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GM Crops & Food
Biotechnology in Agriculture and the Food Chain
Volume 13, 2022 - Issue 1
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Research Article

Broad-spectrum resistance against multiple PVY-strains by CRSIPR/Cas13 system in Solanum tuberosum crop

, , , , , & ORCID Icon show all
Pages 97-111 | Received 18 Feb 2022, Accepted 17 May 2022, Published online: 02 Jun 2022

References

  • Quenouille J, Vassilakos N, Moury B. P otato virus Y: a major crop pathogen that has provided major insights into the evolution of viral pathogenicity. Mol Plant Pathol. 2013;14(5):439–52. doi:10.1111/mpp.12024.
  • Wei T, Zhang C, Hong J, Xiong R, Kasschau KD, Zhou X, Carrington JC, Wang A. Formation of complexes at plasmodesmata for potyvirus intercellular movement is mediated by the viral protein P3N-PIPO. PLoS Pathog. 2010;6(6):e1000962. doi:10.1371/journal.ppat.1000962.
  • Davie K, Holmes R, Pickup J, Lacomme C. Dynamics of PVY strains in field grown potato: impact of strain competition and ability to overcome host resistance mechanisms. Virus Res. 2017;241:95–104. doi:10.1016/j.virusres.2017.06.012.
  • Karasev AV, Gray SM. Continuous and emerging challenges of Potato virus Y in potato. Annu Rev Phytopathol. 2013;51(1):571–86. doi:10.1146/annurev-phyto-082712-102332.
  • Takakura Y, Udagawa H, Shinjo A, Koga K. Mutation of a Nicotiana tabacum L. eukaryotic translation-initiation factor gene reduces susceptibility to a resistance-breaking strain of potato virus Y. Mol Plant Pathol. 2018;19(9):2124–33. doi:10.1111/mpp.12686.
  • Pooggin MM. RNAi-mediated resistance to viruses: a critical assessment of methodologies. Curr Opin Virol. 2017;26:28–35. doi:10.1016/j.coviro.2017.07.010.
  • Kenesi E, Carbonell A, Lózsa R, Vértessy B, Lakatos L. A viral suppressor of RNA silencing inhibits ARGONAUTE 1 function by precluding target RNA binding to pre-assembled RISC. Nucleic Acids Res. 2017;45(13):7736–50. doi:10.1093/nar/gkx379.
  • Hille F, Charpentier E. CRISPR-Cas: biology, mechanisms and relevance. Philos Trans Royal Soc B Biol Sci. 2016;371(1707):20150496. doi:10.1098/rstb.2015.0496.
  • Van Der Oost J, Westra ER, Jackson RN, Wiedenheft B. Unravelling the structural and mechanistic basis of CRISPR–Cas systems. Nat Rev Microbiol. 2014;12(7):479–92. doi:10.1038/nrmicro3279.
  • Edwardson J. Inclusion bodies. Potyvirus Taxon. 1992;5:25–30. ISBN : 978-3-211-82353-8.
  • Harrington LB, Burstein D, Chen JS, Paez-Espino D, Ma E, Witte IP, Cofsky JC, Kyrpides NC, Banfield JF, Doudna JA, et al. Programmed DNA destruction by miniature CRISPR-Cas14 enzymes. Science. 2018;362(6416):839–42. doi:10.1126/science.aav4294.
  • Abudayyeh OO, Gootenberg JS, Essletzbichler P, Han S, Joung J, Belanto JJ, Verdine V, Cox DBT, Kellner MJ, Regev A, et al. RNA targeting with CRISPR–Cas13. Nature. 2017;550(7675):280–84. doi:10.1038/nature24049.
  • Marraffini LA, Sontheimer EJ. Self versus non-self discrimination during CRISPR RNA-directed immunity. Nature. 2010;463(7280):568–71. doi:10.1038/nature08703.
  • Cox DB, Gootenberg JS, Abudayyeh OO, Franklin B, Kellner MJ, Joung J, Zhang F. RNA editing with CRISPR-Cas13. Science. 2017;358(6366):1019–27. doi:10.1126/science.aaq0180.
  • Yan WX, Chong S, Zhang H, Makarova KS, Koonin EV, Cheng DR, Scott DA. 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. doi:10.1016/j.molcel.2018.02.028.
  • Zhang T, Zhao Y, Ye J, Cao X, Xu C, Chen B, An H, Jiao Y, Zhang F, Yang X, et al. Establishing CRISPR /Cas13a immune system conferring RNA virus resistance in both dicot and monocot plants. Plant Biotechnol J. 2019;17(7):1185–87. doi:10.1111/pbi.13095.
