In vivo and in vitro studies of TrpR-DNA interactions

Journal of Molecular Biology

Volumn 258, Issue 1, 1996, Pages 37-52

  Yang, Jie ^a   Gunasekera, Angelo ^a   Lavoie, Teresa A ^a   Jin, Lihua ^a   Lewis, Dale E A ^a   Carey, Jannette ^a  

^a PRINCETON UNIVERSITY   (United States)

Author keywords

Affinity; Compensation; Cooperativity; Footprinting; Stoichiometry

Indexed keywords

DIMETHYL SULFATE; PALINDROMIC DNA; REPRESSOR PROTEIN; TRYPTOPHAN; TRYPTOPHAN REPRESSOR; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; BINDING SITE; CONTROLLED STUDY; DNA BINDING; DNA FLANKING REGION; DNA FOOTPRINTING; DNA METHYLATION; DNA SEQUENCE; ESCHERICHIA COLI; GENE EXPRESSION REGULATION; NONHUMAN; OPERATOR GENE; PRIORITY JOURNAL; PROTEIN DNA BINDING; SERRATIA MARCESCENS; STOICHIOMETRY; X RAY DIFFRACTION;

EID: 0029927845     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0232     Document Type: Article

References (59)

1. Bass, S., Sugiono, P., Arvidson, D. N., Gunsalus, R. P. & Youderian, P. (1987). DNA specificity determinants of Escherichia coli tryptophan repressor binding. Genes Dev. 1, 565-572.
2. Bass, S., Sorrells, V. & Youderian, P. (1988). Mutant trp repressors with new DNA-binding specificities. Science, 242, 240-245.
3. Bennett, G. N. & Yanofsky, C. (1978). Sequence analysis of operator constitutive mutants of the tryptophan operon of Escherichia coli. J. Mol. Biol. 121, 179-192.
4. Brewer, A. C., Mason, P. J. & Patient, R. F. (1990). A simplified method for in vivo footprinting using DMS. Nucl. Acids Res. 18, 5574-5574.
5. Cann, J. R. (1989). Phenomenological theory of gel electrophoresis of protein-nucleic acid complexes. J. Biol. Chem. 264, 17032-17040.
6. Carey, J. (1988). Gel retardation at low pH resolves trp repressor-DNA complexes for quantitative study. Proc. Natl Acad. Sci. USA, 85, 975-979.
7. Carey, J. (1989). trp Repressor arms contribute binding energy without occupying unique locations on DNA. J. Biol. Chem. 264, 1941-1945.
8. Carey, J., Lewis, D. E. A., Lavoie, T. A. & Yang, J. (1991). How does trp repressor bind to its operator? J. Biol. Chem. 266, 24509-24513.
9. Carey, J., Combatti, N., Lewis, D. & Lawson, C. L. (1993). Cocrystals of Escherichia coli trp repressor bound to an alternative operator DNA sequence. J. Mol. Biol. 234, 496-498.
10. Cho, K.-O. & Yanofsky, C. (1988). Development of a trp promoter-strength measuring system and its use in comparison of the trp EDCBA, trp R, and aro H promoters. J. Mol. Biol. 204, 41-50.
11. Chou, W.-Y. & Matthews, K. S. (1989). Serine to cysteine mutations in trp repressor protein alter tryptophan and operator binding. J. Biol. Chem. 264, 18314-18319.
12. Czernick, P., Shin, D. S. & Hurlburt, B. K. (1994). Functional selection and characterization of DNA binding sites for trp repressor of Escherichia coli. J. Biol. Chem. 269, 27869-27875.
13. Elledge, S. J. & Davis, R. W. (1989). Position and density effects on repression by stationary and mobile DNA-binding proteins. Genes Dev. 3, 185-197.
14. Ephrussi, A., Church, G. M., Tonegawa, S. & Gilbert, W. (1985). Lineage-specific interactions of an immunoglobulin enhancer with cellular factors in vivo. Science, 227, 134-140.
15. Gunsalus, R. P. & Yanofsky, C. (1980). Nucleotide sequence and expression of Escherichia coli trpR, the structural gene for the trp aporepressor. Proc. Natl Acad. Sci. USA, 77, 7117-7121.
16. Gunsalus, R. P., Zurawski, G. & Yanofsky, C. (1979). Structural and functional analysis of cloned deoxyribonucleic acid containing the trpR-thr region of the E. coli chromosome. J. Bacteriol. 140, 106-113.
