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. 1996 Jun 15;24(12):2395–2403. doi: 10.1093/nar/24.12.2395

Interactions of the yeast centromere and promoter factor, Cpf1p, with the cytochrome c1 upstream region and functional implications on regulated gene expression.

U Oechsner 1, W Bandlow 1
PMCID: PMC145936  PMID: 8710512

Abstract

The upstream activation site (UAS) of the cytochrome c1 gene, CYT1, contains sequences for DNA-binding of several transcription factors. Among them are the heme-dependent protein, Hap1p, and the multiprotein complex, Hap2/3/4/5, which mediate transcriptional induction under aerobic conditions and after exhaustion of glucose, respectively. The multiple interactions of nuclear proteins with the UAS region of CYT1 observed in electrophoretic mobility shift experiments are influenced by carbon source and oxygen tension, but are independent of both regulators, Hap1p and Hap2/3/4/5. All protein-DNA complexes obtained are solely due to the association of the centromere and promoter factor 1 (Cpf1p) with the centromere determining element (CDE I)-like motif at the 5' boundary of the UAS(CYT1). This motif overlaps with a consensus sequence for the binding of the general factor Abf1p. Functional analyses after the separate introduction of point mutations into both elements reveal no role for the latter protein and only a minor role for Cpf1p in the regulated expression of CYT1/lacZ chimaeric proteins. However, in cpf1-mutants, induction of CYT1 reaches higher steady state levels and adaptation to aerobic conditions occurs faster than in wild-type. Thus, Cpf1p seems to reduce CYT1 promoter activity under partly inducing conditions, e.g. when only one of the activators, Hap1p or the Hap2 complex, exerts its function.

