Molecular Genetics and Genomics

, Volume 273, Issue 5, pp 382–393 | Cite as

Transcriptional profiling of Saccharomyces cerevisiae cells under adhesion-inducing conditions

  • Malte Kleinschmidt
  • Olav Grundmann
  • Nils Blüthgen
  • Hans-Ulrich Mösch
  • Gerhard H. Braus
Original Paper

Abstract

The ability to adhere to other cells is one of the most prominent determinants of fungal pathogenicity. Thus, adherence of fungi to human tissues or plastics triggers hospital-acquired fungal infections, which are an increasing clinical problem, especially in immunocompromised persons. In the model fungus Saccharomyces cerevisiae adhesion can be induced by starvation for amino acids, and depends on the transcriptional activator of the general amino acid control system, Gcn4p. However, not much is known about the transcriptional program that mediates adhesive growth under such conditions. In this study, we present a genome-wide transcriptional analysis of Σ1278b yeast cells that were subjected to adhesion-inducing conditions imposed by amino acid starvation. Twenty-two novel genes were identified as inducible by amino acid starvation; 72 genes belonging to different functional groups, which were not previously known to be regulated by Gcn4p, require Gcn4p for full transcriptional induction under adhesion-inducing conditions. In addition, several genes were identified in Σ1278b cells that were inducible by amino acid starvation in a Gcn4p-independent manner. Our data suggest that adhesion of yeast cells induced by amino acid starvation is regulated by a complex, Σ1278b-specific transcriptional response.

Keywords

Saccharomyces cerevisiae Transcriptional profiling Adhesion Gcn4 Amino acid starvation 

Supplementary material

Supplementary Fig. 1 Expression profiles of yeast cells under non-starvation conditions

438_2005_1139_ESM_supp_f1.pdf (161 kb)
(PDF 161 KB)

Supplementary Table 1 Condition GCN4 / gcn4

438_2005_1139_ESM_supp_t1.xls (700 kb)
(Excel 701 KB)

Supplementary Table 2 Condition wt + / - 10 mM 3AT; 8h

438_2005_1139_ESM_supp_t2.xls (664 kb)
(Excel 665 KB)

Supplementary Table 3 Condition gcn4 + / - 10 mM 3AT; 8h

438_2005_1139_ESM_supp_t3.xls (736 kb)
(Excel 736 KB)

Supplementary Table 4 Condition GCN4 + 10 mM 3AT / gcn4 + 10 mM 3AT; 8h

438_2005_1139_ESM_supp_t4.xls (730 kb)
(Excel 731 KB)

