Skip to main content
Genetics logoLink to Genetics
. 1996 Apr;142(4):1069–1082. doi: 10.1093/genetics/142.4.1069

Functional Analysis of the Put3 Transcriptional Activator of the Proline Utilization Pathway in Saccharomyces Cerevisiae

SAG des-Etages 1, D A Falvey 1, R J Reece 1, M C Brandriss 1
PMCID: PMC1207108  PMID: 8846888

Abstract

Proline can serve as a nitrogen source for the yeast Saccharomyces cerevisiae when preferred sources of nitrogen are absent from the growth medium. PUT3, the activator of the proline utilization pathway, is required for the transcription of the genes encoding the enzymes that convert proline to glutamate. PUT3 is a 979 amino acid protein that constitutively binds a short DNA sequence in the promoters of its target genes, but does not activate their expression in the absence of induction by proline and in the presence of preferred sources of nitrogen. To understand how PUT3 is converted from an inactive to an active state, a dissection of its functional domains has been undertaken. Biochemical and molecular tests, domain swapping experiments, and an analysis of activator-constitutive and activator-defective mutant proteins indicate that PUT3 is dimeric and activates transcription with its negatively charged carboxyterminus, which does not appear to contain a proline-responsive domain. A mutation in the conserved central domain found in many fungal activators interferes with activation without affecting DNA binding or protein stability. Intragenic suppressors of the central domain mutation have been isolated and analyzed.

