Recent advances in synthetic biology

doi:10.11949/j.issn.0438-1157.20150648

Abstract

Abstract:

Synthetic biology is the engineering design and construction of standardized parts, devices and modules to modify the natural life systems or the de novo synthesis of new life systems. Synthetic biology has been widely applied to the fields of chemical synthesis (including materials, biofuels and natural compounds), medical industry, agriculture and environmental protection. Biological parts are used to construct synthetic modules such as toggle switch, synthetic oscillator, genetic amplifier, biologic gates and cellular counter. These synthetic modules reprogram life systems to perform specific functions. Modularized metabolic pathways are optimized in the cellular chassis to realize the biological production of bulk and fine chemicals, such as butanol, isobutanol, artemisinin, and taxol. In recent years, researchers have also developed several genome-editing and DNA assembly techniques, making it possible to perform the precise editing and synthesis of genomes. Moreover, genomes of bacteriophage, Mycoplasma genitalium and Saccharomyces cerevisiae have also been successfully synthesized. In the next 50—100 years, synthetic biology will have significant influence on medical industry, chemical (including drugs) synthesis and military affairs. Synthetic biology will have a gradual but disruptive meaning to the world.

Key words: synthetic biology, biochemical engineering, metablism, parts and devices, modules, genetic circuit, chemical synthesis, genome

摘要：

合成生物学是以工程化设计思路,构建标准化的元器件和模块,改造已存在的天然系统或者从头合成全新的人工生命体系,实现在化学品合成(包括材料、能源和天然化合物)、医学、农业、环境等领域的应用。人们利用基本的生物学元件设计和构建了基因开关、振荡器、放大器、逻辑门、计数器等合成器件,实现对生命系统的重新编程并执行特殊功能。模块化处理生物的代谢途径,并在底盘细胞上进行组装和优化,可以实现大宗化学品和精细化学品的合成。目前人们已经在丁醇、异丁醇、青蒿素和紫杉醇等化合物的生物合成上取得了重要进展。近年来还发展了多种基因组编辑和组装技术,可精确地对基因组进行编辑,人们还成功地合成了噬菌体基因组、支原体基因组和酵母基因组。在未来的50～100年内,合成生物学将对人类的医疗、化学品制造(含药品)、军事产生渐进性的、渗透性的但颠覆性的意义。

关键词: 合成生物学, 生化工程, 代谢, 元器件, 模块, 基因线路, 化学品合成, 基因组

CLC Number:

LIN Zhanglin, ZHANG Yan, WANG Xu, LIU Peng. Recent advances in synthetic biology[J]. CIESC Journal, 2015, 66(8): 2863-2871.

林章凛, 张艳, 王胥, 刘鹏. 合成生物学研究进展[J]. 化工学报, 2015, 66(8): 2863-2871.

