|本期目录/Table of Contents|

[1]王培霞,马渊,吴毅.大DNA体内组装技术进展[J].生物加工过程,2019,17(01):15-22.[doi:10.3969/j.issn.1672-3678.2019.01.003]
 WANG Peixia,MA Yuan,WU Yi.Advances in large DNA in vivo assembly[J].Chinese Journal of Bioprocess Engineering,2019,17(01):15-22.[doi:10.3969/j.issn.1672-3678.2019.01.003]
点击复制

大DNA体内组装技术进展()
分享到:

《生物加工过程》[ISSN:1672-3678/CN:32-1706/Q]

卷:
17
期数:
2019年01期
页码:
15-22
栏目:
出版日期:
2019-01-30

文章信息/Info

Title:
Advances in large DNA in vivo assembly
文章编号:
1672-3678(2019)01-0015-08
作者:
王培霞12马渊12吴毅12
1. 天津大学 化工学院 系统生物工程教育部重点实验室,天津 300072; 2. 天津大学 天津化学化工协同创新中心 合成生物学研究平台,天津 300072
Author(s):
WANG Peixia12MA Yuan12WU Yi12
1.Key Laboratory of Systems Bioengineering of the Ministry of Education,School of Chemical Engineering and Technology, Tianjin University,Tianjin 300072,China; 2.Frontier Science Center for Synthetic Biology,Collaborative Innovation Center of Chemical Science and Engineering(Tianjin),Tianjin University,Tianjin 300072,China
关键词:
DNA组装 染色体合成 合成基因组学 合成生物学
分类号:
O621.3;Q812
DOI:
10.3969/j.issn.1672-3678.2019.01.003
文献标志码:
A
摘要:
DNA组装技术是合成生物学的关键共性技术。目前,小分子DNA组装大多采用体外组装策略,而大分子DNA的组装则更多地借助宿主自身的重组机制在体内完成,常用的宿主包括酿酒酵母、大肠杆菌和枯草芽孢杆菌等。本文中,笔者综述了近年来体内大分子DNA组装的研究进展。

参考文献/References:

