Browse > Article
http://dx.doi.org/10.14348/molcells.2021.0237

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)
Publication Information
Molecules and Cells / v.44, no.12, 2021 , pp. 911-919 More about this Journal
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
CRISPR/Cas9; heritable plant genome editing; ribosomal protein S 5A promoter; tobacco rattle virus; virus-induced genome editing;
Citations & Related Records
Times Cited By KSCI : 1  (Citation Analysis)
연도 인용수 순위
1 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.   DOI
2 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.   DOI
3 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.
4 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.   DOI
5 Senthil-Kumar, M. and Mysore, K.S. (2014). Tobacco rattle virus-based virus-induced gene silencing in Nicotiana benthamiana. Nat. Protoc. 9, 1549-1562.   DOI
6 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   DOI
7 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.   DOI
8 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.   DOI
9 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.   DOI
10 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.   DOI
11 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.   DOI
12 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.   DOI
13 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.   DOI
14 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.   DOI
15 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.   DOI
16 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.   DOI
17 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.   DOI
18 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.   DOI
19 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.   DOI
20 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.   DOI
21 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.   DOI
22 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.
23 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.   DOI
24 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.   DOI
25 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   DOI
26 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.   DOI
27 Oh, Y., Kim, H., and Kim, S.G. (2021a). Virus-induced plant genome editing. Curr. Opin. Plant Biol. 60, 101992.   DOI
28 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.   DOI
29 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.   DOI
30 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.   DOI
31 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.   DOI
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.   DOI
33 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.   DOI
34 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.   DOI
35 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.   DOI
36 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.   DOI
37 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.   DOI
38 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.   DOI
39 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.   DOI
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.   DOI
41 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.   DOI