Near-critical phenomena in intracellular metabolite pools

Biophysical Journal

Volumn 84, Issue 1, 2003, Pages 154-170

  Elf, Johan ^a   Paulsson, Johan ^b   Berg, Otto G ^c   Ehrenberg, Måns ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b PRINCETON UNIVERSITY   (United States)

^c EBC   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME;

ARTICLE; CELL; CORRELATION ANALYSIS; ENZYME MECHANISM; ENZYME SUBSTRATE; ENZYME SUBSTRATE COMPLEX; METABOLITE; MICHAELIS MENTEN KINETICS; MONTE CARLO METHOD; RELAXATION TIME; STATISTICS;

EID: 12244269687     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(03)74839-5     Document Type: Article

References (49)

1. Becskei, A., and L. Serrano. 2000. Engineering stability in gene networks by autoregulation. Nature. 405:590-593.
2. Berg, O. G. 1978. A model for the statistical fluctuations of protein numbers in a microbial population. J. Theor. Biol. 71:587-603.
3. Berg, O. G., J. Paulsson, and M. Ehrenberg. 2000. Fluctuations and quality of control in biological cells: Zero-order ultrasensitivity reinvestigated. Biophys. J. 79:1228-1236.
4. Cluzel, P., M. Surette, and S. Leibler. 2000. An ultrasensitive bacterial motor revealed by monitoring signaling proteins in single cells. Science. 287:1652-1655.
5. Cook, D. L., A. N. Gerber, and S. J. Tapscott. 1998. Modeling stochastic gene expression: Implications for haploinsufficiency. Proc. Natl. Acad. Sci. USA. 95:15641-15646.
6. Cornish-Bowden, A. 1995. Fundamentals of Enzyme Kinetics. Portland Press, Seattle, Washington.
7. Cornish-Bowden, A., and M. L. Cárdenas. 2001. Information transfer in metabolic pathways. Eur. J. Biochem. 268:6616-6624.
8. Dogterom, M., and S. Leibler. 1993. Physical aspects of the growth and regulation of microtubule structures. Phys. Rev. Lett. 70:1347-1350.
9. Edwards, J. S., R. U. Ibarra, and B. O. Palsson. 2001. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat. Biotechnol. 19: 125-130.
10. Ehrenberg, M., and C. G. Kurland. 1984. Costs of accuracy determined by a maximal growth rate constraint. Q. Rev. Biophys. 17:45-82.
11. Elf, J., O. G. Berg, and M. Ehrenberg. 2001. Comparison of repressor and transcriptional attenuator systems for control of amino acid biosynthetic operons. J. Mol. Biol. 313:941-954.
12. Elowitz, M. B., A. J. Levine, E. D. Siggia, and P. S. Swain. 2002. Stochastic gene expression in a single cell. Science. 297:1183-1186.
13. Fano, U. 1947. Ionization yield of rations. II. The fluctuations of the number of ions. Phys. Rev. 72:26-29.
14. Fell, D. 1997. Understanding the Control of Metabolism. Portland Press, London, England.
15. Gardiner, C. 1985. Handbook of Stochastic Methods. Springer Verlag, Berlin, Germany.
16. Gardner, T., C. Cantor, and J. Collins. 2000. Construction of a genetic toggle switch in Escherichia coli. Nature. 403:339-342.
17. Gillespie, D. 1977. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81:2340-2361.
18. Goldbeter, A., and D. E. Koshland, Jr. 1981. An amplified sensitivity arising from covalent modification in biological systems. Proc. Natl. Acad. Sci. USA. 78:6840-6844.
19. Goldbeter, A., and D. E. Koshland, Jr. 1982. Sensitivity amplification in biochemical systems. Q. Rev. Biophys. 15:555-591.
20. Guptasarama, P. 1995. Does replication-induced transcription regulate the myriad of low copy number proteins of Escherichia coli? Bioessays. 17:987-997.
21. Haken, H. 1982. Nonequilibrium phase transitions and self-organization in biological systems. In Thermodynamics and Kinetics of Biological Processes. A. Zotin, editor. Walter de Gruyter, Berlin, Germany.
22. Hasty, J., J. Pradines, M. Dolnik, and J. J. Collins. 2000. Noise-based switches and amplifiers for gene expression. Proc. Natl. Acad. Sci. USA. 97:2075-2080.
