Effect of phenotypic selection on stochastic gene expression

Journal of Physical Chemistry B

Volumn 117, Issue 42, 2013, Pages 13194-13205

  Mora, Thierry ^a   Walczak, Aleksandra M ^a  

^a CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

STOCHASTIC SYSTEMS; SWITCHING FREQUENCY;

EXPRESSION LEVELS; EXTERNAL SIGNALS; INDUCED STRESS; REGULATORY MODEL; STEADY-STATE DISTRIBUTIONS; STOCHASTIC GENE EXPRESSIONS; SWITCHING RATES; VARIABLE NUMBER;

GENE EXPRESSION;

PROTEIN;

ARTICLE; BIOLOGICAL MODEL; GENE EXPRESSION; GENETICS; METABOLISM; PHENOTYPE;

GENE EXPRESSION; MODELS, GENETIC; PHENOTYPE; PROTEINS;

EID: 84886677830     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp403231f     Document Type: Article

References (47)

1. Fraser, D.; Karen, M. A Chance at Survival: Gene Expression Noise and Phenotypic Diversification Strategies Mol. Microbiol. 2009, 71, 1333-1340
2. Eldar, A.; Elowitz, M. B. Functional Roles for Noise in Genetic Circuits Nature 2010, 467, 167-173
3. Süel, G. M.; Garcia-Ojalvo, J.; Liberman, L. M.; Elowitz, M. B. An Excitable Gene Regulatory Circuit Induces Transient Cellular Differentiation Nature 2006, 440, 545-550
4. Cagatay, T.; Garcia-Ojalvo, J.; Süel, G. M. Architecture-Dependent Noise Discriminates Functionally Analogous Differentiation Circuits Cell 2009, 139, 512-522
5. Balaban, N. Q.; Merrin, J.; Chait, R.; Kowalik, L.; Leibler, S. Bacterial Persistence As a Phenotypic Switch Science 2004, 305, 1622-1625
6. Rotema, E.; Loingera, A.; Ronina, I.; Levin-Reismana, I.; Gabaya, C.; Shoreshd, N.; Bihama, O.; Balaban, N. Q. Regulation of Phenotypic Variability by a Threshold-Based Mechanism Underlies Bacterial Persistence Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 12541-12546
7. Gefen, O.; Balaban, N. Q. The Importance of Being Persistent: Heterogeneity of Bacterial Populations under Antibiotic Stress FEMS Microbiol. Rev. 2009, 33, 704-717
8. Sato, K.; Ito, Y.; Yomo, T.; Kaneko, K. On the Relation between Fluctuation and Response in Biological Systems Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 14086-14090
9. Ito, Y.; Toyota, H.; Kaneko, K.; Yomo, T. How Selection Affects Phenotypic Fluctuation Mol. Syst. Biol. 2009, 5, 264
10. Kashiwagi, A.; Urabe, I.; Kaneko, K.; Yomo, T. Adaptive Response of a Gene Network to Environmental Changes by Fitness-Induced Attractor Selection PLoS ONE 2006, 1, e49
11. Shimizu, Y.; Tsuru, S.; Ito, Y.; Ying, B.-W.; Yomo, T. Stochastic Switching Induced Adaptation in a Starved Escherichia coli Population PLoS ONE 2011, 6, e23953
12. Thattai, M.; van Oudenaarden, A. Stochastic Gene Expression in Fluctuating Environments Genetics 2004, 167, 523-530
13. Kussell, E.; Kishony, R.; Balaban, N. Q.; Leibler, S. Bacterial Persistence Genetics 2005, 169, 1807-1814
14. Kussell, E.; Leibler, S. Phenotypic Diversity, Population Growth, and Information in Fluctuating Environments Science 2005, 309, 2075-2078
15. Leibler, S.; Kussell, E. Individual Histories and Selection in Heterogeneous Populations Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 13183-13188
16. Rivoire, O.; Leibler, S. The Value of Information for Populations in Varying Environments J. Stat. Phys. 2010, 142, 1124-1166
17. Sato, K.; Kaneko, K. On the Distribution of State Values of Reproducing Cells Phys. Biol. 2006, 3, 74-82
18. Tanase-Nicola, S.; ten Wolde, P. R. Regulatory Control and the Costs and Benefits of Biochemical Noise PLoS Comput. Biol. 2008, 4, e1000125
19. Elowitz, M. B.; Levine, A. J.; Siggia, E. D.; Swain, P. S. Stochastic Gene Expression in a Single Cell Science 2002, 297, 1183-1186
20. Ozbudak, E. M.; Thattai, M.; Kurtser, I.; Grossman, A. D.; van Oudenaarden, A. Regulation of Noise in the Expression of a Single Gene Nat. Genet. 2002, 31, 69-73
21. Raser, J. M.; O'Shea, E. K. Control of Stochasticity in Eukaryotic Gene Expression Science 2004, 304, 1811-1814
