Anti-CRISPR: discovery, mechanism and function

Abstract

CRISPR–Cas adaptive immune systems are widespread among bacteria and archaea. Recent studies have shown that these systems have minimal long-term evolutionary effects in limiting horizontal gene transfer. This suggests that the ability to evade CRISPR–Cas immunity must also be widespread in phages and other mobile genetic elements. In this Progress article, we discuss recent discoveries that highlight how phages inactivate CRISPR–Cas systems by using anti-CRISPR proteins, and we outline evolutionary and biotechnological implications of their activity.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: Anti-CRISPR gene discovery.
Figure 2: Inhibition of CRISPR–Cas systems by anti-CRISPR proteins is a common strategy across CRISPR–Cas system types and bacterial phylogeny.

References

  1. 1

    Van Valen, L. A new evolutionary law. Evol. Theory 1, 1–30 (1973).

    Google Scholar 

  2. 2

    Kruger, D. H. & Bickle, T. A. Bacteriophage survival: multiple mechanisms for avoiding the deoxyribonucleic acid restriction systems of their hosts. Microbiol. Rev. 47, 345–360 (1983).

    CAS  PubMed  PubMed Central  Google Scholar 

  3. 3

    Drozdz, M., Piekarowicz, A., Bujnicki, J. M. & Radlinska, M. Novel non-specific DNA adenine methyltransferases. Nucleic Acids Res. 40, 2119–2130 (2012).

    CAS  Article  PubMed  Google Scholar 

  4. 4

    Kahmann, R. The mom gene of bacteriophage Mu. Curr. Top. Microbiol. Immunol. 108, 29–47 (1984).

    CAS  PubMed  Google Scholar 

  5. 5

    Studier, F. W. & Movva, N. R. SAMase gene of bacteriophage T3 is responsible for overcoming host restriction. J. Virol. 19, 136–145 (1976).

    CAS  PubMed  PubMed Central  Google Scholar 

  6. 6

    Otsuka, Y. & Yonesaki, T. Dmd of bacteriophage T4 functions as an antitoxin against Escherichia coli LsoA and RnlA toxins. Mol. Microbiol. 83, 669–681 (2012).

    CAS  Article  PubMed  Google Scholar 

  7. 7

    Blower, T. R., Evans, T. J., Przybilski, R., Fineran, P. C. & Salmond, G. P. Viral evasion of a bacterial suicide system by RNA-based molecular mimicry enables infectious altruism. PLoS Genet. 8, e1003023 (2012).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  8. 8

    Bondy-Denomy, J., Pawluk, A., Maxwell, K. L. & Davidson, A. R. Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system. Nature 493, 429–432 (2013).

    CAS  Article  PubMed  Google Scholar 

  9. 9

    Pawluk, A. et al. Naturally occurring off-switches for CRISPR-Cas9. Cell 167, 1829–1838.e9 (2016).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  10. 10

    Pawluk, A., Bondy-Denomy, J., Cheung, V. H., Maxwell, K. L. & Davidson, A. R. A new group of phage anti-CRISPR genes inhibits the type I-E CRISPR-Cas system of Pseudomonas aeruginosa. mBio 5, e00896 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  11. 11

    Pawluk, A. et al. Inactivation of CRISPR-Cas systems by anti-CRISPR proteins in diverse bacterial species. Nat. Microbiol. 1, 16085 (2016).

    CAS  Article  PubMed  Google Scholar 

  12. 12

    Rauch, B. J. et al. Inhibition of CRISPR-Cas9 with bacteriophage proteins. Cell 168, 150–158.e10 (2017).

    CAS  Article  PubMed  Google Scholar 

  13. 13

    Hynes, A. P. et al. An anti-CRISPR from a virulent streptococcal phage inhibits Streptococcus pyogenes Cas9. Nat. Microbiol. http://dx.doi.org/10.1038/s41564-017-0004-7 (2017).

  14. 14

    Samson, J. E., Magadan, A. H., Sabri, M. & Moineau, S. Revenge of the phages: defeating bacterial defences. Nat. Rev. Microbiol. 11, 675–687 (2013).

    CAS  Article  PubMed  Google Scholar 

  15. 15

    Garneau, J. E. et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468, 67–71 (2010).

