酿酒酵母染色体设计与合成研究进展

doi:10.16288/j.yczz.17-199

遗传 ›› 2017, Vol. 39 ›› Issue (10): 865-876.doi: 10.16288/j.yczz.17-199

• 特邀综述 • 下一篇

酿酒酵母染色体设计与合成研究进展

徐赫鸣^1,²(),谢泽雄^1,²,刘夺^1,²,吴毅^1,²,李炳志^1,²,元英进^1,²()

收稿日期:2017-05-31 修回日期:2017-09-10 出版日期:2017-09-21 发布日期:2017-09-22
作者简介:徐赫鸣,硕士研究生,专业方向：合成生物学。
基金资助:
国家自然科学基金(21390203);国家自然科学基金(21576198)

Design and synthesis of yeast chromosomes

Xu Heming^1,²(),Xie Zexiong^1,²,Liu Duo^1,²,Wu Yi^1,²,Li Bingzhi^1,²,Yuan Yingjin^1,²()

Received:2017-05-31 Revised:2017-09-10 Online:2017-09-21 Published:2017-09-22
Supported by:
Supported by the National Natural Science Foundation of China(21390203);Supported by the National Natural Science Foundation of China(21576198)

摘要/Abstract

摘要：

随着合成生物学的蓬勃发展,基因组学的研究正在由读取基因组信息拓展到以编写基因组信息为主的合成基因组学时代。2009年,由Jef D. Boeke教授提出的人工合成酵母基因组计划(Sc2.0)旨在合成世界上首个真核生物基因组。在美、中、英、法、澳大利亚、新加坡等多国科学家的努力下,目前已经完成1/3的酵母染色体的人工合成。本文从合成基因组学领域的发展历程出发,介绍了Sc2.0计划中酿酒酵母(Saccharomyces cerevisiae)染色体设计与合成的最新进展,包括酿酒酵母9号染色体右臂、3号染色体、2号染色体、5号染色体、6号染色体、10号染色体和12号染色体的设计与合成过程,阐述了其各自的合成策略以及生物学意义,以期为合成基因组学的深入开展提供借鉴与参考。

关键词: 合成基因组学, 合成酵母基因组计划(Sc2.0), 合成型酵母染色体

Abstract:

With the rapid growth and development of synthetic biology, research in the genomics is advancing from genome sequencing to genome synthesis. In 2009, Professor Jef D. Boeke proposed the Synthetic Yeast Genome Project (Sc2.0), which aims to synthesize the world’s first eukaryotic genome. With the efforts of scientists from the United States, China, Britain, France, Australia, Singapore and other countries, a third of the Saccharomyces cerevisiae chromosomes has now been synthesized. In the perspectives of synthetic genomics, we here review the recent progress in the Sc2.0 project, including discussion on the right arm of chromosome Ⅸ, and chromosomes Ⅱ, Ⅴ, Ⅵ, Ⅹ, Ⅻ, in terms of their designs and synthetic strategy as well as the biological significance, thereby providing a reference for further research in synthetic genomics.

Key words: synthetic genomics, synthetic yeast genome project (Sc2.0), synthetic yeast chromosomes

徐赫鸣,谢泽雄,刘夺,吴毅,李炳志,元英进. 酿酒酵母染色体设计与合成研究进展[J]. 遗传, 2017, 39(10): 865-876.

Xu Heming,Xie Zexiong,Liu Duo,Wu Yi,Li Bingzhi,Yuan Yingjin. Design and synthesis of yeast chromosomes[J]. Hereditas(Beijing), 2017, 39(10): 865-876.

