Skip to main content
Log in

The Expanding Class 2 CRISPR Toolbox: Diversity, Applicability, and Targeting Drawbacks

  • Review Article
  • Published:
BioDrugs Aims and scope Submit manuscript

Abstract

The class 2 clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system, one of the prokaryotic adaptive immune systems, has sparked a lot of attention for its use as a gene editing tool. Currently, type II, V, and VI effector modules of this class have been characterized and extensively tested for nucleic acid editing, imaging, and disease diagnostics. Due to the unique composition of their nuclease catalytic center, the effector modules substantially vary in their function and possible biotechnology applications. In this review, we discuss the structural and functional diversity in class 2 CRISPR effectors, and debate their suitability for nucleic acid targeting and their shortcomings as gene editing tools.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

References

  1. Hille F, Richter H, Wong SP, Bratovič M, Ressel S, Charpentier E. The biology of CRISPR-Cas: backward and forward. Cell. 2018;172(6):1239–59.

    CAS  PubMed  Google Scholar 

  2. Nuñez JK, Kranzusch PJ, Noeske J, Wright AV, Davies CW, Doudna JA. Cas1–Cas2 complex formation mediates spacer acquisition during CRISPR–Cas adaptive immunity. Nat Struct Mol Biol. 2014;21(6):528.

    PubMed  PubMed Central  Google Scholar 

  3. Koonin EV, Makarova KS, Zhang F. Diversity, classification and evolution of CRISPR-Cas systems. Curr Opin Microbiol. 2017;37:67–78.

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Makarova KS, Zhang F, Koonin EV. SnapShot: class 1 CRISPR-Cas systems. Cell. 2017;168(5):946.e1.

    Google Scholar 

  5. Makarova KS, Zhang F, Koonin EV. SnapShot: class 2 CRISPR-Cas systems. Cell. 2017;168(1):328.e1.

    Google Scholar 

  6. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, et al. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013;339(6121):819–23.

    CAS  PubMed  PubMed Central  Google Scholar 

  7. Knott GJ, Doudna JA. CRISPR-Cas guides the future of genetic engineering. Science. 2018;361(6405):866–9.

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Shmakov S, Smargon A, Scott D, Cox D, Pyzocha N, Yan W, et al. Diversity and evolution of class 2 CRISPR–Cas systems. Nat Rev Microbiol. 2017;15(3):169.

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, Saunders SJ, et al. An updated evolutionary classification of CRISPR–Cas systems. Nat Rev Microbiol. 2015;13(11):722.

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Yan WX, Hunnewell P, Alfonse LE, Carte JM, Keston-Smith E, Sothiselvam S, et al. Functionally diverse type V CRISPR-Cas systems. Science. 2019;363(6422):88–91.

    CAS  PubMed  Google Scholar 

  11. Konermann S, Lotfy P, Brideau NJ, Oki J, Shokhirev MN, Hsu PD. Transcriptome engineering with RNA-targeting type VI-D CRISPR effectors. Cell. 2018;173(3):665–676.e14.

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Shmakov S, Abudayyeh OO, Makarova KS, Wolf YI, Gootenberg JS, Semenova E, et al. Discovery and functional characterization of diverse class 2 CRISPR-Cas systems. Mol Cell. 2015;60(3):385–97.

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Smargon AA, Cox DB, Pyzocha NK, Zheng K, Slaymaker IM, Gootenberg JS, et al. Cas13b is a type VI-B CRISPR-associated RNA-guided RNase differentially regulated by accessory proteins Csx27 and Csx28. Mol Cell. 2017;65(4):618–630.e7.

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Yan WX, Chong S, Zhang H, Makarova KS, Koonin EV, Cheng DR, et al. Cas13d is a compact RNA-targeting type VI CRISPR effector positively modulated by a WYL-domain-containing accessory protein. Mol Cell. 2018;70(2):327–339.e5.

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Zhang H, Dong C, Li L, Wasney GA, Min J. Structural insights into the modulatory role of the accessory protein WYL1 in the type VI-D CRISPR-Cas system. Nucleic Acids Res. 2019;47(10):5420–8.

    PubMed  PubMed Central  Google Scholar 

  16. Nishimasu H, Ran FA, Hsu PD, Konermann S, Shehata SI, Dohmae N, et al. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell. 2014;156(5):935–49.