References 58

[1]	Huang G T. 10 emerging technologies that will change your world [J]. Technology Review, 2004, 107(1): 32-50.
[2]	Singh V. Recent advancements in synthetic biology: current status and challenges [J]. Gene, 2014, 535(1): 1-11.
[3]	Purnick P E M, Weiss R. The second wave of synthetic biology: from modules to systems [J]. Nature Reviews Molecular Cell Biology, 2009, 10(6): 410-422.
[4]	Miksch G, Bettenworth F, Friehs K, Flaschel E, Saalbach A, Nattkemper T W. A rapid reporter system using GFP as a reporter protein for identification and screening of synthetic stationary-phase promoters in Escherichia coli [J]. Applied Microbiology and Biotechnology, 2006, 70(2): 229-236.
[5]	Miksch G, Bettenworth F, Friehs K, Flaschel E, Saalbach A, Twellmann T, Nattkemper T W. Libraries of synthetic stationary-phase and stress promoters as a tool for fine-tuning of expression of recombinant proteins in Escherichia coli [J]. Journal of Biotechnology, 2005, 120(1): 25-37.
[6]	Chen Y J, Liu P, Nielsen A A K, Brophy J A N, Clancy K, Peterson T, Voigt C A. Characterization of 582 natural and synthetic terminators and quantification of their design constraints [J]. Nature Methods, 2013, 10(7): 659-664.
[7]	Levin-Karp A, Barenholz U, Bareia T, Dayagi M, Zelcbuch L, Antonovsky N, Noor E, Milo R. Quantifying translational coupling in E. coli synthetic operons using RBS modulation and fluorescent reporters [J]. ACS Synthetic Biology, 2013, 2(6): 327-336.
[8]	Wittmann A, Suess B. Engineered riboswitches: expanding researchers' toolbox with synthetic RNA regulators [J]. FEBS Letters, 2012, 586(15): 2076-2083.
[9]	Gardner T S, Cantor C R, Collins J J. Construction of a genetic toggle switch in Escherichia coli [J]. Nature, 2000, 403(6767): 339-342.
[10]	Levskaya A, Chevalier A A, Tabor J J, Simpson Z B, Lavery L A, Levy M, Davidson E A, Scouras A, Ellington A D, Marcotte E M, Voigt C A. Synthetic biology: engineering Escherichia coli to see light [J]. Nature, 2005, 438(7067): 441-442.
[11]	Elowitz M B, Leibler S. A synthetic oscillatory network of transcriptional regulators [J]. Nature, 2000, 403(6767): 335-338.
[12]	Nistala G J, Wu K, Rao C V, Bhalerao K D. A modular positive feedback-based gene amplifier [J]. Journal of Biological Engineering, 2010, 4: 4.
[13]	Wang B J, Kitney R I, Joly N, Buck M. Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology [J]. Nature Communications, 2011, 2: 508.
[14]	Ikeda R A, Richardson C C. Interactions of a proteolytically nicked RNA-polymerase of bacteriophage-T7 with its promoter [J]. Journal of Biological Chemistry, 1987, 262(8): 3800-3808.
[15]	Segall-Shapiro T H, Meyer A J, Ellington A D, Sontag E D, Voigt C A. A ‘resource allocator' for transcription based on a highly fragmented T7 RNA polymerase [J]. Molecular Systems Biology, 2014, 10: 742.
[16]	Shis D L, Bennett M R. Synthetic biology: the many facets of T7 RNA polymerase [J]. Molecular Systems Biology, 2014, 10(7): 745.
[17]	Friedland A E, Lu T K, Wang X, Shi D, Church G, Collins J J. Synthetic gene networks that count [J]. Science, 2009, 324(5931): 1199-1202.
[18]	Daniel R, Rubens J R, Sarpeshkar R, Lu T K. Synthetic analog computation in living cells [J]. Nature, 2013, 497(7451): 619-623.
[19]	Li F, Hinderberger J, Seedorf H, Zhang J, Buckel W, Thauer R K. Coupled ferredoxin and crotonyl coenzyme a (CoA) reduction with NADH catalyzed by the butyryl-CoA dehydrogenase/Etf complex from Clostridium kluyveri [J]. Journal of Bacteriology, 2008, 190(3): 843-850.
[20]	Lan E I, Liao J C. Microbial synthesis of n-butanol, isobutanol, and other higher alcohols from diverse resources [J]. Bioresource Technology, 2013, 135: 339-349.
[21]	Atsumi S, Hanai T, Liao J C. Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels [J]. Nature, 2008, 451(7174): 86-89.
[22]	Baez A, Cho K M, Liao J C. High-flux isobutanol production using engineered Escherichia coli: a bioreactor study with in situ product removal [J]. Applied Microbiology and Biotechnology, 2011, 90(5): 1681-1690.
[23]	Martin V J J, Pitera D J, Withers S T, Newman J D, Keasling J D. Engineering a mevalonate pathway in Escherichia coli for production of terpenoids [J]. Nature Biotechnology, 2003, 21(7): 796-802.