References

  1. Abeijon C, Hirschberg CB (1992) Topography of glycosylation reactions in the endoplasmic reticulum. Trends Biochem Sci 17:32–36Google Scholar
  2. Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K (1993) Current protocols in molecular biology. Greene Publishing Associates-Wiley Interscience, New YorkGoogle Scholar
  3. Baillie GS, Douglas LJ (2000) Matrix polymers of Candida biofilms and their possible role in biofilm resistance to antifungal agents. J Antimicrob Chemother 46:397–403Google Scholar
  4. Brachmann CB, Davies A, Cost GJ, Caputon 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 14:115–132Google Scholar
  5. Braus GH, Grundmann O, Brückner S, Mösch HU (2003) Amino acid starvation and Gcn4p regulate adhesive growth and FLO11 gene expression in Saccharomyces cerevisiae. Mol Biol Cell 14:4272–4284Google Scholar
  6. Breitkreutz A, Boucher L, Breitkreutz BJ, Sultan M, Jurisica I, Tyers M (2003) Phenotypic and transcriptional plasticity directed by a yeast mitogen-activated protein kinase network. Genetics 165:997–1015Google Scholar
  7. Bürglin TR (1991) The TEA domain: a novel, highly conserved DNA-binding motif. Cell 66:11–12Google Scholar
  8. Chandra J, Kuhn DM, Mukherjee PK, Hoyer LL, McCormick T, Ghannoum MA (2001) Biofilm formation by the fungal pathogen Candida albicans: development, architecture, and drug resistance. J Bacteriol 183:5385–5394Google Scholar
  9. Cormack BP, Ghori N, Falkow S (1999) An adhesin of the yeast pathogen Candida glabrata mediating adherence to human epithelial cells. Science 285:578–582Google Scholar
  10. Cullen PJ, Sprague GF Jr (2000) Glucose depletion causes haploid invasive growth in yeast. Proc Natl Acad Sci USA 97:13619–13624Google Scholar
  11. Cross FR, Tinkelenberg AH (1991) A potential positive feedback loop controlling CLN1 and CLN2 gene expression at the start of the yeast cell cycle. Cell 65:875–883Google Scholar
  12. Dever TE, Feng L, Wek RC, Cigan AM, Donahue TF, Hinnebusch AG (1992) Phosphorylation of initiation factor 2 alpha by protein kinase GCN2 mediates gene-specific translational control of GCN4 in yeast. Cell 68:585–596Google Scholar
  13. Douglas LJ (2003) Candida biofilms and their role in infection. Trends Microbiol 11:30–36Google Scholar
  14. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11:124241–124257Google Scholar
  15. Garcia-Sanchez S, Aubert S, Iraqui I, Janbon G, Ghigo JM, d’Enfert C (2004) Candida albicans biofilms: a developmental state associated with specific and stable gene expression patterns. Eukaryot Cell 3:536–545Google Scholar
  16. Gavrias V, Andrianopoulos A, Gimeno CJ, Timberlake WE (1996) Saccharomyces cerevisiae TEC1 is required for pseudohyphal growth. Mol Microbiol 19:1255–1263Google Scholar
  17. Gimeno CJ, Fink GR (1994) Induction of pseudohyphal growth by overexpression of PHD1, a Saccharomyces cerevisiae gene related to transcriptional regulators of fungal development. Mol Cell Biol 14:2100–2112Google Scholar
  18. Gimeno CJ, Ljungdahl PO, Styles CA, Fink GR (1992) Unipolar cell divisions in the yeast S. cerevisiae lead to filamentous growth: regulation by starvation and RAS. Cell 68:1077–1090Google Scholar
  19. Guo B, Styles CA, Feng Q, Fink GR (2000) A Saccharomyces gene family involved in invasive growth, cell-cell adhesion, and mating. Proc Natl Acad Sci USA 97:12158–12163Google Scholar
  20. Grundmann O, Mösch HU, Braus GH (2001) Repression of GCN4 mRNA translation by nitrogen starvation in S. cerevisiae. J Biol Chem 276:25661–25671Google Scholar
  21. Halliwell B, Gutteridge JMC (1989) Free radicals in biology and medicine, 2nd edn. Clarendon Press, OxfordGoogle Scholar
  22. Harashima T, Heitman J (2002) The Galpha protein Gpa2 controls yeast differentiation by interacting with kelch repeat proteins that mimic Gbeta subunits. Mol Cell 10:163–173Google Scholar
  23. Hashimoto H, Sakakibara A, Yamasaki M, Yoda K (1997) Saccharomyces cerevisiae VIG9 encodes GDP-mannose pyrophosphorylase, which is essential for protein glycosylation. J Biol Chem 272:16308–16314Google Scholar
  24. Higgins VJ, Beckhouse AG, Oliver AD, Rogers PJ, Dawes IW (2003) Yeast genome-wide expression analysis identifies a strong ergosterol and oxidative stress response during the initial stages of an industrial lager fermentation. Appl Environ Microbiol 69:4777–4787Google Scholar
  25. Hinnebusch AG (1986) Multiple levels of gene regulation in the control of amino acid biosynthesis in Saccharomyces cerevisiae. Bioessays 5:57–62Google Scholar
