CRISPR/Cas9基因编辑技术在真菌中的应用
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摘要
CRISPR/Cas系统是一种新型基因编辑技术,因为它制作成本低廉、操作过程简单、快捷且易于掌握的特点,迅速地在动物、植物和微生物等多种生物中成功实现了基因组定点修饰。简述了Ⅱ型CRISPR/Cas系统的结构、作用机理,对CRISPR/Cas9在真菌基因组编辑中的应用进展进行了概述,并对该技术存在的问题及应用前景进行了展望。
CRISPR/Cas system is a novel gene editing technology. Because of its low cost, simple and quick operation process, and being easy to master, this technology has been successfully used for genome-based modification in a variety of organisms such as animal, plant and microorganism. In this paper, the structure and action mechanism of type-Ⅱ CRISPR/Cas system are briefly described, the application progresses of CRISPR/Cas9 in fungal genome editing are summarized, and the existing problems and application prospects of this technology are discussed.
CRISPR/Cas system is a novel gene editing technology. Because of its low cost, simple and quick operation process, and being easy to master, this technology has been successfully used for genome-based modification in a variety of organisms such as animal, plant and microorganism. In this paper, the structure and action mechanism of type-Ⅱ CRISPR/Cas system are briefly described, the application progresses of CRISPR/Cas9 in fungal genome editing are summarized, and the existing problems and application prospects of this technology are discussed.
引文
[1] 贾琪,孙新立.植物基因打靶的研究与应用[J]. 福建农林大学学报:自然科学版,2014,43(5):449-455.
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[3] Mussolino C, Cathomen T. RNA guides genome engineering[J]. Nature Biotechnology, 2013, 31(3): 208-209.
[4] Svitashev S, Young J K, Schwartz C, et al. Targeted mutagenesis, precise gene editing, and site-specific gene insertion in maize using Cas9 and guide RNA[J]. Plant Physiology, 2015, 169(2): 931-945.
[5] Svitashev S, Schwartz C, Lenderts B, et al. Genome editing in maize directed by CRISPR-Cas9 ribonucleoprotein complexes[J]. Nature Communications, 2016, 16(7): 13274.
[6] Wang F, Wang C, Liu P, et al. Enhanced rice blast resistance by CRISPR/Cas9-targeted mutagenesis of the ERF transcription factor gene OsERF922[J]. PLoS One, 2016, 11(4): e0154027.
[7] Macovei A, Sevilla N R, Cantos C, et al. Novel alleles of rice eIF4G generated by CRISPR/Cas9-targeted mutagenesis confer resistance to rice tungro spherical virus[J]. Plant Biotechnol Journal, 2018, 16(11): 1918-1927.
[8] 黄娟,邓国富,高利军,等.CRISPR/Cas9系统及其在作物育种中的应用[J].南方农业学报,2018,49(1),14-21.
[9] Li W, Teng F, Li T, et al. Simultaneous generation and germline transmission of multiple gene mutations in rat using CRISPR-Cas systems[J]. Nat Biotechnol, 2013, 31(8): 684-686.
[10] Platt R J, Chen S,Zhou Y, et al. CRISPR-Cas9 knock in mice for genome editing and cancer modeling[J]. Cell, 2014, 159(2): 440-455.
[11] Khalili K, Kaminski R, Gordon J, et al. Genome editing strategies: potential tools for eradicating HIV-1/AIDS[J]. Journal of Neurovirology, 2015, 21(3): 310-321.
[12] Maddalo D, Manchado E, Concepcion C P, et al. In vivo engineering of oncogenic chromosomal rearrangements with the CRISPR/Cas9 system[J]. Nature, 2014, 516(7531): 423-427.
[13] Xie F, Ye L, Chang J C, et al. Seamless gene correction of β-thalassemia mutations in patient-specific iPSCs using CRISPR/Cas9 and piggyBac[J]. Genome Res, 2014, 24(9): 1526.
[14] Lina J G, Giedrius G. Design of a CRISPR-Cas system to increase resistance of Bacillus subtilis to bacteriophage SPP1[J]. J Ind Microbiol Biotechnol, 2016, 43(8): 1183-1188.
