Relevance of phenotypic noise to adaptation and evolution

IET Systems Biology

Volumn 2, Issue 5, 2008, Pages 234-246

  Kaneko, K ^a,c   Furusawa, C ^b,c  

^a UNIVERSITY OF TOKYO   (Japan)

^b OSAKA UNIVERSITY   (Japan)

^c JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BIOACTIVITY; CELLS; CONCENTRATION (PROCESS); CYTOLOGY; GENE EXPRESSION; GROWTH KINETICS; NETWORK PROTOCOLS; SENSOR NETWORKS; SIGNAL PROCESSING; SIGNAL TRANSDUCTION; STOCHASTIC PROGRAMMING;

ADAPTIVE; ADAPTIVE STATES; BIOLOGICAL PROCESSES; CELLULAR STATES; GENE EXPRESSION NETWORKS; GENE NETWORKS; GENERIC MECHANISMS; GROWTH AND DEVELOPMENTS; MODEL SIMULATIONS; PROTEIN CONCENTRATIONS; SIMPLE STOCHASTIC; STOCHASTIC; STOCHASTICITY; THRESHOLD LEVELS;

CELL GROWTH;

CELL GROWTH; CELL MATURATION; CELL SURVIVAL; CELLULAR STRESS RESPONSE; COMPUTER PROGRAM; COMPUTER SIMULATION; CONFERENCE PAPER; EVOLUTIONARY ADAPTATION; GENE EXPRESSION REGULATION; GENE MUTATION; GENE REGULATORY NETWORK; GROWTH RATE; MATHEMATICAL COMPUTING; NOISE; NONHUMAN; PHENOTYPE; PROTEIN DEGRADATION; PROTEIN EXPRESSION; PROTEIN SYNTHESIS; SIGNAL TRANSDUCTION; STOCHASTIC MODEL;

ADAPTATION, PHYSIOLOGICAL; ANIMALS; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION; HUMANS; MODELS, GENETIC; MODELS, STATISTICAL; MUTATION; PHENOTYPE; PROTEOME; SIGNAL TRANSDUCTION; STOCHASTIC PROCESSES;

EID: 54049118842     PISSN: 17518849     EISSN: None     Source Type: Journal    
DOI: 10.1049/iet-syb:20070078     Document Type: Conference Paper

References (75)

