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中国生物工程杂志

CHINA BIOTECHNOLOGY
中国生物工程杂志
中国生物工程杂志  2022, Vol. 42 Issue (7): 101-112    DOI: 10.13523/j.cb.2203026
综述     
基于酿酒酵母的大片段DNA组装与转移技术进展*
田方方1,2,何博1,2,吴毅1,2,**()
1. 天津大学化工学院 天津 300072
2. 教育部合成生物学前沿科学中心和系统生物工程重点实验室 天津 300072
Advances in Large DNA Assembly and Transfer Based on Saccharomyces cerevisiae
Fang-fang TIAN1,2,Bo HE1,2,Yi WU1,2,**()
1. School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
2. Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin 300072, China
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摘要：

DNA组装与转移技术是合成生物学的核心使能技术之一,生命体设计改造的复杂度不断提升,使得对大片段DNA组装与转移技术的需求也日益旺盛。小片段DNA的组装与转移技术目前已经比较成熟,大片段DNA由于其分子量大、易断裂,使得体外操作繁琐且效率低下。聚焦酿酒酵母体内组装和转移的技术进展,详细介绍了基于酿酒酵母一次组装和迭代组装的不同方法,并从导入与导出的角度介绍了大片段DNA的转移技术,便于研究者更好地理解和选择酿酒酵母体内组装与转移技术。此外,还展望了将酿酒酵母开发为大片段DNA组装与转移通用平台实现更多物种基因组大尺度设计改造的愿景。
关键词： 大片段DNA组装;  大片段DNA转移;  酿酒酵母    
Abstract:

DNA assembly and transfer techniques are one of the core enabling technologies for synthetic biology. The increasing degree of complexity in the design and modification of living organisms has led to a growing demand for large DNA assembly and transfer methods. Nowadays,the assembly and transfer techniques of small DNA are well developed, while the manipulation of large DNA in vitro is complicated and inefficient due to DNA high molecular weight and ease to break. This review focuses on advances in large DNA assembly and transfer techniques in Saccharomyces cerevisiae and transfer technology. The methods of one-step assembly and iterative assembly in S. cerevisiae are introduced in detail. The transfer methods from the aspect of transfer in and out are highlighted, and researchers can better understand and choose these methods. In addition, the authors envisage that it is possible to make S. cerevisiae become a universal platform for assembly and transfer of large DNA, which enables large-scale genomic design and modification of more organisms.
Key words: Large DNA assembly    Large DNA transfer    Saccharomyces cerevisiae
收稿日期: 2022-03-11 出版日期: 2022-08-03
ZTFLH:  Q812  
基金资助: *国家重点研发计划(2021YFC2102500);国家自然科学基金(31971351)
通讯作者: 吴毅     E-mail: yi.wu@tju.edu.cn
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田方方,何博,吴毅. 基于酿酒酵母的大片段DNA组装与转移技术进展*[J]. 中国生物工程杂志, 2022, 42(7): 101-112.

Fang-fang TIAN,Bo HE,Yi WU. Advances in Large DNA Assembly and Transfer Based on Saccharomyces cerevisiae. China Biotechnology, 2022, 42(7): 101-112.

