The different (sur)faces of Rap1p

Molecular Genetics and Genomics

Volumn 268, Issue 6, 2003, Pages 791-798

  Pina B ^a   Fernandez Larrea J ^a   Garcia Reyero N ^a   Idrissi, F Z ^a  

^a INSTITUT DE BIOLOGIA MOLECULAR DE BARCELONA   (Spain)

Author keywords

DNA sequence analysis; Ribosomal genes; Saccharomyces cerevisiae; Telomeres; Transcriptional regulation

Indexed keywords

FUNGAL DNA; RAP PROTEIN;

ARTICLE; BINDING SITE; CHROMATIN; DNA SEQUENCE; FUNGAL GENE; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN FUNCTION; PROTEIN STRUCTURE; SURFACE PROPERTY; TELOMERE; TRANSCRIPTION REGULATION;

SACCHAROMYCES CEREVISIAE;

EID: 0037361634     PISSN: 16174615     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00438-002-0801-3     Document Type: Article

References (67)

1. Aronson B, Fisher AL, Blechman K, Caudy M, Gergen J (1997) Groucho-dependent and -independent repression activities of Runt domain proteins. Mol Cell Biol 17:5581-5587
2. Bi X, Broach JR (1999) UASrpg can function as a heterochromatin boundary element in yeast. Genes Dev 13:1089-1101
3. Boscheron C, Maillet L, Marcand S, Tsai-Pflugfelder M, Gasser SM, Gilson E (1996) Cooperation at a distance between silencers and proto-silencers at the yeast HML locus. EMBO J 15:2184-2195
4. Branden C, Tooze J (1999) Introduction to protein structure (2nd edn). Garland Publishing, New York
5. Carmen AA, Milne L, Grunstein M (2002) Acetylation of the yeast histone H4 N-terminus regulates its binding to heterochromatin protein SIR3. J Biol Chem 277:4778-4781
6. Cooper J (2000) Telomere transitions in yeast: the end of the chromosome as we know it. Curr Opin Genet Dev 10:169-177
7. De Sanctis V, La Terra S, Bianchi A, Shore D, Burderi L, Di Mauro E, Negri R (2002) In vivo topography of Rap1p-DNA complex at Saccharomyces cerevisiae TEF2UAS(RPG) during transcriptional regulation. J Mol Biol 318:333-349
8. Devlin C, Tice-Baldwin K, Shore D, Arndt KT (1991) RAP1 is required for BAS1/BAS2- and GCN4-dependent transcription of the yeast HIS4 gene. Mol Cell Biol 11:3642-3651
9. Drazinic CM, Smerage JB, López MC, Baker HV (1996) Activation mechanism of the multifunctional transcription factor repressor-activator protein 1 (Rap1p). Mol Cell Biol 16:3187-3196
10. Dubnicoff T, Valentine S, Chen G, Shi T, Lengyel J, Paroush Z, Courey A (1997) Conversion of Dorsal from activator to repressor by the global corepressor Groucho. Genes Dev 11:2952-2957
11. Fernandes L, Rodrigues-Pousada C, Struhl K (1997) Yap, a novel family of eight bZIP proteins in Saccharomyces cerevisiae. Mol Cell Biol 17:6982-6993
12. Freeman K, Gwadz M, Shore D (1995) Molecular and genetic analysis of the toxic effect of RAP1 overexpression in yeast. Genetics 141:1253-1262
13. Gartenberg M (2000) The Sir proteins of Saccharomyces cerevisiae: mediators of transcriptional silencing and much more. Curr Opin Microbiol 3:132-137
14. Giesman D, Best L, Tatchell K (1991) The role of RAP1 in the regulation of the MAT alpha locus. Mol Cell Biol 11:1069-1079
15. Gonçalves P, Maurer K, van Nieuw Amerongen G, Bergkamp-Steffens K, Mager W, Planta R (1996) C-terminal domains of general regulatory factors Abflp and Rap1p in Saccharomyces cerevisiae display functional similarity. Mol Microbiol 19:535-543
16. Graham IR, Chambers A (1994) Use of a selection technique to identify the diversity of binding sites for the yeast RAP1 transcription factor. Nucleic Acids Res 22:124-130
17. Graham I, Haw RA, Spink KG, Halden KA, Chambers A (1999) In vivo analysis of functional regions within yeast Rap1p. Mol Cell Biol 19:7481-7490
18. Grossi S, Bianchi A, Damay P, Shore D (2001) Telomere formation by Rap1p binding site arrays reveals end-specific length regulation requirements and active telomeric recombination. Mol Cell Biol 21:8117-8128
19. Ha N, Helauer K, Turcotte B (1996) Mutations in target DNA elements of yeast HAP1 modulate its transcriptional activity without affecting DNA binding. Nucleic Acids Res 24:1453-1459
