Noise-limited frequency signal transmission in gene circuits

Biophysical Journal

Volumn 93, Issue 11, 2007, Pages 3753-3761

  Tan, Cheemeng ^a   Reza, Faisal ^a,b   You, Lingchong ^a,b  

^a Duke University   (United States)

^b DUKE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CYTOLOGY; FREQUENCY MODULATION; GENE CONTROL; GENETIC MODEL; NOISE; PARAMETER; SIGNAL PROCESSING; SIGNAL TRANSDUCTION; SOUND TRANSMISSION;

EID: 36849003440     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.107.110403     Document Type: Article

References (69)

1. Harmer, S. L., S. Panda, and S. A. Kay. 2001. Molecular bases of circadian rhythms. Annu. Rev. Cell Dev. Biol. 17:215-253.
2. Pourquie, O. 2003. The segmentation clock: converting embryonic time into spatial pattern. Science. 301:328-330.
3. Berridge, M. J., M. D. Bootman, and H. L. Roderick. 2003. Calcium signalling: dynamics, homeostasis and remodelling. Nat. Rev. Mol. Cell Biol. 4:517-529.
4. Berridge, M. J. 1997. The AM and FM of calcium signalling. Nature. 386:759-760.
5. Lahav, G., N. Rosenfeld, A. Sigal, N. Geva-Zatorsky, A. J. Levine, M. B. Elowitz, and U. Alon. 2004. Dynamics of the p53-Mdm2 feedback loop in individual cells. Nat. Genet. 36:147-150.
6. Nelson, D. E., A. E. Ihekwaba, M. Elliott, J. R. Johnson, C. A. Gibney, B. E. Foreman, G. Nelson, V. See, C. A. Horton, D. G. Spiller, S. W. Edwards, H. P. McDowell, J. F. Unitt, E. Sullivan, R. Grimley, N. Benson, D. Broomhead, D. B. Kell, and M. R. White. 2004. Oscillations in NF-kappaB signaling control the dynamics of gene expression. Science. 306:704-708.
7. Holtzendorff, J., D. Hung, P. Brende, A. Reisenauer, P. H. Viollier, H. H. McAdams, and L. Shapiro. 2004. Oscillating global regulators control the genetic circuit driving a bacterial cell cycle. Science. 304:983-987.
8. Klevecz, R. R., and D. B. Murray. 2001. Genome wide oscillations in expression. Wavelet analysis of time series data from yeast expression arrays uncovers the dynamic architecture of phenotype. Mol. Biol. Rep. 28:73-82.
9. Klevecz, R. R., J. Bolen, G. Forrest, and D. B. Murray. 2004. A genomewide oscillation in transcription gates DNA replication and cell cycle. Proc. Natl. Acad. Sci. USA. 101:1200-1205.
10. Jouve, C., I. Palmeirim, D. Henrique, J. Beckers, A. Gossler, D. Ish-Horowicz, and O. Pourquie. 2000. Notch signalling is required for cyclic expression of the hairy-like gene HES1 in the presomitic mesoderm. Development. 127:1421-1429.
11. Morales, A. V., Y. Yasuda, and D. Ish-Horowicz. 2002. Periodic Lunatic fringe expression is controlled during segmentation by a cyclic transcriptional enhancer responsive to notch signaling. Dev. Cell. 3:63-74.
12. Palmeirim, I., D. Henrique, D. Ish-Horowicz, and O. Pourquie. 1997. Avian hairy gene expression identifies a molecular clock linked to vertebrate segmentation and somitogenesis. Cell. 91:639-648.
13. Forsberg, H., F. Crozet, and N. A. Brown. 1998. Waves of mouse Lunatic fringe expression, in four-hour cycles at two-hour intervals, precede somite boundary formation. Curr. Biol. 8:1027-1030.
14. Jiang, Y. J., B. L. Aerne, L. Smithers, C. Haddon, D. Ish-Horowicz, and J. Lewis. 2000. Notch signalling and the synchronization of the somite segmentation clock. Nature. 408:475-479.
15. Conlon, R. A., A. G. Reaume, and J. Rossant. 1995. Notch1 is required for the coordinate segmentation of somites. Development. 121:1533-1545.
16. Oka, C., T. Nakano, A. Wakeham, J. L. de la Pompa, C. Mori, T. Sakai, S. Okazaki, M. Kawaichi, K. Shiota, T. W. Mak, and T. Honjo. 1995. Disruption of the mouse RBP-J κ gene results in early embryonic death. Development. 121:3291-3301.
17. Jen, W. C., D. Wettstein, D. Turner, A. Chitnis, and C. Kintner. 1997. The Notch ligand, X-Δ-2, mediates segmentation of the paraxial mesoderm in Xenopus embryos. Development. 124:1169-1178.
