Phylogenetic conservation and homology modeling help reveal a novel domain within the budding yeast heterochromatin protein sir1

Molecular and Cellular Biology

Volumn 29, Issue 3, 2009, Pages 687-702

  Hou, Zhonggang ^a   Danzer, John R ^a   Mendoza, Liza ^a   Bose, Melissa E ^a   Müller, Ulrika ^a   Williams, Barry ^b   Fox, Catherine A ^a  

^a UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE AND PUBLIC HEALTH   (United States)

^b MICHIGAN STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ORIGIN RECOGNITION COMPLEX; PROTEIN ORC1; PROTEIN SIR1; SILENT INFORMATION REGULATOR PROTEIN; UNCLASSIFIED DRUG; ORC1 PROTEIN, S CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEIN; SIR1 PROTEIN, S CEREVISIAE; SIR3 PROTEIN, S CEREVISIAE;

AMINO ACID SUBSTITUTION; AMINO TERMINAL SEQUENCE; ARTICLE; CONTROLLED STUDY; DNA SEQUENCE; FUNGAL STRAIN; HETEROCHROMATIN; IN VITRO STUDY; IN VIVO STUDY; MOLECULAR PHYLOGENY; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN INTERACTION; PROTEIN STRUCTURE; SACCHAROMYCES CEREVISIAE; ALLELE; AMINO ACID SEQUENCE; CHEMICAL STRUCTURE; CHEMISTRY; CYTOLOGY; GENE SILENCING; GENETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; SEQUENCE HOMOLOGY; SILENCER ELEMENT; STRUCTURAL HOMOLOGY; TWO HYBRID SYSTEM;

SACCHAROMYCETALES;

ALLELES; AMINO ACID SEQUENCE; CONSERVED SEQUENCE; GENE SILENCING; HETEROCHROMATIN; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; ORIGIN RECOGNITION COMPLEX; PHYLOGENY; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; SILENCER ELEMENTS, TRANSCRIPTIONAL; SILENT INFORMATION REGULATOR PROTEINS, SACCHAROMYCES CEREVISIAE; STRUCTURAL HOMOLOGY, PROTEIN; TWO-HYBRID SYSTEM TECHNIQUES;

EID: 59249100791     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/MCB.00202-08     Document Type: Article

References (57)

