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Article

Phylogenetic Conservation and Homology Modeling Help Reveal a Novel Domain within the Budding Yeast Heterochromatin Protein Sir1

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Pages 687-702 | Received 07 Feb 2008, Accepted 10 Nov 2008, Published online: 21 Mar 2023

REFERENCES

  • 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.
  • Bell, S. P. 2002. The origin recognition complex: from simple origins to complex functions. Genes Dev. 16:659–672.
  • 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.
  • 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.
  • Brent, G. A., D. D. Moore, and P. R. Larsen. 1991. Thyroid hormone regulation of gene expression. Annu. Rev. Physiol. 53:17–35.
  • 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.
  • 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.
  • 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.
  • Chien, C. T., S. Buck, R. Sternglanz, and D. Shore. 1993. Targeting of SIR1 protein establishes transcriptional silencing at HM loci and telomeres in yeast. Cell 75:531–541.
  • 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.
  • 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.
  • 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.
  • 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.
  • Cubizolles, F., F. Martino, S. Perrod, and S. M. Gasser. 2006. A homotrimer-heterotrimer switch in Sir2 structure differentiates rDNA and telomeric silencing. Mol. Cell 21:825–836.
  • Delano, W. L. 2002. The PyMol molecular graphics system. DeLano Scientific, San Carlos, CA.
  • Denu, J. M. 2003. Linking chromatin function with metabolic networks: Sir2 family of NAD(+)-dependent deacetylases. Trends Biochem. Sci. 28:41–48.
  • 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.
  • 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.
  • 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.
  • Fox, C. A., and K. H. McConnell. 2005. Toward biochemical understanding of a transcriptionally silenced chromosomal domain in Saccharomyces cerevisiae. J. Biol. Chem. 280:8629–8632.
  • Gardner, K. A., and C. A. Fox. 2001. The Sir1 protein's association with a silenced chromosome domain. Genes Dev. 15:147–157.
  • 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.
  • Gasser, S. M., and M. M. Cockell. 2001. The molecular biology of the SIR proteins. Gene 279:1–16.
  • Gavin, K. A., M. Hidaka, and B. Stillman. 1995. Conserved initiator proteins in eukaryotes. Science 270:1667–1671.
  • 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 98:8584–8589.
  • Goodwin, G. H., and R. H. Nicolas. 2001. The BAH domain, polybromo and the RSC chromatin remodelling complex. Gene 268:1–7.
  • Grunstein, M. 1997. Molecular model for telomeric heterochromatin in yeast. Curr. Opin. Cell Biol. 9:383–387.
  • Guthrie, C., and G. R. Fink. 1991. Guide to yeast genetics and molecular biology. Academic Press, San Diego, CA.
  • Harlow, E., and D. Lane. 1999. Using antibodies: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
  • 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.
  • Hou, Z., J. R. Danzer, C. A. Fox, and J. L. Keck. 2006. Structure of the Sir3 protein bromo adjacent homology (BAH) domain from S. cerevisiae at 1.95 A resolution. Protein Sci. 15:1182–1186.
  • 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.
  • 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.
  • Kim, D. E., D. Chivian, and D. Baker. 2004. Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res. 32:W526–W531.
  • 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.
  • Leatherwood, J., and A. Vas. 2003. Connecting ORC and heterochromatin: why? Cell Cycle 2:573–575.
  • 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.
  • 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 Saccharomyces cerevisiae. Yeast 14:953–961.
  • McNally, F. J., and J. Rine. 1991. A synthetic silencer mediates SIR-dependent functions in Saccharomyces cerevisiae. Mol. Cell. Biol. 11:5648–5659.
  • 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.
  • 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.)
  • 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.
  • Palacios DeBeer, M. A., and C. A. Fox. 1999. A role for a replicator dominance mechanism in silencing. EMBO J. 18:3808–3819.
  • 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.
  • Rudner, A. D., B. E. Hall, T. Ellenberger, and D. Moazed. 2005. A nonhistone protein-protein interaction required for assembly of the SIR complex and silent chromatin. Mol. Cell. Biol. 25:4514–4528.
  • 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.
  • 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.
  • 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.
  • Sasaki, T., and D. M. Gilbert. 2007. The many faces of the origin recognition complex. Curr. Opin. Cell Biol. 19:337–343.
  • 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.
  • 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.
  • 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.
  • 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.
  • Thomas, B. J., and R. Rothstein. 1989. Elevated recombination rates in transcriptionally active DNA. Cell 56:619–630.
  • Triolo, T., and R. Sternglanz. 1996. Role of interactions between the origin recognition complex and Sir1 in transcriptional silencing. Nature 381:251–253.
  • 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.
  • 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 epigenetic silencing. EMBO J. 21:4600–4611.

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