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The promise of synthetic biology

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Abstract

DNA synthesis has become one of the technological bases of a new concept in biology: synthetic biology. The vision of synthetic biology is a systematic, hierarchical design of artificial, biology-inspired systems using robust, standardized, and well-characterized building blocks. The design concept and examples from four fields of application (genetic circuits, protein design, platform technologies, and pathway engineering) are discussed, which demonstrate the usefulness and the promises of synthetic biology. The vision of synthetic biology is to develop complex systems by simplified solutions using available material and knowledge. Synthetic biology also opens a door toward new biomaterials that do not occur in nature.

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References

  • Alvarez M, Rhodes SJ, Bidwell JP (2003) Context-dependent transcription: all politics is local. Gene 313:43–57

    Article  CAS  PubMed  Google Scholar 

  • Astier Y, Bayley H, Howorka S (2005) Protein components for nanodevices. Curr Opin Chem Biol 9:576–584

    Article  CAS  PubMed  Google Scholar 

  • Austin DW, Allen MS, McCollum JM, Dar RD, Wilgus JR, Sayler GS, Samatova NF, Cox CD, Simpson ML (2006) Gene network shaping of inherent noise spectra. Nature 439:608–611

    Article  CAS  PubMed  Google Scholar 

  • Ball P (2004) Synthetic biology: starting from scratch. Nature 431:624–626

    Article  CAS  PubMed  Google Scholar 

  • Ball P (2005) Synthetic biology for nanotechnology. Nanotechnology 16:R1–R8

    Article  CAS  Google Scholar 

  • Basu S, Gerchman Y, Collins CH, Arnold FH, Weiss R (2005) A synthetic multicellular system for programmed pattern formation. Nature 434:1130–1134

    Article  CAS  PubMed  Google Scholar 

  • Benner SA (2004) Understanding nucleic acids using synthetic chemistry. Acc Chem Res 37:784–797

    Article  CAS  PubMed  Google Scholar 

  • Benner SA, Sismour AM (2005) Synthetic biology. Nat Rev Genet 6:533–543

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bolon DN, Voigt CA, Mayo SL (2002) De novo design of biocatalysts. Curr Opin Chem Biol 6:125–129

    Article  CAS  PubMed  Google Scholar 

  • Brent R (2004) A partnership between biology and engineering. Nat Biotechnol 22:1211–1214

    Article  CAS  PubMed  Google Scholar 

  • Coincon M, Heitz A, Chiche L, Derreumaux P (2005) The beta alpha beta alpha beta alpha elementary Supersecondary structure of the Rossmann fold from porcine lactate dehydrogenase exhibits characteristics of a molten globule. Proteins Struct Funct Bioinform 60:740–745

    Article  CAS  Google Scholar 

  • Dattelbaum JD, Looger LL, Benson DE, Sali KM, Thompson RB, Hellinga HW (2005) Analysis of allosteric signal transduction mechanisms in an engineered fluorescent maltose biosensor. Protein Sci 14:284–291

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dueber JE, Yeh BJ, Bhattacharyya RP, Lim WA (2004) Rewiring cell signaling: the logic and plasticity of eukaryotic protein circuitry. Curr Opin Struct Biol 14:690–699

    Article  CAS  PubMed  Google Scholar 

  • Dwyer MA, Looger LL, Hellinga HW (2004) Computational design of a biologically active enzyme. Science 304:1967–1971

    Article  CAS  PubMed  Google Scholar 

  • Endy D (2005) Foundations for engineering biology. Nature 438:449–453

    Article  CAS  PubMed  Google Scholar 

  • Endy D, You L, Yin J, Molineux IJ (2000) Computation, prediction, and experimental tests of fitness for bacteriophage T7 mutants with permuted genomes. Proc Natl Acad Sci USA 97:5375–5380

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ferber D (2004) Synthetic biology. Microbes made to order. Science 303:158–161

    Article  CAS  PubMed  Google Scholar 

  • Gil R, Silva FJ, Pereto J, Moya A (2004) Determination of the core of a minimal bacterial gene set. Microbiol Mol Biol Rev 68:518–537

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gilmore MA, Steward LE, Chamberlin AR (1999) Incorporation of noncoded amino acids by in vitro protein biosynthesis. In: Schmidtchen FP (ed) Implementation and redesign of catalytic function in biopolymers. Springer, Berlin

