Abstract
Yeast genes of phospholipid biosynthesis are negatively regulated by repressor protein Opi1 when precursor molecules inositol and choline (IC) are available. Opi1-triggered gene repression is mediated by recruitment of the Sin3 corepressor complex. In this study, we systematically investigated the regulatory contribution of subunits of Sin3 complexes and identified Pho23 as important for IC-dependent gene repression. Two non-overlapping regions within Pho23 mediate its direct interaction with Sin3. Previous work has shown that Sin3 recruits the histone deacetylase (HDAC) Rpd3 to execute gene repression. While deletion of SIN3 strongly alleviates gene repression by IC, an rpd3 null mutant shows almost normal regulation. We thus hypothesized that various HDACs may contribute to Sin3-mediated repression of IC-regulated genes. Indeed, a triple mutant lacking HDACs, Rpd3, Hda1 and Hos1, could phenocopy a sin3 single mutant. We show that these proteins are able to contact Sin3 in vitro and in vivo and mapped three distinct HDAC interaction domains, designated HID1, HID2 and HID3. HID3, which is identical to the previously described structural motif PAH4 (paired amphipathic helix), can bind all HDACs tested. Chromatin immunoprecipitation studies finally confirmed that Hda1 and Hos1 are recruited to promoters of phospholipid biosynthetic genes INO1 and CHO2.
Similar content being viewed by others
References
Ambroziak J, Henry SA (1994) INO2 and INO4 gene products, positive regulators of phospholipid biosynthesis in Saccharomyces cerevisiae, form a complex that binds to the INO1 promoter. J Biol Chem 269:15344–15349
Carrozza MJ, Florens L, Swanson SK, Shia WJ, Anderson S, Yates J, Washburn MP, Workman JL (2005a) Stable incorporation of sequence specific repressors Ash1 and Ume6 into the Rpd3L complex. Biochim Biophys Acta 1731:77–87
Carrozza MJ, Li B, Florens L, Suganuma T, Swanson SK, Lee KK, Shia WJ, Anderson S, Yates J, Washburn MP, Workman JL (2005b) Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 123:581–592
Chen M, Hancock LC, Lopes JM (2007) Transcriptional regulation of yeast phospholipid biosynthetic genes. Biochim Biophys Acta 1771:310–321
Cliften P, Sudarsanam P, Desikan A, Fulton L, Fulton B, Majors J, Waterston R, Cohen BA, Johnston M (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301:71–76
Cobb J, van Attikum H (2010) Mapping genomic targets of DNA helicases by chromatin immunoprecipitation in Saccharomyces cerevisiae. Methods Mol Biol 587:113–126
Colina AR, Young D (2005) Raf60, a novel component of the Rpd3 histone deacetylase complex required for Rpd3 activity in Saccharomyces cerevisiae. J Biol Chem 280:42552–42556
Davie JK, Edmondson DG, Coco CB, Dent SY (2003) Tup1-Ssn6 interacts with multiple class I histone deacetylases in vivo. J Biol Chem 278:50158–50162
De Antoni A, Gallwitz D (2000) A novel multi-purpose cassette for repeated integrative epitope tagging of genes in Saccharomyces cerevisiae. Gene 246:179–185
De Nadal E, Zapater M, Alepuz PM, Sumoy L, Mas G, Posas F (2004) The MAPK Hog1 recruits Rpd3 histone deacetylase to activate osmoresponsive genes. Nature 427:370–374
Dietz M, Heyken WT, Hoppen J, Geburtig S, Schüller HJ (2003) TFIIB and subunits of the SAGA complex are involved in transcriptional activation of phospholipid biosynthetic genes by the regulatory protein Ino2 in the yeast Saccharomyces cerevisiae. Mol Microbiol 48:1119–1130
Grzenda A, Lomberk G, Zhang JS, Urrutia R (2009) Sin3: master scaffold and transcriptional corepressor. Biochim Biophys Acta 1789:443–450
Heyken WT, Repenning A, Kumme J, Schüller HJ (2005) Constitutive expression of yeast phospholipid biosynthetic genes by variants of Ino2 activator defective for interaction with Opi1 repressor. Mol Microbiol 56:696–707
Hildmann C, Riester D, Schwienhorst A (2007) Histone deacetylases-an important class of cellular regulators with a variety of functions. Appl Microbiol Biotechnol 75:487–497