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Selected References

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  1. Arcangioli B., Lescure B. Identification of proteins involved in the regulation of yeast iso- 1-cytochrome C expression by oxygen. EMBO J. 1985 Oct;4(10):2627–2633. doi: 10.1002/j.1460-2075.1985.tb03980.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Baker R. E., Fitzgerald-Hayes M., O'Brien T. C. Purification of the yeast centromere binding protein CP1 and a mutational analysis of its binding site. J Biol Chem. 1989 Jun 25;264(18):10843–10850. [PubMed] [Google Scholar]
  3. Beckmann H., Kadesch T. Identification of a yeast protein with properties similar to those of the immunoglobulin heavy-chain enhancer-binding protein NF-muE3. Mol Cell Biol. 1989 Oct;9(10):4535–4540. doi: 10.1128/mcb.9.10.4535. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bradford M. M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem. 1976 May 7;72:248–254. doi: 10.1006/abio.1976.9999. [DOI] [PubMed] [Google Scholar]
  5. Bram R. J., Kornberg R. D. Isolation of a Saccharomyces cerevisiae centromere DNA-binding protein, its human homolog, and its possible role as a transcription factor. Mol Cell Biol. 1987 Jan;7(1):403–409. doi: 10.1128/mcb.7.1.403. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Cai M. J., Davis R. W. Purification of a yeast centromere-binding protein that is able to distinguish single base-pair mutations in its recognition site. Mol Cell Biol. 1989 Jun;9(6):2544–2550. doi: 10.1128/mcb.9.6.2544. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Chambers A., Stanway C., Tsang J. S., Henry Y., Kingsman A. J., Kingsman S. M. ARS binding factor 1 binds adjacent to RAP1 at the UASs of the yeast glycolytic genes PGK and PYK1. Nucleic Acids Res. 1990 Sep 25;18(18):5393–5399. doi: 10.1093/nar/18.18.5393. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Chasman D. I., Lue N. F., Buchman A. R., LaPointe J. W., Lorch Y., Kornberg R. D. A yeast protein that influences the chromatin structure of UASG and functions as a powerful auxiliary gene activator. Genes Dev. 1990 Apr;4(4):503–514. doi: 10.1101/gad.4.4.503. [DOI] [PubMed] [Google Scholar]
  9. Chen E. Y., Seeburg P. H. Supercoil sequencing: a fast and simple method for sequencing plasmid DNA. DNA. 1985 Apr;4(2):165–170. doi: 10.1089/dna.1985.4.165. [DOI] [PubMed] [Google Scholar]
  10. De Winde J. H., Van Leeuwen H. C., Grivell L. A. The multifunctional regulatory proteins ABF1 and CPF1 are involved in the formation of a nuclease-hypersensitive region in the promoter of the QCR8 gene. Yeast. 1993 Aug;9(8):847–857. doi: 10.1002/yea.320090805. [DOI] [PubMed] [Google Scholar]
  11. Diffley J. F., Cocker J. H. Protein-DNA interactions at a yeast replication origin. Nature. 1992 May 14;357(6374):169–172. doi: 10.1038/357169a0. [DOI] [PubMed] [Google Scholar]
  12. Dorsman J. C., van Heeswijk W. C., Grivell L. A. Identification of two factors which bind to the upstream sequences of a number of nuclear genes coding for mitochondrial proteins and to genetic elements important for cell division in yeast. Nucleic Acids Res. 1988 Aug 11;16(15):7287–7301. doi: 10.1093/nar/16.15.7287. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Forsburg S. L., Guarente L. Communication between mitochondria and the nucleus in regulation of cytochrome genes in the yeast Saccharomyces cerevisiae. Annu Rev Cell Biol. 1989;5:153–180. doi: 10.1146/annurev.cb.05.110189.001101. [DOI] [PubMed] [Google Scholar]
  14. Gonçalves P. M., Griffioen G., Minnee R., Bosma M., Kraakman L. S., Mager W. H., Planta R. J. Transcription activation of yeast ribosomal protein genes requires additional elements apart from binding sites for Abf1p or Rap1p. Nucleic Acids Res. 1995 May 11;23(9):1475–1480. doi: 10.1093/nar/23.9.1475. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Guarente L., Lalonde B., Gifford P., Alani E. Distinctly regulated tandem upstream activation sites mediate catabolite repression of the CYC1 gene of S. cerevisiae. Cell. 1984 Feb;36(2):503–511. doi: 10.1016/0092-8674(84)90243-5. [DOI] [PubMed] [Google Scholar]
  16. 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]
  17. Iyer V., Struhl K. Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure. EMBO J. 1995 Jun 1;14(11):2570–2579. doi: 10.1002/j.1460-2075.1995.tb07255.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Jung S. Y., Yoo H. Y., Kim Y. H., Kim J., Rho H. M. The glucose-dependent transactivation activity of ABF1 on the expression of the TDH3 gene in yeast. Curr Genet. 1995 Mar;27(4):312–317. doi: 10.1007/BF00352099. [DOI] [PubMed] [Google Scholar]
  19. Lorch Y., Lue N. F., Kornberg R. D. Interchangeable RNA polymerase I and II enhancers. Proc Natl Acad Sci U S A. 1990 Nov;87(21):8202–8206. doi: 10.1073/pnas.87.21.8202. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Lundin M., Nehlin J. O., Ronne H. Importance of a flanking AT-rich region in target site recognition by the GC box-binding zinc finger protein MIG1. Mol Cell Biol. 1994 Mar;14(3):1979–1985. doi: 10.1128/mcb.14.3.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Ma H., Kunes S., Schatz P. J., Botstein D. Plasmid construction by homologous recombination in yeast. Gene. 1987;58(2-3):201–216. doi: 10.1016/0378-1119(87)90376-3. [DOI] [PubMed] [Google Scholar]
