Stochastic delay accelerates signaling in gene networks

PLoS Computational Biology

Volumn 7, Issue 11, 2011, Pages

  Josić, Krešimir ^a   López, José Manuel ^a   Ott, William ^a   Shiau, LieJune ^b   Bennett, Matthew R ^c  

^a University of Houston   (United States)

^b UNIVERSITY OF HOUSTON CLEAR LAKE   (United States)

^c RICE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DELAY CIRCUITS; FEEDBACK; QUEUEING THEORY; STOCHASTIC MODELS; STOCHASTIC SYSTEMS; TRANSCRIPTION;

DISTRIBUTED DELAYS; DYNAMIC PROCESS; GENE NETWORKS; GENE REGULATORY NETWORKS; PROTEIN FOLDINGS; RANDOMLY DISTRIBUTED; REACTION CHAINS; STOCHASTIC DELAY; STOCHASTIC NATURE; WAITING TIME;

PROTEINS;

ACCELERATION; ARTICLE; CONTROLLED STUDY; GENE REGULATORY NETWORK; GENETIC TRANSCRIPTION; NEGATIVE FEEDBACK; OSCILLATION; POSITIVE FEEDBACK; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN SYNTHESIS; SIGNAL TRANSDUCTION; STATISTICAL ANALYSIS; ANIMAL; COMPUTER SIMULATION; GENETICS; HUMAN; STATISTICS;

ANIMALS; COMPUTER SIMULATION; GENE REGULATORY NETWORKS; HUMANS; PROTEIN BIOSYNTHESIS; SIGNAL TRANSDUCTION; STOCHASTIC PROCESSES; TRANSCRIPTION, GENETIC;

EID: 81355154066     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002264     Document Type: Article

References (48)

