Research Advances in Gene Editing and Plant-virus Interaction and Their Application in Breeding Virus-resistant Crops

doi:10.13560/j.cnki.biotech.bull.1985.2018-0462

Abstract

Abstract: Viral diseases impose serious threat to crop production and the best management strategy is to breed virus-resistant crop varieties for production. Research on plant-virus interaction has revealed mechanistic insights on the interactions between viral and plant genes which are essential for viruses to complete their life cycle. Once a virus enters its host plant cells, its particle disassembly, gene expression, genome replication, and ribonucleoprotein complex movement through plasmodesmata and phloem tissue are all dependent on interactions between viral products and specific plant genes. The recessive mutation of those plant genes can confer viral resistance to plants. Such mutation exists in plant natural population and can be directly employed in breeding viral resistant crops. CRISPR/Cas-mediated gene editing enables targeted gene mutagenesis in both plants and animals in vivo and there has been an explosion in the development of this technology in the past five years. It allows precise mutation and editing of the plant genes required for virus infection, thus to effectively create virus-resistant crop. In this review, we aim to summarize recent advancements in gene editing research and current knowledge on plant-virus interaction and provide guidelines for creating viral resistant crops using gene editing technology.

Key words: gene editing, plant-virus interaction, virus, virus-resistant breeding

YANG Yi-zhou, LI Wei, YI Tu-yong, LI Feng. Research Advances in Gene Editing and Plant-virus Interaction and Their Application in Breeding Virus-resistant Crops[J]. Biotechnology Bulletin, 2018, 34(8): 8-16.

