1887

Abstract

Yeast cells can use γ-aminobutyric acid (GABA), a non-protein amino acid, as a nitrogen source that is mainly imported by the permease Uga4 and catabolized by the enzymes GABA transaminase and succinate-semialdehyde dehydrogenase, encoded by the and genes, respectively. The three genes are inducible by GABA and subject to nitrogen catabolite repression. Hence, their regulation occurs through two mechanisms, one dependent on the inducer and the other on nitrogen source quality. The aim of this work was to better understand the molecular mechanisms of transcription factors acting on different regulatory elements present in promoters, such as Uga3, Dal81, Leu3 and the GATA factors, and to establish the mechanism of the concerted action between them. We found that Gat1 plays an important role in the induction of transcription by GABA and that Gzf3 has an effect in cells grown in a poor nitrogen source such as proline and that this effect is positive on expression. We also found that Gln3 and Dal80 affect the interaction of Uga3 and Dal81 on promoters. Moreover, our results indicated that the repressing activity of Leu3 on and occurs through Dal80 since we demonstrated that Leu3 facilitates Dal80 interaction with DNA. However, when the expression of GATA factors is null or negligible, Leu3 functions as an activator.

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2017-11-01
2024-04-19
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References

  1. Ljungdahl PO, Daignan-Fornier B. Regulation of amino acid, nucleotide, and phosphate metabolism in Saccharomyces cerevisiae . Genetics 2012; 190:885–929 [View Article][PubMed]
    [Google Scholar]
  2. Cooper TG. Transmitting the signal of excess nitrogen in Saccharomyces cerevisiae from the Tor proteins to the GATA factors: connecting the dots. FEMS Microbiol Rev 2002; 26:223–238 [View Article][PubMed]
    [Google Scholar]
  3. Georis I, Feller A, Vierendeels F, Dubois E. The yeast GATA factor Gat1 occupies a central position in nitrogen catabolite repression-sensitive gene activation. Mol Cell Biol 2009; 29:3803–3815 [View Article][PubMed]
    [Google Scholar]
  4. Ramos F, El Guezzar M, Grenson M, Wiame JM. Mutations affecting the enzymes involved in the utilization of 4-aminobutyric acid as nitrogen source by the yeast Saccharomyces cerevisiae . Eur J Biochem 1985; 149:401–404 [View Article][PubMed]
    [Google Scholar]
  5. André B. The UGA3 gene regulating the GABA catabolic pathway in Saccharomyces cerevisiae codes for a putative zinc-finger protein acting on RNA amount. Mol Gen Genet 1990; 220:269–276 [View Article][PubMed]
    [Google Scholar]
  6. André B, Talibi D, Soussi Boudekou S, Hein C, Vissers S et al. Two mutually exclusive regulatory systems inhibit UASGATA, a cluster of 5'-GAT(A/T)A-3' upstream from the UGA4 gene of Saccharomyces cerevisiae . Nucleic Acids Res 1995; 23:558–564 [View Article][PubMed]
    [Google Scholar]
  7. Cunningham TS, Dorrington RA, Cooper TG. The UGA4 UASNTR site required for GLN3-dependent transcriptional activation also mediates DAL80-responsive regulation and DAL80 protein binding in Saccharomyces cerevisiae . J Bacteriol 1994; 176:4718–4725 [View Article][PubMed]
    [Google Scholar]
  8. Talibi D, Grenson M, André B. Cis- and trans-acting elements determining induction of the genes of the gamma-aminobutyrate (GABA) utilization pathway in Saccharomyces cerevisiae . Nucleic Acids Res 1995; 23:550–557 [View Article][PubMed]
    [Google Scholar]
  9. Vissers S, Andre B, Muyldermans F, Grenson M. Positive and negative regulatory elements control the expression of the UGA4 gene coding for the inducible 4-aminobutyric-acid-specific permease in Saccharomyces cerevisiae . Eur J Biochem 1989; 181:357–361 [View Article][PubMed]
    [Google Scholar]
  10. Cardillo SB, Correa García S, Bermúdez Moretti M. Common features and differences in the expression of the three genes forming the UGA regulon in Saccharomyces cerevisiae . Biochem Biophys Res Commun 2011; 410:885–889 [View Article][PubMed]
    [Google Scholar]
  11. Cardillo SB, Bermúdez Moretti M, Correa García S. Uga3 and Uga35/Dal81 transcription factors regulate UGA4 transcription in response to gamma-aminobutyric acid and leucine. Eukaryot Cell 2010; 9:1262–1271 [View Article][PubMed]
    [Google Scholar]
