基因组再造与重排构建细胞工厂

谢泽雄; 陈祥荣; 肖文海; 李炳志; 元英进

doi:10.11949/0438-1157.20190702

您当前的位置：

首页 >

文章列表页 >

基因组再造与重排构建细胞工厂

综述与专论 | 更新时间：2026-07-24

- 基因组再造与重排构建细胞工厂
- Cell factory construction accelerated by genome synthesis and rearrangement
- 化工学报 2019年70卷第10期页码：3712-3721
- 作者机构：
  
  1.教育部合成生物学前沿科学中心，天津 300072
  2.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
- 作者简介：
  
  谢泽雄（1990—），男，博士，副教授，xzx@tju.edu.cn
  元英进（1963—），男，博士，教授，yjyuan@tju.edu.cn
- 基金信息：
  
  国家自然科学基金项目(21621004;21750001)
- DOI：10.11949/0438-1157.20190702
  中图分类号： TQ 033
- 收稿：2019-06-21，
  
  修回：2019-08-31，
  
  网络首发：2026-07-24，
  
  纸质出版：2019-10-05
- 稿件说明：
移动端阅览
谢泽雄, 陈祥荣, 肖文海, 李炳志, 元英进. 基因组再造与重排构建细胞工厂[J]. 化工学报, 2019, 70(10): 3712-3721

XIE Zexiong, CHEN Xiangrong, XIAO Wenhai, LI Bingzhi, YUAN Yingjin. Cell factory construction accelerated by genome synthesis and rearrangement[J]. CIESC Journal, 2019, 70(10): 3712-3721
谢泽雄, 陈祥荣, 肖文海, 李炳志, 元英进. 基因组再造与重排构建细胞工厂[J]. 化工学报, 2019, 70(10): 3712-3721 DOI： 10.11949/0438-1157.20190702.

XIE Zexiong, CHEN Xiangrong, XIAO Wenhai, LI Bingzhi, YUAN Yingjin. Cell factory construction accelerated by genome synthesis and rearrangement[J]. CIESC Journal, 2019, 70(10): 3712-3721 DOI： 10.11949/0438-1157.20190702.

摘要

细胞工厂能利用微生物细胞制备人类所需能源、药物和化学品。底盘细胞和外源代谢路径的适配是构建高效细胞工厂的核心难题。基因组再造指利用化学合成的核苷酸分子“自下而上”构建生物基因组，基因组诱导重排指通过在全基因组尺度进行DNA序列与结构的人为调控。基因组再造和诱导重排实现了对生命体的创造，增强了模式底盘细胞的遗传稳定性和操作柔性。基因组的适度精简和密码子简化改善细胞对底物、能量的利用效率，提高细胞生理性能的预测性和可控性。基因组重排可诱导染色体发生随机删除、复制、移位和倒置等结构变异，可产生大量性状优良的模式底盘细胞，进而加速代谢路径优化，提高路径和底盘细胞的适配性，为人工细胞工厂快速构建和优化提供了新策略。

Abstract

Cell factories can use microbial cells to produce the energy

drugs

and chemicals that humans need. The adaptation of chassis cells to exogenous metabolic pathways is a core challenge in building efficient cell factories. Genome synthesis refers to the bottom-up construction of a genome from chemically synthesized nucleotides. Genomic induced rearrangement refers to the customized regulation of DNA sequences and structures in genome scale. Genome synthesis and inducible rearrangement have enabled the creation of organisms

enhanced the flexibility of model chassis. Proper genome simplification and codon simplification improve the utilization efficiency of substrates and energy

and improve the predictability and controllability of cell physiological performance. Genomic rearrangement can generate structural variations such as random deletion

replication

translocation and inversion. The rearrangements of synthetic genome accelerate the rapid evolution of chassis and the optimization of metabolic pathways

and improve the adaptability between chassis and pathway. The genome synthesis and inducible rearrangement provide a new strategy for the construction and optimization of cell factories.

