New insights into DNA-binding behavior of Wilms Tumor Protein (WT1) - A dual study

Biophysical Chemistry

Volumn 145, Issue 2-3, 2009, Pages 116-125

  Nurmemmedov, Elmar ^a   Yengo, Raymond K ^a   Uysal, Hüseyin ^a   Karlsson, Robert ^b   Thunnissen, Marjolein M G M ^a  

^a LUND UNIVERSITY   (Sweden)

^b GE Healthcare Bio Sciences AB   (Sweden)

Author keywords

Bacterial 1 hybrid system; DNA binding; Surface plasmon resonance; Transcription factor; WT1; Zinc finger

Indexed keywords

TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; WILMS TUMOR SUPPRESSOR PROTEIN; ZINC FINGER PROTEIN;

ARTICLE; BINDING AFFINITY; BINDING KINETICS; CONTROLLED STUDY; DNA BINDING; DNA PROTEIN COMPLEX; GENE DELETION; GENE FUNCTION; HYBRID; MOLECULAR INTERACTION; MOLECULAR RECOGNITION; MOLECULAR STABILITY; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; SURFACE PLASMON RESONANCE;

AMINO ACID SEQUENCE; BASE SEQUENCE; BINDING SITES; CLONING, MOLECULAR; DNA; GENE DELETION; KINETICS; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; SURFACE PLASMON RESONANCE; WT1 PROTEINS; ZINC FINGERS;

BACTERIA (MICROORGANISMS);

EID: 70350189932     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2009.09.009     Document Type: Article

References (63)