References

[1] Ruud J, Embden JDAV, Gasstra W, et al.Identification of genes that are associated with DNA repeats in prokaryotes[J]. Molecular Microbiology, 2002, 43(6):1565-1575.
[2] Amitai G, Sorek R.CRISPR-Cas adaptation:insights into the mechanism of action[J]. Nat Rev Microbiol, 2016, 2:67-76.
[3] 李铁民. RNA干扰介导原核细胞适应性免疫[J]. 中国细胞生物学学报, 2008, 30(3):287-290.
[4] Makarova KS, Haft DH, Barrangou R, et al.Evolution and classification of the CRISPR-Cas systems[J]. Nature Review Microbiology, 2011, 9(6):467-477.
[5] Shmakov S, Smargon A, Scott D, et al.Diversity and evolution of class 2 CRISPR-Cas systems[J]. Nature Reviews Microbiology, 2017, 15(3):169-182.
[6] Nishimasu H, Ran FA, Hsu P, et al.Crystal structure of Cas9 in complex with guide RNA and target DNA[J]. Cell, 2014, 156(5):935-949.
[7] Jiang F, Doudna JA.The structural biology of CRISPR-Cas systems[J]. Curr Opin Struct Biol, 2015, 30:100-111.
[8] Jiang F, Zhou K, Ma L, et al.A Cas9-guide RNA complex preorganized for target DNA recognition[J]. Science, 2015, 348(6242):1477-1481.
[9] Komor AC, Badran AH, Liu DR.CRISPR-based technologies for the manipulation of eukaryotic genomes[J]. Cell, 2017, 3:559.
[10] Jiang F, Taylor DW, Chen JS, et al.Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage[J]. Science, 2016, 351(6275):867-871.
[11] Nishimasu H, Nureki O.Structures and mechanisms of CRISPR RNA-guided effector nucleases[J]. Current Opinion in Structural Biology, 2017, 43:68-78.
[12] Swarts DC, Oost JVD, Jinek M.Structural basis for guide RNA processing and seed-dependent DNA targeting by CRISPR-Cas12a[J]. Mol Cell, 2017, 66(2):221-233 e4.
[13] Abudayyeh OO, Gootenberg JS, Konermann S, et al. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector[J]. Science, 2016, 353(6299):aaf5573.
[14] East-Seletsky A, O’Connell MR, Knight SC, et al. Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection[J]. Nature, 2016, 538(7624):270-273.
[15] Liu L, Li X, Wang J, et al.Two distant catalytic sites are responsible for C2c2 RNase activities[J]. Science Foundation in China, 2017, 168(2):121-134 e12.
[16] Liu L, Li X, Ma J, et al.The molecular architecture for RNA-guided RNA cleavage by Cas13a[J]. Cell, 2017, 4:714-726 e10.
[17] Wright AV, Nunez JK, Doudna JA.Biology and applications of CRISPR systems:Harnessing nature’s toolbox for genome engineering[J]. Cell, 2016, 164(1/2):29-44.
[18] Ran YD, Liang Z, Gao CX.Current and future editing reagent delivery systems for plant genome editing[J]. Science China:Life Sciences, 2017, 60(5):490-505.
[19] Cong L, Ran FA, et al.Multiplex genome engineering using CRISPR/Cas systems[J]. Science, 2013, 6121:819-823.
[20] Hwang WY, Fu Y, Reyon D, et al.Efficient genome editing in zebrafish using a CRISPR-Cas system[J]. Nat Biotechnol, 2013, 31(3):227-229.
[21] Mali P, Yang L, et al.RNA-guided human genome engineering via Cas9[J]. Science, 2013, 339(6121):823-826.
[22] Wang H, Yang H, Shivalila CS, et al.One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering[J]. Cell, 2013, 153(4):910-918.
[23] Li JF, Norvill JE, Aach J, et al.Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9[J]. Nat Biotechnol, 2013, 31(8):688-691.
[24] Nekrasov V, Staskawicz B, Weigel D.Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease[J]. Nat Biotechnol, 2013, 31(8):691-693.
[25] Shan Q, Wang Y, Li J, et al.Targeted genome modification of crop plants using a CRISPR-Cas system[J]. Nat Biotechnol, 2013, 31(8):686-688.
[26] Wang M, Mao Y, et al.Multiplex gene editing in rice using the CRISPR-Cpf1 System[J]. Mol Plant, 2017, 7:1011-1013.
[27] Tang X, Lowder LG, Zhang T, et al.A CRISPR-Cpf1 system for efficient genome editing and transcriptional repression in plants[J]. Nat Plants, 2017, 3:17018.
[28] Endo A, Masafumi M, Kaya H, et al.Efficient targeted mutagenesis of rice and tobacco genomes using Cpf1 from Francisella novicida[J]. Sci Rep, 2016, 6:38169.
[29] Li H, Xie K.Recent progresses in CRISPR genome editing in plants[J]. Chinese Journal of Biotechnology, 2017, 33(10):1700-1711.
[30] Komor AC, Kim YB, Packer MS, et al.Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage[J]. Nature, 2016, 533(7603):420-424.
[31] Lu YM, Zhu JK.Precise editing of a target base in the rice genome using a modified CRISPR/Cas9 system[J]. Molecular Plant, 2017, 10(3):523-525.
[32] Zong Y, Wang YP, Li C, et al.Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion[J]. Nat Biotechnol, 2017, 35(5):438-440.
[33] Kim YB, Komore AC, et al.Increasing the genome-targeting scope and precision of base editing with engineered Cas9-cytidine deaminase fusions[J]. Nat Biotechnol, 2017, 35(4):371-376.
[34] Shimatani Z, Kashojiya S, Takayama M, et al.Targeted base editing in rice and tomato using a CRISPR-Cas9 cytidine deaminase fusion[J]. Nat Biotechnol, 2017, 35(5):441-443.
[35] Nishida K, Arazoe T, Yachie N, et al. Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems[J]. Science, 2016, 353(6305):aaf8729.
[36] Gaudelli NM, Komor AC, Rees HA, et al.Programmable base editing of A*T to G*C in genomic DNA without DNA cleavage[J]. Nature, 2017, 551(7681):464-471.
