The promise of synthetic biology

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.

[1]  E M Judd,et al.  Toggles and oscillators: new genetic circuit designs. , 2000, BioEssays : news and reviews in molecular, cellular and developmental biology.

[2]  R. Weiss,et al.  Advances in synthetic biology: on the path from prototypes to applications. , 2005, Current opinion in biotechnology.

[3]  Pasquale Stano,et al.  Approaches to semi-synthetic minimal cells: a review , 2005, Naturwissenschaften.

[4]  M. Elowitz,et al.  Reconstruction of genetic circuits , 2005, Nature.

[5]  Sarah J Kodumal,et al.  Total synthesis of long DNA sequences: synthesis of a contiguous 32-kb polyketide synthase gene cluster. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[6]  L. Serrano,et al.  Engineering stability in gene networks by autoregulation , 2000, Nature.

[7]  Philip Ball,et al.  Synthetic biology: Starting from scratch , 2004, Nature.

[8]  A. P. Sergeyko,et al.  Rational design of macrolides by virtual screening of combinatorial libraries generated through in silico manipulation of polyketide synthases. , 2006, Journal of medicinal chemistry.

[9]  J. Shanks,et al.  Metabolic engineering of plants for alkaloid production. , 2002, Metabolic engineering.

[10]  Christopher M Thomas,et al.  The bacterial ParA-ParB partitioning proteins. , 2001, Journal of biotechnology.

[11]  R. Weiss,et al.  Directed evolution of a genetic circuit , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[12]  S. Howorka,et al.  Protein components for nanodevices. , 2005, Current opinion in chemical biology.

[13]  S. Basu,et al.  Spatiotemporal control of gene expression with pulse-generating networks. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[14]  S. Irmler,et al.  Indole alkaloid biosynthesis in Catharanthus roseus: new enzyme activities and identification of cytochrome P450 CYP72A1 as secologanin synthase. , 2000, The Plant journal : for cell and molecular biology.

[15]  Improvement of the pBRINT-Ts plasmid family to obtain marker-free chromosomal insertion of cloned DNA in E. coli. , 2001, BioTechniques.

[16]  L Serrano,et al.  Design of a 20-amino acid, three-stranded beta-sheet protein. , 1998, Science.

[17]  Steven A Benner,et al.  Understanding nucleic acids using synthetic chemistry. , 2004, Accounts of chemical research.

[18]  J. Keasling,et al.  Engineering a mevalonate pathway in Escherichia coli for production of terpenoids , 2003, Nature Biotechnology.

[19]  B. Wanner,et al.  One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[20]  Loren L Looger,et al.  Computational design of receptors for an organophosphate surrogate of the nerve agent soman. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[21]  B. Höcker,et al.  Mimicking enzyme evolution by generating new (betaalpha)8-barrels from (betaalpha)4-half-barrels. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Martin Fussenegger,et al.  Semi-synthetic mammalian gene regulatory networks. , 2005, Metabolic engineering.

[23]  C. Khosla,et al.  Manipulation and analysis of polyketide synthases. , 2004, Methods in enzymology.

[24]  Kazuo Tanaka,et al.  DNA logic gates. , 2004, Journal of the American Chemical Society.

[25]  M. Elowitz,et al.  Combinatorial Synthesis of Genetic Networks , 2002, Science.

[26]  Xueyan Ma,et al.  Heterologous expression of a Rauvolfia cDNA encoding strictosidine glucosidase, a biosynthetic key to over 2000 monoterpenoid indole alkaloids. , 2002, European journal of biochemistry.

[27]  Christopher A. Voigt,et al.  De novo design of biocatalysts. , 2002, Current opinion in chemical biology.

[28]  S. Basu,et al.  A synthetic multicellular system for programmed pattern formation , 2005, Nature.

[29]  Jürgen Eck,et al.  Metagenomics and industrial applications , 2005, Nature Reviews Microbiology.

[30]  R. Reid,et al.  Redesign, synthesis and functional expression of the 6-deoxyerythronolide B polyketide synthase gene cluster , 2005, Journal of Industrial Microbiology and Biotechnology.

[31]  Michael J MacCoss,et al.  Computational analysis of shotgun proteomics data. , 2005, Current opinion in chemical biology.

[32]  Peter G Schultz,et al.  Adding amino acids to the genetic repertoire. , 2005, Current opinion in chemical biology.

[33]  B. Persson,et al.  A promiscuous glutathione transferase transformed into a selective thiolester hydrolase. , 2006, Organic & biomolecular chemistry.

[34]  J. Collins,et al.  Programmable cells: interfacing natural and engineered gene networks. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[35]  Wendell A Lim,et al.  The modular logic of signaling proteins: building allosteric switches from simple binding domains. , 2002, Current opinion in structural biology.

[36]  Sven Panke,et al.  Advances in biocatalytic synthesis of pharmaceutical intermediates. , 2005, Current opinion in chemical biology.

[37]  Donald Hilvert,et al.  An Active Enzyme Constructed from a 9-Amino Acid Alphabet* , 2005, Journal of Biological Chemistry.

[38]  Farren J. Isaacs,et al.  Synthetic biology evolves. , 2004, Trends in biotechnology.

[39]  K. Strømgaard,et al.  Site‐Specific Incorporation of Unnatural Amino Acids into Proteins , 2004, Chembiochem : a European journal of chemical biology.

[40]  J. Chin,et al.  Cellular logic with orthogonal ribosomes. , 2005, Journal of the American Chemical Society.

[41]  D. Lane,et al.  The parAB gene products of Pseudomonas putida exhibit partition activity in both P. putida and Escherichia coli , 2002, Molecular microbiology.