  • Khan MZ, Amin I, Hameed A, Mansoor S. CRISPR–Cas13a: prospects for plant virus resistance. Trends Biotechnol. 2018;36(12):1207–10. doi:10.1016/j.tibtech.2018.05.005.
  • Li J-F, Norville JE, Aach J, McCormack M, Zhang D, Bush J, Church GM, Sheen J. Multiplex and homologous recombination–mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nat Biotechnol. 2013;31(8):688. doi:10.1038/nbt.2654.
  • Xing H-L, Dong L, Wang Z-P, Zhang H-Y, Han C-Y, Liu B, Wang X-C, Chen Q-J. A CRISPR/Cas9 toolkit for multiplex genome editing in plants. BMC Plant Biol. 2014;14(1):327. doi:10.1186/s12870-014-0327-y.
  • Zhou H, Liu B, Weeks DP, Spalding MH, Yang B. Large chromosomal deletions and heritable small genetic changes induced by CRISPR/Cas9 in rice. Nucleic Acids Res. 2014;42(17):10903–14. doi:10.1093/nar/gku806.
  • Ma X, Zhang Q, Zhu Q, Liu W, Chen Y, Qiu R, Wang B, Yang Z, Li H, Lin Y, et al. A robust CRISPR/Cas9 system for convenient, high-efficiency multiplex genome editing in monocot and dicot plants. Mol Plant. 2015;8(8):1274–84. doi:10.1016/j.molp.2015.04.007.
  • O’Connell MR. Molecular mechanisms of RNA targeting by Cas13-containing type VI CRISPR–Cas systems. J Mol Biol. 2019;431(1):66–87. doi:10.1016/j.jmb.2018.06.029.
  • Aman R, Ali Z, Butt H, Mahas A, Aljedaani F, Khan MZ, Ding S, Mahfouz M. RNA virus interference via CRISPR/Cas13a system in plants. Genome Biol. 2018;19(1):1. doi:10.1186/s13059-017-1381-1.
  • East-Seletsky A, O’Connell MR, Knight SC, Burstein D, Cate JHD, Tjian R, Doudna JA. Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection. Nature. 2016;538(7624):270–73. doi:10.1038/nature19802.
  • Cui X, Wei T, Chowda-Reddy RV, Sun G, Wang A. The Tobacco etch virus P3 protein forms mobile inclusions via the early secretory pathway and traffics along actin microfilaments. Virology. 2010;397(1):56–63. doi:10.1016/j.virol.2009.11.015.
  • Andersen K, Johansen IE. A single conserved amino acid in the coat protein gene of pea seed-borne mosaic potyvirus modulates the ability of the virus to move systemically inChenopodium quinoa. Virology. 1998;241(2):304–11. doi:10.1006/viro.1997.8967.
  • Kieu NP, Lenman M, Wang ES, Petersen BL, Andreasson E. Mutations introduced in susceptibility genes through CRISPR/Cas9 genome editing confer increased late blight resistance in potatoes. Sci Rep. 2021;11(1):1–12. doi:10.1038/s41598-021-83972-w.
  • Subramoni S, Nathoo N, Klimov E, Yuan Z-C. Agrobacterium tumefaciens responses to plant-derived signaling molecules. Front Plant Sci. 2014;5:322. doi:10.3389/fpls.2014.00322.
  • Cho H, Winans SC. VirA and VirG activate the Ti plasmid repABC operon, elevating plasmid copy number in response to wound-released chemical signals. Proc Nat Acad Sci. 2005;102(41):14843–48. doi:10.1073/pnas.0503458102.
  • Wang ES, Kieu NP, Lenman M, Andreasson E. Tissue culture and refreshment techniques for improvement of transformation in local tetraploid and diploid potato with late blight resistance as an example. Plants. 2020;9(6):695. doi:10.3390/plants9060695.
  • Bruce MA, Rupp JLS. Agrobacterium-mediated transformation of Solanum tuberosum L., potato. In: Transgenic plants. Springer; 2019. p. 203–23. doi:10.1007/978-1-4939-8778-8_15.
  • Liu P, Nester EW. Indoleacetic acid, a product of transferred DNA, inhibits vir gene expression and growth of Agrobacterium tumefaciens C58. Proc Nat Acad Sci. 2006;103(12):4658–62. doi:10.1073/pnas.0600366103.
  • Albrecht T, Argueso CT. Should I fight or should I grow now? The role of cytokinins in plant growth and immunity and in the growth–defence trade-off. Ann Bot. 2017;119(5):725–35. doi:10.1093/aob/mcw211.
  • Hill K, Schaller GE. Enhancing plant regeneration in tissue culture: a molecular approach through manipulation of cytokinin sensitivity. Plant Signal Behav. 2013;8(10):212–24. doi:10.4161/psb.25709.