1. Spudich, J.L., and KosCland, D.E.: 'Non-genetic individuality: chance in the single cell', Nature, 1976, 262, p. 467-471 0028-0836
2. Oosawa, F.: 'Effect of the field fluctuation on a macromolecular system', J. Theor. Biol., 1975, 52, p. 175
3. Ko, E., Yomo, T., and Urabe, I.: 'Dynamic clustering of bacterail population', Physica D, 1994, 75, p. 81-88 0167-2789
4. Kaneko, K., and Yomo, T.: 'Cell division, differentiation and dynamic clustering'm', Physica D, 1994, 75, p. 89-102 0167-2789
5. Elowitz, M.B., Levine, A.J., Siggia, E.D., and Swain, P.S.: 'Stochastic gene expression in a single cell', Science, 2002, 297, p. 1183-1187 10.1126/science.1070919 0036-8075
6. Hasty, J., Pradines, J., Dolnik, M., and Collins, J.J.: 'Noise-based switches and amplifiers for gene expression', Proc. Natl. Acad. Sci. USA, 2000, 97, p. 2075-2080 0027-8424
7. McAdams, H.H., and Arkin, A.: 'Stochastic mechanisms in gene expression', Proc. Natl. Acad. Sci. USA, 1997, 94, p. 814-819 0027-8424
8. Raser, J.M., and O'ShOa, E.K.: 'Noise in gene expression: origins, consequences and control', Science, 2005, 23, p. 2010-2013 0036-8075
9. Ozbudak, E.M., Thattai, M., Kurtser, I., Grossman, A.D., and van Oudenaarden, A.: 'Regulation of noise in the expression of a single gene', Nat. Genet., 2002, 31, p. 69-73
10. Korobkova, E., Emonet, T., Vilar, J.M.G., Shimizu, T.S., and Cluzel, P.: 'From molecular noise to behavioural variability in a single bacterium', Nature, 2004, 428, p. 574-578 10.1038/nature02404 0028-0836
11. Arkin, A., Ross, J., and McAdams, H.H.: 'Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells', Genetics, 1998, 149, p. 1633-1648
12. Tkacik, G., Callan, C.G. Jr, Bialek W.: 'Information flow and optimization in transcriptional control', arXiv:q-bio.0709.4209
13. Ziv, E., Nemenman, I., and Wiggins, C.: 'Optimal signal processing in small stochastic biochemical networks', PLoS ONE, 2007, 2, p. e1077
14. Kussell, E., and Leibler, S.: 'Phenotypic diversity, population growth, and information in fluctuating environments', Science, 2005, 309, p. 2075-2078 0036-8075
15. Furusawa, C., Suzuki, T., Kashiwagi, A., Yomo, T., and Kaneko, K.: 'Ubiquity of lognormal distributions in intra-cellular reaction dynamics', Biophysics, 2005, 1, p. 25-31 0006-3509
16. Krishna, S., Banerjee, B., Ramakrishnan, T.V., and Shivashankar, G.V.: 'Stochastic simulations of the origins and implications of long-tailed distributions in gene expression', Proc. Natl. Acad. Sci. USA, 2005, 102, p. 4771-4776 0027-8424
17. Bar-Even, A., Paulsson, J., and Maheshri, N.: Et al. 'Noise in protein expression scales with natural protein abundance', Nat. Genet., 2006, 38, p. 636-643
18. KAneko, K.: 'Life: an introduction to complex systems biology', (Springer, Heidelberg and New York 2006)
19. Kaern, M., Elston, T.C., Blake, W.J., and Collins, J.J.: 'Stochasticity in gene expression: From theories to phenotypes', Nat. Rev. Genet., 2005, 6, p. 451-464
20. Ueda, M., Sako, Y., Tanaka, T., Devreotes, P., and Yanagida, T.: 'Single-molecule analysis of chemotactic signaling in Dictyostelium cells', Science, 2001, 294, p. 864-867 0036-8075
21. Kaneko, K., and Yomo, T.: 'Isologous diversification for robust development of cell society', J. Theor. Biol., 1999, 199, p. 243-256
22. Horsthemke, W., and Lefever, R.: 'Noise-induced transitions', (Springer, Berlin 1984)
23. Kaneko, K.: 'Adiabatic elimination by the eigenfunction expansion method', Prog. Theor. Phys., 1981, 66, p. 129-142 10.1143/PTP.66.129 0033-068X
24. Matsumoto, K., and Tsuda, I.: 'Noise-induced order', J. Stat. Phys., 1983, 31, p. 87 10.1007/BF01010923 0022-4715