链接本文:

https://manu60.magtech.com.cn/biotech/CN/10.13523/j.cb.2203026    或    https://manu60.magtech.com.cn/biotech/CN/Y2022/V42/I7/101

图1  基于酿酒酵母的导入-组装-导出DNA片段的影响因素
图2  CasHRA方法流程图(a)和SwAP-In组装染色体synX流程图(b)
分类 方法 原理 应用 组装大小 引文
酵母一次
组装		 组装成质
粒形式		 DNA组装器(DNA assembler,TAR) 多个待组装的DNA片段(两侧有同源序列)与载体在酿酒酵母体内直接利用同源重组形成环形质粒 多基因调控的生化途径组装,途径文库构建 约50 kb [40][41-43][44-47]
结合Golden Gate(VEGAS) 将启动子、基因、终止子在体外用Golden Gate组装成转录单元模块,再在酿酒酵母体内组装多模块 模块化组装多个转录单元,构建途径文库 约50 kb [51]
结合Gibson 将商业合成的短片段用多次Gibson组装至百kb,再通过酿酒酵母组装 完整基因组 约583 kb [50]
结合蓝白斑筛选(RADOM) 酿酒酵母组装后混合质粒通过大肠杆菌蓝白斑筛选减轻筛选工作 快速构建3~10 kb的DNA片段 3~10 kb [52]
靶向整合
至基因组		 内切核酸酶辅助(I-SceI-assisted integration) 用I-SceI在目标染色体基因座处引入双链断裂,从而促进组装构建体的整合 基因组上的多基因生化途径组装 约35 kb [53]
CRISPR/Cas9辅助(CasEMBLR/CrEdit/Di-CRISPR等) CRISPR/Cas9系统在基因组多位点同时引入双链断裂,促进多位点同时组装 基因组上多位点无标记的多基因生化途径组装 - [54] [57-59]
酵母迭代组装 内切核酸
酶辅助(reiterative recombination)		 用两种内切核酸酶HO和I-SceI,设计两种正交切割质粒,交替使用它们在基因组上引入双链断裂,逐步将DNA片段靶向整合至基因组 基因组上多基因途径文库的构建 - [62]
CRISPR/Cas9辅助(CasHRA) 通过原生质体融合将大质粒共同导入单个细胞,再利用CRISPR/Cas9系统释放出线性DNA进行同源重组组装 大肠杆菌基因组 约1 Mb [60]
逐步转换营养标签组装(SwAP-In) 在待组装DNA片段一侧设计不同的营养标签,每一次组装时都用新的营养标签替换先前的营养标签,通过直接筛选营养标签获得组装正确的菌株 合成型酵母染色体synII、synIII、synV、synVI、synX组装 约770 kb、
约273 kb、
约536 kb、
约243 kb、
约707 kb		 [3-9]
酵母交配、减数分裂重组介导的组装(MRA) 利用二倍体中减数分裂时期姐妹染色单体发生交叉互换的可能性进行组装 人源TCRαβ基因座、合成型染色体synXII 约1 Mb [7, 61]
表1  基于酿酒酵母同源重组的大片段DNA组装方法
分类 方法 转移介质 转移大小 优点 缺点 引文
导入 化学
方法		 PEG-醋酸锂转化 PEG3350/LiOAc 约50 kb 可同时导入多片段,技术成熟 转移尺度小 [26]
PEG-原生质体转化 PEG8000 约200 kb 可同时导入多片段,转移尺度较大 操作复杂,效率低 [66]
阳离子聚合物包埋 阳离子聚合物 约15 kb 能使带负电荷的DNA分子聚集 通用性差,效率低 [67-68]
物理
方法		 酵母原生质体电穿孔转化 山梨醇溶液 约200 kb 操作简单,转移尺度大 酵母致死率高 [69]
完整酵母电穿孔转化 缓冲溶液 约15 kb 操作简单,不需要制备原生质体 酵母致死率高 [70]
基因枪 — 约5 kb 直接导入至细胞核 需要昂贵的精密仪器,效率低 [71-73]
生物
方法		 酵母-酵母原生质体融合 酵母原生质体 Mb级别 转移尺度大,不需要体外操作 供体酵母基因组可能干扰受体基因组,效率低 [60]
酵母交配(mating) — Mb级别 转移尺度大,不需要体外操作 局限于酵母之间 [7, 61]
细菌-酵母原生质体融合 酵母原生质体 Mb级别 转移尺度大,不需要体外操作 效率低 [74-75]
导出 从酵
母中
提取
出后
递送
至其
他宿
主		 电穿孔转移 常规方法提取,通过缓冲溶液电转 约200 kb 可用于其他方法难以转染的细胞系 需要昂贵的细胞电转仪,难操作 [85]
脂质体转染 常规方法提取,通过脂质体转染 约300 kb 有商业化的试剂盒 脂质材料对细胞有毒性 [88-89]
显微注射转移 琼脂糖包埋法提取纯化后注射 约600 kb 转移尺度大,直接转到细胞器(线粒体)或细胞核中 无法高通量操作,对细胞伤害大,需要昂贵的激光设备 [86-87]
阳离子聚合物包埋转移 琼脂糖包埋法提取纯化后通过阳离子聚合物转移 Mb级别 可进行大尺度DNA转移,不需要高级设备 重复性差 [90]
从酵母
中直接
递送至
目的宿
主		 酵母交配(mating) — Mb级别 转移尺度大,不需要体外操作 局限于酵母之间 [94-95]
酵母原生质体-哺乳动物细胞融合 酵母原生质体 Mb级别 转移尺度大,不需要体外操作 供体酵母基因组可能干扰受体基因组,效率低 [96-99]
表2  基于酿酒酵母的大片段DNA转移方法
[1] 赵国屏. 合成生物学: 开启生命科学“会聚”研究新时代. 中国科学院院刊, 2018, 33(11): 1135-1149.
