Abstract
Yeast cells respond to the presence of amino acids in their environment by inducing transcription of several amino acid permease genes including AGP1, BAP2, and BAP3. The signaling pathway responsible for this induction involves Ssy1, a permease-like sensor of external amino acids, and culminates with proteolytic cleavage and translocation to the nucleus of the zinc-finger proteins Stp1 and Stp2, the lack of which abolishes induction of BAP2 and BAP3. Here we show that Stp1-but not Stp2-plays an important role in AGP1 induction, although significant induction of AGP1 by amino acids persists in stp1 and stp1 stp2 mutants. This residual induction depends on the Uga35/Dal81 transcription factor, indicating that the external amino acid signaling pathway activates not only Stp1 and Stp2, but also another Uga35/Dal81-dependent transcriptional circuit. Analysis of the AGP1 gene's upstream region revealed that Stp1 and Uga35/Dal81 act synergistically through a 21-bp cis-acting sequence similar to the UAS(AA) element previously found in the BAP2 and BAP3 upstream regions. Although cells growing under poor nitrogen-supply conditions display much higher induction of AGP1 expression than cells growing under good nitrogen-supply conditions, the UAS(AA) itself is totally insensitive to nitrogen availability. Nitrogen-source control of AGP1 induction is mediated by the GATA factor Gln3, likely acting through adjacent 5'-GATA-3' sequences, to amplify the positive effect of UAS(AA). Our data indicate that Stp1 may act in combination with distinct sets of transcription factors, according to the gene context, to promote induction of transcription in response to external amino acids. The data also suggest that Uga35/Dal81 is yet another transcription factor under the control of the external amino acid sensing pathway. Finally, the data show that the TOR pathway mediating global nitrogen control of transcription does not interfere with the external amino acid signaling pathway.
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- André B., Hein C., Grenson M., Jauniaux J. C. Cloning and expression of the UGA4 gene coding for the inducible GABA-specific transport protein of Saccharomyces cerevisiae. Mol Gen Genet. 1993 Feb;237(1-2):17–25. doi: 10.1007/BF00282779. [DOI] [PubMed] [Google Scholar]
- André B., Jauniaux J. C. Nucleotide sequence of the DURM gene coding for a positive regulator of allophanate-inducible genes in Saccharomyces cerevisiae. Nucleic Acids Res. 1990 Dec 11;18(23):7136–7136. doi: 10.1093/nar/18.23.7136. [DOI] [PMC free article] [PubMed] [Google Scholar]
- André B., Talibi D., Soussi Boudekou S., Hein C., Vissers S., Coornaert D. 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 Feb 25;23(4):558–564. doi: 10.1093/nar/23.4.558. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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 Jan;220(2):269–276. doi: 10.1007/BF00260493. [DOI] [PubMed] [Google Scholar]
- Andréasson Claes, Ljungdahl Per O. Receptor-mediated endoproteolytic activation of two transcription factors in yeast. Genes Dev. 2002 Dec 15;16(24):3158–3172. doi: 10.1101/gad.239202. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Barnes D., Lai W., Breslav M., Naider F., Becker J. M. PTR3, a novel gene mediating amino acid-inducible regulation of peptide transport in Saccharomyces cerevisiae. Mol Microbiol. 1998 Jul;29(1):297–310. doi: 10.1046/j.1365-2958.1998.00931.x. [DOI] [PubMed] [Google Scholar]
- Bechet J., Greenson M., Wiame J. M. Mutations affecting the repressibility of arginine biosynthetic enzymes in Saccharomyces cerevisiae. Eur J Biochem. 1970 Jan;12(1):31–39. doi: 10.1111/j.1432-1033.1970.tb00817.x. [DOI] [PubMed] [Google Scholar]
- Beck T., Hall M. N. The TOR signalling pathway controls nuclear localization of nutrient-regulated transcription factors. Nature. 1999 Dec 9;402(6762):689–692. doi: 10.1038/45287. [DOI] [PubMed] [Google Scholar]
