Genome design and synthesis: from replication to rational design

WANG Junyi; WU Xiaole; CAO Yueyang; LI Bingzhi

doi:10.12211/2096-8208.2020-051

您当前的位置：

首页 >

文章列表页 >

Genome design and synthesis: from replication to rational design

Invited Review | 更新时间：2025-03-20

- Genome design and synthesis: from replication to rational design
- Synthetic Biology Journal Vol. 2, Issue 2, Pages: 247-255(2021)
- 作者机构：
  
  教育部合成生物学前沿科学中心，系统生物工程教育部重点实验室，天津大学化工学院，天津　300072
- 作者简介：
- 基金信息：
- DOI：10.12211/2096-8208.2020-051
  CLC： Q81
- Received：17 June 2020，
  
  Revised：2020-12-25，
  
  Published：30 April 2021
- 稿件说明：
移动端阅览
汪君仪, 武晓乐, 曹月阳, 李炳志. 基因组设计与合成：从复写到理性设计[J]. 合成生物学, 2021, 2(2): 247-255

WANG Junyi, WU Xiaole, CAO Yueyang, LI Bingzhi. Genome design and synthesis: from replication to rational design[J]. Synthetic Biology Journal, 2021, 2(2): 247-255
汪君仪, 武晓乐, 曹月阳, 李炳志. 基因组设计与合成：从复写到理性设计[J]. 合成生物学, 2021, 2(2): 247-255 DOI： 10.12211/2096-8208.2020-051.

WANG Junyi, WU Xiaole, CAO Yueyang, LI Bingzhi. Genome design and synthesis: from replication to rational design[J]. Synthetic Biology Journal, 2021, 2(2): 247-255 DOI： 10.12211/2096-8208.2020-051.

摘要

基因组合成相关技术的进步推动人工基因组合成能力不断取得突破，合成基因组学成为了近年来的研究热点，逐步完成了病毒、原核生物基因组的全合成，真核生物基因组设计合成也取得了阶段性突破。在基因组合成的研究过程中，基因组设计的原则不断拓展，基因组设计的尺度由病毒及噬菌体基因组成功复写发展到蕈状支原体JCVI-syn3.0基因组大幅度简化，在真核生物酿酒酵母基因组合成中探索多种基因组设计原则。本文主要综述了人工基因组设计的相关进展，主要内容包括：①人工基因组密码子的改变：外源基因密码子的优化，密码子丰度转变原则的探究，大肠杆菌中密码子的删除；②人工标签的添加及应用：利用同义密码子替换在合成型基因组中添加标签以区分合成型与野生型基因组；③人工位点的添加：酿酒酵母合成型染色体重组系统的开发，优化及应用；④基因组简化方面的研究；⑤对基因组理性设计、基因组简化规律挖掘等进行了展望。

Abstract

With the advancement of related technologies for gene assembly

artificial genome assembly capabilities have made breakthroughs continuously

and synthetic genomics has been developed as a research hotspot in recent years. The chemical synthesis of genomes for several viruses and prokaryotes have been completed gradually

and the synthesis of eukaryotic genomes has also been explored. In the study of synthetic genomics

researchers continue to explore principles for genome design and increase its scale and depth

from the successful replication of virus and bacteriophage genomes

the substantial simplification in the

Mycoplasma mycoides

JCVI-syn3.0 genome to exploring multiple genome design principles in the eukaryotic

Saccharomyces cerevisiae

. This article summarizes the related progress of artificial genome design

with its main contents focused on: the change of artificial genome codons

the addition of artificial tags

the insertion of artificial sites and the research of genome simplification. In 2016

Church's group used synonymous codons to replace seven codons within the entire genome of

E. coli

but the

E. coli

strain could not survive. In 2019

Chin's research group completed the synthesis of

E. coli

containing 61 codons using the method of complete genome synthesis

and the

E. coli

strain can survive normally. Four "watermark" sequences were introduced into the synthetic

M. mycoides

genome

and a large number of PCR tags were introduced into

the synthetic

Saccharomyces cerevisiae

genome to distinguish between synthetic and wild-type genomes. A highlight of the synthetic yeast chromosome design in the Sc2.0 is the insertion of a reverse symmetric artificial site-loxPsym sequence after the stop codon of each non-essential gene. As a result

a SCRaMbLE (Synthetic Chromosome Rearrangement and Modification by LoxPsym-mediated Evolution) system that can rapidly perform genome rearrangement including deletion

duplication

inversion and translocation was formed in the synthetic yeast. The system has been continuously improved in applications

gradually making it an effective mean to optimize the host

increase the yield and enhance stress tolerance of the strain. In addition

the prospect of the rational design of genomes and rules for genome simplification is also discussed.

