Operator search by mutant Lac repressors

Journal of Molecular Biology

Volumn 278, Issue 3, 1998, Pages 549-558

  Barker, Andrew ^a   Fickert, Reimund ^a,b   Oehler, Stefan ^a,c   Müller Hill, Benno ^a  

^a UNIVERSITY OF COLOGNE   (Germany)

^b SGP   (Germany)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

DNA protein interactions; gal operon; lac operon; Operator binding specificity; Operator search mechanisms

Indexed keywords

BACTERIAL PROTEIN; DIMER; DNA; DNA BINDING PROTEIN; MUTANT PROTEIN; REPRESSOR PROTEIN; TETRAMER;

ARTICLE; BINDING AFFINITY; CONTROLLED STUDY; ESCHERICHIA COLI; LACTOSE OPERON; NONHUMAN; OPERATOR GENE; OPERON; PRIORITY JOURNAL; PROTEIN DNA BINDING;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 0032496385     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1729     Document Type: Article

References (63)

1. Adler K., Beyreuther K., Fanning E., Geisler N., Gronenborn B., Klemm A., Müller-Hill B., Pfahl M., Schmitz A. How lac repressor binds to DNA. Nature. 237:1972;322-327.
2. Aki T., Choy H. E., Adhya S. Histone-like protein HU as a specific transcriptional regulator: co-factor role in repression of gal transcription by Gal repressor. Genes Cells. 1:1996;179-188.
3. Alberti S., Oehler S., von Wilcken-Bergmann B., Krämer H., Müller-Hill B. Dimer-to-tetramer assembly of Lac repressor involves a leucine heptad repeat. New Biologist, 3:1991;57-62.
4. Aslanidis C., Schmitt R. Regulatory elements of the Raffinose operon: nucleotide sequences of operator and repressor genes. J. Bacteriol. 172:1990;2178-2180.
5. Bellomy G. R., Mossing M. C., Record M. T. Jr. Physical properties of DNA in vivo as probed by the length dependence of the lac operator looping process. Biochemistry, 27:1988;3900-3906.
6. Berg O. G., Winter R. B., von Hippel P. H. Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory. Biochemistry, 20:1981;6929-6948.
7. Brenowitz M., Jamison E., Majumdar A., Adhya S. Interaction of the Escherichia coli Gal repressor protein with its DNA operators in vitro. Biochemistry. 29:1990;3374-3383.
8. Brenowitz M., Mandal N., Pickar A., Jamison E., Adhya S. DNA-binding properties of a Lac repressor mutant incapable of forming tetramers. J. Biol. Chem. 266:1991;1281-1288.
9. Butler A. P., Rezvin A., von Hippel P. H. Molecular parameters characterising the interaction of Escherichia coli lac repressor with non-operator DNA and inducer. Biochemistry. 16:1977;4757-4768.
10. Chakerian A. E., Mathews K. S. Characterisation of mutations in oligomerisation domain of Lac repressor protein. J. Biol. Chem. 266:1991;22206-22214.
11. Chin A. M., Feucht B. U., Saier M. H. Jr. Evidence for the regulation of gluconeogenesis by the fructose phosphotransferase system in Salmonella typhimurium. J. Bacteriol. 169:1987;897-899.
12. Choy H. E., Adhya S. Control of gal transcription through DNA looping: inhibition of the initial transcribing complex. Proc. Natl Acad. Sci. USA. 89:1992;11264-11268.
13. Cortay J.-C., Nègre D., Scarabel M., Ramseier T. M., Vartak N. B., Reizer J., Saier M. H. Jr, Cozzone A. J. In vitro asymmetric binding of the pleiotropic regulatory protein, FruR, to the ace operator controlling glyoxylate shunt enzyme synthesis. J. Biol. Chem. 269:1994;14885-14891.
14. Eismann E., von Wilcken-Bergmann B., Müller-Hill B. Specific destruction of the second lac operator decreases repression of the lac operon inEscherichia coli fivefold. J. Mol. Biol. 195:1987;949-952.
15. Ferré-D'Amaré A. R., Burley S. K. DNA recognition by helix-lop-helix proteins. Nucl. Acids Mol. Biol. 7:1994;285-298.
16. Fickert R. Untersuchung zur beschleunigten Operatorsuche durch Lac repressor in Escherichia coli. PhD thesis. 1992;University of Cologne.
17. Fickert R., Müller-Hill B. How Lac repressor finds lac operator in vitro. J. Mol. Biol. 226:1992;59-68.