[42]  J. Richardson,et al.  De novo design, expression, and characterization of Felix: a four-helix bundle protein of native-like sequence. , 1990, Science.

[43]  S. Rhodes,et al.  Context-dependent transcription: all politics is local. , 2003, Gene.

[44]  Sung-Hun Nam,et al.  Design and Evolution of New Catalytic Activity with an Existing Protein Scaffold , 2006, Science.

[45]  Guy Plunkett,et al.  Engineering a reduced Escherichia coli genome. , 2002, Genome research.

[46]  J Craig Venter,et al.  Generating a synthetic genome by whole genome assembly: φX174 bacteriophage from synthetic oligonucleotides , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[47]  D. Cane,et al.  Precursor-directed biosynthesis: biochemical basis of the remarkable selectivity of the erythromycin polyketide synthase toward unsaturated triketides. , 2002, Chemistry & biology.

[48]  S. Herrera.  Synthetic biology offers alternative pathways to natural products , 2005, Nature Biotechnology.

[49]  D. E. Benson,et al.  Analysis of allosteric signal transduction mechanisms in an engineered fluorescent maltose biosensor , 2005, Protein science : a publication of the Protein Society.

[50]  Philip Ball,et al.  Synthetic biology for nanotechnology , 2004 .

[51]  R. Langer,et al.  Designing materials for biology and medicine , 2004, Nature.

[52]  P G Schultz,et al.  Expanding the Genetic Code of Escherichia coli , 2001, Science.

[53]  H. Hellinga,et al.  Periplasmic binding proteins: a versatile superfamily for protein engineering. , 2004, Current opinion in structural biology.

[54]  Dan Ferber,et al.  Synthetic biology. Microbes made to order. , 2004, Science.

[55]  G. Church,et al.  Accurate multiplex gene synthesis from programmable DNA microchips , 2004, Nature.

[56]  Christopher A. Voigt,et al.  Synthetic biology: Engineering Escherichia coli to see light , 2005, Nature.

[57]  Wendell A Lim,et al.  Rewiring cell signaling: the logic and plasticity of eukaryotic protein circuitry. , 2004, Current opinion in structural biology.

[58]  D. Endy.  Foundations for engineering biology , 2005, Nature.

[59]  Dan Ferber,et al.  Microbes Made to Order , 2004, Science.

[60]  C. Hutchison,et al.  Essential genes of a minimal bacterium. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[61]  P. Laflamme,et al.  The expanding universe of alkaloid biosynthesis. , 2001, Current opinion in plant biology.

[62]  A. Moya,et al.  Determination of the Core of a Minimal Bacterial Gene Set , 2004, Microbiology and Molecular Biology Reviews.

[63]  A. Chamberlin,et al.  Incorporation of Noncoded Amino Acids by In Vitro Protein Biosynthesis , 1999 .

[64]  Tanja Kortemme,et al.  Design of a 20-Amino Acid, Three-Stranded β-Sheet Protein , 1998 .

[65]  M. L. Simpson,et al.  Frequency domain analysis of noise in autoregulated gene circuits , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[66]  Tony Pawson,et al.  Synthetic modular systems – reverse engineering of signal transduction , 2005, FEBS letters.

[67]  P. Derreumaux,et al.  The βαβαβ elementary supersecondary structure of the Rossmann fold from porcine lactate dehydrogenase exhibits characteristics of a molten globule , 2005 .

[68]  J. Memelink,et al.  Biotransformation of tryptamine and secologanin into plant terpenoid indole alkaloids by transgenic yeast , 2001, Applied Microbiology and Biotechnology.

[69]  D. Endy,et al.  Computation, prediction, and experimental tests of fitness for bacteriophage T7 mutants with permuted genomes. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[70]  E. Pichersky,et al.  Characterization of Geraniol Synthase from the Peltate Glands of Sweet Basil1 , 2004, Plant Physiology.

[71]  Loren L Looger,et al.  Computational Design of a Biologically Active Enzyme , 2004, Science.

[72]  D. Baker,et al.  Design of a Novel Globular Protein Fold with Atomic-Level Accuracy , 2003, Science.

[73]  Sheldon Park,et al.  Advances in computational protein design. , 2004, Current opinion in structural biology.

[74]  Tony Pawson,et al.  Redirecting tyrosine kinase signaling to an apoptotic caspase pathway through chimeric adaptor proteins , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[75]  J. Collins,et al.  Gene regulation: Neutralizing noise in gene networks , 2000, Nature.

[76]  J. Keasling,et al.  The in vivo synthesis of plant sesquiterpenes by Escherichia coli. , 2001, Biotechnology and Bioengineering.

[77]  C M Kao,et al.  Engineered intermodular and intramodular polyketide synthase fusions. , 1997, Chemistry & biology.

[78]  D J Newman,et al.  Natural products in drug discovery and development. , 1997, Journal of natural products.

[79]  C. M. Summa,et al.  INAUGURAL ARTICLE by a Recently Elected Academy Member:Retrostructural analysis of metalloproteins: Application to the design of a minimal model for diiron proteins , 2000 .

[80]  Roger Brent,et al.  A partnership between biology and engineering , 2004, Nature Biotechnology.

[81]  J. Collins,et al.  Construction of a genetic toggle switch in Escherichia coli , 2000, Nature.

[82]  M. L. Simpson,et al.  Gene network shaping of inherent noise spectra , 2006, Nature.

[83]  A. Svendsen.  Enzyme Functionality : Design: Engineering, and Screening , 2003 .