Skip to main content
PMC home page
Journal of Biological Physics logoLink to Journal of Biological Physics
. 2002 Dec;28(4):701–712. doi: 10.1023/A:1021251125101

Field Hypothesis on the Self-regulation of Gene Expression

K Yoshikawa 1
PMCID: PMC3456465  PMID: 23345807

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.

Keywords: DNA condensation, environmental parameter, first-order phase transition of DNA, higher-order structure of DNA, on/off regulation, segregation in a chain

Full Text

The Full Text of this article is available as a PDF (142.8 KB).

References

  • 1.Jacob F., Monod J. Genetic Regulatory Mechanisms in the Synthesis of Proteins. J. Mol. Biol. 1961;3:318–356. doi: 10.1016/s0022-2836(61)80072-7. [DOI] [PubMed] [Google Scholar]
  • 2.Britten R.J., Davidson E.H. Gene Regulation for Higher Cells: A Theory. Science. 1969;165:349–357. doi: 10.1126/science.165.3891.349. [DOI] [PubMed] [Google Scholar]
  • 3.Nicolis G., Prigogine I. Self-Organization in Nonequilibrium Systems. New York: JohnWiley & Sons; 1977. pp. 354–426. [Google Scholar]
  • 4.Goldbeter, A.: Biochemical Oscillations and Cellular Rhythms, Cambridge University Press, 1996.
  • 5.Murray J.D. Mathematical Biology. Berlin: Springer-Verlag; 1990. [Google Scholar]
  • 6.Elowitz M.B., Leibler S. A Synthetic Oscillatory Network of Transcriptional Regulators. Nature. 2000;403:335–338. doi: 10.1038/35002125. [DOI] [PubMed] [Google Scholar]
  • 7.Gardner T.S., Cantor C.R., Collins J.J. Construction of a Genetic Toggle Switch in Escherichia coli. 2000;403:339–342. doi: 10.1038/35002131. [DOI] [PubMed] [Google Scholar]
  • 8.Hasty J., Pradines J., Dolnik M., Collins J.J. Noise-Based Switches and Amplifiers for Gene Expression. Proc. Natl. Acad. Sci., USA. 2000;97:2075–2080. doi: 10.1073/pnas.040411297. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 9.von Dassow G., Meir E., Munro E.M., Odell G.M. The Segment Polarity Network is a Robust Developmental Module. Nature. 2000;406:188–192. doi: 10.1038/35018085. [DOI] [PubMed] [Google Scholar]
  • 10.Dziarmaga J. Stochastic Gene Expression: Density of Defects Frozen into Permanent Turing Patterns. Phys. Rev. E. 2000;63:011909. doi: 10.1103/PhysRevE.63.011909. [DOI] [PubMed] [Google Scholar]
  • 11.Brooks R. The Relationship between Matter and Life. Nature. 2001;409:409–411. doi: 10.1038/35053196. [DOI] [PubMed] [Google Scholar]
  • 12.McAdams H.H., Arkin A. Stochastic Mechanisms in Gene Expression. Proc. Natl. Acad. Sci., USA. 1997;94:814–819. doi: 10.1073/pnas.94.3.814. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 13.Endy D., Brent R. Modeling Cellular Behavior. Nature. 2001;409:391–395. doi: 10.1038/35053181. [DOI] [PubMed] [Google Scholar]
  • 14.Widom J., Baldwin R.J. Monomolecular Condensation of DNA Induced by Cobalt Hexamine. Biopolymers. 1983;22:1595–1620. doi: 10.1002/bip.360220612. [DOI] [PubMed] [Google Scholar]
  • 15.Bloomfield V.A. DNA Condensation. Curr. Opin. Struct. Biol. 1996;6:334–341. doi: 10.1016/s0959-440x(96)80052-2. [DOI] [PubMed] [Google Scholar]
  • 16.Vasilevskaya V.V., Khokhlov A.R., Matsuzawa Y., Yoshikawa K. Collapse of Single DNA in poly(ethylene glycol), Solutions. J. Chem. Phys. 1995;102:6595–6602. [Google Scholar]