[37] Hua K, TAO X, Yuan F, et al.Precise A^. T to G^. C base editing in the rice genome[J]. Molecular Plant, 2018, 11(4):627-630.
[38] Yan F, Kuang Y, Ren B, et al.High-efficient A. T to G. C base editing by Cas9n-guided tRNA adenosine deaminase in rice[J]. Molecular Plant, 2018, 11(4):631-634.
[39] Wang A.Dissecting the molecular network of virus-plant interactions:the complex roles of host factors[J]. Annual Review of Phytopathology, 2015, 53(1):45-66.
[40] Alam SB, Rochon DA.Cucumber necrosis virus recruits cellular heat shock protein 70 homologs at several stages of infection[J]. J Virol, 2016, 90(7):3302-3317.
[41] Alam SB, Rochon DA.Evidence that Hsc70 is associated with cucumber necrosis virus particles and plays a role in particle disassembly[J]. J Virol, 2017, 91(2):01555-16.
[42] Sanfacon H.Plant translation factors and virus resistance[J]. Viruses, 2015, 7(7):3392-3419.
[43] Hashimoto M, Neriya Y, et al.EXA1, a GYF domain protein, is res-ponsible for loss-of-susceptibility to Plantago asiatica mosaic virus in Arabidopsis thaliana[J]. Plant J, 2016, 88(1):120-131.
[44] Pogany J, Nagy D.Activation of tomato bushy stunt virus RNA-dependent RNA polymerase by cellular heat shock protein 70 is enhanced by phospholipids in vitro[J]. J Virol, 2015, 89(10):5714-5723.
[45] Imura Y, Molho M, Chuang C, et al.Cellular Ubc2/Rad6 E2 ubiquitin-conjugating enzyme facilitates tombusvirus replication in yeast and plants[J]. Virology, 2015, 484:265-275.
[46] Xu K, Nagy D.RNA virus replication depends on enrichment of phosphatidylethanolamine at replication sites in subcellular membranes[J]. Proc Natl Acad Sci USA, 2015, 112(14):E1782-E1791.
[47] Tian M, Sasvani Z, Gonzalez PA, et al.Salicylic acid inhibits the replication of tomato bushy stunt virus by directly targeting a host component in the replication complex[J]. Mol Plant Microbe Interact, 2015, 28(4):379-386.
[48] Hanley-Bowdoin L, Bejarano ER, Robertson D, et al.Geminiviruses:masters at redirecting and reprogramming plant processes[J]. Nat Rev Microbiol, 2013, 11(11):777-788.
[49] Rizvi I, Choudhury NR, Tuteja N.Insights into the functional characteristics of geminivirus rolling-circle replication initiator protein and its interaction with host factors affecting viral DNA replication[J]. Archives of Virology, 2015, 160(2):375-387.
[50] Fridborg I, Grainger J, Page A, et al.TIP, a novel host factor linking callose degradation with the cell-to-cell movement of potato virus X[J]. Mol Plant Microbe Interact, 2003, 16(2):132-140.
[51] Bubici G, Carluccio AV, Cillo F, et al.Virus-induced gene silencing of pectin methylesterase protects Nicotiana benthamiana from lethal symptoms caused by Tobacco mosaic virus[J]. European Journal of Plant Pathology, 2015, 141(2):339-347.
[52] Ishikawa K, et al.Dual targeting of a virus movement protein to ER and plasma membrane subdomains is essential for plasmodesmata localization[J]. PLoS Pathogens, 2017, 13(6):e1006463.
[53] Levy A, Zheng JY, Lazarowitzl SG.Synaptotagmin SYTA forms ER-plasma membrane junctions that are recruited to plasmodesmata for plant virus movement[J]. Curr Biol, 2015, 15:2018-2025.
[54] Pitzalis N, Heinlein M.The roles of membranes and associated cytoskeleton in plant virus replication and cell-to-cell movement
[J]. J Exp Bot, 2017, 69(1):117-132.
[55] Ueki S, Spektor R, Natale DM, et al.ANK, a host cytoplasmic receptor for the tobacco mosaic virus cell-to-cell movement protein, facilitates intercellular transport through plasmodesmata[J]. PLoS Pathogens, 2010, 6(11):e1001201.
[56] Guiu-Aragones C, Sánchez-Pina MA, et al.cmv1 is a gate for Cucumber mosaic virus transport from bundle sheath cells to phloem in melon[J]. Mol Plant Pathol, 2016, 17(6):973-984.
[57] Pyott DE, Sheehan E, Molnar A.Engineering of CRISPR/Cas9-mediated potyvirus resistance in transgene-free Arabidopsis plants[J]. Mol Plant Pathol, 2016, 17(8):1276-1288.
[58] Chandrasekaran J, Brumin M, Wolf D, et al.Development of broad virus resistance in non-transgenic cucumber using CRISPR/Cas9 technology[J]. Mol Plant Pathol, 2016, 17(7):1140-1153.
[59] Wittmann S, Chatel H, et al.Interaction of the viral protein genome linked of turnip mosaic potyvirus with the translational eukaryotic initiation factor(iso)4E of Arabidopsis thaliana using the yeast two-hybrid system[J]. Virology, 1997, 1:84-92.
[60] Lellis AD, Kasschau KD, et al.Loss-of-susceptibility mutants of Ar-abidopsis thaliana reveal an essential role for eIF(iso)4E during potyvirus infection[J]. Curr Biol, 2002, 12(12):1046-1051.
[61] Hashimoto M, Neriya Y, Yamaji Y, et al.Recessive resistance to plant viruses:potential resistance genes beyond translation initiation factors[J]. Front Microbiol, 2016, 7:1695.
[62] Deng Y, Liu M, Li X, et al.microRNA-mediated R gene regulation:molecular scabbards for double-edged swords[J]. Science China Life Science, 2018, 61(2):138-147.
[63] Khalid A, Zhang Q, Yasir M, et al.Small RNA based genetic engineering for plant viral resistance:application in crop protection[J]. Front Microbiol, 2017, 8:43.