关键词

Keywords

references

Breitling R , Takano E . Synthetic biology advances for pharmaceutical production [J ] . Curr. Opin. Biotechnol ., 2015 , 35 : 46 - 51 .

Chang M C , Eachus R A , Trieu W , et al . Engineering Escherichia coli for production of functionalized terpenoids using plant P450s [J ] . Nat. Chem. Biol ., 2007 , 3 ( 5 ): 274 - 277 .

Paddon C J , Keasling J D . Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development [J ] . Nat. Rev. Microbiol ., 2014 , 12 ( 5 ): 355 - 367 .

Hong K K , Nielsen J . Metabolic engineering of Saccharomyces cerevisiae : a key cell factory platform for future biorefineries [J ] . Cell Mol . Life Sci ., 2012 , 69 ( 16 ): 2671 - 2690 .

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

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 .

Pennisi E . Building the ultimate yeast genome [J ] . Science , 2014 , 343 ( 6178 ): 1426 - 1429 .

Sliva A , Yang H , Boeke J D , et al . Freedom and responsibility in synthetic genomics: the synthetic yeast project [J ] . Genetics , 2015 , 200 ( 4 ): 1021 - 1028 .

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 designer eukaryotic chromosome [J ] . Science , 2014 , 344 ( 6179 ): 55 - 58 .

Oliver S G , van der Aart Q J , Agostoni-Carbone M L , et al . The complete DNA sequence of yeast chromosome III [J ] . Nature , 1992 , 357 ( 6373 ): 38 - 46 .

Mercy G , Mozziconacci J , Scolari V F , et al . 3D organization of synthetic and scrambled chromosomes [J ] . Science , 2017 , 355 ( 6329 ): eaaf4597 .

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 .

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

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 .

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 .

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 .

Xie Z X , Liu D , Li B Z , et al . Design and chemical synthesis of eukaryotic chromosomes [J ] . Chem. Soc. Rev ., 2017 , 46 ( 23 ): 7191 - 7207 .

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

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 .

Hutchison C A 3rd , Chuang R Y , Noskov V N , et al . Design and synthesis of a minimal bacterial genome [J ] . Science , 2016 , 351 ( 6280 ): aad6253 .

Goffeau A , Barrell B G , Bussey H , et al . Life with 6000 genes [J ] . Science , 1996 , 274 ( 5287 ): 546 - 547, 563 .

Giaever G , Chu A M , Ni L , et al . Functional profiling of the Saccharomyces cerevisiae genome [J ] . Nature , 2002 , 418 ( 6896 ): 387 - 391 .

Tong A H , Evangelista M , Parsons A B , et al . Systematic genetic analysis with ordered arrays of yeast deletion mutants [J ] . Science , 2001 , 294 ( 5550 ): 2364 - 2368 .

Tong A H , Lesage G , Bader G D , et al . Global mapping of the yeast genetic interaction network [J ] . Science , 2004 , 303 ( 5659 ): 808 - 813 .

Costanzo M , Baryshnikova A , Bellay J , et al . The genetic landscape of a cell [J ] . Science , 2010 , 327 ( 5964 ): 425 - 431 .

Costanzo M , VanderSluis B , Koch E N , et al . A global genetic interaction network maps a wiring diagram of cellular function [J ] . Science , 2016 , 353 ( 6306 ): aaf1420 .

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: X174 bacteriophage from synthetic oligonucleotides [J ] . Proc. Natl. Acad. Sci. USA , 2003 , 100 ( 26 ): 15440 - 15445 .

Chan L Y , Kosuri S , Endy D . Refactoring bacteriophage T7 [J ] . Mol . Syst . Biol ., 2005 , 1 ( 1 ): 2005 . 0018 .

Becker M M , Graham R L , Donaldson E F , et al . Synthetic recombinant bat SARS-like coronavirus is infectious in cultured cells and in mice [J ] . Proc. Natl. Acad. Sci. USA , 2008 , 105 ( 50 ): 19944 - 19949 .

