A perspective of synthetic biology: Assembling building blocks for novel functions

Biotechnology Journal

Volumn 1, Issue 6, 2006, Pages 690-699

  Fu, Pengcheng ^a  

^a UNIVERSITY OF HAWAII   (United States)

Author keywords

Biomaterials; Genetic circuits; Minimal genome; Synthetic biology; Systems biology

Indexed keywords

APPLICATION AREA; BIOLOGICAL PARTS; BUILDING BLOCKES; ENGINEERING DISCIPLINES; FUNCTIONAL ELEMENTS; GENETIC CIRCUITS; LIFE FORM; LIVING SYSTEMS; NOVEL FUNCTIONS; SYNTHETIC BIOLOGY; SYSTEMS BIOLOGY;

BIOLOGICAL MATERIALS; BIOMATERIALS; GENETIC ENGINEERING;

BIOLOGY;

BIOLOGICAL MODEL; BIOMIMETICS; BIOTECHNOLOGY; COMPUTER SIMULATION; GENETIC ENGINEERING; METHODOLOGY; REVIEW; SYSTEM ANALYSIS; SYSTEMS BIOLOGY;

BIOMIMETICS; BIOTECHNOLOGY; COMPUTER SIMULATION; GENETIC ENGINEERING; MODELS, BIOLOGICAL; SYSTEMS BIOLOGY; SYSTEMS INTEGRATION;

EID: 33750796181     PISSN: 18606768     EISSN: 18607314     Source Type: Journal    
DOI: 10.1002/biot.200600019     Document Type: Review

References (95)

