Cost-benefit theory and optimal design of gene regulation functions

Physical Biology

Volumn 4, Issue 4, 2007, Pages 229-245

  Kalisky, Tomer ^a   Dekel, Erez ^a   Alon, Uri ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

REGULATOR PROTEIN;

ARTICLE; CELL INTERACTION; COST BENEFIT ANALYSIS; ESCHERICHIA COLI; GENE CONTROL; GENE EXPRESSION; GENE FUNCTION; MOLECULAR EVOLUTION; NOISE; NONHUMAN; OPERON; POSITIVE FEEDBACK; PRIORITY JOURNAL; SIGNAL TRANSDUCTION;

EID: 38049146129     PISSN: 14783967     EISSN: 14783975     Source Type: Journal    
DOI: 10.1088/1478-3975/4/4/001     Document Type: Article

References (55)

1. Elena S F and Lenski R E 2003 Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation Nat. Rev. Genet. 4 457-69
2. Orr H A 2005 The genetic theory of adaptation: a brief history Nat. Rev. Genet. 6 119-27
3. Ibarra R U, Edwards J S and Palsson B O 2002 Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth Nature 420 186-9
4. Koch A L 1983 The protein burden of lac operon products J. Mol. Evol. 19 455-62
5. Dekel E and Alon U 2005 Optimality and evolutionary tuning of the expression level of a protein Nature 436 588-92
6. Dekel E, Mangan S and Alon U 2005 Environmental selection of the feed-forward loop circuit in gene-regulation networks Phys. Biol. 2 81-8
7. Thattai M and van Oudenaarden A 2004 Stochastic gene expression in fluctuating environments Genetics 167 523-30
8. Wolf D M, Vazirani V V and Arkin A P 2005 Diversity in times of adversity: probabilistic strategies in microbial survival games J. Theor. Biol. 234 227-53
9. Jacob F and Monod J 1961 Genetic regulatory mechanisms in the synthesis of proteins J. Mol. Biol. 3 318-56
10. Muller-Hill B 1996 The Lac Operon: A Short History of a Genetic Paradigm (Berlin: Walter de Gruyter) p 207
11. Alon U 2006 An Introduction to Systems Biology: Design Principles of Biological Circuits (Mathematical and Computational Biology Series) 1st edn (Boca Raton, FL: CRC Press)
12. Mayo A E, Setty Y, Shavit S, Zaslaver A and Alon U 2006 Plasticity of the cis-regulatory input function of a gene PLoS Biol. 4 e45
13. Setty Y, Mayo A E, Surette M G and Alon U 2003 Detailed map of a cis-regulatory input function Proc. Natl Acad. Sci. USA 100 7702-7
14. Wang X G, Olsen L R and Roderick S L 2002 Structure of the lac operon galactoside acetyltransferase Structure 10 581-8
15. Andrews K J and Lin E C 1976 Thiogalactoside transacetylase of the lactose operon as an enzyme for detoxification J. Bacteriol. 128 510-3
16. Santillan M and Mackey M C 2004 Influence of catabolite repression and inducer exclusion on the bistable behavior of the lac operon Biophys. J. 86 1282-92
17. Yildirim N and Mackey M C 2003 Feedback regulation in the lactose operon: a mathematical modeling study and comparison with experimental data Biophys. J. 84 2841-51
18. Wong P, Gladney S and Keasling J D 1997 Mathematical model of the lac operon: inducer exclusion, catabolite repression, and diauxic growth on glucose and lactose Biotechnol. Prog. 13 132-43
19. Yagil G and Yagil E 1971 On the relation between effector concentration and the rate of induced enzyme synthesis Biophys. J. 11 11-27
20. Vilar J M and Leibler S 2003 DNA looping and physical constraints on transcription regulation J. Mol. Biol. 331 981-9
21. Mangan S and Alon U 2003 Structure and function of the feed-forward loop network motif Proc. Natl Acad. Sci. USA 100 11980-5
22. Savageau M A 2001 Design principles for elementary gene circuits: elements, methods, and examples Chaos 11 142-59
23. Kussell E and Leibler S 2005 Phenotypic diversity, population growth, and information in fluctuating environments Science 309 2075-8
24. Kaern M, Elston T C, Blake W J and Collins J J 2005 Stochasticity in gene expression: from theories to phenotypes Nat. Rev. Genet. 6 451-64
25. Sigal A, Milo R, Cohen A, Geva-Zatorsky N, Klein Y, Liron Y, Rosenfeld N, Danon T, Perzov N and Alon U 2006 Variability and memory of protein levels in human cells Nature 444 643-6
26. Bar-Even A, Paulsson J, Maheshri N, Carmi M, O'Shea E, Pilpel Y and Barkai N 2006 Noise in protein expression scales with natural protein abundance Nat. Genet. 38 636-43