17. Gunsalus, R. P., Miguel, A. G. & Gunsalus, G. L. (1986). Intracellular Trp repressor levels in Escherichia coli. J. Bacteriol. 167, 272-278.
18. Haran, T. E., Joachimiak, A. & Sigler, P. B. (1992). The DNA target of the trp repressor. EMBO J. 11, 3021-3030.
19. Haydock, P. V., Bogosian, G., Brechling, K. & Somerville, R. L. (1983). Studies on the interaction of trp holorepressor with several operators. J. Mol. Biol. 170, 1019-1030.
20. Heatwole, V. M. & Somerville, R. L. (1991a). Cloning, nucleotide sequence, and characterization of mtr, the structural gene for a tryptophan-specific permease of Escherichia coli K-12. J. Bacteriol. 173, 108-115.
21. Heatwole, V. M. & Somerville, R. L. (1991b). The tryptophan-specific permease gene, mtr, is differentially regulated by the tryptophan and tyrosine repressors in E. coli K12. J. Bacteriol. 173, 3601-3604.
22. Heatwole, V. M. & Somerville, R. L. (1992). Synergism between the trp repressor and tyr repressor in repression of the aroL promoter of Escherichia coli K-12. J. Bacteriol. 174, 331-335.
23. 2-terminal arms of trp repressor participate in repressor/operator association. Nucl. Acids Res. 20, 337-341.
24. Joachimiak, A., Kelley, R. L., Gunsalus, R. P., Yanofsky, C. & Sigler, P. (1983). Purification and characterization of trp aporepressor. Proc. Natl Acad. Sci. USA, 80, 668-672.
25. Joachimiak, A., Haran, T. E. & Sigler, P. B. (1994). Mutagenesis supports water-mediated recognition in the trp repressor-operator system. EMBO J. 13, 367-372.
26. Kelley, R. L. & Yanofsky, C. (1982). trp aporepressor production is controlled by autogenous regulation and inefficient translation. Proc. Natl Acad. Sci. USA, 79, 3120-3124.
27. Kelley, R. L. & Yanofsky, C. (1985). Mutational studies with the trp repressor of E. coli support the helix-turn-helix model of repressor recognition of operator DNA. Proc. Natl Acad. Sci. USA, 82, 483-487.
28. Klig, L. S., Carey, J. & Yanofsky, C. (1988). trp repressor interactions with the trp, aroH, and trpR operators. J. Mol. Biol. 202, 769-777.
29. Kumamoto, A., Miller, W. & Gunsalus, R. P. (1987). E. coli tryptophan repressor binds multiple sites within the aroH and trp operators. Genes Dev. 1, 556-564.
30. Lawley, B. & Pittard, A. J. (1994). Regulation of aroL expression by TyrR protein and Trp repressor in E. coli K12. J. Bacteriol. 176, 6921-6930.
31. Lawson, C. L. & Carey J. (1993). Tandem binding in crystals of a trp repressor/operator half-site complex. Nature, 366, 178-182.
32. LeTilly, V. & Royer, C. A. (1993). Fluorescence anisotropy assays implicate protein-protein interactions in regulating trp repressor DNA binding. Biochemistry 32, 7753-7758.
33. Lewis, D. E. A. & Carey, J. (1993). Analysis of trp repressor-DNA interactions using gel electrophoresis. Electrophoresis, 14, 713-719.
34. Liu, Y.-C. & Matthews, K. S. (1993). Dependence of trp repressor-operator affinity stoichiometry and apparent cooperativity on DNA sequence and size. J. Biol. Chem. 268, 23239-23249.
35. Maniatis, T., Fritsch, E. F. & Sambrook, J. (1982). Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
36. Marmorstein, R. Q., Sprinzl, M. & Sigler, P. B. (1991). An alkaline phosphatase protection assay to investigate trp repressor/operator interactions. Biochemistry, 30, 1141-1148.
37. Maxam, A. M. & Gilbert, W. (1980). Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 65, 499-560.
38. Nichols, B. P. & Yanofsky, C. (1983). Plasmids containing the trp promoters of Escherichia coli and Serratia marcescens and their use in expressing cloned genes. Methods Enzymol. 101, 155-164.
