Skip to main content
Molecular and Cellular Biology logoLink to Molecular and Cellular Biology
. 1991 May;11(5):2609–2619. doi: 10.1128/mcb.11.5.2609

Analysis of constitutive and noninducible mutations of the PUT3 transcriptional activator.

J E Marczak 1, M C Brandriss 1
PMCID: PMC360030  PMID: 2017167

Abstract

The Saccharomyces cerevisiae PUT3 gene encodes a transcriptional activator that binds to DNA sequences in the promoters of the proline utilization genes and is required for the basal and induced expression of the enzymes of this pathway. The sequence of the wild-type PUT3 gene revealed the presence of one large open reading frame capable of encoding a 979-amino-acid protein. The protein contains amino-terminal basic and cysteine-rich domains homologous to the DNA-binding motifs of other yeast transcriptional activators. Adjacent to these domains is an acidic domain with a net charge of -17. A second acidic domain with a net charge of -29 is located at the carboxy terminus. The midsection of the PUT3 protein has homology to other activators including GAL4, LAC9, PPR1, and PDR1. Mutations in PUT3 causing aberrant (either constitutive or noninducible) expression of target genes in this system have been analyzed. One activator-defective and seven activator-constitutive PUT3 alleles have been retrieved from the genome and sequenced to determine the nucleotide changes responsible for the altered function of the protein. The activator-defective mutation is a single nucleotide change within codon 409, replacing glycine with aspartic acid. One activator-constitutive mutation is a nucleotide change at codon 683, substituting phenylalanine for serine. The remaining constitutive mutations resulted in amino acid substitutions or truncations of the protein within the carboxy-terminal 76 codons. Mechanisms for regulating the activation function of the PUT3 protein are discussed.