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Nishimasu H, Cong L, Yan WX, Ran FA, Zetsche B, Li Y, et al. Crystal structure of Staphylococcus aureus Cas9. Cell. 2015;162(5):1113–26.

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Fonfara I, Le Rhun A, Chylinski K, Makarova KS, Lecrivain A-L, Bzdrenga J, et al. Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems. Nucleic Acids Res. 2013;42(4):2577–90.

    PubMed  PubMed Central  Google Scholar 

  19. Jinek M, Jiang F, Taylor DW, Sternberg SH, Kaya E, Ma E, et al. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science. 2014;343(6176):1247997.

    PubMed  PubMed Central  Google Scholar 

  20. Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS, Essletzbichler P, et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell. 2015;163(3):759–71.

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Gao P, Yang H, Rajashankar KR, Huang Z, Patel DJ. Type V CRISPR-Cas Cpf1 endonuclease employs a unique mechanism for crRNA-mediated target DNA recognition. Cell Res. 2016;26(8):901.

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Dong D, Ren K, Qiu X, Zheng J, Guo M, Guan X, et al. The crystal structure of Cpf1 in complex with CRISPR RNA. Nature. 2016;532(7600):522.

    CAS  PubMed  Google Scholar 

  23. Yang H, Gao P, Rajashankar KR, Patel DJ. PAM-dependent target DNA recognition and cleavage by C2c1 CRISPR-Cas endonuclease. Cell. 2016;167(7):1814–1828.e12.

    CAS  PubMed  PubMed Central  Google Scholar 

  24. Liu J-J, Orlova N, Oakes BL, Ma E, Spinner HB, Baney KL, et al. CasX enzymes comprise a distinct family of RNA-guided genome editors. Nature. 2019;566(7743):218.

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Chen JS, Ma E, Harrington LB, Da Costa M, Tian X, Palefsky JM, et al. CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science. 2018;360(6387):436–9.

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Li S-Y, Cheng Q-X, Liu J-K, Nie X-Q, Zhao G-P, Wang J. CRISPR-Cas12a has both cis-and trans-cleavage activities on single-stranded DNA. Cell Res. 2018;28(4):491.

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Swarts DC, Jinek M. Mechanistic Insights into the cis-and trans-acting DNase activities of Cas12a. Mol Cell. 2019;73(3):589–600.e4.

    CAS  PubMed  PubMed Central  Google Scholar 

  28. Harrington LB, Burstein D, Chen JS, Paez-Espino D, Ma E, Witte IP, et al. Programmed DNA destruction by miniature CRISPR-Cas14 enzymes. Science. 2018;362(6416):839–42.

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Liu L, Li X, Wang J, Wang M, Chen P, Yin M, et al. Two distant catalytic sites are responsible for C2c2 RNase activities. Cell. 2017;168(1–2):121–134.e12.

    CAS  PubMed  Google Scholar 

  30. Zhang B, Ye W, Ye Y, Zhou H, Saeed AF, Chen J, et al. Structural insights into Cas13b-guided CRISPR RNA maturation and recognition. Cell Res. 2018;28(12):1198.

    PubMed  PubMed Central  Google Scholar 

  31. Zhang C, Konermann S, Brideau NJ, Lotfy P, Wu X, Novick SJ, et al. Structural basis for the RNA-guided ribonuclease activity of CRISPR-Cas13d. Cell. 2018;175(1):212–223.e17.

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Slaymaker IM, Mesa P, Kellner MJ, Kannan S, Brignole E, Koob J, et al. High-resolution structure of Cas13b and biochemical characterization of RNA targeting and cleavage. Cell Rep. 2019;26(13):3741–3751.e5.

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNA–guided DNA endonuclease in adaptive bacterial immunity. Science. 2012;337(6096):816–21.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y, Pirzada ZA, et al. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature. 2011;471(7340):602.

    CAS  PubMed  PubMed Central  Google Scholar 

  35. O’Connell M. Molecular mechanisms of RNA-Targeting by Cas13-containing type VI CRISPR-Cas systems. J Mol Biol. 2019;431(1):66–87.