[15] Wen Z, Minton N P, Zhang Y, et al. Enhanced solvent production by metabolic engineering of a twin-clostridial consortium[J]. Metab Eng, 2017(39): 3848.
[16] Wang S, Dong S, Wang P, et al. Genome editing in Clostridium saccharoperbutylacetonicum N1-4 using CRISPR-Cas9 system[J]. Appl Environ Microbiol, 2017, 83(10): e00233-e00317.
[17] Ishino Y, Shinagawa H, Makino K, et al. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product[J]. Journal of Bacteriology, 1987, 169(12): 5429-5433.
[18] Jansen R, Embden J, Gaastra W, et al. Identification of genes that are associated with DNA repeats in prokaryotes[J]. Molecular microbiology, 2002, 43(6): 1565-1575.
[19] Grissa I, Vergnaud G, Pourcel C. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats[J]. BMC Bioinformatics, 2007, 8(1): 172.
[20] Barrangou R, Fremaux C, Deveau H, et al. CRISPR provides acquired resistance against viruses in prokaryotes[J]. Science, 2007, 315(5819): 1709-1712.
[21] Marraffini L A, Sontheimer E J. CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA[J]. Science, 2008, 322(5909): 1843-1845.
[22] Cong L, Ran F A, Cox D, et al. Multiplex genome engineering using CRISPR/Cas systems[J]. Science, 2013, 39(6121): 197-217.
[23] Mali P, Yang L, Esvelt K M, et al. RNA-guided human genome engineering via Cas9[J]. Science, 2013, 339(6121): 823-826.
[24] Sinkunas T, Gasiunas G, Fremaux C, et al. Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system[J]. EMBO J, 2011, 30(7): 1335-1342.
[25] Anantharaman V, Iyer L M, Aravind L. Presence of a classical RRM-fold palm domain in Thg1-type 3′-5′ nucleic acid polymerases and the origin of the GGDEF and CRISPR polymerase domains[J]. Biol Direct, 2010(5): 43.
[26] Garneau J E, Dupuis M E, Villion M, et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA[J]. Nature, 2010, 468(7320): 67-71.
[27] 方锐,畅飞,孙照霖,等.CRISPR/Cas9介导的基因组定点编辑技术[J].生物化学与生物物理进展,2013,40(8):691-702.
[28] 李铁民,杜波.CRISPR-Cas系统与细菌和噬菌体的共进化[J].遗传,2011,33(3):213-218.
[29] Jiang F, Doudna J A. The structural biology of CRISPR-Cas systems[J]. Curr Opin Struct Biol, 2015(30): 100-111.
[30] DiCarlo J E, Norville J E, Mali P, et al. Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems[J]. Nucleic Acids Research, 2013, 41(7): 4336-4343.
[31] Bao Z, Xiao H, Liang J, et al. Homology-integrated CRISPR-Cas (HI-CRISPR)system for one-step multigene disruption in Saccharomyces cerevisiae[J]. ACS Synth Biol, 2015, 4(5): 585-594.
[32] Jacobs J Z, Ciccaglione K M, Tournier V, et al. Implementation of the CRISPR-Cas9 system in fission yeast[J]. Nature Communications, 2014(5): 5344.
[33] Shapiro R S, Chavez A, Porter C B M, et al. A CRISPR-Cas9-based gene drive platform for genetic interaction analysis in Candida albicans[J]. Nature Microbiology, 2018, 3(1): 73.
[34] Liu R, Chen L, Jiang Y, et al. Efficient genome editing in filamentous fungus Trichoderma reesei using the CRISPR/Cas9 system[J]. Cell Discovery, 2015(1): 15007.
[35] Katayama T, Tanaka Y, Okabe T, et al. Development of a genome editing technique using the CRISPR/Cas9 system in the industrial filamentous fungus Aspergillus oryzae[J]. Biotechnology Letters, 2016, 38(4): 637-642.
[36] Zhang C, Meng X, Wei X, et al. Highly efficient CRISPR mutagenesis by microhomology-mediated end joining in Aspergillus fumigatus[J]. Fungal Genetics and Biology, 2016(86): 47-57.