Full text

PDF
2615

Selected References

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

  1. Andrianopoulos A., Hynes M. J. Sequence and functional analysis of the positively acting regulatory gene amdR from Aspergillus nidulans. Mol Cell Biol. 1990 Jun;10(6):3194–3203. doi: 10.1128/mcb.10.6.3194. [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. Bach M. L., Lacroute F. Direct selective techniques for the isolation of pyrimidine auxotrophs in yeast. Mol Gen Genet. 1972;115(2):126–130. doi: 10.1007/BF00277292. [DOI] [PubMed] [Google Scholar]
  4. Balzi E., Chen W., Ulaszewski S., Capieaux E., Goffeau A. The multidrug resistance gene PDR1 from Saccharomyces cerevisiae. J Biol Chem. 1987 Dec 15;262(35):16871–16879. [PubMed] [Google Scholar]
  5. Baum J. A., Geever R., Giles N. H. Expression of qa-1F activator protein: identification of upstream binding sites in the qa gene cluster and localization of the DNA-binding domain. Mol Cell Biol. 1987 Mar;7(3):1256–1266. doi: 10.1128/mcb.7.3.1256. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Bennetzen J. L., Hall B. D. Codon selection in yeast. J Biol Chem. 1982 Mar 25;257(6):3026–3031. [PubMed] [Google Scholar]
  7. Beri R. K., Whittington H., Roberts C. F., Hawkins A. R. Isolation and characterization of the positively acting regulatory gene QUTA from Aspergillus nidulans. Nucleic Acids Res. 1987 Oct 12;15(19):7991–8001. doi: 10.1093/nar/15.19.7991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Birnboim H. C., Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 1979 Nov 24;7(6):1513–1523. doi: 10.1093/nar/7.6.1513. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Blumberg H., Eisen A., Sledziewski A., Bader D., Young E. T. Two zinc fingers of a yeast regulatory protein shown by genetic evidence to be essential for its function. 1987 Jul 30-Aug 5Nature. 328(6129):443–445. doi: 10.1038/328443a0. [DOI] [PubMed] [Google Scholar]
  10. 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]
  11. 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]
  12. Brandriss M. C. Isolation and preliminary characterization of Saccharomyces cerevisiae proline auxotrophs. J Bacteriol. 1979 Jun;138(3):816–822. doi: 10.1128/jb.138.3.816-822.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Brandriss M. C., Krzywicki K. A. Amino-terminal fragments of delta 1-pyrroline-5-carboxylate dehydrogenase direct beta-galactosidase to the mitochondrial matrix in Saccharomyces cerevisiae. Mol Cell Biol. 1986 Oct;6(10):3502–3512. doi: 10.1128/mcb.6.10.3502. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. 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]
  15. 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]
  16. 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]
  17. Carlson M., Botstein D. Two differentially regulated mRNAs with different 5' ends encode secreted with intracellular forms of yeast invertase. Cell. 1982 Jan;28(1):145–154. doi: 10.1016/0092-8674(82)90384-1. [DOI] [PubMed] [Google Scholar]
  18. 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]
  19. Cherry J. R., Johnson T. R., Dollard C., Shuster J. R., Denis C. L. Cyclic AMP-dependent protein kinase phosphorylates and inactivates the yeast transcriptional activator ADR1. Cell. 1989 Feb 10;56(3):409–419. doi: 10.1016/0092-8674(89)90244-4. [DOI] [PubMed] [Google Scholar]
  20. Chou P. Y., Fasman G. D. Prediction of the secondary structure of proteins from their amino acid sequence. Adv Enzymol Relat Areas Mol Biol. 1978;47:45–148. doi: 10.1002/9780470122921.ch2. [DOI] [PubMed] [Google Scholar]
  21. Cohen P. Protein phosphorylation and hormone action. Proc R Soc Lond B Biol Sci. 1988 Jul 22;234(1275):115–144. doi: 10.1098/rspb.1988.0040. [DOI] [PubMed] [Google Scholar]
  22. Denis C. L., Gallo C. Constitutive RNA synthesis for the yeast activator ADR1 and identification of the ADR1-5c mutation: implications in posttranslational control of ADR1. Mol Cell Biol. 1986 Nov;6(11):4026–4030. doi: 10.1128/mcb.6.11.4026. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Devereux J., Haeberli P., Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. doi: 10.1093/nar/12.1part1.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Edelman A. M., Blumenthal D. K., Krebs E. G. Protein serine/threonine kinases. Annu Rev Biochem. 1987;56:567–613. doi: 10.1146/annurev.bi.56.070187.003031. [DOI] [PubMed] [Google Scholar]
  25. Fitzgerald M., Shenk T. The sequence 5'-AAUAAA-3'forms parts of the recognition site for polyadenylation of late SV40 mRNAs. Cell. 1981 Apr;24(1):251–260. doi: 10.1016/0092-8674(81)90521-3. [DOI] [PubMed] [Google Scholar]
  26. Friden P., Schimmel P. LEU3 of Saccharomyces cerevisiae encodes a factor for control of RNA levels of a group of leucine-specific genes. Mol Cell Biol. 1987 Aug;7(8):2708–2717. doi: 10.1128/mcb.7.8.2708. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Garnier J., Osguthorpe D. J., Robson B. Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J Mol Biol. 1978 Mar 25;120(1):97–120. doi: 10.1016/0022-2836(78)90297-8. [DOI] [PubMed] [Google Scholar]
