Response delays and the structure of transcription networks

Journal of Molecular Biology

Volumn 329, Issue 4, 2003, Pages 645-654

  Rosenfeld, Nitzan ^a   Alon, Uri ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

Computational biology; Design principles; Network motifs; Systems biology

Indexed keywords

GREEN FLUORESCENT PROTEIN;

ACCURACY; ARTICLE; BACTERIAL KINETICS; CELL CYCLE; DATA BASE; DROSOPHILA MELANOGASTER; ESCHERICHIA COLI; GENE EXPRESSION REGULATION; GENE REPRESSION; GENETIC TRANSCRIPTION; MATHEMATICAL ANALYSIS; NONHUMAN; PRIORITY JOURNAL; REPORTER GENE; RESPONSE TIME; SACCHAROMYCES CEREVISIAE; SEA URCHIN;

DROSOPHILA MELANOGASTER; ECHINOIDEA; ESCHERICHIA COLI; MELANOGASTER; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 0038392724     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(03)00506-0     Document Type: Article

References (54)

1. Savageau M.A. Parameter sensitivity as a criterion for evaluating and comparing the performance of biochemical systems. Nature. 229:1971;542-544.
2. Savageau M.A. Comparison of classical and autogenous systems of regulation in inducible operons. Nature. 252:1974;546-549.
3. Savageau M.A. Design of molecular control mechanisms and the demand for gene expression. Proc. Natl Acad. Sci. USA. 74:1977;5647-5651.
4. Arnone M.I., Davidson E.H. The hardwiring of development: organization and function of genomic regulatory systems. Development. 124:1997;1851-1864.
5. Savageau M. Design principles for elementary gene circuits: elements, methods, and examples. Chaos. 11:2001;142-159.
6. Thieffry D., Huerta A.M., Perez-Rueda E., Collado-Vides J. From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli. Bioessays. 20:1998;433-440.
7. Hartwell L.H., Hopfield J.J., Leibler S., Murray A.W. From molecular to modular cell biology. Nature. 402:1999;C47-C52.
8. McAdams H.H., Arkin A. Towards a circuit engineering discipline. Curr. Biol. 10:2000;R318-R320.
9. Barkai N., Leibler S. Robustness in simple biochemical networks. Nature. 387:1997;913-917.
10. Alon U., Surette M.G., Barkai N., Leibler S. Robustness in bacterial chemotaxis. Nature. 397:1999;168-171.
11. Yi T.M., Huang Y., Simon M.I., Doyle J. Robust perfect adaptation in bacterial chemotaxis through integral feedback control. Proc. Natl Acad. Sci. USA. 97:2000;4649-4653.
12. Barkai N., Leibler S. Circadian clocks limited by noise. Nature. 403:2000;267-268.
13. Vilar J.M., Kueh H.Y., Barkai N., Leibler S. Mechanisms of noise-resistance in genetic oscillators. Proc. Natl Acad. Sci. USA. 99:2002;5988-5992.
14. Wyrick J.J., Young R.A. Deciphering gene expression regulatory networks. Curr. Opin. Genet. Dev. 12:2002;130-136.
15. Shen-Orr S.S., Milo R., Mangan S., Alon U. Network motifs in the transcriptional regulation network of Escherichia coli. Nature Genet. 31:2002;64-68.
16. Milo R., Shen-Orr S., Itzkovitz S., Kashtan N., Chklovskii D., Alon U. Network motifs: simple building blocks of complex networks. Science. 298:2002;824-827.
17. Wagner A., Fell D.A. The small world inside large metabolic networks. Proc. R. Soc. ser. B. 268:2001;1803-1810.
18. Guelzim N., Bottani S., Bourgine P., Kepes F. Topological and causal structure of the yeast transcriptional regulatory network. Nature Genet. 31:2002;60-63.
19. Newman M.E., Strogatz S.H., Watts D.J. Random graphs with arbitrary degree distributions and their applications. Phys. Rev. ser. E. 64:2001;026118.
20. Maslov S., Sneppen K. Specificity and stability in topology of protein networks. Science. 296:2002;910-913.
21. Lee T.I., Rinaldi N.J., Robert F., Odom D.T., Bar-Joseph Z., Gerber G.K., et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science. 298:2002;799-804.
22. Yokobayashi Y., Weiss R., Arnold F.H. Directed evolution of a genetic circuit. Proc. Natl Acad. Sci. USA. 99:2002;16587-16591.
23. Costanzo M.C., Crawford M.E., Hirschman J.E., Kranz J.E., Olsen P., Robertson L.S., et al. YPD, PombePD and WormPD: model organism volumes of the BioKnowledge library, an integrated resource for protein information. Nucl. Acids Res. 29:2001;75-79.