20. Hardy CF, Balderes D, Shore D (1992) Dissection of a carboxyterminal region of the yeast regulatory protein RAP1 with effects on both transcriptional activation and silencing. Mol Cell Biol 12:1209-1217
21. Hermann-Le Denmat S, Werner M, Sentenac A, Thuriaux P (1994) Suppression of yeast RNA polymerase III mutations by FHL1, a gene coding for a forkhead protein involved in rRNA processing. Mol Cel Biol 14:2905-2913
22. Huie MA, Scott EW, Drazinic CM, López MC, Hornstra IK, Yang TP, Baker HV (1992) Characterization of the DNA-binding activity of GCR1: in vivo evidence for two GCR1-binding sites in the upstream activating sequence of TPI of Saccharomyces cerevisiae. Mol Cell Biol 12:2690-2700
23. Idrissi F-Z (1999) Structural and functional polymorphism of DNA sequences bound to the S. cerevisiae protein Rap1p (PhD Thesis, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain)
24. Idrissi F-Z, Piña B (1999) Functional divergence between the half-sites of the DNA binding sequence for Rap1p. Biochem J 341:477-482
25. Idrissi F-Z, Fernández-Larrea JB, Piña B (1998) Structural and functional heterogeneity of Rap1p complexes with telomeric and UASrpg-like DNA sequences. J Mol Biol 284:925-935
26. Idrissi F-Z, García-Reyero N, Fernández-Larrea J, Piña B (2001) Alternative mechanisms of transcriptional activation by Rap1p. J Biol Chem 276:26090-26098
27. +-dependent histone acetylase. Nature 403:795-800
28. Jansen R, Gerstein M (2000) Analysis of the yeast transcriptome with structural and functional categories: characterizing highly expressed proteins. Nucleic Acids Res 28:1481-1488
29. König P, Rhodes D (1997) Recognition of telomeric DNA. Trends Biochem Sci 22:43-47
30. König P, Giraldo R, Chapman L, Rhodes D (1996) The crystal structure of the DNA-binding domain of yeast RAP1 in complex with telomeric DNA. Cell 85:125-136
31. Kosoy A., Pagans S, Espinás M, Azorín F, Bernués J (2002) GAGA factor down regulates its own promoter. J Biol Chem 277:42280-42282
32. Krauskopf A, Blackburn EH (1996) Control of telomere growth by interactions of RAP1 with the most distal telomeric repeats. Nature 383:354-357
33. Kurtz S, Shore D (1991) RAP1 protein activates and silences transcription of mating-type genes in yeast. Genes Dev 5:616-628
34. Kyrion G, Liu K, Liu C, Lustig AJ (1993) RAP1 and telomere structure regulate telomere position effects in Saccharomyces cerevisiae. Genes Dev 7:1146-1159
35. Lascaris RF, Mager WH, Planta RJ (1999) DNA-binding requirements of the yeast protein Rap1p as selected in silico from ribosomal protein gene promoter sequences. Bioinformatics 15:2657-2677
36. Lee T, et al (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298:799-804
37. Lefstin JA, Yamamoto KR (1998) Allosteric effects of DNA on transcriptional regulators. Nature 392:885-888
38. Lieb JD, Liu X, Botstein D, Brown PO (2001) Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet 26:327-334
39. López MC, Smerage JB, Baker HV (1998) Multiple domains of repressor activator protein 1 contribute to facilitated binding of glycolysis regulatory protein 1. Proc Natl Acad Sci USA 95:14112-14117
40. Loven MA, Likhite VS, Choi I, Nardulli AM (2001) Estrogen response elements alter coactivator recruitment through allosteric modulation of estrogen receptor beta conformation. J Biol Chem 276:45282-45288
41. Lukens AK, King DA, Marmorstein R (2000) Structure of HAP1-PC7 bound to DNA: implications for DNA recognition and allosteric effects of DNA-binding on transcriptional activation. Nucleic Acids Res 28, 3853-3863
42. Luo K, Vega-Palas M, Grunstein M (2002) Rap1-Sir4 binding independent of other Sir, yKu, or histone interactions initiates the assembly of telomeric heterochromatin in yeast. Genes Dev 16:1528-1539
43. Martin SG, Laroche T, Suka N, Grunstein M, Gasser SM (1999) Relocalization of telomeric Ku and SIR proteins in response to DNA strand breaks in yeast. Cell 97:621-633
