Modular approaches to expanding the functions of living matter

Nature Chemical Biology

Volumn 2, Issue 6, 2006, Pages 304-311

  Chin, Jason W ^a  

^a MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GREEN FLUORESCENT PROTEIN; REPRESSOR PROTEIN; RNA; TRANSCRIPTION FACTOR;

CELL COMMUNICATION; DNA BINDING; DNA DAMAGE; ESCHERICHIA COLI; FLUORESCENCE; GENE CONTROL; GENE EXPRESSION; GENE FUNCTION; GENETIC CODE; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN FUNCTION; REPRESSOR GENE; REVIEW; SIGNAL TRANSDUCTION; SYNTHESIS; THERMODYNAMICS;

ESCHERICHIA COLI;

EID: 33646877664     PISSN: 15524450     EISSN: 15524469     Source Type: Journal    
DOI: 10.1038/nchembio789     Document Type: Review

References (63)

1. Hartwell, L.H., Hopfield, J.J., Leibler, S. & Murray, A.W. From molecular to modular cell biology. Nature 402, C47-C52 (1999).
2. Kashtan, N. & Alon, U. Spontaneous evolution of modularity and network motifs. Proc. Natl. Acad. Sci. USA 102, 13773-13778 (2005).
3. Gardner, T.S., Cantor, C.R. & Collins, J.J. Construction of a genetic toggle switch in Escherichia coli. Nature 403, 339-342 (2000).
4. Kobayashi, H. et al. Programmable cells: interfacing natural and engineered gene networks. Proc. Natl. Acad. Sci. USA 101, 8414-8419 (2004).
5. Kramer, B.P. et al. An engineered epigenetic transgene switch in mammalian cells. Nat. Biotechnol. 22, 867-870 (2004).
6. Elowitz, M.B. & Leibler, S. A synthetic oscillatory network of transcriptional regulators. Nature 403, 335-338 (2000).
7. Atkinson, M.R., Savageau, M.A., Myers, J.T. & Ninfa, A.J. Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell 113, 597-607 (2003).
8. Fung, E. et al. A synthetic gene-metabolic oscillator. Nature 435, 118-122 (2005).
9. Kaern, M., Blake, W.J. & Collins, J.J. The engineering of gene regulatory networks. Annu. Rev. Biomed. Eng. 5, 179-206 (2003).
10. Becskei, A. & Serrano, L. Engineering stability in gene networks by autoregulation. Nature 405, 590-593 (2000).
11. Elowitz, M.B., Levine, A.J., Siggia, E.D. & Swain, P.S. Stochastic gene expression in a single cell. Science 297, 1183-1186 (2002).
12. Swain, P.S., Elowitz, M.B. & Siggia, E.D. Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc. Natl. Acad. Sci. USA 99, 12795-12800 (2002).
13. Rosenfeld, N., Young, J.W., Alon, U., Swain, P.S. & Elowitz, M.B. Gene regulation at the single-cell level. Science 307, 1962-1965 (2005).
14. Pedraza, J.M. & van Oudenaarden, A. Noise propagation in gene networks. Science 307, 1965-1969 (2005).
15. Ozbudak, E.M., Thattai, M., Kurtser, I., Grossman, A.D. & van Oudenaarden, A. Regulation of noise in the expression of a single gene. Nat. Genet. 31, 69-73 (2002).
16. Isaacs, F.J., Hasty, J., Cantor, C.R. & Collins, J.J. Prediction and measurement of an autoregulatory genetic module. Proc. Natl. Acad. Sci. USA 100, 7714-7719 (2003).
17. Blake, W.J., Kaern, M., Cantor, C.R. & Collins, J.J. Noise in eukaryotic gene expression. Nature 422, 633-637 (2003).
18. Raser, J.M. & O'Shea, E.K. Control of stochasticity in eukaryotic gene expression. Science 304, 1811-1814 (2004).
19. Rao, C.V., Wolf, D.M. & Arkin, A.P. Control, exploitation and tolerance of intracellular noise. Nature 420, 231-237 (2002).
