농업과학연구 (Korean Journal of Agricultural Science)

  • 제46권4호
  • /
  • Pages.885-895
  • /
  • 2019
  • /
  • 2466-2402(pISSN)
  • /
  • 2466-2410(eISSN)
충남대학교 농업과학연구소 (Institute of Agricultural Science, CNU)
권호 표지
DOI QR코드

DOI QR Code

Current status of CRISPR/Cas9 base editor technologies and their applications in crop precision breeding

  • Kim, Rigyeong (Metabolic Engineering Division, National Institute of Agricultural Sciences, Rural Development Administration) ;
  • Song, Jaeeun (Metabolic Engineering Division, National Institute of Agricultural Sciences, Rural Development Administration) ;
  • Ga, Eunji (Metabolic Engineering Division, National Institute of Agricultural Sciences, Rural Development Administration) ;
  • Min, Myung Ki (Metabolic Engineering Division, National Institute of Agricultural Sciences, Rural Development Administration) ;
  • Lee, Jong-Yeol (Metabolic Engineering Division, National Institute of Agricultural Sciences, Rural Development Administration) ;
  • Lim, Sun-Hyung (Metabolic Engineering Division, National Institute of Agricultural Sciences, Rural Development Administration) ;
  • Kim, Beom-Gi (Metabolic Engineering Division, National Institute of Agricultural Sciences, Rural Development Administration)
  • 투고 : 2019.09.10
  • 심사 : 2019.10.22
  • 발행 : 2019.12.31
PDF 다운로드
⟨ 이전 논문 다음 논문 ⟩

초록

Plant biotechnologists have long dreamed of technologies to manipulate genes in plants at will. This dream has come true partly through the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology, which now has been used to edit genes in several important crops. However, there are many restrictions in editing a gene precisely using the CRISPR/Cas9 technology because CRISPR/Cas9 may cause deletions or additions in some regions of the target gene. Several other technologies have been developed for gene targeting and precision editing. Among these, base editors might be the most practically and efficiently used compared to others. Base editors are tools which are able to cause a transition from cytosine into thymine, or from adenine into guanine very precisely on specific sequences. Cytosine base editors basically consist of nCas9, cytosine deaminase, and uracil DNA glycosylase inhibitor (UGI). Adenine base editors consist of nCas9 and adenine deaminase. These were first developed for human cells and have since also been applied successfully to crops. Base editors have been successfully applied for productivity improvement, fortification and herbicide resistance of crops. Thus, base editor technologies start to open a new era for precision gene editing or breeding in crops and might result in revolutionary changes in crop breeding and biotechnology.