44. Mencia M, Moqtaderi Z, Geisberg J, Kuras L, Struhl K (2002) Activator-specific recruitment of TFIID and regulation of ribosomal protein genes in yeast. Mol Cell 9:823-833
45. Mishra K, Shore D (1999) Yeast Ku protein plays a direct role in telomeric silencing and counteracts inhibition by Rif proteins. Curt Biol 9:1123-1126
46. Mizuta K, Tsujii R, Warner JR, Nishiyama M (1998) The C-terminal silencing domain of Rap1p is essential for the repression of ribosomal protein genes in response to a defect in the secretory pathway. Nucleic Acids Res 26:1063-1069
47. Moehle CM, Hinnebusch AG (1991) Association of RAP1 binding sites with stringent control of ribosomal protein gene transcription in Saccharomyces cerevisiae. Mol Cell Biol 11:2723-2735
48. Moretti P, Shore D (2001) Multiple interactions in Sir protein recruitment by Rap1p at silencers and telomeres in yeast. Mol Cell Biol 21:8082-8094
49. Moretti P, Freeman K, Coodly L, Shore D (1994) Evidence that a complex of SIR proteins interact with the silencer and telomerebinding protein Raplp. Genes Dev 8:2257-2269
50. Morse RH (2000) RAP, RAP, open up! New wrinkles for RAP1 in yeast. Trends Genet 15:51-54
51. O'Reilly M, Teichmann SA, Rhodes D (1999) Telomerases. Curr Opin Struct Biol 9:56-65
52. Palladino F, Laroche T, Gilson E, Axelrod A, Pillus L, Gasser SM (1993a) SIR3 and SIR4 proteins are required for the positioning and integrity of yeast telomeres. Cell 75:543-555
53. Palladino F, Laroche T, Gilson E, Pillus L, Gasser SM (1993b) The positioning of yeast telomeres depends on SIR3, SIR4, and the integrity of the nuclear membrane. Cold Spring Harbor Symp Quant Biol 58:733-746
54. Reid JL, Iyer VR, Brown PO, Struhl K (2000) Coordinate regulation of yeast ribosomal protein genes is associated with targeted recruitment of Esa1 histone acetylase. Mol Cell 6:1297-307
55. Rossetti L, Cacchione S, De Menna A, Chapman L, Rhodes D, Savino M (2001) Specific interactions of the telomeric protein Rap1p with nucleosomal binding sites. J Mol Biol 305:903-913
56. Ryan MP, Stafford GA, Yu L, Morse RH (2000) Artificially recruited TATA-binding protein fails to remodel chromatin and does not activate three promoters that require chromatin remodeling. Mol Cell Biol 20:5847-5857
57. Schwabe JW, Chapman L, Rhodes D (1995) The oestrogen receptor recognizes an imperfectly palindromic response element through an alternative side-chain conformation. Structure 3:201-213
58. Shore D (1994) RAPI: a protean regulator in yeast. Trends Genet 10:408-412
59. Stavenhagen JB, Zakian VA (1994) Internal tracts of telomeric DNA act as silencers in Sacchacromyces cerevisiae. Genes Dev 8:1411-1422
60. Taylor HO, O'Reilly M, Leslie AG, Rhodes D (2000) How the multifunctional yeast Rap1p discriminates between DNA target sites: a crystallographic analysis. J Mol Biol 303:693-707
61. Vignais ML, Woudt LP, Wassenaar GM, Mager WH, Sentenac A, Planta RJ (1987) Specific binding of TUF factor to upstream activation sites of yeast ribosomal protein genes. EMBO J 6:1451-1457
62. Vignais ML, Huet J, Buhler JM, Sentenac A (1990) Contacts between the factor TUF and RPG sequences. J Biol Chem 265:14669-14674
63. Wahlin J, Cohn M (2000) Saccharomyces cerevisiae RAP1 binds to telomeric sequences with spatial flexibility. Nucleic Acids Res 28:2292-2301
64. Warner JR (1999) The economics of ribosome biosynthesis in yeast. Trends Biochem Sci 24:437-440
65. Wood JR, Greene GL, Nardulli AM (1998) Estrogen response elements function as allosteric modulators of estrogen receptor concentration. Mol Cell Biol 18:1927-1934
66. Wotton D, Shore D (1997) A novel Rap1p-interacting factor, Rif2p, cooperates with Rif1p to regulate telomere length in Saccharomyces cerevisiae. Genes Dev 11:748-760
67. Yu L, Sabet N, Chambers A, Morse RH (2001) The N-terminal and C-terminal domains of RAP1 are dispensable for chromatin opening and GCN4-mediated HIS4 activation in budding yeast. J Biol Chem 276:33257-33264