Molecular Genetics and Genomics

, Volume 283, Issue 3, pp 211–221 | Cite as

Mediator subunits and histone methyltransferase Set2 contribute to Ino2-dependent transcriptional activation of phospholipid biosynthesis in the yeast Saccharomyces cerevisiae

  • Anne Dettmann
  • Yvonne Jäschke
  • Ivonne Triebel
  • Jessica Bogs
  • Ireen Schröder
  • Hans-Joachim Schüller
Original Paper

Abstract

To activate eukaryotic genes, several pathways which modify chromatin and recruit general factors of the transcriptional machinery are utilized. We investigated the factors required for activation of yeast phospholipid biosynthetic genes, depending on activator protein Ino2 which binds to the inositol/choline-responsive element (ICRE) upstream promoter motif together with its partner protein Ino4. We used a set of 15 strains each defective for one of the non essential subunits of yeast mediator complex and identified med2, med3, med15, med18 and med19 as impaired for inositol biosynthesis. In these mutants, ICRE-dependent gene activation was reduced to 13–22% of the wild-type level. We also demonstrate synthetic growth and activation defects among mediator mutants and mutants lacking defined histone modifications (snf1, gcn5) and transcriptional coactivators (sub1). Analysis of mutants defective for histone methylation (set1, set2 and dot1) and demethylation (jhd1, jhd2, gis1, rph1 and ecm5) revealed the importance of the H3 Lys36-specific Set2 methyltransferase for ICRE-dependent gene expression. Although defined mediator subunits are critical for gene activation, we could not detect their interaction with Ino2. In contrast, Ino2 directly binds to the Set2 histone methyltransferase. Mapping of interaction domains revealed the importance of the SET core domain which was necessary and sufficient for binding Ino2.

Keywords

Phospholipid biosynthesis Saccharomyces cerevisiae Transcriptional activation Ino2 Mediator Histone methyltransferase 

