Positive-Feedback Loops as a Flexible Biological Module

Current Biology

Volumn 17, Issue 8, 2007, Pages 668-677

  Ingolia, Nicholas T ^a   Murray, Andrew W ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

EVO_ECOL; MICROBIO; SYSBIO

Indexed keywords

PEPTIDE;

ARTICLE; FEEDBACK SYSTEM; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; MATING FACTOR; METABOLISM; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION;

FEEDBACK, BIOCHEMICAL; GENE EXPRESSION REGULATION, FUNGAL; GENE REGULATORY NETWORKS; MAP KINASE SIGNALING SYSTEM; PEPTIDES; SACCHAROMYCES CEREVISIAE;

SACCHAROMYCETALES;

EID: 34047258309     PISSN: 09609822     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cub.2007.03.016     Document Type: Article

References (43)

1. Strogatz S. Nonlinear Dynamics and Chaos: With Applications to Physics, Biology, Chemistry, and Engineering (1994), Perseus Publishing, Cambridge, MA
2. Delbrück M. Unités biologiques douées de continuité génétique. Colloq. Int. CNRS 8 (1949) 33-35
3. Monod J., and Jacob F. General conclusions: Teleonomic mechanisms in cellular metabolism, growth, and differentiation. Cold Spring Harb. Symp. Quant. Biol. 26 (1961) 389-401
4. Glass L., and Kauffman S.A. The logical analysis of continuous, non-linear biochemical control networks. J. Theor. Biol. 39 (1973) 103-129
5. Ptashne M. A Genetic Switch: Gene Control and Phage λ (1986), Cell Press, Cambridge, MA
6. Pomerening J.R., Kim S.Y., and Ferrell J.J.E. Systems-level dissection of the cell-cycle oscillator: Bypassing positive feedback produces damped oscillations. Cell 122 (2005) 565-578
7. Pomerening J.R., Sontag E.D., and Ferrell J.J.E. Building a cell cycle oscillator: Hysteresis and bistability in the activation of Cdc2. Nat. Cell Biol. 5 (2003) 346-351
8. Sha W., Moore J., Chen K., Lassaletta A.D., Yi C.S., Tyson J.J., and Sible J.C. Hysteresis drives cell-cycle transitions in Xenopus laevis egg extracts. Proc. Natl. Acad. Sci. USA 100 (2003) 975-980
9. Novick A., and Weiner M. Enzyme induction as an all-or-none phenomenon. Proc. Natl. Acad. Sci. USA 43 (1957) 553-566
10. Acar M., Becskei A., and v Oudenaarden A. Enhancement of cellular memory by reducing stochastic transitions. Nature 435 (2005) 228-232
11. Ozbudak E.M., Thattai M., Lim H.N., Shraiman B.I., and v Oudenaarden A. Multistability in the lactose utilization network of Escherichia coli. Nature 427 (2004) 737-740
12. Thomas R., and Kaufman M. Multistationarity, the basis of cell differentiation and memory. I. Structural conditions of multistationarity and other nontrivial behavior. Chaos 11 (2001) 170-179
13. Becskei A., Séraphin B., and Serrano L. Positive feedback in eukaryotic gene networks: Cell differentiation by graded to binary response conversion. EMBO J. 20 (2001) 2528-2535
14. Atkinson M.R., Savageau M.A., Meyers J.T., and Ninfa A.J. Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell 113 (2003) 597-607
15. Isaacs F.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
16. Kramer B.P., and Fussenegger M. Hysteresis in a synthetic mammalian gene network. Proc. Natl. Acad. Sci. USA 102 (2005) 9517-9522
17. Gardner T.S., Cantor C.R., and Collins J.J. Construction of a genetic toggle switch in Eschicheria coli. Nature 403 (2000) 339-342
18. Bardwell L. A walk-through of the yeast mating pheromone response pathway. Peptides 25 (2004) 1465-1476
19. Ferrell J.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
20. Bhalla U.S., Ram P.T., and Iyengar R. MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network. Science 297 (2002) 1018-1023
21. Cairns B.R., Ramer S.W., and Kornberg R.D. Order of action of components in the yeast pheromone response pathway revealed with a dominant allele of the STE11 kinase and the multiple phosphorylation of the STE7 kinase. Genes Dev. 6 (1992) 1305-1318