Orlinger K K , Holzer G W , Schwaiger J , et al . An inactivated West Nile Virus vaccine derived from a chemically synthesized cDNA system [J ] . Vaccine , 2010 , 28 ( 19 ): 3318 - 3324 .

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 .

Gibson D G , Smith H O , Hutchison C A , et al . Chemical synthesis of the mouse mitochondrial genome [J ] . Nat . Methods , 2010 , 7 ( 11 ): 901 - 903 .

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

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 ] . Nat . Commun ., 2018 , 9 ( 1 ): 1936 .

Dymond J , Boeke J . The Saccharomyces cerevisiae SCRaMbLE system and genome minimization [J ] . Bioeng. Bugs ., 2012 , 3 ( 3 ): 168 - 171 .

Hoess R H , Wierzbicki A , Abremski K . The role of the loxP spacer region in P1 site-specific recombination [J ] . Nucleic. Acids. Res ., 1986 , 14 ( 5 ): 2287 - 2300 .

Testa G , Stewart A F . Creating a transloxation [J ] . Embo . Reports , 2000 , 1 ( 2 ): 120 - 121 .

Glass J I , Assad-Garcia N , Alperovich N , et al . Essential genes of a minimal bacterium [J ] . Proc. Natl. Acad. Sci. USA , 2006 , 103 ( 2 ): 425 - 430 .

Lajoie M J , Kosuri S , Mosberg J A , et al . Probing the limits of genetic recoding in essential genes [J ] . Science , 2013 , 342 ( 6156 ): 361 - 363 .

Neumann H , Hancock S M , Buning R , et al . A method for genetically installing site-specific acetylation in recombinant histones defines the effects of H3 K56 acetylation [J ] . Mol . Cell , 2009 , 36 ( 1 ): 153 - 163 .

Park H S , Hohn M J , Umehara T , et al . Expanding the genetic code of Escherichia coli with phosphoserine [J ] . Science , 2011 , 333 ( 6046 ): 1151 - 1154 .

Xie J , Schultz P G . A chemical toolkit for proteins—an expanded genetic code [J ] . Nat . Rev . Mol . Cell Biol ., 2006 , 7 ( 10 ): 775 - 782 .

Wang L , Xie J , Schultz P G . Expanding the genetic code [J ] . Annu. Rev. Biophys. Biomol. Struct ., 2006 , 35 : 225 - 249 .

Maxmen A . Synthetic yeast chromosomes help probe mysteries of evolution [J ] . Nature , 2017 , 543 ( 7645 ): 298 - 299 .

Isaacs F J , Carr P A , Wang H H , et al . Precise manipulation of chromosomes in vivo enables genome-wide codon replacement [J ] . Science , 2011 , 333 ( 6040 ): 348 - 353 .

Wang H H , Isaacs F J , Carr P A , et al . Programming cells by multiplex genome engineering and accelerated evolution [J ] . Nature , 2009 , 460 ( 7257 ): 894 - 898 .

Mandell D J , Lajoie M J , Mee M T , et al . Biocontainment of genetically modified organisms by synthetic protein design [J ] . Nature , 2015 , 518 ( 7537 ): 55 - 60 .

Rovner A J , Haimovich A D , Katz S R , et al . Recoded organisms engineered to depend on synthetic amino acids [J ] . Nature , 2015 , 518 ( 7537 ): 89 - 93 .

Ma N J , Moonan D W , Isaacs F J . Precise manipulation of bacterial chromosomes by conjugative assembly genome engineering [J ] . Nat. Protoc ., 2014 , 9 ( 10 ): 2285 - 2300 .

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

Salim H M , Ring K L , Cavalcanti A R . Patterns of codon usage in two ciliates that reassign the genetic code: Tetrahymena thermophila and Paramecium tetraurelia [J ] . Protist , 2008 , 159 ( 2 ): 283 - 298 .

