A Novel DNA Binding Motif for Yeast Zinc Cluster Proteins: the Leu3p and Pdr3p Transcriptional Activators Recognize Everted Repeats

REFERENCES

• Ausubel, F. M., R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl. 1989. Current protocols in molecular biology. Greene Publishing Associates and Wiley-Interscience, New York.
   Google Scholar
• Baleja, J. D., R. Marmorstein, S. C. Harrison, and G. Wagner. 1992. Solution structure of the DNA-binding domain of Cd2-GAL4 from S. cerevisiae. Nature (London) 356:450–453.
   PubMedGoogle Scholar
• Bram, R. J., N. F. Lue, and R. D. Kornberg. 1986. A GAL family of upstream activating sequences in yeast: roles in both induction and repression of transcription. EMBO J. 5:603–608.
   PubMedGoogle Scholar
• Brisco, P. R., and G. B. Kohlhaw. 1990. Regulation of yeast LEU2. Total deletion of regulatory gene LEU3 unmasks GCN4-dependent basal level expression of LEU2. J. Biol. Chem. 265:11667–11675.
   PubMedGoogle Scholar
• Corton, J. C., and S. A. Johnston. 1989. Altering DNA-binding specificity of GAL4 requires sequences adjacent to the zinc finger. Nature (London) 340:724–727.
   PubMedGoogle Scholar
• Creusot, F., J. Verdiere, M. Gaisne, and P. P. Slonimski. 1988. CYP1 (HAP1) regulator of oxygen-dependent gene expression in yeast. I. Overall organization of the protein sequence displays several novel structural domains. J. Mol. Biol. 204:263–276.
   PubMedGoogle Scholar
• Delahodde, A., T. Delaveau, and C. Jacq. 1995. Positive autoregulation of the yeast transcription factor Pdr3p, which is involved in control of drug resistance. Mol. Cell. Biol. 15:4043–4050.
   PubMedGoogle Scholar
• Delaveau, T., A. Delahodde, E. Carvajal, J. Subik, and C. Jacq. 1994. PDR3, a new yeast regulatory gene, is homologous to PDR1 and controls the multidrug resistance phenomenon. Mol. Gen. Genet. 244:501–511.
   PubMedGoogle Scholar
• Delaveau, T., C. Jacq, and J. Perea. 1992. Sequence of a 12.7 kb segment of yeast chromosome II identifies a PDR-like gene and several new open reading frames. Yeast 8:761–768.
   PubMedGoogle Scholar
• Forsburg, S. L., and L. Guarente. 1988. Mutational analysis of upstream activation sequence 2 of the CYC1 gene of Saccharomyces cerevisiae: a HAP2-HAP3-responsive site. Mol. Cell. Biol. 8:647–654.
   PubMedGoogle Scholar
• Friden, P., and P. Schimmel. 1987. LEU3 of Saccharomyces cerevisiae encodes a factor for control of RNA levels of a group of leucine-specific genes. Mol. Cell. Biol. 7:2708–2717.
   PubMedGoogle Scholar
• Friden, P., and P. Schimmel. 1988. LEU3 of Saccharomyces cerevisiae activates multiple genes for branched-chain amino acid biosynthesis by binding to a common decanucleotide core sequence. Mol. Cell. Biol. 8:2690–2697.
   PubMedGoogle Scholar
• Guarente, L., and T. Mason. 1983. Heme regulates transcription of the CYC1 gene of S. cerevisiae via an upstream activation site. Cell 32:1279–1286.
   PubMed Web of Science ®Google Scholar
• Ha, N., K. Hellauer, and B. Turcotte. 1996. Mutations in target DNA elements of yeast HAP1 modulate its transcriptional activity without affecting DNA binding. Nucleic Acids Res. 24:1453–1459.
   PubMedGoogle Scholar
• Hakes, D. J., and J. E. Dixon. 1992. New vectors for high level expression of recombinant proteins in bacteria. Anal. Biochem. 202:293–298.
   PubMed Web of Science ®Google Scholar
• Halvorsen, Y. C., K. Nandablan, and R. C. Dickson. 1991. Identification of base and backbone contacts used for DNA sequence recognition and high-affinity binding by LAC9, a transcription activator containing a C6 finger. Mol. Cell. Biol. 11:1777–1784.
   PubMedGoogle Scholar
• Hu, Y., T. G. Cooper, and G. B. Kohlhaw. 1995. The Saccharomyces cerevisiae LEU3 protein activates expression of GDH1, a key gene in nitrogen assimilation. Mol. Cell. Biol. 15:52–57.
