Regulatory Dynamics of Synthetic Gene Networks with Positive Feedback

Journal of Molecular Biology

Volumn 359, Issue 4, 2006, Pages 1107-1124

  Maeda, Yusuke T ^a   Sano, Masaki ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

dynamics; hysteresis; positive feedback; synthetic biology; systems biology

Indexed keywords

SYNTHETIC DNA;

ARTICLE; CHEMICAL REACTION; ESCHERICHIA COLI; GENE CONTROL; GENE EXPRESSION; GENE SWITCHING; MATHEMATICAL MODEL; NONHUMAN; POSITIVE FEEDBACK; PRIORITY JOURNAL;

ESCHERICHIA COLI;

EID: 33744794380     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.03.064     Document Type: Article

References (42)

1. Shen-Orr S.S., Milo R., Mangan S., and Alon U. Network motifs in the transcriptional regulation network of Escherichia coli. Nature Genet. 31 (2002) 64-68
2. Milo R., Shen-Orr S.S., Itzkovitz S., Kashtan N., Chklovskii D., and Alon U. Network motifs: simple building blocks of complex networks. Science 298 (2002) 824-827
3. Becskei A., and Serrano L. Engineering stability in gene networks by autoregulation. Nature 405 (2000) 590-593
4. Becskei A., Seraphin B., and Serrano L. Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion. EMBO J. 20 (2001) 2528-2535
5. Ferrell J.E. Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability. Curr. Opin. Cell Biol. 14 (2002) 140-148
6. Austin D.W., Allen M.S., McCollum J.M., Dar R.D., Wilgus J.R., Sayler G.S., et al. Gene network shaping of inherent noise spectra. Nature 439 (2006) 608-611
7. Rosenfeld N., Elowitz M.B., and Alon U. Negative autoregulation speeds the response times of transcription networks. J. Mol. Biol. 323 (2002) 785-793
8. Gardner T.S., Canter C.R., and Collins J.J. Construction of a genetic toggle switch in Escherichia coli. Nature 403 (2000) 339-342
9. Kramer B.P., Viretta a.U., Baba M.D.-E., Aubel D., Weber W., and Fussenegger M. An engineered epigenetic transgene switch in mammalian cells. Nature Biotechnol. 22 (2004) 867-870
10. Johnston Jr. R.J., Chang S., Etchberger J.F., Ortiz C.O., and Hobert O. MicroRNAs acting in a double-negative feedback loop to control a neuronal cell fate decision. Proc. Natl Acad. Sci. USA 102 (2005) 12449-12454
11. Angeli D., Ferrell J.E., and Sontag E.D. Detection of multistability, bifurcations,and hysteresis in a large class of biological positive-feedback systems. Proc. Natl Acad. Sci. USA 101 (2004) 1822-1827
12. Isaacs J., Hasty J., Cantor C.R., and Collins J.J. Prediction and measurement of an autoregulatory genetic module. Proc. Natl Acad. Sci. USA 100 (2003) 7714-7719
13. Ptashne M. Genetic Switch: Phage Lambda and Higher Organisms (1992), Blackwell Science, Cambridge
14. Ozbudak E.M., Thattai M., Lim H.N., Shraiman B.I., and Oudenaarden A. Multistability in the lactose utilization network of Escherichia coli. Nature 427 (2004) 737-740
15. Siegele D.E., and Hu J.C. Gene expression from plasmids containing the araBAD promoter at subsaturating inducer concentrations represents mixed populations. Proc. Natl Acad. Sci. USA 94 (1997) 8168-8172
16. Acar M., Becskei A., and Oudenaarden A. Enhancement of cellular memory by reducing stochastic transitions. Nature 435 (2005) 228-232
17. Ferrell J.E., and Machleder E.M. The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes. Science 280 (1998) 895-898
18. Xiong W., and Ferrell J.E. A positive-feedback-based bistable "memory module" that governs a cell fate decision. Nature 426 (2003) 460-464
19. Bagowski C.P., and Ferrell J.E. Bistability in the JNK cascade. Curr. Biol. 11 (2001) 1176-1182