关键词

Keywords

references

SANGER F , NICKLEN S , COULSON A R . DNA sequencing with chain-terminating inhibitors [J ] . Proceedings of the National Academy of Sciences of the United States of America , 1977 , 74 ( 12 ): 5463 - 5467 .

STEUERNAGEL B , TAUDIEN S , GUNDLACH H , et al . De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley [J ] . BMC Genomics , 2009 , 10 ( 1 ): 547 .

ROTHBERG J M , HINZ W , REARICK T M , et al . An integrated semiconductor device enabling non-optical genome sequencing [J ] . Nature , 2011 , 475 ( 7356 ): 348 - 352 .

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 ( 5583 ): 1016 - 1018 .

SMITH H O , HUTCHISON C A , PFANNKOCH C , et al . Generating a synthetic genome by whole genome assembly: φX174 bacteriophage from synthetic oligonucleotides [J ] . Proceedings of the National Academy of Sciences of the United States of America , 2003 , 100 ( 26 ): 15440 - 15445 .

THAO T T N , LABROUSSAA F , EBERT N , et al . Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform [J ] . Nature , 2020 .

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 ( 5867 ): 1215 - 1220 .

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 ( 5987 ): 52 - 56 .

ZIMMER R , GIBBINS A M . Construction and characterization of a large-fragment chicken bacterial artificial chromosome library [J ] . Genomics , 1997 , 42 ( 2 ): 217 - 226 .

DE LISE A M , TUAN R S . Electroporation-mediated DNA transfection of embryonic chick limb mesenchymal cells [J ] . Methods in Molecular Biology , 2000 : 377 - 382 .

CO D O , BOROWSKI A H , LEUNG J D , et al . Generation of transgenic mice and germline transmission of a mammalian artificial chromosome introduced into embryos by pronuclear microinjection [J ] . Chromosome Research , 2000 , 8 ( 3 ): 183 - 191 .

PAULIS M . Chromosome transfer via cell fusion [J ] . Methods of Molecular Biology , 2011 , 738 : 57 - 67 .

BROWN D M , CHAN Y A , DESAI P J , et al . Efficient size-independent chromosome delivery from yeast to cultured cell lines [J ] . Nucleic Acids Research , 2016 ( 7 ): e50 .

SUZUKI T , KAZUKI Y , HARA T , et al . Current advances in microcell-mediated chromosome transfer technology and its applications [J ] . Experimental Cell Research , 2020 , 390 ( 1 ): 111915 .

LAJOIE M J , ROVNER A J , GOODMAN D B , et al . Genomically recoded organisms expand biological functions [J ] . Science , 2013 , 342 ( 6156 ): 357 - 360 .

OSTROV N , LANDON M , GUELL M , et al . Design, synthesis, and testing toward a 57-codon genome [J ] . Science , 2016 , 353 ( 6301 ): 819 - 822 .

WANG K , FREDENS J , BRUNNER S F , et al . Defining synonymous codon compression schemes by genome recoding [J ] . Nature , 2016 , 539 ( 7627 ): 59 - 64 .

FREDENS J , WANG K , DE LA TORRE D , et al . Total synthesis of Escherichia coli with a recoded genome [J ] . Nature , 2019 , 569 ( 7757 ): 514 - 518 .

HUTCHISON C A , CHUANG R Y , NOSKOV V N , et al . Design and synthesis of a minimal bacterial genome [J ] . Science , 2016 , 351 ( 6280 ).

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 ( 7365 ): 471 - 476 .

