The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks

Journal of Molecular Biology

Volumn 334, Issue 2, 2003, Pages 197-204

  Mangan, S ^a   Zaslaver, A ^a   Alon, U ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

Computational biology; Design principles; Network motifs; Systems biology

Indexed keywords

ARABINOSE; CYCLIC AMP; GREEN FLUORESCENT PROTEIN;

ARTICLE; ENZYME ACTIVITY; ESCHERICHIA COLI; KINETICS; PRIORITY JOURNAL; PROTEIN MOTIF; SIGNAL TRANSDUCTION;

EID: 0242364231     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2003.09.049     Document Type: Article

References (43)

1. Hartwell L.H., Hopfield J.J., Leibler S., Murray A.W. From molecular to modular cell biology. Nature. 402:1999;47-52.
2. 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.
3. 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.
4. Ouzounis C.A., Karp P.D. Global properties of the metabolic map of Escherichia coli. Genome Res. 10:2000;568-576.
5. Rao C.V., Arkin A.P. Control motifs for intracellular regulatory networks. Annu. Rev. Biomed. Eng. 3:2001;391-419.
6. 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.
7. Mangan, S. & Alon, W. (2003). Structure and function of the feed-forward loop network motif. Proc. Natl Acad. Sci. USA, 100, 11980-11985.
8. Yuh C.H., Bolouri H., Davidson E.H. Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene. Science. 279:1998;1896-1902.
9. Buchler N.E., Gerland U., Hwa T. On schemes of combinatorial transcription logic. Proc. Natl Acad. Sci. USA. 100:2003;5136-5141.
10. Setty Y., Mayo A., Surette M., Alon U. Detailed map of a cis-regulatory input function. Proc. Natl Acad. Sci. USA. 100:2003;7702-7707.
11. Wilcox G., Meuris P., Bass R., Englesbe E. Regulation of L-arabinose operon Bad in vitro. J. Biol. Chem. 249:1974;2946-2952.
12. Casadaban M.J. Regulation of regulatory gene for arabinose pathway, Arac. J. Mol. Biol. 104:1976;557-566.
13. Johnson C.M., Schleif R.F. In vivo induction kinetics of the arabinose promoters in Escherichia coli. J. Bacteriol. 177:1995;3438-3442.
14. Schleif R. Two positively regulated systems, ara and mal. Neidhardt F.C. Escherichia coli and Salmonella. vol. 1:1996;1300-1309 ASM Press, Washington, DC.
15. Schleif R. Regulation of the L-arabinose operon of Escherichia coli. Trends Genet. 16:2000;559-565.
16. Beckwith J. The lactose operon. Neidhardt F.C. Escherichia coli and Salmonella: cellular and Molecular Biology. vol. 2:1987;1444-1452 ASM Press, Washington, DC.
17. Vilar J.M.G., Guet C.C., Leibler S. Modeling network dynamics: the lac operon, a case study. J. Cell Biol. 161:2003;471-476.
18. 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.
19. 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.
20. Salgado H., Santos-Zavaleta A., Gama-Castro S., Millan-Zarate D., Diaz-Peredo E., Sanchez-Solano F., et al. RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12. Nucl. Acids Res. 29:2001;72-74.
21. Rosenfeld N., Elowitz M.B., Alon U. Negative autoregulation speeds the response times of transcription networks. J. Mol. Biol. 323:2002;785-793.
22. Rosenfeld N., Alon U. Response delays and the structure of teranscription networks. J. Mol. Biol. 329:2003;645-654.
23. Savageau M. Genetic regulatory mechanisms and the ecological niche of Escherichia coli. Proc. Natl Acad. Sci. USA. 71:1974;2453-2455.
24. Savageau M.A. Design of molecular control mechanisms and the demand for gene expression. Proc. Natl Acad. Sci. USA. 74:1977;5647-5651.
25. Savageau, M. (1989). Are there rules governing patterns of gene regulation? Theoretical Biology-Epigenetics and Evolutionary Order (Goodwin, B. C. & Saundres, P. T., eds), pp. 42-66, Edinburgh University Press.
26. Savageau M. Design principles for elementary gene circuits: elements, methods and examples. Chaos. 11:2001;142-159.
27. Babu M.M., Teichmann S.A. Evolution of transcription factors and the gene regulatory network in Escherichia coli. Nucl. Acids Res. 31:2003;1234-1244.
28. Conant, G. C. & Wagner, A. (2003). Convergent evolution of gene circuits. Nat. Genetics, 34, 264-266.
29. Duggan A., Ma C., Chalfie M. Regulation of touch receptor differentiation by the Caenorhabditis elegans mec-3 and unc-86 genes. Development. 125:1998;4107-4119.
30. Altun-Gultekin Z., Andachi Y., Tsalik E.L., Pilgrim D., Kohara Y., Hobert O. A regulatory cascade of three homeobox genes, ceh-10, ttx-3 and ceh-23, controls cell fate specification of a defined interneuron class in C. elegans. Development. 128:2001;1951-1969.
31. Davidson E.H., Rast J.P., Oliveri P., Ransick A., Calestani C., Yuh C.H. A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo. Dev. Biol. 246:2002;162-190.
32. Moroni M.C., Hickman E.S., Denchi E.L., Caprara G., Colli E., Cecconi F., et al. Apaf-1 is a transcriptional target for E2F and p53. Nature Cell. Biol. 3:2001;552-558.
33. Mullen A.C., Hutchins A.S., High F.A., Lee H.W., Sykes K.J., Chodosh L.A., Reiner S.L. Hlx is induced by and genetically interacts with T-bet to promote heritable T(H)1 gene induction. Nature Immunol. 3:2002;652-658.
34. White J.G. Neuronal connectivity in Caenorhabditis elegans. Trends Neurosci. 8:1985;277-283.
35. Alberts, B., Bray, D., Lewis, J., Raff, M., Roberts, K., & Watson, J. D. Molecular Biology of the Cell. 4th edit, Gerland Science, New York, pp. 859-861.
36. Blattner F.R., Plunkett G. 3rd, Bloch C.A., Perna N.T., Burland V., Riley M., et al. The complete genome sequence of Escherichia coli K-12. Science. 277:1997;1453-1474.
37. Cormack B.P., Valdivia R.H., Falkow S. FACS-optimized mutants of the green fluorescent protein (GFP). Gene. 173:1996;33-38.
38. Lobell R.B., Schleif R.F. DNA looping and unlooping by AraC protein. Science. 250:1990;528-532.
39. McAdams H.H., Arkin A. Simulation of prokaryotic genetic circuits. Annu. Rev. Biophys. Biomol. Struct. 27:1998;199-224.
40. Tyson J.J., Chen K.C., Novak B. Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr. Opin. Cell. Biol. 15:2003;221-231.
41. Thomas R., D'Ari R. Biological Feedback. 1990;CRC Press, Boca Raton, FL.
42. Bremer H., Dennis P.P. Modulation of chemical composition and other parameters of the cell by growth rate. Neidhardt F.C. Escherichia coli and Salmonella: Cellular and Molecular Biology. vol. 2:1987;1553-1569 ASM Press, Washington, DC.
43. Vilar, J. M. & Leibler, S. (2003). DNA looping and physical constraints on transcription regulation. J. Mol. Biol. 331, 981-989.