References

  1. Adam M, Robert F, Larochelle M, Gaudreau L (2001) H2A.Z is required for global chromatin integrity and for recruitment of RNA polymerase II under specific conditions. Mol Cell Biol 21:6270–6279PubMedCrossRefGoogle Scholar
  2. 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 269:15344–15349PubMedGoogle Scholar
  3. Barbaric S, Luckenbach T, Schmid A, Blaschke D, Hörz W, Korber P (2007) Redundancy of chromatin remodeling pathways for the induction of the yeast PHO5 promoter in vivo. J Biol Chem 282:27610–27621PubMedCrossRefGoogle Scholar
  4. Berger SL (2007) The complex language of chromatin regulation during transcription. Nature 447:407–412PubMedCrossRefGoogle Scholar
  5. Bhaumik SR, Raha T, Aiello DP, Green MR (2004) In vivo target of a transcriptional activator revealed by fluorescence resonance energy transfer. Genes Dev 18:333–343PubMedCrossRefGoogle Scholar
  6. Biswas D, Dutta-Biswas R, Mitra D, Shibata Y, Strahl BD, Formosa T, Stillman DJ (2006) Opposing roles for Set2 and yFACT in regulating TBP binding at promoters. EMBO J 25:4479–4489PubMedCrossRefGoogle Scholar
  7. Biswas D, Takahata S, Xin H, Dutta-Biswas R, Yu Y, Formosa T, Stillman DJ (2008) A role for Chd1 and Set2 in negatively regulating DNA replication in Saccharomyces cerevisiae. Genetics 178:649–659PubMedCrossRefGoogle Scholar
  8. Björklund S, Gustafsson CM (2005) The yeast Mediator complex and its regulation. Trends Biochem Sci 30:240–244PubMedCrossRefGoogle Scholar
  9. Brachmann CB, Davies A, Cost GJ, Caputo E, Li J, Hieter P, Boeke JD (1998) Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 14:115–132PubMedCrossRefGoogle Scholar
  10. Brent R, Ptashne M (1985) A eukaryotic transcriptional activator bearing the DNA specificity of a prokaryotic repressor. Cell 43:729–736PubMedCrossRefGoogle Scholar
  11. Carrozza MJ, Li B, Florens L, Suganuma T, Swanson SK, Lee KK, Shia WJ, Anderson S, Yates J, Washburn MP, Workman JL (2005) Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 123:581–592PubMedCrossRefGoogle Scholar
  12. Chen M, Hancock LC, Lopes JM (2007) Transcriptional regulation of yeast phospholipid biosynthetic genes. Biochim Biophys Acta 1771:310–321PubMedGoogle Scholar
  13. Chuikov S, Kurash JK, Wilson JR, Xiao B, Justin N, Ivanov GS, McKinney K, Tempst P, Prives C, Gamblin SJ, Barlev NA, Reinberg D (2004) Regulation of p53 activity through lysine methylation. Nature 432:353–360PubMedCrossRefGoogle Scholar
  14. 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 48:1119–1130PubMedCrossRefGoogle Scholar
  15. Dotson MR, Yuan CX, Roeder RG, Myers LC, Gustafsson CM, Jiang YW, Li Y, Kornberg RD, Asturias FJ (2000) Structural organization of yeast and mammalian mediator complexes. Proc Natl Acad Sci USA 97:14307–14310PubMedCrossRefGoogle Scholar
  16. Drysdale CM, Jackson BM, McVeigh R, Klebanow ER, Bai Y, Kokubo T, Swanson M, Nakatani Y, Weil PA, Hinnebusch AG (1998) The Gcn4p activation domain interacts specifically in vitro with RNA polymerase II holoenzyme, TFIID, and the Adap-Gcn5p coactivator complex. Mol Cell Biol 18:1711–1724PubMedGoogle Scholar
  17. Ebbert R, Birkmann A, Schüller HJ (1999) The product of the SNF2/SWI2 paralogue INO80 of Saccharomyces cerevisiae required for efficient expression of various yeast structural genes is part of a high-molecular-weight protein complex. Mol Microbiol 32:741–751PubMedCrossRefGoogle Scholar
  18. Flaus A, Owen-Hughes T (2001) Mechanisms for ATP-dependent chromatin remodelling. Curr Opin Genet Dev 11:148–154PubMedCrossRefGoogle Scholar
  19. Govind CK, Yoon S, Qiu H, Govind S, Hinnebusch AG (2005) Simultaneous recruitment of coactivators by Gcn4p stimulates multiple steps of transcription in vivo. Mol Cell Biol 25:5626–5638PubMedCrossRefGoogle Scholar
  20. Guglielmi B, van Berkum NL, Klapholz B, Bijma T, Boube M, Boschiero C, Bourbon HM, Holstege FC, Werner M (2004) A high resolution protein interaction map of the yeast mediator complex. Nucleic Acids Res 32:5379–5391PubMedCrossRefGoogle Scholar
  21. Güldener U, Heck S, Fielder T, Beinhauer J, Hegemann JH (1996) A new efficient gene disruption cassette for repeated use in budding yeast. Nucleic Acids Res 24:2519–2524PubMedCrossRefGoogle Scholar
  22. Hampsey M (1998) Molecular genetics of the RNA polymerase II general transcriptional machinery. Microbiol Mol Biol Rev 62:465–503PubMedGoogle Scholar
  23. 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 56:696–707PubMedCrossRefGoogle Scholar
  24. 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 22:601–613PubMedCrossRefGoogle Scholar
