CRISPR/Cas: aplicaciones y perspectivas para el mejoramiento genético de plantas
Resumen
El desarrollo vertiginoso de la tecnología CRISPR/Cas en los últimos años, desde su descubrimiento como sistema inmune microbiano hasta su evolución como herramienta versátil y potente para la modificación de la función génica, constituye un manifiesto sobre cómo investigaciones básicas de impacto moderado pueden revolucionar las investigaciones biológicas. A partir de su aplicación como plataforma para la edición génica guiada por ARN, el sistema CRISPR/Cas se ha extendido hacia campos tan diversos como la regulación de la expresión génica, edición del epigenoma y visualización in vivo de la cromatina. En este artículo se introduce la tecnología CRISPR/Cas con énfasis en el sistema de tipo II CRISPR/Cas9 y se discuten susprincipales aplicaciones en el mejoramiento genético en plantas. Igualmente, se destacan los avances y limitaciones del uso de la tecnología en plantas, y se delinean las futuras perspectivas en el campo del mejoramiento genético.
Palabras clave:edición de genoma, estrés biótico y abiótico, ingeniería genética, modificación de función génica
Referencias
Abudayyeh OO, Gootenberg JS, Konermann S, Joung J, Slaymaker IM, Cox DB, Severinov K (2016) C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science 353(6299): 0aaf5573; doi:10.1126/science.aaf5573
Alagoz Y, Gurkok T, Zhang B, Unver T (2016) Manipulating the biosynthesis of bioactive compound alkaloids for next-generation metabolic engineering in opium poppy using CRISPR-Cas 9 genome editing technology. Sci Rep 6: 30910; doi:10.1038/srep30910
Ali Z, Abulfaraj A, Idris A, Ali S, Tashkandi M, Mahfouz MM (2015) CRISPR/Cas9-mediated viral interference in plants. Genome Biology 16:238; doi:10.1186/s13059-015-0799-6
Anders C, Niewoehner O, Duerst A, Jinek M (2014) Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature 513(7519): 569; doi:10.1038/nature13579
Baltes NJ, Hummel AW, Konecna E, Cegan R, Bruns AN, Bisaro DM, Voytas DF (2015) Conferring resistance to geminiviruses with the CRISPR–Cas prokaryotic immune system. Nature Plants 1: 15145; doi:10.1038/nplants.2015.145
Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Horvath P (2007) CRISPR provides acquired resistance against viruses in prokaryotes. Science 315(5819): 1709-1712; doi:10.1126/science.1138140
Bondy-Denomy J, Pawluk A, Maxwell KL, Davidson AR (2013) Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system. Nature 493(7432): 429; doi:10.1038/nature11723
Bortesi L, Zhu C, Zischewski J, Perez L, Bassié L, Nadi R, Medina V (2016) Patterns of CRISPR/Cas9 activity in plants, animals and microbes. Plant Biotechnology Journal 14(12): 2203-2216; doi:10.1111/pbi.12634
Chandrasekaran J, Brumin M, Wolf D, Leibman D, Klap C, Pearlsman M (2016) Development of broad virus resistance in non-transgenic cucumber using CRISPR/Cas9 technology. Mol Plant Pathol 17: 1140–1153; doi:10.1111/mpp.12375
Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W (2013) Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 155: 1479–91; doi:10.1016/j.cell.2013.12.001
Chen JS, Doudna JA (2017) The chemistry of Cas9 and its CRISPR colleagues. Nat Rev Chem 1: 0078; doi:10.1038/s41570-017-0078
Cho SW, Kim S, Kim JM, Kim JS (2013) Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nature biotechnology 31(3): 230; doi:10.1038/nbt.2507
Choudhury SR, Cui Y, Lubecka K, Stefanska B, Irudayaraj J (2016) CRISPR-dCas9 mediated TET1 targeting for selective DNA demethylation at BRCA1 promoter. Oncotarget 7: 46545–56; doi:10.18632/oncotarget.10234
