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. 1998 Apr 1;26(7):1731–1740. doi: 10.1093/nar/26.7.1731

Sequence-specific DNA recognition by the myb-like domain of the human telomere binding protein TRF1: a model for the protein-DNA complex.

P König 1, L Fairall 1, D Rhodes 1
PMCID: PMC147458  PMID: 9512546

Abstract

Telomeres consist of tandem arrays of short G-rich sequence motifs packaged by specific DNA binding proteins. In humans the double-stranded telomeric TTAGGG repeats are specifically bound by TRF1 and TRF2. Although telomere binding proteins from evolutionarily distant species are not sequence homologues, they share a Myb-like DNA binding motif. Here we have used gel retardation, primer extension and DNase I footprinting analyses to define the binding site of the isolated Myb-like domain of TRF1 and present a three-dimensional model for its interaction with human telomeric DNA. Our results suggest that the Myb-like domain of TRF1 recognizes a binding site centred on the sequence GGGTTA and that its DNA binding mode is similar to that of the homeodomain-like motifs of the yeast telomere binding protein RAP1. The implications of these findings for recognition of telomeric DNA in general are discussed.

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Selected References

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  1. Ades S. E., Sauer R. T. Differential DNA-binding specificity of the engrailed homeodomain: the role of residue 50. Biochemistry. 1994 Aug 9;33(31):9187–9194. doi: 10.1021/bi00197a022. [DOI] [PubMed] [Google Scholar]
  2. Ades S. E., Sauer R. T. Specificity of minor-groove and major-groove interactions in a homeodomain-DNA complex. Biochemistry. 1995 Nov 7;34(44):14601–14608. doi: 10.1021/bi00044a040. [DOI] [PubMed] [Google Scholar]
  3. Affolter M., Percival-Smith A., Müller M., Leupin W., Gehring W. J. DNA binding properties of the purified Antennapedia homeodomain. Proc Natl Acad Sci U S A. 1990 Jun;87(11):4093–4097. doi: 10.1073/pnas.87.11.4093. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Berman J., Tachibana C. Y., Tye B. K. Identification of a telomere-binding activity from yeast. Proc Natl Acad Sci U S A. 1986 Jun;83(11):3713–3717. doi: 10.1073/pnas.83.11.3713. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Bianchi A., Smith S., Chong L., Elias P., de Lange T. TRF1 is a dimer and bends telomeric DNA. EMBO J. 1997 Apr 1;16(7):1785–1794. doi: 10.1093/emboj/16.7.1785. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Bilaud T., Koering C. E., Binet-Brasselet E., Ancelin K., Pollice A., Gasser S. M., Gilson E. The telobox, a Myb-related telomeric DNA binding motif found in proteins from yeast, plants and human. Nucleic Acids Res. 1996 Apr 1;24(7):1294–1303. doi: 10.1093/nar/24.7.1294. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Broccoli D., Chong L., Oelmann S., Fernald A. A., Marziliano N., van Steensel B., Kipling D., Le Beau M. M., de Lange T. Comparison of the human and mouse genes encoding the telomeric protein, TRF1: chromosomal localization, expression and conserved protein domains. Hum Mol Genet. 1997 Jan;6(1):69–76. doi: 10.1093/hmg/6.1.69. [DOI] [PubMed] [Google Scholar]
  8. Broccoli D., Smogorzewska A., Chong L., de Lange T. Human telomeres contain two distinct Myb-related proteins, TRF1 and TRF2. Nat Genet. 1997 Oct;17(2):231–235. doi: 10.1038/ng1097-231. [DOI] [PubMed] [Google Scholar]