  • 17.Yoshikawa K., Takahashi M., Vasilevskaya V.V., Khokhlov A.R. Large Discrete Transition in a Single DNA Molecule Appears Continuous in the Ensemble. Phys. Rev. Lett. 1996;76:3029–3031. doi: 10.1103/PhysRevLett.76.3029. [DOI] [PubMed] [Google Scholar]
  • 18.Yoshikawa K., Kidoaki S., Takahashi M., Vasilevskaya V.V., Khokhlov A.R. Marked Discreteness on the Coil-Globule Transition of Single Duplex DNA. Ber. Bunsen-Ges. Phys. Chem. 1996;100:876–880. [Google Scholar]
  • 19.Takahashi M., Yoshikawa K., Vasilevskaya V.V., Khokhlov A.R. Discrete Coil-Globule Transition of Single Duplex DNAs induced by Polyamine. J. Phys. Chem. B. 1997;101:9396–9401. [Google Scholar]
  • 20.Yoshikawa Y., Yoshikawa K. Diaminoalkanes with an Odd Number of Carbon Atoms induce Compaction of a Single Double-Stranded DNA chain. FEBS Lett. 1995;361:277–281. doi: 10.1016/0014-5793(95)00190-k. [DOI] [PubMed] [Google Scholar]
  • 21.Yamasaki Y., Yoshikawa K. Higher Order Structure of DNA Controlled by the Redox State of Fe2+/Fe3+ J. Am. Chem. Soc. 1997;119:10573–10578. [Google Scholar]
  • 22.Mel'nikov S.M., Sergeyev V.G., Yoshikawa K. Discrete Coil-Globule Transition of Large DNA by Cationic Surfactant. J. Am. Chem. Soc. 1995;117:2401–2408. [Google Scholar]
  • 23.Mel'nikov S.M., Sergeyev V.G., Yoshikawa K., Takahashi H., Hatta I. Cooperativity or Phase Transition? Unfolding Transition of DNA Cationic Surfactant Complex. J. Chem. Phys. 1997;107:6917–6924. [Google Scholar]
  • 24.Mel'nikov S.M., Yoshikawa K. First-Order Phase Transition in Large Single Duplex DNA induced by a Nonionic Surfactant. Biochem. Biophys. Res. Commun. 1997;230:514–517. doi: 10.1006/bbrc.1996.5993. [DOI] [PubMed] [Google Scholar]
  • 25.Grosberg A., Khokhlov A.R. Statistical Physics of Macromolecules. N.Y.: AIP Press; 1994. [Google Scholar]
  • 26.Yamasaki Y., Teramoto Y., Yoshikawa K. Disappearance of the Negative Charge in Giant DNA with a Folding Transition. Biophys. J. 2001;80:2823–2832. doi: 10.1016/S0006-3495(01)76249-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 27.Makita N., Yoshikawa K. ATP/ADP Switches the Higher-Order Structure of DNA in the Presence of Spermidine. FEBS Lett. 1999;460:333–337. doi: 10.1016/s0014-5793(99)01368-x. [DOI] [PubMed] [Google Scholar]
  • 28.Tsumoto T., Yoshikawa K. RNA Switches the Higher-Order Structure of DNA. Biophys. Chem. 1999;82:1–8. doi: 10.1016/s0301-4622(99)00098-8. [DOI] [PubMed] [Google Scholar]
  • 29.Takagi S., Yoshikawa K. Stepwise Collapse of Polyelectrolyte Chains Entrapped in a Finite Space as Predicted by Theoretical Considerations. Langmuir. 1999;15:4143–4146. [Google Scholar]
  • 30.Oana H., Ueda M., 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. 1999;265:140–143. doi: 10.1006/bbrc.1999.1614. [DOI] [PubMed] [Google Scholar]
  • 31.Yoshikawa Y., Velichiko Y., Ichiba Y., Yoshikawa K. Self-Assembled Pearling Structure of Long Duplex DNA with Histone H1. Eur. J. Biochem. 2001;268:2593–2599. doi: 10.1046/j.1432-1327.2001.02144.x. [DOI] [PubMed] [Google Scholar]
  • 32.Yoshikawa K., Yoshikawa Y., Koyama Y., Kanbe T. Highly Effective Compaction of Long Duplex DNA Induced by Polyethylene Glycol with Pendant Amino Groups. J. Am. Chem. Soc. 1997;119:6473–6477. [Google Scholar]
  • 33.Wolffe, A.: Chromatin, Structure & Function, 2nd ed., Academic Press, 1995.

Articles from Journal of Biological Physics are provided here courtesy of Springer Science+Business Media B.V.

RESOURCES