Gorter de Vries A R , Pronk J T , Daran J G . Industrial relevance of chromosomal copy number variation in Saccharomyces yeasts [J ] . Appl . Environ . Microbiol ., 2017 , 83 ( 11 ): e03206 - 16 .

Takagi A , Harashima S , Oshima Y . Construction and characterization of isogenic series of Saccharomyces cerevisiae polyploid strains [J ] . Appl. Environ. Microbiol ., 1983 , 45 ( 3 ): 1034 - 1040 .

Li Y , Wu Y , Ma L , et al . Loss of heterozygosity by SCRaMbLEing [J ] . Sci . China Life Sci ., 2019 , 62 ( 3 ): 381 - 393 .

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

Luo J , Sun X , Cormack B P , et al . Karyotype engineering by chromosome fusion leads to reproductive isolation in yeast [J ] . Nature , 2018 , 560 ( 7718 ): 392 - 396 .

Neurohr G , Naegeli A , Titos I , et al . A midzone-based ruler adjusts chromosome compaction to anaphase spindle length [J ] . Science , 2011 , 332 ( 6028 ): 465 - 468 .

Wang J , Xie Z X , Ma Y , et al . Ring synthetic chromosome V SCRaMbLE [J ] . Nat . Commun ., 2018 , 9 ( 1 ): 3783 .

Weischenfeldt J , Symmons O , Spitz F , et al . Phenotypic impact of genomic structural variation: insights from and for human disease [J ] . Nat. Rev. Genet ., 2013 , 14 ( 2 ): 125 - 138 .

Blount B A , Gowers G F , Ho J C H , et al . Rapid host strain improvement by in vivo rearrangement of a synthetic yeast chromosome [J ] . Nat . Commun ., 2018 , 9 ( 1 ): 1932 .

Jia B , Wu Y , Li B Z , et al . Precise control of SCRaMbLE in synthetic haploid and diploid yeast [J ] . Nat . Commun ., 2018 , 9 ( 1 ): 1933 .

Jullesson D , David F , Pfleger B , et al . Impact of synthetic biology and metabolic engineering on industrial production of fine chemicals [J ] . Biotechnol. Adv ., 2015 , 33 ( 7 ): 1395 - 1402 .

Luo Z , Wang L , Wang Y , et al . Identifying and characterizing SCRaMbLEd synthetic yeast using ReSCuES [J ] . Nat . Commun ., 2018 , 9 ( 1 ): 1930 .

Ma L , Li Y , Chen X , et al . SCRaMbLE generates evolved yeasts with increased alkali tolerance [J ] . Microb . Cell Fact ., 2019 , 18 ( 1 ): 52 .

Shen M J , Wu Y , Yang K , et al . Heterozygous diploid and interspecies SCRaMbLEing [J ] . Nat . Commun ., 2018 , 9 ( 1 ): 1934 .

Fisher A K , Freedman B G , Bevan D R , et al . A review of metabolic and enzymatic engineering strategies for designing and optimizing performance of microbial cell factories [J ] . Comput. Struct. Biotechnol. J ., 2014 , 11 ( 18 ): 91 - 99 .

Wu Y , Zhu R Y , Mitchell L A , et al . In vitro DNA SCRaMbLE [J ] . Nat . Commun ., 2018 , 9 ( 1 ): 1935 .

Hochrein L , Mitchell L A , Schulz K , et al . L-SCRaMbLE as a tool for light-controlled cre-mediated recombination in yeast [J ] . Nat . Commun ., 2018 , 9 ( 1 ): 1931 .

浏览量

下载量

CSCD

文章被引用时，请邮件提醒。

提交

工具集

关联资源

维生素A生物合成的研究进展

代谢工程改造解脂耶氏酵母生产脂肪酸及其衍生物

黑曲霉作为分泌蛋白细胞工厂的研究进展

化学品绿色制造核心技术——合成生物学

过渡金属基氮掺杂炭的构筑及其脱硫性能研究