ANNALURU N , MULLER H , MITCHELL L A , et al . Total synthesis of a functional d esigner eukaryotic chromosome [J ] . Science , 2014 , 344 ( 6179 ): 55 - 58 .

SHEN Y , WANG Y , CHEN T , et al . Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome [J ] . Science , 2017 , 355 ( 6329 ): eaaf4791 .

XIE Z X , LI B Z , MITCHELL L A , et al . " Perfect" designer chromosome V and behavior of a ring derivative [J ] . Science , 2017 , 355 ( 6329 ): eaaf4704 .

MITCHELL L A , WANG A , STRACQUADANIO G , et al . Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond [J ] . Science , 2017 , 355 ( 6329 ): eaaf4831 .

WU Y , LI B Z , ZHAO M , et al . Bug mapping and fitness testing of chemically synthesized chromosome X [J ] . Science , 2017 , 355 ( 6329 ): eaaf4706 .

ZHANG W , ZHAO G , LUO Z , et al . Engineering the ribosomal DNA in a megabase synthetic chromosome [J ] . Science , 2017 , 355 ( 6329 ): eaaf3981 .

SHAO Y , LU N , WU Z , et al . Creating a functional single-chromosome yeast [J ] . Nature , 2018 , 560 ( 7718 ): 331 - 335 .

SHAO Y , LU N , CAI C , et al . A single circular chromosome yeast [J ] . Cell Research , 2019 , 29 ( 1 ): 87 - 89 .

OSTROV N , BEAL J , ELLIS T , et al . Technological challenges and milestones for writing genomes [J ] . Science , 2019 , 366 ( 6463 ): 310 - 312 .

柴梦哲 , 贾斌 , 李炳志 , 等 . 人工基因组合成与重排研究进展 [J ] . 生命科学 , 2019 , 31 ( 4 ): 46 - 53 .

CHAI M Z , JIA B , LI B Z , et al . Progress in research on artificial gene assembly and rearrangement [J ] . Chinese Bulletin Life Science , 2019 , 31 ( 4 ): 46 - 53 .

罗周卿 , 戴俊彪 . 合成基因组学:设计与合成的艺术 [J ] . 生物工程学报 , 2017 , 33 ( 3 ): 331 - 342 .

LUO Z Q , DAI J B . Synthetic genomics: the art of design and synthesis [J ] . Chinese Journal of Biotechnology , 2017 , 33 ( 3 ): 331 - 342 .

GUSTAFSSON C , GOVINDARAJAN S , MINSHULL J . Codon bias and heterologous protein expression [J ] . Trends in Biotechnology , 2004 , 22 ( 7 ): 346 - 353 .

CHIN J X , CHUNG B K S , Lee D Y . Codon Optimization OnLine (COOL): a web-based multi-objective optimization platform for synthetic gene design [J ] . Bioinformatics , 2014 , 30 ( 15 ): 2210 - 2212 .

CANNAROZZI G , SCHRAUDOLPH N N , FATY M , et al . A role for codon order in translation dynamics [J ] . Cell , 2010 , 141 ( 2 ): 355 - 367 .

RICHARDSON S M , MITCHELL L A , STRACQUADANIO G , et al . Design of a synthetic yeast genome [J ] . Science , 2017 , 355 ( 6329 ): 1040 - 1044 .

LUO Z , WANG L , WANG Y , et al . Identifying and characterizing SCRaMbLEd synthetic yeast using ReSCuES [J ] . Nature Communications , 2018 , 9 ( 1 ): 1 - 10 .

MA L , LI Y , CHEN X , et al . SCRaMbLE generates evolved yeasts with increased alkali tolerance [J ] . Microbial Cell Factories , 2019 , 18 ( 1 ): 52 .

HOESS R H , WIERZBICKI A , ABREMSKI K . The role of the loxP spacer region in PI site-specific recombination [J ] . Nucleic Acids Research , 1986 , 14 ( 5 ): 2287 - 2300 .

SHEN Y , STRACQUADANIO G , WANG Y , et al . SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes [J ] . Genome Research , 2016 , 26 ( 1 ): 36 - 49 .

JIA B , WU Y , LI B Z , et al . Precise control of SCRaMbLE in synthetic haploid and diploid yeast [J ] . Nature Communications , 2018 , 9 ( 1 ): 1 - 13 .