  26. Hinnebusch AG (1992) General and pathway-specific regulatory mechanisms controlling the synthesis of amino acid biosynthetic enzymes in Saccharomyces cerevisiae. In: Broach JR, Jones EW, Pringle JR (eds) The Molecular and cellular biology of the yeast Saccharomyces cerevisae: gene expression. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp319–414Google Scholar
  27. Hinnebusch AG (1997) Translational regulation of yeast GCN4. A window on factors that control initiator-tRNA binding to the ribosome. J Biol Chem 272:21661–21664Google Scholar
  28. Hope IA, Struhl K (1985) GCN4 protein, synthesized in vitro, binds HIS3 regulatory sequences: implications for general control of amino acid biosynthetic genes in yeast. Cell 43:177–188Google Scholar
  29. Ito H, Fukuda Y, Murata K, Kimura A (1983) Transformation of intact yeast cells treated with alkali cations. J Bacteriol 153:163–168Google Scholar
  30. Jia MH, Larossa RA, Lee JM, Rafalski A, Derose E, Gonye G, Xue Z (2000) Global expression profiling of yeast treated with an inhibitor of amino acid biosynthesis, sulfometuron methyl. Physiol Genomics 3:83–92Google Scholar
  31. Klis FM, Mol P, Hellingwerf K, Brul S (2002) Dynamics of cell wall structure in Saccharomyces cerevisiae. FEMS Microbiol Rev 26:239–256Google Scholar
  32. Kuchin S, Vyas VK, Carlson M (2002) Snf1 protein kinase and the repressors Nrg1 and Nrg2 regulate FLO11, haploid invasive growth, and diploid pseudohyphal differentiation. Mol Cell Biol 22:3994–4000Google Scholar
  33. Kuchin S, Vyas VK, Carlson M (2003) Role of the yeast Snf1 protein kinase in invasive growth. Biochem Soc Trans 31:175–177Google Scholar
  34. Kuranda MJ, Robbins PW (1991) Chitinase is required for cell separation during growth of Saccharomyces cerevisiae. J Biol Chem 266:19758–19767Google Scholar
  35. Lamb TM, Mitchell AP (2003) The transcription factor Rim101p governs ion tolerance and cell differentiation by direct repression of the regulatory genes NRG1 and SMP1 in Saccharomyces cerevisiae. Mol Cell Biol 23:677–686Google Scholar
  36. Liu H, Styles CA, Fink GR (1993) Elements of the yeast pheromone response pathway required for filamentous growth of diploids. Science 262:1741–1744Google Scholar
  37. Liu H, Styles CA, Fink GR (1996) Saccharomyces cerevisiae S288C has a mutation in FLO8, a gene required for filamentous growth. Genetics 144:967–978Google Scholar
  38. Lo WS, Dranginis AM (1998) The cell surface flocculin Flo11 is required for pseudohyphae formation and invasion by Saccharomyces cerevisiae. Mol Biol Cell 9:161–171Google Scholar
  39. Madhani HD, Fink GR (1997) Combinatorial control required for the specificity of yeast MAPK signaling. Science 275:1314–1317Google Scholar
  40. Madhani HD, Galitski T, Lander ES, Fink GR (1999) Effectors of a developmental mitogen-activated protein kinase cascade revealed by expression signatures of signaling mutants. Proc Natl Acad Sci USA 96:12530–12535Google Scholar
  41. Marton MJ, DeRisi JL, Bennett HA, Iyer VR, Meyer MR, Roberts CJ, Stoughton R, Burchard J, Slade D, Dai H, Bassett DE Jr, Hartwell LH, Brown PO, Friend SH (1998) Drug target validation and identification of secondary drug target effects using DNA microarrays. Nat Med 4:1293–1301Google Scholar
  42. Meussdoerffer F, Fink GR (1983) Structure and expression of two aminoacyl-tRNA synthetase genes from Saccharomyces cerevisiae. J Biol Chem 258:6293–6299Google Scholar
  43. Mirande M, Waller JP (1988) The yeast lysyl-tRNA synthetase gene. Evidence for general amino acid control of its expression and domain structure of the encoded protein. J Biol Chem 263:18443–18451Google Scholar
  44. Mösch HU, Fink GR (1997) Dissection of filamentous growth by transposon mutagenesis in Saccharomyces cerevisiae. Genetics 145:671–684Google Scholar
  45. Mösch HU, Scheier B, Lahti R, Mantsala P, Braus GH (1991) Transcriptional activation of yeast nucleotide biosynthetic gene ADE4 by GCN4. J Biol Chem 266:20453–20460Google Scholar
  46. Mösch HU, Kübler E, Krappmann S, Fink GR, Braus GH (1999) Crosstalk between the Ras2p-controlled mitogen-activated protein kinase and cAMP pathways during invasive growth of Saccharomyces cerevisiae. Mol Biol Cell 10:1325–1335Google Scholar
  47. Natarajan K, Meyer MR, Jackson BM, Slade D, Roberts C, Hinnebusch AG, Marton MJ (2001) Transcriptional profiling shows that Gcn4p is a master regulator of gene expression during amino acid starvation in yeast. Mol Cell Biol 13:4347–4368Google Scholar