[37] Arazoe T, Miyoshi K, Yamato T, et al. Tailor-made CRISPR/Cas system for highly efficient targeted gene replacement in the rice blast fungus[J]. Biotechnology and Bioengineering, 2015, 112(12): 2543-2549.
[38] Schuster M, Schweizer G, Reissmann S, et al. Genome editing in Ustilago maydis using the CRISPR-Cas system[J]. Fungal Genetics and Biology, 2016(89): 3 -9.
[39] Waltz E. Gene-edited CRISPR mushroom escapes US regulation[J]. Nature, 2016, 532(7599): 293.
[40] Sugano S S, Suzuki H, Shimokita E, et al. Genome editing in the mushroom-forming basidiomycete Coprinopsis cinerea, optimized by a high-throughput transformation system[J]. Scientific Reports, 2017, 7(1): 1260.
[41] 刘建雨,刘建辉,张丹,等.农杆菌介导的 Cas9 基因转化金针菇的研究[J].食用菌学报,2017,24(3):25-29.
[42] Qin H, Xiao H, Zou G, et al. CRISPR-Cas9 assisted gene disruption in the higher fungus Ganoderma species[J]. Process Biochemistry, 2017(56): 57-61.
[43] 孙丹.蛹虫草遗传转化体系的建立及营养缺陷型菌株的创制[D].长春:吉林农业大学,2017.
[44] Chen B X, Wei T, Ye Z W, et al. Efficient CRISPR-Cas9 gene disruption system in edible-medicinal mushroom Cordyceps militaris[J]. Frontiers in Microbiology, 2018(9): 1157.
[45] Zhou H B, Liu B, Weeks D P, et al. Large chromosomal deletions and heritable small genetic changes induced by CRISPR/Cas9 in rice[J]. Nucleic Acids Research, 2014, 42(17): 1233-1236.
[46] Hsu P D, Scott D A, Weinstein J A, et al. DNA targeting specificity of RNA-guided Cas9 nucleases[J]. Nat Biotechnol, 2013, 31(9): 827-832.
[47] Müller M, Lee C M, Gasiunas G, et al. Streptococcus thermophilus, CRISPR-Cas9 systems enable specific editing of the human genome[J]. Molecular Therapy, 2016, 24(3): 636-644.
[48] Paix A, Folkmann A, Goldman D H, et al. Precision genome editing using synthesis-dependent repair of Cas9-induced DNA breaks[J]. Proceedings of the National Academy of Sciences, 2017, 114(50): E10745-E10754.
[49] Matsuura T, Baek M, Kwon J, et al. Efficient gene editing in Neurospora crassa with CRISPR technology[J]. Fungal Biology & Biotechnology, 2015, 2(1): 4-11.
[2] 常振仪,严维,刘东风,等.CRISPR/Cas技术研究进展[J].农业生物技术学报,2015,23(9):1196-1206.
[3] Mussolino C, Cathomen T. RNA guides genome engineering[J]. Nature Biotechnology, 2013, 31(3): 208-209.
[4] Svitashev S, Young J K, Schwartz C, et al. Targeted mutagenesis, precise gene editing, and site-specific gene insertion in maize using Cas9 and guide RNA[J]. Plant Physiology, 2015, 169(2): 931-945.
[5] Svitashev S, Schwartz C, Lenderts B, et al. Genome editing in maize directed by CRISPR-Cas9 ribonucleoprotein complexes[J]. Nature Communications, 2016, 16(7): 13274.
[6] Wang F, Wang C, Liu P, et al. Enhanced rice blast resistance by CRISPR/Cas9-targeted mutagenesis of the ERF transcription factor gene OsERF922[J]. PLoS One, 2016, 11(4): e0154027.
[7] Macovei A, Sevilla N R, Cantos C, et al. Novel alleles of rice eIF4G generated by CRISPR/Cas9-targeted mutagenesis confer resistance to rice tungro spherical virus[J]. Plant Biotechnol Journal, 2018, 16(11): 1918-1927.
[8] 黄娟,邓国富,高利军,等.CRISPR/Cas9系统及其在作物育种中的应用[J].南方农业学报,2018,49(1),14-21.