Full Text

The Full Text of this article is available as a PDF (4.0 MB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Alani E., Cao L., Kleckner N. A method for gene disruption that allows repeated use of URA3 selection in the construction of multiply disrupted yeast strains. Genetics. 1987 Aug;116(4):541–545. doi: 10.1534/genetics.112.541.test. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Axelrod J. D., Majors J., Brandriss M. C. Proline-independent binding of PUT3 transcriptional activator protein detected by footprinting in vivo. Mol Cell Biol. 1991 Jan;11(1):564–567. doi: 10.1128/mcb.11.1.564. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Baleja J. D., Marmorstein R., Harrison S. C., Wagner G. Solution structure of the DNA-binding domain of Cd2-GAL4 from S. cerevisiae. Nature. 1992 Apr 2;356(6368):450–453. doi: 10.1038/356450a0. [DOI] [PubMed] [Google Scholar]
  4. Bartel P., Chien C. T., Sternglanz R., Fields S. Elimination of false positives that arise in using the two-hybrid system. Biotechniques. 1993 Jun;14(6):920–924. [PubMed] [Google Scholar]
  5. 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]
  6. Brandriss M. C. Evidence for positive regulation of the proline utilization pathway in Saccharomyces cerevisiae. Genetics. 1987 Nov;117(3):429–435. doi: 10.1093/genetics/117.3.429. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Brandriss M. C., Magasanik B. Genetics and physiology of proline utilization in Saccharomyces cerevisiae: enzyme induction by proline. J Bacteriol. 1979 Nov;140(2):498–503. doi: 10.1128/jb.140.2.498-503.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Brandriss M. C., Magasanik B. Genetics and physiology of proline utilization in Saccharomyces cerevisiae: mutation causing constitutive enzyme expression. J Bacteriol. 1979 Nov;140(2):504–507. doi: 10.1128/jb.140.2.504-507.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Brandriss M. C., Magasanik B. Proline: an essential intermediate in arginine degradation in Saccharomyces cerevisiae. J Bacteriol. 1980 Sep;143(3):1403–1410. doi: 10.1128/jb.143.3.1403-1410.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Brandriss M. C. Proline utilization in Saccharomyces cerevisiae: analysis of the cloned PUT2 gene. Mol Cell Biol. 1983 Oct;3(10):1846–1856. doi: 10.1128/mcb.3.10.1846. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Chasman D. I., Kornberg R. D. GAL4 protein: purification, association with GAL80 protein, and conserved domain structure. Mol Cell Biol. 1990 Jun;10(6):2916–2923. doi: 10.1128/mcb.10.6.2916. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Coffman J. A., el Berry H. M., Cooper T. G. The URE2 protein regulates nitrogen catabolic gene expression through the GATAA-containing UASNTR element in Saccharomyces cerevisiae. J Bacteriol. 1994 Dec;176(24):7476–7483. doi: 10.1128/jb.176.24.7476-7483.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Daugherty J. R., Rai R., el Berry H. M., Cooper T. G. 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 Jan;175(1):64–73. doi: 10.1128/jb.175.1.64-73.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Dingwall C., Laskey R. A. Nuclear targeting sequences--a consensus? Trends Biochem Sci. 1991 Dec;16(12):478–481. doi: 10.1016/0968-0004(91)90184-w. [DOI] [PubMed] [Google Scholar]
  15. Friden P., Reynolds C., Schimmel P. A large internal deletion converts yeast LEU3 to a constitutive transcriptional activator. Mol Cell Biol. 1989 Sep;9(9):4056–4060. doi: 10.1128/mcb.9.9.4056. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Grenson M., Hou C., Crabeel M. Multiplicity of the amino acid permeases in Saccharomyces cerevisiae. IV. Evidence for a general amino acid permease. J Bacteriol. 1970 Sep;103(3):770–777. doi: 10.1128/jb.103.3.770-777.1970. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Griggs D. W., Johnston M. Promoter elements determining weak expression of the GAL4 regulatory gene of Saccharomyces cerevisiae. Mol Cell Biol. 1993 Aug;13(8):4999–5009. doi: 10.1128/mcb.13.8.4999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Jauniaux J. C., Grenson M. GAP1, the general amino acid permease gene of Saccharomyces cerevisiae. Nucleotide sequence, protein similarity with the other bakers yeast amino acid permeases, and nitrogen catabolite repression. Eur J Biochem. 1990 May 31;190(1):39–44. doi: 10.1111/j.1432-1033.1990.tb15542.x. [DOI] [PubMed] [Google Scholar]
  19. Jauniaux J. C., Vandenbol M., Vissers S., Broman K., Grenson M. Nitrogen catabolite regulation of proline permease in Saccharomyces cerevisiae. Cloning of the PUT4 gene and study of PUT4 RNA levels in wild-type and mutant strains. Eur J Biochem. 1987 May 4;164(3):601–606. doi: 10.1111/j.1432-1033.1987.tb11169.x. [DOI] [PubMed] [Google Scholar]
  20. Johnston M., Dover J. Mutational analysis of the GAL4-encoded transcriptional activator protein of Saccharomyces cerevisiae. Genetics. 1988 Sep;120(1):63–74. doi: 10.1093/genetics/120.1.63. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Kaput J., Brandriss M. C., Prussak-Wieckowska T. In vitro import of cytochrome c peroxidase into the intermembrane space: release of the processed form by intact mitochondria. J Cell Biol. 1989 Jul;109(1):101–112. doi: 10.1083/jcb.109.1.101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Laemmli U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. doi: 10.1038/227680a0. [DOI] [PubMed] [Google Scholar]
