Advances in synthetic biology: On the path from prototypes to applications

Current Opinion in Biotechnology

Volumn 16, Issue 4, 2005, Pages 476-483

  McDaniel, Ryan ^a   Weiss, Ron ^a  

^a PRINCETON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOSENSING; GENETIC CIRCUITS; METABOLIC NETWORKS; SYNTHETIC BIOLOGY;

DRUG PRODUCTS; GENES; GENETIC ENGINEERING; MOLECULAR BIOLOGY; OPTIMIZATION; PROTEINS; SYNTHESIS (CHEMICAL); SYSTEMS ANALYSIS;

BIOTECHNOLOGY;

DNA; PROTEIN;

CELL COMMUNICATION; DNA BINDING; ESCHERICHIA COLI; GENE AMPLIFICATION; GENE CONTROL; GENE EXPRESSION PROFILING; MOLECULAR BIOLOGY; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN ENGINEERING; PROTEIN MOTIF; PROTEIN SYNTHESIS; REPRESSOR GENE; REVIEW; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION; STEADY STATE; TRANSCRIPTION INITIATION; VIBRIO FISCHERI;

GENE EXPRESSION REGULATION; MODELS, BIOLOGICAL; MODELS, CHEMICAL; PROTEIN ENGINEERING;

EID: 23444461901     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.copbio.2005.07.002     Document Type: Review

References (50)