Zhao G P. Synthetic biology: unsealing the convergence era of life science research. Bulletin of Chinese Academy of Sciences, 2018, 33(11): 1135-1149.
[2] Gibson D G, Glass J I, Lartigue C, et al. Creation of a bacterial cell controlled by a chemically synthesized genome. Science, 2010, 329(5987): 52-56.
doi: 10.1126/science.1190719
[3] Dymond J S, Richardson S M, Coombes C E, et al. Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature, 2011, 477(7365): 471-476.
doi: 10.1038/nature10403
[4] Wu Y, Li B Z, Zhao M, et al. Bug mapping and fitness testing of chemically synthesized chromosome X. Science, 2017, 355(6329): eaaf4706.
[5] Shen Y, Wang Y, Chen T, et al. Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome. Science, 2017, 355(6329): eaaf4791.
doi: 10.1126/science.aaf4791
[6] Richardson S M, Mitchell L A, Stracquadanio G, et al. Design of a synthetic yeast genome. Science, 2017, 355(6329): 1040-1044.
doi: 10.1126/science.aaf4557 pmid: 28280199
[7] Zhang W M, Zhao G H, Luo Z Q, et al. Engineering the ribosomal DNA in a megabase synthetic chromosome. Science, 2017, 355(6329): eaaf3981.
doi: 10.1126/science.aaf3981
[8] Xie Z X, Li B Z, Mitchell L A, et al. “Perfect” designer chromosome V and behavior of a ring derivative. Science, 2017, 355(6329): eaaf4704.
doi: 10.1126/science.aaf4704
[9] Mitchell L A, Wang A, Stracquadanio G, et al. Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond. Science, 2017, 355(6329): eaaf4831.
doi: 10.1126/science.aaf4831
[10] Fredens J, Wang K H, de la Torre D, et al. Total synthesis of Escherichia coli with a recoded genome. Nature, 2019, 569(7757): 514-518.
doi: 10.1038/s41586-019-1192-5
[11] Luo Z Q, Jiang S Y, Dai J B. Chromosomal rearrangements of synthetic yeast by SCRaMbLE. Methods in Molecular Biology (Clifton, N J), 2021, 2196: 153-165.
[12] Shen M J, Wu Y, Yang K, et al. Heterozygous diploid and inter species SCRaMbLEing. Nature Communications, 2018, 9: 1934.
doi: 10.1038/s41467-018-04157-0
[13] Li Y X, Wu Y, Ma L, et al. Loss of heterozygosity by SCRaMbLEing. Science China Life Sciences, 2019, 62(3): 381-393.
doi: 10.1007/s11427-019-9504-5
[14] Jia B, Wu Y, Li B Z, et al. Precise control of SCRaMbLE in synthetic haploid and diploid yeast. Nature Communications, 2018, 9: 1933.
doi: 10.1038/s41467-018-03084-4
[15] Wang J, Xie Z X, Ma Y, et al. Ring synthetic chromosome V SCRaMbLE. Nature Communications, 2018, 9(1): 3783.
doi: 10.1038/s41467-018-06216-y
[16] Wang P X, Xu H, Li H, et al. SCRaMbLEing of a synthetic yeast chromosome with clustered essential genes reveals synthetic lethal interactions. ACS Synthetic Biology, 2020, 9(5): 1181-1189.
doi: 10.1021/acssynbio.0c00059
[17] 盛晓菁, 齐晓雪, 徐蕾, 等. 基因克隆及组装技术的研究进展. 中国生物工程杂志, 2020, 40(1-2): 133-139.
Sheng X J, Qi X X, Xu L, et al. The research progress of gene cloning and assembly. China Biotechnology, 2020, 40(1-2): 133-139.
