A computational study of λ-lac mutants

Physical Biology

Volumn 6, Issue 4, 2009, Pages

  Werner, Maria ^a   Aurell, Erik ^a  

^a ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

HYDROLASE; REPRESSOR PROTEIN;

ARTICLE; BACTERIOPHAGE LAMBDA; GENE CONSTRUCT; MATHEMATICAL MODEL; NONHUMAN; PRIORITY JOURNAL; THEORETICAL STUDY; THERMODYNAMICS; COMPUTER SIMULATION; GENE EXPRESSION REGULATION; GENETICS; MUTATION;

ENTEROBACTERIA PHAGE LAMBDA;

BACTERIOPHAGE LAMBDA; COMPUTER SIMULATION; GENE EXPRESSION REGULATION, BACTERIAL; GENE EXPRESSION REGULATION, VIRAL; MUTATION; REPRESSOR PROTEINS; THERMODYNAMICS;

EID: 70350722026     PISSN: 14783967     EISSN: 14783975     Source Type: Journal    
DOI: 10.1088/1478-3975/6/4/046007     Document Type: Article

References (39)

1. Echols H 2001 Operators and Promoters. The Story of Molecular Biology and its Creators (Berkeley, CA: University of California Press)
2. Gottesman M E and Weisberg R A 2004 Little lambda, who made thee? Microbiol. Mol. Biol. Rev. 68 796-813
3. Ptashne M and Gann A 2002 Genes and Signals (New York: Cold Spring Harbor Laboratory Press)
4. Ptashne M 1992 A Genetic Switch 2nd edn (Cambridge: Blackwell Scientific)
5. Lederberg E M and Lederberg J 1953 Genetic studies of lysogenicity in escherichia coli Genetics 38 51-64
6. Lwoff A 1953 Lysogeny Bacteriol. Rev. 17 269-332
7. Shea M A and Ackers G K 1985 The OR control system of bacteriophage lambda. A physical-chemical model for gene regulation J. Mol. Biol. 181 211-30
8. Reinitz J and Vaisnys J R 1990 Theoretical and experimental analysis of the phage lambda genetic switch implies missing levels of co-operativity J. Theor. Biol. 145 295-318
9. Aurell E, Brown S, Johanson J and Sneppen K 2002 Stability puzzles in phage λ Phys. Rev. E 65 051914
10. Zhu X M, Yin L, Hood L and Ao P 2004 Calculating biological behaviors of epigenetic states in the phage λ life cycle Funct. Integr. Genomics 4 188-95
11. Saiz L and Vilar J 2006 Stochastic dynamics of macromolecular-assembly networks Mol. Syst. Biol. 2 2006.0024
12. Bintu L, Buchler N E, GarciaH G, Gerland U, Hwa T, Kondev J and Philips R 2005 Transcriptional regulation by the numbers: models Curr. Opin. Genet. Dev. 15 116-24
13. Bintu L, Buchler N E, GarciaH G, Gerland U, Hwa T, Kondev J and Philips R 2005 Transcriptional regulation by the numbers: applications Curr. Opin. Genet. Dev. 15 125-35
14. Alon Uri 2007 An Introduction to Systems Biology: Design Principles of Biological Circuits (London: Chapman and Hall)
15. Atsumi S and Little J W 2004 Regulatory circuit design and evolution using phage lambda Genes Dev. 18 2086-94
16. Atsumi S and Little J W 2006 Role of the lytic repressor in prophage induction of phage lambda as analyzed by a module-replacement approach Proc. Natl. Acad. Sci. 103 4558-63
17. Revet B, von Wilcken-Bergmann B, Bessert H, Barker A and Muller-Hill B 1999 Four dimers of λ repressor bound to two suitably spaced pairs of λ operators form octamers and DNA loops over large distances Curr. Biol. 9 151-4
18. Dodd I B, Perkins A J, Tsemitsidis D and Egan J B 2001 Octamerization of λ CI repressor is needed for effective repression of PRM and efficient switching from lysogeny Genes Dev. 15 3013-22