参考文献

[1]	Cello J, Paul AV, Wimmer E . Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template. Science, 2002,297(5583):1016-1018.
[2]	Smith HO, Hutchison CA, Pfannkoch C, Venter JC . Generating a synthetic genome by whole genome assembly: φX174 bacteriophage from synthetic oligonucleotides. Proc Natl Acad Sci USA, 2003,100(26):15440-15445.
[3]	Chan LY, Kosuri S, Endy D . Refactoring bacteriophage T7. Mol Syst Biol, 2005,1(1): 2005.0018.
[4]	Tumpey TM, Basler CF, Aguilar PV, Zeng H, Solórzano A, Swayne DE, Cox NJ, Katz JM, Taubenberger JK, Palese P, García-Sastre A . Characterization of the reconstructed 1918 Spanish influenza pandemic virus. Science, 2005,310(5745):77-80.
[5]	Gibson DG, Benders GA, Andrews-Pfannkoch C, Denisova EA, Baden-Tillson H, Zaveri J, Stockwell TB, Brownley A, Thomas DW, Algire MA, Merryman C, Young L, Noskov VN, Glass JI, Venter JC, Hutchison III CA, Smith HO . Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome Science, 2008,319(5867):1215-1220.
[6]	Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA, Benders GA, Montague MG, Ma L, Moodie MM, Merryman C, Vashee S, Krishnakumar R, Assad-Garcia N, Andrews-Pfannkoch C, Denisova EA, Young L, Qi ZQ, Segall-Shapiro TH, Calvey CH, Parmar PP, Hutchison CA, Smith HO, Venter JC . Creation of a bacterial cell controlled by a chemically synthesized genome. Science, 2010,329(5987):52-56.
[7]	Gibson DG, Smith HO, Hutchison III CA, Venter JC, Merryman C . Chemical synthesis of the mouse mitochondrial genome. Nat Methods, 2010,7(11):901-903.
[8]	Hutchison III CA, Chuang RY, Noskov VN, Assad-Garcia N, Deerinck TJ, Ellisman MH, Gill J, Kannan K, Karas BJ, Ma L, Pelletier JF, Qi ZQ, Richter RA, Strychalski EA, Sun LJ, Suzuki Y, Tsvetanova B, Wise KS, Smith HO, Glass JI, Merryman C, Gibson DG, Venter JC . Design and synthesis of a minimal bacterial genome. Science, 2016, 351(6280): aad6253.
[9]	Ostrov N, Landon M, Guell M, Kuznetsov G, Teramoto J, Cervantes N, Zhou M, Singh K, Napolitano MG, Moosburner M, Shrock E, Pruitt BW, Conway N, Goodman DB, Gardner CL, Tyree G, Gonzales A, Wanner BL, Norville JE, Lajoie MJ, Church GM . Design, synthesis, and testing toward a 57-codon genome. Science, 2016,353(6301):819-822.
[10]	Young TS, Schultz PG . Beyond the canonical 20 amino acids: expanding the genetic lexicon. J Biol Chem, 2010,285(15):11039-11044.
[11]	Lee KB, Hou CY, Kim CE, Kim DM, Suga H, Kang TJ . Genetic code expansion by degeneracy reprogramming of arginyl codons. ChemBioChem, 2016,17(13):1198-1201.
[12]	Dymond JS, Richardson SM, Coombes CE, Babatz T, Muller H, Annaluru N, Blake WJ, Schwerzmann JW, Dai JB, Lindstrom DL, Boeke AC, Gottschling DE, Chandrasegaran S, Bader JS, Boeke JD . Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature, 2011,477(7365):471-476.
[13]	Mitchell LA, Wang A, Stracquadanio G, Kuang Z, Wang XY, Yang K, Richardson S, Martin JA, Zhao Y, Walker R, Luo YS, Dai HJ, Dong K, Tang ZJ, Yang YL, Cai YZ, Heguy A, Ueberheide B, Feny? D, Dai JB, Bader JS, Boeke JD. Synthesis, debugging, effects of synthetic chromosome consolidation: synVI and beyond.Science, 2017, 355(6329): eaaf4831.
[14]	Shen Y, Wang Y, Chen T, Gao F, Gong JH, Abramczyk D, Walker R, Zhao HC, Chen SH, Liu W, Luo YS, Müller CA, Paul-Dubois-Taine A, Alver B, Stracquadanio G, Mitchell LA, Luo ZQ, Fan YQ, Zhou BJ, Wen B, Tan FJ, Wang YJ, Zi J, Xie ZX, Li BZ, Yang K, Richardson SM, Jiang H, French CE, Nieduszynski CA, Koszul R, Marston AL, Yuan YJ, Wang J, Bader JS, Dai JB, Boeke JD, Xu X, Cai YZ, Yang HM . Deep functional analysis of synII,a 770-kilobase synthetic yeast chromosome. Science, 2017, 355(6329): eaaf4791.