25. Benzi, R., Parisi, G., Sutera, A., and Vulpiani, A.: 'A theory of stochastic resonance in climatic change', SIAM J. Appl. Math., 1983, 43, (3), p. 565-578 10.1137/0143037 0036-1399
26. Mcnamara, B., and Wiesenfeld, K.: 'Theory of stochastic resonance', Phys. Rev. A, 1989, 39, p. 4854-4869
27. Kaneko, K.: 'Dominance of milnor attractors and noise-induced selection in a multiattractor system', Phys. Rev. Lett., 1997, 78, p. 2736-2739 0031-9007
28. Kashiwagi, A., Urabe, I., Kaneko, K., and Yomo, T.: 'Adaptive response of a gene network to environmental changes by attractor selection', PLoS ONE, 2006, 1, p. e49
29. Furusawa, C., and Kaneko, K.: 'A generic mechanism for adaptive growth regulation', PLoS Comput. Biol., 2008, 4, p. e3
30. Jacob, F., and Monod, J.: 'Genetic regulatory mechanisms in the synthesis of proteins', J. Mol. Biol., 1961, 3, p. 318-356
31. Bochner, B.R., Gadzinski, P., and Pnomitros, E.: 'Phenotype microarrays for highthroughput phenotypic testing and assay of gene function', Genome Res., 2001, 11, p. 1246-1255
32. Zhou, L., Lei, X., Bochner, B.R., and Wanner, B.L.: 'Phenotype microarray analysis of Escherichia coli K-12 mutants with deletions of all two-component systems', J. Bacteriol., 2003, 185, (16), p. 4956-4972
33. Tatusov, R.L., Fedorova, N.D., and Jackson, J.D.: Et al. 'The COG database: An updated version includes eukaryotes', BMC Bioinformatics, 2003, 4, p. 41
34. Stolovicki, E., Dror, T., Brenner, N., and Braun, E.: 'Synthetic gene-recruitment reveals adaptive reprogramming of gene regulation in yeast', Genetics, 2006, 173, p. 75-85
35. Stem, S., Dror, T., Stolovicki, E., Brenner, N., and Braun, E.: 'Genome-wide transcriptional plasticity underlies cellular adaptation to novel challenge', Mol. Syst. Biol., 2007, 3, p. 106
36. Narang, A.: 'The dynamical analogy between microbial growth on mixtures of substrated abd population growth of competeing species', Biotechnol. Bioeng., 1998, 59, p. 116-121
37. Marr, A.G.: 'Growth rate of Escherichia coli', Microbiol. Rev., 1991, 55, (2), p. 316-333
38. Pakula, T.M., Salonen, K., Uusitalo, J., and Penttila, M.: 'The effect of specific growth rate on protein synthesis and secretion in the filamentous fungus Trichoderma reesei', Microbiology, 2005, 151, p. 135-143
39. Edwards, J.S., and Palsson, B.O.: 'The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities', Proc. Natl. Acad. Sci. USA, 2000, 97, p. 5528-5533 0027-8424
40. Ibarra, R.U., Edwards, J.S., and Palsson, B.O.: 'Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth', Nature, 2002, 420, p. 186-189 0028-0836
41. Fong, S.S., and Palsson, B.O.: 'Metabolic gene deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes', Nat. Genet., 2004, 36, p. 1056-1058
42. Kirschner, M.W., and Gerhart, J.C.: 'The plausibility of life', (Yale University Press 2005)
43. West-Eberhard, M.J.: 'Developmental plasticity and evolution', (Oxford University Press 2003)
44. Ancel, L.W.: 'Undermining the Baldwin Dxpediting effect: does phenotypic plasticity accelerate evolution?', Theor. Popul. Biol., 2000, 58, p. 307-319
45. Callahan, H.S., Pigliucci, M., and Schlichting, C.D.: 'Developmental phenotypic plasticity: Where ecology and evolution meet molecular biology', Bioessays, 1997, 19, p. 519-525
46. Einstein, A., and Furth, R.: 'Investigation on the theory of Brownian movement', (Collection of papers) (Dover 1956) (republication from 1926).
47. Kubo, R., Toda, M., and Hashitsume, N.: 'Statistical physics II', (Springer 1985), English translation
48. Paulsson, J.: 'Summing up the noise in gene networks', Nature, 2004, 427, p. 415 0028-0836
49. Marconi, U.M.B., Puglisi, A., Rondoni, L., and Vulpiani, A.: 'Fluctuation-dissipation: Response theory in statistical physics', Physics Reports, 2008, 462, (3), p. 67-121