Christian M, Cermak T, Doyle EL, Schmidt C, Zhang F, Hummel A, Voytas DF (2010) Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186(2): 757-761; doi:10.1534/genetics.110.120717
Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Zhang F (2013) Multiplex genome engineering using CRISPR/Cas systems. Science 339(6121):819-823; doi:10.1126/science.1231143
de Toledo DP, Brail Q, Dahlbeck D, Staskawicz BJ (2016) CRISPR-Cas9 mediated mutagenesis of a DMR6 ortholog in tomato confers broad-spectrum disease resistance. bioRxiv 064824:0; doi:10.1101/064824
Feng Z, Zhang B, Ding W, Liu X, Yang DL, Wei P (2013) Efficient genome editing in plants using a CRISPR/Cas system. Cell Res 23: 1229–1232; doi:10.1038/cr.2013.114
Fonfara I, Richter H, Bratovič M, Le Rhun A, Charpentier E (2016) The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA. Nature 532(7600): 517; doi:10.1038/nature17945
Freisleben R, Lein A (1942) Uber die Auffindung einer Mehltauresistenten Mutante nach Rontgenbestrahlung einer Anfalligen Reinen Linie von Sommergerste. Naturwissenschaften 30(40): 608-608; doi:10.1007/BF01488231
Garneau JE, Dupuis ME, Villion M, Romero DA, Barrangou R, Boyaval P, Fremaux C, Horvath P, Magada´n AH, Moineau S (2010) The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468: 67–71; doi:10.1038/nature09523
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(7681): 464; doi:0.1038/nature24644
Gil‐Humanes J, Wang Y, Liang Z, Shan Q, Ozuna CV, Sánchez‐León S, Voytas DF (2017) High‐efficiency gene targeting in hexaploid wheat using DNA replicons and CRISPR/Cas9. The Plant Journal 89(6): 1251-1262; doi:10.1111/tpj.13446
Groenen PM, Bunschoten AE, Soolingen DV, Errtbden JDV (1993) Nature of DNA polymorphism in the direct repeat cluster of Mycobacterium tuberculosis, application for strain differentiation by a novel typing method. Molecular Microbiology 10(5): 1057-1065; doi:10.1111/j.1365-2958.1993.tb00976.x
Guilinger JP, Thompson DB, Liu DR (2014) Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification. Nature Biotechnology 32(6): 577; doi:10.1038/nbt.2909
Hilton IB, D’Ippolito AM, Vockley CM, Thakore PI, Crawford GE (2015) Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nat Biotechnol 33: 510–17; doi:10.1038/nbt.3199
Hirano H, Gootenberg JS, Horii T, Abudayyeh OO, Kimura M, Hsu PD, Nishimasu, H (2016) Structure and engineering of Francisella novicida Cas9. Cell 164(5): 950-961; doi:10.1016/j.cell.2016.01.039
Hoe N, Nakashima K, Grigsby D, Pan X, Dou SJ, Naidich S, Musser JM (1999) Rapid molecular genetic subtyping of serotype M1 group A Streptococcus strains. Emerg Infect Dis 5: 254-263; doi:10.3201/eid0502.990210
Hou Z, Zhang Y, Propson NE, Howden SE, Chu LF, Sontheimer EJ, Thomson JA (2013) Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis. Proc Natl Acad Sci 110(39): 15644-15649; doi:10.1073/pnas.1313587110
Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, Cradick TJ (2013) DNA targeting specificity of RNA-guided Cas9 nucleases. Nature Biotechnology 31(9): 827; doi:10.1038/nbt.2647
Hwang WY, Fu Y, Reyon D, Maeder ML, Tsai SQ, Sander JD, Joung JK (2013) Efficient genome editing in zebrafish using a CRISPR-Cas system. Nature Biotechnology 31(3): 227; doi:10.1038/nbt.2501
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. J Bacteriol 169(12): 5429-33; doi:10.1128/jb.169.12.5429-5433.1987