    Google Scholar 

  • Glass JI, Assad-Garcia N, Alperovich N, Yooseph S, Lewis MR, Maruf M, Hutchison CA 3rd, Smith HO, Venter JC (2006) Essential genes of a minimal bacterium. Proc Natl Acad Sci USA 103:425–430

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hecht MH, Richardson JS, Richardson DC, Ogden RC (1990) De novo design, expression, and characterization of Felix: a four-helix bundle protein of native-like sequence. Science 249:884–891

    Article  CAS  PubMed  Google Scholar 

  • Hederos S, Tegler L, Carlsson J, Persson B, Viljanen J, Broo KS (2006) A promiscuous glutathione transferase transformed into a selective thiolester hydrolase. Org Biomol Chem 4:90–97

    Article  CAS  PubMed  Google Scholar 

  • Herrera S (2005) Synthetic biology offers alternative pathways to natural products. Nat Biotechnol 23:270–271

    Article  CAS  PubMed  Google Scholar 

  • Hocker B, Claren J, Sterner R (2004) Mimicking enzyme evolution by generating new (betaalpha)8-barrels from (betaalpha)4-half-barrels. Proc Natl Acad Sci USA 101:16448–16453

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Howard PL, Chia MC, Del Rizzo S, Liu FF, Pawson T (2003) Redirecting tyrosine kinase signaling to an apoptotic caspase pathway through chimeric adaptor proteins. Proc Natl Acad Sci USA 100:11267–11272

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kodumal SJ, Patel KG, Reid R, Menzella HG, Welch M, Santi DV (2004) Total synthesis of long DNA sequences: synthesis of a contiguous 32-kb polyketide synthase gene cluster. Proc Natl Acad Sci USA 101:15573–15578

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kolisnychenko V, Plunkett G 3rd, Herring CD, Feher T, Posfai J, Blattner FR, Posfai G (2002) Engineering a reduced Escherichia coli genome. Genome Res 12:640–647

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kortemme T, Ramirez-Alvarado M, Serrano L (1998) Design of a 20-amino acid, three-stranded beta-sheet protein. Science 281:253–256

    Article  CAS  PubMed  Google Scholar 

  • Kramer BP, Fischer M, Fussenegger M (2005) Semi-synthetic mammalian gene regulatory networks. Metab Eng 7:241–250

    Article  CAS  PubMed  Google Scholar 

  • Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D (2003) Design of a novel globular protein fold with atomic-level accuracy. Science 302:1364–1368

    Article  CAS  PubMed  Google Scholar 

  • Langer R, Tirrell DA (2004) Designing materials for biology and medicine. Nature 428:487–492

    Article  CAS  PubMed  Google Scholar 

  • Levskaya A, Chevalier AA, Tabor JJ, Simpson ZB, Lavery LA, Levy M, Davidson EA, Scouras A, Ellington AD, Marcotte EM, Voigt CA (2005) Synthetic biology: engineering Escherichia coli to see light. Nature 438:441–442

    Article  CAS  PubMed  Google Scholar 

  • Lim WA (2002) The modular logic of signaling proteins: building allosteric switches from simple binding domains. Curr Opin Struct Biol 12:61–68

    Article  CAS  PubMed  Google Scholar 

  • Lombardi A, Summa CM, Geremia S, Randaccio L, Pavone V, DeGrado WF (2000) Inaugural article: retrostructural analysis of metalloproteins: application to the design of a minimal model for diiron proteins. Proc Natl Acad Sci USA 97:6298–6305

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lorenz P, Eck J (2005) Metagenomics and industrial applications. Nat Rev Microbiol 3:510–516

    Article  CAS  PubMed  Google Scholar 

  • Luisi PL, Ferri F, Stano P (2006) Approaches to semi-synthetic minimal cells: a review. Naturwissenschaften 93:1–13

    Article  CAS  PubMed  Google Scholar 

  • McDaniel R, Weiss R (2005) Advances in synthetic biology: on the path from prototypes to applications. Curr Opin Biotechnol 16:476–483

    Article  CAS  PubMed  Google Scholar 

  • Menzella HG, Reisinger SJ, Welch M, Kealey JT, Kennedy J, Reid R, Tran CQ, Santi DV (2006) Redesign, synthesis and functional expression of the 6-deoxyerythronolide B polyketide synthase gene cluster. J Ind Microbiol Biotechnol 33:22–28