1. F. Jacob, and J. Monod Genetic regulatory mechanisms in the synthesis of proteins J Mol Biol 3 1961 318 356
2. J. Monod, and F. Jacob Teleonomic mechanisms in cellular metabolism, growth, and differentiation Cold Spring Harb Symp Quant Biol 26 1961 389 401
3. H.H. McAdams, and L. Shapiro Circuit simulation of genetic networks Science 269 1995 650 656
4. R. Lutz, T. Lozinski, T. Ellinger, and H. Bujard Dissecting the functional program of Escherichia coli promoters: the combined mode of action of Lac repressor and AraC activator Nucleic Acids Res 29 2001 3873 3881
5. R. Lutz, and H. Bujard Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements Nucleic Acids Res 25 1997 1203 1210
6. U. Baron, M. Gossen, and H. Bujard Tetracycline-controlled transcription in eukaryotes: novel transactivators with graded transactivation potential Nucleic Acids Res 25 1997 2723 2729
7. R. Weiss, and S. Basu The device physics of cellular logic gates First Workshop on Non-Silicon Computation 2002 54 61
8. Y. Yokobayashi, R. Weiss, and F.H. Arnold Directed evolution of a genetic circuit Proc Natl Acad Sci USA 99 2002 16587 16591 Describes the rationale for and application of directed evolution towards the fine-tuning and optimization of synthetic gene networks.
9. C.Y. Huang, and J.E. Ferrell Jr. Ultrasensitivity in the mitogen-activated protein kinase cascade Proc Natl Acad Sci USA 93 1996 10078 10083
10. S. Hooshangi, S. Thiberge, and R. Weiss Ultrasensitivity and noise propagation in a synthetic transcriptional cascade Proc Natl Acad Sci USA 102 2005 3581 3586
11. N. Rosenfeld, and U. Alon Response delays and the structure of transcription networks J Mol Biol 329 2003 645 654
12. S.S. Shen-Orr, R. Milo, S. Mangan, and U. Alon Network motifs in the transcriptional regulation network of Escherichia coli Nat Genet 31 2002 64 68
13. J.M. Pedraza, and A. van Oudenaarden Noise propagation in gene networks Science 307 2005 1965 1969
14. N. Rosenfeld, J.W. Young, U. Alon, P.S. Swain, and M.B. Elowitz Gene regulation at the single-cell level Science 307 2005 1962 1965
15. W.J. Blake, M. Kærn, C.R. Cantor, and J.J. Collins Noise in eukaryotic gene expression Nature 422 2003 633 637
16. S. Basu, R. Mehreja, S. Thiberge, M.T. Chen, and R. Weiss Spatiotemporal control of gene expression with pulse-generating networks Proc Natl Acad Sci USA 101 2004 6355 6360
17. S. Mangan, A. Zaslaver, and U. Alon The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks J Mol Biol 334 2003 197 204
18. A. Becskei, and L. Serrano Engineering stability in gene networks by autoregulation Nature 405 2000 590 593
19. N. Rosenfeld, M.B. Elowitz, and U. Alon Negative autoregulation speeds the response times of transcription networks J Mol Biol 323 2002 785 793
20. T.S. Gardner, C.R. Cantor, and J.J. Collins Construction of a genetic toggle switch in Escherichia coli Nature 403 2000 339 342
21. B.P. Kramer, A.U. Viretta, M. Daoud-El-Baba, D. Aubel, W. Weber, and M. Fussenegger An engineered epigenetic transgene switch in mammalian cells Nat Biotechnol 22 2004 867 870
22. M.B. Elowitz, and S. Leibler A synthetic oscillatory network of transcriptional regulators Nature 403 2000 335 338
23. M.B. Elowitz, A.J. Levine, E.D. Siggia, and P.S. Swain Stochastic gene expression in a single cell Science 297 2002 1183 1186 Describes methods for determining a Gene Regulatory Function (GRF) of a promoter by quantifying the relationship between input and output. Also furthered the understanding of both intrinsic and extrinsic noise as they relate to fluctuations in the GRF.
24. M.R. Atkinson, M.A. Savageau, J.T. Myers, and A.J. Ninfa Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli Cell 113 2003 597 607
25. A. Becskei, B. Seraphin, and L. Serrano Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion EMBO J 20 2001 2528 2535
26. M.B. Miller, and B.L. Bassler Quorum sensing in bacteria Annu Rev Microbiol 55 2001 165 199
27. R. Weiss, and T.F. Knight Engineered communications for microbial robotics DNA6: Sixth International Meeting on DNA Based Computers 2000 1 15
28. H. Kobayashi, M. Kaern, M. Araki, K. Chung, T.S. Gardner, C.R. Cantor, and J.J. Collins Programmable cells: interfacing natural and engineered gene networks Proc Natl Acad Sci USA 101 2004 8414 8419 Describes the design and implementation of a few synthetic gene networks that utilize cell-cell communication and a toggle switch to process inputs and affect cell behavior in a programmable fashion in order to realize novel behaviors.
29. J. Garcia-Ojalvo, M.B. Elowitz, and S.H. Strogatz Modeling a synthetic multicellular clock: repressilators coupled by quorum sensing Proc Natl Acad Sci USA 101 2004 10955 10960
30. D. McMillen, N. Kopell, J. Hasty, and J.J. Collins Synchronizing genetic relaxation oscillators by intercell signalling Proc Natl Acad Sci USA 99 2002 679 684
31. S. Basu, Y. Gerchman, C. Collins, F. Arnold, and R. Weiss A synthetic multicellular system for programmed pattern formation Nature 434 2005 1130 1134 Describes an engineered multicellular system that programs E. coli to spatially regulate gene expression using cell-cell communication and form several user-defined artificial patterns.
32. D. Karig, and R. Weiss Signal-amplifying genetic circuit enables in vivo observation of weak promoter activation in the Rhl quorum sensing system Biotechnol Bioeng 89 2005 709 718
33. T. Bulter, S.G. Lee, W.W. Wong, E. Fung, M.R. Connor, and J.C. Liao Design of artificial cell-cell communication using gene and metabolic networks Proc Natl Acad Sci USA 101 2004 2299 2304
34. L. You, R.S. Cox III, R. Weiss, and F.H. Arnold Programmed population control by cell-cell communication and regulated killing Nature 428 2004 868 871
35. S.H. Park, A. Zarrinpar, and W.A. Lim Rewiring MAP kinase pathways using alternative scaffold assembly mechanisms Science 299 2003 1061 1064 The authors engineered a novel fusion scaffold using proteins from yeast signaling pathways, providing insight into normal scaffold function and creating a new input/output signaling module in yeast.
36. L.L. Looger, M.A. Dwyer, J.J. Smith, and H.W. Hellinga Computational design of receptor and sensor proteins with novel functions Nature 423 2003 185 190
37. V.J. Martin, D.J. Pitera, S.T. Withers, J.D. Newman, and J.D. Keasling Engineering a mevalonate pathway in Escherichia coli for production of terpenoids Nat Biotechnol 21 2003 796 802 Describes an engineered pathway that creates a precursor to the drug artemisinin. This system has immediate application in supplementing the short supply of this malarial cure.
38. E.S. Gilbert, A.W. Walker, and J.D. Keasling A constructed microbial consortium for biodegradation of the organophosphorus insecticide parathion Appl Microbiol Biotechnol 61 2003 77 81
39. M.A. Dwyer, L.L. Looger, and H.W. Hellinga Computational design of a biologically active enzyme Science 304 2004 1967 1971
40. U. Alon Biological networks: the tinkerer as an engineer Science 301 2003 1866 1867
41. M. Kaern, W.J. Blake, and J.J. Collins The engineering of gene regulatory networks Annu Rev Biomed Eng 5 2003 179 206
42. H.H. McAdams, and A. Arkin Simulation of prokaryotic genetic circuits Annu Rev Biophys Biomol Struct 27 1998 199 224
43. X.J. Feng, S. Hooshangi, D. Chen, G. Li, R. Weiss, and H. Rabitz Optimizing genetic circuits by global sensitivity analysis Biophys J 87 2004 2195 2202
44. H.H. McAdams, and A. Arkin Towards a circuit engineering discipline Curr Biol 10 2000 R318 R320
45. C.H. Collins, F.H. Arnold, and J.R. Leadbetter Directed evolution of Vibrio fischeri LuxR for increased sensitivity to a broad spectrum of acyl-homoserine lactones Mol Microbiol 55 2005 712 723
46. A. Crameri, G. Dawes, E. Rodriguez Jr., S. Silver, and W.P. Stemmer Molecular evolution of an arsenate detoxification pathway by DNA shuffling Nat Biotechnol 15 1997 436 438
47. C.C. Guet, M.B. Elowitz, W. Hsing, and S. Leibler Combinatorial synthesis of genetic networks Science 296 2002 1466 1470
48. P.A. Carr, J.S. Park, Y.J. Lee, T. Yu, S. Zhang, and J.M. Jacobson Protein-mediated error correction for de novo DNA synthesis Nucleic Acids Res 32 2004 e162
49. J. Tian, H. Gong, N. Sheng, X. Zhou, E. Gulari, X. Gao, and G. Church Accurate multiplex gene synthesis from programmable DNA microchips Nature 432 2004 1050 1054 Improves the cost and error correction capabilities of DNA synthesis to enable affordable, high-fidelity construction of long DNA segments with arbitrary sequences, which should alleviate perhaps the most important bottleneck in synthetic biology.
50. W.P. Stemmer, A. Crameri, K.D. Ha, T.M. Brennan, and H.L. Heyneker Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides Gene 164 1995 49 53