    PubMed  Google Scholar 

  36. Yin K, Gao C, Qiu J-L. Progress and prospects in plant genome editing. Nat Plants. 2017;3(8):17107.

    CAS  PubMed  Google Scholar 

  37. Zhang Y, Long C, Li H, McAnally JR, Baskin KK, Shelton JM, et al. CRISPR-Cpf1 correction of muscular dystrophy mutations in human cardiomyocytes and mice. Sci Adv. 2017;3(4):e1602814.

    PubMed  PubMed Central  Google Scholar 

  38. Hu X, Wang C, Liu Q, Fu Y, Wang K. Targeted mutagenesis in rice using CRISPR-Cpf1 system. J Genet Genom. 2017;44(1):71–3.

    Google Scholar 

  39. O’connell MR, Oakes BL, Sternberg SH, East-Seletsky A, Kaplan M, Doudna JA. Programmable RNA recognition and cleavage by CRISPR/Cas9. Nature. 2014;516(7530):263.

    PubMed  PubMed Central  Google Scholar 

  40. Dugar G, Leenay RT, Eisenbart SK, Bischler T, Aul BU, Beisel CL, et al. CRISPR RNA-dependent binding and cleavage of endogenous RNAs by the Campylobacter jejuni Cas9. Mol Cell. 2018;69(5):893–905.e7.

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Rousseau BA, Hou Z, Gramelspacher MJ, Zhang Y. Programmable RNA cleavage and recognition by a natural CRISPR-Cas9 system from Neisseria meningitidis. Mol Cell. 2018;69(5):906–914.e4.

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Strutt SC, Torrez RM, Kaya E, Negrete OA, Doudna JA. RNA-dependent RNA targeting by CRISPR-Cas9. Elife. 2018;7:e32724.

    PubMed  PubMed Central  Google Scholar 

  43. Abudayyeh OO, Gootenberg JS, Essletzbichler P, Han S, Joung J, Belanto JJ, et al. RNA targeting with CRISPR–Cas13. Nature. 2017;550(7675):280.

    PubMed  PubMed Central  Google Scholar 

  44. Abudayyeh OO, Gootenberg JS, Konermann S, Joung J, Slaymaker IM, Cox DB, et al. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science. 2016;353(6299):aaf5573.

    PubMed  PubMed Central  Google Scholar 

  45. Gootenberg JS, Abudayyeh OO, Lee JW, Essletzbichler P, Dy AJ, Joung J, et al. Nucleic acid detection with CRISPR-Cas13a/C2c2. Science. 2017;356(6336):438–42.

    CAS  PubMed  PubMed Central  Google Scholar 

  46. Myhrvold C, Freije CA, Gootenberg JS, Abudayyeh OO, Metsky HC, Durbin AF, et al. Field-deployable viral diagnostics using CRISPR-Cas13. Science. 2018;360(6387):444–8.

    CAS  PubMed  PubMed Central  Google Scholar 

  47. Gootenberg JS, Abudayyeh OO, Kellner MJ, Joung J, Collins JJ, Zhang F. Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6. Science. 2018;360(6387):439–44. https://doi.org/10.1126/science.aaq0179.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell. 2013;152(5):1173–83.

    CAS  PubMed  PubMed Central  Google Scholar 

  49. Gilbert LA, Larson MH, Morsut L, Liu Z, Brar GA, Torres SE, et al. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell. 2013;154(2):442–51.

    CAS  PubMed  PubMed Central  Google Scholar 

  50. Liu XS, Wu H, Ji X, Stelzer Y, Wu X, Czauderna S, et al. Editing DNA methylation in the mammalian genome. Cell. 2016;167(1):233–247.e17.

    CAS  PubMed  PubMed Central  Google Scholar 

  51. Lei Y, Zhang X, Su J, Jeong M, Gundry MC, Huang Y-H, et al. Targeted DNA methylation in vivo using an engineered dCas9-MQ1 fusion protein. Nat Commun. 2017;8:16026.

    CAS  PubMed  PubMed Central  Google Scholar 

  52. Choudhury SR, Cui Y, Lubecka K, Stefanska B, Irudayaraj J. CRISPR-dCas9 mediated TET1 targeting for selective DNA demethylation at BRCA1 promoter. Oncotarget. 2016;7(29):46545.

    PubMed  PubMed Central  Google Scholar 

  53. Hilton IB, D’ippolito AM, Vockley CM, Thakore PI, Crawford GE, Reddy TE, et al. Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nat Biotechnol. 2015;33(5):510.

