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. 1995 Apr 25;23(8):1426–1433. doi: 10.1093/nar/23.8.1426

INO1-100: an allele of the Saccharomyces cerevisiae INO1 gene that is transcribed without the action of the positive factors encoded by the INO2, INO4, SWI1, SWI2 and SWI3 genes.

S Swift 1, P McGraw 1
PMCID: PMC306872  PMID: 7753636

Abstract

A dominant allele of the INO1 locus, INO1-100, does not require the positive regulators encoded by INO2 and INO4 for expression. Sequence analysis showed that INO1-100 had a 239 bp deletion in the INO1 promoter. INO1-100 suppressed the inositol auxotrophy of ino2, ino4, swi1, swi2 and swi3 mutants. Transcription of INO1-100 was constitutive and independent of these regulators. A 20 bp deletion from -247 to -228 caused a similar phenotype. A 38 bp deletion from -245 to -208 suppressed the inositol auxotrophy of an ino2 mutant, but not an ino4 mutant, indicating that Ino2p and Ino4p may function alone as well as in a complex. A 40 bp deletion from -287 to -248 that removed a URS1 site caused constitutive transcription that required INO2 and INO4. A deletion from -167 to -128 suppressed the inositol auxotrophy of swi, ino2 and ino4 mutants, indicating the presence of a previously unidentified URS1. Mutation of the specific negative regulator of phospholipid synthesis encoded by OPI1 suppressed the inositol auxotrophy of swi2 mutants. This study indicates that negative regulation of INO1 is chromatin mediated and provides in vivo information on the interaction of both general and specific regulatory factors that function to accomplish negative and positive regulation of the INO1 promoter in response to inositol.