[18] Horton R M, Hunt H D, Ho S N, et al. Engineering hybrid genes without the use of restriction enzymes: gene splicing by overlap extension. Gene, 1989, 77(1): 61-68.
pmid: 2744488
[19] Quan J Y, Tian J D. Circular polymerase extension cloning of complex gene libraries and pathways. PLoS One, 2009, 4(7): e6441.
doi: 10.1371/journal.pone.0006441
[20] Engler C, Kandzia R, Marillonnet S. A one pot, one step, precision cloning method with high throughput capability. PLoS One, 2008, 3(11): e3647.
doi: 10.1371/journal.pone.0003647
[21] Shetty R P, Endy D, Knight T F Jr. Engineering BioBrick vectors from BioBrick parts. Journal of Biological Engineering, 2008, 2: 5.
doi: 10.1186/1754-1611-2-5
[22] Gibson D G, Young L, Chuang R Y, et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nature Methods, 2009, 6(5): 343-345.
doi: 10.1038/nmeth.1318
[23] Li M Z, Elledge S J. Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC. Nature Methods, 2007, 4(3): 251-256.
doi: 10.1038/nmeth1010
[24] Xia Y Z, Li K, Li J J, et al. T 5 exonuclease-dependent assembly offers a low-cost method for efficient cloning and site-directed mutagenesis. Nucleic Acids Research, 2019, 47(3): e15.
doi: 10.1093/nar/gky1169
[25] Juhas M, Ajioka J W. High molecular weight DNA assembly in vivo for synthetic biology applications. Critical Reviews in Biotechnology, 2017, 37(3): 277-286.
doi: 10.3109/07388551.2016.1141394
[26] Hinnen A, Hicks J B, Fink G R. Transformation of yeast. PNAS, 1978, 75(4): 1929-1933.
pmid: 347451
[27] Orr-Weaver T L, Szostak J W, Rothstein R J. Yeast transformation: a model system for the study of recombination. PNAS, 1981, 78(10): 6354-6358.
pmid: 6273866
[28] Gibson D G. Gene and genome construction in yeast. Current Protocols in Molecular Biology, 2011, 94(1): 3.22.1-3.22.17.
[29] Eckert-Boulet N, Rothstein R, Lisby M. Cell biology of homologous recombination in yeast. Methods in Molecular Biology (Clifton, N J), 2011, 745: 523-536.
[30] Pâques F, Haber J E. Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae. Microbiology and Molecular Biology Reviews: MMBR, 1999, 63(2): 349-404.
doi: 10.1128/MMBR.63.2.349-404.1999
[31] Fishman-Lobell J, Rudin N, Haber J E. Two alternative pathways of double-strand break repair that are kinetically separable and independently modulated. Molecular and Cellular Biology, 1992, 12(3): 1292-1303.
doi: 10.1128/mcb.12.3.1292-1303.1992 pmid: 1545810
[32] Löbs A K, Schwartz C, Wheeldon I. Genome and metabolic engineering in non-conventional yeasts: current advances and applications. Synthetic and Systems Biotechnology, 2017, 2(3): 198-207.
doi: 10.1016/j.synbio.2017.08.002
[33] Ploessl D, Zhao Y X, Cao M F, et al. A repackaged CRISPR platform increases homology-directed repair for yeast engineering. Nature Chemical Biology, 2022, 18(1): 38-46.
doi: 10.1038/s41589-021-00893-5
[34] Mitchell L A, McCulloch L H, Pinglay S, et al. De novo assembly and delivery to mouse cells of a 101 kb functional human gene. Genetics, 2021, 218(1): iyab038.
doi: 10.1093/genetics/iyab038
[35] Gibson D G, Benders G A, Axelrod K C, et al. One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome. Proceedings of the National Academy of Sciences of the United States of America, 2008, 105(51): 20404-20409.
[36] Hutchison C A 3rd, Chuang R Y, Noskov V N, et al. Design and synthesis of a minimal bacterial genome. Science, 2016, 351(6280): aad6253.
doi: 10.1126/science.aad6253
[37] Sugawara N, Haber J E. Characterization of double-strand break-induced recombination: homology requirements and single-stranded DNA formation. Molecular and Cellular Biology, 1992, 12(2): 563-575.
doi: 10.1128/mcb.12.2.563-575.1992 pmid: 1732731
[38] Manivasakam P, Weber S C, McElver J, et al. Micro-homology mediated PCR targeting in Saccharomyces cerevisiae. Nucleic Acids Research, 1995, 23(14): 2799-2800.
pmid: 7651842
[39] Jiang S, Tang Y, Xiang L, et al. Efficient de novo assembly and modification of large DNA fragments. Science China Life Sciences, 2021: 2021Dec16.