  • Gaspar T, Kevers C, Penel C, Greppin H, Reid DM, Thorpe TA. Plant hormones and plant growth regulators in plant tissue culture. In Vitro Cell Dev Biol-Plant. 1996;32(4):272–89. doi:10.1007/BF02822700.
  • Uzair M, Long H, Zafar SA, Patil SB, Chun Y, Li L, Fang J, Zhao J, Peng L, Yuan S, et al. Narrow Leaf21, encoding ribosomal protein RPS3A, controls leaf development in rice. Plant Physiol. 2021;186(1):497–518. doi:10.1093/plphys/kiab075.
  • Sugimoto K, Meyerowitz EM. Regeneration in Arabidopsis tissue culture. Methods Mol Biol. 2013;959:265-75. doi:10.1007/978-1-62703-221-6_18. PMID: 23299682
  • Xi J, Patel M, Dong S, Que Q, Qu R. Acetosyringone treatment duration affects large T-DNA molecule transfer to rice callus. BMC Biotechnol. 2018;18(1):1–8. doi:10.1186/s12896-018-0459-5.
  • Zhan X, Zhang F, Zhong Z, Chen R, Wang Y, Chang L, Bock R, Nie B, Zhang J. Generation of virus-resistant potato plants by RNA genome targeting. Plant Biotechnol J. 2019;17(9):1814–22. doi:10.1111/pbi.13102.
  • Gao Z, Herrera-Carrillo E, Berkhout B. Improvement of the CRISPR-Cpf1 system with ribozyme-processed crRNA. RNA Biol. 2018;15(12):1458–67. doi:10.1080/15476286.2018.1551703.
  • Xie K, Minkenberg B, Yang Y. Boosting CRISPR/Cas9 multiplex editing capability with the endogenous tRNA-processing system. Proc Nat Acad Sci. 2015;112(11):3570–75. doi:10.1073/pnas.1420294112.
  • Wolter F, Puchta H. The CRISPR/Cas revolution reaches the RNA world: cas13, a new Swiss Army knife for plant biologists. Plant J. 2018;94(5):767–75. doi:10.1111/tpj.13899.
  • Zhang T, Zheng Q, Yi X, An H, Zhao Y, Ma S, Zhou G. Establishing RNA virus resistance in plants by harnessing CRISPR immune system. Plant Biotechnol J. 2018;16(8):1415–23. doi:10.1111/pbi.12881.
  • Abudayyeh OO, Gootenberg JS, Konermann S, Joung J, Slaymaker IM, Cox DBT, Shmakov S, Makarova KS, Semenova E, Minakhin L, et al. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science. 2016;353(6299):aaf5573. doi:10.1126/science.aaf5573.
  • Xu C, Zhou, Y., Xiao, Q, et al. Programmable RNA editing with compact CRISPR–Cas13 systems from uncultivated microbes. Nat Methods. 2021;18:499–506.
  • Pandita D, Puli COR, Palakolanu SR. CRISPR/Cas13: A Novel and Emerging Tool for RNA Editing in Plants. In: Tang, G., Teotia, S., Tang, X., Singh, D. (eds) RNA-Based Technologies for Functional Genomics in Plants. Concepts and Strategies in Plant Sciences. Springer, Cham. https://doi.org/10.1007/978-3-030-64994-4_14
  • Zhang J, Khan SA, Hasse C, Ruf S, Heckel DG, Bock R. Full crop protection from an insect pest by expression of long double-stranded RNAs in plastids. Science. 2015;347(6225):991–94. doi:10.1126/science.1261680.
  • Porebski S, Bailey LG, Baum BR. Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant Mol Biol Rep. 1997;15(1):8–15. doi:10.1007/BF02772108.
  • Chen L, Cai Y, Zhou G, Shi X, Su J, Chen G, Lin K. Rapid Sanger sequencing of the 16S rRNA gene for identification of some common pathogens. PloS one. 2014;9(2):e88886. doi:10.1371/journal.pone.0088886.
  • Nie X, Singh RP, Singh M. Molecular and pathological characterization of N: o isolates of the Potato virus Y from Manitoba, Canada. Can J Plant Pathol. 2004;26(4):573–83. doi:10.1080/07060660409507178.
  • Wang J, Meng F, Chen R, Liu J, Nie X, Nie B. RT-PCR differentiation, molecular and pathological characterization of Andean and ordinary strains of Potato virus S in potatoes in China. Plant Dis. 2016;100(8):1580–85. doi:10.1094/PDIS-11-15-1257-RE.
  • Bilgin DD, DeLucia EH, Clough SJ. A robust plant RNA isolation method suitable for Affymetrix GeneChip analysis and quantitative real-time RT-PCR. Nat Protoc. 2009;4(3):333–40. doi:10.1038/nprot.2008.249.