DNA looping increases the range of bistability in a stochastic model of the lac genetic switch

Physical Biology

Volumn 10, Issue 2, 2013, Pages

  Earnest, Tyler M ^a   Roberts, Elijah ^b,c   Assaf, Michael ^a   Dahmen, Karin ^a,d   Luthey Schulten, Zaida ^a,b  

^a University of Illinois at Urbana Champaign   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^c JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d HEBREW UNIVERSITY OF JERUSALEM   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

ESCHERICHIA COLI;

BACTERIAL DNA; LAC REPRESSOR; MESSENGER RNA;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; ESCHERICHIA COLI; GENETICS; LACTOSE OPERON; STATISTICS;

ALGORITHMS; COMPUTER SIMULATION; DNA, BACTERIAL; ESCHERICHIA COLI; LAC OPERON; LAC REPRESSORS; MODELS, GENETIC; NUCLEIC ACID CONFORMATION; RNA, MESSENGER; STOCHASTIC PROCESSES;

EID: 84876242563     PISSN: 14783967     EISSN: 14783975     Source Type: Journal    
DOI: 10.1088/1478-3975/10/2/026002     Document Type: Article

References (57)

1. Novick A and Weiner M 1957 Enzyme induction as an all-or-none phenomenon Proc. Natl Acad. Sci. 43 553-66
2. Jacob F and Monod J 1961 Genetic regulatory mechanisms in the synthesis of proteins J. Mol. Biol. 3 318-56
3. Choi P J, Cai L, Frieda K and Xie X S 2008 A stochastic single-molecule event triggers phenotype switching of a bacterial cell Science 322 442-6
4. Oehler S, Alberti S and Müller-Hill B 2006 Induction of the lac promoter in the absence of DNA loops and the stoichiometry of induction Nucl. Acids Res. 34 606-12
5. Vilar J M G and Saiz L 2005 DNA looping in gene regulation: from the assembly of macromolecular complexes to the control of transcriptional noise Curr. Opin. Genet. Dev. 15 136-44
6. Oehler S, Amouyal M, Kolkhof P, von Wilcken-Bergmann B and Müller-Hill B 1994 Quality and position of the three lac operators of E. coli define efficiency of repression EMBO J. 13 3348-55
7. Acar M, Mettetal J T and van Oudenaarden A 2008 Stochastic switching as a survival strategy in fluctuating environments Nature Genet. 40 471-5
8. Dekel E and Alon U 2005 Optimality and evolutionary tuning of the expression level of a protein Nature 436 588-92
9. Thattai M 2004 Stochastic gene expression in fluctuating environments Genetics 167 523-30
10. 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
11. Matthews K S 1992 DNA looping Microbiol. Rev. 56 123-36
12. Schleif R 1992 DNA Looping Annu. Rev. Biochem. 61 199-223
13. Choi P J, Xie X S and Shakhnovich E I 2010 Stochastic switching in gene networks can occur by a single-molecule event or many molecular steps J. Mol. Biol. 396 230-44
14. Stamatakis M and Mantzaris N V 2009 Comparison of deterministic and stochastic models of the lac operon genetic network Biophys. J. 96 887-906
15. Mettetal J T, Muzzey D, Pedraza J M, Ozbudak E M and van Oudenaarden A 2006 Predicting stochastic gene expression dynamics in single cells Proc. Natl Acad. Sci. 103 7304-9
16. Vilar J M G, Guet C C and Leibler S 2003 Modeling network dynamics: the lac operon, a case study J. Cell Biol. 161 471-6
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. Pressé S, Ghosh K and Dill K A 2011 Modeling stochastic dynamics in biochemical systems with feedback using maximum caliber J. Phys. Chem. B 115 6202-12
20. Pressé S, Ghosh K, Phillips R and Dill K A 2010 Dynamical fluctuations in biochemical reactions and cycles Phys. Rev. E 82 031905
21. Raser J M and O'Shea E K 2005 Noise in gene expression: origins, consequences, and control Science 309 2010-3
22. 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
23. McAdams H H and Arkin A 1997 Stochastic mechanisms in gene expression Proc. Natl Acad. Sci. 94 814-9
24. Assaf M, Roberts E and Luthey-Schulten Z 2011 Determining the stability of genetic switches: explicitly accounting for mRNA noise Phys. Rev. Lett. 106 248102
25. Shahrezaei V and Swain P S 2008 Analytical distributions for stochastic gene expression Proc. Natl Acad. Sci. 105 17256-61
26. 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
27. Hornos J E M, Schultz D, Innocentini G C P, Wang J, Walczak A M, Onuchic J N and Wolynes P G 2005 Self-regulating gene: an exact solution Phys. Rev. E 72 051907