    CAS  Article  PubMed  Google Scholar 

  16. 16

    Marraffini, L. A. & Sontheimer, E. J. CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322, 1843–1845 (2008).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  17. 17

    Barrangou, R. et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315, 1709–1712 (2007).

    CAS  Article  PubMed  Google Scholar 

  18. 18

    Edgar, R. & Qimron, U. The Escherichia coli CRISPR system protects from λ lysogenization, lysogens, and prophage induction. J. Bacteriol. 192, 6291–6294 (2010).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  19. 19

    Brouns, S. J. et al. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321, 960–964 (2008).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  20. 20

    Marraffini, L. A. CRISPR-Cas immunity in prokaryotes. Nature 526, 55–61 (2015).

    CAS  Article  PubMed  Google Scholar 

  21. 21

    Mohanraju, P. et al. Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems. Science 353, aad5147 (2016).

    Article  PubMed  Google Scholar 

  22. 22

    Wright, A. V., Nunez, J. K. & Doudna, J. A. Biology and applications of CRISPR systems: harnessing nature's toolbox for genome engineering. Cell 164, 29–44 (2016).

    CAS  Article  PubMed  Google Scholar 

  23. 23

    Makarova, K. S. et al. An updated evolutionary classification of CRISPR-Cas systems. Nat. Rev. Microbiol. 13, 722–736 (2015).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  24. 24

    Koonin, E. V., Makarova, K. S. & Zhang, F. Diversity, classification and evolution of CRISPR-Cas systems. Curr. Opin. Microbiol. 37, 67–78 (2017).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  25. 25

    Wang, H., La Russa, M. & Qi, L. S. CRISPR/Cas9 in genome editing and beyond. Annu. Rev. Biochem. 85, 227–264 (2016).

    CAS  Article  PubMed  Google Scholar 

  26. 26

    Bikard, D., Hatoum-Aslan, A., Mucida, D. & Marraffini, L. A. CRISPR interference can prevent natural transformation and virulence acquisition during in vivo bacterial infection. Cell Host Microbe 12, 177–186 (2012).

    CAS  Article  PubMed  Google Scholar 

  27. 27

    Wozniak, R. A. & Waldor, M. K. Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow. Nat. Rev. Microbiol. 8, 552–563 (2010).

    CAS  Article  PubMed  Google Scholar 

  28. 28

    Dobrindt, U., Hochhut, B., Hentschel, U. & Hacker, J. Genomic islands in pathogenic and environmental microorganisms. Nat. Rev. Microbiol. 2, 414–424 (2004).

    CAS  Article  PubMed  Google Scholar 

  29. 29

    Juhas, M. et al. Genomic islands: tools of bacterial horizontal gene transfer and evolution. FEMS Microbiol. Rev. 33, 376–393 (2009).

    CAS  Article  PubMed  Google Scholar 

  30. 30

    Sun, C. L. et al. Phage mutations in response to CRISPR diversification in a bacterial population. Environ. Microbiol. 15, 463–470 (2013).

    CAS  Article  PubMed  Google Scholar 

  31. 31

    van Houte, S. et al. The diversity-generating benefits of a prokaryotic adaptive immune system. Nature 532, 385–388 (2016).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  32. 32

    Fineran, P. C. et al. Degenerate target sites mediate rapid primed CRISPR adaptation. Proc. Natl Acad. Sci. USA 111, E1629–E1638 (2014).

    CAS  Article  PubMed  Google Scholar 

  33. 33

    Gophna, U. et al. No evidence of inhibition of horizontal gene transfer by CRISPR-Cas on evolutionary timescales. ISME J. 9, 2021–2027 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  34. 34

    Touchon, M., Bernheim, A. & Rocha, E. P. Genetic and life-history traits associated with the distribution of prophages in bacteria. ISME J. 10, 2744–2754 (2016).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  35. 35

    Touchon, M. et al. Antibiotic resistance plasmids spread among natural isolates of Escherichia coli in spite of CRISPR elements. Microbiology 158, 2997–3004 (2012).

    CAS  Article  PubMed  Google Scholar 

  36. 36

    Dang, T. N. et al. Uropathogenic Escherichia coli are less likely than paired fecal E. coli to have CRISPR loci. Infect. Genet. Evol. 19, 212–218 (2013).