24. Elowitz M.B., Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature. 403:2000;335-338.
25. Gardner T.S., Cantor C.R., Collins J.J. Construction of a genetic toggle switch in Escherichia coli. Nature. 403:2000;339-342.
26. Becskei A., Serrano L. Engineering stability in gene networks by autoregulation. Nature. 405:2000;590-593.
27. Rosenfeld N., Elowitz M.B., Alon U. Negative autoregulation speeds the response times of transcription networks. J. Mol. Biol. 323:2002;785-793.
28. Guet C.C., Elowitz M.B., Hsing W., Leibler S. Combinatorial synthesis of genetic networks. Science. 296:2002;1466-1470.
29. Simon I., Barnett J., Hannett N., Harbison C.T., Rinaldi N.J., Volkert T.L., et al. Serial regulation of transcriptional regulators in the yeast cell cycle. Cell. 106:2001;697-708.
30. Davidson E.H., Rast J.P., Oliveri P., Ransick A., Calestani C., Yuh C.H., et al. A genomic regulatory network for development. Science. 295:2002;1669-1678.
31. Cormack B.P., Valdivia R.H., Falkow S. FACS-optimized mutants of the green fluorescent protein (GFP). Gene. 173:1996;33-38.
32. Kalir S., McClure J., Pabbaraju K., Southward C., Ronen M., Leibler S., et al. Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria. Science. 292:2001;2080-2083.
33. Ronen M., Rosenberg R., Shraiman B.I., Alon U. Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics. Proc. Natl Acad. Sci. USA. 99:2002;10555-10560.
34. McAdams H.H., Arkin A. Simulation of prokaryotic genetic circuits. Annu. Rev. Biophys. Biomol. Struct. 27:1998;199-224.
35. Monod J., Pappenheimer A., Cohen-Bazire G. La cinetique de la biosynthese de la b-Galactosidase chez E. coli consideree comme fonction de la croissance. Biochim. Biophys. Acta. 1953;9.
36. Thomas R. Boolean formalization of genetic control circuits. J. Theor. Biol. 42:1973;563-585.
37. Schimke R. On the roles of synthesis and degradation in regulation of enzyme levels in mammalian tissues. Curr. Top. Cell. Regul. 1:1969;77-124.
38. Judd E.M., Laub M.T., McAdams H.H. Toggles and oscillators: new genetic circuit designs. Bioessays. 22:2000;507-509.
39. Aldridge P., Hughes K.T. Regulation of flagellar assembly. Curr. Opin. Microbiol. 5:2002;160-165.
40. Aizawa S.I., Kubori T. Bacterial flagellation and cell division. Genes Cells. 3:1998;625-634.
41. Little J.W., Mount D.W. The SOS regulatory system of Escherichia coli. Cell. 29:1982;11-22.
42. Courcelle J., Khodursky A., Peter B., Brown P.O., Hanawalt P.C. Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli. Genetics. 158:2001;41-64.
43. Makarova K.S., Mironov A.A., Gelfand M.S. Conservation of the binding site for the arginine repressor in all bacterial lineages. Genome Biol. 2:2001;13.
44. Laub M.T., McAdams H.H., Feldblyum T., Fraser C.M., Shapiro L. Global analysis of the genetic network controlling a bacterial cell cycle. Science. 290:2000;2144-2148.
45. Ferrell J.E. Jr, Machleder E.M. The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes. Science. 280:1998;895-898.
46. Bourke Arnvig K., Pedersen S., Sneppen K. Thermodynamics of heat-shock response. Phys. Rev. Letters. 84:2000;3005-3008.
47. Lawrence P. The Making of a Fly. 1992;Blackwell Science Inc, Oxford.
48. Maduro M.F., Rothman J.H. Making worm guts: the gene regulatory network of the Caenorhabditis elegans endoderm. Dev. Biol. 246:2002;68-85.
49. Kim S.K., Lund J., Kiraly M., Duke K., Jiang M., Stuart J.M., et al. A gene expression map for Caenorhabditis elegans. Science. 293:2001;2087-2092.
50. Rothenberg E.V., Anderson M.K. Elements of transcription factor network design for T-lineage specification. Dev. Biol. 246:2002;29-44.
51. Tomancak, P., Beaton, A., Weiszmann, R., Kwan, E., Shu, S., Lewis, S. E. et al. (2002). Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol, 3, research0088.1-research0088.14.
52. Stragier P., Losick R. Cascades of sigma factors revisited. Mol. Microbiol. 4:1990;1801-1806.
53. Lutz R., Bujard H. Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. Nucl. Acids Res. 25:1997;1203-1210.
54. Cluzel P., Surette M., Leibler S. An ultrasensitive bacterial motor revealed by monitoring signaling proteins in single cells. Science. 287:2000;1652-1655.