1. Hofmeyr, J. H., Westerhoff, H. V., Building the cellular puzzle: control in multi-level reaction networks. J. Theor. Biol. 2001, 208, 261-285.
2. Doyle J. C., Robustness and dynamics in biological networks, in: The First International Conference on Systems Biology. Japan Science and Technology Corporation, MIT Press, New York 2000.
3. Wiener N., Cybernetics - Control and Communication in the Animal and the Machine. John Wiley & Sons, New York 1948.
4. Kitano H., Systems biology: A brief overview. Science 2002, 295, 1662-1664.
5. Dorf, R. C., Mandell, J. D., Bioengineering at the University of Santa Clara. Proceedings of the Annual Conference on Engineering in Medicine and Biology. The Conference Committee for the 19th ACEMB, San Francisco, USA, Aug. 9-12, 1966.
6. Encyclopaedia Britannica, 15th edn. Encyclopaedia Britannica, Inc., Chicago 1994.
7. Cuello, J. L., The Descent of Biological Engineering. Proceedings of the Institute of Biological Engineering, IBE Publications, Athens 2002.
8. Cohenm S. N., Chang, A. C. Y., Boyer, H., Helling, R. B., Construction of biologically functional bacterial plasmids in vitro. Proc. Natl. Acad. Sci. USA 1973, 70, 3240-3244.
9. Rodgers, M., The pandora's box congress. Rolling Stone 1975, 189, 37-77.
10. Hobom, B., Surgery of genes. At the doorstep of synthetic biology. Med. Klin. 1980. 75, 14-21.
11. Sullins, J., Synthetic biology: the technoscience of artificial life, in: Proceeding of the 20th World Congress of Philosophy, Boston, Massachusetts, USA 10-15 August, 1998.
12. Rawls, R., "Synthetic biology" makes its debut. Chem. Eng. News 2000, 49-51.
13. Covert M. W., Schilling C. H., Famili, I., Edwards, J. S. et al., Metabolic modeling of microbial strains in silico. Trends Biochem. Sci. 2001, 26, 179-186.
14. Zazopoulos, E., Huang, K., Staffa, A., Liu, W. et al., A genomics-guided approach for discovering and expressing cryptic metabolic pathways. Nat. Biotechnol. 2003. 21, 187-190.
15. Yeger-Lotem, E., Sattath, S., Kashtan, N., Itzkovitz, S. et al., Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. Proc. Natl. Acad. Sci. USA 2004. 101, 5934-5939.
16. Brazhnik, P., de la Fuente, A., Mendes, P., Gene networks: how to put the function in genomics. Trends Biotechnol. 2002, 11, 467-472.
17. Wolf, D. M., Eeckman, F. H., On the relationship between genomic regulatory element organization and gene regulatory dynamics. J. Theor. Biol. 1998, 195, 167-186.
18. Wall, M. E., Hlavacek, W. S., Savageau, M. A., Design of gene circuits: lessons from bacteria. Nat. Rev. Genet. 2004. 5, 34-42.
19. Alm E., Arkin, A. P.. Biological networks. Curr. Opin. Struct. Biol. 2003, 13, 193-202.
20. McAdams H. H., Arkin, A. P., Gene regulation: towards a circuit engineering discipline. Curr. Biol. 2000, 10, R318-R320.
21. Bray, D., Molecular networks: the top-down view. Science 2003, 301, 1864-1865.
22. Alon, U., Biological networks: the tinkerer as an engineer. Science 2003. 301, 1866-1867.
23. Bar-Joseph, Z., Gerber, G. K., Lee, T. I., Rinaldi, N. J. et al., Computational discovery of gene modules and regulatory networks. Nat. Biotechnol. 2003, 21, 1337-1342.
24. Liang, S., Fuhrman, S., Somogyi, R., REVEAL, a general reverse engineering algorithm for inference of genetic network architectures. Biocomputing '98: Proc. Pac. Symp. Biocomput., Maui, Hawaii, January 4-9, 1998, 3, 18-29.
25. Akutsu, T., Miyano, S., Kuhara, S., Identification of genetic networks from a small number of gene expression patterns under the Boolean network model. Biocomputing '99: Proc. Pac. Symp. Biocomput., Mauna Lani, Hawaii, January 4-9, 1999, 4, 17-28.
26. Wahde, M., Hertz, J., Coarse-grained Reverse Engineering of Genetic Regulatory Networks. BioSystems 2000, 55, 129-136.
27. Ren, B. R., Wyrick, F., Aparicio, J. J., Jennings, O. et al., Genomewide location and function of DNA binding proteins. Science 2000. 290, 2306-2309.
28. de Jong, H., Page, M., Qualitative simulation of large and complex genetic regulatory systems. Proceedings of the 14th European Conference on Artificial Intelligence (ECAI), Berlin, Germany, August 20-25, 2000, IOS Press.
29. Gardner, T.S., di Bernardo, Lorenz, D., Collins, D., James, J., Inferring genetic networks and identifying compound mode of action via expression profiling. Science 2003, 301), 102-105.
30. Imoto, S., Goto, T., Miyano, S., Estimation of genetic networks and functional structures between genes by using Bayesian networks and nonparametric regression, in: Proceedings of the 7th Pacific Symposiun on Biocomputing (PSB 2002), Lihue, Hawaii, USA, January 3-7, 2002.
31. Salisbury, M. W., Get ready for synthetic biology. Genome Technol. 2006, Jan/Feb, 26-33.
32. Davidson, E. H. et al., A Provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo. Dev. Biol. 2002. 246, 162-190.