19. Platt T, Miller J H and Weber K 1970 In vivo degradation of mutant Lac repressor Nature 228 1154-6
20. Pakula A A, Young V B and Sauer R T 1986 Bacteriophage λ cro mutations: effects on activity and intracellular degradation Proc. Natl. Acad, Sci. 83 8829-33
21. Wilson C J, Zhan H, Swint-Kruse L and Matthews K S 2007 The lactose repressor system: paradigms for regulation, allosteric behavior and protein folding Cell. Mol. Life Sci. 64 3-16
22. Chen J and Matthews K S 1992 Deletion of lactose repressor carboxyl-terminal domain affects tetramer formation J. Biol. Chem. 267 13843-50
23. Betz J L, Sasmor H M, Buck F, Insley M Y and Caruthers M H 1986 Base substitution mutants of the lac operator: in vivo and in vitro affinities for lac repressor Gene 50 123-32
24. O'Gorman R B, Rosenberg J M, Kallai O B, Dickerson R E, Itakura K, Riggs A D and Matthews K S 1980 Equilibrium binding of inducer to lac repressor-operator DNA complex J. Biol. Chem. 255 10107-14
25. Bourgeois S and Pfahl M 1976 Repressors Adv. Protein Chem. 30 1-99
26. Dunaway M, Olson J S, Rosenberg J M, Kallai O B, Dickerson R E and Matthews K S 1980 Kinetic studies of inducer binding to lac repressor-operator complex J. Biol. Chem. 255 10115-9
27. Koblan K S and Ackers G K 1991 Energetics of subunit dimerization in bacteriophage λ cI repressor: Linkage to protons, temperature and KCl Biochemistry 30 7817-21
28. Koblan K S and Ackers G K 1992 Site-specific enthalpic regulation of DNA transcription at bacteriophage λOR Biochemistry 31 57-65
29. Senear D F, Brenowitz M, Shea M A and Ackers G K 1986 Energetics of cooperative protein-DNA interactions: comparison between quantitative deoxyribonuclease footprint titration and filter binding Biochemistry 25 7344-54
30. Dodd I B, Shearwin K E, Perkins A J, Burr T, Hochschild A and Egan J B 2004 Cooperativity in long-range gene regulation by the lambda CI repressor Genes Dev. 18 344-54
31. Aurell E and Sneppen K 2002 Epigenetics as a first exit problem Phys. Rev. Lett. 88 048101
32. Takeda Y, Sarai A and Rivera V M 1989 Analysis of the sequence-specific interactions between Cro repressor and operator DNA by systematic base substitution experiments Proc. Natl. Acad. Sci 86 439-43
33. Jana R, Hazbun T R, Mollah A K M M and Mossing M C 1997 A folded monomeric intermediate in the formation of lambda Cro dimer-DNA complexes J. Mol. Biol. 273 402-16
34. Shean C S and Gottesman M E 1992 Translation of the prophage λ cI transcript Cell 70 513-22
35. Gardner T S, Cantor C R and Collins J J 2000 Construction of a genetic toggle switch in Escherichia coli Nature 403 339-42
36. Kennell D and Reizman H 1977 Transcription and translation initiation frequencies of the Escherichia coli lacOperon J. Mol. Biol. 114 1-21
37. Barrick D, Villanueba K, Childs J, Kalil R, Schneider T D, Lawrence C E, Gold L and Stormo G D 1994 Quantitative analysis of ribosome binding sites in E.coli Nucleic Acid Res. 22 1287-95
38. Svenningsen S L, Costantino N, Court D L and Adhya S 2005 On the role of Cro in λ prophage induction Proc. Natl. Acad. Sci. 102 4465-9
39. Schubert R A, Dodd I B, Egan J B and Shearwin K E 2007 Cro's role in the CI-Cro bistable switch is critical for λ's transition from lysogeny to lytic development Genes Dev. 21 2461-72