[1] JUHAS M,AJIOKA J W.High molecular weight DNA assembly in vivo for synthetic biology applications[J].Crit Rev Biotechnol,2017,37(3):277-286.
[2] O’CONNOR M,PEIFER M,BENDER W.Construction of large DNA segments in Escherichia coli[J].Science,1989,244:1307-1312.
[3] ZHANG Y,BUCHHOLZ F,MUYRERS J P P,et al.A new logic for DNA engineering using recombination in Escherichia coli[J].Nat Genet,1998,20(2):123-128.
[4] YU D,ELLIS H M,LEE E C,et al.An efficient recombination system for chromosome engineering in Escherichia coli[J].Proc Natl Acad Sci USA,2000,97(11):5978-5983.
[5] MURPHY K C.The λ Gam protein inhibits RecBCD binding to dsDNA ends[J].J Mol Biol,2007,371(1):19-24.
[6] SAUER B,HENDERSON N.Site-specific DNA recombination in mammalian cells by the Cre recombinase of bacteriophage P1[J].Proc Natl Acad Sci USA,1988,85(14):5166-5170.
[7] HOANAG T T,KARKHOFF-SCHWEIZER R R,KUTCHMA A J,et al.A broad-host-range Flp-FRT,recombination system for site-specific excision of chromosomally-located DNA sequences:application for isolation of unmarked Pseudomonas aeruginosa,mutants[J].Gene,1998,212(1):77-86.
[8] WENZEL S C,GROSS F,ZHANG Y,et al.Heterologous expression of a myxobacterial natural products assembly line in Pseudomonads via Red/ET recombineering[J].Chem Biol,2005,12(3):349-356.
[9] SMAILUS D E,WARREN R L,HOLT R A.Constructing large DNA segments by iterative clone recombination[J].Syst Synth Biol,2007,1(3):139-144.
[10] FU J,BIAN X,HU S,et al.Full-length RecE enhances linear-linear homologous recombination and facilitates direct cloning for bioprospecting[J].Nat Biotechnol,2012,30(5):440-446.
[11] HINNEN A,HICKS J B,FINK G R.Transformation of yeast[J].Proc Natl Acad Sci USA,1978,75(4):1929-1933.
[12] ORR-WEAVER T L,SZOSTAK J W,ROTHSTEIN R J.Yeast transformation:a model system for the study of recombination[J].Proc Natl Acad Sci USA,1981,78(10):6354-6358.
[13] GIBSON D G.Gene and genome construction in yeast[J].Curr Protoc Mol Biol,2011,doi:10.1002/0471142727.mb0322s94.
[14] SHAO Z,ZHAO H,ZHAO H.DNA assembler,an in vivo genetic method for rapid construction of biochemical pathways[J].Nucleic Acids Res,2009,37(2):e16.
[15] GUO Y,DONG J,ZHOU T,et al.YeastFab:the design and construction of standard biological parts for metabolic engineering in Saccharomyces cerevisiae[J].Nucleic Acids Res,2015,43(13):e88.
[16] DYMOND J S,RICHARDSON S M,COOMBES C E,et al.Synthetic chromosome arms function in yeast and generate phenotypic diversity by design[J].Nature,2011,477:471-476.
[17] LIN Q,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[J].ACS Synth Biol,2016,4(3):213-220.
[18] JAKOCˇINAS T,RAJKUMAR A S,ZHANG J,et al.CasEMBLR:Cas9-facilitated multiloci genomic integration of in vivo assembled DNA parts in Saccharomyces cerevisiae[J].ACS Synth Biol,2015,4(11):1226-1234.
[19] KUIJPERS N G,CHROUMPI S,VOS T,et al.One-step assembly and targeted integration of multigene constructs assisted by the I-SceI meganuclease in Saccharomyces cerevisiae[J].FEMS Yeast Res,2013,13(8):769-781.
[20] STORICI F,LEWIS L K,RESNICK M A.In vivo site-directed mutagenesis using oligonucleotides[J].Nat Biotechnol,2001,19(8):773-776.
[21] ZHOU J,WU R,XUE X,et al.CasHRA(Cas9-facilitated homologous recombination assembly)method of constructing megabase-sized DNA[J].Nucleic Acids Res,2016,44(14):e124.
[22] YADAV T,CARRASCO B,SERRANO E,et al.Roles of Bacillus subtilis DprA and SsbA in RecA-mediated genetic recombination[J].J Biol Chem,2014,289(40):27640-27652.
[23] ITAYA M.Toward a bacterial genome technology:integration of the Escherichia coli prophage lambda genome into the Bacillus subtilis 168 chromosome[J].Mol General Genet,1995,248(1):9-16.
[24] ITAYA M,NAGATA T,SHIROISHI T,et al.Efficient cloning and engineering of giant DNAs in a novel Bacillus subtilis genome vector[J].J Biochem,2000,128(5):869-875.
[25] IWATA T,KANEKO S,SHIWA Y,et al.Bacillus subtilis genome vector-based complete manipulation and reconstruction of genomic DNA for mouse transgenesis[J].BMC Genomics,2013,14:300.
[26] ITAYA M,TSUGE K,KOIZUMI M,et al.Combining two genomes in one cell:stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome[J].Proc Natl Acad Sci USA,2005,102(44):15971-15976.