   PubMedGoogle Scholar
• Kaltzmann, D. J., P. E. Burnett, J. Golin, Y. Mahe, and W. S. Moye-Rowley. 1994. Transcriptional control of the yeast PDR5 gene by the PDR3 product. Mol. Cell. Biol. 14:4653–4661.
   PubMedGoogle Scholar
• Kirkpatrick, C. R., and P. Schimmel. 1995. Detection of leucine-independent DNA site occupancy of the yeast Leu3p transcriptional activator in vivo. Mol. Cell. Biol. 15:4021–4030.
   PubMedGoogle Scholar
• Kraulis, P. J., A. R. Raine, P. L. Gadhavi, and E. D. Laue. 1992. Structure of the DNA-binding domain of zinc GAL4. Nature (London) 356:448–450.
   PubMedGoogle Scholar
• Kunkel, T. A. 1985. Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc. Natl. Acad. Sci. USA 82:488–492.
   PubMed Web of Science ®Google Scholar
• Lodi, T., and B. Guiard. 1991. Complex transcriptional regulation of the Saccharomyces cerevisiae CYB2 gene encoding cytochrome b2: CYP1 (HAP1) activator binds to the CYB2 upstream activation site UAS1-B2. Mol. Cell. Biol. 11:3762–3772.
   PubMedGoogle Scholar
• Marmorstein, R., M. Carey, M. Ptashne, and S. C. Harrison. 1992. DNA recognition by GAL4: structure of a protein-DNA complex. Nature (London) 356:408–414.
   PubMed Web of Science ®Google Scholar
• Marmorstein, R., and S. C. Harrison. 1994. Crystal structure of a PPR1-DNA complex: DNA recognition by proteins containing a Zn2Cys6 binuclear cluster. Genes Dev. 8:2504–2512.
   PubMed Web of Science ®Google Scholar
• Pfeifer, K., B. Arcangioli, and L. Guarente. 1987. Yeast HAP1 activator competes with the factor RC2 for binding to the upstream activation site UAS1 of the CYC1 gene. Cell 49:9–18.
   PubMed Web of Science ®Google Scholar
• Pfeifer, K., K. S. Kim, S. Kogan, and L. Guarente. 1989. Functional dissection and sequence of yeast HAP1 activator. Cell 56:291–301.
   PubMed Web of Science ®Google Scholar
• Pfeifer, K., T. Prezant, and L. Guarente. 1987. Yeast HAP1 activator binds to two upstream activation sites of different sequence. Cell 49:19–27.
   PubMedGoogle Scholar
• Prezant, T., K. Pfeifer, and L. Guarente. 1987. Organization of the regulatory region of the yeast CYC7 gene: multiple factors are involved in regulation. Mol. Cell. Biol. 7:3252–3259.
   PubMedGoogle Scholar
• Reece, R. J., and M. Ptashne. 1993. Determinants of binding-site specificity among yeast C6 zinc cluster proteins. Science 261:909–911.
   PubMedGoogle Scholar
• Remboutsika, E., and G. B. Kohlhaw. 1994. Molecular architecture of a Leu3p-DNA complex in solution: a biochemical approach. Mol. Cell. Biol. 14:5547–5557.
   PubMedGoogle Scholar
• Roy, A., F. Exinger, and R. Losson. 1990. cis- and trans-acting regulatory elements of the yeast URA3 promoter. Mol. Cell. Biol. 10:5257–5270.
   PubMedGoogle Scholar
• Schneider, J. C., and L. Guarente. 1991. Regulation of the yeast CYT1 gene encoding cytochrome c1 by HAP1 and HAP2/3/4. Mol. Cell. Biol. 11:4934–4942.
   PubMedGoogle Scholar
• Sherman, F., G. R. Fink, and J. B. Hicks. 1986. Methods in yeast genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
   Google Scholar
• Siddiqui, A. H., and M. C. Brandriss. 1989. The Saccharomyces cerevisiae PUT3 activator protein associates with proline-specific upstream activation sequences. Mol. Cell. Biol. 9:4706–4712.
   PubMedGoogle Scholar
• Sikorski, R. S., and P. Hieter. 1989. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122:19–27.
   PubMed Web of Science ®Google Scholar
• Strich, R., R. T. Surosky, C. Steber, E. Dubois, F. Messenguy, and R. E. Esposito. 1994. UME6 is a key regulator of nitrogen repression and meiotic development. Genes Dev. 8:796–810.
   PubMed Web of Science ®Google Scholar
• Sze, J. Y., M. Woontner, J. A. Jaehning, and G. B. Kohlhaw. 1992. In vitro transcriptional activation by a metabolic intermediate: activation by LEU3 depends on alpha-isopropylmalate. Science 258:1143–1145.
   PubMedGoogle Scholar
• Timmerman, J. E., B. Guiard, E. Shechter, M. A. Delsuc, J. Y. Lallemand, and M. Gervais. 1994. The DNA-binding domain of the yeast Saccharomyces cerevisiae CYP1(HAP1) transcription factor possesses two zinc ions which are complexed in a zinc cluster. Eur. J. Biochem. 225:593–599.
   PubMedGoogle Scholar
• Tini, M., G. Otulakowski, M. L. Breitman, L.-C. Tsui, and V. Giguère. 1993. An everted repeat mediates retinoic acid induction of the γF-crystallin gene: evidence of a direct role for retinoids in lens development. Genes Dev. 7:295–307.
   PubMed Web of Science ®Google Scholar
• Tu, H., and M. J. Casadaban. 1990. The upstream activating sequence for L-leucine gene regulation in Saccharomyces cerevisiae. Nucleic Acids Res. 18:3923–3931.
   PubMedGoogle Scholar
• Vallee, B. L., J. E. Coleman, and D. S. Auld. 1991. Zinc fingers, zinc clusters, and zinc twists in DNA-binding protein domains. Proc. Natl. Acad. Sci. USA 88:999–1003.
   PubMed Web of Science ®Google Scholar
• Vashee, S., H. Xu, S. A. Johnston, and T. Kodadek. 1993. How do “Zn2 cys6” proteins distinguish between similar upstream activation sites? Comparison of the DNA-binding specificity of the GAL4 protein in vitro and in vivo. J. Biol. Chem. 268:24699–24706.
   PubMedGoogle Scholar
• Winkler, H., G. Adam, E. Mattes, M. Schanz, A. Hartig, and H. Ruis. 1988. Co-ordinate control of synthesis of mitochondrial and nonmitochondrial hemoproteins: a binding site for the HAP1 (CYP1) protein in the UAS region of the yeast catalase T gene (CTT1). EMBO J. 7:1799–1804.
   PubMed Web of Science ®Google Scholar
• Witte, M. M., and R. C. Dickson. 1990. The C6 zinc finger and adjacent amino acids determine DNA-binding specificity and affinity in the yeast activator proteins LAC9 and PPR1. Mol. Cell. Biol. 10:5128–5137.
   PubMedGoogle Scholar
• Zhang, L., O. Bermingham-McDonogh, B. Turcotte, and L. Guarente. 1993. Antibody-promoted dimerization bypasses the regulation of DNA binding by the heme domain of the yeast transcriptional activator HAP1. Proc. Natl. Acad. Sci. USA 90:2851–2855.
   PubMedGoogle Scholar
• Zhang, L., and L. Guarente. 1994. The yeast activator HAP1—a GAL4 family member—binds DNA in a directly repeated orientation. Genes Dev. 8:2110–2119.
   PubMedGoogle Scholar
• Zhou, K., P. R. Brisco, A. E. Hinkkanen, and G. B. Kohlhaw. 1987. Structure of yeast regulatory gene LEU3 and evidence that LEU3 itself is under general amino acid control. Nucleic Acids Res. 15:5261–5273.
   PubMedGoogle Scholar
• Zhou, K. M., Y. L. Bai, and G. B. Kohlhaw. 1990. Yeast regulatory protein LEU3: a structure-function analysis. Nucleic Acids Res. 18:291–298.
   PubMed Web of Science ®Google Scholar
• Zhou, K. M., and G. B. Kohlhaw. 1990. Transcriptional activator LEU3 of yeast. Mapping of the transcriptional activation function and significance of activation domain tryptophans. J. Biol. Chem. 265:17409–17412.
   PubMedGoogle Scholar
• Zitomer, R. S., J. W. Sellers, D. W. McCarter, G. A. Hastings, P. Wick, and C. V. Lowry. 1987. Elements involved in oxygen regulation of the Saccharomyces cerevisiae CYC7 gene. Mol. Cell. Biol. 7:2212–2220.
   PubMedGoogle Scholar