  12. Cardillo SB, Levi CE, Bermúdez Moretti M, Correa García S. Interplay between the transcription factors acting on the GATA- and GABA-responsive elements of Saccharomyces cerevisiae UGA promoters. Microbiology 2012; 158:925–935 [View Article][PubMed]
    [Google Scholar]
  13. Kohlhaw GB. Leucine biosynthesis in fungi: entering metabolism through the back door. Microbiol Mol Biol Rev 2003; 67:1–15 [View Article][PubMed]
    [Google Scholar]
  14. Boer VM, Daran JM, Almering MJ, de Winde JH, Pronk JT. Contribution of the Saccharomyces cerevisiae transcriptional regulator Leu3p to physiology and gene expression in nitrogen- and carbon-limited chemostat cultures. FEMS Yeast Res 2005; 5:885–897 [View Article][PubMed]
    [Google Scholar]
  15. MacPherson S, Larochelle M, Turcotte B. A fungal family of transcriptional regulators: the zinc cluster proteins. Microbiol Mol Biol Rev 2006; 70:583–604 [View Article][PubMed]
    [Google Scholar]
  16. Coffman JA, Rai R, Loprete DM, Cunningham T, Svetlov V et al. Cross regulation of four GATA factors that control nitrogen catabolic gene expression in Saccharomyces cerevisiae . J Bacteriol 1997; 179:3416–3429 [View Article][PubMed]
    [Google Scholar]
  17. Coffman JA, Rai R, Cunningham T, Svetlov V, Cooper TG. Gat1p, a GATA family protein whose production is sensitive to nitrogen catabolite repression, participates in transcriptional activation of nitrogen-catabolic genes in Saccharomyces cerevisiae . Mol Cell Biol 1996; 16:847–858 [View Article][PubMed]
    [Google Scholar]
  18. Daugherty JR, Rai R, El Berry HM, Cooper TG. Regulatory circuit for responses of nitrogen catabolic gene expression to the GLN3 and DAL80 proteins and nitrogen catabolite repression in Saccharomyces cerevisiae . J Bacteriol 1993; 175:64–73 [View Article][PubMed]
    [Google Scholar]
  19. Levi CE, Cardillo SB, Bertotti S, Ríos C, Correa García S et al. GABA induction of the Saccharomyces cerevisiae UGA4 gene depends on the quality of the carbon source: role of the key transcription factors acting in this process. Biochem Biophys Res Commun 2012; 421:572–577 [View Article][PubMed]
    [Google Scholar]
  20. Abdel-Sater F, Iraqui I, Urrestarazu A, André B. The external amino acid signaling pathway promotes activation of Stp1 and Uga35/Dal81 transcription factors for induction of the AGP1 gene in Saccharomyces cerevisiae . Genetics 2004; 166:1727–1739 [View Article][PubMed]
    [Google Scholar]
  21. Small AJ, Todd RB, Zanker MC, Delimitrou S, Hynes MJ et al. Functional analysis of TamA, a coactivator of nitrogen-regulated gene expression in Aspergillus nidulans . Mol Genet Genomics 2001; 265:636–646[PubMed] [Crossref]
    [Google Scholar]
  22. Polotnianka R, Monahan BJ, Hynes MJ, Davis MA. TamA interacts with LeuB, the homologue of Saccharomyces cerevisiae Leu3p, to regulate gdhA expression in Aspergillus nidulans . Mol Genet Genomics 2004; 272:452–459 [View Article][PubMed]
    [Google Scholar]
  23. Davis MA, Small AJ, Kourambas S, Hynes MJ. The tamA gene of Aspergillus nidulans contains a putative zinc cluster motif which is not required for gene function. J Bacteriol 1996; 178:3406–3409 [View Article][PubMed]
    [Google Scholar]
  24. Downes DJ, Davis MA, Kreutzberger SD, Taig BL, Todd RB. Regulation of the NADP-glutamate dehydrogenase gene gdhA in Aspergillus nidulans by the Zn(II)2Cys6 transcription factor LeuB. Microbiology 2013; 159:2467–2480 [View Article][PubMed]
    [Google Scholar]
  25. Wach A. PCR-synthesis of marker cassettes with long flanking homology regions for gene disruptions in S. cerevisiae . Yeast 1996; 12:259–265 [View Article][PubMed]
    [Google Scholar]
  26. Wach A, Brachat A, Pöhlmann R, Philippsen P. New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae . Yeast 1994; 10:1793–1808 [View Article][PubMed]
    [Google Scholar]
  27. Longtine MS, Mckenzie A, Demarini DJ, Shah NG, Wach A et al. Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae . Yeast 1998; 14:953–961 [View Article][PubMed]
    [Google Scholar]
  28. Goldstein AL, Mccusker JH. Three new dominant drug resistance cassettes for gene disruption in Saccharomyces cerevisiae . Yeast 1999; 15:1541–1553 [View Article][PubMed]
    [Google Scholar]
  29. Christianson TW, Sikorski RS, Dante M, Shero JH, Hieter P. Multifunctional yeast high-copy-number shuttle vectors. Gene 1992; 110:119–122 [View Article][PubMed]
    [Google Scholar]
  30. Miller JH. Experiments in Molecular Genetics Cold Spring Harbor, NY: Cold Spring Harbor Laboratory; 1972 pp. 403