Hoppen J, Repenning A, Albrecht A, Geburtig S, Schüller HJ (2005) Comparative analysis of promoter regions containing binding sites of the heterodimeric transcription factor Ino2/Ino4 involved in yeast phospholipid biosynthesis. Yeast 22:601–613
James P, Halladay J, Craig EA (1996) Genomic libraries and a host strain designed for highly efficient two-hybrid selection in yeast. Genetics 144:1425–1436
Jäschke Y, Schwarz J, Clausnitzer D, Müller C, Schüller HJ (2011) Pleiotropic corepressors Sin3 and Ssn6 interact with repressor Opi1 and negatively regulate transcription of genes required for phospholipid biosynthesis in the yeast Saccharomyces cerevisiae. Mol Genet Genomics 285:91–100
Joshi AA, Struhl K (2005) Eaf3 chromodomain interaction with methylated H3-K36 links histone deacetylation to Pol II elongation. Mol Cell 20:971–978
Kadosh D, Struhl K (1997) Repression by Ume6 involves recruitment of a complex containing Sin3 corepressor and Rpd3 histone deacetylase to target promoters. Cell 89:365–371
Kim SJ, Swanson MJ, Qiu H, Govind CK, Hinnebusch AG (2005) Activator Gcn4p and Cyc8p/Tup1p are interdependent for promoter occupancy at ARG1 in vivo. Mol Cell Biol 25:11171–11183
Kodaki T, Hosaka K, Nikawa J, Yamashita S (1991) Identification of the upstream activation sequences responsible for the expression and regulation of the PEM1 and PEM2 genes encoding the enzymes of the phosphatidylethanolamine methylation pathway in Saccharomyces cerevisiae. J Biochem 109:276–287
Kumme J, Dietz M, Wagner C, Schüller HJ (2008) Dimerization of yeast transcription factors Ino2 and Ino4 is regulated by precursors of phospholipid biosynthesis mediated by Opi1 repressor. Curr Genet 54:35–45
Kuzmichev A, Zhang Y, Erdjument-Bromage H, Tempst P, Reinberg D (2002) Role of the Sin3-histone deacetylase complex in growth regulation by the candidate tumor suppressor p33(ING1). Mol Cell Biol 22:835–848
Laherty CD, Yang WM, Sun JM, Davie JR, Seto E, Eisenman RN (1997) Histone deacetylases associated with the mSin3 corepressor mediate mad transcriptional repression. Cell 89:349–356
Lau WTW, Schneider KR, O’Shea EK (1998) A genetic study of signaling processes for repression of PHO5 transcription in Saccharomyces cerevisiae. Genetics 150:1349–1359
Loewith R, Smith JS, Meijer M, Williams TJ, Bachman N, Boeke JD, Young D (2001) Pho23 is associated with the Rpd3 histone deacetylase and is required for its normal function in regulation of gene expression and silencing in Saccharomyces cerevisiae. J Biol Chem 276:24068–24074
Lopes JM, Schulze KL, Yates JW, Hirsch JP, Henry SA (1993) The INO1 promoter of Saccharomyces cerevisiae includes an upstream repressor sequence (URS1) common to a diverse set of yeast genes. J Bacteriol 175:4235–4238
Malavé TM, Dent SY (2006) Transcriptional repression by Tup1-Ssn6. Biochem Cell Biol 84:437–443
Mumberg D, Müller R, Funk M (1994) Regulatable promoters of Saccharomyces cerevisiae: comparison of transcriptional activity and their use for heterologous expression. Nucl Acids Res 22:5767–5768
Rundlett SE, Carmen AA, Kobayashi R, Bavykin S, Turner BM, Grunstein M (1996) HDA1 and RPD3 are members of distinct yeast histone deacetylase complexes that regulate silencing and transcription. Proc Natl Acad Sci USA 93:14503–14508
Rundlett SE, Carmen AA, Suka N, Turner BM, Grunstein M (1998) Transcriptional repression by UME6 involves deacetylation of lysine 5 of histone H4 by RPD3. Nature 392:831–835
Schüller HJ, Hahn A, Tröster F, Schütz A, Schweizer E (1992) Coordinate genetic control of yeast fatty acid synthase genes FAS1 and FAS2 by an upstream activation site common to genes involved in membrane lipid biosynthesis. EMBO J 11:107–114
Schwank S, Ebbert R, Rautenstrauss K, Schweizer E, Schüller HJ (1995) Yeast transcriptional activator INO2 interacts as an Ino2p/Ino4p basic helix-loop-helix heteromeric complex with the inositol/choline-responsive element necessary for expression of phospholipid biosynthetic genes in Saccharomyces cerevisiae. Nucl Acids Res 23:230–237