[9] Li W, Teng F, Li T, et al. Simultaneous generation and germline transmission of multiple gene mutations in rat using CRISPR-Cas systems[J]. Nat Biotechnol, 2013, 31(8): 684-686.
[10] Platt R J, Chen S,Zhou Y, et al. CRISPR-Cas9 knock in mice for genome editing and cancer modeling[J]. Cell, 2014, 159(2): 440-455.
[11] Khalili K, Kaminski R, Gordon J, et al. Genome editing strategies: potential tools for eradicating HIV-1/AIDS[J]. Journal of Neurovirology, 2015, 21(3): 310-321.
[12] Maddalo D, Manchado E, Concepcion C P, et al. In vivo engineering of oncogenic chromosomal rearrangements with the CRISPR/Cas9 system[J]. Nature, 2014, 516(7531): 423-427.
[13] Xie F, Ye L, Chang J C, et al. Seamless gene correction of β-thalassemia mutations in patient-specific iPSCs using CRISPR/Cas9 and piggyBac[J]. Genome Res, 2014, 24(9): 1526.
[14] Lina J G, Giedrius G. Design of a CRISPR-Cas system to increase resistance of Bacillus subtilis to bacteriophage SPP1[J]. J Ind Microbiol Biotechnol, 2016, 43(8): 1183-1188.
[15] Wen Z, Minton N P, Zhang Y, et al. Enhanced solvent production by metabolic engineering of a twin-clostridial consortium[J]. Metab Eng, 2017(39): 3848.
[16] Wang S, Dong S, Wang P, et al. Genome editing in Clostridium saccharoperbutylacetonicum N1-4 using CRISPR-Cas9 system[J]. Appl Environ Microbiol, 2017, 83(10): e00233-e00317.
[17] Ishino Y, Shinagawa H, Makino K, et al. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product[J]. Journal of Bacteriology, 1987, 169(12): 5429-5433.
[18] Jansen R, Embden J, Gaastra W, et al. Identification of genes that are associated with DNA repeats in prokaryotes[J]. Molecular microbiology, 2002, 43(6): 1565-1575.
[19] Grissa I, Vergnaud G, Pourcel C. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats[J]. BMC Bioinformatics, 2007, 8(1): 172.
[20] Barrangou R, Fremaux C, Deveau H, et al. CRISPR provides acquired resistance against viruses in prokaryotes[J]. Science, 2007, 315(5819): 1709-1712.
[21] Marraffini L A, Sontheimer E J. CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA[J]. Science, 2008, 322(5909): 1843-1845.
[22] Cong L, Ran F A, Cox D, et al. Multiplex genome engineering using CRISPR/Cas systems[J]. Science, 2013, 39(6121): 197-217.
[23] Mali P, Yang L, Esvelt K M, et al. RNA-guided human genome engineering via Cas9[J]. Science, 2013, 339(6121): 823-826.
[24] Sinkunas T, Gasiunas G, Fremaux C, et al. Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system[J]. EMBO J, 2011, 30(7): 1335-1342.
[25] Anantharaman V, Iyer L M, Aravind L. Presence of a classical RRM-fold palm domain in Thg1-type 3′-5′ nucleic acid polymerases and the origin of the GGDEF and CRISPR polymerase domains[J]. Biol Direct, 2010(5): 43.
[26] Garneau J E, Dupuis M E, Villion M, et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA[J]. Nature, 2010, 468(7320): 67-71.
[27] 方锐,畅飞,孙照霖,等.CRISPR/Cas9介导的基因组定点编辑技术[J].生物化学与生物物理进展,2013,40(8):691-702.
[28] 李铁民,杜波.CRISPR-Cas系统与细菌和噬菌体的共进化[J].遗传,2011,33(3):213-218.
[29] Jiang F, Doudna J A. The structural biology of CRISPR-Cas systems[J]. Curr Opin Struct Biol, 2015(30): 100-111.
[30] DiCarlo J E, Norville J E, Mali P, et al. Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems[J]. Nucleic Acids Research, 2013, 41(7): 4336-4343.
