Delay-induced anomalous fluctuations in intracellular regulation

Nature Communications

Volumn 2, Issue 1, 2011, Pages

  Grönlund, Andreas ^a   Lötstedt, Per ^a   Elf, Johan ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOSYNTHESIS; CELL FUNCTION; DOWNSTREAM PROCESSING; INTRACELLULAR SIGNALING; MOLECULAR MECHANICS; NEGATIVE FEEDBACK; REGULATORY MECHANISM; TRANSCRIPTION REGULATION; BIOLOGICAL MODEL; CHEMISTRY; GENE EXPRESSION REGULATION; GENETICS; INTRACELLULAR SPACE; KINETICS; METABOLISM; PROTEIN SYNTHESIS;

RNA;

GENE EXPRESSION REGULATION; INTRACELLULAR SPACE; KINETICS; MODELS, GENETIC; PROTEIN BIOSYNTHESIS; RNA;

EID: 80052412641     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms1422     Document Type: Article

References (23)

1. Lestas, I., Vinnicombe, G. & Paulsson, J. Fundamental limits on the suppression of molecular fluctuations. Nature 467, 174-178 (2010
2. Parker, J., Pollard, J. W., Friesen, J. D. & Stanners, C. P. Stuttering: high-level mistranslation in animal and bacterial cells. Proc. Natl Acad. Sci. USA 75, 1091-1095 (1978 (Pubitemid 8305213)
3. O'Farrell, P. H. The suppression of defective translation by ppgpp and its role in the stringent response. Cell 14, 545-557 (1978
4. Elf, J. & Ehrenberg, M. Near-critical behaviour of aminoacyl-RNA pools in E. coli at rate-limiting supply of amino acids. Biophys. J. 88, 132-146 (2005 (Pubitemid 40070664)
5. Lestas, I., Paulsson, J., Ross, N. E. & Vinnicombe, G. Noise in gene regulatory networks. IEEE Trans. Autom. Control 53 (Special Issue), 189-200 (2008 (Pubitemid 351314549)
6. Grönlund, A., Lötstedt, P. & Elf, J. Costs and constraints from time-delayed feedback in small gene regulatory motifs. Proc. Natl Acad. Sci. 107, 8171-8176 (2010
7. Paulsson, J. & Elf, J. System Modeling in Cellular Biology Chapter: Stochastic Modeling of Intracellular Kinetics.MIT Press, (2005
8. Novak, B. & Tyson, J. J. Design principles of biochemical oscillators. Nat. Rev. Mol. Cell Biol. 9, 981-991 (2008
9. Tiana, G., Krishna, S., Pigolotti, S., Jensen, M. H. & Sneppen, K. Oscillations and temporal signalling in cells. Phys. Biol. 4, R1 (2007
10. Danino, T., Mondragon-Palomino, O., Tsimring, L. & Hasty, J. A synchronized quorum of genetic clocks. Nature 463, 326-330 (2010
11. Stricker, J., Cookson, S., Bennett, M. R., Mather, W. H., Tsimring, L. S. & Hasty, J. A fast, robust and tunable synthetic gene oscillator. Nature 456, 516-519 (2008 (Pubitemid 352759003)
12. Bratsun, D., Volfson, D., Tsimring, L. S. & Hasty, J. Delay-induced stochastic oscillations in gene regulation. Proc. Natl Acad. Sci. USA 102, 14593-14598 (2005 (Pubitemid 41457102)
13. Tian, T., Burrage, K., Burrage, P. M. & Carletti, M. Stochastic delay differential equations for genetic regulatory networks. J. Comput. Appl. Math. 205, 696-707 (2007 (Pubitemid 46719713)
14. Gillespie, D. T. A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J. Comput. Phys. 22, 403-434 (1976
15. Murray, J. D. Mathematical Biology, I: An Introduction. Interdisciplinary Applied Mathematics 3rd edn.Springer, (2002
16. van Kampen, N. G. Stochastic Processes in Physics and Chemistry 5th edn.Elsevier, (2004
17. Gadgil, C., Hyeong, C. & Othmer, H. G. A stochastic analysis of first-order reaction networks. Bull. Math. Biol. 67, 901-946 (2005 (Pubitemid 40912459)
18. Jahnke, T. & Huisinga, W. Solving the chemical master equation for monomolecular reaction systems analytically. J. Math. Biol. 54, 1-26 (2007 (Pubitemid 44951311)
19. Elf, J. & Ehrenberg, M. What makes ribosome-mediated transcriptional attenuation sensitive to amino acid limitation? PLoS Comput. Biol. 1, e2 (2005
20. Paulsson, J. Summing up the noise in gene networks. Nature 427, 415-418 (2004 (Pubitemid 38168488)
21. Paulsson, J., Berg, O. G. & Ehrenberg, M. Stochastic focusing: fluctuation-enhanced sensitivity of intracellular regulation. Proc. Natl Acad. Sci. 97, 7148-7153 (2000 (Pubitemid 30431432)
22. Fender, A., Elf, J., Hampel, K., Zimmermann, B., Gerhart, E. & Wagner, H. RNAs actively cycle on the sm-like protein hfq. Genes Dev. 24, 2621-2626 (2010
23. Elf, J. & Ehrenberg, M. Fast evaluation of fluctuations in biochemical networks with the linear noise approximation. Genome Res. 13, 2475-2484 (2003) (Pubitemid 37428272)