[40] Shao Z Y, Zhao H, Zhao H M. DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways. Nucleic Acids Research, 2009, 37(2): e16.
doi: 10.1093/nar/gkn991
[41] Du J, Yuan Y B, Si T, et al. Customized optimization of metabolic pathways by combinatorial transcriptional engineering. Nucleic Acids Research, 2012, 40(18): e142.
doi: 10.1093/nar/gks549
[42] Kim B, Du J, Eriksen D T, et al. Combinatorial design of a highly efficient xylose-utilizing pathway in Saccharomyces cerevisiae for the production of cellulosic biofuels. Applied and Environmental Microbiology, 2013, 79(3): 931-941.
doi: 10.1128/AEM.02736-12
[43] Eriksen D T, Hsieh P C H, Lynn P, et al. Directed evolution of a cellobiose utilization pathway in Saccharomyces cerevisiae by simultaneously engineering multiple proteins. Microbial Cell Factories, 2013, 12: 61.
doi: 10.1186/1475-2859-12-61 pmid: 23802545
[44] Larionov V, Kouprina N, Solomon G, et al. Direct isolation of human BRCA2 gene by transformation-associated recombination in yeast. PNAS, 1997, 94(14): 7384-7387.
pmid: 9207100
[45] Larionov V, Kouprina N, Graves J, et al. Specific cloning of human DNA as yeast artificial chromosomes by transformation-associated recombination. Proceedings of the National Academy of Sciences of the United States of America, 1996, 93(1): 491-496.
[46] Kouprina N, Annab L, Graves J, et al. Functional copies of a human gene can be directly isolated by transformation-associated recombination cloning with a small 3' end target sequence. Proceedings of the National Academy of Sciences of the United States of America, 1998, 95(8): 4469-4474.
[47] Kouprina N, Larionov V. TAR cloning: insights into gene function, long-range haplotypes and genome structure and evolution. Nature Reviews Genetics, 2006, 7(10): 805-812.
pmid: 16983376
[48] Kouprina N, Larionov V. Transformation-associated recombination (TAR) cloning for genomics studies and synthetic biology. Chromosoma, 2016, 125(4): 621-632.
doi: 10.1007/s00412-016-0588-3 pmid: 27116033
[49] Kouprina N, Larionov V. TAR cloning: perspectives for functional genomics, biomedicine, and biotechnology. Molecular Therapy - Methods & Clinical Development, 2019, 14: 16-26.
[50] Gibson D G, Benders G A, Andrews-Pfannkoch C, et al. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science, 2008, 319(5867): 1215-1220.
doi: 10.1126/science.1151721
[51] Mitchell L A, Chuang J, Agmon N, et al. Versatile genetic assembly system (VEGAS) to assemble pathways for expression in S.cerevisiae. Nucleic Acids Research, 2015, 43(13): 6620-6630.
doi: 10.1093/nar/gkv466 pmid: 25956652
[52] Lin Q H, Jia B, Mitchell L A, et al. RADOM, an efficient in vivo method for assembling designed DNA fragments up to 10 kb long in Saccharomyces cerevisiae. ACS Synthetic Biology, 2015, 4(3): 213-220.
doi: 10.1021/sb500241e
[53] Kuijpers N G A, Chroumpi S, Vos T, et al. One-step assembly and targeted integration of multigene constructs assisted by the I-SceI meganuclease in Saccharomyces cerevisiae. FEMS Yeast Research, 2013, 13(8): 769-781.
doi: 10.1111/1567-1364.12087 pmid: 24028550
[54] Jakočiunas T, Rajkumar A S, Zhang J, et al. CasEMBLR: Cas9-facilitated multiloci genomic integration of in vivo assembled DNA parts in Saccharomyces cerevisiae. ACS Synthetic Biology, 2015, 4(11): 1226-1234.