[15]	Annaluru N, Muller H, Mitchell LA, Ramalingam S, Stracquadanio G, Richardson SM, Dymond JS, Kuang Z, Scheifele LZ, Cooper EM, Cai YZ, Zeller K, Agmon N, Han JS, Hadjithomas M, Tullman J, Caravelli K, Cirelli K, Guo ZY, London V, Yeluru A, Murugan S, Kandavelou K, Agier N, Fischer G, Yang K, Martin JA, Bilgel M, Bohutskyi P, Boulier KM, Capaldo BJ, Chang J, Charoen K, Choi WJ, Deng P , DiCarlo JE, Doong J, Dunn J, Feinberg JI, Fernandez C, Floria CE, Gladowski D, Hadidi P, Ishizuka I, Jabbari J, Lau CYL, Lee PA, Li S, Lin D, Linder ME, Ling J, Liu J, Liu J, London M, Ma H, Mao J, McDade JE, McMillan A, Moore AM, Oh WC, Ouyang Y, Patel R, Paul M, Paulsen LC, Qiu J, Rhee A, Rubashkin MG, Soh IY, Sotuyo NE, Srinivas V, Suarez A, Wong A, Wong R, Xie WR, Xu YJ, Yu AT, Koszul R, Bader JS, Boeke JD, Chandrasegaran S. Total synthesis of a functional designer eukaryotic chromosome. Science, 2014,344(6179):55-58.
[16]	Wu Y, Li BZ, Zhao M, Mitchell LA, Xie ZX, Lin QH, Wang X, Xiao WH, Wang Y, Zhou X, Liu H, Li X, Ding MZ, Liu D, Zhang L, Liu BL, Wu XL, Li FF, Dong XT, Jia B, Zhang WZ, Jiang GZ, Liu Y, Bai X, Song TQ, Chen Y, Zhou SJ, Zhu RY, Gao F, Kuang Z, Wang XY, Shen M, Yang K, Stracquadanio G, Richardson SM, Lin YC, Wang LH, Walker R, Luo YS, Ma PS, Yang HM, Cai YZ, Dai JB, Bader JS, Boeke JD, Yuan YJ . Bug mapping and fitness testing of chemically synthesized chromosome X. Science, 2017,355(6329):eaaf4706.
[17]	Xie ZX, Li BZ, Mitchell LA, Wu Y, Qi X, Jin Z, Jia B, Wang X, Zeng BX, Liu HM, Wu XL, Feng Q, Zhang WZ, Liu W, Ding MZ, Li X, Zhao GR, Qiao JJ, Cheng JS, Zhao M, Kuang Z, Wang XY, Martin JA, Stracquadanio G, Yang K, Bai X, Zhao J, Hu ML, Lin QH, Zhang WQ, Shen MH, Chen S, Su W, Wang EX, Guo R, Zhai F, Guo XJ, Du HX, Zhu JQ, Song TQ, Dai JJ, Li FF, Jiang GZ, Han SL, Liu SY, Yu ZC, Yang XN, Chen K, Hu C, Li DS, Jia N, Liu Y, Wang LT, Wang S, Wei XT, Fu MQ, Qu LM, Xin SY, Liu T, Tian KR, Li XN, Zhang JH, Song LX, Liu JG, Lv JF, Xu H, Tao R, Wang Y, Zhang TT, Deng YX, Wang YR, Li T, Ye GX, Xu XR, Xia ZB, Zhang W, Yang SL, Liu YL, Ding WQ, Liu ZN, Zhu JQ, Liu NZ, Walker R, Luo YS, Wang Y, Shen Y, Yang HM, Cai YZ, Ma PS, Zhang CT, Bader JS, Boeke JD , Yuan YJ. "Perfect" designer chromosome V and behavior of a ring derivative. Science, 2017,355(6329): eaaf4704.
[18]	Zhang WM, Zhao GH, Luo ZQ, Lin YC, Wang LH, Guo YK, Wang A, Jiang SY, Jiang QW, Gong JH, Wang Y, Hou S, Huang J, Li TY, Qin YR, Dong JK, Qin Q, Zhang JY, Zou XZ, He X, Zhao L, Xiao YB, Xu M, Cheng EC, Huang N, Zhou T, Shen Y, Walker R, Luo YS, Kuang Z, Mitchell LA, Yang K, Richardson SM, Wu Y, Li BZ, Yuan YJ, Yang HM, Lin JW, Chen GQ, Wu QY, Bader JS, Cai YZ, Boeke JD , Dai JB. Engineering the ribosomal DNA in a megabase synthetic chromosome. Science, 2017,355(6329): eaaf3981.
[19]	Richardson SM, Mitchell LA, Stracquadanio G, Yang K, Dymond JS , DiCarlo JE, Lee D, Huang CLV, Chandrasegaran S, Cai YZ, Boeke JD, Bader JS. Design of a synthetic yeast genome. Science, 2017,355(6329):1040-1044.
[20]	Dymond J, Boeke J . The Saccharomyces cerevisiae SCRaMbLE system and genome minimization Bioeng Bugs, 2012,3(3):168-171.
[21]	Shen Y, Stracquadanio G, Wang Y, Yang K, Mitchell LA, Xue YX, Cai YZ, Chen T, Dymond JS, Kang K, Gong JH, Zeng XF, Zhang YF, Li YR, Feng Q, Xu X, Wang J, Wang J, Yang HM, Boeke JD, Bader JS . SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes. Genome Res, 2016,26(1):36-49.
