Binding linkage in a telomere DNA-protein complex at the ends of Oxytricha nova chromosomes

Journal of Molecular Biology

Volumn 350, Issue 5, 2005, Pages 938-952

  Buczek, Pawel ^a   Orr, Rochelle S ^a   Pyper, Sean R ^a   Shum, Mili ^a   Kimmel, Emily ^a   Ota, Irene ^a   Gerum, Shawn E ^a   Horvath, Martin P ^a  

^a UNIVERSITY OF UTAH   (United States)

Author keywords

Binding linkage; Protein engineering; Protein DNA interactions; Protein protein interactions; Telomere binding protein

Indexed keywords

HYBRID PROTEIN; SINGLE STRANDED DNA; TELOMERE BINDING PROTEIN;

ALPHA CHAIN; ARTICLE; BETA CHAIN; BINDING AFFINITY; CARBOXY TERMINAL SEQUENCE; CHROMOSOME ANALYSIS; CHROMOSOME STRUCTURE; CILIATE; CRYSTAL STRUCTURE; DNA BINDING; DNA PROTEIN COMPLEX; MOLECULAR STABILITY; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN DOMAIN; PROTEIN ENGINEERING; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEIN SYNTHESIS; TELOMERE;

STERKIELLA NOVA;

EID: 21744446086     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.05.040     Document Type: Article

References (65)

1. E.H. Blackburn Structure and function of telomeres Nature 350 1991 569 573
2. J. Lingner, and T.R. Cech Telomerase and chromosome end maintenance Curr. Opin. Genet. Dev. 8 1998 226 232
3. L.A. Klobutcher, M.T. Swanton, P. Donini, and D.M. Prescott All gene-sized DNA molecules in four species of hypotrichs have the same terminal sequence and an unusual 3′ terminus Proc. Natl Acad. Sci. USA 78 1981 3015 3019
4. E.R. Henderson, and E.H. Blackburn An overhanging 3′ terminus is a conserved feature of telomeres Mol. Cell Biol. 9 1989 345 348
5. R. McElligott, and R.J. Wellinger The terminal DNA structure of mammalian chromosomes EMBO J. 16 1997 3705 3714
6. G. Kyrion, K. Liu, C. Liu, and A.J. Lustig RAP1 and telomere structure regulate telomere position effects in Saccharomyces cerevisiae Genes Dev. 7 1993 1146 1159
7. A. Krauskopf, and E.H. Blackburn Rap1 protein regulates telomere turnover in yeast Proc. Natl Acad. Sci. USA 95 1998 12486 12491
8. J. Wahlin, and M. Cohn Saccharomyces cerevisiae RAP1 binds to telomeric sequences with spatial flexibility Nucl. Acids Res. 28 2000 2292 2301
9. B. Li, S. Oestreich, and T. de Lange Identification of human Rap1: implications for telomere evolution Cell 101 2000 471 483
10. B. van Steensel, A. Smogorzewska, and T. de Lange TRF2 protects human telomeres from end-to-end fusions Cell 92 1998 401 413
11. D. Broccoli, A. Smogorzewska, L. Chong, and T. de Lange Human telomeres contain two distinct Myb-related proteins, TRF1 and TRF2 Nature Genet. 17 1997 231 235
12. A. Bianchi, S. Smith, L. Chong, P. Elias, and T. de Lange TRF1 is a dimer and bends telomeric DNA EMBO J. 16 1997 1785 1794
13. D.E. Gottschling, and V.A. Zakian Telomere proteins: specific recognition and protection of the natural termini of Oxytricha macronuclear DNA Cell 47 1986 195 205
14. C.M. Price, and T.R. Cech Telomeric DNA-protein interactions of Oxytricha macronuclear DNA Genes Dev. 1 1987 783 793
15. J.J. Lin, and V.A. Zakian The Saccharomyces CDC13 protein is a single-strand TG1-3 telomeric DNA-binding protein in vitro that affects telomere behavior in vivo Proc. Natl Acad. Sci. USA 93 1996 13760 13765
16. P. Baumann, and T.R. Cech Pot1, the putative telomere end-binding protein in fission yeast and humans Science 292 2001 1171 1175
17. W.I. Sundquist, and A. Klug Telomeric DNA dimerizes by formation of guanine tetrads between hairpin loops Nature 342 1989 825 829
18. G.N. Parkinson, M.P. Lee, and S. Neidle Crystal structure of parallel quadruplexes from human telomeric DNA Nature 417 2002 876 880
19. S. Neidle, and G.N. Parkinson The structure of telomeric DNA Curr. Opin. Struct. Biol. 13 2003 275 283
20. J.D. Griffith, L. Comeau, S. Rosenfield, R.M. Stansel, A. Bianchi, H. Moss, and T. de Lange Mammalian telomeres end in a large duplex loop Cell 97 1999 503 514
21. T. Nikitina, and C.L. Woodcock Closed chromatin loops at the ends of chromosomes J. Cell Biol. 166 2004 161 165
22. T. de Lange T-loops and the origin of telomeres Nature Rev. Mol. Cell Biol. 5 2004 323 329
23. C.M. Counter, A.A. Avilion, C.E. LeFeuvre, N.G. Stewart, C.W. Greider, C.B. Harley, and S. Bacchetti Telomere shortening associated with chromosome instability is arrested in immortal cells which express telomerase activity EMBO J. 11 1992 1921 1929
24. A.G. Bodnar, M. Ouellette, M. Frolkis, S.E. Holt, C.P. Chiu, and G.B. Morin Extension of life-span by introduction of telomerase into normal human cells Science 279 1998 349 352
25. J. Karlseder, A. Smogorzewska, and T. de Lange Senescence induced by altered telomere state, not telomere loss Science 295 2002 2446 2449
26. E.H. Blackburn Telomere states and cell fates Nature 408 2000 53 56
27. C.M. Counter The roles of telomeres and telomerase in cell life span Mutat. Res. 366 1996 45 63
28. C.B. Harley, H. Vaziri, C.M. Counter, and R.C. Allsopp The telomere hypothesis of cellular aging Expt. Gerontol. 27 1992 375 382
29. J.T. Gray, D.W. Celander, C.M. Price, and T.R. Cech Cloning and expression of genes for the Oxytricha telomere-binding protein: specific subunit interactions in the telomeric complex Cell 67 1991 807 814
30. G. Fang, and T.R. Cech Oxytricha telomere-binding protein: DNA-dependent dimerization of the alpha and beta subunits Proc. Natl Acad. Sci. USA 90 1993 6056 6060
31. G. Fang, J.T. Gray, and T.R. Cech Oxytricha telomere-binding protein: separable DNA-binding and dimerization domains of the alpha-subunit Genes Dev. 7 1993 870 882
32. M.P. Horvath, V.L. Schweiker, J.M. Bevilacqua, J.A. Ruggles, and S.C. Schultz Crystal structure of the Oxytricha nova telomere end binding protein complexed with single strand DNA Cell 95 1998 963 974
33. S. Classen, J.A. Ruggles, and S.C. Schultz Crystal structure of the N-terminal domain of Oxytricha nova telomere end-binding protein alpha subunit both uncomplexed and complexed with telomeric ssDNA J. Mol. Biol. 314 2001 1113 1125
34. O.B. Peersen, J.A. Ruggles, and S.C. Schultz Dimeric structure of the Oxytricha nova telomere end-binding protein alpha-subunit bound to ssDNA Nature Struct. Biol. 9 2002 182 187