  23. Lasko P. F., Brandriss M. C. Proline transport in Saccharomyces cerevisiae. J Bacteriol. 1981 Oct;148(1):241–247. doi: 10.1128/jb.148.1.241-247.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Laughon A., Gesteland R. F. Isolation and preliminary characterization of the GAL4 gene, a positive regulator of transcription in yeast. Proc Natl Acad Sci U S A. 1982 Nov;79(22):6827–6831. doi: 10.1073/pnas.79.22.6827. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Leuther K. K., Johnston S. A. Nondissociation of GAL4 and GAL80 in vivo after galactose induction. Science. 1992 May 29;256(5061):1333–1335. doi: 10.1126/science.1598579. [DOI] [PubMed] [Google Scholar]
  26. Leuther K. K., Salmeron J. M., Johnston S. A. Genetic evidence that an activation domain of GAL4 does not require acidity and may form a beta sheet. Cell. 1993 Feb 26;72(4):575–585. doi: 10.1016/0092-8674(93)90076-3. [DOI] [PubMed] [Google Scholar]
  27. Ma J., Ptashne M. Deletion analysis of GAL4 defines two transcriptional activating segments. Cell. 1987 Mar 13;48(5):847–853. doi: 10.1016/0092-8674(87)90081-x. [DOI] [PubMed] [Google Scholar]
  28. Marczak J. E., Brandriss M. C. Analysis of constitutive and noninducible mutations of the PUT3 transcriptional activator. Mol Cell Biol. 1991 May;11(5):2609–2619. doi: 10.1128/mcb.11.5.2609. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Marczak J. E., Brandriss M. C. Isolation of constitutive mutations affecting the proline utilization pathway in Saccharomyces cerevisiae and molecular analysis of the PUT3 transcriptional activator. Mol Cell Biol. 1989 Nov;9(11):4696–4705. doi: 10.1128/mcb.9.11.4696. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Minehart P. L., Magasanik B. Sequence and expression of GLN3, a positive nitrogen regulatory gene of Saccharomyces cerevisiae encoding a protein with a putative zinc finger DNA-binding domain. Mol Cell Biol. 1991 Dec;11(12):6216–6228. doi: 10.1128/mcb.11.12.6216. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Reece R. J., Ptashne M. Determinants of binding-site specificity among yeast C6 zinc cluster proteins. Science. 1993 Aug 13;261(5123):909–911. doi: 10.1126/science.8346441. [DOI] [PubMed] [Google Scholar]
  32. Rosenberg A. H., Lade B. N., Chui D. S., Lin S. W., Dunn J. J., Studier F. W. Vectors for selective expression of cloned DNAs by T7 RNA polymerase. Gene. 1987;56(1):125–135. doi: 10.1016/0378-1119(87)90165-x. [DOI] [PubMed] [Google Scholar]
  33. Sadowski I., Bell B., Broad P., Hollis M. GAL4 fusion vectors for expression in yeast or mammalian cells. Gene. 1992 Sep 1;118(1):137–141. doi: 10.1016/0378-1119(92)90261-m. [DOI] [PubMed] [Google Scholar]
  34. Salmeron J. M., Jr, Johnston S. A. Analysis of the Kluyveromyces lactis positive regulatory gene LAC9 reveals functional homology to, but sequence divergence from, the Saccharomyces cerevisiae GAL4 gene. Nucleic Acids Res. 1986 Oct 10;14(19):7767–7781. doi: 10.1093/nar/14.19.7767. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Salmeron J. M., Jr, Langdon S. D., Johnston S. A. Interaction between transcriptional activator protein LAC9 and negative regulatory protein GAL80. Mol Cell Biol. 1989 Jul;9(7):2950–2956. doi: 10.1128/mcb.9.7.2950. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Siddiqui A. H., Brandriss M. C. A regulatory region responsible for proline-specific induction of the yeast PUT2 gene is adjacent to its TATA box. Mol Cell Biol. 1988 Nov;8(11):4634–4641. doi: 10.1128/mcb.8.11.4634. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Siddiqui A. H., Brandriss M. C. The Saccharomyces cerevisiae PUT3 activator protein associates with proline-specific upstream activation sequences. Mol Cell Biol. 1989 Nov;9(11):4706–4712. doi: 10.1128/mcb.9.11.4706. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Stanbrough M., Magasanik B. Transcriptional and posttranslational regulation of the general amino acid permease of Saccharomyces cerevisiae. J Bacteriol. 1995 Jan;177(1):94–102. doi: 10.1128/jb.177.1.94-102.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Stone G., Sadowski I. GAL4 is regulated by a glucose-responsive functional domain. EMBO J. 1993 Apr;12(4):1375–1385. doi: 10.1002/j.1460-2075.1993.tb05782.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Wang S. S., Brandriss M. C. Proline utilization in Saccharomyces cerevisiae: analysis of the cloned PUT1 gene. Mol Cell Biol. 1986 Jul;6(7):2638–2645. doi: 10.1128/mcb.6.7.2638. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Wang S. S., Brandriss M. C. Proline utilization in Saccharomyces cerevisiae: sequence, regulation, and mitochondrial localization of the PUT1 gene product. Mol Cell Biol. 1987 Dec;7(12):4431–4440. doi: 10.1128/mcb.7.12.4431. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Xu S., Falvey D. A., Brandriss M. C. Roles of URE2 and GLN3 in the proline utilization pathway in Saccharomyces cerevisiae. Mol Cell Biol. 1995 Apr;15(4):2321–2330. doi: 10.1128/mcb.15.4.2321. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Yocum R. R., Hanley S., West R., Jr, Ptashne M. Use of lacZ fusions to delimit regulatory elements of the inducible divergent GAL1-GAL10 promoter in Saccharomyces cerevisiae. Mol Cell Biol. 1984 Oct;4(10):1985–1998. doi: 10.1128/mcb.4.10.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES