The DNA-binding domain of the ultraspiracle drives deformation of the response element whereas the DNA-binding domain of the ecdysone receptor is responsible for a slight additional change of the preformed structure

Biochemistry

Volumn 45, Issue 3, 2006, Pages 668-675

  Dobryszycki, Piotr ^a   Grad, Iwona ^a,b   Krusiński, Tomasz ^a   Michaluk, Piotr ^a,c   Sawicka, Dorota ^a   Kowalska, Agnieszka ^a   Orłowski, Marek ^a   Jakób, Michał ^a   Rymarczyk, Grzegorz ^a   Kochman, Marian ^a   Ozyhar, Andrzej ^a  

^a WROCLAW UNIVERSITY OF TECHNOLOGY   (Poland)

^b UNIVERSITY OF GENEVA   (Switzerland)

^c NENCKI INSTITUTE OF EXPERIMENTAL BIOLOGY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

DIMERS; ENZYMES; FLUORESCENCE; GELS; GENES; PROTEINS;

FLUORESCENCE DECAY; FLUORESCENCE RESONANCE ENERGY TRANSFER (FRET); GEL RETARDATION; METAMORPHOSIS;

DNA;

CELL NUCLEUS RECEPTOR; ECDYSONE RECEPTOR; ECDYSTEROID; INSECT PROTEIN; PALINDROMIC DNA; ULTRASPIRACLE PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; DNA BINDING MOTIF; DNA FOOTPRINTING; DNA RESPONSIVE ELEMENT; FLUORESCENCE RESONANCE ENERGY TRANSFER; GENE; HSP27 GENE; METAMORPHOSIS; MOLTING; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DNA BINDING; PROTEIN STRUCTURE; STEADY STATE;

ANIMALS; BASE SEQUENCE; BINDING SITES; DNA; DNA-BINDING PROTEINS; FLUORESCENCE RESONANCE ENERGY TRANSFER; HEAT-SHOCK PROTEINS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; RECEPTORS, STEROID; RESPONSE ELEMENTS; STRUCTURE-ACTIVITY RELATIONSHIP; TRANSCRIPTION FACTORS;

HEXAPODA; INSECTA;

EID: 31044441892     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi051354b     Document Type: Article

References (43)

