Synthetic circuits, devices and modules

The aim of synthetic biology is to design artificial biological systems for novel applications. From an engineering perspective, construction of biological systems of defined functionality in a hierarchical way is fundamental to this emerging field. Here, we highlight some current advances on design of several basic building blocks in synthetic biology including the artificial gene control elements, synthetic circuits and their assemblies into devices and modules. Such engineered basic building blocks largely expand the synthetic toolbox and contribute to our understanding of the underlying design principles of living cells.

[1]  S. K. Desai,et al.  Genetic screens and selections for small molecules based on a synthetic riboswitch that activates protein translation. , 2004, Journal of the American Chemical Society.

[2]  J. Liao,et al.  A synthetic gene–metabolic oscillator , 2005, Nature.

[3]  R. Herbst‐Irmer,et al.  Synthesis of chiroptical molecular switches by pd-catalyzed domino reactions. , 2009, Journal of the American Chemical Society.

[4]  Martin Fussenegger,et al.  Self-sufficient control of urate homeostasis in mice by a synthetic circuit , 2010, Nature Biotechnology.

[5]  D. Lafontaine,et al.  Therapeutic applications of ribozymes and riboswitches. , 2010, Current opinion in pharmacology.

[6]  R. Mitra,et al.  TATA is a modular component of synthetic promoters. , 2010, Genome research.

[7]  James C. Liao,et al.  Expanding metabolism for biosynthesis of nonnatural alcohols , 2008, Proceedings of the National Academy of Sciences.

[8]  V. Scaria,et al.  Modulation of microRNA function by synthetic ribozymes. , 2010, Molecular bioSystems.

[9]  Thomas H Segall-Shapiro,et al.  Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome , 2010, Science.

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

[11]  S. Altman,et al.  Rapid selection of accessible and cleavable sites in RNA by Escherichia coli RNase P and random external guide sequences , 2008, Proceedings of the National Academy of Sciences.

[12]  Timothy S. Ham,et al.  Production of the antimalarial drug precursor artemisinic acid in engineered yeast , 2006, Nature.

[13]  C-M Ghim,et al.  Two-component genetic switch as a synthetic module with tunable stability. , 2009, Physical review letters.

[14]  Kate S. Carroll,et al.  Chemical Dissection of an Essential Redox Switch in Yeast , 2022 .

[15]  D. Endy,et al.  Refactoring bacteriophage T7 , 2005, Molecular systems biology.

[16]  E. Siggia,et al.  Analysis of Combinatorial cis-Regulation in Synthetic and Genomic Promoters , 2008, Nature.

[17]  J. Micklefield,et al.  Reengineering orthogonally selective riboswitches , 2010, Proceedings of the National Academy of Sciences.

[18]  N. Ban,et al.  Multiple conformational switches in a GTPase complex control co-translational protein targeting , 2009, Proceedings of the National Academy of Sciences.

[19]  Jason Gertz,et al.  Environment-specific combinatorial cis-regulation in synthetic promoters , 2009, Molecular systems biology.

[20]  J. Keasling,et al.  Microbial production of fatty-acid-derived fuels and chemicals from plant biomass , 2010, Nature.

[21]  Nicolas E. Buchler,et al.  Protein sequestration generates a flexible ultrasensitive response in a genetic network , 2009, Molecular systems biology.

[22]  F. Blattner,et al.  Emergent Properties of Reduced-Genome Escherichia coli , 2006, Science.

[23]  S. Lowe,et al.  Probing tumor phenotypes using stable and regulated synthetic microRNA precursors , 2005, Nature Genetics.

[24]  R. Weiss,et al.  Ultrasensitivity and noise propagation in a synthetic transcriptional cascade. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[25]  E. Winfree,et al.  Construction of an in vitro bistable circuit from synthetic transcriptional switches , 2006, Molecular systems biology.

[26]  J. Stelling,et al.  A tunable synthetic mammalian oscillator , 2009, Nature.