28. Thattai M and van Oudenaarden A 2001 Intrinsic noise in gene regulatory networks Proc. Natl Acad. Sci. 98 8614-9
29. Kepler T B and Elston T C 2001 Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations Biophys. J. 81 3116-36
30. Peccoud J and Ycart B 1995 Markovian modeling of gene-product synthesis Theor. Popul. Biol. 48 222-34
31. Berg O G 1978 A model for the statistical fluctuations of protein numbers in a microbial population J. Theor. Biol. 71 587-603
32. Munsky B and Khammash M 2006 The finite state projection algorithm for the solution of the chemical master equation J. Chem. Phys. 124 044104
33. Roberts E, Magis A, Ortiz J O, Baumeister W and Luthey-Schulten Z 2011 Noise contributions in an inducible genetic switch: a whole-cell simulation study PLoS Comput. Biol. 7 e1002010
34. Newby J M 2012 Isolating intrinsic noise sources in a stochastic genetic switch Phys. Biol. 9 026002
35. van Kampen N G 2007 Stochastic Processes in Physics and Chemistry (North-Holland Personal Library) 3rd edn (Amsterdam: North Holland)
36. Bender C M and Orszag S A 1999 Advanced Mathematical Methods for Scientists and Engineers: Asymptotic Methods and Perturbation Theory vol 1 (Berlin: Springer)
37. Dykman M I, Mori E, Ross J and Hunt P M 1994 Large fluctuations and optimal paths in chemical kinetics J. Chem. Phys. 100 5735-50
38. Assaf M and Meerson B 2010 Extinction of metastable stochastic populations Phys. Rev. E 81 021116
39. Escudero C and Kamenev A 2009 Switching rates of multistep reactions Phys. Rev. E 79 041149
40. Mehta P, Mukhopadhyay R and Wingreen N S 2008 Exponential sensitivity of noise-driven switching in genetic networks Phys. Biol. 5 026005
41. Morelli M J, Allen R J, Tanase-Nicola S and ten Wolde P R 2008 Eliminating fast reactions in stochastic simulations of biochemical networks: a bistable genetic switch J. Chem. Phys. 128 045105
42. MacNamara S, Bersani A M, Burrage K and Sidje R B 2008 Stochastic chemical kinetics and the total quasi-steady-state assumption: application to the stochastic simulation algorithm and chemical master equation J. Chem. Phys. 129 095105
43. Paulsson J and Ehrenberg M 2000 Random signal fluctuations can reduce random fluctuations in regulated components of chemical regulatory networks Phys. Rev. Lett. 84 5447-50
44. Sánchez A and Kondev J 2008 Transcriptional control of noise in gene expression Proc. Natl Acad. Sci. 105 5081-6
45. MacNamara S, Burrage K and Sidje R 2008 Multiscale modeling of chemical kinetics via the master equation Multiscale Model. Simul. 6 1146-68
46. Dandach S H and Khammash M 2010 Analysis of stochastic strategies in bacterial competence: a master equation approach PLoS Comput. Biol. 6 e1000985
47. Munsky B and Khammash M 2007 A multiple time interval finite state projection algorithm for the solution to the chemical master equation J. Comput. Phys. 226 818-35
48. Sidje R B 1998 Expokit. A software package for computing matrix exponentials ACM Trans. Math. Softw. 24 130-56
49. Micheelsen M A, Mitarai N, Sneppen K and Dodd I B 2010 Theory for the stability and regulation of epigenetic landscapes Phys. Biol. 7 026010
50. Walczak A M, Onuchic J N and Wolynes P G 2005 Absolute rate theories of epigenetic stability Proc. Natl Acad. Sci. 102 18926-31
51. Aurell E and Sneppen K 2002 Epigenetics as a first exit problem Phys. Rev. Lett. 88 048101
52. Munsky B and Khammash M 2008 Transient analysis of stochastic switches and trajectories with applications to gene regulatory networks IET Syst. Biol. 2 323-33
53. Gillespie D T 1977 Exact stochastic simulation of coupled chemical reactions J. Phys. Chem. 81 2340-61
54. Eismann E R and Müller-Hill B 1990 lac repressor forms stable loops in vitro with supercoiled wild-type lac DNA containing all three natural lac operators J. Mol. Biol. 213 763-75
55. Vilar J and Leibler S 2003 DNA looping and physical constraints on transcription regulation J. Mol. Biol. 331 981-9
56. Johnson S, Lindén M and Phillips R 2012 Sequence dependence of transcription factor-mediated DNA looping Nucleic Acids Res. 40 1-11
57. Haeusler A R, Goodson K A, Lillian T D, Wang X, Goyal S, Perkins N C and Kahn J D 2012 Fret studies of a landscape of lac repressor-mediated DNA loops Nucleic Acids Res. 40 4432-45