22. Swain, P. S.; Elowitz, M. B.; Siggia, E. D. Intrinsic and Extrinsic Contributions to Stochasticity in Gene Expression Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 12795-12800
23. Sasai, M.; Wolynes, P. G. Stochastic Gene Expression As a Many-Body Problem Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 2374-2379
24. Kepler, T. B.; Elston, T. C. Stochasticity in Transcriptional Regulation: Origins, Consequences, And Mathematical Representations Biophys. J. 2001, 81, 3116-3136
25. Zwicker, D.; Lubensky, D. K.; ten Wolde, P.-R. Robust Circadian Clocks from Coupled Protein-Modification and Transcription-Translation Cycles Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 22540-22545
26. Friedman, N.; Cai, L.; Xie, X. S. Linking Stochastic Dynamics to Population Distribution: An Analytical Framework of Gene Expression Phys. Rev. Lett. 2006, 97, 168302
27. Walczak, A. M.; Sasai, M.; Wolynes, P. G. Self-Consistent Proteomic Field Theory of Stochastic Gene Switches Biophys. J. 2005, 88, 828-850
28. Cooper, S.; Helmstetter, C. E. Chromosome Replication and the Division Cycle of Escherichia coli B/r J. Mol. Biol. 1968, 31, 519-540
29. Price, G. R. Fisher's 'Fundamental Theorem' Made Clear Annu. Human Genet. 1972, 36, 129-140
30. Gillespie, D. T. Exact Stochastic Simulation of Coupled Chemical Reactions J. Phys. Chem. 1977, 81, 2340-2361
31. Bortz, A. B.; Kalos, M. H.; Lebowitz, J. L. A New Algorithm for Monte Carlo Simulation of Ising Spin Systems J Comput Phys 1975, 17, 10-18
32. Nevozhay, D.; Adams, R. M.; Itallie, E. V.; Bennett, M. R.; Balázsi, G. Mapping the Environmental Fitness Landscape of a Synthetic Gene Circuit PLoS Comput Biol 2012, 8, e1002480
33. Blake, W. J.; Kaern, M.; Cantor, C. R.; Collins, J. J. Noise in Eukaryotic Gene Expression Nature 2003, 422, 633-637
34. Weinberger, L. S.; Dar, R. D.; Simpson, M. L. Transient-Mediated Fate Determination in a Transcriptional Circuit of HIV Nat. Genet. 2008, 40, 466-470
35. Acar, M.; Mettetal, J. T.; van Oudenaarden, A. Stochastic Switching As a Survival Strategy in Fluctuating Environments Nat. Genet. 2008, 40, 471-475
36. Golding, I.; Cox, E. C. Eukaryotic Transcription: What Does It Mean for a Gene to Be 'On'? Curr. Biol. 2006, 16, R371-R373
37. Golding, I.; Paulsson, J.; Zawilski, S. M.; Cox, E. C. Real-Time Kinetics of Gene Activity in Individual Bacteria Cell 2005, 123, 1025-1030
38. Cai, L.; Friedman, N.; Xie, X. S. Stochastic Protein Expression in Individual Cells at the Single Molecule Level Nature 2006, 440, 358-362
39. Chubb, J. R.; Trcek, T.; Shenoy, S. M.; Singer, R. H. Transcriptional Pulsing of a Developmental Gene Curr. Biol. 2006, 16, 1018-1025
40. Walczak, A. M.; Sasai, M.; Wolynes, P. G. Self-Consistent Proteomic Field Theory of Stochastic Gene Switches Biophys. J. 2005, 88, 828-850
41. Hornos, J. E. M.; Schultz, D.; Innocentini, G. C. P.; J. Wang, A. M. W.; Onuchic, J. N.; Wolynes, P. G. Self-Regulating Gene: An Exact Solution Phys. Rev. E 2005, 72, 051907
42. Walczak, A. M.; Mugler, A.; Wiggins, C. H. Analytic Methods for Modeling Stochastic Regulatory Networks. in Methods in Molecular Biology; Betterton, M.; Liu, X., Eds.; Springer Verlag: New York, 2012; Vol. 880.
43. Miekisz, J.; Szymanska, P. Gene Expression in Self-Repressing System with Multiple Gene Copies Bull. Math. Biol. 2013, 75, 317330
44. Abramowitz, M.; Stegun, I. A. Handbook of Mathematical Functions; Applied Mathematics Series; National Bureau of Standards: Gaithersburg, MD, 1972; Vol. 55.
45. Losick, R.; Desplan, C. Stochasticity and Cell Fate Science 2008, 320, 65-68
46. Bialek, W. Stability and Noise in Biochemical Switches. Advances in Neural Information Processing; Massachuetts Institute of Technology: Cambridge, MA, 2001; Vol. 13, pp 103-109.
47. Aurell, E.; Sneppen, K. Epigenetics as a First Exit Problem Phys. Rev. Lett. 2002, 88, 048101