 4931913 (free full text).