18. Friedman A. M., Fischmann T. O., Steitz T. A. Crystal structure of lac repressor core tetramer and its implications for DNA looping. Science. 268:1995;1721-1727.
19. Fritz H.-J., Bicknäse B., Gleumes B., Heibach C., Rosahl S., Ehring R. Characterisation of two mutations in the Escherichia coli galE gene inactivating the second galactose operator and comparitive studies of repressor binding. EMBO J. 2:1983;2129-2135.
20. Haber R., Adhya S. Interaction of spatially separated protein-DNA complexes for control of gene expression: operator conversions. Proc. Natl Acad. Sci. USA. 85:1988;9683-9687.
21. Hohn B. In vitro packaging of λ and cosmid DNA. Methods Enzymol. 68:1979;299-309.
22. adiand the native dimeric Gal repressor. J. Biol. Chem. 272:1997;22092-22096.
23. Irani M. H., Orosz L., Adhya S. A control element within a structural gene: the gal operon of Escherichia coli. Cell. 32:1983;783-788.
24. Jacob F., Monod J. Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 3:1961;318-356.
25. Jaenicke R., Muiznieks I., Aslanidis C., Schmitt R. Ultracentrifugal analysis of the quaternary structure of the raf repressor from Escherichia coli. FEBS Letters. 260:1990;233-235.
26. Jobe A., Bourgeois S. The lac repressor-operator interaction VII. A repressor with unique binding properties: the X86 repressor. J. Mol. Biol. 72:1972;139-152.
27. Law S. M., Bellomy G. R., Schlax P. J., Record M. T. Jr. In vivo thermodynamic analysis of repression with and without looping in lac constructs. J. Mol. Biol. 230:1993;161-173.
28. Lehming N., Sartorius J., Niemöller M., Genenger G., von Wilcken-Bergmann B., Müller-Hill B. The interaction of the recognition helix of lac repressor with lac operator. EMBO J. 6:1987;3145-3153.
29. Lehming N., Sartorius J., Oehler S., von Wilcken-Bergmann B., Müller-Hill B. Recognition helices of lac and λ repressor are oriented in opposite directions and recognise similar DNA sequences. Proc. Natl Acad. Sci. USA. 85:1988;7947-7951.
30. Lehming N., Sartorius J., Kisters-Woike B., von Wilcken-Bergmann B., Müller-Hill B. Mutant lac repressors with new specificities hint at rules for protein-DNA recognition. EMBO J. 9:1990;615-621.
31. symoperatores to a LacI tetramer: evidence for contributions of non-operator DNA binding by wrapping and looping. J. Mol. Biol. 260:1996;697-717.
32. Lewis M., Chang G., Horton N. C., Kercher M. A., Pace H. C., Schumacher M. A., Brennan R. G., Lu P. Crystal structure of the lactose operon repressor and its complexes with DNA and inducer. Science. 271:1996;1247-1254.
33. Lieberman B. A., Nordeen S. K. DNA intersegment transfer, how steroid receptors search for a target site. J. Biol. Chem. 272:1997;1061-1068.
34. Majumdar A., Adhya S. Demonstration of two operator elements in gal: in vitro repressor binding studies. Proc. Natl Acad. Sci. USA. 81:1984;6100-6104.
35. L-galR fusion in pKC31 plasmid vector. J. Biol. Chem. 262:1987;2326-2331.
36. Mandal N., Su W., Haber R., Adhya S., Echols H. Genes Dev. 4:1990;410-418.
37. Miller J. H. Experiments in Molecular Genetics. 1972;Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
38. Müller J., Oehler S., Müller-Hill B. Repression of lac promoter as a function of distance, phase and quality of an auxiliary lac operator. J. Mol. Biol. 257:1996;21-29.
39. Müller-Hill B. Sequence homology between Lac and Gal repressors and three sugar-binding periplasmic proteins. Nature. 302:1983;163-164.
40. Müller-Hill B., Beyreuther K., Gilbert W. Lac repressor from Escherichia coli. Methods Enzymol. 21:1971;483-487.
41. Nakanishi S., Adhya S., Gottesman M. E., Pastan I. In vitro repression of the transcription of gal operon by purified gal repressor. Proc. Natl Acad. Sci. USA. 70:1973;334-338.
42. Nègre D., Bonod-Bidaud C., Geourjon C., Deléage G., Cozzone A. J., Cortay J.-C. Definition of a consensus DNA-binding site for the Escherichia coli pleiotropic regulatory protein, FruR. Mol. Microbiol. 21:1996;257-266.