[31] Bao Z, Xiao H, Liang J, et al. Homology-integrated CRISPR-Cas (HI-CRISPR)system for one-step multigene disruption in Saccharomyces cerevisiae[J]. ACS Synth Biol, 2015, 4(5): 585-594.
[32] Jacobs J Z, Ciccaglione K M, Tournier V, et al. Implementation of the CRISPR-Cas9 system in fission yeast[J]. Nature Communications, 2014(5): 5344.
[33] Shapiro R S, Chavez A, Porter C B M, et al. A CRISPR-Cas9-based gene drive platform for genetic interaction analysis in Candida albicans[J]. Nature Microbiology, 2018, 3(1): 73.
[34] Liu R, Chen L, Jiang Y, et al. Efficient genome editing in filamentous fungus Trichoderma reesei using the CRISPR/Cas9 system[J]. Cell Discovery, 2015(1): 15007.
[35] Katayama T, Tanaka Y, Okabe T, et al. Development of a genome editing technique using the CRISPR/Cas9 system in the industrial filamentous fungus Aspergillus oryzae[J]. Biotechnology Letters, 2016, 38(4): 637-642.
[36] Zhang C, Meng X, Wei X, et al. Highly efficient CRISPR mutagenesis by microhomology-mediated end joining in Aspergillus fumigatus[J]. Fungal Genetics and Biology, 2016(86): 47-57.
[37] Arazoe T, Miyoshi K, Yamato T, et al. Tailor-made CRISPR/Cas system for highly efficient targeted gene replacement in the rice blast fungus[J]. Biotechnology and Bioengineering, 2015, 112(12): 2543-2549.
[38] Schuster M, Schweizer G, Reissmann S, et al. Genome editing in Ustilago maydis using the CRISPR-Cas system[J]. Fungal Genetics and Biology, 2016(89): 3 -9.
[39] Waltz E. Gene-edited CRISPR mushroom escapes US regulation[J]. Nature, 2016, 532(7599): 293.
[40] Sugano S S, Suzuki H, Shimokita E, et al. Genome editing in the mushroom-forming basidiomycete Coprinopsis cinerea, optimized by a high-throughput transformation system[J]. Scientific Reports, 2017, 7(1): 1260.
[41] 刘建雨,刘建辉,张丹,等.农杆菌介导的 Cas9 基因转化金针菇的研究[J].食用菌学报,2017,24(3):25-29.
[42] Qin H, Xiao H, Zou G, et al. CRISPR-Cas9 assisted gene disruption in the higher fungus Ganoderma species[J]. Process Biochemistry, 2017(56): 57-61.
[43] 孙丹.蛹虫草遗传转化体系的建立及营养缺陷型菌株的创制[D].长春:吉林农业大学,2017.
[44] Chen B X, Wei T, Ye Z W, et al. Efficient CRISPR-Cas9 gene disruption system in edible-medicinal mushroom Cordyceps militaris[J]. Frontiers in Microbiology, 2018(9): 1157.
[45] Zhou H B, Liu B, Weeks D P, et al. Large chromosomal deletions and heritable small genetic changes induced by CRISPR/Cas9 in rice[J]. Nucleic Acids Research, 2014, 42(17): 1233-1236.
[46] Hsu P D, Scott D A, Weinstein J A, et al. DNA targeting specificity of RNA-guided Cas9 nucleases[J]. Nat Biotechnol, 2013, 31(9): 827-832.
[47] Müller M, Lee C M, Gasiunas G, et al. Streptococcus thermophilus, CRISPR-Cas9 systems enable specific editing of the human genome[J]. Molecular Therapy, 2016, 24(3): 636-644.
[48] Paix A, Folkmann A, Goldman D H, et al. Precision genome editing using synthesis-dependent repair of Cas9-induced DNA breaks[J]. Proceedings of the National Academy of Sciences, 2017, 114(50): E10745-E10754.
[49] Matsuura T, Baek M, Kwon J, et al. Efficient gene editing in Neurospora crassa with CRISPR technology[J]. Fungal Biology & Biotechnology, 2015, 2(1): 4-11.