    [Google Scholar]
  31. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔC T method. Methods 2001; 25:402–408 [View Article][PubMed]
    [Google Scholar]
  32. Medina-Rivera A, Defrance M, Sand O, Herrmann C, Castro-Mondragon JA et al. RSAT 2015: regulatory sequence analysis tools. Nucleic Acids Res 2015; 43:W50–W56 [View Article][PubMed]
    [Google Scholar]
  33. Teixeira MC, Monteiro PT, Guerreiro JF, Gonçalves JP, Mira NP et al. The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae . Nucleic Acids Res 2014; 42:D161–D166 [View Article][PubMed]
    [Google Scholar]
  34. Zhu J, Zhang MQ. SCPD: a promoter database of the yeast Saccharomyces cerevisiae . Bioinformatics 1999; 15:607–611 [View Article][PubMed]
    [Google Scholar]
  35. Idicula AM, Blatch GL, Cooper TG, Dorrington RA. Binding and activation by the zinc cluster transcription factors of Saccharomyces cerevisiae. Redefining the UASGABA and its interaction with Uga3p. J Biol Chem 2002; 277:45977–45983 [View Article][PubMed]
    [Google Scholar]
  36. Georis I, Feller A, Tate JJ, Cooper TG, Dubois E. Nitrogen catabolite repression-sensitive transcription as a readout of Tor pathway regulation: the genetic background, reporter gene and GATA factor assayed determine the outcomes. Genetics 2009; 181:861–874 [View Article][PubMed]
    [Google Scholar]
  37. Luzzani C, Cardillo SB, Bermúdez Moretti M, Correa García S. New insights into the regulation of the Saccharomyces cerevisiae UGA4 gene: two parallel pathways participate in carbon-regulated transcription. Microbiology 2007; 153:3677–3684 [View Article][PubMed]
    [Google Scholar]
  38. Palavecino MD, Correa-García SR, Bermúdez-Moretti M. Genes of different catabolic pathways are coordinately regulated by Dal81 in Saccharomyces cerevisiae . J Amino Acids 2015; 2015:1–8 [View Article][PubMed]
    [Google Scholar]
  39. Springael JY, Penninckx MJ. Nitrogen-source regulation of yeast gamma-glutamyl transpeptidase synthesis involves the regulatory network including the GATA zinc-finger factors Gln3, Nil1/Gat1 and Gzf3. Biochem J 2003; 371:589–595 [View Article][PubMed]
    [Google Scholar]
  40. Staschke KA, Dey S, Zaborske JM, Palam LR, McClintick JN et al. Integration of general amino acid control and target of rapamycin (TOR) regulatory pathways in nitrogen assimilation in yeast. J Biol Chem 2010; 285:16893–16911 [View Article][PubMed]
    [Google Scholar]
  41. André B, Hein C, Grenson M, Jauniaux JC. Cloning and expression of the UGA4 gene coding for the inducible GABA-specific transport protein of Saccharomyces cerevisiae . Mol Gen Genet 1993; 237:17–25 [View Article][PubMed]
    [Google Scholar]
  42. Cunningham TS, Rai R, Cooper TG. The level of DAL80 expression down-regulates GATA factor-mediated transcription in Saccharomyces cerevisiae . J Bacteriol 2000; 182:6584–6591 [View Article][PubMed]
    [Google Scholar]
  43. Soussi-Boudekou S, Vissers S, Urrestarazu A, Jauniaux JC, André B. Gzf3p, a fourth GATA factor involved in nitrogen-regulated transcription in Saccharomyces cerevisiae . Mol Microbiol 1997; 23:1157–1168 [View Article][PubMed]
    [Google Scholar]
  44. Georis I, Tate JJ, Cooper TG, Dubois E. Tor pathway control of the nitrogen-responsive DAL5 gene bifurcates at the level of Gln3 and Gat1 regulation in Saccharomyces cerevisiae . J Biol Chem 2008; 283:8919–8929 [View Article][PubMed]
    [Google Scholar]
  45. Magasanik B, Kaiser CA. Nitrogen regulation in Saccharomyces cerevisiae . Gene 2002; 290:1–18 [View Article][PubMed]
    [Google Scholar]
  46. Bechet J, Greenson M, Wiame JM. Mutations affecting the repressibility of arginine biosynthetic enzymes in Saccharomyces cerevisiae . Eur J Biochem 1970; 12:31–39 [View Article][PubMed]
    [Google Scholar]
  47. Grenson M. 4-Aminobutyric acid (GABA) uptake in Baker's yeast Saccharomyces cerevisiae is mediated by the general amino acid permease, the proline permease and a GABA specific permease integrated into the GABA-catabolic pathway. Life Sci Adv Biochem 1987; 6:35–39
    [Google Scholar]
  48. Coornaert D, Vissers S, André B, Grenson M. The UGA43 negative regulatory gene of Saccharomyces cerevisiae contains both a GATA-1 type zinc finger and a putative leucine zipper. Curr Genet 1992; 21:301–307 [View Article][PubMed]
    [Google Scholar]
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