    Article  CAS  PubMed  Google Scholar 

  • Panke S, Wubbolts M (2005) Advances in biocatalytic synthesis of pharmaceutical intermediates. Curr Opin Chem Biol 9:188–194

    Article  CAS  Google Scholar 

  • Park S, Yang X, Saven JG (2004) Advances in computational protein design. Curr Opin Struct Biol 14:487–494

    Article  CAS  PubMed  Google Scholar 

  • Park HS, Nam SH, Lee JK, Yoon CN, Mannervik B, Benkovic SJ, Kim HS (2006) Design and evolution of new catalytic activity with an existing protein scaffold. Science 311:535–538

    Article  CAS  PubMed  Google Scholar 

  • Pawson T, Linding R (2005) Synthetic modular systems—reverse engineering of signal transduction. FEBS Lett 579:1808–1814

    Article  CAS  PubMed  Google Scholar 

  • Raab RM, Tyo K, Stephanopoulos G (2005) Metabolic engineering. Adv Biochem Eng Biotechnol 100:1–17

    CAS  PubMed  Google Scholar 

  • Rackham O, Chin JW (2005) Cellular logic with orthogonal ribosomes. J Am Chem Soc 127:17584–17585

    Article  CAS  PubMed  Google Scholar 

  • Scott P (2003) The wrong stuff?: attempts at flight before (& after) the Wright brothers. Hylas Publishing, New York

    Google Scholar 

  • Simpson ML, Cox CD, Sayler GS (2003) Frequency domain analysis of noise in autoregulated gene circuits. Proc Natl Acad Sci USA 100:4551–4556

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Smith HO, Hutchison CA 3rd, Pfannkoch C, Venter JC (2003) Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides. Proc Natl Acad Sci USA 100:15440–15445

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sprinzak D, Elowitz MB (2005) Reconstruction of genetic circuits. Nature 438:443–448

    Article  CAS  PubMed  Google Scholar 

  • Stromgaard A, Jensen AA, Stromgaard K (2004) Site-specific incorporation of unnatural amino acids into proteins. Chembiochem 5:909–916

    Article  CAS  PubMed  Google Scholar 

  • Svendsen A (2004) Enzyme functionality: design, engineering, and screening. CRC, Boca Raton, FL

    Google Scholar 

  • Tian J, Gong H, Sheng N, Zhou X, Gulari E, Gao X, Church G (2004) Accurate multiplex gene synthesis from programmable DNA microchips. Nature 432:1050–1054

    Article  CAS  PubMed  Google Scholar 

  • Walter KU, Vamvaca K, Hilvert D (2005) An active enzyme constructed from a 9-amino acid alphabet. J Biol Chem 280:37742–37746

    Article  CAS  PubMed  Google Scholar 

  • Wang L, Brock A, Herberich B, Schultz PG (2001) Expanding the genetic code of Escherichia coli. Science 292:498–500

    Article  CAS  PubMed  Google Scholar 

  • Xie J, Schultz PG (2005) Adding amino acids to the genetic repertoire. Curr Opin Chem Biol 9:548–554

    Article  CAS  PubMed  Google Scholar 

  • Yokobayashi Y, Weiss R, Arnold FH (2002) Directed evolution of a genetic circuit. Proc Natl Acad Sci USA 99:16587–16591

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zotchev SB, Stepanchikova AV, Sergeyko AP, Sobolev BN, Filimonov DA, Poroikov VV (2006) Rational design of macrolides by virtual screening of combinatorial libraries generated through in silico manipulation of polyketide synthases. J Med Chem 49:2077–2087

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

Inspiration and financial support from the EU-NEST program on synthetic biology (EUROBIOSYN) are greatly acknowledged. I am especially grateful for the fruitful discussions with Homme W. Hellinga and Sven Panke and for the constructive criticism by the unknown reviewers.

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  1. Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany

    Jürgen Pleiss

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Pleiss, J. The promise of synthetic biology. Appl Microbiol Biotechnol 73, 735–739 (2006). https://doi.org/10.1007/s00253-006-0664-3

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  • DOI: https://doi.org/10.1007/s00253-006-0664-3

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