43. Oehler S., Eismann E. R., Krämer H., Müller-Hill B. The three operators of the lac operon cooperate in repression. EMBO J. 9:1990;973-979.
44. Oehler S., Amouyal M., Kolkhof P., von Wilcken-Bergmann B., Müller-Hill B. Quality and position of the three lac operators of E. coli define efficiency of repression. EMBO J. 13:1994;3348-3355.
45. Ptashne M. A Genetic Switch. 1992;Blackwell Scientific Publications Inc. Cambridge.
46. Ramseier T., M. Bledig, S. Michotey, V. Feghali, R. Saier, M. H. Jr. The global regulatory protein FruR modulates the direction of carbon flow in Escherichia coli. Mol. Microbiol. 16:1995;1157-1169.
47. Riggs A. D., Bourgeois S., Cohn M. The lac repressor-operator interaction III. Kinetic studies. J. Mol. Biol. 53:1970a;401-417.
48. Riggs A. D., Suzuki H., Bourgeois S. lac repressor-operator interaction. I. Equilibrium studies. J. Mol. Biol. 48:1970b;67-83.
49. Royer C. A., Chakerian A. E., Matthews K. S. Macromolecular binding equilibria in the lac repressor system: studies using high-pressure fluorescence spectroscopy. Biochemistry, 29:1990;4959-4966.
50. Ruusala T., Crothers D. M. Sliding and intermolecular transfer of the lac repressor: kinetic peturbation of a reaction intermediate by a distant DNA sequence. Proc. Natl Acad. Sci. USA. 89:1992;4903-4907.
51. Sadler J. R., Sasmor H., Betz J. L. A perfectly symmetric lac operator binds the lac repressor very tightly. Proc. Natl Acad. Sci. USA. 80:1983;6785-6789.
52. Sambrook J., Fritsch E. F., Maniatis T. Molecular Cloning; A Laboratory Manual. 1989;Cold Spring Harbor Laboratory Press. Cold Spring Harbor.
53. Schlax P. J., Capp M. W., Record M. T. Jr. Inhibition of transcription initiation by lac repressor. J. Mol. Biol. 245:1995;331-350.
54. Schumacher M. A., Choi K. Y., Zalkin H., Brennan R. G. Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by α helices. Science. 266:1994;763-770.
55. Schumacher M. A., Choi K. Y., Lu F., Zalkin H., Brennan R. G. Mechanism of corepressor-mediated specific DNA binding by the purine repressor. Cell. 83:1995;147-155.
56. Sieg K., Kun J., Pohl I., Scherf A., Müler-Hill B. A versatile phage lambda expression vector system for cloning in Escherichia coli. Gene. 75:1989;261-270.
57. Simons A., Tils D., von Wilcken-Bergmann B., Müller-Hill B. Possible ideal lac operator: Escherichia coli lac operator-like sequences from eukaryotic genomes lack the central G-C pair. Proc. Natl Acad. Sci. USA. 81:1984;1624-1628.
58. Slijper M., Bonvin A. M. J. J., Boelens R., Kaptein R. Refined structure of lac repressor headpiece (1-56) determined by relaxation matrix calculations from 2D and 3D NOE data: change of tertiary structure upon binding to the lac operator. J. Mol. Biol. 259:1996;761-773.
59. Slijper M., Boelens R., Davis A. L., Konings R. N. H., van der Marel G. A., van Boom J. H., Kaptein R. Backbone and side chain dynamics of lac repressor headpiece (1-56) and its complex with DNA. Biochemistry. 36:1997;249-254.
60. Weickert M. J., Adhya S. A family of bacterial regulators homologous to Gal and Lac repressors. J. Biol. Chem. 267:1992;15869-15874.
61. von Hippel P. H., Revzin A., Gross C. A., Wang A. C. Non-specific binding of genome regulating proteins as a biological control mechanism. 1. The lac operon: equilibrium aspects. Proc. Natl Acad. Sci. USA. 71:1974;4808-4812.
62. von Wilcken-Bergmann B., Müller-Hill B. Sequence of galR gene indicates a common evolutionary origin of lac and gal repressor inEscherichia coli. Proc. Natl Acad. Sci. USA. 79:1982;2427-2431.
63. Winter R. B., Berg O. G., von Hippel P. H. Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli lac repressor-operator interaction: kinetic measurements and conclusions. Biochemistry. 20:1981;6961-6977.