39. Oppenheim, D. S., Bennett, G. N. & Yanofsky, C. (1980). Escherichia coli RNA polymerase and trp repressor interaction with the promoter-operator region of the tryptophan operon of Salmonella typhimurium. J. Mol. Biol. 144, 133-142.
40. Otwinowski, Z., Schevitz, R. W., Zhang, R.-G., Lawson, C. L., Joachimiak, A., Marmorstein, R. Q., Luisi, B. F. & Sigler, P. B. (1988). Crystal structure of trp repressor/operator complex at atomic resolution. Nature, 335, 321-329.
41. Paluh, J. L. & Yanofsky, C. (1986). High-level production and rapid purification of the E. coli trp repressor. Nucl. Acids Res. 14, 7851-7860.
42. Pearson, W. R. & Lipman, D. J. (1988). Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA, 85, 2444-2448.
43. Reynolds, J. A., Gilbert, D. B. & Tanford, C. (1974). Empirical correlation between hydrophobic free energy and aqueous cavity surface area. Proc. Natl Acad. Sci. USA, 71, 2925-2927.
44. Sarsero, J. P., Wookey, P. J. & Pittard, A. J. (1991). Regulation of expression of Escherichia coli K-12 mtr gene by TyrR protein and trp repressor. J. Bacteriol. 173, 4133-4143.
45. Sasse-Dwight, S. & Gralla, J. D. (1991). Footprinting protein-DNA complexes in vivo. Methods Enzymol. 208, 146-168.
46. Schneider, T. D., Stormo, G. D., Gold, L. & Ehrenfeucht, A. (1986). Information content of binding sites on nucleotide sequences. J. Mol. Biol. 188, 415-431.
47. Senear, D. F. & Brenowitz, M. (1991). Determination of binding constants for cooperative site-specific protein-DNA interactions using the gel mobility-shift assay. J. Biol. Chem. 266, 13661-13671.
48. Spolar, R. S. & Record, M. T. (1994). Coupling of local folding to site specific binding of proteins to DNA. Science, 263, 777-784.
49. Squires, C. L., Lee, F. D. & Yanofsky, C. (1975). Interaction of the trp repressor and RNA polymerase with the trp operon. J. Mol. Biol. 92, 93-111.
50. Staacke, D., Walter, B., Kisters-Woike, B., Wilcken-Bergmann, B. V. & Muller-Hill, B. (1990). How trp repressor binds to its operator. EMBO J. 9, 1963-1967.
51. Sutton, C. L., Mazumder, A., Chen, C. H. & Sigman, D. S. (1993). Transforming the E. coli trp repressor into a site-specific nuclease. Biochemistry, 32, 4225-4230.
52. von Hippel, P. H. & Berg, O. G. (1986). On the specificity of DNA-protein interactions. Proc. Natl Acad. Sci. USA, 83, 1608-1612.
53. Weber, G. (1993). Protein Interactions. Chapman & Hall, New York.
54. Wissman, A. & Hillen, W. (1992). DNA contacts probed by modification protection and interference studies. Methods Enzymol. 208, 365-379.
55. Yang, J. (1995). In vivo and in vitro studies of TrpR-DNA interactions. PhD. Thesis, Princeton University, Princeton, N.J.
56. Yang, J. & Carey, J. (1995). Footprint phenotypes: structural models of DNA-binding proteins from chemical modification analysis of DNA. Methods Enzymol. 259, 452-468.
57. Yang, W., Ni, L. & Somerville, R. L. (1993). A stationary-phase protein of Escherichia coli that affects the mode of association between the trp repressor protein and operator-bearing DNA. Proc. Natl Acad. Sci. USA, 90, 5796-5800.
58. Zurawski, G., Gunsalus, R. P., Brown, K. D. & Yanofsky, C. (1981). Structure and regulation of aroH, the structural gene for the tryptophan-repressible 3-deoxy-D-arabino-heptulosonic acid-7-phosphate synthetase of Escherichia coli. J. Mol. Biol. 145, 47-53.
59. Zwieb, C. & Adhya, S. (1994). Improved plasmid vectors for the analysis of protein-induced DNA bending. Methods. Mol. Biol. 30, 281-294.