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RPS5A Promoter-Driven Cas9 Produces Heritable Virus-Induced Genome Editing in Nicotiana attenuata

  • Oh, Youngbin (Department of Biological Sciences, Korea Advanced Institute for Science and Technology) ;
  • Kim, Sang-Gyu (Department of Biological Sciences, Korea Advanced Institute for Science and Technology)
  • Received : 2021.09.13
  • Accepted : 2021.09.30
  • Published : 2021.12.31

Abstract

The virus-induced genome editing (VIGE) system aims to induce targeted mutations in seeds without requiring any tissue culture. Here, we show that tobacco rattle virus (TRV) harboring guide RNA (gRNA) edits germ cells in a wild tobacco, Nicotiana attenuata, that expresses Streptococcus pyogenes Cas9 (SpCas9). We first generated N. attenuata transgenic plants expressing SpCas9 under the control of 35S promoter and infected rosette leaves with TRV carrying gRNA. Gene-edited seeds were not found in the progeny of the infected N. attenuata. Next, the N. attenuata ribosomal protein S5 A (RPS5A) promoter fused to SpCas9 was employed to induce the heritable gene editing with TRV. The RPS5A promoter-driven SpCas9 successfully produced monoallelic mutations at three target genes in N. attenuata seeds with TRV-delivered guide RNA. These monoallelic mutations were found in 2%-6% seeds among M1 progenies. This editing method provides an alternative way to increase the heritable editing efficacy of VIGE.

Keywords

Acknowledgement

We thank Emily Wheeler, for editorial assistance and Joohee Kim, for technical assistance. The targeted deep sequencing was supported by Bio Core facilities in KAIST. Y.O. and S.G.K. have filed a patent application based on this work. This work was supported by KAIST-funded Global Singularity Research Program (N11200021) and the Samsung Science & Technology Foundation (SSTF-BA1901-10).