  9. Carra J. H., Privalov P. L. Energetics of folding and DNA binding of the MAT alpha 2 homeodomain. Biochemistry. 1997 Jan 21;36(3):526–535. doi: 10.1021/bi962206b. [DOI] [PubMed] [Google Scholar]
  10. Chong L., van Steensel B., Broccoli D., Erdjument-Bromage H., Hanish J., Tempst P., de Lange T. A human telomeric protein. Science. 1995 Dec 8;270(5242):1663–1667. doi: 10.1126/science.270.5242.1663. [DOI] [PubMed] [Google Scholar]
  11. Cooper J. P., Nimmo E. R., Allshire R. C., Cech T. R. Regulation of telomere length and function by a Myb-domain protein in fission yeast. Nature. 1997 Feb 20;385(6618):744–747. doi: 10.1038/385744a0. [DOI] [PubMed] [Google Scholar]
  12. Dubendorff J. W., Studier F. W. Controlling basal expression in an inducible T7 expression system by blocking the target T7 promoter with lac repressor. J Mol Biol. 1991 May 5;219(1):45–59. doi: 10.1016/0022-2836(91)90856-2. [DOI] [PubMed] [Google Scholar]
  13. Fairall L., Rhodes D. A new approach to the analysis of DNase I footprinting data and its application to the TFIIIA/5S DNA complex. Nucleic Acids Res. 1992 Sep 25;20(18):4727–4731. doi: 10.1093/nar/20.18.4727. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Florence B., Handrow R., Laughon A. DNA-binding specificity of the fushi tarazu homeodomain. Mol Cell Biol. 1991 Jul;11(7):3613–3623. doi: 10.1128/mcb.11.7.3613. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Gehring W. J., Affolter M., Bürglin T. Homeodomain proteins. Annu Rev Biochem. 1994;63:487–526. doi: 10.1146/annurev.bi.63.070194.002415. [DOI] [PubMed] [Google Scholar]
  16. Gerchman S. E., Graziano V., Ramakrishnan V. Expression of chicken linker histones in E. coli: sources of problems and methods for overcoming some of the difficulties. Protein Expr Purif. 1994 Jun;5(3):242–251. doi: 10.1006/prep.1994.1037. [DOI] [PubMed] [Google Scholar]
  17. Howe K. M., Reakes C. F., Watson R. J. Characterization of the sequence-specific interaction of mouse c-myb protein with DNA. EMBO J. 1990 Jan;9(1):161–169. doi: 10.1002/j.1460-2075.1990.tb08092.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Jones T. A., Zou J. Y., Cowan S. W., Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A. 1991 Mar 1;47(Pt 2):110–119. doi: 10.1107/s0108767390010224. [DOI] [PubMed] [Google Scholar]
  19. Kim J., Zwieb C., Wu C., Adhya S. Bending of DNA by gene-regulatory proteins: construction and use of a DNA bending vector. Gene. 1989 Dec 21;85(1):15–23. doi: 10.1016/0378-1119(89)90459-9. [DOI] [PubMed] [Google Scholar]
  20. Kissinger C. R., Liu B. S., Martin-Blanco E., Kornberg T. B., Pabo C. O. Crystal structure of an engrailed homeodomain-DNA complex at 2.8 A resolution: a framework for understanding homeodomain-DNA interactions. Cell. 1990 Nov 2;63(3):579–590. doi: 10.1016/0092-8674(90)90453-l. [DOI] [PubMed] [Google Scholar]
  21. Konig P., Giraldo R., Chapman L., Rhodes D. The crystal structure of the DNA-binding domain of yeast RAP1 in complex with telomeric DNA. Cell. 1996 Apr 5;85(1):125–136. doi: 10.1016/s0092-8674(00)81088-0. [DOI] [PubMed] [Google Scholar]
  22. Krauskopf A., Blackburn E. H. Control of telomere growth by interactions of RAP1 with the most distal telomeric repeats. Nature. 1996 Sep 26;383(6598):354–357. doi: 10.1038/383354a0. [DOI] [PubMed] [Google Scholar]