Jansen R, Embden JDAV, Gaastra W, Schouls LM (2002) Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol 43: 1565–1575; doi:10.1046/j.1365-2958.2002.02839.x
Jiang W, Zhou H, Bi H, Fromm M, Yang B, Weeks DP (2013) Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice. Nucleic Acids Research 41(20): e188-e188; doi:10.1093/nar/gkt780
Jiang F, Doudna JA (2017) CRISPR–Cas9 structures and mechanisms. Annual review of biophysics 46: 505-529; doi:10.1146/annurev-biophys-062215-010822
Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337: 816–821; doi:10.1126/science.1225829
Jinek M, East A, Cheng A, Lin S, Ma E, Doudna J (2013) RNA-programmed genome editing in human cells. eLife 2: e00471; doi:10.7554/eLife.00471
Jinek M, Jiang F, Taylor DW, Sternberg SH, Kaya E, Ma E, Kaplan M (2014) Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science 343(6176): 1247997; doi:10.1126/science.1247997
Kim YG, Cha J, Chandrasegaran S (1996) Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proc Natl Acad Sci 93: 1156–1160; doi:10.1073/pnas.93.3.1156
Kim E, Koo T, Park SW, Kim D, Kim K, Cho HY, Kim JH (2017) In vivo genome editing with a small Cas9 orthologue derived from Campylobacter jejuni. Nature Communications 8: 14500
Koonin EV, Makarova KS, Zhang F (2017) Diversity, classification and evolution of CRISPR-Cas systems. Current Opinion in Microbiology 37: 67-78; doi:10.1016/j.mib.2017.05.008
Kleinstiver BP, Prew MS, Tsai SQ, Topkar VV, Nguyen NT, Zheng Z, Aryee MJ (2015) Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature 523(7561): 481; doi:10.1038/nature14592
Kleinstiver BP, Pattanayak V, Prew MS, Tsai SQ, Nguyen NT, Zheng Z, Joung JK (2016) High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects. Nature 529(7587): 490; doi:10.1038/nature16526
Knight SC, Xie L, Deng W, Guglielmi B, Witkowsky LB, Bosanac L, Liu Z (2015) Dynamics of CRISPR-Cas9 genome interrogation in living cells. Science 350(6262): 823-826; doi:10.1126/science.aac6572
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(7603): 420; doi:10.1038/nature17946
Kuscu C, Parlak M, Tufan T, Yang J, Szlachta K, Wei X, Adli M (2017) CRISPR-STOP: gene silencing through base-editing-induced nonsense mutations. Nature Methods 14(7): 710; doi:10.1038/nmeth.4327
Li JF, Norville JE, Aach J, McCormack M, Zhang D, Bush J, Sheen J (2013) Multiplex and homologous recombination–mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nature Biotechnology 31(8): 688; doi:10.1038/nbt.2654
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(3): 526-529; doi:0.1038/srep43320
Liang Z, Chen K, Li T, Zhang Y, Wang Y, Zhao Q, Gao C (2017) Efficient DNA-free genome editing of bread wheat using CRISPR/Cas9 ribonucleoprotein complexes. Nature Communications 8: 14261; doi:10.1038/ncomms14261
Liu D, Chen X, Liu J, Ye J, Guo Z (2012) The rice ERF transcription factor OsERF922 negatively regulates resistance to Magnaporthe oryzae and salt tolerance. J Exp Bot, 63:3899–911; doi:10.1093/jxb/ers079
Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, Saunders SJ, Koonin EV (2015) An updated evolutionary classification of CRISPR–Cas systems. Nat Rev Microbiol 13(11): 722–736; doi:10.1038/nrmicro3569
Mali P, Aach J, Stranges PB, Esvelt KM, Moosburner M, Kosuri S, Church GM (2013) CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nature Biotechnology 31(9): 833; doi:10.1038/nbt.2675
Marraffini LA, Sontheimer EJ (2008) CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322(5909): 1843-1845; doi:10.1126/science.1165771