[22]	Michelson AM, Todd AR . Nucleotides part XXXII. Synthesis of a dithymidine dinucleotide containing a 3°: 5°- internucleotidic linkage. J Chem Soc, 1955: 2632-2638.
[23]	Beaucage SL, Caruthers MH . ChemInform abstract: Deoxynucleoside phosphoramidites. A new class of key intermediates for deoxypolynucleotide synthesis. ChemInform, 1981,12(36), doi: 10.1002/chin.198136353.
[24]	Fodor SP, Read JL, Pirrung MC, Stryer L, Lu AT, Solas D . Light-directed, spatially addressable parallel chemical synthesis. Science, 1991,251(4995):767-773.
[25]	Shetty RP, Endy D, Knight TF Jr . Engineering BioBrick vectors from BioBrick parts. J Biol Eng, 2008,2:5.
[26]	Engler C, Kandzia R, Marillonnet S . A one pot, one step, precision cloning method with high throughput capability. PLoS One, 2008,3(11):e3647.
[27]	Gibson DG, Young L, Chuang RY, Venter JC, Hutchison III CA, Smith HO . Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods, 2009,6(5):343-345.
[28]	Fu J, Bian XY, Hu SB, Wang HL, Huang F, Seibert PM, Plaza A, Xia LQ, Müller R, Stewart AF, Zhang YM . Full-length RecE enhances linear-linear homologous recombination and facilitates direct cloning for bioprospecting. Nat Biotechnol, 2012,30(5):440-446.
[29]	Wang HL, Li Z, Jia RN, Hou Y, Yin J, Bian XY, Li AY, Müller R, Stewart AF, Fu J, Zhang YM . RecET direct cloning and Redαβ recombineering of biosynthetic gene clusters, large operons or single genes for heterologous expression. Nat Protoc, 2016,11(7):1175-1190.
[30]	Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E . A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science, 2012,337(6096):816-821.
[31]	Cong L, Ran FA, Cox D, Lin SL, Barretto R, Habib N, Hsu PD, Wu XB, Jiang WY, Marraffini LA, Zhang F . Multiplex genome engineering using CRISPR/Cas systems. Science, 2013,339(6121):819-823.
[32]	Mali P, Yang LH, Esvelt KM, Aach J, Guell M , DiCarlo JE, Norville JE, Church GM. RNA-guided human genome engineering via Cas9. Science, 2013,339(6121):823-826.
[33]	Cobb RE, Wang YJ, Zhao HM . High-efficiency multiplex genome editing of Streptomyces species using an engineered CRISPR/Cas system. ACS Synth Biol, 2015,4(6):723-728.
[34]	Zhou JT, Wu RH, Xue XL, Qin ZJ . CasHRA (Cas9-facilitated homologous recombination assembly) method of constructing megabase-sized DNA. Nucleic Acids Res, 2016,44(14):e124.
[35]	Sternberg N . Bacteriophage P1 site-specific recombination: III. Strand exchange during recombination at lox sites J Mol Biol, 1981,150(4):603-608.
[36]	Sternberg N, Hamilton D . Bacteriophage P1 site-specific recombination: I. Recombination between loxP sites J Mol Biol, 1981,150(4):467-486.
[37]	Sternberg N, Hamilton D, Hoess R . Bacteriophage P1 site-specific recombination: II. Recombination between loxP and the bacterial chromosome J Mol Biol, 1981,150(4):487-507.
[38]	Abremski K, Hoess R . Bacteriophage P1 site-specific recombination. Purification and properties of the Cre recombinase protein. J Biol Chem, 1984,259(3):1509-1514.
[39]	Abremski K, Wierzbicki A, Frommer B, Hoess RH . Bacteriophage P1 Cre-loxP site-specific recombination. Site-specific DNA topoisomerase activity of the Cre recombination protein. J Biol Chem, 1986,261(1):391-396.
[40]	Kuhstoss S, Rao RN . Analysis of the integration function of the streptomycete bacteriophage φC31. J Mol Biol, 1991,222(4):897-908.

编辑推荐

Metrics

www.chinagene.cn
备案号：京ICP备09063187号-4
总访问:,今日访问:,当前在线:

酿酒酵母染色体设计与合成研究进展

Design and synthesis of yeast chromosomes

RichHTML

PDF (PC)

可视化

被引次数

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 0

编辑推荐

Metrics