1. Claessens, F., and Gewirth, D. T. (2004) DNA recognition by nuclear receptors, Essays Biochem. 40, 59-72.
2. Lane, D., Prentki, P., and Chandler, M. (1992) Use of gel retardation to analyze protein-nucleic acid interactions, Microbiol. Rev. 56, 509-528.
3. Potthoff, S. J., Romine, L. E., and Nardulli, A. M. (1996) Effects of wild type and mutant estrogen receptors on DNA flexibility, DNA bending, and transcription activation, Mol. Endocrinol. 10, 1095-1106.
4. Shulemovich, K., Dimaculangan, D. D., Katz, D., and Lazar, M. A. (1995) DNA bending by thyroid hormone receptor: influence of half-site spacing and RXR, Nucleic Acids Res. 23, 811-818.
5. Petz, L. N., Nardulli, A. M., Kim, J., Horwitz, K. B., Freedman, L. P., and Shapiro, D. J. (1997) DNA bending is induced by binding of the glucocorticoid receptor DNA binding domain and progesterone receptors to their response element, J. Steroid Biochem. Mol. Biol. 60, 31-41.
6. Prendergast, P., Pan, Z., and Edwards, D. P. (1996) Progesterone receptor-induced bending of its target DNA: distinct effects of the A and B receptor forms, Mol. Endocrinol. 10, 393-407.
7. Aguinaldo, A. M., Turbeville, J. M., Linford, L. S., Rivera, M. C., Garey, J. R., Raff, R. A., and Lake, J. A. (1997) Evidence for a clade of nematodes, arthropods and other moulting animals, Nature 387, 489-493.
8. Yao, T. P., Segraves, W. A., Oro, A. E., McKeown, M., and Evans, R. M. (1992) Drosophila ultraspiracle modulates ecdysone receptor function via heterodimer formation, Cell 71, 63-72.
9. Thomas, H. E., Stunnenberg, H. G., and Stewart, A. F. (1993) Heterodimerization of the Drosophila ecdysone receptor with retinoid X receptor and ultraspiracle, Nature 362, 471-475.
10. Andres, A. J., Fletcher, J. C., Karim, F. D., and Thummel, C. S. (1993) Molecular analysis of the initiation of insect metamorphosis: a comparative study of Drosophila ecdysteroid-regulated transcription, Dev. Biol. 160, 388-404.
11. Hu, X., Cherbas, L., and Cherbas, P. (2003) Transcription activation by the ecdysone receptor (EcR/USP): identification of activation functions, Mol. Endocrinol. 17, 716-731.
12. Niedziela-Majka, A., Kochman, M., and Ożyhar, A. (2000) Polarity of the ecdysone receptor complex interaction with the palindromic response element from the hsp27 gene promoter, Eur. J. Biochem. 267, 507-519.
13. Khorasanizadeh, S., and Rastinejad, F. (2001) Nuclear-receptor interactions on DNA-response elements, Trends Biochem. Sci. 26, 384-390.
14. Riddihough, G., and Pelham, H. R. B. (1987) An ecdysone response element in the Drosophila hsp27 promoter, EMBO J. 6, 3729-3734.
15. Ożyhar, A., Strangmann-Diekmann, M., Kiltz, H. H., and Pongs, O. (1991) Characterization of a specific ecdysteroid receptor-DNA complex reveals common properties for invertebrate and vertebrate hormone-receptor/DNA interactions, Eur. J. Biochem. 200, 329-335.
16. Ozers, M. S., Hill, J. J., Ervin, K., Wood, J. R., Nardulli, A. M., Royer, C. A., and Gorski, J. (1997) Equilibrium binding of estrogen receptor with DNA using fluorescence anisotropy, J. Biol. Chem. 272, 30405-30411.
17. Wang, X., Graveland-Bikker, J. F., de Kruif, C. G., and Robillard, G. T. (2004) Oligomerization of hydrophobin SC3 in solution: from soluble state to self-assembly, Protein Sci. 13, 810-821.
18. Grad, I., Niedziela-Majka, A., Kochman, M., and Ożyhar, A. (2001) Analysis of Usp DNA binding domain targeting reveals critical determinants of the ecdysone receptor complex interaction with the response element, Eur. J. Biochem. 268, 3751-3758.
19. Niedziela-Majka, A., Rymarczyk, G., Kochman, M., and Ożyhar, A. (1998) Pure, bacterially expressed DNA-binding domains of the functional ecdysteroid receptor capable of interacting synergistically with the hsp27 20-hydroxyecdysone response element. GST-Induced dimerization of DNA-binding domains alters characteristics of their interaction with DNA, Protein Expression Purif. 14, 208-220.
20. Kim, J., Zwieb, C., Wu, C., and Adhya, S. (1989) Bending of DNA by gene-regulatory proteins: construction and use of a DNA bending vector, Gene 85, 15-23.