Masepohl B, Görlitz K, Böhme H (1996) Long tandemly repeated repetitive (LTRR) sequences in the filamentous cyanobacterium Anabaena sp. PCC 7120. Biochimica et Biophysica Acta (BBA)-Gene Structure and Expression 1307(1): 26-30; doi:10.1007/s002030050301
Miao J, Guo D, Zhang J, Huang Q, Qin G, Zhang X (2013) Targeted mutagenesis in rice using CRISPR-Cas system. Cell Res 23: 1233–1236; doi:10.1038/cr.2013.123
Mojica FJM, Ferrer C, Juez G, Rodriguez‐Valera F (1995) Long stretches of short tandem repeats are present in the largest replicons of the Archaea Haloferax mediterranei and Haloferax volcanii and could be involved in replicon partitioning. Molecular Microbiology 17(1): 85-93; doi:10.1111/j.1365-2958.1995.mmi_17010085.x
Mojica FJ, Diez-Villasenor C, Garcia-Martinez J, Almendros C (2009) Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 155: 733–740
Nakade S, Yamamoto T, Sakuma T (2017) Cas9, Cpf1 and C2c1/2/3―What's next?. Bioengineered 8(3): 265-273; doi:10.1080/21655979.2017.1282018
Nekrasov V, Staskawicz B, Weigel D, Jones JD, Kamoun S (2013) Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9-guided endonuclease. Nat Biotechnol 31: 691–693; doi:10.1038/nbt.2655
Nekrasov V, Wang C, Win J, Lanz C,nWeigel D, Kamoun S (2017) Rapid generation of a transgene-free powdery mildew resistant tomato by genome deletion. Sci Rep 7: 482; doi:10.1038/s41598-017-00578-x
Nishimasu H, Ran FA, Hsu PD, Konermann S, Shehata SI, Dohmae N, Nureki O (2014) Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell 156(5): 935-949; doi:10.1016/j.cell.2014.02.001
Osakabe Y, Osakabe K (2017) Genome editing to improve abiotic stress responses in plants. Progress Mol. Biol. Trans Sci 149: 1877-1173; doi:10.1016/bs.pmbts.2017.03.007
Pattanayak V, Lin S, Guilinger JP, Ma E, Doudna JA, Liu DR (2013) High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nature Biotechnology 31(9): 839; doi:10.1038/nbt.2673
Peng A, Chen S, Lei T, Xu L, He Y (2017) Engineering canker-resistant plants through CRISPR/Cas9-targeted editing of the susceptibility gene CsLOB1 promoter in citrus. Plant Biotechnol J 15:1509–19; doi:10.1111/pbi.12733
Piatek A, Ali Z, Baazim H, Li L, Abulfaraj A (2015) RNA-guided transcriptional regulation in planta via synthetic dCas9-based transcription factors. Plant Biotechnol J 13: 578–89; doi:10.1111/pbi.12284
Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA (2013) Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152(5): 1173-1183; doi:10.1016/j.cell.2013.02.022
Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA, Zhang F (2013) Genome engineering using the CRISPR-Cas9 system. Nature protocols 8(11): 2281; doi:10.1038/nprot.2013.143
Sander JD, Joung JK (2014) CRISPR-Cas systems for editing, regulating and targeting genomes. Nature Biotechnology 32(4): 347; doi:10.1038/nbt.2842
Shmakov S, Smargon A, Scott D, Cox D, Pyzocha N, Yan W, Severinov K (2017) Diversity and evolution of class 2 CRISPR–Cas systems. Nature Reviews Microbiology 15(3): 169; doi:10.1038/nrmicro.2016.184
Shan Q, Wang Y, Li J, Zhang Y, Chen K, Liang Z (2013) Targeted genome modification of crop plants using a CRISPR-Cas system. Nat Biotechnol 31: 686–688; doi:10.1038/nbt.2650
Slaymaker IM, Gao L, Zetsche B, Scott DA, Yan WX, Zhang F (2016) Rationally engineered Cas9 nucleases with improved specificity. Science 351(6268): 84-88; doi:10.1126/science.aad5227
Steinert J, Schiml S, Puchta H (2016) Homology-based double-strand break-induced genome engineering in plants. Plant Cell Reports 35(7): 1429-1438; doi:10.1007/s00299-016-1981-3
