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Synthetic biology: putting synthesis into biology

Advanced Review

Jing Liang, Yunzi Luo, Huimin Zhao

Published Online: Jul 13 2010

DOI: 10.1002/wsbm.104

Full article on Wiley Online Library: HTML PDF

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The ability to manipulate living organisms is at the heart of a range of emerging technologies that serve to address important and current problems in environment, energy, and health. However, with all its complexity and interconnectivity, biology has for many years been recalcitrant to engineering manipulations. The recent advances in synthesis, analysis, and modeling methods have finally provided the tools necessary to manipulate living systems in meaningful ways and have led to the coining of a field named synthetic biology. The scope of synthetic biology is as complicated as life itself—encompassing many branches of science and across many scales of application. New DNA synthesis and assembly techniques have made routine customization of very large DNA molecules. This in turn has allowed the incorporation of multiple genes and pathways. By coupling these with techniques that allow for the modeling and design of protein functions, scientists have now gained the tools to create completely novel biological machineries. Even the ultimate biological machinery—a self‐replicating organism—is being pursued at this moment. The aim of this article is to dissect and organize these various components of synthetic biology into a coherent picture. WIREs Syst Biol Med 2011 3 7–20 DOI: 10.1002/wsbm.104

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Figure 1.

Overview of synthetic biology. This scheme describes the relationship among the various methods used in synthetic biology and different applications of synthetic biology on different levels.

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Figure 2.

Synthesis of large DNA molecules in yeast. (a) Yeast homologous recombination mechanism. DNA fragments sharing an overlap region at 3^′‐ and 5^′‐ends with the neighboring DNA fragments can be assembled into a single larger DNA molecule. (b) Construction of a synthetic M. genitalium genome. Twenty‐five different overlapping DNA segments (blue arrows, 17–35 kb each) composing the genome were co‐transformed into yeast followed by assembly of the entire genome in a single step.

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Figure 3.

Analog‐to‐digital converter. (a) In this example system, the two toggle switches are initially ‘off’, i.e., repressor 2 and repressor 4 are expressed. Separately in a sensor array, repressor 1 has an input dependent promoter with a low input threshold. When input concentration rises above its threshold, repressor 1 is expressed, switching the state of toggle switch 1 to ‘on’. Using another input dependent promoter that has a higher threshold, switch 2 is toggled ‘on’ at a higher input concentration. (b) The corresponding digital response of the example gene switches.

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Figure 4.

Artemisinin biosynthetic pathway. The mevalonate‐based FPP biosynthetic pathway has been assembled from S. cerevisiae (HMG‐CoA synthase, hmgS; N‐terminally truncated HMG‐CoA reductase, thmgR; mevalonate kinase, mk; phosphomevalonate kinase, pmk; and mevalonate diphosphate decarboxylase, mpd) and E. coli (acetoacetyl‐CoA synthase, atoB; IPP isomerase, idi; and FPP synthase, ispA), and expressed in E. coli. The pathway is assembled in two operons, one is responsible for converting acetyl‐CoA to mevalonate, and the other is responsible for converting mevalonate to FPP. Further introduction of amorphadiene synthase (ads), oxidase (p450), and redox partner (cpr) allows the strain to convert FPP to artemisinic acid which can be chemically converted to artemisinin..

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Figure 5.

A synthetic predator–prey ecosystem. The system consists of two engineered bacterial populations that control each other's survival and death. CcdB is a cytotoxic protein that kills the cell and CcdA is its antidote. In the predator, CcdB is constitutively expressed, and will die off without an external signal. The antidote CcdA is expressed only when the predator receives signaling molecules (3OC6HSL) from the prey. At high enough prey concentration, the predator will survive. However, the prey also receives signaling molecules (3OC12HSL) from the predator. In the prey, CcdB is expressed in response to the predator signal. Therefore, in high enough predator concentration, the prey will die.

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References

What`s in a name?. Nat Biotechnol 2009, 27: 1071–1073.
Keasling, JD. Synthetic biology for synthetic chemistry. ACS Chem Biol 2008, 3: 64–76.
Young, E, Alper, H. Synthetic biology: tools to design, build, and optimize cellular processes. J Biomed Biotechnol 2010, 12.
Mukherji, S, van Oudenaarden, A. Synthetic biology: understanding biological design from synthetic circuits. Nat Rev Genet 2009, 10: 859–871.
Yeh, BJ, Lim, WA. Synthetic biology: lessons from the history of synthetic organic chemistry. Nat Chem Biol 2007, 3: 521–525.
Tigges, M, Fussenegger, M. Recent advances in mammalian synthetic biology—design of synthetic transgene control networks. Curr Opin Biotechnol 2009, 20: 449–460.
Purnick, PEM, Weiss, R. The second wave of synthetic biology: from modules to systems. Nat Rev Mol Cell Biol 2009, 10: 410–422.
Benner, SA, Sismour, AM. Synthetic biology. Nat Rev Genet 2005, 6: 533–543.
Marchisio, MA, Stelling, J. Computational design tools for synthetic biology. Curr Opin Biotechnol 2009, 20: 479–485.
Khalil, AS, Collins, JJ. Synthetic biology: applications come of age. Nat Rev Genet 2010, 11: 367–379.
Neumann, H, Neumann‐Staubitz, P. Synthetic biology approaches in drug discovery and pharmaceutical biotechnology. Appl Microbiol Biotechnol 2010, DOI: 10.1007/s00253‐010‐2578‐3
May, M. Engineering a new business. Nat Biotechnol 2009, 27: 1112–1120.
Mueller, S, Coleman, JR, Wimmer, E. Putting synthesis into biology: a viral view of genetic engineering through de novo gene and genome synthesis. Chem Biol 2009, 16: 337–347.
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, CA, Smith, HO. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 2008, 319: 1215–1220.
Gibson, DG, Benders, GA, Axelrod, KC, Zaveri, J, Algire, MA, Moodie, M, Montague, MG, Venter, JC, Smith, HO, Hutchison, CA. One‐step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome. P Natl Acad Sci USA 2008, 105: 20404–20409.
Shao, Z, Zhao, H. Zhao, H. DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways. Nucleic Acids Res 2009, 37: e16.
Dougherty, MJ, Arnold, FH. Directed evolution: new parts and optimized function. Curr Opin Biotechnol 2009, 20: 486–491.
Schmidt‐Dannert, C. Directed evolution of single proteins, metabolic pathways, and viruses. Biochemistry‐US 2001, 40: 13125–13136.
Rubin‐Pitel, SB, Zhao, HM. Recent advances in biocatalysis by directed enzyme evolution. Comb Chem High Throughput Screen 2006, 9: 247–257.
Shivange, AV, Marienhagen, J, Mundhada, H, Schenk, A, Schwaneberg, U. Advances in generating functional diversity for directed protein evolution. Curr Opin Chem Biol 2009, 13: 19–25.
Arnold, FH. Design by directed evolution. Acc Chem Res 1998, 31: 125–131.
Zhao, HM, Chockalingam, K, Chen, ZL. Directed evolution of enzymes and pathways for industrial biocatalysis. Curr Opin Biotechnol 2002, 13: 104–110.
Chockalingam, K, Chen, ZL, Katzenellenbogen, JA, Zhao, HM. Directed evolution of specific receptor‐ligand pairs for use in the creation of gene switches. Proc Natl Acad Sci USA 2005, 102: 5691–5696.
Reetz, MT, Carballeira, JD. Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes. Nat Protoc 2007, 2: 891–903.
Herman, A, Tawfik, DS. Incorporating Synthetic Oligonucleotides via Gene Reassembiv (ISOR): a versatile tool forgenerating targeted libraries. Protein Eng Des Sel 2007, 20: 219–226.
Hidalgo, A, Schliessmann, A, Molina, R, Hermoso, J, Bornscheuer, UT. A one‐pot, simple methodology for cassette randomisation and recombination for focused directed evolution. Protein Eng Des Sel 2008, 21: 567–576.
Kumar, R, Rajagopal, K. Single‐step overlap‐primer‐walk polymerase chain reaction for multiple mutagenesis without overlap extension. Anal Biochem 2008, 377: 105–107.
Deng, QW, Luo, WS, Donnenberg, MS. Rapid site site‐directed domain scanning mutagenesis of enteropathogenic Escherichia coli espD. Biol Proced Online 2007, 18–26.
Röthlisberger, D, Khersonsky, O, Wollacott, AM, Jiang, L, DeChancie, J, Betker, J, Gallaher, JL, Althoff, EA, Zanghellini, A, Dym, O, Albeck, S, Houk, KN, Tawfik, DS, Baker, D. Kemp elimination catalysts by computational enzyme design. Nature 2008, 453: 190–195.
Pitera, DJ, Paddon, CJ, Newman, JD, Keasling, JD. Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli. Metab Eng 2007, 9: 193–207.
Bennett, MR, Hasty, J. Overpowering the component problem. Nat Biotechnol 2009, 27: 450–451.
Ellis, T, Wang, X, Collins, JJ. Diversity‐based, model‐guided construction of synthetic gene networks with predicted functions. Nat Biotechnol 2009, 27: 465–471.
Dueber, JE, Wu, GC, Malmirchegini, GR, Moon, TS, Petzold, CJ, Ullal, AV, Prather, KLJ, Keasling, JD. Synthetic protein scaffolds provide modular control over metabolic flux. Nat Biotechnol 2009, 27: 753–759.
Landrain, TE, Carrera, J, Kirov, B, Rodrigo, G, Jaramillo, A. Modular model‐based design for heterologous bioproduction in bacteria. Curr Opin Biotechnol 2009, 20: 272–279.
Pósfai, G, Plunkett, G, Fehér, T, Frisch, D, Keil, GM, Umenhoffer, K, Kolisnychenko, V, Stahl, B, Sharma, SS, de Arruda, M, Burland, V, Harcum, SW, Blattner, FR. Emergent properties of reduced‐genome Escherichia coli. Science 2006, 312: 1044–1046.
Itaya, M, Tsuge, K, Koizumi, M, Fujita, K. Combining two genomes in one cell: Stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome. Proc Natl Acad Sci USA 2005, 102: 15971–15976.
Chan, LY, Kosuri, S, Endy, D. Refactoring bacteriophage T7. Mol Syst Biol 2005, 1.
Zhang, YX, Perry, K, Vinci, VA, Powell, K, Stemmer, WPC, del Cardayre, SB. Genome shuffling leads to rapid phenotypic improvement in bacteria. Nature 2002, 415: 644–646.
Wang, HH, Isaacs, FJ, Carr, PA, Sun, ZZ, Xu, G, Forest, CR, Church, GM. Programming cells by multiplex genome engineering and accelerated evolution. Nature 2009, 460: 894–898.
Forêt, S, Kassahn, KS, Grasso, LC, Hayward, DC, Iguchi, A, Ball, EE, Miller, DJ. Genomic and microarray approaches to coral reef conservation biology. Coral Reefs 2007, 26: 475–486.
Weniger, M, Engelmann, JC, Schultz, J. Genome expression pathway analysis tool—analysis and visualization of microarray gene expression data under genomic, proteomic and metabolic context. BMC Bioinformatics 2007, 8: 179.
Grandori, C, Mac, J, Siebelt, F, Ayer, DE, Eisenman, RN. Myc‐Max heterodimers activate a DEAD box gene and interact with multiple E box‐related sites in vivo. EMBO J 1996, 15: 4344–4357.
Collas, P. The current state of chromatin immunoprecipitation. Mol Biotechnol 2010, 45: 87–100.
Trapnell, C, Salzberg, SL. How to map billions of short reads onto genomes. Nat Biotechnol 2009, 27: 455–457.
Farnham, PJ. Insights from genomic profiling of transcription factors. Nat Rev Genet 2009, 10: 605–616.
Park, PJ. ChIP‐seq: advantages and challenges of a maturing technology. Nat Rev Genet 2009, 10: 669–680.
Griffiths, WJ, Wang, Y. Mass spectrometry: from proteomics to metabolomics and lipidomics. Chem Soc Rev 2009, 38: 1882–1896.
Domon, B. Mass spectrometry and protein analysis. Science 2006, 312: 212–217.
Bantscheff, M, Schirle, M, Sweetman, G, Rick, J, Kuster, B. Quantitative mass spectrometry in proteomics: a critical review. Anal Bioanal Chem 2007, 389: 1017–1031.
Gygi, SP, Rist, B, Gerber, SA, Turecek, F, Gelb, MH, Aebersold, R. Quantitative analysis of complex protein mixtures using isotope‐coded affinity tags. Nat Biotechnol 1999, 17: 994–999.
Mann, M. Functional and quantitative proteomics using SILAC. Nat Rev Mol Cell Biol 2006, 7: 952–958.
Simon, GM, Cravatt, BF. Activity‐based proteomics of enzyme superfamilies: serine hydrolases as a case study. J Biol Chem 2010, 285: 11051–11055.
Cravatt, BF, Wright, AT, Kozarich, JW. Activity‐based protein profiling: From enzyme chemistry. Annu Rev Biochem 2008, 77: 383–414.
Goldsmith, P, Fenton, H, Morris‐Stiff, G, Ahmad, N, Fisher, J, Prasad, KR. Metabonomics: a useful tool for the future surgeon. J Surg Res 2008, 160: 122–132.
Kizer, L, Pitera, DJ, Pfleger, BF, Keasling, JD. Application of functional genomics to pathway optimization for increased isoprenoid production. Appl Environ Microbiol 2008, 74: 3229–3241.
Kaznessis, YN. Computational methods in synthetic biology. Biotechnol J 2009, 4: 1392–1405.
Cooling, MT, Rouilly, V, Misirli, G, Lawson, J, Yu, T, Hallinan, J, Wipat, A. Standard virtual biological parts: a repository of modular modeling components for synthetic biology. Bioinformatics 2010, 26: 925–931.
Chou, CH, Chang, WC, Chiu, CM, Huang, CC, Huang, HD. FMM: a web server for metabolic pathway reconstruction and comparative analysis. Nucleic Acids Res 2009, 37: W129–W134.
Zhang, Z, Buckler, ES, Casstevens, TM, Bradbury, PJ. Software engineering the mixed model for genome‐wide association studies on large samples. Brief Bioinform 2009, 10: 664–675.
Lehner, B. Modelling genotype–phenotype relationships and human disease with genetic interaction networks. J Exp Biol 2007, 210: 1559–1566.
Durot, M, Bourguignon, PY, Schachter, V. Genome‐scale models of bacterial metabolism: reconstruction and applications. FEMS Microbiol Rev 2009, 33: 164–190.
Mo, ML, Palsson, BO. Understanding human metabolic physiology: a genome‐to‐systems approach. Trends Biotechnol 2009, 27: 37–44.
Appella, DH. Non‐natural nucleic acids for synthetic biology. Curr Opin Chem Biol 2009, 13: 687–696.
Wang, L, Chen, S, Xu, T, Taghizadeh, K, Wishnok, JS, Zhou, X, You, D, Deng, Z, Dedon, PC. Phosphorothioation of DNA in bacteria by dnd genes. Nat Chem Biol 2007, 3: 709–710.
Shaw, BR, Dobrikov, M, Wang, X, Wan, J, He, K, Lin, JL, Li, P, Rait, V, Sergueeva, ZA, Sergueev, D. Reading, writing, and modulating genetic information with boranophosphate mimics of nucleotides, DNA, and RNA. Ann NY Acad Sci 2003, 1002: 12–29.
Renders, M, Lievrouw, R, Krecmerová, M, Holý, A, Herdewijn, P. Enzymatic polymerization of phosphonate nucleosides. Chembiochem 2008, 9: 2883–2888.
Benner, SA. Understanding nucleic acids using synthetic chemistry. Acc Chem Res 2004, 37: 784–797.
Yang, Z, Hutter, D, Sheng, P, Sismour, AM, Benner, SA. Artificially expanded genetic information system: a new base pair with an alternative hydrogen bonding pattern. Nucleic Acids Res 2006, 34: 6095–6101.
Wang, L, Brock, A, Herberich, B, Schultz, PG. Expanding the genetic code of Escherichia coli. Science 2001, 292: 498–500.
Hirao, I, Ohtsuki, T, Fujiwara, T, Mitsui, T, Yokogawa, T, Okuni, T, Nakayama, H, Takio, K, Yabuki, T, Kigawa, T, Kodama, K, Yokogawa, T, Nishikawa, K, Yokoyama, S. An unnatural base pair for incorporating amino acid analogs into proteins. Nat Biotechnol 2002, 20: 177–182.
Ibba, M, Hennecke, H. Towards engineering proteins by site‐directed incorporation in vivo of non‐natural amino acids. Biotechnology (NY) 1994, 12: 678–682.
Liu, W, Brock, A, Chen, S, Chen, S, Schultz, PG. Genetic incorporation of unnatural amino acids into proteins in mammalian cells. Nat Methods 2007, 4: 239–244.
Wang, Q, Parrish, AR, Wang, L. Expanding the genetic code for biological studies. Chem Biol 2009, 16: 323–336.