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Selected References

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  1. Ambroziak J., Henry S. A. INO2 and INO4 gene products, positive regulators of phospholipid biosynthesis in Saccharomyces cerevisiae, form a complex that binds to the INO1 promoter. J Biol Chem. 1994 May 27;269(21):15344–15349. [PubMed] [Google Scholar]
  2. Ashburner B. P., Lopes J. M. Autoregulated expression of the yeast INO2 and INO4 helix-loop-helix activator genes effects cooperative regulation on their target genes. Mol Cell Biol. 1995 Mar;15(3):1709–1715. doi: 10.1128/mcb.15.3.1709. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bailis A. M., Poole M. A., Carman G. M., Henry S. A. The membrane-associated enzyme phosphatidylserine synthase is regulated at the level of mRNA abundance. Mol Cell Biol. 1987 Jan;7(1):167–176. doi: 10.1128/mcb.7.1.167. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bowdish K. S., Mitchell A. P. Bipartite structure of an early meiotic upstream activation sequence from Saccharomyces cerevisiae. Mol Cell Biol. 1993 Apr;13(4):2172–2181. doi: 10.1128/mcb.13.4.2172. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Cairns B. R., Kim Y. J., Sayre M. H., Laurent B. C., Kornberg R. D. A multisubunit complex containing the SWI1/ADR6, SWI2/SNF2, SWI3, SNF5, and SNF6 gene products isolated from yeast. Proc Natl Acad Sci U S A. 1994 Mar 1;91(5):1950–1954. doi: 10.1073/pnas.91.5.1950. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Carlson M., Laurent B. C. The SNF/SWI family of global transcriptional activators. Curr Opin Cell Biol. 1994 Jun;6(3):396–402. doi: 10.1016/0955-0674(94)90032-9. [DOI] [PubMed] [Google Scholar]
  7. Culbertson M. R., Henry S. A. Inositol-requiring mutants of Saccharomyces cerevisiae. Genetics. 1975 May;80(1):23–40. doi: 10.1093/genetics/80.1.23. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Côté J., Quinn J., Workman J. L., Peterson C. L. Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF complex. Science. 1994 Jul 1;265(5168):53–60. doi: 10.1126/science.8016655. [DOI] [PubMed] [Google Scholar]
  9. Dean-Johnson M., Henry S. A. Biosynthesis of inositol in yeast. Primary structure of myo-inositol-1-phosphate synthase (EC 5.5.1.4) and functional analysis of its structural gene, the INO1 locus. J Biol Chem. 1989 Jan 15;264(2):1274–1283. [PubMed] [Google Scholar]
  10. Donahue T. F., Henry S. A. myo-Inositol-1-phosphate synthase. Characteristics of the enzyme and identification of its structural gene in yeast. J Biol Chem. 1981 Jul 10;256(13):7077–7085. [PubMed] [Google Scholar]
  11. Elion E. A., Warner J. R. The major promoter element of rRNA transcription in yeast lies 2 kb upstream. Cell. 1984 Dec;39(3 Pt 2):663–673. doi: 10.1016/0092-8674(84)90473-2. [DOI] [PubMed] [Google Scholar]
  12. Fascher K. D., Schmitz J., Hörz W. Role of trans-activating proteins in the generation of active chromatin at the PHO5 promoter in S. cerevisiae. EMBO J. 1990 Aug;9(8):2523–2528. doi: 10.1002/j.1460-2075.1990.tb07432.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Greenberg M. L., Goldwasser P., Henry S. A. Characterization of a yeast regulatory mutant constitutive for synthesis of inositol-1-phosphate synthase. Mol Gen Genet. 1982;186(2):157–163. doi: 10.1007/BF00331845. [DOI] [PubMed] [Google Scholar]
  14. Greenberg M. L., Reiner B., Henry S. A. Regulatory mutations of inositol biosynthesis in yeast: isolation of inositol-excreting mutants. Genetics. 1982 Jan;100(1):19–33. doi: 10.1093/genetics/100.1.19. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Hill J. E., Myers A. M., Koerner T. J., Tzagoloff A. Yeast/E. coli shuttle vectors with multiple unique restriction sites. Yeast. 1986 Sep;2(3):163–167. doi: 10.1002/yea.320020304. [DOI] [PubMed] [Google Scholar]
  16. Hirsch J. P., Henry S. A. Expression of the Saccharomyces cerevisiae inositol-1-phosphate synthase (INO1) gene is regulated by factors that affect phospholipid synthesis. Mol Cell Biol. 1986 Oct;6(10):3320–3328. doi: 10.1128/mcb.6.10.3320. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Hirschhorn J. N., Brown S. A., Clark C. D., Winston F. Evidence that SNF2/SWI2 and SNF5 activate transcription in yeast by altering chromatin structure. Genes Dev. 1992 Dec;6(12A):2288–2298. doi: 10.1101/gad.6.12a.2288. [DOI] [PubMed] [Google Scholar]
  18. Hoffman C. S., Winston F. A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli. Gene. 1987;57(2-3):267–272. doi: 10.1016/0378-1119(87)90131-4. [DOI] [PubMed] [Google Scholar]