1. Jacob F, Monod J, (1961) Genetic regulatory mechanisms in synthesis of proteins. J Mol Biol 3: 318-356.
2. Alon U, (2007) Network motifs: theory and experimental approaches. Nat Rev Genet 8: 450-461.
3. De Jong H, (2002) Modeling and simulation of genetic regulatory systems: a literature review. J Comp Biol 9: 67-103.
4. Kærn M, Blake WJ, Collins JJ, (2003) The engineering of gene regulatory networks. Annu Rev Biomed Eng 5: 179-206.
5. Gillespie DT, (1977) Exact stochastic simulation of coupled chemical reactions. J Phys Chem 81: 2340-2361.
6. Kepler TB, Elston TC, (2001) Stochasticity in transcriptional regulation: origins consequences, and mathematical representations. Biophys J 81: 3116-3136.
7. Bundschuh R, Hayot F, Jayaprakash C, (2003) Fluctuations and slow variables in genetic networks. Biophys J 84: 1606-1615.
8. Bennett MR, Volfson D, Tsimring L, Hasty J, (2007) Transient dynamics of genetic regulatory networks. Biophys J 92: 3501-3512.
9. Lan YH, Elston TC, Papoian GA, (2008) Elimination of fast variables in chemical Langevin equations. J Chem Phys 129: 214115.
10. McAdams HH, Shapiro L, (1995) Circuit simulation of genetic networks. Science 269: 650-656.
11. Goodwin BC, (1965) Oscillatory behavior in enzymatic control processes. Adv Enzyme Regul 3: 425-438.
12. Mahaffy JM, Pao CV, (1984) Models of genetic control by repression with time delays and spatial effects. J Math Biol 20: 39-57.
13. Chen L, Aihara K, (2002) Stability of genetic regulatory networks with time delay. IEEE Trans Circ Syst 49: 602-608.
14. Smolen P, Baxter DA, Byrne JH, (1999) Effects of macromolecular transport and stochastic uctuations on dynamics of genetic regulatory systems. Am J Physiol Cell Physiol 277: C777-C790.
15. Monk NA, (2003) Oscillatory expression of Hes1, p53, and NF-κB driven by transcriptional time delays. Curr Biol 13: 1409-1413.
16. Lewis J, (2003) Autoinhibition with transcriptional delay: A simple mechanism for the zebrafish somitogeneis oscillator. Curr Biol 13: 1398-1408.
17. Mather W, Bennett MR, Hasty J, Tsimring LS, (2009) Delay-induced degrade-and-fire oscillations in small genetic circuits. Phys Rev Lett 102: 068105.
18. Amir A, Meshner S, Beatus T, Stavans J, (2010) Damped oscillations in the adaptive response of the iron homeostasis network in E. coli. Molec Microbiol 76: 428-436.
19. Stricker J, Cookson S, Bennett MR, Mather WH, Tsimring LS, et al. (2008) A fast, robust and tunable synthetic gene oscillator. Nature 456: 516-519.
20. Tigges M, Marquez-Lago TT, Stelling J, Fussenegger M, (2009) A tunable synthetic mammalian oscillator. Nature 457: 309-12.
21. Larson DR, Zenklusen D, Wu B, Chao JA, Singer RH, (2011) Real-time observation of transcription initiation and elongation on an endogenous yeast gene. Science 332: 475-478.
22. Smolen P, Baxter DA, Byrne JH, (2002) A reduced model clarifies the role of feedback loops and time delays in the drosophila circadian oscillator. Biophys J 83: 2349-2359.
23. Sriram K, Gopinathan MS, (2004) A two variable delay model for the circadian rhythm of neurospora crassa. J Theor Biol 231: 23-38.
24. Ukai-Tadenuma M, Yamada RG, Xu H, Ripperger JA, Liu AC, et al. (2011) Delay in feedback repression by Cryptochrome 1 is required for circadian clock function. Cell 144: 268-281.
25. Chen KC, Csikasz-Nagy A, Gyorffy B, Val J, Novak B, et al. (2000) Kinetic analysis of a molecular model of the budding yeast cell cycle. Molec Biol Cell 11: 369-391.
26. Sevim V, Gong XW, Socolar JES, (2010) Reliability of transcriptional cycles and the yeast cell-cycle oscillator. PLoS Comp Biol 6: e1000842.
27. Tiana G, Jensen MH, Sneppen K, (2002) Time delay as a key to apoptosis induction in the p53 network. Eur Phys J 29: 135-140.
28. Bratsun D, Volfson D, Tsimring LS, Hasty J, (2005) Delay-induced stochastic oscillations in gene regulation. Proc Natl Acad Sci U S A 102: 14593-14598.
29. Maithreye R, Sarkar RR, Parnaik V, Sinha S, (2008) Delay-induced transient increase and heterogeneity in gene expression in negatively auto-regulated gene circuits. PLoS One 3: e2972.
30. Scott M, (2009) Long delay times in reaction rates increase intrinsic uctuations. Phys Rev E 80: 031129.
31. Grönlund A, Lötstedt P, Elf J, (2010) Costs and constraints from time-delayed feedback in small regulatory motifs. Proc Natl Acad Sci U S A 107: 8171-8176.
32. Schlicht R, Winkler G, (2008) A delay stochastic process with applications in molecular biology. J Math Biol 57: 613-648.
33. Arazi A, Ben-Jacob E, Yechiali U, (2004) Bridging genetic networks and queueing theory. Physica A 332: 585-616.
34. Levine E, Hwa T, (2007) Stochastic uctuations in metabolic pathways. Proc Natl Acad Sci USA 104: 9224-9229.
35. Mather WH, Cookson NA, Hasty J, Tsimring LS, Williams RJ, (2010) Correlation resonance by coupled enzymatic processing. Biophys J 99: 3172-3181.
36. Zhu R, Ribeiro AS, Salahub D, Kauffman SA, (2007) Studying genetic regulatory networks at the molecular level: Delayed reaction stochastic models. J Theor Biol 246: 725-745.
37. Zhu R, Salahub D, (2008) Delay stochastic simulation of single-gene expression reveals detailed relationship between protein noise and mean abundance. FEBS Lett 582: 2905-2910.
38. Bel G, Munsky M, Nemenman I, (2010) The simplicity of completion time distributions for common complex biochemical processes. Phys Biol 7: 016003.
39. Elowitz MB, Levine AJ, Siggia ED, Swain PS, (2002) Stochastic gene expression in a single cell. Science 297: 1183-1186.
40. Gross D, Shortle J, Thompson J, Harris C, (2008) Fundamentals of queueing theory. 4th edition Hoboken, New Jersey John Wiley & Sons Inc.
41. Thattai M, van Oudenaarden A, (2002) Attenuation of noise in ultrasensitive signaling cascades. Biophys J 82: 2943-2950.
42. Hooshangi S, Thiberge S, Weiss R, (2005) Ultrasensitivity and noise propogation in a synthetic transcriptional cascade. Proc Natl Acad Sci U S A 102: 3581-3586.
43. Mangan S, Alon U, (2003) Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci U S A 100: 11980-11985.
44. Mangan S, Itzkovitz S, Zaslaver A, Alon U, (2006) The incoherent feed-forward loop accelerates the response-time of the gal system in escherichia coli. J Mol Biol 356: 1073-1081.
45. Goentoro L, Shoval O, Kirschner MW, Alon U, (2009) The incoherent feedforward loop can provide fold-change detection in gene regulation. Mol Cell 36: 894-899.
46. Amir A, Kobiler O, Rokney A, Oppenheim AB, Stavans J, (2007) Noise in timing and precision of gene activities in a genetic cascade. Mol Syst Biol 3: 71.
47. Golding I, Paulsson J, Zawilski SM, Cox EC, (2005) Real-time kinetics of gene activity in individual bacteria. Cell 123: 1025-1036.
48. Cai X, (2007) Exact stochastic simulation of coupled chemical reactions with delays. J Chem Phys 126: 124108.