21. Förster, T. (1948) Intermolecular energy migration and fluorescence, Ann. Phys. (Lepzig) 2, 55-75.
22. Fairclough, R. H., and Cantor, C. R. (1977) in Methods in Enzymology (Hirs, C. H. W., and Timasheff, S. N., Eds.) pp 347-379, Academic Press, New York.
23. Clegg, R. M., Murchie, A. I., Zechel, A., and Lilley, D. M. (1993) Observing the helical geometry of double-stranded DNA in solution by fluorescence resonance energy transfer, Proc. Natl. Acad. Sci. U.S.A. 90, 2994-2998.
24. Gohlke, C., Murchie, A. I., Lilley, D. M., and Clegg, R. M. (1994) Kinking of DNA and RNA helices by bulged nucleotides observed by fluorescence resonance energy transfer, Proc. Natl. Acad. Sci. U.S.A. 91, 11660-11664.
25. Vamosi, G., Gohlke, C., and Clegg, R. M. (1996) Fluorescence characteristics of 5-carboxytetramethylrhodamine linked covalently to the 5′ end of oligonucleotides: multiple conformers of single-stranded and double-stranded dye-DNA complexes, Biophys. J. 71, 972-994.
26. Lorenz, M., Hillisch, A., Goodman, S. D., and Diekmann, S. (1999) Global structure similarities of intact and nicked DNA complexed with IHF measured in solution by fluorescence resonance energy transfer, Nucleic Acids Res. 27, 4619-4625.
27. Lakowicz, J. R. (1999) Priciples of Fluorescence Spectroscopy, Kluwer Academic Plenum Publishers, New York.
28. Wu, J., Parkhurst, K. M., Powell, R. M., Brenowitz, M., and Parkhurst, L. J. (2001) DNA bends in TATA-binding protein-TATA complexes in solution are DNA sequence-dependent, J. Biol. Chem. 276, 14614-14622.
29. Grad, I., Kochman, M., and Ożyhar, A. (2002) Functionality versus strength-Has functional selection taken place in the case of the ecdysteroid receptor response element?, Acta Biochim. Pol. 49, 747-756.
30. Ferrari, S., Harley, V. R., Pontiggia, A., Goodfellow, P. N., Lovell-Badge, R., and Bianchi, M. E. (1992) SRY, like HMG1, recognizes sharp angles in DNA, EMBO J. 11, 4497-4506.
31. Mischati, C., Feriotto, G., Bianchi, N., and Gambari, R. (1995) A non-radioactive automated protocol to study protein-DNA interactions by DNase I footprinting, Int. J. Oncol. 6, 153-156.
32. Melcher, S. E., Wilson, T. J., and Lilley, D. M. (2003) The dynamic nature of the four-way junction of the hepatitis C virus IRES, RNA 9, 809-820.
33. Wu, H. M., and Crothers, D. M. (1984) The locus of sequence-directed and protein-induced DNA bending, Nature 308, 509-513.
34. Ożyhar, A., and Pongs, O. (1993) Mutational analysis of the interaction between ecdysteroid receptor and its response element, J. Steroid Biochem. Mol. Biol. 46, 135-145.
35. Devarakonda, S., Harp, J. M., Kim, Y., Ożyhar, A., and Rastinejad, F. (2003) Structure of the heterodimeric ecdysone receptor DNA-binding complex, EMBO J. 22, 5827-5840.
36. Lu, X. J., and Olson, W. K. (2003) 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures, Nucleic Acids Res. 31, 5108-5121.
37. Strahs, D., and Schlick, T. (2000) A-Tract bending: insights into experimental structures by computational models, J. Mol. Biol 301, 643-663.
38. Dragan, A. I., Liu, Y., Makeyeva, E. N., and Privalov, P. L. (2004) DNA-binding domain of GCN4 induces bending of both the ATF/ CREB and AP-1 binding sites of DNA, Nucleic Acids Res. 32, 5192-5197.
39. Wright, P. E., and Dyson, H. J. (1999) Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm, J. Mol. Biol. 293, 321-331.
40. Tompa, P. (2003) Intrinsically unstructured proteins evolve by repeat expansion, BioEssays 25, 847-855.
41. Tompa, P. (2005) The interplay between structure and function in intrinsically unstructured proteins, FEBS Lett. 579, 3346-3354.
42. Orłowski, M., Szyszka, M., Kowalska, A., Grad, I., Zoglowek, A., Rymarczyk, G., Dobryszycki, P., Krowarsch, D., Rastinejad, F., Kochman, M., and Ożyhar, A. (2004) Plasticity of the ecdysone receptor DNA binding domain, Mol. Endocrinol. 18, 2166-2184.
43. Vlahovicek, K., Kajan, L., and Pongor, S. (2003) DNA analysis servers: plot.it, bend.it, model.it and IS, Nucleic Acids Res. 31, 3686-3687.