doi: 10.1021/acssynbio.5b00007
[55] Postma E D, Dashko S, van Breemen L, et al. A supernumerary designer chromosome for modular in vivo pathway assembly in Saccharomyces cerevisiae. Nucleic Acids Research, 2021, 49(3): 1769-1783.
doi: 10.1093/nar/gkaa1167 pmid: 33423048
[56] Postma E D, Hassing E J, Mangkusaputra V, et al. Modular, synthetic chromosomes as new tools for large scale engineering of metabolism. Metabolic Engineering, 2022, 72: 1-13.
doi: 10.1016/j.ymben.2021.12.013 pmid: 35051627
[57] Ronda C, Maury J, Jakočiunas T, et al. CrEdit: CRISPR mediated multi-loci gene integration in Saccharomyces cerevisiae. Microbial Cell Factories, 2015, 14: 97.
doi: 10.1186/s12934-015-0288-3
[58] Shi S B, Liang Y Y, Zhang M M, et al. A highly efficient single-step, markerless strategy for multi-copy chromosomal integration of large biochemical pathways in Saccharomyces cerevisiae. Metabolic Engineering, 2016, 33: 19-27.
doi: 10.1016/j.ymben.2015.10.011
[59] Huang S C, Geng A L. High-copy genome integration of 2, 3-butanediol biosynthesis pathway in Saccharomyces cerevisiae via in vivo DNA assembly and replicative CRISPR-Cas9 mediated delta integration. Journal of Biotechnology, 2020, 310: 13-20.
doi: 10.1016/j.jbiotec.2020.01.014
[60] Zhou J T, Wu R H, Xue X L, et al. CasHRA (Cas9-facilitated Homologous Recombination Assembly)method of constructing megabase-sized DNA. Nucleic Acids Research, 2016, 44(14): e124.
doi: 10.1093/nar/gkw475
[61] Li L P, Lampert J C, Chen X J, et al. Transgenic mice with a diverse human T cell antigen receptor repertoire. Nature Medicine, 2010, 16(9): 1029-1034.
doi: 10.1038/nm.2197
[62] Wingler L M, Cornish V W.Reiterative Recombination for the in vivo assembly of libraries of multigene pathways. Proceedings of the National Academy of Sciences of the United States of America, 2011, 108(37): 15135-15140.
[63] Luo J C, Sun X J, Cormack B P, et al. Karyotype engineering by chromosome fusion leads to reproductive isolation in yeast. Nature, 2018, 560(7718): 392-396.
doi: 10.1038/s41586-018-0374-x
[64] Shao Y Y, Lu N, Wu Z F, et al. Creating a functional single-chromosome yeast. Nature, 2018, 560(7718): 331-335.
doi: 10.1038/s41586-018-0382-x
[65] Shao Y Y, Lu N, Cai C, et al. A single circular chromosome yeast. Cell Research, 2019, 29(1): 87-89.
doi: 10.1038/s41422-018-0110-y
[66] Gietz R D, Schiestl R H, Willems A R, et al. Studies on the transformation of intact yeast cells by the LiAc/SS-DNA/PEG procedure. Yeast, 1995, 11(4): 355-360.
pmid: 7785336
[67] Broach J R, Strathern J N, Hicks J B. Transformation in yeast: development of a hybrid cloning vector and isolation of the can1 gene. Gene, 1979, 8(1): 121-133.
pmid: 395029
[68] Khan N C, Sen S P. Genetic transformation in yeasts. Journal of General Microbiology, 1974, 83(2): 237-250.
pmid: 4610082
[69] Karube I, Tamiya E, Matsuoka H. Transformation of Saccharomyces cerevisiae spheroplasts by high electric pulse. FEBS Letters, 1985, 182(1): 90-94.
doi: 10.1016/0014-5793(85)81160-1
[70] Delorme E. Transformation of Saccharomyces cerevisiae by electroporation. Applied and Environmental Microbiology, 1989, 55(9): 2242-2246.
doi: 10.1128/aem.55.9.2242-2246.1989 pmid: 2679384
[71] Johnston S A, Anziano P Q, Shark K, et al. Mitochondrial transformation in yeast by bombardment with microprojectiles. Science, 1988, 240(4858): 1538-1541.
pmid: 2836954
[72] Armaleo D, Ye G N, Klein T M, et al. Biolistic nuclear transformation of Saccharomyces cerevisiae and other fungi. Current Genetics, 1990, 17(2): 97-103.
pmid: 2138934
[73] Bonnefoy N, Fox T D. Directed alteration of Saccharomyces cerevisiae mitochondrial DNA by biolistic transformation and homologous recombination. Methods in Molecular Biology (Clifton, N J), 2007, 372: 153-166.