1. Matsunaga E. Genetics of Wilms' tumor. Hum. Genet. 57 (1981) 231-246
2. Call K.M., Glaser T., Ito C.Y., Buckler A.J., Pelletier J., et al. Isolation and characterization of a zinc finger polypeptide gene at the human chromosome 11 Wilms' tumor locus. Cell 60 (1990) 509-520
3. Gessler M., Poustka A., Cavenee W., Neve R.L., Orkin S.H., et al. Homozygous deletion in Wilms tumours of a zinc-finger gene identified by chromosome jumping. Nature 343 (1990) 774-778
4. Madden S.L., Cook D.M., Morris J.F., Gashler A., Sukhatme V.P., et al. Transcriptional repression mediated by the WT1 Wilms tumor gene product. Science 253 (1991) 1550-1553
5. Rauscher III F.J., Morris J.F., Tournay O.E., Cook D.M., and Curran T. Binding of the Wilms' tumor locus zinc finger protein to the EGR-1 consensus sequence. Science 250 (1990) 1259-1262
6. Huang A., Campbell C.E., Bonetta L., McAndrews-Hill M.S., Chilton-MacNeill S., et al. Tissue, developmental, and tumor-specific expression of divergent transcripts in Wilms tumor. Science 250 (1990) 991-994
7. Pelletier J., Schalling M., Buckler A.J., Rogers A., Haber D.A., et al. Expression of the Wilms' tumor gene WT1 in the murine urogenital system. Genes Dev. 5 (1991) 1345-1356
8. Oka Y., and Kawase I. Cancer antigen WT1-targeting treatment for the malignancies. Nihon Rinsho Meneki Gakkai Kaishi 31 (2008) 375-382
9. Chaise C., Buchan S.L., Rice J., Marquet J., Rouard H., et al. DNA vaccination induces WT1-specific T-cell responses with potential clinical relevance. Blood 112 (2008) 2956-2964
10. Menke A., McInnes L., Hastie N.D., and Schedl A. The Wilms' tumor suppressor WT1: approaches to gene function. Kidney Int. 53 (1998) 1512-1518
11. Lee S.B., and Haber D.A. Wilms tumor and the WT1 gene. Exp. Cell Res. 264 (2001) 74-99
12. Borel F., Barilla K.C., Hamilton T.B., Iskandar M., and Romaniuk P.J. Effects of Denys-Drash syndrome point mutations on the DNA binding activity of the Wilms' tumor suppressor protein WT1. Biochemistry 35 (1996) 12070-12076
13. Hamilton T.B., Barilla K.C., and Romaniuk P.J. High affinity binding sites for the Wilms' tumour suppressor protein WT1. Nucleic Acids Res. 23 (1995) 277-284
14. Nakagama H., Heinrich G., Pelletier J., and Housman D.E. Sequence and structural requirements for high-affinity DNA binding by the WT1 gene product. Mol. Cell. Biol. 15 (1995) 1489-1498
15. Pavletich N.P., and Pabo C.O. Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A. Science 252 (1991) 809-817
16. Ladomery M., Sommerville J., Woolner S., Slight J., and Hastie N. Expression in Xenopus oocytes shows that WT1 binds transcripts in vivo, with a central role for zinc finger one. J. Cell Sci. 116 (2003) 1539-1549
17. Morrison A.A., Venables J.P., Dellaire G., and Ladomery M.R. The Wilms tumour suppressor protein WT1 (+ KTS isoform) binds alpha-actinin 1 mRNA via its zinc-finger domain. Biochem. Cell Biol. 84 (2006) 789-798
18. Iuchi S. Three classes of C2H2 zinc finger proteins. Cell. Mol. Life Sci. 58 (2001) 625-635
19. Wolfe S.A., Nekludova L., and Pabo C.O. DNA recognition by Cys2His2 zinc finger proteins. Annu. Rev. Biophys. Biomol. Struct. 29 (2000) 183-212
20. Laity J.H., Dyson H.J., and Wright P.E. Molecular basis for modulation of biological function by alternate splicing of the Wilms' tumor suppressor protein. Proc. Natl. Acad. Sci. U. S. A. 97 (2000) 11932-11935
21. Zhai G., Iskandar M., Barilla K., and Romaniuk P.J. Characterization of RNA aptamer binding by the Wilms' tumor suppressor protein WT1. Biochemistry 40 (2001) 2032-2040
22. Yang W.P., Wu H., and Barbas III C.F. Surface plasmon resonance based kinetic studies of zinc finger-DNA interactions. J. Immunol. Methods 183 (1995) 175-182
23. Nurmemmedov E., and Thunnissen M. Expression, purification, and characterization of the 4 zinc finger region of human tumor suppressor WT1. Protein Expr. Purif. 46 (2006) 379-389
24. Meng X., Brodsky M.H., and Wolfe S.A. A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors. Nat. Biotechnol. 23 (2005) 988-994
25. Bondeson K., Frostell-Karlsson A., Fagerstam L., and Magnusson G. Lactose repressor-operator DNA interactions: kinetic analysis by a surface plasmon resonance biosensor. Anal. Biochem. 214 (1993) 245-251
26. Cornille F., Emery P., Schuler W., Lenoir C., Mach B., et al. DNA binding properties of a chemically synthesized DNA binding domain of hRFX1. Nucleic Acids Res. 26 (1998) 2143-2149
27. Hamdan S.M., Marintcheva B., Cook T., Lee S.J., Tabor S., et al. A unique loop in T7 DNA polymerase mediates the binding of helicase-primase, DNA binding protein, and processivity factor. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 5096-5101
28. Persson B., Stenhag K., Nilsson P., Larsson A., Uhlen M., et al. Analysis of oligonucleotide probe affinities using surface plasmon resonance: a means for mutational scanning. Anal. Biochem. 246 (1997) 34-44
29. Witte G., Urbanke C., and Curth U. DNA polymerase III chi subunit ties single-stranded DNA binding protein to the bacterial replication machinery. Nucleic Acids Res. 31 (2003) 4434-4440
30. Young E.T., Kacherovsky N., and Cheng C. An accessory DNA binding motif in the zinc finger protein Adr1 assists stable binding to DNA and can be replaced by a third finger. Biochemistry 39 (2000) 567-574
31. Moss T. DNA-protein interactions, principles and protocols. Methods in Molecular Biology. 2nd ed. (2001), Humana Press, Totowa NJ
32. Oda M., Furukawa K., Sarai A., and Nakamura H. Construction of an artificial tandem protein of the c-Myb DNA-binding domain and analysis of its DNA binding specificity. Biochem. Biophys. Res. Commun. 262 (1999) 94-97