1. Altaf, M., R. T. Utley, N. Lacoste, S. Tan, S. D. Briggs, and J. Cote. 2007. Interplay of chromatin modifiers on a short basic patch of histone H4 tail defines the boundary of telomeric heterochromatin. Mol. Cell 28:1002-1014.
2. Bell, S. P. 2002. The origin recognition complex: from simple origins to complex functions. Genes Dev. 16:659-672.
3. Bell, S. P., J. Mitchell, J. Leber, R. Kobayashi, and B. Stillman. 1995. The multidomain structure of Orc1p reveals similarity to regulators of DNA replication and transcriptional silencing. Cell 83:563-568.
4. Bose, M. E., K. H. McConnell, K. A. Gardner-Aukema, U. Muller, M. Weinreich, J. L. Keck, and C. A. Fox. 2004. The origin recognition complex and Sir4 protein recruit Sir1p to yeast silent chromatin through independent interactions requiring a common Sir1p domain. Mol. Cell. Biol. 24:774-786.
5. Brent, G. A., D. D. Moore, and P. R. Larsen. 1991. Thyroid hormone regulation of gene expression. Annu. Rev. Physiol. 53:17-35.
6. Callebaut, I., J. C. Courvalin, and J. P. Mornon. 1999. The BAH (bromo- adjacent homology) domain: a link between DNA methylation, replication and transcriptional regulation. FEBS Lett. 446:189-193.
7. Carmen, A. A., L. Milne, and M. Grunstein. 2002. Acetylation of the yeast histone H4 N terminus regulates its binding to heterochromatin protein SIR3. J. Biol. Chem. 277:4778-4781.
8. Casey, L., E. E. Patterson, U. Muller, and C. A. Fox. 2008. Conversion of a replication origin to a silencer through a pathway shared by a forkhead transcription factor and an S phase cyclin. Mol. Biol. Cell 19:608-622.
9. Chien, C. T., S. Buck, R. Sternglanz, and D. Shore. 1993. TargetingofSIR1 protein establishes transcriptional silencing at HM loci and telomeres in yeast. Cell 75:531-541.
10. Chivian, D., and D. Baker. 2006. Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection. Nucleic Acids Res. 34:e112.
11. Chivian, D.,D. E. Kim, L. Malmstrom, P. Bradley, T. Robertson, P. Murphy, C. E. Strauss, R. Bonneau, C. A. Rohl, and D. Baker. 2003. Automated prediction of CASP-5 structures using the Robetta server. Proteins 53(Suppl. 6):524-533.
12. Chivian, D., D. E. Kim, L. Malmstrom, J. Schonbrun, C. A. Rohl, and D. Baker. 2005. Prediction of CASP6 structures using automated Robetta protocols. Proteins 61(Suppl. 7):157-166.
13. Connelly, J. J., P. Yuan, H. C. Hsu, Z. Li, R. M. Xu, and R. Sternglanz. 2006. Structure and function of the Saccharomyces cerevisiae Sir3 BAH domain. Mol. Cell. Biol. 26:3256-3265.
14. Cubizolles, F., F. Martino, S. Perrod, and S. M. Gasser. 2006. A homotri-mer-heterotrimer switch in Sir2 structure differentiates rDNA and telomeric silencing. Mol. Cell 21:825-836.
15. Delano, W. L. 2002. The PyMol molecular graphics system. DeLano Scientific, San Carlos, CA.
16. Denu, J. M. 2003. Linking chromatin function with metabolic networks: Sir2 family of NAD( + )-dependent deacetylases. Trends Biochem. Sci. 28:41-48.
17. Dhillon, N., and R. T. Kamakaka. 2000. A histone variant, Htz1p, and a Sir1p-like protein, Esc2p, mediate silencing at HMR. Mol. Cell 6:769-780.
18. Fox, C. A., A. E. Ehrenhofer-Murray, S. Loo, and J. Rine. 1997. The Origin recognition complex, SIR1, and the S phase requirement for silencing. Science 276:1547-1551.
19. Fox, C. A., S. Loo, A. Dillin, and J. Rine. 1995. The origin recognition complex has essential functions in transcriptional silencing and chromosomal replication. Genes Dev. 9:911-924.
20. Fox, C. A., and K. H. McConnell. 2005. Toward biochemical understanding of a transcriptionally silenced chromosomal domain in Saccharomyces cer- evisiae. J. Biol. Chem. 280:8629-8632.
21. Gardner, K. A., and C. A. Fox. 2001. The Sir1 protein's association with a silenced chromosome domain. Genes Dev. 15:147-157.
22. Gardner, K. A., J. Rine, and C. A. Fox. 1999. A region of the Sir1 protein dedicated to recognition of a silencer and required for interaction with the Orc1 protein in Saccharomyces cerevisiae. Genetics 151:31-44.
23. Gasser, S. M., and M. M. Cockell. 2001. The molecular biology of the SIR proteins. Gene 279:1-16.
24. Gavin, K. A., M. Hidaka, and B. Stillman. 1995. Conserved initiator proteins in eukaryotes. Science 270:1667-1671.
25. Georgel, P. T., M. A. Palacios DeBeer, G. Pietz, C. A. Fox, and J. C. Hansen. 2001. Sir3-dependent assembly of supramolecular chromatin structures in vitro. Proc. Natl. Acad. Sci. USA 98:858-8589.
26. Goodwin, G. H., and R. H. Nicolas. 2001. The BAH domain, polybromo and the RSC chromatin remodelling complex. Gene 268:1-7.
27. Grunstein, M. 1997. Molecular model for telomeric heterochromatin in yeast. Curr. Opin. Cell Biol. 9:383-387.
28. Guthrie, C., and G. R. Fink. 1991. Guide to yeast genetics and molecular biology. Academic Press, San Diego, CA.
29. Harlow, E., and D. Lane. 1999. Using antibodies: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
