Abstract
The mechanism of the self-regulation of gene expression in living cells is generally explained by considering complicated networks of key-lock relationships, and in fact there is a large body of evidence on a hugenumber of key-lock relationships. However, in the present article we stress that with the network hypothesis alone it is impossible to fully explain the mechanism of self-regulation in life. Recently, it has been established that individual giant DNA molecules, larger than several tens of kilo base pairs, undergo a large discrete transition in their higher-order structure. It has become clear that nonspecific weak interactions with various chemicals, suchas polyamines, small salts, ATP and RNA, cause on/off switching in the higher-order structure of DNA. Thus, the field parameters of the cellular environment should play important roles in the mechanism of self-regulation, in addition to networks of key and locks. This conformational transition induced by field parameters may be related to rigid on/off regulation, whereas key-lock relationships may be involved in a more flexible control of gene expression.
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Jacob, F. and Monod, J.: Genetic Regulatory Mechanisms in the Synthesis of Proteins, J. Mol. Biol. 3 (1961), 318–356.
Britten, R.J. and Davidson, E.H.: Gene Regulation for Higher Cells: A Theory, Science 165 (1969), 349–357.
Nicolis, G. and Prigogine, I.: Self-Organization in Nonequilibrium Systems, JohnWiley & Sons, New York, 1977, pp. 354–426.
Goldbeter, A.: Biochemical Oscillations and Cellular Rhythms, Cambridge University Press, 1996.
Murray, J.D.: Mathematical Biology, Springer-Verlag, Berlin, 1990.
Elowitz, M.B. and Leibler, S.: A Synthetic Oscillatory Network of Transcriptional Regulators, Nature 403 (2000), 335–338.
Gardner, T.S., Cantor, C.R. and Collins, J.J.: Construction of a Genetic Toggle Switch in Escherichia coli, 403 (2000), 339–342.
Hasty, J., Pradines, J., Dolnik, M. and Collins, J.J.: Noise-Based Switches and Amplifiers for Gene Expression, Proc. Natl. Acad. Sci., USA 97 (2000), 2075–2080.
von Dassow, G., Meir, E., Munro, E.M. and Odell, G.M.: The Segment Polarity Network is a Robust Developmental Module, Nature 406 (2000), 188–192.
Dziarmaga, J.: Stochastic Gene Expression: Density of Defects Frozen into Permanent Turing Patterns, Phys. Rev. E 63 (2000), 011909.
Brooks, R.: The Relationship between Matter and Life, Nature 409 (2001), 409–411.
McAdams, H.H. and Arkin, A.: Stochastic Mechanisms in Gene Expression, Proc. Natl. Acad. Sci., USA 94 (1997), 814–819.
Endy, D. and Brent, R.: Modeling Cellular Behavior, Nature 409 (2001), 391–395.
Widom, J. and Baldwin, R.J.: Monomolecular Condensation of DNA Induced by Cobalt Hexamine, Biopolymers 22 (1983), 1595–1620.
Bloomfield, V.A.: DNA Condensation, Curr. Opin. Struct. Biol. 6 (1996), 334–341.
Vasilevskaya, V.V., Khokhlov, A.R., Matsuzawa, Y. and Yoshikawa, K.: Collapse of Single DNA in poly(ethylene glycol), Solutions, J. Chem. Phys. 102 (1995), 6595–6602.
Yoshikawa, K., Takahashi, M., Vasilevskaya, V.V. and Khokhlov, A.R.: Large Discrete Transition in a Single DNA Molecule Appears Continuous in the Ensemble, Phys. Rev. Lett. 76 (1996), 3029–3031.
Yoshikawa, K., Kidoaki, S., Takahashi, M., Vasilevskaya, V.V. and Khokhlov, A.R.: Marked Discreteness on the Coil-Globule Transition of Single Duplex DNA, Ber. Bunsen-Ges. Phys. Chem. 100 (1996), 876–880.
Takahashi, M., Yoshikawa, K., Vasilevskaya, V.V. and Khokhlov, A.R.: Discrete Coil-Globule Transition of Single Duplex DNAs induced by Polyamine, J. Phys. Chem. B 101 (1997), 9396–9401.
Yoshikawa, Y. and Yoshikawa, K.: Diaminoalkanes with an Odd Number of Carbon Atoms induce Compaction of a Single Double-Stranded DNA chain, FEBS Lett. 361 (1995), 277–281.
Yamasaki, Y. and Yoshikawa, K.: Higher Order Structure of DNA Controlled by the Redox State of Fe2+/Fe3+, J. Am. Chem. Soc. 119 (1997), 10573–10578.
Mel'nikov, S.M., Sergeyev, V.G. and Yoshikawa, K.: Discrete Coil-Globule Transition of Large DNA by Cationic Surfactant, J. Am. Chem. Soc. 117 (1995), 2401–2408.
Mel'nikov, S.M., Sergeyev, V.G., Yoshikawa, K., Takahashi, H. and Hatta, I.: Cooperativity or Phase Transition? Unfolding Transition of DNA Cationic Surfactant Complex, J. Chem. Phys. 107 (1997), 6917–6924.
Mel'nikov, S.M. and Yoshikawa, K.: First-Order Phase Transition in Large Single Duplex DNA induced by a Nonionic Surfactant, Biochem. Biophys. Res. Commun. 230 (1997), 514–517.
Grosberg, A.Yu. and Khokhlov, A.R.: Statistical Physics of Macromolecules, AIP Press, N.Y., 1994.
Yamasaki, Y., Teramoto, Y. and Yoshikawa, K.: Disappearance of the Negative Charge in Giant DNA with a Folding Transition, Biophys. J. 80 (2001), 2823–2832.
Makita, N. and Yoshikawa, K.: ATP/ADP Switches the Higher-Order Structure of DNA in the Presence of Spermidine, FEBS Lett. 460 (1999), 333–337.
Tsumoto, T. and Yoshikawa, K.: RNA Switches the Higher-Order Structure of DNA, Biophys. Chem. 82 (1999), 1–8.
Takagi, S. and Yoshikawa, K.: Stepwise Collapse of Polyelectrolyte Chains Entrapped in a Finite Space as Predicted by Theoretical Considerations, Langmuir 15 (1999), 4143–4146.
Oana, H., Ueda, M. and Washizu, M.: Visualization of Specific Sequence on a Single Large DNA Molecule using Fluorescence Microscopy based on a New DNA-Stretching Method, Biochem. Biophys. Res. Commun. 265 (1999), 140–143.
Yoshikawa, Y., Velichiko, Yu.S., Ichiba, Y. and Yoshikawa, K.: Self-Assembled Pearling Structure of Long Duplex DNA with Histone H1, Eur. J. Biochem. 268 (2001), 2593–2599.
Yoshikawa, K., Yoshikawa, Y., Koyama, Y. and Kanbe; T.: Highly Effective Compaction of Long Duplex DNA Induced by Polyethylene Glycol with Pendant Amino Groups, J. Am. Chem. Soc. 119 (1997), 6473–6477.
Wolffe, A.: Chromatin, Structure & Function, 2nd ed., Academic Press, 1995.
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Yoshikawa, K. Field Hypothesis on the Self-regulation of Gene Expression. Journal of Biological Physics 28, 701–712 (2002). https://doi.org/10.1023/A:1021251125101
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DOI: https://doi.org/10.1023/A:1021251125101