18. Pourquie, O., and K. Kusumi. 2001. When body segmentation goes wrong. Clin. Genet. 60:409-416.
19. Franken, P., L. Lopez-Molina, L. Marcacci, U. Schibler, and M. Tafti. 2000. The transcription factor DBP affects circadian sleep consolidation and rhythmic EEG activity. J. Neurosci. 20:617-625.
20. Richardson, G. S. 2005. The human circadian system in normal and disordered sleep. J. Clin. Psychiatry. 66(Suppl. 9):3-9.
21. Dolmetsch, R. E., K. Xu, and R. S. Lewis. 1998. Calcium oscillations increase the efficiency and specificity of gene expression. Nature. 392:933-936.
22. Kupzig, S., S. A. Walker, and P. J. Cullen. 2005. The frequencies of calcium oscillations are optimized for efficient calcium-mediated activation of Ras and the ERK/MAPK cascade. Proc. Natl. Acad. Sci. USA. 102:7577-7582.
23. Samoilov, M., A. Arkin, and J. Ross. 2002. Signal processing by simple chemical systems. J. Phys. Chem. A. 106:10205-10221.
24. Kaern, M., T. C. Elston, W. J. Blake, and J. J. Collins. 2005. Stochasticity in gene expression: from theories to phenotypes. Nat. Rev. Genet. 6:451-464.
25. Raser, J. M., and E. K. O'Shea. 2005. Noise in gene expression: origins, consequences, and control. Science. 309:2010-2013.
26. Rao, C. V., D. M. Wolf, and A. P. Arkin. 2002. Control, exploitation and tolerance of intracellular noise. Nature. 420:231-237.
27. Paulsson, J. 2004. Summing up the noise in gene networks. Nature. 427:415-418.
28. Bahar, R., C. H. Hartmann, K. A. Rodriguez, A. D. Denny, R. A. Busuttil, M. E. Dolle, R. B. Calder, G. B. Chisholm, B. H. Pollock, C. A. Klein, and J. Vijg. 2006. Increased cell-to-cell variation in gene expression in ageing mouse heart. Nature. 441:1011-1014.
29. Bialek, W., and S. Setayeshgar. 2005. Physical limits to biochemical signaling. Proc. Natl. Acad. Sci. USA. 102:10040-10045.
30. Colman-Lerner, A., A. Gordon, E. Serra, T. Chin, O. Resnekov, D. Endy, C. G. Pesce, and R. Brent. 2005. Regulated cell-to-cell variation in a cell-fate decision system. Nature. 437:699-706.
31. Rosenfeld, N., J. W. Young, U. Alon, P. S. Swain, and M. B. Elowitz. 2005. Gene regulation at the single-cell level. Science. 307:1962-1965.
32. Barkai, N., and S. Leibler. 2000. Circadian clocks limited by noise. Nature. 403:267-268.
33. Hooshangi, S., S. Thiberge, and R. Weiss. 2005. Ultrasensitivity and noise propagation in a synthetic transcriptional cascade. Proc. Natl. Acad. Sci. USA. 102:3581-3586.
34. Pedraza, J. M., and A. van Oudenaarden. 2005. Noise propagation in gene networks. Science. 307:1965-1969.
35. Simpson, M. L., C. D. Cox, and G. S. Sayler. 2003. Frequency domain analysis of noise in autoregulated gene circuits. Proc. Natl. Acad. Sci. USA. 100:4551-4556.
36. Austin, D. W., M. S. Allen, J. M. McCollum, R. D. Dar, J. R. Wilgus, G. S. Sayler, N. F. Samatova, C. D. Cox, and M. L. Simpson. 2006. Gene network shaping of inherent noise spectra. Nature. 439:608-611.
37. Andrews, B. W., T. M. Yi, and P. A. Iglesias. 2006. Optimal noise filtering in the chemotactic response of Escherichia coli. PLoS Comput. Biol. 2:e154.
38. Alter, O., P. O. Brown, and D. Botstein. 2000. Singular value decomposition for genome-wide expression data processing and modeling. Proc. Natl. Acad. Sci. USA. 97:10101-10106.
39. Klevecz, R. R. 2000. Dynamic architecture of the yeast cell cycle uncovered by wavelet decomposition of expression microarray data. Funct. Integr. Genomics. 1:186-192.
40. Tan, C., H. Song, J. Niemi, and L. You. 2007. A synthetic biology challenge: making cells compute. Mol. Biosyst. 3:343-353.
41. Lipan, O., and W. H. Wong. 2005. The use of oscillatory signals in the study of genetic networks. Proc. Natl. Acad. Sci. USA. 102:7063-7068.