30. Hou, Z., D. A. Bernstein, C. A. Fox, and J. L. Keck. 2005. Structural basis of the Sir1-origin recognition complex interaction in transcriptional silencing. Proc. Natl. Acad. Sci. USA 102:8489-8494.
31. Hou, Z., J. R. Danzer, C. A. Fox, and J. L. Keck. 2006. Structure ofthe Sir3 protein bromo adjacent homology (BAH) domain from S. cerevisiae at 1.95 A resolution. Protein Sci. 15:1182-1186.
32. Hsu, H. C., B. Stillman, and R. M. Xu. 2005. Structural basis for origin recognition complex 1 protein-silence information regulator 1 protein interaction in epigenetic silencing. Proc. Natl. Acad. Sci. USA 102:8519-8524.
33. James, P., J. Halladay, and E. A. Craig. 1996. Genomic libraries and a host strain designed for highly efficient two-hybrid selection in yeast. Genetics 144:1425-1436.
34. Kim, D. E., D. Chivian, and D. Baker. 2004. Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res. 32: W526-W531.
35. Kitazono, A. A., B. T. Tobe, H. Kalton, N. Diamant, and S. J. Kron. 2002. Marker-fusion PCR for one-step mutagenesis of essential genes in yeast. Yeast 19:141-149.
36. Leatherwood, J., and A. Vas. 2003. Connecting ORC and heterochromatin: why? Cell Cycle 2:573-575.
37. Liou, G. G., J. C. Tanny, R. G. Kruger, T. Walz, and D. Moazed. 2005. Assembly of the SIR complex and its regulation by O-acetyl-ADP-ribose, a product of NAD-dependent histone deacetylation. Cell 121:515-527.
38. Longtine, M. S., A. McKenzie III, D. J. Demarini, N. G. Shah, A. Wach, A. Brachat, P. Philippsen, and J. R. Pringle. 1998. Additional modules for versatile and economical PCR-based gene deletion and modification in Sac- charomyces cerevisiae. Yeast 14:953-961.
39. McNally, F. J., and J. Rine. 1991. A synthetic silencer mediates SIR-depen- dent functions in Saccharomyces cerevisiae. Mol. Cell. Biol. 11:5648-5659.
40. Moazed, D., A. Kistler, A. Axelrod, J. Rine, and A. D. Johnson. 1997. Silent information regulator protein complexes in Saccharomyces cerevisiae: a SIR2/SIR4 complex and evidence for a regulatory domain in SIR4 that inhibits its interaction with SIR3. Proc. Natl. Acad. Sci. USA 94:2186-2191.
41. Moazed, D., A. D. Rudner, J. Huang, G. J. Hoppe, and J. C. Tanny. 2004. A model for step-wise assembly of heterochromatin in yeast. Novartis Found. Symp. 259:48-56. (Discussion, 259:56-62, 163-169.)
42. Onishi, M., G. G. Liou, J. R. Buchberger, T. Walz, and D. Moazed. 2007. Role of the conserved Sir3-BAH domain in nucleosome binding and silent chromatin assembly. Mol. Cell 28:1015-1028.
43. Palacios DeBeer, M. A., and C. A. Fox. 1999. A role for a replicator dominance mechanism in silencing. EMBO J. 18:3808-3819.
44. Rohl, C. A., C. E. Strauss, D. Chivian, and D. Baker. 2004. Modeling structurally variable regions in homologous proteins with Rosetta. Proteins 55:656-677.
45. Rudner, A. D., B. E. Hall, T. Ellenberger, and D. Moazed. 2005. A nonhis- tone protein-protein interaction required for assembly of the SIR complex and silent chromatin. Mol. Cell. Biol. 25:4514-4528.
46. Rusche, L. N., A. L. Kirchmaier, and J. Rine. 2003. The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae. Annu. Rev. Biochem. 72:481-516.
47. Rusche, L. N., A. L. Kirchmaier, and J. Rine. 2002. Ordered nucleation and spreading of silenced chromatin in Saccharomyces cerevisiae. Mol. Biol. Cell 13:2207-2222.
48. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
49. Sasaki, T., and D. M. Gilbert. 2007. The manyfaces of the origin recognition complex. Curr. Opin. Cell Biol. 19:337-343.
50. Sharp, J. A., D. C. Krawitz, K. A. Gardner, C. A. Fox, and P. D. Kaufman. 2003. The budding yeast silencing protein Sir1 is a functional component of centromeric chromatin. Genes Dev. 17:2356-2361.
51. Sikorski, R. S., and P. Hieter. 1989. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122:19-27.
52. Stone, E. M., M. J. Swanson, A. M. Romeo, J. B. Hicks, and R. Sternglanz. 1991. The SIR1 gene of Saccharomyces cerevisiae and its role as an extragenic suppressor of several mating-defective mutants. Mol. Cell. Biol. 11:2253-2262.
53. Taylor, S. S., J. A. Buechler, and W. Yonemoto. 1990. cAMP-dependent protein kinase: framework for a diverse family of regulatory enzymes. Annu. Rev. Biochem. 59:971-1005.
54. Thomas, B. J., and R. Rothstein. 1989. Elevated recombination rates in transcriptionally active DNA. Cell 56:619-630.
55. Triolo, T., and R. Sternglanz. 1996. Role of interactions between the origin recognition complex and Sir1 in transcriptional silencing. Nature 381:251-253.
56. Xu, W., J. G. Aparicio, O. M. Aparicio, and S. Tavare. 2006. Genome-wide mapping of ORC and Mcm2p binding sites on tiling arrays and identification of essential ARS consensus sequences in S. cerevisiae. BMC Genomics 7:276.
57. Zhang, Z., M. K. Hayashi, O. Merkel, B. Stillman, and R. M. Xu. 2002. Structure and function of the BAH-containing domain of Orc1p in epige-netic silencing. EMBO J. 21:4600-4611.