  25. Hoshizaki DK, Hill JE, Henry SA (1990) The Saccharomyces cerevisiae INO4 gene encodes a small, highly basic protein required for derepression of phospholipid biosynthesis enzymes. J Biol Chem 265:4736–4745PubMedGoogle Scholar
  26. Huang J, Perez-Burgos L, Placek BJ, Sengupta R, Richter M, Dorsey JA, Kubicek S, Opravil S, Jenuwein T, Berger SL (2006) Repression of p53 activity by Smyd2 mediated methylation. Nature 444:629–632PubMedCrossRefGoogle Scholar
  27. Jenuwein T, Allis CD (2001) Translating the histone code. Science 293:1074–1080PubMedCrossRefGoogle Scholar
  28. Kang JS, Kim SH, Hwang MS, Han SJ, Lee YC, Kim YJ (2001) The structural and functional organization of the yeast mediator complex. J Biol Chem 276:42003–42010PubMedCrossRefGoogle Scholar
  29. Kizer KO, Phatnani HP, Shibata Y, Hall H, Greenleaf AL, Strahl BD (2005) A novel domain in Set2 mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation. Mol Cell Biol 25:3305–3316PubMedCrossRefGoogle Scholar
  30. Klose RJ, Zhang Y (2007) Regulation of histone methylation by demethylimination and demethylation. Nat Rev Mol Cell Biol 8:307–318PubMedCrossRefGoogle Scholar
  31. Knaus R, Pollock R, Guarente L (1996) Yeast SUB1 is a suppressor of TFIIB mutations and has homology to the human co-activator PC4. EMBO J 15:1933–1940PubMedGoogle Scholar
  32. Kodaki T, Hosaka K, Nikawa J, Yamashita S (1995) The SNF2/SWI2/GAM1/TYE3/RIC1 gene is involved in the coordinate regulation of phospholipid synthesis in Saccharomyces cerevisiae. J Biochem 117:362–368PubMedCrossRefGoogle Scholar
  33. Koh SS, Ansari AZ, Ptashne M, Young RA (1998) An activator target in the RNA polymerase II holoenzyme. Mol Cell 1:895–904PubMedCrossRefGoogle Scholar
  34. Kornberg RD (2005) Mediator and the mechanism of transcriptional activation. Trends Biochem Sci 30:235–239PubMedCrossRefGoogle Scholar
  35. Kouskouti A, Scheer E, Staub A, Tora L, Talianidis I (2004) Gene-specific modulation of TAF10 function by SET9-mediated methylation. Mol Cell 14:175–182PubMedCrossRefGoogle Scholar
  36. 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 54:35–45PubMedCrossRefGoogle Scholar
  37. Kurdistani SK, Grunstein M (2003) Histone acetylation and deacetylation in yeast. Nat Rev Mol Cell Biol 4:276–284PubMedCrossRefGoogle Scholar
  38. Lee TI, Causton HC, Holstege FC, Shen WC, Hannett N, Jennings EG, Winston F, Green MR, Young RA (2000) Redundant roles for the TFIID and SAGA complexes in global transcription. Nature 405:701–704PubMedCrossRefGoogle Scholar
  39. Leroy C, Cormier L, Kuras L (2006) Independent recruitment of mediator and SAGA by the activator Met4. Mol Cell Biol 26:3149–3163PubMedCrossRefGoogle Scholar
  40. Li J, Moazed D, Gygi SP (2002) Association of the histone methyltransferase Set2 with RNA polymerase II plays a role in transcription elongation. J Biol Chem 277:49383–49388PubMedCrossRefGoogle Scholar
  41. Lo WS, Gamache ER, Henry KW, Yang D, Pillus L, Berger SL (2005) Histone H3 phosphorylation can promote TBP recruitment through distinct promoter-specific mechanisms. EMBO J 24:997–1008PubMedCrossRefGoogle Scholar
  42. Loewen CJ, Gaspar ML, Jesch SA, Delon C, Ktistakis NT, Henry SA, Levine TP (2004) Phospholipid metabolism regulated by a transcription factor sensing phosphatidic acid. Science 304:1644–1647PubMedCrossRefGoogle Scholar
  43. Martin C, Zhang Y (2005) The diverse functions of histone lysine methylation. Nat Rev Mol Cell Biol 6:838–849PubMedCrossRefGoogle Scholar
  44. Melcher K, Johnston SA (1995) GAL4 interacts with TATA-binding protein and coactivators. Mol Cell Biol 15:2839–2848PubMedGoogle Scholar
  45. Mumberg D, Müller R, Funk M (1994) Regulatable promoters of Saccharomyces cerevisiae: comparison of transcriptional activity and their use for heterologous expression. Nucleic Acids Res 22:5767–5768PubMedCrossRefGoogle Scholar
  46. Myers LC, Gustafsson CM, Hayashibara KC, Brown PO, Kornberg RD (1999) Mediator protein mutations that selectively abolish activated transcription. Proc Natl Acad Sci USA 96:67–72PubMedCrossRefGoogle Scholar
  47. Nelson CJ, Santos-Rosa H, Kouzarides T (2006) Proline isomerization of histone H3 regulates lysine methylation and gene expression. Cell 126:905–916PubMedCrossRefGoogle Scholar
  48. Nikoloff DM, McGraw P, Henry SA (1992) The INO2 gene of Saccharomyces cerevisiae encodes a helix-loop-helix protein that is required for activation of phospholipid synthesis. Nucleic Acids Res 20:3253PubMedCrossRefGoogle Scholar