[27]  Tomoaki Hara,et al.  Synthetic translational regulation by an L7Ae-kink-turn RNP switch. , 2010, Nature chemical biology.

[28]  Wade C Winkler,et al.  Riboswitches and the role of noncoding RNAs in bacterial metabolic control. , 2005, Current opinion in chemical biology.

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

[30]  B Demple,et al.  Redox-operated genetic switches: the SoxR and OxyR transcription factors. , 2001, Trends in biotechnology.

[31]  Ji Hee Ha,et al.  Chemical sensing of DNT by engineered olfactory yeast strain. , 2007, Nature chemical biology.

[32]  R. Sprengel,et al.  Tetracycline-controlled genetic switches. , 2007, Handbook of experimental pharmacology.

[33]  J. Collins,et al.  Tuning and controlling gene expression noise in synthetic gene networks , 2010, Nucleic acids research.

[34]  Haisu Ma,et al.  Synthesizing a novel genetic sequential logic circuit: a push-on push-off switch , 2010, Molecular systems biology.

[35]  A. Paul,et al.  Chemical Synthesis of Poliovirus cDNA: Generation of Infectious Virus in the Absence of Natural Template , 2002, Science.

[36]  Chase L. Beisel,et al.  Model-guided design of ligand-regulated RNAi for programmable control of gene expression , 2008, Molecular systems biology.

[37]  W. Stemmer,et al.  Multivalent avimer proteins evolved by exon shuffling of a family of human receptor domains , 2005, Nature biotechnology.

[38]  Christopher A. Voigt,et al.  Spatiotemporal Control of Cell Signalling Using A Light-Switchable Protein Interaction , 2009, Nature.

[39]  L. Tsimring,et al.  A synchronized quorum of genetic clocks , 2009, Nature.

[40]  R. D'Amato,et al.  Exogenous control of mammalian gene expression through modulation of RNA self-cleavage , 2004, Nature.

[41]  M. Elowitz,et al.  A synthetic oscillatory network of transcriptional regulators , 2000, Nature.

[42]  Y. Sugiura,et al.  Design and synthesis of artificial zinc finger proteins. , 2007, Methods in molecular biology.

[43]  B. Suess,et al.  A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo. , 2004, Nucleic acids research.

[44]  G. Georgiou.  How to Flip the (Redox) Switch , 2002, Cell.

[45]  E. Andrianantoandro,et al.  Synthetic biology: new engineering rules for an emerging discipline , 2006, Molecular systems biology.

[46]  Shohei Koide,et al.  Design of protein function leaps by directed domain interface evolution , 2008, Proceedings of the National Academy of Sciences.

[47]  Sangdun Choi,et al.  Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy , 2005, Nature Biotechnology.

[48]  Yukio Sugiura,et al.  New redesigned zinc-finger proteins: design strategy and its application. , 2008, Chemistry.

[49]  Wendell A. Lim,et al.  Rewiring MAP Kinase Pathways Using Alternative Scaffold Assembly Mechanisms , 2003, Science.

[50]  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.

[51]  G. Church,et al.  Synthetic Gene Networks That Count , 2009, Science.

[52]  T. Sera.  Generation of cell-permeable artificial zinc finger protein variants. , 2010, Methods in molecular biology.

[53]  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.

[54]  S. Altman,et al.  Inactivation of expression of several genes in a variety of bacterial species by EGS technology , 2009, Proceedings of the National Academy of Sciences.

[55]  James C Liao,et al.  Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde , 2009, Nature Biotechnology.

[56]  Timothy B. Stockwell,et al.  Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome , 2008, Science.

[57]  Wei Ge,et al.  Synthetic shRNAs as potent RNAi triggers , 2005, Nature Biotechnology.

[58]  M. Bennett,et al.  A fast, robust, and tunable synthetic gene oscillator , 2008, Nature.

[59]  Wendell A. Lim,et al.  Rapid Diversification of Cell Signaling Phenotypes by Modular Domain Recombination , 2010, Science.