- Bernard F., André B. Genetic analysis of the signalling pathway activated by external amino acids in Saccharomyces cerevisiae. Mol Microbiol. 2001 Jul;41(2):489–502. doi: 10.1046/j.1365-2958.2001.02538.x. [DOI] [PubMed] [Google Scholar]
- Bernard F., André B. Ubiquitin and the SCF(Grr1) ubiquitin ligase complex are involved in the signalling pathway activated by external amino acids in Saccharomyces cerevisiae. FEBS Lett. 2001 May 11;496(2-3):81–85. doi: 10.1016/s0014-5793(01)02412-7. [DOI] [PubMed] [Google Scholar]
- Bricmont P. A., Daugherty J. R., Cooper T. G. The DAL81 gene product is required for induced expression of two differently regulated nitrogen catabolic genes in Saccharomyces cerevisiae. Mol Cell Biol. 1991 Feb;11(2):1161–1166. doi: 10.1128/mcb.11.2.1161. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Cliften Paul, Sudarsanam Priya, Desikan Ashwin, Fulton Lucinda, Fulton Bob, Majors John, Waterston Robert, Cohen Barak A., Johnston Mark. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science. 2003 May 29;301(5629):71–76. doi: 10.1126/science.1084337. [DOI] [PubMed] [Google Scholar]
- Coffman J. A., Rai R., Loprete D. M., Cunningham T., Svetlov V., Cooper T. G. Cross regulation of four GATA factors that control nitrogen catabolic gene expression in Saccharomyces cerevisiae. J Bacteriol. 1997 Jun;179(11):3416–3429. doi: 10.1128/jb.179.11.3416-3429.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Cooper Terrance G. Transmitting the signal of excess nitrogen in Saccharomyces cerevisiae from the Tor proteins to the GATA factors: connecting the dots. FEMS Microbiol Rev. 2002 Aug;26(3):223–238. doi: 10.1111/j.1574-6976.2002.tb00612.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Coornaert D., Vissers S., André B. The pleiotropic UGA35(DURL) regulatory gene of Saccharomyces cerevisiae: cloning, sequence and identity with the DAL81 gene. Gene. 1991 Jan 15;97(2):163–171. doi: 10.1016/0378-1119(91)90048-g. [DOI] [PubMed] [Google Scholar]
- Crespo José L., Hall Michael N. Elucidating TOR signaling and rapamycin action: lessons from Saccharomyces cerevisiae. Microbiol Mol Biol Rev. 2002 Dec;66(4):579-91, table of contents. doi: 10.1128/MMBR.66.4.579-591.2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Davis M. A., Small A. J., Kourambas S., Hynes M. J. The tamA gene of Aspergillus nidulans contains a putative zinc cluster motif which is not required for gene function. J Bacteriol. 1996 Jun;178(11):3406–3409. doi: 10.1128/jb.178.11.3406-3409.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Didion T., Regenberg B., Jørgensen M. U., Kielland-Brandt M. C., Andersen H. A. The permease homologue Ssy1p controls the expression of amino acid and peptide transporter genes in Saccharomyces cerevisiae. Mol Microbiol. 1998 Feb;27(3):643–650. doi: 10.1046/j.1365-2958.1998.00714.x. [DOI] [PubMed] [Google Scholar]
- Dorrington R. A., Cooper T. G. The DAL82 protein of Saccharomyces cerevisiae binds to the DAL upstream induction sequence (UIS). Nucleic Acids Res. 1993 Aug 11;21(16):3777–3784. doi: 10.1093/nar/21.16.3777. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Forsberg H., Gilstring C. F., Zargari A., Martínez P., Ljungdahl P. O. The role of the yeast plasma membrane SPS nutrient sensor in the metabolic response to extracellular amino acids. Mol Microbiol. 2001 Oct;42(1):215–228. doi: 10.1046/j.1365-2958.2001.02627.x. [DOI] [PubMed] [Google Scholar]
- Forsberg H., Ljungdahl P. O. Genetic and biochemical analysis of the yeast plasma membrane Ssy1p-Ptr3p-Ssy5p sensor of extracellular amino acids. Mol Cell Biol. 2001 Feb;21(3):814–826. doi: 10.1128/MCB.21.3.814-826.2001. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Forsberg H., Ljungdahl P. O. Sensors of extracellular nutrients in Saccharomyces cerevisiae. Curr Genet. 2001 Sep;40(2):91–109. doi: 10.1007/s002940100244. [DOI] [PubMed] [Google Scholar]