Rowe, L, Ensor, M, Mehl, R, Daunert, S. Modulating the bioluminescence emission of photoproteins by in vivo site‐directed incorporation of non‐natural amino acids. ACS Chem Biol 2010, DOI: 10.1021/cb9002909
Taira, H, Fukushima, M, Hohsaka, T, Sisido, M. Four‐base codon‐mediated incorporation of non‐natural amino acids into proteins in a eukaryotic cell‐free translation system. J Biosci Bioeng 2005, 99: 473–476.
Leloup, JC, Goldbeter, A. A model for circadian rhythms in Drosophila incorporating the formation of a complex between the PER and TIM proteins. J Biol Rhythms 1998, 13: 70–87.
Hasty, J, McMillen, D, Collins, JJ. Engineered gene circuits. Nature 2002, 420: 224–230.
Lu, TK, Khalil, AS, Collins, JJ. Next‐generation synthetic gene networks. Nat Biotechnol 2009, 27: 1139–1150.
Cadatay, T, Turcotte, M, Elowitz, MB, Garcia‐Ojalvo, J, Süel, GM. Architecture‐dependent noise discriminates functionally analogous differentiation circuits. Cell 2009, 139: 512–522.
Tsuruta, H, Paddon, CJ, Eng, D, Lenihan, JR, Horning, T, Anthony, LC, Regentin, R, Keasling, JD, Renninger, NS, Newman, JD. High‐level production of amorpha‐4,11‐diene, a precursor of the antimalarial agent artemisinin, in Escherichia coli. PLoS ONE 2009, 4: e4489.
van Zyl, WH, Lynd, LR, Den Haan, R, McBride, JE. Consolidated bioprocessing for bioethanol production using Saccharomyces cerevisiae. Adv Biochem Eng Biotechnol 2007, 108: 205–235.
Carere, CR, Sparling, R, Cicek, N, Levin, DB. Third generation biofuels via direct cellulose fermentation. Int J Mol Sci 2008, 9: 1342–1360.
Glass, JI, Assad‐Garcia, N, Alperovich, N, Yooseph, S, Lewis, MR, Maruf, M, Hutchison, CA 3rd, Smith, HO, Venter, JC. Essential genes of a minimal bacterium. Proc Natl Acad Sci USA 2006, 103: 425–430.
Marshall, A. The sorcerer of synthetic genomes. Nat Biotechnol 2009, 27: 1121–1124.
Gibson, DG, Glass, JI, Lartigue, C, Noskov, VN, Chuang, R‐Y, 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 3rd, Smith, HO, Venter, JC. Creation of a bacterial cell controlled by a chemically synthesized genome. Science, DOI: 2010:10.1126/science.1190719
Wimmer, E, Mueller, S, Tumpey, TM, Taubenberger, JK. Synthetic viruses: a new opportunity to understand and prevent viral disease. Nat Biotechnol 2009, 27: 1163–1172.
Budin, I, Szostak, JW. Expanding roles for diverse physical phenomena during the origin of life. Annu Rev Biophys 2010, 39: 245–263.
Balagaddé, FK, Song, H, Ozaki, J, Collins, CH, Barnet, M, Arnold, FH, Quake, SR, You, L. A synthetic Escherichia coli predator‐prey ecosystem. Mol Syst Biol 2008, 4: 187.
Brenner, K, You, L, Arnold, FH. Engineering microbial consortia: a new frontier in synthetic biology. Trends Biotechnol 2008, 26: 483–489.
Alper, H, Stephanopoulos, G. Engineering for biofuels: exploiting innate microbial capacity or importing biosynthetic potential? Nat Rev Microbiol 2009, 7: 715–723.
Morrison, M, Pope, PB, Denman, SE, McSweeney, CS. Plant biomass degradation by gut microbiomes: more of the same or something new? Curr Opin Biotechnol 2009, 20: 358–363.
Eiteman, MA, Lee, SA, Altman, E. A co‐fermentation strategy to consume sugar mixtures effectively. J Biol Eng 2008, 2: 3.

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Jens Nielsen

Jens Nielsen
is a Professor in the Department of Biology and Biological Engineering at Chalmers University of Technology in Göteborg, Sweden. His research focus is on systems biology of metabolism. The yeast Saccharomyces cerevisiae is the lab’s key organism for experimental research, but they also work with Aspergilli oryzae.

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