References

  1. Ahn, Y.K., Yoon, M.K., and Jeon, J.S. (2013). Development of an efficient Agrobacterium-mediated transformation system and production of herbicide-resistant transgenic plants in garlic (Allium sativum L.). Mol. Cells 36, 158-162. https://doi.org/10.1007/s10059-013-0142-6
  2. Ali, Z., Abul-faraj, A., Li, L., Ghosh, N., Piatek, M., Mahjoub, A., Aouida, M., Piatek, A., Baltes, N.J., Voytas, D.F., et al. (2015). Efficient virus-mediated genome editing in plants using the CRISPR/Cas9 system. Mol. Plant 8, 1288-1291. https://doi.org/10.1016/j.molp.2015.02.011
  3. Ali, Z., Eid, A., Ali, S., and Mahfouz, M.M. (2018). Pea early-browning virus-mediated genome editing via the CRISPR/Cas9 system in Nicotiana benthamiana and Arabidopsis. Virus Res. 244, 333-337. https://doi.org/10.1016/j.virusres.2017.10.009
  4. Alonso, J.M. and Ecker, J.R. (2006). Moving forward in reverse: genetic technologies to enable genome-wide phenomic screens in Arabidopsis. Nat. Rev. Genet. 7, 524-536. https://doi.org/10.1038/nrg1893
  5. Altpeter, F., Springer, N.M., Bartley, L.E., Blechl, A.E., Brutnell, T.P., Citovsky, V., Conrad, L.J., Gelvin, S.B., Jackson, D.P., Kausch, A.P., et al. (2016). Advancing crop transformation in the era of genome editing. Plant Cell 28, 1510-1520. https://doi.org/10.1105/tpc.16.00196
  6. Ariga, H., Toki, S., and Ishibashi, K. (2020). Potato virus X vector-mediated DNA-free genome editing in plants. Plant Cell Physiol. 61, 1946-1953. https://doi.org/10.1093/pcp/pcaa123
  7. Bae, S., Park, J., and Kim, J.S. (2014). Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics 30, 1473-1475. https://doi.org/10.1093/bioinformatics/btu048
  8. Baltes, N., Hummel, A., Konecna, E., Cegan, R., Bruns, A.N., Bisaro, D.M., and Voytas, D.F. (2015). Conferring resistance to geminiviruses with the CRISPR-Cas prokaryotic immune system. Nat. Plants 1, 15145. https://doi.org/10.1038/nplants.2015.145
  9. Cody, W.B., Scholthof, H.B., and Mirkov, T.E. (2017). Multiplexed gene editing and protein overexpression using a Tobacco mosaic virus viral vector. Plant Physiol. 175, 23-35. https://doi.org/10.1104/pp.17.00411
  10. Ellison, E.E., Nagalakshmi, U., Gamo, M.E., Huang, P.J., Dinesh-Kumar, S., and Voytas, D.F. (2020). Multiplexed heritable gene editing using RNA viruses and mobile single guide RNAs. Nat. Plants 6, 620-624. https://doi.org/10.1038/s41477-020-0670-y
  11. Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J.A., and Charpentier, E. (2012). A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816-821. https://doi.org/10.1126/science.1225829
  12. Kang, B.C., Yun, J.Y., Kim, S.T., Shin, Y., Ryu, J., Choi, M., Woo, J.W., and Kim, J.S. (2018). Precision genome engineering through adenine base editing in plants. Nat. Plants 4, 427-431. https://doi.org/10.1038/s41477-018-0178-x
  13. Kang, M., Ahn, H., Rothe, E., Baldwin, I.T., and Kim, S.G. (2020). A robust genome-editing method for wild plant species Nicotiana attenuata. Plant Biotechnol. Rep. 14, 585-598. https://doi.org/10.1007/s11816-020-00634-5
  14. Kim, H., Kim, S.T., Ryu, J., Choi, M.K., Kweon, J., Kang, B.C., Ahn, H.M., Bae, S., Kim, J., Kim, J.S., et al. (2016). A simple, flexible and high-throughput cloning system for plant genome editing via CRISPR-Cas system. J. Integr. Plant Biol. 58, 705-712. https://doi.org/10.1111/jipb.12474
  15. Krugel, T., Lim, M., Gase, K. Halitschke, R., and Baldwin, I.T. (2002). Agrobacterium-mediated transformation of Nicotiana attenuata, a model ecological expression system. Chemoecology 12, 177-183. https://doi.org/10.1007/PL00012666
  16. Lei, J., Dai, P., Li, Y., Zhang, W., Zhou, G., Liu, C., and Liu, X. (2021). Heritable gene editing using FT mobile guide RNAs and DNA viruses. Plant Methods 17, 20. https://doi.org/10.1186/s13007-021-00719-4
  17. Li, J.F., Norville, J., Aach, J., McCormack, M., Zhang, D., Bush, J., Church, G.M., and Sheen, J. (2013). Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nat. Biotechnol. 31, 688-691. https://doi.org/10.1038/nbt.2654
  18. Li, T., Hu, J., Sun, Y., Li, B., Zhang, D., Li, W., Liu, J., Li, D., Gao, C., Zhang, Y., et al. (2021). Highly efficient heritable genome editing in wheat using an RNA virus and bypassing tissue culture. Mol. Plant 2021 Jul 15 [Epub]. https://doi.org/10.1016/j.molp.2021.07.010
  19. Ma, X., Zhang, X., Liu, H., and Li, Z. (2020). Highly efficient DNA-free plant genome editing using virally delivered CRISPR-Cas9. Nat. Plants 6, 773-779. https://doi.org/10.1038/s41477-020-0704-5
  20. Mao, Y., Zhang, Z., Feng, Z., Wei, P., Zhang, H., Botella, J.R., and Zhu, J.K. (2016). Development of germ-line-specific CRISPR-Cas9 systems to improve the production of heritable gene modifications in Arabidopsis. Plant Biotechnol. J. 14, 519-532. https://doi.org/10.1111/pbi.12468