  19. Hoshizaki D. K., Hill J. E., Henry S. A. The Saccharomyces cerevisiae INO4 gene encodes a small, highly basic protein required for derepression of phospholipid biosynthetic enzymes. J Biol Chem. 1990 Mar 15;265(8):4736–4745. [PubMed] [Google Scholar]
  20. Hudak K. A., Lopes J. M., Henry S. A. A pleiotropic phospholipid biosynthetic regulatory mutation in Saccharomyces cerevisiae is allelic to sin3 (sdi1, ume4, rpd1). Genetics. 1994 Feb;136(2):475–483. doi: 10.1093/genetics/136.2.475. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. KENNEDY E. P., WEISS S. B. The function of cytidine coenzymes in the biosynthesis of phospholipides. J Biol Chem. 1956 Sep;222(1):193–214. [PubMed] [Google Scholar]
  22. Klig L. S., Homann M. J., Carman G. M., Henry S. A. Coordinate regulation of phospholipid biosynthesis in Saccharomyces cerevisiae: pleiotropically constitutive opi1 mutant. J Bacteriol. 1985 Jun;162(3):1135–1141. doi: 10.1128/jb.162.3.1135-1141.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Kruger W., Herskowitz I. A negative regulator of HO transcription, SIN1 (SPT2), is a nonspecific DNA-binding protein related to HMG1. Mol Cell Biol. 1991 Aug;11(8):4135–4146. doi: 10.1128/mcb.11.8.4135. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Lai K., McGraw P. Dual control of inositol transport in Saccharomyces cerevisiae by irreversible inactivation of permease and regulation of permease synthesis by INO2, INO4, and OPI1. J Biol Chem. 1994 Jan 21;269(3):2245–2251. [PubMed] [Google Scholar]
  25. Lamping E., Lückl J., Paltauf F., Henry S. A., Kohlwein S. D. Isolation and characterization of a mutant of Saccharomyces cerevisiae with pleiotropic deficiencies in transcriptional activation and repression. Genetics. 1994 May;137(1):55–65. doi: 10.1093/genetics/137.1.55. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Laurent B. C., Carlson M. Yeast SNF2/SWI2, SNF5, and SNF6 proteins function coordinately with the gene-specific transcriptional activators GAL4 and Bicoid. Genes Dev. 1992 Sep;6(9):1707–1715. doi: 10.1101/gad.6.9.1707. [DOI] [PubMed] [Google Scholar]
  27. Li Z., Brendel M. Co-regulation with genes of phospholipid biosynthesis of the CTR/HNM1-encoded choline/nitrogen mustard permease in Saccharomyces cerevisiae. Mol Gen Genet. 1993 Dec;241(5-6):680–684. doi: 10.1007/BF00279911. [DOI] [PubMed] [Google Scholar]
  28. Loewy B. S., Henry S. A. The INO2 and INO4 loci of Saccharomyces cerevisiae are pleiotropic regulatory genes. Mol Cell Biol. 1984 Nov;4(11):2479–2485. doi: 10.1128/mcb.4.11.2479. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Lopes J. M., Henry S. A. Interaction of trans and cis regulatory elements in the INO1 promoter of Saccharomyces cerevisiae. Nucleic Acids Res. 1991 Jul 25;19(14):3987–3994. doi: 10.1093/nar/19.14.3987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Lopes J. M., Hirsch J. P., Chorgo P. A., Schulze K. L., Henry S. A. Analysis of sequences in the INO1 promoter that are involved in its regulation by phospholipid precursors. Nucleic Acids Res. 1991 Apr 11;19(7):1687–1693. doi: 10.1093/nar/19.7.1687. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Lopes J. M., Schulze K. L., Yates J. W., Hirsch J. P., Henry S. A. The INO1 promoter of Saccharomyces cerevisiae includes an upstream repressor sequence (URS1) common to a diverse set of yeast genes. J Bacteriol. 1993 Jul;175(13):4235–4238. doi: 10.1128/jb.175.13.4235-4238.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Luche R. M., Sumrada R., Cooper T. G. A cis-acting element present in multiple genes serves as a repressor protein binding site for the yeast CAR1 gene. Mol Cell Biol. 1990 Aug;10(8):3884–3895. doi: 10.1128/mcb.10.8.3884. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. McGraw P., Henry S. A. Mutations in the Saccharomyces cerevisiae opi3 gene: effects on phospholipid methylation, growth and cross-pathway regulation of inositol synthesis. Genetics. 1989 Jun;122(2):317–330. doi: 10.1093/genetics/122.2.317. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Mitchell A. P. Control of meiotic gene expression in Saccharomyces cerevisiae. Microbiol Rev. 1994 Mar;58(1):56–70. doi: 10.1128/mr.58.1.56-70.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Nasmyth K., Stillman D., Kipling D. Both positive and negative regulators of HO transcription are required for mother-cell-specific mating-type switching in yeast. Cell. 1987 Feb 27;48(4):579–587. doi: 10.1016/0092-8674(87)90236-4. [DOI] [PubMed] [Google Scholar]