  49. Park JM, Kim HS, Han SJ, Hwang MS, Lee YC, Kim YJ (2000) In vivo requirement of activator-specific binding targets of mediator. Mol Cell Biol 20:8709–8719PubMedCrossRefGoogle Scholar
  50. Pillai B, Sampath V, Sharma N, Sadhale P (2001) Rpb4, a non-essential subunit of core RNA polymerase II of Saccharomyces cerevisiae is important for activated transcription of a subset of genes. J Biol Chem 276:30641–30647PubMedCrossRefGoogle Scholar
  51. Sampath V, Rekha N, Srinivasan N, Sadhale P (2003) The conserved and non-conserved regions of Rpb4 are involved in multiple phenotypes in Saccharomyces cerevisiae. J Biol Chem 278:51566–51576PubMedCrossRefGoogle Scholar
  52. Scafe C, Nonet M, Young RA (1990) RNA polymerase II mutants defective in transcription of a subset of genes. Mol Cell Biol 10:1010–1016PubMedGoogle Scholar
  53. Schaft D, Roguev A, Kotovic KM, Shevchenko A, Sarov M, Shevchenko A, Neugebauer KM, Stewart AF (2003) The histone 3 lysine 36 methyltransferase, SET2, is involved in transcriptional elongation. Nucleic Acids Res 31:2475–2482PubMedCrossRefGoogle Scholar
  54. Schüller HJ, Schorr R, Hoffmann B, Schweizer E (1992) Regulatory gene INO4 of yeast phospholipid biosynthesis is positively autoregulated and functions as a trans-activator of fatty acid synthase genes FAS1 and FAS2 from Saccharomyces cerevisiae. Nucleic Acids Res 20:5955–5961PubMedCrossRefGoogle Scholar
  55. Schüller HJ, Richter K, Hoffmann B, Ebbert R, Schweizer E (1995) DNA binding site of the yeast heteromeric Ino2p/Ino4p basic helix-loop-helix transcription factor: structural requirements as defined by saturation mutagenesis. FEBS Lett 370:149–152PubMedCrossRefGoogle Scholar
  56. 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. Nucleic Acids Res 23:230–237PubMedCrossRefGoogle Scholar
  57. Shi X, Kachirskaia I, Yamaguchi H, West LE, Wen H, Wang EW, Dutta S, Appella E, Gozani O (2007) Modulation of p53 function by SET8-mediated methylation at lysine 382. Mol Cell 27:636–646PubMedCrossRefGoogle Scholar
  58. Song W, Treich I, Qian N, Kuchin S, Carlson M (1996) SSN genes that affect transcriptional repression in Saccharomyces cerevisiae encode SIN4, ROX3, and SRB proteins associated with RNA polymerase II. Mol Cell Biol 16:115–120PubMedGoogle Scholar
  59. Stillman DJ, Dorland S, Yu Y (1994) Epistasis analysis of suppressor mutations that allow HO expression in the absence of the yeast SWI5 transcriptional activator. Genetics 136:781–788PubMedGoogle Scholar
  60. Strahl BD, Grant PA, Briggs SD, Sun ZW, Bone JR, Caldwell JA, Mollah S, Cook RG, Shabanowitz J, Hunt DF, Allis CD (2002) Set2 is a nucleosomal histone H3-selective methyltransferase that mediates transcriptional repression. Mol Cell Biol 22:1298–1306PubMedCrossRefGoogle Scholar
  61. Takagi Y, Kornberg RD (2006) Mediator as a general transcription factor. J Biol Chem 281:80–89PubMedCrossRefGoogle Scholar
  62. Tompa R, Madhani HD (2007) Histone H3 lysine 36 methylation antagonizes silencing in Saccharomyces cerevisiae independently of the Rpd3S histone deacetylase complex. Genetics 175:585–593PubMedCrossRefGoogle Scholar
  63. Tschiersch B, Hofmann A, Krauss V, Dorn R, Korge G, Reuter G (1994) The protein encoded by the Drosophila position-effect variegation suppressor gene Su(var)3–9 combines domains of antagonistic regulators of homeotic gene complexes. EMBO J 13:3822–3831PubMedGoogle Scholar
  64. Wach A, Brachat A, Pöhlmann R, Philippsen P (1994) New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae. Yeast 10:1793–1808PubMedCrossRefGoogle Scholar
  65. 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 41:155–166PubMedCrossRefGoogle Scholar
  66. Wu WH, Hampsey M (1999) An activation-specific role for transcription factor TFIIB in vivo. Proc Natl Acad Sci USA 96:2764–2769PubMedCrossRefGoogle Scholar
  67. Xiao T, Hall H, Kizer KO, Shibata Y, Hall MC, Borchers CH, Strahl BD (2003) Phosphorylation of RNA polymerase II CTD regulates H3 methylation in yeast. Genes Dev 17:654–663PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Anne Dettmann
    • 1
    • 2
  • Yvonne Jäschke
    • 1
  • Ivonne Triebel
    • 1
    • 3
  • Jessica Bogs
    • 1
    • 4
  • Ireen Schröder
    • 1
    • 5
  • Hans-Joachim Schüller
    • 1
  1. 1.Institut für Genetik und Funktionelle GenomforschungGreifswaldGermany
  2. 2.Institut für Mikrobiologie und GenetikGöttingenGermany
  3. 3.Institut für PharmakologieGreifswaldGermany
  4. 4.Friedrich-Loeffler-InstitutGreifswald-Insel RiemsGermany
  5. 5.Julius Wolff InstitutCampus Virchow-KlinikumBerlinGermany

Personalised recommendations