27. Raser J M and O'Shea E K 2005 Noise in gene expression: origins, consequences, and control Science 309 2010-3
28. Thattai M and van Oudenaarden A 2001 Intrinsic noise in gene regulatory networks Proc. Natl Acad. Sci. USA 98 8614-9
29. Volfson D, Marciniak J, Blake W J, Ostroff N, Tsimring L S and Hasty J 2006 Origins of extrinsic variability in eukaryotic gene expression Nature 439 861-4
30. Cai L, Friedman N and Xie X S 2006 Stochastic protein expression in individual cells at the single molecule level Nature 440 358-62
31. Elowitz M B, Levine A J, Siggia E D and Swain P S 2002 Stochastic gene expression in a single cell Science 297 1183-6
32. Friedman N, Cai L and Xie X S 2006 Linking stochastic dynamics to population distribution: an analytical framework of gene expression Phys. Rev. Lett. 97 168302
33. McAdams H H and Arkin A 1997 Stochastic mechanisms in gene expression Proc. Natl Acad. Sci. USA 94 814-9
34. Swain P S, Elowitz M B and Siggia E D 2002 Intrinsic and extrinsic contributions to stochasticity in gene expression Proc. Natl Acad. Sci. USA 99 12795-800
35. Rosenfeld N, Elowitz M B and Alon U 2002 Negative autoregulation speeds the response times of transcription networks J. Mol. Biol. 323 785-93
36. Rosenfeld N, Young J W, Alon U, Swain P S and Elowitz M B 2005 Gene regulation at the single-cell level Science 307 1962-5
37. Dong H, Nilsson L and Kurland C G 1995 Gratuitous overexpression of genes in Escherichia coli leads to growth inhibition and ribosome destruction J. Bacteriol. 177 1497-504
38. Shen-Orr S S, Milo R, Mangan S and Alon U 2002 Network motifs in the transcriptional regulation network of Escherichia coli Nat. Genet. 31 64-8
39. Kalir S, Mangan S and Alon U 2005 A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli Mol. Syst. Biol. 1 E1-6
40. Mangan S, Itzkovitz S, Zaslaver A and Alon U 2006 The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli J. Mol. Biol. 356 1073-81
41. Mangan S, Zaslaver A and Alon U 2003 The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks J. Mol. Biol. 334 197-204
42. Alon U 2007 Network motifs: theory and experimental approaches Nat. Rev. Genet. 8 450-61
43. Debarbouille M and Schwartz M 1979 The use of gene fusions to study the expression of malT the positive regulator gene of the maltose regulon J. Mol. Biol. 132 521-34
44. Richet E and Raibaud O 1987 Purification and properties of the MalT protein, the transcription activator of the Escherichia coli maltose regulon J. Biol. Chem. 262 12647-53
45. Casadaban M J 1976 Regulation of the regulatory gene for the arabinose pathway, araC J. Mol. Biol. 104 557-66
46. Hahn S and Schleif R 1983 In vivo regulation of the Escherichia coli araC promoter J. Bacteriol. 155 593-600
47. Kolodrubetz D and Schleif R 1981 Identification of araC protein and two-dimensional gels, its in vivo instability and normal level J. Mol. Biol. 149 133-9
48. Geanacopoulos M and Adhya S 1997 Functional characterization of roles of GalR and GalS as regulators of the gal regulon J. Bacteriol. 179 228-34
49. Kar S and Adhya S 2001 Recruitment of HU by piggyback: a special role of GalR in repressosome assembly Genes Dev. 15 2273-81
50. Shinar G, Dekel E, Tlusty T and Alon U 2006 Rules for biological regulation based on error minimization Proc. Natl Acad. Sci. USA 103 3999-4004
51. Zaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, Shavit S, Liebermeister W, Surette M G and Alon U 2006 A comprehensive library of fluorescent transcriptional reporters for Escherichia coli Nat. Method 3 623-8
52. Balagadde F K, You L, Hansen C L, Arnold F H and Quake S R 2005 Long-term monitoring of bacteria undergoing programmed population control in a microchemostat Science 309 137-40
53. Ozbudak E M, Thattai M, Lim H N, Shraiman B I and Van Oudenaarden A 2004 Multistability in the lactose utilization network of Escherichia coli Nature 427 737-40
54. Valentine F A 1946 The problem of Lagrange with differential inequalities as added side conditions Contributions to the Calculus of Variations (1933-1937) ed G A Bliss (Chicago: University of Chicago Press) pp 407-48
55. Desai J P 1998 Motion planning and control of cooperative robotic systems Mechanical Engineering and Applied Mechanics (Philadelphia, PA: University of Pennsylvania) p 180