33. Gill S.C., and von Hippel P.H. Calculation of protein extinction coefficients from amino acid sequence data. Anal. Biochem. 182 (1989) 319-326
34. Bradford M.M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72 (1976) 248-254
35. Lowry O.H., Rosebrough N.J., Farr A.L., and Randall R.J. Protein measurement with the Folin phenol reagent. J. Biol. Chem. 193 (1951) 265-275
36. Meng X., and Wolfe S.A. Identifying DNA sequences recognized by a transcription factor using a bacterial one-hybrid system. Nat Protoc 1 (2006) 30-45
37. Bailey T.L., Boden M., Buske F.A., Frith M., Grant C.E., et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37 (2009) W202-W208
38. Crooks G.E., Hon G., Chandonia J.M., and Brenner S.E. WebLogo: a sequence logo generator. Genome Res. 14 (2004) 1188-1190
39. Karlsson R., Katsamba P.S., Nordin H., Pol E., and Myszka D.G. Analyzing a kinetic titration series using affinity biosensors. Anal. Biochem. 349 (2006) 136-147
40. Kriwacki R.W., Schultz S.C., Steitz T.A., and Caradonna J.P. Sequence-specific recognition of DNA by zinc-finger peptides derived from the transcription factor Sp1. Proc. Natl. Acad. Sci. U. S. A. 89 (1992) 9759-9763
41. Schaufler L.E., and Klevit R.E. Mechanism of DNA binding by the ADR1 zinc finger transcription factor as determined by SPR. J. Mol. Biol. 329 (2003) 931-939
42. Beerli R.R., and Barbas III C.F. Engineering polydactyl zinc-finger transcription factors. Nat. Biotechnol. 20 (2002) 135-141
43. Blancafort P., Magnenat L., and Barbas III C.F. Scanning the human genome with combinatorial transcription factor libraries. Nat. Biotechnol. 21 (2003) 269-274
44. Pabo C.O., Peisach E., and Grant R.A. Design and selection of novel Cys2His2 zinc finger proteins. Annu. Rev. Biochem. 70 (2001) 313-340
45. Clemens K.R., Wolf V., McBryant S.J., Zhang P., Liao X., et al. Molecular basis for specific recognition of both RNA and DNA by a zinc finger protein. Science 260 (1993) 530-533
46. Setzer D.R., Menezes S.R., Del Rio S., Hung V.S., and Subramanyan G. Functional interactions between the zinc fingers of Xenopus transcription factor IIIA during 5S rRNA binding. RNA 2 (1996) 1254-1269
47. Theunissen O., Rudt F., and Pieler T. Structural determinants in 5S RNA and TFIIIA for 7S RNP formation. Eur. J. Biochem. 258 (1998) 758-767
48. Theunissen O., Rudt F., Guddat U., Mentzel H., and Pieler T. RNA and DNA binding zinc fingers in Xenopus TFIIIA. Cell 71 (1992) 679-690
49. Searles M.A., Lu D., and Klug A. The role of the central zinc fingers of transcription factor IIIA in binding to 5S RNA. J. Mol. Biol. 301 (2000) 47-60
50. Del Rio S., Menezes S.R., and Setzer D.R. The function of individual zinc fingers in sequence-specific DNA recognition by transcription factor IIIA. J. Mol. Biol. 233 (1993) 567-579
51. Hamilton T.B., Turner J., Barilla K., and Romaniuk P.J. Contribution of individual amino acids to the nucleic acid binding activities of the Xenopus zinc finger proteins TFIIIIA and p43. Biochemistry 40 (2001) 6093-6101
52. Zang W.Q., Veldhoen N., and Romaniuk P.J. Effects of zinc finger mutations on the nucleic acid binding activities of Xenopus transcription factor IIIA. Biochemistry 34 (1995) 15545-15552
53. Wang H., Sun R., Liu G., Yao M., Fei J., et al. Characterization of the target DNA sequence for the DNA-binding domain of zinc finger protein 191. Acta Biochim. Biophys. Sin. (Shanghai) 40 (2008) 704-710
54. Hamilton T.B., Borel F., and Romaniuk P.J. Comparison of the DNA binding characteristics of the related zinc finger proteins WT1 and EGR1. Biochemistry 37 (1998) 2051-2058
55. Laity J.H., Chung J., Dyson H.J., and Wright P.E. Alternative splicing of Wilms' tumor suppressor protein modulates DNA binding activity through isoform-specific DNA-induced conformational changes. Biochemistry 39 (2000) 5341-5348
56. Hammes A., Guo J.K., Lutsch G., Leheste J.R., Landrock D., et al. Two splice variants of the Wilms' tumor 1 gene have distinct functions during sex determination and nephron formation. Cell 106 (2001) 319-329
57. Reynolds P.A., Smolen G.A., Palmer R.E., Sgroi D., Yajnik V., et al. Identification of a DNA-binding site and transcriptional target for the EWS-WT1(+ KTS) oncoprotein. Genes Dev. 17 (2003) 2094-2107
58. Li H., Smolen G.A., Beers L.F., Xia L., Gerald W., et al. Adenosine transporter ENT4 is a direct target of EWS/WT1 translocation product and is highly expressed in desmoplastic small round cell tumor. PLoS ONE 3 (2008) e2353
59. Stoll R., Lee B.M., Debler E.W., Laity J.H., Wilson I.A., et al. Structure of the Wilms tumor suppressor protein zinc finger domain bound to DNA. J. Mol. Biol. 372 (2007) 1227-1245
60. Bardeesy N., and Pelletier J. Overlapping RNA and DNA binding domains of the wt1 tumor suppressor gene product. Nucleic Acids Res. 26 (1998) 1784-1792
61. Gerald W.L., and Haber D.A. The EWS-WT1 gene fusion in desmoplastic small round cell tumor. Semin. Cancer Biol. 15 (2005) 197-205
62. Fairall L., Harrison S.D., Travers A.A., and Rhodes D. Sequence-specific DNA binding by a two zinc-finger peptide from the Drosophila melanogaster Tramtrack protein. J. Mol. Biol. 226 (1992) 349-366
63. Sakaguchi K., Appella E., Omichinski J.G., Clore G.M., and Gronenborn A.M. Specific DNA binding to a major histocompatibility complex enhancer sequence by a synthetic 57-residue double zinc finger peptide from a human enhancer binding protein. J. Biol. Chem. 266 (1991) 7306-7311