35. M.C. Willis, B.J. Hicke, O.C. Uhlenbeck, T.R. Cech, and T.H. Koch Photocrosslinking of 5-iodouracil-substituted RNA and DNA to proteins Science 262 1993 1255 1257
36. B.J. Hicke, M.C. Willis, T.H. Koch, and T.R. Cech Telomeric protein-DNA point contacts identified by photo-cross-linking using 5-bromodeoxyuridine Biochemistry 33 1994 3364 3373
37. L. Laporte, J. Stultz, and G.J. Thomas Jr Solution conformations and interactions of alpha and beta subunits of the Oxytricha nova telomere binding protein: investigation by Raman spectroscopy Biochemistry 36 1997 8053 8059
38. A. Fontana, G. Fassina, C. Vita, D. Dalzoppo, M. Zamai, and M. Zambonin Correlation between sites of limited proteolysis and segmental mobility in thermolysin Biochemistry 25 1986 1847 1851
39. S.J. Hubbard, S.F. Campbell, and J.M. Thornton Molecular recognition. Conformational analysis of limited proteolytic sites and serine proteinase protein inhibitors J. Mol. Biol. 220 1991 507 530
40. S.J. Hubbard, F. Eisenmenger, and J.M. Thornton Modeling studies of the change in conformation required for cleavage of limited proteolytic sites Protein Sci. 3 1994 757 768
41. F.W. Smith, and J. Feigon Quadruplex structure of Oxytricha telomeric DNA oligonucleotides Nature 356 1992 164 168
42. S. Haider, G.N. Parkinson, and S. Neidle Crystal structure of the potassium form of an Oxytricha nova G-quadruplex J. Mol. Biol. 320 2002 189 200
43. M.P. Horvath, and S.C. Schultz DNA G-quartets in a 1.86 Å resolution structure of an Oxytricha nova telomeric protein-DNA complex J. Mol. Biol. 310 2001 367 377
44. C. Bohr, K.A. Hasselbalch, and A. Krogh Ueber einen in biologischer Beziehung wichtigen Einfluss, den die Kohlensaurespannung des Blutes aufdessen Sauerstoffbindung ubt Skand. Arch. Physiol. 16 1904 402 412
45. K. Imai, and T. Yonetani PH dependence of the Adair constants of human hemoglobin. Nonuniform contribution of successive oxygen bindings to the alkaline Bohr effect J. Biol. Chem. 250 1975 2227 2231
46. E.R. Kantrowitz, and W.N. Lipscomb Escherichia coli aspartate transcarbamylase: the relation between structure and function Science 241 1988 669 674
47. S.J. Froelich-Ammon, B.A. Dickinson, J.M. Bevilacqua, S.C. Schultz, and T.R. Cech Modulation of telomerase activity by telomere DNA-binding proteins in Oxytricha Genes Dev. 12 1998 1504 1514
48. B. Hicke, R. Rempel, J. Maller, R.A. Swank, J.R. Hamaguchi, and E.M. Bradbury Phosphorylation of the Oxytricha telomere protein: possible cell cycle regulation Nucl. Acids Res. 23 1995 1887 1893
49. W. Wang, R. Skopp, M. Scofield, and C. Price Euplotes crassus has genes encoding telomere-binding proteins and telomere-binding protein homologs Nucl. Acids Res. 20 1992 6621 6629
50. M. Lei, P. Baumann, and T.R. Cech Cooperative binding of single-stranded telomeric DNA by the Pot1 protein of Schizosaccharomyces pombe Biochemistry 41 2002 14560 14568
51. D. Loayza, H. Parsons, J. Donigian, K. Hoke, and T. de Lange DNA binding features of human POT1: a nonamer 5′-TAGGGTTAG-3′ minimal binding site, sequence specificity, and internal binding to multimeric sites J. Biol. Chem. 279 2004 13241 13248
52. A.G. Murzin OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences EMBO J. 12 1993 861 867
53. M. Lei, E.R. Podell, and T.R. Cech Structure of human POT1 bound to telomeric single-stranded DNA provides a model for chromosome end-protection Nature Struct. Mol. Biol. 11 2004 1223 1229
54. M. Lei, E.R. Podell, P. Baumann, and T.R. Cech DNA self-recognition in the structure of Pot1 bound to telomeric single-stranded DNA Nature 426 2003 198 203
55. R.M. Mitton-Fry, E.M. Anderson, T.R. Hughes, V. Lundblad, and D.S. Wuttke Conserved structure for single-stranded telomeric DNA recognition Science 296 2002 145 147
56. D.L. Theobald, and D.S. Wuttke Prediction of multiple tandem OB-fold domains in telomere end-binding proteins Pot1 and Cdc13 Structure (Camb) 12 2004 1877 1879
57. D.L. Theobald, R.B. Cervantes, V. Lundblad, and D.S. Wuttke Homology among telomeric end-protection proteins Structure (Camb) 11 2003 1049 1050
58. D. Loayza, and T. De Lange POT1 as a terminal transducer of TRF1 telomere length control Nature 423 2003 1013 1018
59. D. Liu, A. Safari, M.S. O'Connor, D.W. Chan, A. Laegeler, J. Qin, and Z. Songyang PTOP interacts with POT1 and regulates its localization to telomeres Nature Cell Biol. 6 2004 673 680
60. R.M. Stansel, T. de Lange, and J.D. Griffith T-loop assembly in vitro involves binding of TRF2 near the 3′ telomeric overhang EMBO J 20 2001 5532 5540
61. R.C. Wang, A. Smogorzewska, and T. de Lange Homologous recombination generates T-loop-sized deletions at human telomeres Cell 119 2004 355 368
62. Q. Yang, Y.L. Zheng, and C.C. Harris POT1 and TRF2 cooperate to maintain telomeric integrity Mol. Cell Biol. 25 2005 1070 1080
63. S.C. Gill, and P.H. von Hippel Calculation of protein extinction coefficients from amino acid sequence data Anal. Biochem. 182 1989 319 326
64. H. Schagger, and G. von Jagow Tricine-sodium dodecyl sulfate- polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa Anal. Biochem. 166 1987 368 379
65. D.W. Marquardt An algorithm for least-squares estimation of non-linear parameters J. Soc. Ind. Appl. Math. 11 1963 431 441