    CAS  PubMed  PubMed Central  Google Scholar 

  54. Chen X, Wei M, Liu X, Song S, Wang L, Yang X, et al. Construction and validation of the CRISPR/dCas9-EZH2 system for targeted H3K27Me3 modification. Biochem Biophys Res Commun. 2019;511(2):246–52.

    CAS  PubMed  Google Scholar 

  55. Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature. 2016;533(7603):420.

    CAS  PubMed  PubMed Central  Google Scholar 

  56. Cox DB, Gootenberg JS, Abudayyeh OO, Franklin B, Kellner MJ, Joung J, et al. RNA editing with CRISPR-Cas13. Science. 2017;358(6366):1019–27.

    CAS  PubMed  PubMed Central  Google Scholar 

  57. Gaudelli NM, Komor AC, Rees HA, Packer MS, Badran AH, Bryson DI, et al. Programmable base editing of A• T to G• C in genomic DNA without DNA cleavage. Nature. 2017;551(7681):464.

    CAS  PubMed  PubMed Central  Google Scholar 

  58. Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W, Li G-W, et al. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell. 2013;155(7):1479–91.

    CAS  PubMed  PubMed Central  Google Scholar 

  59. Nelles DA, Fang MY, O’Connell MR, Xu JL, Markmiller SJ, Doudna JA, et al. Programmable RNA tracking in live cells with CRISPR/Cas9. Cell. 2016;165(2):488–96.

    CAS  PubMed  PubMed Central  Google Scholar 

  60. Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, et al. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol. 2013;31(9):827.

    CAS  PubMed  PubMed Central  Google Scholar 

  61. Casini A, Olivieri M, Petris G, Montagna C, Reginato G, Maule G, et al. A highly specific SpCas9 variant is identified by in vivo screening in yeast. Nat Biotechnol. 2018;36(3):265.

    CAS  PubMed  PubMed Central  Google Scholar 

  62. Chen JS, Dagdas YS, Kleinstiver BP, Welch MM, Sousa AA, Harrington LB, et al. Enhanced proofreading governs CRISPR–Cas9 targeting accuracy. Nature. 2017;550(7676):407.

    CAS  PubMed  PubMed Central  Google Scholar 

  63. Kosicki M, Tomberg K, Bradley A. Repair of double-strand breaks induced by CRISPR–Cas9 leads to large deletions and complex rearrangements. Nat Biotechnol. 2018;36(8):765.

    CAS  PubMed  PubMed Central  Google Scholar 

  64. Cullot G, Boutin J, Toutain J, Prat F, Pennamen P, Rooryck C, et al. CRISPR-Cas9 genome editing induces megabase-scale chromosomal truncations. Nat Commun. 2019;10(1):1136.

    PubMed  PubMed Central  Google Scholar 

  65. Jin S, Zong Y, Gao Q, Zhu Z, Wang Y, Qin P et al. Cytosine, but not adenine, base editors induce genome-wide off-target mutations in rice. Science. 2019;364(6437):292–5.

    CAS  PubMed  Google Scholar 

  66. Zuo E, Sun Y, Wei W, Yuan T, Ying W, Sun H et al. Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos. Science. 2019;364(6437):289–92.

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We would like to acknowledge Lora Starrs and Alexander McKay for fruitful discussions and critical reading of the manuscript. Dr. Burgio’s research program is supported by the National Health and Medical Research Council of Australia (APP1143008), the Australian Research Council (DP180101494), and the National Collaborative Research Infrastructure Strategy (NCRIS) via the Australian Phenomics Network. Arash Hajizadeh Dastjerdi is supported by a JCSMR postgraduate scholarship, and Anthony Newman is supported by a Research Training Program domestic scholarship. We finally wish to acknowledge two anonymous reviewers and the editor for their helpful and excellent suggestions on the manuscript.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Gaetan Burgio.

Ethics declarations

Funding

No funding was received for the preparation of this review.

Conflict of interest

AHD, AN, and GB declare that they have no conflict of interest.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Hajizadeh Dastjerdi, A., Newman, A. & Burgio, G. The Expanding Class 2 CRISPR Toolbox: Diversity, Applicability, and Targeting Drawbacks. BioDrugs 33, 503–513 (2019). https://doi.org/10.1007/s40259-019-00369-y

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s40259-019-00369-y

Navigation