  22. Masison D. C., Baker R. E. Meiosis in Saccharomyces cerevisiae mutants lacking the centromere-binding protein CP1. Genetics. 1992 May;131(1):43–53. doi: 10.1093/genetics/131.1.43. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. McBroom L. D., Sadowski P. D. DNA bending by Saccharomyces cerevisiae ABF1 and its proteolytic fragments. J Biol Chem. 1994 Jun 10;269(23):16461–16468. [PubMed] [Google Scholar]
  24. McNabb D. S., Xing Y., Guarente L. Cloning of yeast HAP5: a novel subunit of a heterotrimeric complex required for CCAAT binding. Genes Dev. 1995 Jan 1;9(1):47–58. doi: 10.1101/gad.9.1.47. [DOI] [PubMed] [Google Scholar]
  25. Mellor J., Jiang W., Funk M., Rathjen J., Barnes C. A., Hinz T., Hegemann J. H., Philippsen P. CPF1, a yeast protein which functions in centromeres and promoters. EMBO J. 1990 Dec;9(12):4017–4026. doi: 10.1002/j.1460-2075.1990.tb07623.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Mellor J., Rathjen J., Jiang W., Barnes C. A., Dowell S. J. DNA binding of CPF1 is required for optimal centromere function but not for maintaining methionine prototrophy in yeast. Nucleic Acids Res. 1991 Jun 11;19(11):2961–2969. doi: 10.1093/nar/19.11.2961. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Moncollin V., Stalder R., Verdier J. M., Sentenac A., Egly J. M. A yeast homolog of the human UEF stimulates transcription from the adenovirus 2 major late promoter in yeast and in mammalian cell-free systems. Nucleic Acids Res. 1990 Aug 25;18(16):4817–4823. doi: 10.1093/nar/18.16.4817. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Niedenthal R., Stoll R., Hegemann J. H. In vivo characterization of the Saccharomyces cerevisiae centromere DNA element I, a binding site for the helix-loop-helix protein CPF1. Mol Cell Biol. 1991 Jul;11(7):3545–3553. doi: 10.1128/mcb.11.7.3545. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. O'Connell K. F., Surdin-Kerjan Y., Baker R. E. Role of the Saccharomyces cerevisiae general regulatory factor CP1 in methionine biosynthetic gene transcription. Mol Cell Biol. 1995 Apr;15(4):1879–1888. doi: 10.1128/mcb.15.4.1879. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Oechsner U., Hermann H., Zollner A., Haid A., Bandlow W. Expression of yeast cytochrome c1 is controlled at the transcriptional level by glucose, oxygen and haem. Mol Gen Genet. 1992 Apr;232(3):447–459. doi: 10.1007/BF00266250. [DOI] [PubMed] [Google Scholar]
  31. Pfeifer K., Arcangioli B., Guarente L. Yeast HAP1 activator competes with the factor RC2 for binding to the upstream activation site UAS1 of the CYC1 gene. Cell. 1987 Apr 10;49(1):9–18. doi: 10.1016/0092-8674(87)90750-1. [DOI] [PubMed] [Google Scholar]
  32. Pfeifer K., Kim K. S., Kogan S., Guarente L. Functional dissection and sequence of yeast HAP1 activator. Cell. 1989 Jan 27;56(2):291–301. doi: 10.1016/0092-8674(89)90903-3. [DOI] [PubMed] [Google Scholar]
  33. Pinkham J. L., Olesen J. T., Guarente L. P. Sequence and nuclear localization of the Saccharomyces cerevisiae HAP2 protein, a transcriptional activator. Mol Cell Biol. 1987 Feb;7(2):578–585. doi: 10.1128/mcb.7.2.578. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Schmalix W., Oechsner U., Magdolen V., Bandlow W. Kinetics of the intracellular availability of heme after supplementing a heme-deficient yeast mutant with 5-aminolevulinate. Biol Chem Hoppe Seyler. 1986 May;367(5):379–385. doi: 10.1515/bchm3.1986.367.1.379. [DOI] [PubMed] [Google Scholar]
  35. Sherman F. Getting started with yeast. Methods Enzymol. 1991;194:3–21. doi: 10.1016/0076-6879(91)94004-v. [DOI] [PubMed] [Google Scholar]
  36. Sinclair D. A., Kornfeld G. D., Dawes I. W. Yeast intragenic transcriptional control: activation and repression sites within the coding region of the Saccharomyces cerevisiae LPD1 gene. Mol Cell Biol. 1994 Jan;14(1):214–225. doi: 10.1128/mcb.14.1.214. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Ushinsky S. C., Keng T. A novel allele of HAP1 causes uninducible expression of HEM13 in Saccharomyces cerevisiae. Genetics. 1994 Mar;136(3):819–831. doi: 10.1093/genetics/136.3.819. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Verdière J., Gaisne M., Labbe-Bois R. CYP1 (HAP1) is a determinant effector of alternative expression of heme-dependent transcribed genes in yeast [corrected]. Mol Gen Genet. 1991 Aug;228(1-2):300–306. doi: 10.1007/BF00282480. [DOI] [PubMed] [Google Scholar]
  39. Winter E., Varshavsky A. A DNA binding protein that recognizes oligo(dA).oligo(dT) tracts. EMBO J. 1989 Jun;8(6):1867–1877. doi: 10.1002/j.1460-2075.1989.tb03583.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Zitomer R. S., Lowry C. V. Regulation of gene expression by oxygen in Saccharomyces cerevisiae. Microbiol Rev. 1992 Mar;56(1):1–11. doi: 10.1128/mr.56.1.1-11.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. de Winde J. H., Grivell L. A. Global regulation of mitochondrial biogenesis in Saccharomyces cerevisiae: ABF1 and CPF1 play opposite roles in regulating expression of the QCR8 gene, which encodes subunit VIII of the mitochondrial ubiquinol-cytochrome c oxidoreductase. Mol Cell Biol. 1992 Jun;12(6):2872–2883. doi: 10.1128/mcb.12.6.2872. [DOI] [PMC free article] [PubMed] [Google Scholar]

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