33. Savageau, M. A., Rules for the evolution of gene circuitry. Biocomputing '98: Proc. Pac. Symp. Biocomput., Maui, Hawaii, January 4-9, 1998, 3, 54-65.
34. Romero, P. et al., Computational prediction of human metabolic pathways from the complete human genome. Genome Biol. 2004, 6, R2.1-17.
35. Simpson, M. L., Rewiring the cell: synthetic biology moves towards higher functional complexity. Trends Biotechnol. 2004, 22, 555-557.
36. Jacob, F., Monod, J., Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 1961. 3, 318-356.
37. Kaern, M., Blake, W. J., Collins, J. J., The engineering of gene regulatory networks. Annu. Rev. Biomed. Eng. 2003, 5, 179-206.
38. Canton, B., Engineering the Interface Between Cellular Chassis and Integrated Biological Systems. MIT Synthetic Biology Working Group Reports published online 8 August 2005 (doi: 1721.1/19813).
39. Gardner, T. S., Cantor, C. A., Collins, J. A., Construction of a genetic toggle switch in Escherichia coli. Nature 2000, 403, 339-342.
40. Elowitz, M. B., Leibler, S., A synthetic oscillatory network of transcriptional regulators. Nature 2000, 403, 335-338.
41. Elowitz, M. B., Levine, A. J., Siggia, E. D. et al., Stochastic gene expression in a single cell. Science 2002, 297, 1183-1186.
42. Rosenfeld, N., Elowitz, M. B., Alon, U., Negative autoregulation speeds the response times of transcription networks. J. Mol. Biol. 2002, 323, 785-793.
43. Swain, P. S., Elowitz, M. B., Siggia, E. D., Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc. Natl. Acad. Sci. USA 2002, 99, 12795-12800.
44. Garcia-Ojalvo, J., Elowitz, M. B., Strogatz, S. H., Modeling a synthetic multicellular clock: repressilators coupled by quorum sensing. Proc. Natl. Acad. Sci. USA 2004, 101, 10955-10960.
45. Atkinson, M. R., Savageau, M. A., Myers, J. T. et al., Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell 2003, 113, 597-607.
46. Weiss, R., Basu, S., Kalmbach, A., Hooshangi, S. et al., Genetic circuit building blocks for cellular computation, communications, and signal processing. Natural Comput. 2003, 2, 47-84.
47. Yokobayashi, Y., Collins, C. H., Leadbetter, J. R., Weiss, R. et al., Evolutionary design of genetic circuits and cell-cell communications. Adv. Complex Syst. 2003, 6, 37-45.
48. Levskaya, A., Chevalier, A.A., Tabor, J.J., Simpson, Z.B. et al., Synthetic biology: engineering Escherichia coli to see light. Nature 2005, 438, 441-442.
49. Kobayashi, H., Kaern, M. Araki, M., Chung, K. et al., Programmable cells: interfacing natural and engineered gene networks, Proc. Natl. Acad. Sci. USA 2004, 101, 8414-8419.
50. Miller, M. B., Bassler, B. L., Quorum sensing in bacteria. Annu. Rev. Microbiol. 2001, 55, 165-199.
51. Basu, S., Mehreja, R., Thiberge, S., Chen, M.T. et al., Spatiotemporal control of gene expression with pulse-generating networks. Proc. Natl. Acad. Sci. USA 2004, 101, 6355-6360.
52. Wang, L., Zhang, Z., Brock, A, Schultz, P. G., Addition of the keto functional group to the genetic code of Escherichia coli. Proc. Natl. Acad. Sci. USA 2003, 100, 56-61.
53. Noren, C. J., Anthony-Cahill, S. J., Suich, D. J., Noren, K.A. et al., Invitro suppression of an amber mutation by a chemically aminoacylated transfer RNA prepared by runoff transcription. Nucleic Acids Res. 1990, 18, 83-88.
54. Robertson, S. A., Noren, C. J., Anthony-Cahill, S. J., Griffith, M.C. et al., The use of 5' phospho-2-deoxyribocytidylylriboadenosine as a facile route to chemical aminoacylation of transfer RNA. Nucleic Acids Res. 1989, 17, 9649-9660.
55. Mehl, R. A., Anderson, J. C., Santoro, S. W. et al., Generation of a bacterium with a 21 amino acid genetic code. J. Am. Chem. Soc. 2003, 125, 935-939.
56. Chin, J. W., Cropp, T. A., Anderson, J. C., Mukherji, M. et al., An expanded eukaryotic genetic code. Science 2003, 301, 964-967.
57. Hohsaka, T., Ashizuka, Y., Taira, H., Murakami, H. et al., Incorporation of nonnatural amino acids into proteins by using various fourbase codons in an Escherichia coli in vitro translation system. Biochemistry 2001, 40, 11060-11064.
58. Hohsaka, T., Ashizuka, Y., Murakami, H., Sisidoa, M., Five-base codons for incorporation of nonnatural amino acids into proteins. Nucleic Acids Res, 2001, 29, 3646-3651.
59. Wang L., Schultz, P. G., Expanding the genetic code. Chem. Commun. (Camb) 2002, 1-11.
60. Boyer, P. D., The ATP synthase-A splendid molecular machine. Annu. Rev. Biochem. 1997, 66, 717-749.
61. o steps. Cell 1998, 93, 1117-1124.
62. Soong, R. K., Bachand, G. D., Neves, H. P., Olkhovets, A.G. et al., Powering an inorganic nanodevice with a biomolecular motor. Science 2000, 290, 1555-1558.
63. Soong, R. E., Neves, H. P., Schmidt, J. J., Bachand, G.D. et al., Engineering issues in the fabrication of a hybrid nano-propeller system powered by F1-ATPase. Biomed. Microdevices 2001, 3, 71-73.