50. Sato, K., Ito, Y., Yomo, T., and Kaneko, K.: 'On the relation between fluctuation and response in biological systems', Proc. Nat. Acad. Sci. USA, 2003, 100, p. 14086-14090
51. Kaneko, K., and Furusawa, C.: 'An evolutionary relationship between genetic variation and phenotypic fluctuation', J. Theo. Biol., 2006, 240, p. 78-86
52. Wagner, A.: 'Robustness against mutations in genetic networks of yeast', Nat. Genet., 2000, 24, p. 355-361
53. Ciliberti, S., Martin, O.C., and Wagner, A.: 'Robustness can evolve gradually in complex regulatory gene networks with varying topology', PLOS Comput. Biol., 2007, 3, p. e15
54. de Visser, J.A., Hermisson, J., and Wagner, G.P.: Et al. 'Evolution and detection of genetic robustness', Evolution, 2003, 57, p. 1959-1972
55. Barkai, N., and Leibler, S.: 'Robustness in simple biochemical networks', Nature, 1997, 387, p. 913-917 0028-0836
56. Alon, U., Surette, M.G., Barkai, N., and Leibler, S.: 'Robustness in bacterial chemotaxis', Nature, 1999, 397, p. 168-171 0028-0836
57. Schmalhausen, I.IT: 'Factors of evolution: the theory of stabilizing selection', (University of Chicago Press, Chicago 1949), (reprinted 1986)
58. Waddington, C.H.: 'The strategy of the genes', (Allen & Unwin, London 1957)
59. Waddington, C.H.: 'Genetic assimilation of an acquired character', Evolution, 1953, 7, p. 118-126
60. Ancel, L.W., and Fontana, W.: 'Plasticity, evolvability and modularity in RNA', J. Exp. Zool., 2002, 288, p. 242-283
61. Wagner, G.P., Booth, G., and Bagheri-Chaichian, H.: 'A population genetic theory of canalization', Evolution, 1997, 51, p. 329-347
62. Gibson, G., and Wagner, G.P.: 'CanAlization in evolutionary genetics: a stabilizing theory?', Bioessays, 2000, 22, p. 372-380
63. Kaneko, K.: 'Evolution of robustness to noise and mutation in gene expression dynamics', PLoS ONE, 2007, 2, p. e434
64. Glass, L., and Kauffman, S.A.: 'The logical analysis of continuous, non-linear biochemical control networks', J. Theor. Biol., 1973, 39, p. 103-129
65. Mjolsness, E., Sharp, D.H., and Reisnitz, J.: 'A connectionist model of development', J. Theor. Biol., 1991, 152, p. 429-453
66. Salazar-Ciudad, I., Garcia-Fernandez, J., and Sole, R.V.: 'Gene networks capable of pattern formation: From induction to reaction-diffusion', J. Theor. Biol., 2000, 205, p. 587-603
67. Li, F., Long, T., Lu, Y., Ouyang, Q., and Tang, C.: 'The yeast cell-cycle network is robustly designed', Proc. Nat. Acad. Sci. USA, 2004, 101, p. 10040-10046
68. Wang, J., Huang, B., Xia, X., and Sun, Z.: 'Funneled landscape leads to robustness of cellular networks: MAPK signal transduction', Biophys. J., 2006, 91, p. L54-L56 0006-3495
69. Abe, H., and Go, N.: 'Noninteracting local-structure model of folding and unfolding transition in globular proteins. I. Formulation', Biopolymers, 1980, 20, p. 1013
70. Onuchic, J.N., Wolynes, P.G., Luthey-Schulten, Z., and Socci, N.D.: 'Toward an outline of the topography of a realistic protein-folding funnel', Proc. Natl. Acad. Sci. USA, 1995, 92, p. 3626 0027-8424
71. Baldwin, J.M.: 'A new factor in evolution', Am. Nat., 1896, 30, p. 441-451
72. Bonner, J.T.: 'The evolution of culture in animals', (Princeton University Press 1980)
73. Pigliucci, M., Murren, C.J., and Schlichting, C.D.: 'Phenotypic plasticity and evolution by genetic assimilation', J. Exp. Biol., 2006, 209, p. 2362-2367
74. PigliuccG, M., and Murren, C.J.: 'Perspective: genetic assimilation and a possible evolutionary paradox: Can macroevolution sometimes be so fast as to pass us by?', Evolution, 2003, 57, p. 1455-1464
75. Kaneko, K., and Furusawa, C.: 'Consistency principle in biological dynamical systems theory in bioscience', Theory Biosci., 2008, 127, (2), p. 195-204