- Gaber Richard F., Ottow Kim, Andersen Helge A., Kielland-Brandt Morten C. Constitutive and hyperresponsive signaling by mutant forms of Saccharomyces cerevisiae amino acid sensor Ssy1. Eukaryot Cell. 2003 Oct;2(5):922–929. doi: 10.1128/EC.2.5.922-929.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gietz D., St Jean A., Woods R. A., Schiestl R. H. Improved method for high efficiency transformation of intact yeast cells. Nucleic Acids Res. 1992 Mar 25;20(6):1425–1425. doi: 10.1093/nar/20.6.1425. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Guarente L. Yeast promoters and lacZ fusions designed to study expression of cloned genes in yeast. Methods Enzymol. 1983;101:181–191. doi: 10.1016/0076-6879(83)01013-7. [DOI] [PubMed] [Google Scholar]
- Hein C., Springael J. Y., Volland C., Haguenauer-Tsapis R., André B. NPl1, an essential yeast gene involved in induced degradation of Gap1 and Fur4 permeases, encodes the Rsp5 ubiquitin-protein ligase. Mol Microbiol. 1995 Oct;18(1):77–87. doi: 10.1111/j.1365-2958.1995.mmi_18010077.x. [DOI] [PubMed] [Google Scholar]
- Iraqui I., Vissers S., Bernard F., de Craene J. O., Boles E., Urrestarazu A., André B. Amino acid signaling in Saccharomyces cerevisiae: a permease-like sensor of external amino acids and F-Box protein Grr1p are required for transcriptional induction of the AGP1 gene, which encodes a broad-specificity amino acid permease. Mol Cell Biol. 1999 Feb;19(2):989–1001. doi: 10.1128/mcb.19.2.989. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ito H., Fukuda Y., Murata K., Kimura A. Transformation of intact yeast cells treated with alkali cations. J Bacteriol. 1983 Jan;153(1):163–168. doi: 10.1128/jb.153.1.163-168.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Jacobs E., Dubois E., Wiame J. M. Regulation of ureaamidolyase synthesis in Saccharomyces cerevisiae, RNA analysis, and cloning of the positive regulatory gene DURM. Curr Genet. 1985;9(5):333–339. doi: 10.1007/BF00421602. [DOI] [PubMed] [Google Scholar]
- Jacobs P., Jauniaux J. C., Grenson M. A cis-dominant regulatory mutation linked to the argB-argC gene cluster in Saccharomyces cerevisiae. J Mol Biol. 1980 Jun 5;139(4):691–704. doi: 10.1016/0022-2836(80)90055-8. [DOI] [PubMed] [Google Scholar]
- Jorgensen M. U., Gjermansen C., Andersen H. A., Kielland-Brandt M. C. STP1, a gene involved in pre-tRNA processing in yeast, is important for amino-acid uptake and transcription of the permease gene BAP2. Curr Genet. 1997 Mar;31(3):241–247. doi: 10.1007/s002940050201. [DOI] [PubMed] [Google Scholar]
- Jørgensen M. U., Bruun M. B., Didion T., Kielland-Brandt M. C. Mutations in five loci affecting GAP1-independent uptake of neutral amino acids in yeast. Yeast. 1998 Jan 30;14(2):103–114. doi: 10.1002/(SICI)1097-0061(19980130)14:2<103::AID-YEA203>3.0.CO;2-C. [DOI] [PubMed] [Google Scholar]
- Kellis Manolis, Patterson Nick, Endrizzi Matthew, Birren Bruce, Lander Eric S. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature. 2003 May 15;423(6937):241–254. doi: 10.1038/nature01644. [DOI] [PubMed] [Google Scholar]
- Kodama Yukiko, Omura Fumihiko, Takahashi Keiko, Shirahige Katsuhiko, Ashikari Toshihiko. Genome-wide expression analysis of genes affected by amino acid sensor Ssy1p in Saccharomyces cerevisiae. Curr Genet. 2002 May 7;41(2):63–72. doi: 10.1007/s00294-002-0291-1. [DOI] [PubMed] [Google Scholar]
- Longtine M. S., McKenzie A., 3rd, Demarini D. J., Shah N. G., Wach A., Brachat A., Philippsen P., Pringle J. R. Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast. 1998 Jul;14(10):953–961. doi: 10.1002/(SICI)1097-0061(199807)14:10<953::AID-YEA293>3.0.CO;2-U. [DOI] [PubMed] [Google Scholar]