[27] ITAYA M,FUJITA K,KUROKI A,et al.Bottom-up genome assembly using the Bacillus subtilis genome vector[J].Nat Methods,2008,5(1):41-43.
[28] OHTANI N,HASEGAWA M,SATO M,et al.Serial assembly of Thermus,megaplasmid DNA in the genome of Bacillus subtilis,168:a BAC-based domino method applied to DNA with a high GC content[J].Biotechnol J,2012,7(7):867-876.
[29] OGAWA T,IWATA T,KANEKO S,et al.An inducible recA expression Bacillus subtilis genome vector for stable manipulation of large DNA fragments[J].BMC Genomics,2015,16(1):1-12.
[30] CELLO J,PAUL A V,WIMMER E.Chemical synthesis of Poliovirus cDNA:generation of infectious virus in the absence of natural template[J].Science,2002,297:1016-1018.
[31] WIMMER E,HELLENC U,CAO X.Genetics of Poliovirus[J].Ann Rev Genet,1993,27(4):353-436.
[32] SMITH H O,HUTCHISON C A,PFANNKOCH C,et al.Generating a synthetic genome by whole genome assembly:φX174 bacteriophage from synthetic oligonucleotides[J].Proc Natl Acad Sci USA,2003,100(26):15440-15445.
[33] CHAN L Y,KOSURI S,ENDY D.Refactoring bacteriophage T7[J].Mol Syst Biol,2005,1(1):2005.0018.
[34] FRASER C M,GOCAYNE J D,WHITE O,et al.The minimal gene complement of Mycoplasma genitalium[J].Science,1995,270:397-403.
[35] GIBSON D G,BENDERS G A,ANDREWS-PFANNKOCH C,et al.Complete chemical synthesis,assembly,and cloning of a Mycoplasma genitalium genome[J].Science,2008,319:1215-1220.
[36] LARTIQUE C,VASHEE S,ALGIRE M A,et al.Creating bacterial strains from genomes that have been cloned and engineered in yeast[J].Science,2009,325:1693-1696.
[37] GIBSON D G,GLASS J I,LARTIGUE C,et al.Creation of a bacterial cell controlled by a chemically synthesized genome[J].Science,2010,329:52-56.
[38] HUTCHISON C A,CHUANG R Y,NOSKOV V N,et al.Design and synthesis of a minimal bacterial genome[J].Science,2016,351:aad6253.
[39] 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[J].ACS Synth Biol,2012,1(1):22-28.
[40] TAGWERKER C,DUPONT C L,KARAS B J,et al.Sequence analysis of a complete 1.66 Mb Prochlorococcus marinus MED4 genome cloned in yeast[J].Nucleic Acids Res,2012,40(20):10375-10383.
[41] HEUER T,B?RGER C,MAASS G,et al.Cloning of prokaryotic genomes in yeast artificial chromosomes:application to the population genetics of Pseudomonas aeruginosa[J].Electrophoresis,2010,19(4):486-494.
[42] NOSKOV V N,KARAS B J,YOUNG L,et al.Assembly of large,high G+C bacterial DNA fragments in yeast[J].ACS Synth Biol,2012,1(7):267-273.
[43] ANNALURU N,MULLER H,MITCHELL L A,et al.Total synthesis of a functional designer eukaryotic chromosome[J].Science,2014,344:55-58.
[44] SHEN Y,WANG Y,CHEN T,et al.Deep functional analysis of synII,a 770-kilobase synthetic yeast chromosome[J].Science,2017,doi:10.1126/science.aaf4791.
[45] XIE Z X,LI B Z,MITCHELL L A,et al."Perfect" designer chromosome V and behavior of a ring derivative[J].Science,2017,doi:10.1126/science.aaf4704.
[46] MITCHELL L A,WANG A,STRACQUADANIO G,et al.Synthesis,debugging,and effects of synthetic chromosome consolidation:synVI and beyond[J].Science,2017,doi:10.1126/science.aaf4831.
[47] WU Y,LI B Z,ZHAO M,et al.Bug mapping and fitness testing of chemically synthesized chromosome X[J].Science,2017,doi:10.1126/science.aaf4706.
[48] ZHANG W,ZHAO G,LUO Z,et al.Engineering the ribosomal DNA in a megabase synthetic chromosome.[J].Science,2017,doi:10.1126/science.aaf3981.
[49] KARAS B J,MOLPARIA B,JABLANOVIC J,et al.Assembly of eukaryotic algal chromosomes in yeast[J].J Biol Eng,2013,7(1):1-12.
[50] ALBERTSEN H M,ABDERRAHIM H,CANN H M,et al.Construction and characterization of a yeast artificial chromosome library containing seven haploid human genome equivalents.[J].Proc Natl Acad Sci USA,1990,87(11):4256-4260.
[51] MARSCHALL P,MALIK N,LARIN Z.Transfer of YACs up to 2.3 Mb intact into human cells with polyethylenimine[J].Gene Therapy,1999,6(9):1634-1637.
[52] BOEKE J D,CHURCH G,HESSEL A,et al.Genome engineering:the Genome Project-Write[J].Science,2016,353:126-127.

备注/Memo

备注/Memo:
收稿日期:2018-12-06修回日期:2018-12-21
作者简介:王培霞(1994—),女,福建南安人,硕士研究生,研究方向:合成生物学; 吴毅(联系人),副教授,E-mail:yi.wu@tju.edu.cn
引文格式:王培霞,马渊,吴毅.大DNA体内组装技术进展[J].生物加工过程,2019,17(1):15-22.
WANG Peixia,MA Yuan,WU Yi.Advances in large DNA in vivo assembly[J].Chin J Bioprocess Eng,2019,17(1):15-22..
更新日期/Last Update: 2019-01-30