  36. Nikoloff D. M., Henry S. A. Functional characterization of the INO2 gene of Saccharomyces cerevisiae. A positive regulator of phospholipid biosynthesis. J Biol Chem. 1994 Mar 11;269(10):7402–7411. [PubMed] [Google Scholar]
  37. Nikoloff D. M., McGraw P., Henry S. A. The INO2 gene of Saccharomyces cerevisiae encodes a helix-loop-helix protein that is required for activation of phospholipid synthesis. Nucleic Acids Res. 1992 Jun 25;20(12):3253–3253. doi: 10.1093/nar/20.12.3253. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Orr-Weaver T. L., Szostak J. W., Rothstein R. J. Genetic applications of yeast transformation with linear and gapped plasmids. Methods Enzymol. 1983;101:228–245. doi: 10.1016/0076-6879(83)01017-4. [DOI] [PubMed] [Google Scholar]
  39. Park H. D., Luche R. M., Cooper T. G. The yeast UME6 gene product is required for transcriptional repression mediated by the CAR1 URS1 repressor binding site. Nucleic Acids Res. 1992 Apr 25;20(8):1909–1915. doi: 10.1093/nar/20.8.1909. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Peterson C. L., Dingwall A., Scott M. P. Five SWI/SNF gene products are components of a large multisubunit complex required for transcriptional enhancement. Proc Natl Acad Sci U S A. 1994 Apr 12;91(8):2905–2908. doi: 10.1073/pnas.91.8.2905. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Peterson C. L., Herskowitz I. Characterization of the yeast SWI1, SWI2, and SWI3 genes, which encode a global activator of transcription. Cell. 1992 Feb 7;68(3):573–583. doi: 10.1016/0092-8674(92)90192-f. [DOI] [PubMed] [Google Scholar]
  42. Peterson C. L., Kruger W., Herskowitz I. A functional interaction between the C-terminal domain of RNA polymerase II and the negative regulator SIN1. Cell. 1991 Mar 22;64(6):1135–1143. doi: 10.1016/0092-8674(91)90268-4. [DOI] [PubMed] [Google Scholar]
  43. Rothstein R. J. One-step gene disruption in yeast. Methods Enzymol. 1983;101:202–211. doi: 10.1016/0076-6879(83)01015-0. [DOI] [PubMed] [Google Scholar]
  44. Schüller H. J., Schorr R., Hoffmann B., Schweizer E. Regulatory gene INO4 of yeast phospholipid biosynthesis is positively autoregulated and functions as a transactivator of fatty acid synthase genes FAS1 and FAS2 from Saccharomyces cerevisiae. Nucleic Acids Res. 1992 Nov 25;20(22):5955–5961. doi: 10.1093/nar/20.22.5955. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Vidal M., Strich R., Esposito R. E., Gaber R. F. RPD1 (SIN3/UME4) is required for maximal activation and repression of diverse yeast genes. Mol Cell Biol. 1991 Dec;11(12):6306–6316. doi: 10.1128/mcb.11.12.6306. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Vogel K., Hörz W., Hinnen A. The two positively acting regulatory proteins PHO2 and PHO4 physically interact with PHO5 upstream activation regions. Mol Cell Biol. 1989 May;9(5):2050–2057. doi: 10.1128/mcb.9.5.2050. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Wang H., Nicholson P. R., Stillman D. J. Identification of a Saccharomyces cerevisiae DNA-binding protein involved in transcriptional regulation. Mol Cell Biol. 1990 Apr;10(4):1743–1753. doi: 10.1128/mcb.10.4.1743. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Wang H., Reynolds-Hager L., Stillman D. J. Genetic interactions between SIN3 mutations and the Saccharomyces cerevisiae transcriptional activators encoded by MCM1, STE12, and SWI1. Mol Gen Genet. 1994 Dec 15;245(6):675–685. doi: 10.1007/BF00297274. [DOI] [PubMed] [Google Scholar]
  49. Wang H., Stillman D. J. In vitro regulation of a SIN3-dependent DNA-binding activity by stimulatory and inhibitory factors. Proc Natl Acad Sci U S A. 1990 Dec;87(24):9761–9765. doi: 10.1073/pnas.87.24.9761. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. White M. J., Hirsch J. P., Henry S. A. The OPI1 gene of Saccharomyces cerevisiae, a negative regulator of phospholipid biosynthesis, encodes a protein containing polyglutamine tracts and a leucine zipper. J Biol Chem. 1991 Jan 15;266(2):863–872. [PubMed] [Google Scholar]
  51. Winston F., Carlson M. Yeast SNF/SWI transcriptional activators and the SPT/SIN chromatin connection. Trends Genet. 1992 Nov;8(11):387–391. doi: 10.1016/0168-9525(92)90300-s. [DOI] [PubMed] [Google Scholar]
  52. Yoshimoto H., Ohmae M., Yamashita I. The Saccharomyces cerevisiae GAM2/SIN3 protein plays a role in both activation and repression of transcription. Mol Gen Genet. 1992 May;233(1-2):327–330. doi: 10.1007/BF00587597. [DOI] [PubMed] [Google Scholar]

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