    CAS  Article  PubMed  Google Scholar 

  37. 37

    Bondy-Denomy, J. et al. Multiple mechanisms for CRISPR-Cas inhibition by anti-CRISPR proteins. Nature 526, 136–139 (2015).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  38. 38

    Chowdhury, S. et al. Structure reveals mechanisms of viral suppressors that intercept a CRISPR RNA-guided surveillance complex. Cell 169, 47–57.e11 (2017).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  39. 39

    Peng, R. et al. Alternate binding modes of anti-CRISPR viral suppressors AcrF1/2 to Csy surveillance complex revealed by cryo-EM structures. Cell Res. 27, 853–864 (2017).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  40. 40

    Maxwell, K. L. et al. The solution structure of an anti-CRISPR protein. Nat. Commun. 7, 13134 (2016).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  41. 41

    van Erp, P. B. et al. Mechanism of CRISPR-RNA guided recognition of DNA targets in Escherichia coli. Nucleic Acids Res. 43, 8381–8391 (2015).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  42. 42

    Dong, D. et al. Structural basis of CRISPR-SpyCas9 inhibition by an anti-CRISPR protein. Nature 546, 436–439 (2017).

    CAS  Article  PubMed  Google Scholar 

  43. 43

    Yang, H. & Patel, D. J. Inhibition mechanism of an anti-CRISPR suppressor AcrIIA4 targeting SpyCas9. Mol. Cell 67, 117–127.e5 (2017).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  44. 44

    Shin, J. et al. Disabling Cas9 by an anti-CRISPR DNA mimic. Sci. Adv. 3, e1701620 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  45. 45

    Harrington, L. B. et al. A broad-spectrum inhibitor of CRISPR-Cas9. Cell 170, 1224–1233.e15 (2017).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  46. 46

    Wang, X. et al. Structural basis of Cas3 inhibition by the bacteriophage protein AcrF3. Nat. Struct. Mol. Biol. 23, 868–870 (2016).

    CAS  Article  PubMed  Google Scholar 

  47. 47

    Wang, J. et al. A CRISPR evolutionary arms race: structural insights into viral anti-CRISPR/Cas responses. Cell Res. 26, 1165–1168 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  48. 48

    Burstein, D. et al. Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems. Nat. Commun. 7, 10613 (2016).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  49. 49

    Jiang, W. et al. Dealing with the evolutionary downside of CRISPR immunity: bacteria and beneficial plasmids. PLoS Genet. 9, e1003844 (2013).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  50. 50

    Westra, E. R. et al. Parasite exposure drives selective evolution of constitutive versus inducible defense. Curr. Biol. 25, 1043–1049 (2015).

    CAS  Article  PubMed  Google Scholar 

  51. 51

    Gilbert, L. A. et al. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 154, 442–451 (2013).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  52. 52

    Dominguez, A. A., Lim, W. A. & Qi, L. S. Beyond editing: repurposing CRISPR-Cas9 for precision genome regulation and interrogation. Nat. Rev. Mol. Cell Biol. 17, 5–15 (2016).

    CAS  Article  PubMed  Google Scholar 

  53. 53

    Maxwell, K. L. Phages fight back: inactivation of the CRISPR-Cas bacterial immune system by anti-CRISPR proteins. PLoS Pathog. 12, e1005282 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  54. 54

    Hug, L. A. et al. A new view of the tree of life. Nat. Microbiol. 1, 16048 (2016).

    CAS  Article  PubMed  Google Scholar 

Download references

Acknowledgements

A.P. was supported by a Canadian Institutes of Health Research Doctoral Award. Research in this area in the authors' laboratories is supported by Canadian Institutes of Health Research grants to A.R.D. (MOP-130482) and K.L.M. (MOP-136845).

Author information

Affiliations

Authors

Contributions

A.P. researched the data for the article. A.P. and K.L.M. wrote the article. A.P., K.L.M. and A.R.D. substantially contributed to discussions of the content and reviewed and edited the manuscript before submission.

Corresponding author

Correspondence to Karen L. Maxwell.

Ethics declarations

Competing interests

The authors declare potential competing interest as all authors have a patent pending for anti-CRISPR technologies on which they are inventors.

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Pawluk, A., Davidson, A. & Maxwell, K. Anti-CRISPR: discovery, mechanism and function. Nat Rev Microbiol 16, 12–17 (2018). https://doi.org/10.1038/nrmicro.2017.120

Download citation

Further reading