20. Cai, L., Friedman, N. & Xie, X.S. Stochastic protein expression in individual cells at the single molecule level. Nature 440, 358-362 (2006).
21. Suel, G.M., Garcia-Ojalvo, J., Liberman, L.M. & Elowitz, M.B. An excitable gene regulatory circuit induces transient cellular differentiation. Nature 440, 545-550 (2006).
22. Guet, C.C., Elowitz, M.B., Hsing, W. & Leibler, S. Combinatorial synthesis of genetic networks. Science 296, 1466-1470 (2002).
23. You, L., Cox, R.S., III, Weiss, R. & Arnold, F.H. Programmed population control by cell-cell communication and regulated killing. Nature 428, 868-871 (2004).
24. Anderson, J.C., Clarke, E.J., Arkin, A.P. & Voigt, C.A. Environmentally controlled invasion of cancer cells by engineered bacteria. J. Mol. Biol. 355, 619-627 (2006).
25. Basu, S., Gerchman, Y., Collins, C.H., Arnold, F.H. & Weiss, R. A synthetic multicellular system for programmed pattern formation. Nature 434, 1130-1134 (2005).
26. Basu, S., Mehreja, R., Thiberge, S., Chen, M.T. & Weiss, R. Spatiotemporal control of gene expression with pulse-generating networks. Proc. Natl. Acad. Sci. USA 101, 6355-6360 (2004).
27. Chen, M.T. & Weiss, R. Artificial cell-cell communication in yeast Saccharomyces cerevisiae using signaling elements from Arabidopsis thaliana. Nat. Biotechnol. 23, 1551-1555 (2005).
28. Bulter, T. et al. Design of artificial cell-cell communication using gene and metabolic networks. Proc. Natl. Acad. Sci. USA 101, 2299-2304 (2004).
29. Levskaya, A. et al. Synthetic biology: engineering Escherichia coli to see light. Nature 438, 441-442 (2005).
30. Derr, P., Boder, E. & Goulian, M. Changing the specificity of a bacterial chemoreceptor. J. Mol. Biol. 355, 923-932 (2006).
31. Looger, L.L., Dwyer, M.A., Smith, J.J. & Hellinga, H.W. Computational design of receptor and sensor proteins with novel functions. Nature 423, 185-190 (2003).
32. Desmet, J., Demaeyer, M., Hazes, B. & Lasters, I. The dead-end elimination theorem and its use in protein side-chain positioning. Nature 356, 539-542 (1992).
33. Park, S.H., Zarrinpar, A. & Lim, W.A. Rewiring MAP kinase pathways using alternative scaffold assembly mechanisms. Science 299, 1061-1064 (2003).
34. Bhattacharyya, R.P. et al. The Ste5 scaffold allosterically modulates signaling output of the yeast mating pathway. Science 311, 822-826 (2006).
35. Chin, J.W. et al. An expanded eukaryotic genetic code. Science 301, 964-967 (2003).
36. Wang, L., Brock, A., Herberich, B. & Schultz, P.G. Expanding the genetic code of Escherichia coli. Science 292, 498-500 (2001).
37. Chin, J.W., Cropp, T.A., Chu, S., Meggers, E. & Schultz, P.G. Progress toward an expanded eukaryotic genetic code. Chem. Biol. 10, 511-519 (2003).
38. Kwok, Y. & Wong, J.T. Evolutionary relationship between Halobacterium cutirubrum and eukaryotes determined by use of aminoacyl-tRNA synthetases as phylogenetic probes. Can. J. Biochem. 58, 213-218 (1980).
39. Santoro, S.W., Wang, L., Herberich, B., King, D.S. & Schultz, P.G. An efficient system for the evolution of aminoacyl-tRNA synthetase specificity. Nat. Biotechnol. 20, 1044-1048 (2002).
40. Chin, J.W., Martin, A.B., King, D.S., Wang, L. & Schultz, P.G. Addition of a photo-crosslinking amino acid to the genetic code of Escherichia coli. Proc. Natl. Acad. Sci. USA 99, 11020-11024 (2002).