  28. Hashimoto H., Kikuchi Y., Nogi Y., Fukasawa T. Regulation of expression of the galactose gene cluster in Saccharomyces cerevisiae. Isolation and characterization of the regulatory gene GAL4. Mol Gen Genet. 1983;191(1):31–38. doi: 10.1007/BF00330886. [DOI] [PubMed] [Google Scholar]
  29. 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]
  30. Hope I. A., Struhl K. Functional dissection of a eukaryotic transcriptional activator protein, GCN4 of yeast. Cell. 1986 Sep 12;46(6):885–894. doi: 10.1016/0092-8674(86)90070-x. [DOI] [PubMed] [Google Scholar]
  31. Hopp T. P., Woods K. R. Prediction of protein antigenic determinants from amino acid sequences. Proc Natl Acad Sci U S A. 1981 Jun;78(6):3824–3828. doi: 10.1073/pnas.78.6.3824. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Johnston M., Davis R. W. Sequences that regulate the divergent GAL1-GAL10 promoter in Saccharomyces cerevisiae. Mol Cell Biol. 1984 Aug;4(8):1440–1448. doi: 10.1128/mcb.4.8.1440. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Johnston M., Dover J. Mutations that inactivate a yeast transcriptional regulatory protein cluster in an evolutionarily conserved DNA binding domain. Proc Natl Acad Sci U S A. 1987 Apr;84(8):2401–2405. doi: 10.1073/pnas.84.8.2401. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Johnston M. Genetic evidence that zinc is an essential co-factor in the DNA binding domain of GAL4 protein. Nature. 1987 Jul 23;328(6128):353–355. doi: 10.1038/328353a0. [DOI] [PubMed] [Google Scholar]
  35. Johnston S. A., Hopper J. E. Isolation of the yeast regulatory gene GAL4 and analysis of its dosage effects on the galactose/melibiose regulon. Proc Natl Acad Sci U S A. 1982 Nov;79(22):6971–6975. doi: 10.1073/pnas.79.22.6971. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Johnston S. A., Salmeron J. M., Jr, Dincher S. S. Interaction of positive and negative regulatory proteins in the galactose regulon of yeast. Cell. 1987 Jul 3;50(1):143–146. doi: 10.1016/0092-8674(87)90671-4. [DOI] [PubMed] [Google Scholar]
  37. Kammerer B., Guyonvarch A., Hubert J. C. Yeast regulatory gene PPR1. I. Nucleotide sequence, restriction map and codon usage. J Mol Biol. 1984 Dec 5;180(2):239–250. doi: 10.1016/s0022-2836(84)80002-9. [DOI] [PubMed] [Google Scholar]
  38. Keegan L., Gill G., Ptashne M. Separation of DNA binding from the transcription-activating function of a eukaryotic regulatory protein. Science. 1986 Feb 14;231(4739):699–704. doi: 10.1126/science.3080805. [DOI] [PubMed] [Google Scholar]
  39. Kim J., Michels C. A. The MAL63 gene of Saccharomyces encodes a cysteine-zinc finger protein. Curr Genet. 1988 Oct;14(4):319–323. doi: 10.1007/BF00419988. [DOI] [PubMed] [Google Scholar]
  40. Kohchi C., Toh-e A. Nucleotide sequence of Candida pelliculosa beta-glucosidase gene. Nucleic Acids Res. 1985 Sep 11;13(17):6273–6282. doi: 10.1093/nar/13.17.6273. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Laughon A., Gesteland R. F. Primary structure of the Saccharomyces cerevisiae GAL4 gene. Mol Cell Biol. 1984 Feb;4(2):260–267. doi: 10.1128/mcb.4.2.260. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Lipman D. J., Pearson W. R. Rapid and sensitive protein similarity searches. Science. 1985 Mar 22;227(4693):1435–1441. doi: 10.1126/science.2983426. [DOI] [PubMed] [Google Scholar]
  43. 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]
  44. 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]
  45. Marin O., Meggio F., Marchiori F., Borin G., Pinna L. A. Site specificity of casein kinase-2 (TS) from rat liver cytosol. A study with model peptide substrates. Eur J Biochem. 1986 Oct 15;160(2):239–244. doi: 10.1111/j.1432-1033.1986.tb09962.x. [DOI] [PubMed] [Google Scholar]
  46. Messenguy F., Dubois E., Descamps F. Nucleotide sequence of the ARGRII regulatory gene and amino acid sequence homologies between ARGRII PPRI and GAL4 regulatory proteins. Eur J Biochem. 1986 May 15;157(1):77–81. doi: 10.1111/j.1432-1033.1986.tb09640.x. [DOI] [PubMed] [Google Scholar]
  47. Miller J., McLachlan A. D., Klug A. Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. EMBO J. 1985 Jun;4(6):1609–1614. doi: 10.1002/j.1460-2075.1985.tb03825.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Myers A. M., Tzagoloff A., Kinney D. M., Lusty C. J. Yeast shuttle and integrative vectors with multiple cloning sites suitable for construction of lacZ fusions. Gene. 1986;45(3):299–310. doi: 10.1016/0378-1119(86)90028-4. [DOI] [PubMed] [Google Scholar]
  49. Mylin L. M., Bhat J. P., Hopper J. E. Regulated phosphorylation and dephosphorylation of GAL4, a transcriptional activator. Genes Dev. 1989 Aug;3(8):1157–1165. doi: 10.1101/gad.3.8.1157. [DOI] [PubMed] [Google Scholar]