키워드

참고문헌

  1. Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P. 2007. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315:1709-1712. https://doi.org/10.1126/science.1138140
  2. Belhaj K, Chaparro-Garcia A, Kamoun S, Patron NJ, Nekrasov V. 2015. Editing plant genomes with CRISPR/Cas9. Current Opinion Biotechnology 32:76-84. https://doi.org/10.1016/j.copbio.2014.11.007
  3. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F. 2013. Multiplex genome engineering using CRISPR/Cas systems. Science 339:819-823. https://doi.org/10.1126/science.1231143
  4. Endo M, Mikami M, Endo A, Kaya H, Itoh T, Nishimasu H, Nureki O, Toki S. 2019. Genome editing in plants by engineered CRISPR-Cas9 recognizing NG PAM. Nature Plants 5:14-17. https://doi.org/10.1038/s41477-018-0321-8
  5. Gaudelli NM, Komor AC, Rees HA, Packer MS, Badran AH, Bryson DI, Liu DR. 2017. Programmable base editing of A*T to G*C in genomic DNA without DNA cleavage. Nature 551:464-471. https://doi.org/10.1038/nature24644
  6. Harris RS, Petersen-Mahrt SK, Neuberger MS. 2002. RNA editing enzyme APOBEC1 and some of its homologs can act as DNA mutators. Molecular Cell 10:1247-1253. https://doi.org/10.1016/S1097-2765(02)00742-6
  7. Hu JH, Miller SM, Geurts MH, Tang W, Chen L, Sun N, Zeina CM, Gao X, Rees HA, Lin Z, Liu DR. 2018. Evolved Cas9 variants with broad PAM compatibility and high DNA specificity. Nature 556:57-63. https://doi.org/10.1038/nature26155
  8. Hua K, Tao X, Han P, Wang R, Zhu JK. 2019a. Genome engineering in rice using Cas9 variants that recognize NG PAM sequences. Molecular Plant 12:1003-1014. https://doi.org/10.1016/j.molp.2019.03.009
  9. Hua K, Tao X, Yuan F, Wang D, Zhu JK. 2018. Precise A.T to G.C base editing in the rice genome. Molecular Plant 11:627-630. https://doi.org/10.1016/j.molp.2018.02.007
  10. Hua K, Tao X, Zhu JK. 2019b. Expanding the base editing scope in rice by using Cas9 variants. Plant Biotechnology Journal 17:499-504. https://doi.org/10.1111/pbi.12993
  11. Ishino Y, Shinagawa H, Makino K, Amemura M, Nakata A. 1987. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. Journal of Bacteriology 169:5429-5433. https://doi.org/10.1128/jb.169.12.5429-5433.1987
  12. Jansen R, Embden JD, Gaastra W, Schouls LM. 2002. Identification of genes that are associated with DNA repeats in prokaryotes. Molecular Microbiology 43:1565-1575. https://doi.org/10.1046/j.1365-2958.2002.02839.x
  13. Jiang WZ, Henry IM, Lynagh PG, Comai L, Cahoon EB, Weeks DP. 2017. Significant enhancement of fatty acid composition in seeds of the allohexaploid, Camelina sativa, using CRISPR/Cas9 gene editing. Plant Biotechnology Journal 15:648-657. https://doi.org/10.1111/pbi.12663
  14. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. 2012. A programmable dual-RNAguided DNA endonuclease in adaptive bacterial immunity. Science 337:816-821. https://doi.org/10.1126/science.1225829
  15. Kang BC, Yun JY, Kim ST, Shin Y, Ryu J, Choi M, Woo JW, Kim JS. 2018. Precision genome engineering through adenine base editing in plants. Nature Plants 4:427-431. https://doi.org/10.1038/s41477-018-0178-x
  16. Kim YB, Komor AC, Levy JM, Packer MS, Zhao KT, Liu DR. 2017. Increasing the genome-targeting scope and precision of base editing with engineered Cas9-cytidine deaminase fusions. Nature Biotechnology 35:371-376. https://doi.org/10.1038/nbt.3803
  17. Kleinstiver BP, Prew MS, Tsai SQ, Nguyen NT, Topkar VV, Zheng Z, Joung JK. 2015a. Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition. Nature Biotechnology 33:1293-1298. https://doi.org/10.1038/nbt.3404
  18. Kleinstiver BP, Prew MS, Tsai SQ, Topkar VV, Nguyen NT, Zheng Z, Gonzales AP, Li Z, Peterson RT, Yeh JR, Aryee MJ, Joung JK. 2015b. Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature 523:481-485. https://doi.org/10.1038/nature14592
  19. Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR. 2016. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533:420-424. https://doi.org/10.1038/nature17946
  20. Li C, Zong Y, Wang Y, Jin S, Zhang D, Song Q, Zhang R, Gao C. 2018. Expanded base editing in rice and wheat using a Cas9-adenosine deaminase fusion. Genome Biology 19:59. https://doi.org/10.1186/s13059-018-1443-z
  21. Li J, Sun Y, Du J, Zhao Y, Xia L. 2017. Generation of targeted point mutations in rice by a modified CRISPR/Cas9 system. Molecular Plant 10:526-529. https://doi.org/10.1016/j.molp.2016.12.001