[24]	Ro D K, Paradise E M, Ouellet M, Fisher K J, Newman K L, Ndungu J M, Ho K A, Eachus R A, Ham T S, Kirby J, Chang M C Y, Withers S T, Shiba Y, Sarpong R, Keasling J D. Production of the antimalarial drug precursor artemisinic acid in engineered yeast [J]. Nature, 2006, 440(7086): 940-943.
[25]	Pfleger B F, Pitera D J, D Smolke C, Keasling J D. Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes [J]. Nature Biotechnology, 2006, 24(8): 1027-1032.
[26]	Paddon C J, Westfall P J, Pitera D J, Benjamin K, Fisher K, Mcphee D, Leavell M D, Tai A, Main A, Eng D, Polichuk D R, Teoh K H, Reed D W, Treynor T, Lenihan J, Fleck M, Bajad S, Dang G, Dengrove D, Diola D, Dorin G, Ellens K W, Fickes S, Galazzo J, Gaucher S P, Geistlinger T, Henry R, Hepp M, Horning T, Iqbal T, Jiang H, Kizer L, Lieu B, Melis D, Moss N, Regentin R, Secrest S, Tsuruta H, Vazquez R, Westblade L F, Xu L, Yu M, Zhang Y, Zhao L, Lievense J, Covello P S, Keasling J D, Reiling K K, Renninger N S, Newman J D. High-level semi-synthetic production of the potent antimalarial artemisinin [J]. Nature, 2013, 496(7446): 528-532.
[27]	Dueber J E, Wu G C, Malmirchegini G R, Moon T S, Petzold C J, Ullal A V, Prather K L J, Keasling J D. Synthetic protein scaffolds provide modular control over metabolic flux [J]. Nature Biotechnology, 2009, 27(8): 753-759.
[28]	Ajikumar P K, Xiao W H, Tyo K E, Wang Y, Simeon F, Leonard E, Mucha O, Phon T H, Pfeifer B, Stephanopoulos G. Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli [J]. Science, 2010, 330(6000): 70-74.
[29]	Zhang Y H P. Production of biocommodities and bioelectricity by cell-free synthetic enzymatic pathway biotransformations: challenges and opportunities [J]. Biotechnology and Bioengineering, 2010, 105(4): 663-677.
[30]	Zhang Y H P, Evans B R, Mielenz J R, Hopkins R C, Adams M W W. High-yield hydrogen production from starch and water by a synthetic enzymatic pathway [J]. PLOS ONE, 2007, 2(5): e456.
[31]	Cheng Q, Xiang L, Izumikawa M, Meluzzi D, Moore B S. Enzymatic total synthesis of enterocin polyketides [J]. Nature Chemical Biology, 2007, 3(9): 557-558.
[32]	Balagaddé F K, Song H, Ozaki J, Collins C H, Barnet M, Arnold F H, Quake S R, You L C. A synthetic Escherichia coli predator-prey ecosystem [J]. Molecular Systems Biology, 2008, 4(1): 187.
[33]	Eiteman M A, Lee S A, Altman E. A co-fermentation strategy to consume sugar mixtures effectively [J]. Journal of Biological Engineering, 2008, 2: 3.
[34]	Gasiunas G, Barrangou R, Horvath P, Siksnys V. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria [J]. Proceedings of the National Academy of Sciences of the United States of America, 2012, 109(39): E2579-E2586.
[35]	Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna J A, Charpentier E. A programmable dual-RNA—guided DNA endonuclease in adaptive bacterial immunity [J]. Science, 2012, 337(6096): 816-821.
[36]	Ran F A, Hsu P D, Wright J, Agarwala V, Scott D A, Zhang F. Genome engineering using the CRISPR-Cas9 system [J]. Nature protocols, 2013, 8(11): 2281-2308.
[37]	Boch J, Scholze H, Schornack S, Landgraf A, Hahn S, Kay S, Lahaye T, Nickstadt A, Bonas U. Breaking the code of DNA binding specificity of TAL-Type Ⅲ effectors [J]. Science, 2009, 326(5959): 1509-1512.
[38]	Mali P, Aach J, Stranges P B, Esvelt K M, Moosburner M, Kosuri S, Yang L, Church G M. Cas9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering [J]. Nature Biotechnology, 2013, 31(9): 833-838.
[39]	Wang H H, Isaacs F J, Carr P A, Sun Z Z, Xu G, Forest C R, Church G M. Programming cells by multiplex genome engineering and accelerated evolution [J]. Nature, 2009, 460(7257): 894-898.
[40]	Wang H H, Kim H, Cong L, Jeong J, Bang D, Church G M. Genome-scale promoter engineering by coselection MAGE [J]. Nature Methods, 2012, 9(6): 591-593.
[41]	Isaacs F J, Carr P A, Wang H H, Lajoie M J, Sterling B, Kraal L, Tolonen A C, Gianoulis T A, Goodman D B, Reppas N B. Precise manipulation of chromosomes in vivo enables genome-wide codon replacement [J]. Science, 2011, 333(6040): 348-353.