20. Sha W., Moore J., Chen K., Lassaletta A.D., Yi C.S., and Tyson J.J. Hysteresis drives cell-cycle transitions in Xenopus laevis egg extracts. Proc. Natl Acad. Sci. USA 100 (2003) 975-980
21. Pomerening J.R., Sontag E.D., and Ferrell J.E. Building a cell cycle oscillator: hysteresis and bistability in the activation of Cdc2. Nature Cell. Biol. 5 (2003) 346-351
22. Savageau M.A. Comparison of classical and autogenous systems of regulation in inducible operons. Nature 252 (1974) 546-549
23. Sprinzak D., and Elowitz M.B. Reconstruction of genetic circuits. Nature 438 (2005) 443-448
24. Ackers G.K., Johnson A.D., and Shea M.A. Quantitative model for gene regulation by lambda phage repressor. Proc. Natl Acad. Sci. USA 79 (1982) 1129-1133
25. Rosenfeld N., Young J.W., Alon U., Swain P.S., and Elowitz M.B. Gene regulation at the single-cell level. Science 307 (2005) 1962-1965
26. Atsumi S., and Little J.W. Regulatory circuit design and evolution using phage lambda. Genes Dev. 18 (2004) 2086-2094
27. Sarai A., and Takeda Y. Lambda repressor recognizes the approximately 2-fold symmetric half-operator sequences asymmetrically. Proc. Natl Acad. Sci. USA 86 (1989) 6513-6517
28. Little J.W., Shepley D.P., and Wert D. Robustness of a gene regulatory circuit. EMBO.J. 18 (1999) 4299-4307
29. trc promoters by natural and synthetic inducers. Biotechnol. Prog. 18 (2002) 672-674
30. Aurell E., Brown S., Johanson J., and Sneppen K. Stability puzzles in phage λ. Phys. Rev. E 65 (2002) 051914
31. R control system of bacteriophage lambda: a physical-chemical model for gene regulation. J. Mol. Biol. 181 (1985) 211-230
32. Setty Y., Mayo A.E., Surette M.G., and Alon U. Detailed map of a cis-regulatory input function. Proc. Natl Acad. Sci. USA 100 (2003) 7702-7707
33. Pray T.R., Burz D.S., and Ackers G.K. Cooperative non-specific DNA binding by octamerizing λcI repressors: a site-specific thermodynamic analysis. J. Mol. Biol. 282 (1998) 947-958
34. Kramer B.P., and Fussenegger M. Hysteresis in a synthetic mammalian gene network. Proc. Natl Acad. Sci. USA 102 (2005) 1848-1852
35. Kobiler O., Rokney A., Friedman N., Court D.L., Stavans J., and Oppenheim A.B. Quantitative kinetic analysis of the bacteriophage λ genetic network. Proc. Natl Acad. Sci. USA 102 (2005) 4470-4475
36. Kalir, S., Mangan, S., & Alon, U. (2005). A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli. Molecular Systems Biology, msb4100010-E1-msb 4100010-E6. Publisher, Town.
37. Mangan S., Zaslaver A., and Alon U. The coherent feedforward loop serves as a sign-sensitive delay element in transcriptional networks. J. Mol. Biol. 334 (2003) 197-204
38. Brandman O., Ferrell Jr. J.E., Li R., and Meyer T. Interlinked fast and slow positive feedback loops drive reliable cell decisions. Science 310 (2005) 496-498
39. Hasty J., McMillen D., Isaacs F., and Collins J.J. Computational studies of gene regulatory networks: in numero molecular biology. Nature Rev. Genet. 2 (2001) 268-279
40. Buchler N.E., Gerland U., and Hwa T. Non-linear protein degradation and the function of genetic circuits. Proc. Natl Acad. Sci. USA 102 (2005) 9559-9564
41. Andersen J.B., Sternberg C., Poulsen L.K., Björn S.P., Givskov M., and Molin S. New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria. Appl. Environ. Microbiol. 64 (1998) 2240-2246
42. Sambrook J., and Russell D.W. Molecular Cloning: A Laboratory Manual. 3rd. 3rd edit. (2001), Cold Spring Harbor Laboratory Press, Plainview, NY