  50. Mylin L. M., Johnston M., Hopper J. E. Phosphorylated forms of GAL4 are correlated with ability to activate transcription. Mol Cell Biol. 1990 Sep;10(9):4623–4629. doi: 10.1128/mcb.10.9.4623. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Nakao T., Yamato I., Anraku Y. Nucleotide sequence of putP, the proline carrier gene of Escherichia coli K12. Mol Gen Genet. 1987 Jun;208(1-2):70–75. doi: 10.1007/BF00330424. [DOI] [PubMed] [Google Scholar]
  52. Ogawa N., Oshima Y. Functional domains of a positive regulatory protein, PHO4, for transcriptional control of the phosphatase regulon in Saccharomyces cerevisiae. Mol Cell Biol. 1990 May;10(5):2224–2236. doi: 10.1128/mcb.10.5.2224. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Pan T., Coleman J. E. GAL4 transcription factor is not a "zinc finger" but forms a Zn(II)2Cys6 binuclear cluster. Proc Natl Acad Sci U S A. 1990 Mar;87(6):2077–2081. doi: 10.1073/pnas.87.6.2077. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Pan T., Coleman J. E. Structure and function of the Zn(II) binding site within the DNA-binding domain of the GAL4 transcription factor. Proc Natl Acad Sci U S A. 1989 May;86(9):3145–3149. doi: 10.1073/pnas.86.9.3145. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Pearson W. R., Lipman D. J. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444–2448. doi: 10.1073/pnas.85.8.2444. [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. 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]
  57. 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]
  58. Salmeron J. M., Jr, Leuther K. K., Johnston S. A. GAL4 mutations that separate the transcriptional activation and GAL80-interactive functions of the yeast GAL4 protein. Genetics. 1990 May;125(1):21–27. doi: 10.1093/genetics/125.1.21. [DOI] [PMC free article] [PubMed] [Google Scholar]
  59. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  60. 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]
  61. Sollitti P., Marmur J. Primary structure of the regulatory gene from the MAL6 locus of Saccharomyces carlsbergensis. Mol Gen Genet. 1988 Jul;213(1):56–62. doi: 10.1007/BF00333398. [DOI] [PubMed] [Google Scholar]
  62. Sophianopoulou V., Scazzocchio C. The proline transport protein of Aspergillus nidulans is very similar to amino acid transporters of Saccharomyces cerevisiae. Mol Microbiol. 1989 Jun;3(6):705–714. doi: 10.1111/j.1365-2958.1989.tb00219.x. [DOI] [PubMed] [Google Scholar]
  63. Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
  64. Sprang S. R., Acharya K. R., Goldsmith E. J., Stuart D. I., Varvill K., Fletterick R. J., Madsen N. B., Johnson L. N. Structural changes in glycogen phosphorylase induced by phosphorylation. Nature. 1988 Nov 17;336(6196):215–221. doi: 10.1038/336215a0. [DOI] [PubMed] [Google Scholar]
  65. Taylor W. E., Young E. T. cAMP-dependent phosphorylation and inactivation of yeast transcription factor ADR1 does not affect DNA binding. Proc Natl Acad Sci U S A. 1990 Jun;87(11):4098–4102. doi: 10.1073/pnas.87.11.4098. [DOI] [PMC free article] [PubMed] [Google Scholar]
  66. Vandenbol M., Jauniaux J. C., Grenson M. Nucleotide sequence of the Saccharomyces cerevisiae PUT4 proline-permease-encoding gene: similarities between CAN1, HIP1 and PUT4 permeases. Gene. 1989 Nov 15;83(1):153–159. doi: 10.1016/0378-1119(89)90413-7. [DOI] [PubMed] [Google Scholar]
  67. Verdière J., Gaisne M., Guiard B., Defranoux N., Slonimski P. P. CYP1 (HAP1) regulator of oxygen-dependent gene expression in yeast. II. Missense mutation suggests alternative Zn fingers as discriminating agents of gene control. J Mol Biol. 1988 Nov 20;204(2):277–282. doi: 10.1016/0022-2836(88)90575-x. [DOI] [PubMed] [Google Scholar]
  68. Wray L. V., Jr, Witte M. M., Dickson R. C., Riley M. I. Characterization of a positive regulatory gene, LAC9, that controls induction of the lactose-galactose regulon of Kluyveromyces lactis: structural and functional relationships to GAL4 of Saccharomyces cerevisiae. Mol Cell Biol. 1987 Mar;7(3):1111–1121. doi: 10.1128/mcb.7.3.1111. [DOI] [PMC free article] [PubMed] [Google Scholar]
  69. Yanisch-Perron C., Vieira J., Messing J. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene. 1985;33(1):103–119. doi: 10.1016/0378-1119(85)90120-9. [DOI] [PubMed] [Google Scholar]
  70. Zaret K. S., Sherman F. DNA sequence required for efficient transcription termination in yeast. Cell. 1982 Mar;28(3):563–573. doi: 10.1016/0092-8674(82)90211-2. [DOI] [PubMed] [Google Scholar]
  71. Zhou K., Brisco P. R., Hinkkanen A. E., Kohlhaw G. B. Structure of yeast regulatory gene LEU3 and evidence that LEU3 itself is under general amino acid control. Nucleic Acids Res. 1987 Jul 10;15(13):5261–5273. doi: 10.1093/nar/15.13.5261. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Molecular and Cellular Biology are provided here courtesy of Taylor & Francis

RESOURCES