[74] Karas B J, Jablanovic J, Irvine E, et al. Transferring whole genomes from bacteria to yeast spheroplasts using entire bacterial cells to reduce DNA shearing. Nature Protocols, 2014, 9(4): 743-750.
doi: 10.1038/nprot.2014.045
[75] Karas B J, Jablanovic J, Sun L J, et al. Direct transfer of whole genomes from bacteria to yeast. Nature Methods, 2013, 10(5): 410-412.
doi: 10.1038/nmeth.2433
[76] Wheeler V C, Aitken M, Coutelle C. Modification of the mouse mitochondrial genome by insertion of an exogenous gene. Gene, 1997, 198(1-2): 203-209.
pmid: 9370282
[77] Gupta M, Hoo B. Entire maize chloroplast genome is stably maintained in a yeast artificial chromosome. Plant Molecular Biology, 1991, 17(3): 361-369.
pmid: 1679355
[78] Ketner G, Spencer F, Tugendreich S, et al. Efficient manipulation of the human adenovirus genome as an infectious yeast artificial chromosome clone. Proceedings of the National Academy of Sciences of the United States of America, 1994, 91(13): 6186-6190.
[79] García-Ramírez J J, Ruchti F, Huang H, et al. Dominance of virus over host factors in cross-species activation of human Cytomegalovirus early gene expression. Journal of Virology, 2001, 75(1): 26-35.
pmid: 11119570
[80] Benders G A, Noskov V N, Denisova E A, et al. Cloning whole bacterial genomes in yeast. Nucleic Acids Research, 2010, 38(8): 2558-2569.
doi: 10.1093/nar/gkq119
[81] Karas B J, Tagwerker C, Yonemoto I T, et al. Cloning the Acholeplasma laidlawii PG-8A genome in Saccharomyces cerevisiae as a yeast centromeric plasmid. ACS Synthetic Biology, 2012, 1(1): 22-28.
doi: 10.1021/sb200013j
[82] Tagwerker C, Dupont C L, Karas B J, et al. Sequence analysis of a complete 1.66 Mb Prochlorococcus marinus MED 4 genome cloned in yeast. Nucleic Acids Research, 2012, 40(20): 10375-10383.
doi: 10.1093/nar/gks823
[83] Karas B J, Molparia B, Jablanovic J, et al. Assembly of eukaryotic algal chromosomes in yeast. Journal of Biological Engineering, 2013, 7(1): 30.
doi: 10.1186/1754-1611-7-30
[84] Soltysiak M P M, Meaney R S, Hamadache S, et al. Trans-kingdom conjugation within solid media from Escherichia coli to Saccharomyces cerevisiae. International Journal of Molecular Sciences, 2019, 20(20): 5212.
doi: 10.3390/ijms20205212
[85] Lee E C, Liang Q, Ali H, et al. Complete humanization of the mouse immunoglobulin loci enables efficient therapeutic antibody discovery. Nature Biotechnology, 2014, 32(4): 356-363.
doi: 10.1038/nbt.2825 pmid: 24633243
[86] Yoneji T, Fujita H, Mukai T, et al. Grand scale genome manipulation via chromosome swapping in Escherichia coli programmed by three one megabase chromosomes. Nucleic Acids Research, 2021, 49(15): 8407-8418.
doi: 10.1093/nar/gkab298
[87] Gnirke A, Huxley C, Peterson K, et al. Microinjection of intact 200- to 500-kb fragments of YAC DNA into mammalian cells. Genomics, 1993, 15(3): 659-667.
pmid: 8385648
[88] Mejía J E, Willmott A, Levy E, et al. Functional complementation of a genetic deficiency with human artificial chromosomes. The American Journal of Human Genetics, 2001, 69(2): 315-326.
doi: 10.1086/321977
[89] Logsdon G A, Gambogi C W, Liskovykh M A, et al. Human artificial chromosomes that bypass centromeric DNA. Cell, 2019, 178(3): 624-639.e19.