  23. Kyrion G., Boakye K. A., Lustig A. J. C-terminal truncation of RAP1 results in the deregulation of telomere size, stability, and function in Saccharomyces cerevisiae. Mol Cell Biol. 1992 Nov;12(11):5159–5173. doi: 10.1128/mcb.12.11.5159. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. König P., Rhodes D. Recognition of telomeric DNA. Trends Biochem Sci. 1997 Feb;22(2):43–47. doi: 10.1016/s0968-0004(97)01008-6. [DOI] [PubMed] [Google Scholar]
  25. Larson G. P., Castanotto D., Rossi J. J., Malafa M. P. Isolation and functional analysis of a Kluyveromyces lactis RAP1 homologue. Gene. 1994 Dec 2;150(1):35–41. doi: 10.1016/0378-1119(94)90854-0. [DOI] [PubMed] [Google Scholar]
  26. Liu-Johnson H. N., Gartenberg M. R., Crothers D. M. The DNA binding domain and bending angle of E. coli CAP protein. Cell. 1986 Dec 26;47(6):995–1005. doi: 10.1016/0092-8674(86)90814-7. [DOI] [PubMed] [Google Scholar]
  27. Lutter L. C. Kinetic analysis of deoxyribonuclease I cleavages in the nucleosome core: evidence for a DNA superhelix. J Mol Biol. 1978 Sep 15;124(2):391–420. doi: 10.1016/0022-2836(78)90306-6. [DOI] [PubMed] [Google Scholar]
  28. Ogata K., Morikawa S., Nakamura H., Sekikawa A., Inoue T., Kanai H., Sarai A., Ishii S., Nishimura Y. Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices. Cell. 1994 Nov 18;79(4):639–648. doi: 10.1016/0092-8674(94)90549-5. [DOI] [PubMed] [Google Scholar]
  29. Pabo C. O., Sauer R. T. Transcription factors: structural families and principles of DNA recognition. Annu Rev Biochem. 1992;61:1053–1095. doi: 10.1146/annurev.bi.61.070192.005201. [DOI] [PubMed] [Google Scholar]
  30. Riggs A. D., Suzuki H., Bourgeois S. Lac repressor-operator interaction. I. Equilibrium studies. J Mol Biol. 1970 Feb 28;48(1):67–83. doi: 10.1016/0022-2836(70)90219-6. [DOI] [PubMed] [Google Scholar]
  31. Sandell L. L., Zakian V. A. Loss of a yeast telomere: arrest, recovery, and chromosome loss. Cell. 1993 Nov 19;75(4):729–739. doi: 10.1016/0092-8674(93)90493-a. [DOI] [PubMed] [Google Scholar]
  32. Smith J., Singh M. System for accurate one-dimensional gel analysis including high-resolution quantitative footprinting. Biotechniques. 1996 Jun;20(6):1082–1087. doi: 10.2144/96206bc01. [DOI] [PubMed] [Google Scholar]
  33. Tanikawa J., Yasukawa T., Enari M., Ogata K., Nishimura Y., Ishii S., Sarai A. Recognition of specific DNA sequences by the c-myb protooncogene product: role of three repeat units in the DNA-binding domain. Proc Natl Acad Sci U S A. 1993 Oct 15;90(20):9320–9324. doi: 10.1073/pnas.90.20.9320. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Weston S. A., Lahm A., Suck D. X-ray structure of the DNase I-d(GGTATACC)2 complex at 2.3 A resolution. J Mol Biol. 1992 Aug 20;226(4):1237–1256. doi: 10.1016/0022-2836(92)91064-v. [DOI] [PubMed] [Google Scholar]
  35. Zakian V. A. Telomeres: beginning to understand the end. Science. 1995 Dec 8;270(5242):1601–1607. doi: 10.1126/science.270.5242.1601. [DOI] [PubMed] [Google Scholar]
  36. Zhong Z., Shiue L., Kaplan S., de Lange T. A mammalian factor that binds telomeric TTAGGG repeats in vitro. Mol Cell Biol. 1992 Nov;12(11):4834–4843. doi: 10.1128/mcb.12.11.4834. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. van Steensel B., de Lange T. Control of telomere length by the human telomeric protein TRF1. Nature. 1997 Feb 20;385(6618):740–743. doi: 10.1038/385740a0. [DOI] [PubMed] [Google Scholar]

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