  22. Lu Y, Zhu JK. 2017. Precise editing of a target base in the rice genome using a modified CRISPR/Cas9 system. Molecular Plant 10:523-525. https://doi.org/10.1016/j.molp.2016.11.013
  23. Miao C, Xiao L, Hua K, Zou C, Zhao Y, Bressan RA, Zhu JK. 2018. Mutations in a subfamily of abscisic acid receptor genes promote rice growth and productivity. Proceedings of the National Academy of Sciences of the United States of America 115:6058-6063. https://doi.org/10.1073/pnas.1804774115
  24. Negishi K, Kaya H, Abe K, Hara N, Saika H, Toki S. 2019. An adenine base editor with expanded targeting scope using SpCas9-NGv1 in rice. Plant Biotechnology Journal 17:1476-1478. https://doi.org/10.1111/pbi.13120
  25. Nishida K, Arazoe T, Yachie N, Banno S, Kakimoto M, Tabata M, Mochizuki M, Miyabe A, Araki M, Hara KY, Shimatani Z, Kondo A. 2016. Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems. Science 353:aaf8729. https://doi.org/10.1126/science.aaf8729
  26. Nishimasu H, Shi X, Ishiguro S, Gao L, Hirano S, Okazaki S, Noda T, Abudayyeh OO, Gootenberg JS, Mori H, Oura S, Holmes B, Tanaka M, Seki M, Hirano H, Aburatani H, Ishitani R, Ikawa M, Yachie N, Zhang F, Nureki O. 2018. Engineered CRISPR-Cas9 nuclease with expanded targeting space. Science 361:1259-1262. https://doi.org/10.1126/science.aas9129
  27. Qin R, Li J, Li H, Zhang Y, Liu X, Miao Y, Zhang X, Wei P. 2019. Developing a highly efficient and wildly adaptive CRISPR-SaCas9 toolset for plant genome editing. Plant Biotechnology Journal 17:706-708. https://doi.org/10.1111/pbi.13047
  28. Ran FA, Cong L, Yan WX, Scott DA, Gootenberg JS, Kriz AJ, Zetsche B, Shalem O, Wu X, Makarova KS, Koonin EV, Sharp PA, Zhang F. 2015. In vivo genome editing using Staphylococcus aureus Cas9. Nature 520:186-191. https://doi.org/10.1038/nature14299
  29. Ren B, Liu L, Li S, Kuang Y, Wang J, Zhang D, Zhou X, Lin H, Zhou H. 2019. Cas9-NG greatly expands the targeting scope of the genome-editing toolkit by recognizing NG and other atypical PAMs in rice. Molecular Plant 12:1015-1026. https://doi.org/10.1016/j.molp.2019.03.010
  30. Shimatani Z, Kashojiya S, Takayama M, Terada R, Arazoe T, Ishii H, Teramura H, Yamamoto T, Komatsu H, Miura K, Ezura H, Nishida K, Ariizumi T, Kondo A. 2017. Targeted base editing in rice and tomato using a CRISPR-Cas9 cytidine deaminase fusion. Nature Biotechnology 35:441-443. https://doi.org/10.1038/nbt.3833
  31. Wang X, Li J, Wang Y, Yang B, Wei J, Wu J, Wang R, Huang X, Chen J, Yang L. 2018. Efficient base editing in methylated regions with a human APOBEC3A-Cas9 fusion. Nature Biotechnology 36:946-949. https://doi.org/10.1038/nbt.4198
  32. Xie K, Minkenberg B, Yang Y. 2015. Boosting CRISPR/Cas9 multiplex editing capability with the endogenous tRNA-processing system. Proceedings of the National Academy of Sciences of the United States of America 112:3570-3575. https://doi.org/10.1073/pnas.1420294112
  33. Yan F, Kuang Y, Ren B, Wang J, Zhang D, Lin H, Yang B, Zhou X, Zhou H. 2018. Highly efficient A.T to G.C base editing by Cas9n-Guided tRNA adenosine deaminase in rice. Molecular Plant 11:631-634. https://doi.org/10.1016/j.molp.2018.02.008
  34. Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS, Essletzbichler P, Volz SE, Joung J, van der Oost J, Regev A, Koonin EV, Zhang F. 2015. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163:759-771. https://doi.org/10.1016/j.cell.2015.09.038
  35. Zhong Z, Sretenovic S, Ren Q, Yang L, Bao Y, Qi C, Yuan M, He Y, Liu S, Liu X, Wang J, Huang L, Wang Y, Baby D, Wang D, Zhang T, Qi Y, Zhang Y. 2019. Improving plant genome editing with high-fidelity xCas9 and non-canonical PAM-targeting Cas9-NG. Molecular Plant 12:1027-1036. https://doi.org/10.1016/j.molp.2019.03.011
  36. Zong Y, Song Q, Li C, Jin S, Zhang D, Wang Y, Qiu JL, Gao C. 2018. Efficient C-to-T base editing in plants using a fusion of nCas9 and human APOBEC3A. Nature Biotechnology 36:950-953. https://doi.org/10.1038/nbt.4261
  37. Zong Y, Wang Y, Li C, Zhang R, Chen K, Ran Y, Qiu JL, Wang D, Gao C. 2017. Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion. Nature Biotechnology 35:438-440. https://doi.org/10.1038/nbt.3811

피인용 문헌

  1. Overview of CRISPR/Cas9: a chronicle of the CRISPR system and application to ornamental crops vol.47, pp.4, 2019, https://doi.org/10.7744/kjoas.20200075