- Magasanik Boris, Kaiser Chris A. Nitrogen regulation in Saccharomyces cerevisiae. Gene. 2002 May 15;290(1-2):1–18. doi: 10.1016/s0378-1119(02)00558-9. [DOI] [PubMed] [Google Scholar]
- Nielsen P. S., van den Hazel B., Didion T., de Boer M., Jørgensen M., Planta R. J., Kielland-Brandt M. C., Andersen H. A. Transcriptional regulation of the Saccharomyces cerevisiae amino acid permease gene BAP2. Mol Gen Genet. 2001 Jan;264(5):613–622. doi: 10.1007/s004380000347. [DOI] [PubMed] [Google Scholar]
- Olive M. G., Daugherty J. R., Cooper T. G. DAL82, a second gene required for induction of allantoin system gene transcription in Saccharomyces cerevisiae. J Bacteriol. 1991 Jan;173(1):255–261. doi: 10.1128/jb.173.1.255-261.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Regenberg B., Düring-Olsen L., Kielland-Brandt M. C., Holmberg S. Substrate specificity and gene expression of the amino-acid permeases in Saccharomyces cerevisiae. Curr Genet. 1999 Dec;36(6):317–328. doi: 10.1007/s002940050506. [DOI] [PubMed] [Google Scholar]
- Rowen D. W., Esiobu N., Magasanik B. Role of GATA factor Nil2p in nitrogen regulation of gene expression in Saccharomyces cerevisiae. J Bacteriol. 1997 Jun;179(11):3761–3766. doi: 10.1128/jb.179.11.3761-3766.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Small A. J., Hynes M. J., Davis M. A. The TamA protein fused to a DNA-binding domain can recruit AreA, the major nitrogen regulatory protein, to activate gene expression in Aspergillus nidulans. Genetics. 1999 Sep;153(1):95–105. doi: 10.1093/genetics/153.1.95. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Soussi-Boudekou S., Vissers S., Urrestarazu A., Jauniaux J. C., André B. Gzf3p, a fourth GATA factor involved in nitrogen-regulated transcription in Saccharomyces cerevisiae. Mol Microbiol. 1997 Mar;23(6):1157–1168. doi: 10.1046/j.1365-2958.1997.3021665.x. [DOI] [PubMed] [Google Scholar]
- Stanbrough M., Rowen D. W., Magasanik B. Role of the GATA factors Gln3p and Nil1p of Saccharomyces cerevisiae in the expression of nitrogen-regulated genes. Proc Natl Acad Sci U S A. 1995 Oct 10;92(21):9450–9454. doi: 10.1073/pnas.92.21.9450. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Susan-Resiga Delia, Nowak Thomas. The proton transfer step catalyzed by yeast pyruvate kinase. J Biol Chem. 2003 Jan 31;278(15):12660–12671. doi: 10.1074/jbc.M300257200. [DOI] [PubMed] [Google Scholar]
- 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 Feb 25;23(4):550–557. doi: 10.1093/nar/23.4.550. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Turoscy V., Cooper T. G. Pleiotropic control of five eucaryotic genes by multiple regulatory elements. J Bacteriol. 1982 Sep;151(3):1237–1246. doi: 10.1128/jb.151.3.1237-1246.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Vissers S., Andre B., Muyldermans F., Grenson M. Induction of the 4-aminobutyrate and urea-catabolic pathways in Saccharomyces cerevisiae. Specific and common transcriptional regulators. Eur J Biochem. 1990 Feb 14;187(3):611–616. doi: 10.1111/j.1432-1033.1990.tb15344.x. [DOI] [PubMed] [Google Scholar]
- Wach A. PCR-synthesis of marker cassettes with long flanking homology regions for gene disruptions in S. cerevisiae. Yeast. 1996 Mar 15;12(3):259–265. doi: 10.1002/(SICI)1097-0061(19960315)12:3%3C259::AID-YEA901%3E3.0.CO;2-C. [DOI] [PubMed] [Google Scholar]
- de Boer M., Nielsen P. S., Bebelman J. P., Heerikhuizen H., Andersen H. A., Planta R. J. Stp1p, Stp2p and Abf1p are involved in regulation of expression of the amino acid transporter gene BAP3 of Saccharomyces cerevisiae. Nucleic Acids Res. 2000 Feb 15;28(4):974–981. doi: 10.1093/nar/28.4.974. [DOI] [PMC free article] [PubMed] [Google Scholar]
- van Helden J., André B., Collado-Vides J. Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J Mol Biol. 1998 Sep 4;281(5):827–842. doi: 10.1006/jmbi.1998.1947. [DOI] [PubMed] [Google Scholar]