41. Cropp, T.A. & Schultz, P.G. An expanding genetic code. Trends Genet. 20, 625-630 (2004).
42. Sakamoto, K. et al. Site-specific incorporation of an unnatural amino acid into proteins in mammalian cells. Nucleic Acids Res. 30, 4692-4699 (2002).
43. Hino, N. et al. Protein photo-cross-linking in mammalian cells by site-specific incorporation of a photoreactive amino acid. Nat. Methods 2, 201-206 (2005).
44. Anderson, J.C. et al. An expanded genetic code with a functional quadruplet codon. Proc. Natl. Acad. Sci. USA 101, 7566-7571 (2004).
45. Mehl, R.A. et al. Generation of a bacterium with a 21 amino acid genetic code. J. Am. Chem. Soc. 125, 935-939 (2003).
46. Bayer, T.S. & Smolke, C.D. Programmable ligand-controlled riboregulators of eukaryotic gene expression. Nat. Biotechnol. 23, 337-343 (2005).
47. Isaacs, F.J. et al. Engineered riboregulators enable post-transcriptional control of gene expression. Nat. Biotechnol. 22, 841-847 (2004).
48. Rackham, O. & Chin, J.W. A network of orthogonal ribosome x mRNA pairs. Nat. Chem. Biol. 1, 159-166 (2005).
49. Rackham, O. & Chin, J.W. Cellular logic with orthogonal ribosomes. J. Am. Chem. Soc. 127, 17584-17585 (2005).
50. Rackham, O., Wang, K. & Chin, J.W. Functional epitopes at the ribosome subunit interface. Nat. Chem. Biol. 2, 254-258 (2006).
51. Tian, J. et al. Accurate multiplex gene synthesis from programmable DNA microchips. Nature 432, 1050-1054 (2004).
52. Cello, J., Paul, A.V. & Wimmer, E. Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template. Science 297, 1016-1018 (2002).
53. Smith, H.O., Hutchison, C.A., III, Pfannkoch, C. & Venter, J.C. Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides. Proc. Natl. Acad. Sci. USA 100, 15440-15445 (2003).
54. Kodumal, S.J. et al. Total synthesis of long DNA sequences: synthesis of a contiguous 32-kb polyketide synthase gene cluster. Proc. Natl. Acad. Sci. USA 101, 15573-15578 (2004).
55. Stemmer, W.P., Crameri, A., Ha, K.D., Brennan, T.M. & Heyneker, H.L. Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides. Gene 164, 49-53 (1995).
56. Binkowski, B.F., Richmond, K.E., Kaysen, J., Sussman, M.R. & Belshaw, P.J. Correcting errors in synthetic DNA through consensus shuffling. Nucleic Acids Res. 33, e55 (2005).
57. Endy, D. Foundations for engineering biology. Nature 438, 449-453 (2005).
58. Yokobayashi, Y., Weiss, R. & Arnold, F.H. Directed evolution of a genetic circuit. Proc. Natl. Acad. Sci. USA 99, 16587-16591 (2002).
59. Farmer, W.R. & Liao, J.C. Improving lycopene production in Escherichia coli by engineering metabolic control. Nat. Biotechnol. 18, 533-537 (2000).
60. Mukherjee, K.J., Rowe, D.C., Watkins, N.A. & Summers, D.K. Studies of single-chain antibody expression in quiescent Escherichia coli. Appl. Environ. Microbiol. 70, 3005-3012 (2004).
61. Rowe, D.C. & Summers, D.K. The quiescent-cell expression system for protein synthesis in Escherichia coli. Appl. Environ. Microbiol. 65, 2710-2715 (1999).
62. Guido, N.J. et al. A bottom-up approach to gene regulation. Nature 439, 856-860 (2006).
63. Szostak, J.W., Bartel, D.P. & Luisi, P.L. Synthesizing life. Nature 409, 387-390 (2001).