64. Liu, H., Schmidt, J. J., Bachand, G. G., Rizk, S.S. et al., Control of a biomolecular motor-powered nanodevice with an engineered chemical switch. Nat. Mater. 2003, 1, 173-177.
65. Block, S. M., Real engines of creation. Nature 1997, 386, 217-219.
66. Perkel, J. M., Investigating molecular motors step by step: recent discoveries begin to answer how dyneins, kinesins, and myosins actually work. Scientist 2004, 18, 19-31.
67. Schmidt J. J., Montemagno, C. D., Bionanomechanical systems. Annu. Rev. Mater. Res. 2004, 34, 315-337.
68. Abrahams, J. P., Leslie, A. G. W., Lutter, R., Walker, J.E., Structure at 2.8 Å resolution of F1-ATPase from bovine heart mitochondria. Nature 1994, 370, 621-628.
69. Noji, H., Yasuda, R., Yoshida, M., Kinosita Jr., K., Direct observation of the rotation of F1 ATPase. Nature 1997, 386, 299-302.
70. Duncan, T., Bulygin, V., Zhou, Y., Hutcheon, M. L. et al., Rotation of subunits during catalysis by Escherichia coli F1-ATPase. Proc. Natl. Acad. Sci. USA 1995, 92, 10964-10968.
71. Vale, R. D., Reese, T. S., Sheetz, M. P., Identification of a novel forcegenerating protein, kinesin, involved in microtubule-based motility. Cell 1985, 42, 39-50.
72. Böhm, K. J., Stracke, R., Mühlig, P., Unger, E., Motor protein-driven unidirectional transport of micrometer-sized cargoes across isopolar microtubule arrays. Nanotechnology 2001, 12, 238-244.
73. Kuo, S. C., Gelles, J., Steuer, E., Sheetz, M.P., A model for kinesin movement from nanometer-level movements of kinesin and cytoplasmic dynein and force measurements. J. Cell Sci. Suppl. 1991, 14, 135-138.
74. Dennis, J. R., Howard, J., Vogel, V., Molecular shuttles: directed motion of microtubules across nanoscale kinesin tracks. Nanotechnology 1999, 10, 232-236.
75. Schief, W. R., Clark, R. H., Crevenna, A. H., Howard, J., Inhibition of kinesin motility by ADP and phosphate supports a hand-over-hand mechanism. Proc. Natl. Acad. Sci. USA 2004, 101, 1183-1188.
76. Montemagno, C. D., Nanomachines: A roadmap for realizing the vision. J. Nanoparticle Res. 2001, 3, 1-3.
77. Koonin, E. V., How many genes can make a cell: the minimal-geneset concept. Annu. Rev. Genomics Hum. Genet. 2000, 1, 99-116.
78. Luisi, P. L., Oberholzer, T., Lazcano, A., The notion of a DNA minimal cell: a general discourse and some guidelines for an experimental approach. Helvet. Chim. Acta 2002, 85, 1759-1777.
79. Hutchison, C. A., III, Peterson, S. N., Gill, S. R., Cline, R. T., Global transposon mutagenesis and a minimal mycoplasma genome. Science 1999, 286, 2165-2169.
80. Ji, Y., Zhang, B., von Horn, S.F., Warren, P. et al., Identification of critical staphylococcal genes using conditional phenotypes generated by antisense RNA. Science 2001, 293, 2266-2269.
81. Chandonia, J.-M., Konerding, D. E., Allen, D.G., Computational structural genomics of a complete minimal organism. Genome Informatics 2002, 13, 390-391.
82. Zhang, R., Ou, H.-Y., Zhang, C.T., DEG: a database of essential genes. Nucleic Acids Res. 2004, 32, D271-272.
83. Kobayashi, K., Ehrlich, S. D., Albertini, A., Amati, G. et al., Essential Bacillus subtilis genes. Proc. Natl. Acad. Sci. USA 2003, 100, 4678-4683.
84. Mushegian, A. R., Koonin, E. V., A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc. Natl. Acad. Sci. USA 1996, 93, 10268-10273.
85. Arigoni, F., Talabot, F., Peitsch, M., Edgerton, M. D., Meldrum, E., A genome-based approach for the identification of essential bacterial genes. Nat. Biotechnol. 1998, 16, 851-856.
86. Lazcano, A. The never-ending story. Am. Scientist 2003, 91, no. 5.
87. Deamer, D., A giant step towards artificial life? Trends Biotechnol. 2005, 23, 336-338.
88. Deamer, D., Is this life? Scientist 2006, 20, 30.
89. Rasmussen, S., Chen, L., Deamer, D., Krakauer, D.C. et al., Transitions from nonliving to living matter. Science 2004, 303, 963-965.
90. Smith, H. O., Hutchison, C. A. III, Pfannkoch, C., Venter, J.C., Generating a synthetic genome by whole genome assembly: FX174 bacteriophage from synthetic oligonucleotides. Proc. Natl. Acad. Sci. USA 2003, 100, 15440-15445.
91. Cello, J., Paul, A. V., Wimmer, E., Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template. Science 2002, 297, 1016-1018.
92. Brent, R., A partnership between biology and engineering. Nat. Biotechnol. 2004, 22, 1211-1214.
93. Rinaldi, A., A new code for life: Expansion of the genetic code and artificial assembly of functional genomes are raising important questions about ethics and safety. EMBO Rep. 2004, 5, 336-339.
94. Cho, M. K., Magnus, D., Caplan, A.L., McGee, D., et al., Ethical considerations in synthesizing a minimal genome. Science 1999, 286, 2087-2090.
95. Block, S., Donoho, D., Hwa, T., Joyce, G. et al., DNA barcodes and watermarks, in: Jason Report JSR-03-305, The Mitre Corporation, McLean 2004.