[42]	Ellis T, Adie T, Baldwin G S. DNA assembly for synthetic biology: from parts to pathways and beyond [J]. Integrative Biology, 2011, 3(2): 109-118.
[43]	Shao Z, Zhao H, Zhao H. DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways [J]. Nucleic Acids Research, 2009, 37(2): e16.
[44]	Tsuge K, Matsui K, Itaya M. One step assembly of multiple DNA fragments with a designed order and orientation in Bacillus subtilis plasmid [J]. Nucleic Acids Research, 2003, 31(21): e133.
[45]	Itaya M, Fujita K, Kuroki A, Tsuge K. Bottom-up genome assembly using the Bacillus subtilis genome vector [J]. Nature Methods, 2008, 5(1): 41-43.
[46]	Bryksin A V, Matsumura I. Overlap extension PCR cloning: a simple and reliable way to create recombinant plasmids [J]. Biotechniques, 2010, 48(6): 463-465.
[47]	Quan J, Tian J. Circular polymerase extension cloning of complex gene libraries and pathways [J]. PLOS ONE, 2009, 4(7): e6441.
[48]	Agmon N, Mitchell L A, Cai Y, Ikushima S, Chuang J, Zheng A, Choi W-J, Martin J A, Caravelli K, Stracquadanio G, Boeke J D. Yeast Golden Gate (yGG) for the efficient assembly of S. cerevisiae transcription units [J]. ACS Synthetic Biology, 2015: Article ASAP.
[49]	Engler C, Kandzia R, Marillonnet S. A one pot, one step, precision cloning method with high throughput capability [J]. PLOS ONE, 2008, 3(11): e3647.
[50]	Gibson D G. Enzymatic assembly of overlapping DNA fragments [J]. Methods Enzymol, 2011, 498: 349-361.
[51]	Gibson D G, Smith H O, Hutchison C A Ⅲ, Venter J C, Merryman C. Chemical synthesis of the mouse mitochondrial genome [J]. Nature Methods, 2010, 7(11): 901-903.
[52]	Gibson D G, Young L, Chuang R Y, Venter J C, Hutchison C A Ⅲ, Smith H O. Enzymatic assembly of DNA molecules up to several hundred kilobases [J]. Nature Methods, 2009, 6(5): 343-345.
[53]	Smith H O, Hutchison C A, Pfannkoch C, Venter J C. Generating a synthetic genome by whole genome assembly: FX174 bacteriophage from synthetic oligonucleotides [J]. Proceedings of the National Academy of Sciences of the United States of America, 2003, 100(26): 15440-15445.
[54]	Gibson D G, Benders G A, Andrews-Pfannkoch C, Denisova E A, Baden-Tillson H, Zaveri J, Stockwell T B, Brownley A, Thomas D W, Algire M A, Merryman C, Young L, Noskov V N, Glass J I, Venter J C, Hutchison C A, Smith H O. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome [J]. Science, 2008, 319(5867): 1215-1220.
[55]	Gibson D G, Glass J I, Lartigue C, Noskov V N, Chuang R Y, Algire M A, Benders G A, Montague M G, Ma L, Moodie M M, Merryman C, Vashee S, Krishnakumar R, Assad-Garcia N, Andrews-Pfannkoch C, Denisova E A, Young L, Qi Z Q, Segall-Shapiro T H, Calvey C H, Parmar P P, Hutchison C A, Smith H O, Venter J C. Creation of a bacterial cell controlled by a chemically synthesized genome [J]. Science, 2010, 329(5987): 52-56.
[56]	Annaluru N, Muller H, Mitchell L A, Ramalingam S, Stracquadanio G, Richardson S M, Dymond J S, Kuang Z, Scheifele L Z, Cooper E M, Cai Y Z, Zeller K, Agmon N, Han J S, Hadjithomas M, Tullman J, Caravelli K, Cirelli K, Guo Z Y, London V, Yeluru A, Murugan S, Kandavelou K, Agier N, Fischer G, Yang K, Martin J A, Bilgel M, Bohutski P, Boulier K M, Capaldo B J, Chang J, Charoen K, Choi W J, Deng P, Dicarlo J E, Doong J, Dunn J, Feinberg J I, Fernandez C, Floria C E, Gladowski D, Hadidi P, Ishizuka I, Jabbari J, Lau C Y L, Lee P A, Li S, Lin D, Linder M E, Ling J, Liu J, Liu J, London M, Ma H, Mao J, Mcdade J E, Mcmillan A, Moore A M, Oh W C, Ouyang Y, Patel R, Paul M, Paulsen L C, Qiu J, Rhee A, Rubashkin M G, Soh I Y, Sotuyo N E, Srinivas V, Suarez A, Wong A, Wong R, Xie W R, Xu Y J, Yu A T, Koszul R, Bader J S, Boeke J D, Chandrasegaran S. Total synthesis of a functional designer eukaryotic chromosome [J]. Science, 2014, 344(6179): 55-58.
[57]	Mizoguchi H, Mori H, Fujio T. Escherichia coli minimum genome factory [J]. Biotechnology and Applied Biochemistry, 2007, 46(3): 157-167.
[58]	Morimoto T, Kadoya R, Endo K, Tohata M, Sawada K, Liu S, Ozawa T, Kodama T, Kakeshita H, Kageyama Y, Manabe K, Kanaya S, Ara K, Ozaki K, Ogasawara N. Enhanced recombinant protein productivity by genome reduction in Bacillus subtilis [J]. DNA Research, 2008, 15(2): 73-81.