[90] Marschall P, Malik N, Larin Z. Transfer of YACs up to 2.3 Mb intact into human cells with polyethylenimine. Gene Therapy, 1999, 6(9): 1634-1637.
pmid: 10490774
[91] Montoliu L. Large-scale preparation of yeast agarose plugs to isolate yeast artificial chromosome DNA. Cold Spring Harbor Protocols, 2018, 2018(8). DOI: 10.1101/pdb.prot093955.
doi: 10.1101/pdb.prot093955
[92] Montoliu L. Purification of yeast artificial chromosome DNA for microinjection using pulsed-field gel electrophoresis and ultrafiltration. Cold Spring Harbor Protocols, 2018, 2018(8). DOI: 10.1101/pdb.prot093948.
doi: 10.1101/pdb.prot093948
[93] Montoliu L. Purification of yeast artificial chromosome DNA for microinjection using a two-gel electrophoresis procedure. Cold Spring Harbor Protocols, 2018, 2018(8). DOI: 10.1101/pdb.prot093930.
doi: 10.1101/pdb.prot093930
[94] Zhou S J, Wu Y, Zhao Y, et al. Dynamics of synthetic yeast chromosome evolution shaped by hierarchical chromatin organization. bioRxiv, 2021. DOI: 10.1101/2021.07.19.453002.
doi: 10.1101/2021.07.19.453002
[95] Xu H, Han M Z, Zhou S Y, et al. Chromosome drives via CRISPR-Cas 9 in yeast. Nature Communications, 2020, 11: 4344.
doi: 10.1038/s41467-020-18222-0
[96] Davies N P, Huxley C. YAC transfer into mammalian cells by cell fusion. Methods in Molecular Biology (Clifton, N J), 1996, 54: 281-292.
[97] Jakobovits A, Moore A L, Green L L, et al. Germ-line transmission and expression of a human-derived yeast artificial chromosome. Nature, 1993, 362(6417): 255-258.
doi: 10.1038/362255a0
[98] Li L P, Lampert J C, Chen X J, et al. Transgenic mice with a diverse human T cell antigen receptor repertoire. Nature Medicine, 2010, 16(9): 1029-1034.
doi: 10.1038/nm.2197
[99] Li L P, Blankenstein T. Generation of transgenic mice with megabase-sized human yeast artificial chromosomes by yeast spheroplast-embryonic stem cell fusion. Nature Protocols, 2013, 8(8): 1567-1582.
doi: 10.1038/nprot.2013.093
[100] Brown D M, Chan Y A, Desai P J, et al. Efficient size-independent chromosome delivery from yeast to cultured cell lines. Nucleic Acids Research, 2016, 45(7): e50.
[101] Luo D, Saltzman W M. Synthetic DNA delivery systems. Nature Biotechnology, 2000, 18(1): 33-37.
pmid: 10625387
[102] 柴梦哲, 贾斌, 李炳志, 等. 人工基因组合成与重排研究进展. 生命科学, 2019, 31(4): 364-371.
Chai M Z, Jia B, Li B Z, et al. Advances in synthetic genome and genome rearrangement. Chinese Bulletin of Life Sciences, 2019, 31(4): 364-371.
[103] Kouprina N, Noskov V N, Larionov V. Selective isolation of large segments from individual microbial genomes and environmental DNA samples using transformation-associated recombination cloning in yeast. Nature Protocols, 2020, 15(3): 734-749.
doi: 10.1038/s41596-019-0280-1 pmid: 32005981
[104] Gaida A, Becker M M, Schmid C D, et al. Cloning of the repertoire of individual Plasmodium falciparum var genes using transformation associated recombination (TAR). PLoS One, 2011, 6(3): e17782.
doi: 10.1371/journal.pone.0017782
[105] Ceze L, Nivala J, Strauss K. Molecular digital data storage using DNA. Nature Reviews Genetics, 2019, 20(8): 456-466.
doi: 10.1038/s41576-019-0125-3
[106] Chen W G, Han M Z, Zhou J T, et al. An artificial chromosome for data storage. National Science Review, 2021, 8(5): nwab028.
doi: 10.1093/nsr/nwab028
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