42. Gadgil, C., C. H. Lee, and H. G. Othmer. 2005. A stochastic analysis of first-order reaction networks. Bull. Math. Biol. 67:901-946.
43. Thattai, M., and A. van Oudenaarden. 2001. Intrinsic noise in gene regulatory networks. Proc. Natl. Acad. Sci. USA. 98:8614-8619.
44. Walleczek, J. 2000. Self-Organized Biological Dynamics and Nonlinear Control. Cambridge University Press, Cambridge, UK.
45. Gillespie, D. T. 1977. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81:2340-2361.
46. Tse, A., F. W. Tse, W. Almers, and B. Hille. 1993. Rhythmic exocytosis stimulated by GnRH-induced calcium oscillations in rat gonadotropes. Science. 260:82-84.
47. 2+ spike frequency can optimize gene expression. Nature. 392:936-941.
48. Berridge, M. J. 2005. Unlocking the secrets of cell signaling. Annu. Rev. Physiol. 67:1-21.
49. 2+ oscillation. EMBO J. 22:3825-3832.
50. Hasty, J., M. Dolnik, V. Rottschafer, and J. J. Collins. 2002. Synthetic gene network for entraining and amplifying cellular oscillations. Phys. Rev. Lett. 88:148101.
51. Schimke, R. T. 1969. On the roles of synthesis and degradation in regulation of enzyme levels in mammalian tissues. Curr. Top. Cell. Regul. 1:77-124.
52. Becskei, A., and L. Serrano. 2000. Engineering stability in gene networks by autoregulation. Nature. 405:590-593.
53. Rosenfeld, N., M. B. Elowitz, and U. Alon. 2002. Negative autoregulation speeds the response times of transcription networks. J. Mol. Biol. 323:785-793.
54. Savageau, M. A. 1974. Comparison of classical and autogenous systems of regulation in inducible operons. Nature. 252:546-549.
55. Blake, W. J., M. Kaern, C. R. Cantor, and J. J. Collins. 2003. Noise in eukaryotic gene expression. Nature. 422:633-637.
56. 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.
57. Becskei, A., M. G. Boselli, and A. van Oudenaarden. 2004. Amplitude control of cell-cycle waves by nuclear import. Nat. Cell Biol. 6:451-457.
58. Mangan, S., and U. Alon. 2003. Structure and function of the feed-forward loop network motif. Proc. Natl. Acad. Sci. USA. 100:11980-11985.
59. Elowitz, M. B., and S. Leibler. 2000. A synthetic oscillatory network of transcriptional regulators. Nature. 403:335-338.
60. Wiesenfeld, K., and F. Moss. 1995. Stochastic resonance and the benefits of noise: from ice ages to crayfish and SQUIDs. Nature. 373:33-36.
61. Drummond, D. A., J. D. Bloom, C. Adami, C. O. Wilke, and F. H. Arnold. 2005. Why highly expressed proteins evolve slowly. Proc. Natl. Acad. Sci. USA. 102:14338-14343.
62. You, L., and J. Yin. 2006. Evolutionary design on budget: robustness and optimality of bacteriophage T7. IEE Proc. Syst. Biol. 153:46-52.
63. Lim, K. I., T. Lang, V. Lam, and J. Yin. 2006. Model-based design of growth-attenuated viruses. PLoS Comput. Biol. 2:e116.
64. Volfson, D., J. Marciniak, W. J. Blake, N. Ostroff, L. S. Tsimring, and J. Hasty. 2006. Origins of extrinsic variability in eukaryotic gene expression. Nature. 439:861-864.
65. Spudich, J. L., and D. E. Koshland, Jr. 1976. Non-genetic individuality: chance in the single cell. Nature. 262:467-471.
66. Rosenfeld, N., and U. Alon. 2003. Response delays and the structure of transcription networks. J. Mol. Biol. 329:645-654.
67. Raskin, D. M., and P. A. de Boer. 1999. Rapid pole-to-pole oscillation of a protein required for directing division to the middle of Escherichia coli. Proc. Natl. Acad. Sci. USA. 96:4971-4976.
68. Howard, M., and K. Kruse. 2005. Cellular organization by self-organization: mechanisms and models for Min protein dynamics. J. Cell Biol. 168:533-536.
69. Kerr, R. A., H. Levine, T. J. Sejnowski, and W. J. Rappel. 2006. Division accuracy in a stochastic model of Min oscillations in Escherichia coli. Proc. Natl. Acad. Sci. USA. 103:347-352.