Abstract
Taking the famous genetic toggle switch as an example, we numerically investigated the effect of noise on bistability. We found that extrinsic noise resulting from stochastic fluctuations in synthesis and degradation rates and from the environmental fluctuation in gene regulatory processes can induce coherent switch, and that there is an optimal noise intensity such that the noise not only can induce this switch, but also can amplify a weak input signal. In addition, we found that the intrinsic noise introduced through the Poisson τ-leap algorithm cannot induce such a switch.
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Gammaitoni L, Hänggi P, Jung P, Marchesoni F. Stochastic resonance. Rev Modern Phys, 1998, 70(1): 223–287
Hu G, Ditzinger T, Ning C Z, Haken H. Stochastic resonance without extrinsic periodic force. Phys Rev Lett, 1993, 71(6): 807–810
Zhou T S, Chen L N, Aihara K. Molecular communication through stochastic synchronization induced by extracellular fluctuations. Phys Rev Lett, 2005, 95(17): 178103
Han S K, Yim T G, Postnov D E, Sosnovtseva O V. Interacting coherent resonance oscillators. Phys Rev Lett, 1999, 83(9): 1771–1774
Hasty J, Pradines J, Dolnik M, Collins J J. Noise-based switches and amplifiers for gene expression. Proc Natl Acad Sci USA, 2000, 97(5): 2075–2080
Ptashne M. A Genetic Switch: Phage λ and Higher Organisms (Cell, Cambridge, MA), 1992
McAdams H H, Arkin A. Stochastic mechanisms in gene expression. Proc Natl Acad Sci USA, 1997, 94(3): 814–819
Issacs F J, Hasty J, Cantor C R, Collins J J. Prediction and measurement of an autoregulatory genetic module. Proc Natl Acad Sci USA, 2003, 100(13): 7714–7719
Gardner T S, Cantor C R, Collins J J. Construction of a genetic toggle switch in Escherichia coli. Nature, 2000, 403(6767): 339–342
Kobayashi H, Kærn M, Araki M, Chung K, Gardner T S, Cantor C R, Collins J J. Programmable cells: Interfacing natural and engineered gene networks. Proc Natl Acad Sci USA, 2004, 101(22): 8414–8419
Kramer B P, Viretta A. U, El Baba M D, Aubel D, Weber W, Fussenegger M. An engineered epigenetic transgene switch in mammalian cells. Nat Biotechnol, 2004, 22(7): 867–870
Xiong W, Ferrell Je Jr. A positive-feedback-based bistable ‘memory module’ that governs a cell fate decision. Nature, 2003, 402(6965): 460–464
Bagowski C P, Ferrell J E. Bistability in the JNK cascade. Curr Biol, 2001, 11(15): 1176–1182
Harding A, Tian T, Westbury E, Frische E, Hancock J F. Subcellular localization determines MAP kinase signal output. Curr Biol, 2005, 15(9): 869–873
Markevich N I, Hoek J B, Kholodenko B N. Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades. J Cell Biol, 2004, 164(3): 353–359
Pomerening J R, Sontag E D, Ferrell Je Jr. Building a cell cycle oscillator: Hysteresis and bistability in the activiation of Cdc2. Nat Cell Biol, 2003, 5(4): 346–351
Masaki S, Peter G W. Stochastic gene expression as a many-body problem. Proc Natl Acad Sci USA, 2006, 100(5): 2374–2379
Jonathan M R, Erin K O. Noise in gene expression: Origins, consequences, and control. Science, 2005, 309(5736): 2010–2013
Arkin A, Ross J, McAdams H H. Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-infected Escherichia coli cells. Genetics, 1998, 149(4): 1633–1648
Tian T H, Burrage K. Stochastic models for regulatory networks of the genetic toggle switch. Proc Natl Acad Sci USA, 2006, 103(22): 8372–8377
Hasty J, Isaacs F, Dolnik M, McMillen D, Collins J J. Designer gene networks: Towards fundamental cellular control. Chaos, 2001, 11(1): 207–219
Wang Z W, Hou Z H, Xin H W. Internal signal stochastic resonance in synthetic gene networks. Sci China Ser B-Chem, 2005, 48(3): 189–194
Arkady S, Pikovsky A, Kurths J. Coherence resonance in a noise-driven excitable system. Phys Rev Lett, 1997, 78(5): 775–778
Pikovsky A, Zaikin A. System size resonance in coupled noisy systems and in the Ising model. Phys Rev Lett, 2002, 88(5): 050601
Liu Q, Jia Y. Fluctuations-induced switch in the gene transcriptional regulatory system. Phys Rev E, 2004, 70(4): 041907
Chen J R. Improving the speed of the genetic toggle switch without sacrificing its dynamic stability. Phys Rev E, 2006, 73(4): 041901
Gillespie D T. Approximate accelerated stochastic simulation chemically reacting systems. J Chem Phys, 2001, 115(4): 1716–1733
Elowitz M B, Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature, 2000, 403(6767): 335–338
Ao P. Potential in stochastic differential equations: Novel construction. J Phys A: Math Gen, 2004, 37: L25–L30
Wang J, Huang B, Xia X F, Sun Z R. Funneled landscape leads to robustness of cell networks: Yeast cell cycle. PLoS Comput Biol, 2006, 2(11): 1385–1394
Jung P, Hänggi P. Stochastic nonlinear dynamics modulated by extrinsic periodic forces. Europhys Lett, 1989, 8: 505–510
Zhou T S, Zhang J J, Yuan Z J, Xu A L. Extrinsic stimuli mediate collective rhythms: Artificial control strategies. PLoS One, 2007, 2: e231
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Supported by the National Distinguished PhD Dissertations (200521) and the National Natural Science Foundation of China (Grant No. 60736208)
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Yuan, Z., Zhang, J. & Zhou, T. Noise-induced coherent switch. Sci. China Ser. B-Chem. 51, 562–569 (2008). https://doi.org/10.1007/s11426-007-0134-5
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DOI: https://doi.org/10.1007/s11426-007-0134-5