  21. Mei, Y., Beernink, B.M., Ellison, E.E., Konecna, E., Neelakandan, A.K., Voytas, D.F., and Whitham, S.A. (2019). Protein expression and gene editing in monocots using foxtail mosaic virus vectors. Plant Direct 3, e00181.
  22. Oh, Y., Kim, H., and Kim, S.G. (2021a). Virus-induced plant genome editing. Curr. Opin. Plant Biol. 60, 101992. https://doi.org/10.1016/j.pbi.2020.101992
  23. Oh, Y., Kim, H., Lee, H.J., and Kim, S.G. (2021b). Ribozyme-processed guide RNA enhances virus-mediated plant genome editing. Biotechnol. J. 2021 Jun 8 [Epub]. https://doi.org/10.1002/biot.202100189
  24. Oh, Y., Lee, B., Kim, H., and Kim, S.G. (2020). A multiplex guide RNA expression system and its efficacy for plant genome engineering. Plant Methods 16, 37. https://doi.org/10.1186/s13007-020-00580-x
  25. Park, J., Bae, S., and Kim, J.S. (2015). Cas-Designer: a web-based tool for choice of CRISPR-Cas9 target sites. Bioinformatics 31, 4014-4016. https://doi.org/10.1093/bioinformatics/btv537
  26. Park, J., Lim, K., Kim, J.S., and Bae, S. (2017). Cas-analyzer: an online tool for assessing genome editing results using NGS data. Bioinformatics 33, 286-288. https://doi.org/10.1093/bioinformatics/btw561
  27. Patro, S., Kumar, D., Ranjan, R., Maiti, I.B., and Dey, N. (2012). The development of efficient plant promoters for transgene expression employing plant virus promoters. Mol. Plant 5, 941-944. https://doi.org/10.1093/mp/sss028
  28. Senthil-Kumar, M. and Mysore, K.S. (2014). Tobacco rattle virus-based virus-induced gene silencing in Nicotiana benthamiana. Nat. Protoc. 9, 1549-1562. https://doi.org/10.1038/nprot.2014.092
  29. Sunilkumar, G., Mohr, L., Lopata-Finch, E., Emani, C., and Rathore, K. (2002). Developmental and tissue-specific expression of CaMV 35S promoter in cotton as revealed by GFP. Plant Mol. Biol. 50, 463-479. https://doi.org/10.1023/A:1019832123444
  30. Tsutsui, H. and Higashiyama, T. (2017). pKAMA-ITACHI vectors for highly efficient CRISPR/Cas9-mediated gene knockout in Arabidopsis thaliana. Plant Cell Physiol. 58, 46-56. https://doi.org/10.1093/pcp/pcw191
  31. Uranga, M., Aragones, V., Selma, S., Vazquez-Vilar, M., Orzaez, D., and Daros, J.A. (2021). Efficient Cas9 multiplex editing using unspaced sgRNA arrays engineering in a Potato virus X vector. Plant J. 106, 555-565. https://doi.org/10.1111/tpj.15164
  32. Wang, M., Lu, Y., Botella, J.R., Mao, Y., Hua, K., and Zhu, J. (2017). Gene targeting by homology-directed repair in rice using a geminivirus-based CRISPR/Cas9 system. Mol. Plant 10, 1007-1010. https://doi.org/10.1016/j.molp.2017.03.002
  33. Wilkinson, J.E., Twell, D., and Lindsey, K. (1997). Activities of CaMV 35S and nos promoters in pollen: implications for field release of transgenic plants. J. Exp. Bot. 48, 265-275. https://doi.org/10.1093/jxb/48.2.265
  34. Wu, H., Qu, X., Dong, Z., Luo, L., Shao, C., Forner, J., Lohmann, J.U., Su, M., Xu, M., Liu, X., et al. (2020). WUSCHEL triggers innate antiviral immunity in plant stem cells. Science 370, 227-231. https://doi.org/10.1126/science.abb7360
  35. Yan, L., Wei, S., Wu, Y., Hu, R., Li, H., Yang, W., and Xie, Q. (2015). High-efficiency genome editing in Arabidopsis using YAO promoter-driven CRISPR/Cas9 system. Mol. Plant 8, 1820-1823. https://doi.org/10.1016/j.molp.2015.10.004
  36. Yang, S.J., Carter, S.A., Cole, A.B., Cheng, N.H., and Nelson, R.S. (2004). A natural variant of a host RNA-dependent RNA polymerase is associated with increased susceptibility to viruses by Nicotiana benthamiana. Proc. Natl. Acad. Sci. U. S. A. 101, 6297-6302. https://doi.org/10.1073/pnas.0304346101
  37. Yin, K., Han, T., Liu, G., Chen, T., Wang, Y., Yu, A.Y.L., and Liu, Y. (2015). A geminivirus-based guide RNA delivery system for CRISPR/Cas9 mediated plant genome editing. Sci. Rep. 5, 14926. https://doi.org/10.1038/srep14926
  38. Yoo, S.D., Cho, Y.H., and Sheen, J. (2007). Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis. Nat. Protoc. 2, 1565-1572. https://doi.org/10.1038/nprot.2007.199
  39. Zhang, X., Kang, L., Zhang, Q., Meng, Q., Pan, Y., Yu, Z., Shi, N., Jackson, S., Zhang, X., Wang, H., et al. (2020). An RNAi suppressor activates in planta virus-mediated gene editing. Funct. Integr. Genomics 20, 471-477. https://doi.org/10.1007/s10142-019-00730-y
  40. Zheng, X., Deng, W., Luo, K., Duan, H., Chen, Y., McAvoy, R., Song, S., Pei, Y., and Li, Y. (2007). The cauliflower mosaic virus (CaMV) 35S promoter sequence alters the level and patterns of activity of adjacent tissue- and organ-specific gene promoters. Plant Cell Rep. 26, 1195-1203. https://doi.org/10.1007/s00299-007-0307-x
  41. Zhu, H., Li, C., and Gao, C. (2020). Applications of CRISPR-Cas in agriculture and plant biotechnology. Nat. Rev. Mol. Cell Biol. 21, 661-677.