LIN Q , QI H , WU Y , et al . Robust orthogonal recombination system for versatile genomic elements rearrangement in yeast Saccharomyces cerevisiae [J ] . Scientific Reports , 2015 , 5 : 15249 .

HOCHREIN L , MITCHELL L A , SCHULZ K , et al . L-SCRaMbLE as a tool for light-controlled Cre-mediated recombination in yeast [J ] . Nature Communications , 2018 , 9 ( 1 ): 1 - 10 .

SHEN M J , WU Y , YANG K , et al . Heterozygous diploid and interspecies SCRaMbLEing [J ] . Nature Communications , 2018 , 9 ( 1 ): 1 - 8 .

WU Y , ZHU R Y , Mitchell L A , et al . In vitro DNA SCRaMbLE [J ] . Nature Communications , 2018 , 9 ( 1 ): 1 - 9 .

LIU W , LUO Z , WANG Y , et al . Rapid pathway prototyping and engineering using in vitro and in vivo synthetic genome SCRaMbLE-in methods [J ] . Nature Communications , 2018 , 9 ( 1 ): 1 - 12 .

BLOUNT B A , GOWERS G O F , HO J C H , et al . Rapid host strain improvement by in vivo rearrangement of a synthetic yeast chromosome [J ] . Nature Communications , 2018 , 9 ( 1 ): 1 - 10 .

WANG J , JIA B , XIE Z , et al . Improving prodeoxyviolacein production via multiplex SCRaMbLE iterative cycles [J ] . Frontiers of Chemical Science and Engineering , 2018 , 12 ( 4 ): 806 - 814 .

WANG P X , XU H , LI H , et al . SCRaMbLEing of a synthetic yeast chromosome with clustered essential genes reveals synthetic lethal interactions [J ] . ACS Synthetic Biology , 2020 , 9 ( 5 ): 1181 - 1189 .

LUO Z Q , YU K , XIE S Q , et al . Compacting a synthetic yeast chromosome arm [J ] . Genome Biology , 2021 , 22 . DOI: 10.1186/s 13059-020-02232-8 http://dx.doi.org/10.1186/s13059-020-02232-8 .

GORYSHIN I Y , NAUMANN T A , APODACA J , et al . Chromosomal deletion formation system based on Tn5 double transposition: use for making minimal genomes and essential gene analysis [J ] . Genome Research , 2003 , 13 ( 4 ): 644 - 653 .

KUMAGAI H , SASAKI M , IDIRIS A , et al . Minimum genome factories in Schizosaccharomyces pombe [M ] // Microbial production , Tokyo : Springer , 2014 : 17 - 24 .

BOEKE J D , CHURCH G , HESSEL A , et al . The genome project-write [J ] . Science , 2016 , 353 ( 6295 ): 126 - 127 .

MEINKE G , BOHM A , HAUBER J , et al . Cre recombinase and other tyrosine recombinases [J ] . Chemical Reviews , 2016 , 116 ( 20 ): 12785 - 12820 .

Views

下载量

CSCD

Alert me when the article has been cited

提交

Tools

Publicity Resources

Research progress of synthetic mammalian genomics

Reading, editing, and writing techniques for genome research

Related Author

Jun-Yi WANG

Xiao-le WU

Yue-Yang CAO

Bing-Zhi LI

HE Bo

FU Zongheng

WU Yi

ZHAO Guangrong

Related Institution

Frontiers Science Center for Synthetic Biology， Key Laboratory of Systems Bioengineering （Ministry of Education）， School of Chemical Engineering and Technology， Tianjin University

College of Life Sciences and Oceanography， Shenzhen University

Guangdong Provincial Key Laboratory of Synthetic Genomics， Shenzhen Key Laboratory of Synthetic Genomics， Center for Synthetic Genomics， Shenzhen Institute of Synthetic Biology， Shenzhen Institutes of Advanced Technology， Chinese Academy of Sciences

Frontiers Science Center for Synthetic Biology， Key Laboratory of Systems Bioengineering （Ministry of Education）， School of Chemical Engineering and Technology， Tianjin University

⁰