23. Heinrich, R., and S. Schuster. 1996. The Regulation of Cellular Systems. Chapman and Hall, New York, New York.
24. Horn, R. A., and C. R. Johnson. 1991. Topics in Matrix Analysis. Cambridge University Press, Cambridge, Massachusetts.
25. Ibba, M., and D. Söll. 2000. Aminoacyl-tRNA synthesis. Annu. Rev. Biochem. 69:617-650.
26. Joel, K. 1987. Statistical Thermodynamics of Nonequilibrium Processes. Springer-Verlag, Berlin.
27. Johnson, N., and S. Kotz. 1969. Discrete Distributions. Houghton Mifflin, Boston, Massachusetts.
28. Jordan, A., and P. Reichar. 1998. Ribonucleotide reductases. Annu. Rev. Biochem. 67:71-98.
29. Kacser, H., and J. A. Bums. 1973. The control of flux. Symp. Soc. Exp. Biol. 27:65-104.
30. Kepler, T. B., and T. C. Elston. 2001. Stochasticity in transcriptional regulation: Origins, consequences, and mathematical representations. Biophys. J. 81:3116-3136.
31. Ko, M. S. 1992. Induction mechanism of a single gene molecule: Stochastic or deterministic? Bioessays. 14:341-346.
32. Koshland, D. E., Jr., A. Goldbeter, and J. B. Stock. 1982. Amplification and adaptation in regulatory and sensory systems. Science. 217:220-225.
33. McAdams, H. H., and A. Arkin. 1997. Stochastic mechanisms in gene expression. Proc. Natl. Acad. Sci. USA. 94:814-819.
34. Metzler, R. 2001. The future is noisy: The role of spatial fluctuations in genetic switching. Phys. Rev. Lett. 87:68-103.
35. Morton-Firth, C., and D. Bray. 2001. Stochastic simulation of cell signaling pathways. In Modeling of Genetic and Biochemical Networks. Bower and Bolouri editors. MIT Press, Cambridge, Massachusetts.
36. Neidhardt, F., R. Curtiss, J. Ingraham, E. Lin, K. Low, B. Magasanik, W. Reznikoff, M. Riley, M. Shcaechter, and H. Umbarger. 1996. Escherichia Coli and Salmonella Typhimurium: Cellular and Molecular Biology. ASM Press, Washington, D.C.
37. Ozbudak, E. M., M. Thattai, I. Kurtser, A. D. Grossman, and A. van Oudenaarden. 2002. Regulation of noise in the expression of a single gene. Nat. Genet. 31:69-73.
38. Paulsson, J. 2000. The Stochastic Nature of Intracellular Control Circuits. Uppsala University, Uppsala, Sweden.
39. Paulsson, J., O. G. Berg, and M. Ehrenberg. 2000. Stochastic focusing: Fluctuation-enhanced sensitivity of intracellular regulation. Proc. Natl. Acad. Sci. USA. 97:7148-7153.
40. Paulsson, J., and M. Ehrenberg. 2001. Noise in a minimal regulatory network: Plasmid copy number control. Q. Rev. Biophys. 34:1-59.
41. Risken, H. 1984. The Fokker-Planck Equation. Springer Verlag, Berlin, Germany.
42. Råde, L., and B. Westergren. 1995. Mathematics Handbook for Science and Engineering. studentlitteratur, Lund, Sweden.
43. Savageau, M. A. 1971. Parameter sensitivity as a criterion for evaluating and comparing the performance of biochemical systems. Nature. 229:542-544.
44. Savageau, M. A. 1976. Biochemical Systems Analysis: A Study of Function and Design in Molecular Biology. Addison-Wesley, Reading, Pennsylvania.
45. Strogatz, S. H. 1994. Nonlinear Dynamics and Chaos: With Applications to Physics, Biology, Chemistry, and Engineering. Addison-Wesley, Cambridge, Massachusetts.
46. Surrey, T., F. Nedelec, S. Leibler, and E. Karsenti. 2001. Physical properties determining self-organization of motors and microtubules. Science. 292:1167-1171.
47. Thattai, M., and A. van Oudenaarden. 2001. Intrinsic noise in gene regulatory networks. Proc. Natl. Acad. Sci. USA. 98:8614-8619.
48. van Kampen, N. 1997. Stochastic Processes in Physics and Chemistry, 2nd Ed. Elsevier, Amsterdam, the Netherlands.
49. Vilar, J. M., H. Y. Kueh, N. Barkai, and S. Leibler. 2002. Mechanisms of noise-resistance in genetic oscillators. Proc. Natl. Acad. Sci. USA. 99:5988-5992.