  48. Oehlen LJ, Cross FR (1998) Potential regulation of Ste20 function by the Cln1-Cdc28 and Cln2-Cdc28 cyclin-dependent protein kinases. J Biol Chem 273:25089–25097Google Scholar
  49. Oliphant AR, Brandl CJ,Struhl K (1989) Defining the sequence-specificity of DNA-binding proteins by selecting binding sites from random-sequence oligonucleotides: analysis of yeast GCN4 protein. Mol Cell Biol 9:2944–2949Google Scholar
  50. O’Toole GA, Pratt LA, Watnick PI, Newman DK, Weaver VB, Kolter R (1999) Genetic approaches to study of biofilms. Methods Enzymol 310:91–109Google Scholar
  51. Palecek SP, Parikh AS, Kron SJ (2000) Genetic analysis reveals that FLO11 upregulation and cell polarization independently regulate invasive growth in Saccharomyces cerevisiae. Genetics 156:1005–1023Google Scholar
  52. Pan X, Heitman J (1999) Cyclic AMP-dependent protein kinase regulates pseudohyphal differentiation in Saccharomyces cerevisiae. Mol Cell Biol 19:4874–4887Google Scholar
  53. Pan X, Heitman J (2000) Sok2 regulates yeast pseudohyphal differentiation via a transcription factor cascade that regulates cell-cell adhesion. Mol Cell Biol 20:8364–8372Google Scholar
  54. Ram AF, Van den Ende H, Klis FM (1998) Green fluorescent protein-cell wall fusion proteins are covalently incorporated into the cell wall of Saccharomyces cerevisiae. FEMS Microbiol Lett 162:249–255Google Scholar
  55. Reynolds TB, Fink GR (2001) Bakers’ yeast, a model for fungal biofilm formation. Science 5505:878–881Google Scholar
  56. Roberts RL, Fink GR (1994) Elements of a single MAP kinase cascade in Saccharomyces cerevisiae mediate two developmental programs in the same cell type: mating and invasive growth. Genes Dev 8:2974–2985Google Scholar
  57. Roberts RL, Mösch HU, Fink GR (1997) 14-3-3 proteins are essential for RAS/MAPK cascade signaling during pseudohyphal development in S. cerevisiae. Cell 89:1055–1065Google Scholar
  58. Robertson LS, Fink GR (1998) The three yeast A kinases have specific signaling functions in pseudohyphal growth. Proc Natl Acad Sci USA 95:13783–13787Google Scholar
  59. Rupp S, Summers E, Lo HJ, Madhani H, Fink G (1999) MAP kinase and cAMP filamentation signaling pathways converge on the unusually large promoter of the yeast FLO11 gene. EMBO J 18:1257–1269Google Scholar
  60. Schuldiner O, Yanover C, Benvenisty N (1998) Computer analysis of the entire budding yeast genome for putative targets of the GCN4 transcription factor. Curr Genet 33:16–20Google Scholar
  61. Schulte F, Ciriacy M (1995) HTR1/MTH1 encodes a repressor for HXT genes. Yeast special issue 239Google Scholar
  62. Sundstrom P (2002) Adhesion in Candida spp. Cell Microbiol 4:461–469Google Scholar
  63. Suzuki C, Hori V, Kashiwagi Y (2003) Sreening and characterization of transposon-insertion mutants in a pseudohyphal strain of Saccharomyces cerevisiae. Yeast 20:407–415Google Scholar
  64. Thorpe GW, Fong CS, Alic N, Higgins VJ, Dawes IW (2004) Cells have distinct mechanisms to maintain protection against different reactive oxygen species: oxidative-stress-response genes. Proc Natl Acad Sci USA 101:6564–6569Google Scholar
  65. Tripathi G, Wiltshire C, Macaskill S, Tournu H, Budge S, Brown AJP (2002) Gcn4 co-ordinates morphogenetic and metabolic responses to amino acid starvation in Candida albicans. EMBO J 21:5448–5456Google Scholar
  66. Umebayashi K, Nakano A (2003) Ergosterol is required for targeting of tryptophan permease to the yeast plasma membrane. J Cell Biol 161:1117–1131Google Scholar
  67. Wek SA, Zhu S, Wek RC (1995) The histidyl-tRNA synthetase-related sequence in the eIF-2 alpha protein kinase GCN2 interacts with tRNA and is required for activation in response to starvation for different amino acids. Mol Cell Biol 15:4497–4506Google Scholar

Copyright information

© Springer-Verlag 2005

Authors and Affiliations

  • Malte Kleinschmidt
    • 1
  • Olav Grundmann
    • 1
    • 3
  • Nils Blüthgen
    • 2
  • Hans-Ulrich Mösch
    • 1
    • 4
  • Gerhard H. Braus
    • 1
  1. 1.Institute of Microbiology and GeneticsGeorg-August-UniversityGöttingenGermany
  2. 2.Institute for Theoretical BiologyHumboldt-UniversityBerlinGermany
  3. 3.Department of MicrobiologyMax Planck Institute BremenBremenGermany
  4. 4.Department of GeneticsPhilipps-University MarburgMarburgGermany

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