Sternberg SH, Redding S, Jinek M, Greene EC, Doudna JA (2014) DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 507(7490): 62; doi:10.1038/nature13011
Svitashev S, Schwartz C, Lenderts B, Young JK, Cigan AM (2016) Genome editing in maize directed by CRISPR–Cas9 ribonucleoprotein complexes. Nature Communications 7: 13274; doi:10.1038/ncomms13274
Tang L, Mao B, Li Y, Lv Q, Zhang L, Zhao B (2017) Knockout of OsNramp5 using the CRISPR/Cas9 system produces low Cd-accumulating indica rice without compromising yield. Scientific Reports (7): 14438; doi:10.1038/s41598-017-14832-9
Tsai SQ, Wyvekens N, Khayter C, Foden JA, Thapar V, Reyon D, Joung JK (2014) Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing. Nature biotechnology 32(6): 569; doi:10.1038/nbt.2908
van der Oost J, Westra ER, Jackson RN, Wiedenheft B (2014) Unravelling the structural and mechanistic basis of CRISPR-Cas systems. Nat Rev Microbiol 12: 479–492; doi:10.1038/nrmicro3279
van Schie CCN, Takken FLW (2014) Susceptibility Genes 101: How to Be a Good Host. Annu Rev Phytopathol 52:551–581; doi:10.1146/annurev-phyto-102313-045854
Vouillot L, Thélie A, Pollet N (2015) Comparison of T7E1 and surveyor mismatch cleavage assays to detect mutations triggered by engineered nucleases. G3 Genes, Genomes, Genetics 5(3):407-415; doi:10.1534/g3.114.015834
Waltz E (2016) Gene-edited CRISPR mushroom escapes US regulation. Nature News 532(7599): 293; doi:10.1038/nature.2016.19754
Wang Y, Cheng X, Shan Q, Zhang Y, Liu J, Gao C (2014) Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew. Nat Biotechnol 32: 947–951; doi:10.1038/nbt.2969
Wang F, Wang C, Liu P, Lei C, Hao W, Gao Y, Zhao K (2016) Enhanced rice blast resistance by CRISPR/Cas9-targeted mutagenesis of the ERF transcription factor gene OsERF922. PloS One 11(4): e0154027; doi:10.1371/journal.pone.0154027
Wang M, Lu Y, Botella JR, Mao Y, Hua K, Zhu JK (2017) Gene targeting by homology-directed repair in rice using a geminivirus-based CRISPR/Cas9 system. Mol Plant 10: 1007–10; doi:10.1016/j.molp.2017.03.002
Woo JW, Kim J, Kwon SI, Corvalán C, Cho SW, Kim H, Kim JS (2015) DNA-free genome editing in plants with preassembled CRISPR-Cas9 ribonucleoproteins. Nature biotechnology 33(11): 1162; doi:10.1038/nbt.3389
Xie K, Yang Y (2013) RNA-guided genome editing in plants using a CRISPR/Cas system. Mol Plant 6: 1975–1983; doi:10.1093/mp/sst119
Yamano T, Nishimasu H, Zetsche B, Hirano H, Slaymaker IM, Li Y, Ishitani R (2016) Crystal structure of Cpf1 in complex with guide RNA and target DNA. Cell 165(4): 949-962; doi:10.1016/j.cell.2016.04.003
Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS, Essletzbichler P, Volz SE, Joung J, van der Oost J, Regev A (2015) Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163: 759–771; doi:10.1016/j.cell.2015.09.038
Zischewski J, Fischer R, Bortesi L (2017) Detection of on-target and off-target mutations generated by CRISPR/Cas9 and other sequence-specific nucleases. Biotechnology Advances 35(1): 95-104; doi:10.1016/j.biotechadv.2016.12.003
Copyright (c) 2018 Biotecnología Vegetal
Biotecnología Vegetal eISSN 2074-8647, RNPS: 2154. ISSN 1609-1841, RNPS: 0397 Editada por: Instituto de Biotecnología de las Plantas. Universidad Central Marta Abreu de Las Villas. Carretera a Camajuaní km 5.5, Santa Clara, Villa Clara, Cuba CP 54 830 Tel: 53 42200124, e-mail: info@ibp.co.cu
Biotecnología Vegetal está bajo una Licencia Creative Commons Atribución-NoComercial 4.0 Internacional.