22. Whiteway M., Hougan L., and Thomas D.Y. Overexpression of the STE4 gene leads to mating response in haploid Saccharomyces cerevisiae. Mol. Cell. Biol. 10 (1990) 217-222
23. Chang F., and Herskowitz I. Identification of a gene necessary for cell cycle arrest by a negative growth factor of yeast: FAR1 is an inhibitor of a G1 cyclin, CLN2. Cell 63 (1990) 999-1011
24. Cherkasova V., Lyons D.M., and Elion E.A. Fus3p and Kss1p control G1 arrest in Saccharomyces cerevisiae through a balance of distinct arrest and proliferative functions that operate in parallel with Far1p. Genetics 151 (1999) 989-1004
25. Bishop A.C., Ubersax J.A., Petsch D.T., Matheos D.P., Gray N.S., Blethrow J., Shimuzu E., Tsien J.Z., Schultz P.G., Rose M.D., et al. A chemical switch for inhibitor-sensitive alleles of any protein kinase. Nature 407 (2000) 395-401
26. Elion E.A., Brill J.A., and Fink G.R. FUS3 represses CLN1 and CLN2 and in concert with KSS1 promotes signal transduction. Proc. Natl. Acad. Sci. USA 88 (1991) 9392-9396
27. Alper H., Fischer C., Nevoight E., and Stephanopoulos G. Tuning genetic control through promoter engineering. Proc. Natl. Acad. Sci. USA 102 (2005) 12678-12683
28. Pryciak P.M., and Huntress F.A. Membrane recruitment of the kinase cascade scaffold protein Ste5 by the Gβγ complex underlies activation of the yeast pheromone response pathway. Genes Dev. 12 (1998) 2684-2697
29. Zanolari B., and Riezman H. Quantitation of α-factor internalization and response during Saccharomyces cerevisiae cell cycle. Mol. Cell. Biol. 11 (1991) 5251-5258
30. Oehlen L.J.W.M., and Cross F.R. G1 cyclins CLN1 and CLN2 repress the mating factor response pathway at Start in the yeast cell cycle. Genes Dev. 8 (1994) 1058-1070
31. Colman-Lerner A., Gordon A., Serra E., Chin T., Resnekov O., Endy D., Pesce C.G., and Brent R. Regulated cell-to-cell variation in a cell-fate decision system. Nature 437 (2005) 699-706
32. Volfson D., Marciniak J., Blake W.J., Ostroff N., Tsimring L.S., and Hasty J. Origins of extrinsic variability in eukaryotic gene expression. Nature 439 (2006) 861-864
33. Balaban N.Q., Merrin J., Chait R., Kowalik L., and Leibler S. Bacterial persistence as a phenotypic switch. Science 305 (2004) 1622-1625
34. Zordan R.E., Galgoczy D.J., and Johnson A.D. Epigenetic properties of white-opaque switching in Candida albicans are based on a self-sustaining transcriptional feedback loop. Proc. Natl. Acad. Sci. USA 103 (2006) 12807-12812
35. Huang G., Wang H., Chou S., Nie X., Chen J., and Liu H. Bistable expression of WOR1, a master regulator of white-opaque switching in Candida albicans. Proc. Natl. Acad. Sci. USA 103 (2006) 12813-12818
36. Kussell E., and Leibler S. Phenotypic diversity, population growth, and information in fluctuating environments. Science 309 (2005) 2075-2078
37. Osterfield M., Kirschner M.W., and Flanagan J.G. Graded positional information: Interpretation for both fate and guidance. Cell 113 (2003) 425-428
38. Ashe H.L., and Briscoe J. The interpretation of morphogen gradients. Development 133 (2006) 385-394
39. Von Dassow G., and Odell G.M. Design and constraints of the Drosophila segment polarity module: Robust spatial patterning emerges from intertwined cell state switches. J. Exp. Zool. 294 (2002) 179-215
40. Albert R., and Othmer H.G. The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster. J. Theor. Biol. 223 (2003) 1-18
41. Ingolia N. Robustness and topology in the segment polarity network. PLoS Biol. 2 (2004) 123
42. Guthrie C., and Fink G.R. Guide to Yeast Genetics and Molecular and Cell Biology (2004), Academic Press, San Diego, CA
43. Harju S., Fedosyuk H., and Peterson K.R. Rapid isolation of yeast genomic DNA: Bust n' grab. BMC Biotechnol. 4 (2004) 8