Shevchenko A, Roguev A, Schaft D, Buchanan L, Habermann B, Sakalar C, Thomas H, Krogan NJ, Shevchenko A, Stewart AF (2008) Chromatin central: towards the comparative proteome by accurate mapping of the yeast proteomic environment. Genome Biol 9:R167
Shi X, Hong T, Walter KL, Ewalt M, Michishita E, Hung T, Carney D, Peña P, Lan F, Kaadige MR, Lacoste N, Cayrou C, Davrazou F, Saha A, Cairns BR, Ayer DE, Kutateladze TG, Shi Y, Côté J, Chua KF, Gozani O (2006) ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression. Nature 442:96–99
Silverstein RA, Ekwall K (2005) Sin3: a flexible regulator of global gene expression and genome stability. Curr Genet 47:1–17
Slekar KH, Henry SA (1995) SIN3 works through two different promoter elements to regulate INO1 gene expression in yeast. Nucl Acids Res 23:1964–1969
Sun ZW, Hampsey M (1999) A general requirement for the Sin3-Rpd3 histone deacetylase complex in regulating silencing in Saccharomyces cerevisiae. Genetics 152:921–932
Vannier D, Balderes D, Shore D (1996) Evidence that the transcriptional regulators SIN3 and RPD3, and a novel gene (SDS3) with similar functions, are involved in transcriptional silencing in S. cerevisiae. Genetics 144:1343–1353
Wagner C, Dietz M, Wittmann J, Albrecht A, Schüller HJ (2001) The negative regulator Opi1 of phospholipid biosynthesis in yeast contacts the pleiotropic repressor Sin3 and the transcriptional activator Ino2. Mol Microbiol 41:155–166
Wang H, Clark I, Nicholson PR, Herskowitz I, Stillman DJ (1990) The Saccharomyces cerevisiae SIN3 gene, a negative regulator of HO, contains four paired amphipathic helix motifs. Mol Cell Biol 10:5927–5936
Wang SS, Zhou BO, Zhou JQ (2011) Histone H3 lysine 4 hypermethylation prevents aberrant nucleosome remodeling at the PHO5 promoter. Mol Cell Biol 31:3171–3181
Washburn BK, Esposito RE (2001) Identification of the Sin3-binding site in Ume6 defines a two-step process for conversion of Ume6 from a transcriptional repressor to an activator in yeast. Mol Cell Biol 21:2057–2069
Watson AD, Edmondson DG, Bone JR, Mukai Y, Yu Y, Du W, Stillman DJ, Roth SY (2000) Ssn6-Tup1 interacts with class I histone deacetylases required for repression. Genes Dev 14:2737–2744
Wu J, Carmen AA, Kobayashi R, Suka N, Grunstein M (2001a) HDA2 and HDA3 are related proteins that interact with and are essential for the activity of the yeast histone deacetylase HDA1. Proc Natl Acad Sci USA 98:4391–4396
Wu J, Suka N, Carlson M, Grunstein M (2001b) TUP1 utilizes histone H3/H2B specific HDA1 deacetylase to repress gene activity in yeast. Mol Cell 7:117–126
Xie T, He Y, Korkeamaki H, Zhang Y, Imhoff R, Lohi O, Radhakrishnan I (2011) Structure of the 30-kDa Sin3-associated protein (SAP30) in complex with the mammalian Sin3A corepressor and Its role in nucleic acid binding. J Biol Chem 286:27814–27824
Yang XJ, Seto E (2008) The Rpd3/Hda1 family of lysine deacetylases: from bacteria and yeast to mice and men. Nat Rev Mol Cell Biol 9:206–218
Yang X, Zhang F, Kudlow JE (2002) Recruitment of O-GlcNAc transferase to promoters by corepressor mSin3A: coupling protein O-GlcNAcylation to transcriptional repression. Cell 110:69–80
Zhang Y, Sun ZW, Iratni R, Erdjument-Bromage H, Tempst P, Hampsey M, Reinberg D (1998) SAP30, a novel protein conserved between human and yeast, is a component of a histone deacetylase complex. Mol Cell 1:1021–1031
Acknowledgments
This work has been supported by the Deutsche Forschungsgemeinschaft (DFG). We thank Marius Wanjek for valuable support.
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by H. Ronne.
M. Grigat and Y. Jäschke contributed equally to this work.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Grigat, M., Jäschke, Y., Kliewe, F. et al. Multiple histone deacetylases are recruited by corepressor Sin3 and contribute to gene repression mediated by Opi1 regulator of phospholipid biosynthesis in the yeast Saccharomyces cerevisiae . Mol Genet Genomics 287, 461–472 (2012). https://doi.org/10.1007/s00438-012-0692-x
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00438-012-0692-x