Skip to main content
Molecular and Cellular Biology logoLink to Molecular and Cellular Biology
. 1997 Mar;17(3):1110–1117. doi: 10.1128/mcb.17.3.1110

A basic helix-loop-helix-leucine zipper transcription complex in yeast functions in a signaling pathway from mitochondria to the nucleus.

Y Jia 1, B Rothermel 1, J Thornton 1, R A Butow 1
PMCID: PMC231836  PMID: 9032238

Abstract

The expression of some nuclear genes in Saccharomyces cerevisiae, such as the CIT2 gene, which encodes a glyoxylate cycle isoform of citrate synthase, is responsive to the functional state of mitochondria. Previous studies identified a basic helix-loop-helix-leucine zipper (bHLH/Zip) transcription factor encoded by the RTG1 gene that is required for both basal expression of the CIT2 gene and its increased expression in respiratory-deficient cells. Here, we describe the cloning and characterization of RTG3, a gene encoding a 54-kDa bHLH/Zip protein that is also required for CIT2 expression. Rtg3p binds together with Rtg1p to two identical sites oriented as inverted repeats 28 bp apart in a regulatory upstream activation sequence element (UASr) in the CIT2 promoter. The core binding site for the Rtg1p-Rtg3p heterodimer is 5'-GGTCAC-3', which differs from the canonical E-box site, CANNTG, to which most other bHLH proteins bind. We demonstrate that both of the Rtg1p-Rtg3p binding sites in the UAS(r) element are required in vivo and act synergistically for CIT2 expression. The basic region of Rtg3p conforms well to the basic region of most bHLH proteins, whereas the basic region of Rtg1p does not. These findings suggest that the Rtg1p-Rtg3p complex interacts in a novel way with its DNA target sites.

Full Text

The Full Text of this article is available as a PDF (918.6 KB).

Selected References

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

  1. Ayer D. E., Kretzner L., Eisenman R. N. Mad: a heterodimeric partner for Max that antagonizes Myc transcriptional activity. Cell. 1993 Jan 29;72(2):211–222. doi: 10.1016/0092-8674(93)90661-9. [DOI] [PubMed] [Google Scholar]
  2. Benezra R., Davis R. L., Lockshon D., Turner D. L., Weintraub H. The protein Id: a negative regulator of helix-loop-helix DNA binding proteins. Cell. 1990 Apr 6;61(1):49–59. doi: 10.1016/0092-8674(90)90214-y. [DOI] [PubMed] [Google Scholar]
  3. Blackwood E. M., Eisenman R. N. Max: a helix-loop-helix zipper protein that forms a sequence-specific DNA-binding complex with Myc. Science. 1991 Mar 8;251(4998):1211–1217. doi: 10.1126/science.2006410. [DOI] [PubMed] [Google Scholar]
  4. Chelstowska A., Butow R. A. RTG genes in yeast that function in communication between mitochondria and the nucleus are also required for expression of genes encoding peroxisomal proteins. J Biol Chem. 1995 Jul 28;270(30):18141–18146. doi: 10.1074/jbc.270.30.18141. [DOI] [PubMed] [Google Scholar]
  5. Ellenberger T., Fass D., Arnaud M., Harrison S. C. Crystal structure of transcription factor E47: E-box recognition by a basic region helix-loop-helix dimer. Genes Dev. 1994 Apr 15;8(8):970–980. doi: 10.1101/gad.8.8.970. [DOI] [PubMed] [Google Scholar]
  6. Ferré-D'Amaré A. R., Prendergast G. C., Ziff E. B., Burley S. K. Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain. Nature. 1993 May 6;363(6424):38–45. doi: 10.1038/363038a0. [DOI] [PubMed] [Google Scholar]
  7. Fisher D. E., Parent L. A., Sharp P. A. High affinity DNA-binding Myc analogs: recognition by an alpha helix. Cell. 1993 Feb 12;72(3):467–476. doi: 10.1016/0092-8674(93)90122-7. [DOI] [PubMed] [Google Scholar]
  8. Halazonetis T. D., Kandil A. N. Predicted structural similarities of the DNA binding domains of c-Myc and endonuclease Eco RI. Science. 1992 Jan 24;255(5043):464–466. doi: 10.1126/science.1734524. [DOI] [PubMed] [Google Scholar]
  9. Jayaraman P. S., Hirst K., Goding C. R. The activation domain of a basic helix-loop-helix protein is masked by repressor interaction with domains distinct from that required for transcription regulation. EMBO J. 1994 May 1;13(9):2192–2199. doi: 10.1002/j.1460-2075.1994.tb06496.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Kim J. B., Spotts G. D., Halvorsen Y. D., Shih H. M., Ellenberger T., Towle H. C., Spiegelman B. M. Dual DNA binding specificity of ADD1/SREBP1 controlled by a single amino acid in the basic helix-loop-helix domain. Mol Cell Biol. 1995 May;15(5):2582–2588. doi: 10.1128/mcb.15.5.2582. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Kim K. S., Rosenkrantz M. S., Guarente L. Saccharomyces cerevisiae contains two functional citrate synthase genes. Mol Cell Biol. 1986 Jun;6(6):1936–1942. doi: 10.1128/mcb.6.6.1936. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Kos W., Kal A. J., van Wilpe S., Tabak H. F. Expression of genes encoding peroxisomal proteins in Saccharomyces cerevisiae is regulated by different circuits of transcriptional control. Biochim Biophys Acta. 1995 Oct 17;1264(1):79–86. doi: 10.1016/0167-4781(95)00127-3. [DOI] [PubMed] [Google Scholar]
  13. Kunau W. H., Bühne S., de la Garza M., Kionka C., Mateblowski M., Schultz-Borchard U., Thieringer R. Comparative enzymology of beta-oxidation. Biochem Soc Trans. 1988 Jun;16(3):418–420. doi: 10.1042/bst0160418. [DOI] [PubMed] [Google Scholar]
  14. Lewin A. S., Hines V., Small G. M. Citrate synthase encoded by the CIT2 gene of Saccharomyces cerevisiae is peroxisomal. Mol Cell Biol. 1990 Apr;10(4):1399–1405. doi: 10.1128/mcb.10.4.1399. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Liao X. S., Small W. C., Srere P. A., Butow R. A. Intramitochondrial functions regulate nonmitochondrial citrate synthase (CIT2) expression in Saccharomyces cerevisiae. Mol Cell Biol. 1991 Jan;11(1):38–46. doi: 10.1128/mcb.11.1.38. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Liao X., Butow R. A. RTG1 and RTG2: two yeast genes required for a novel path of communication from mitochondria to the nucleus. Cell. 1993 Jan 15;72(1):61–71. doi: 10.1016/0092-8674(93)90050-z. [DOI] [PubMed] [Google Scholar]
  17. Lusska A., Shen E., Whitlock J. P., Jr Protein-DNA interactions at a dioxin-responsive enhancer. Analysis of six bona fide DNA-binding sites for the liganded Ah receptor. J Biol Chem. 1993 Mar 25;268(9):6575–6580. [PubMed] [Google Scholar]
  18. Ma P. C., Rould M. A., Weintraub H., Pabo C. O. Crystal structure of MyoD bHLH domain-DNA complex: perspectives on DNA recognition and implications for transcriptional activation. Cell. 1994 May 6;77(3):451–459. doi: 10.1016/0092-8674(94)90159-7. [DOI] [PubMed] [Google Scholar]
  19. Marshall P. A., Krimkevich Y. I., Lark R. H., Dyer J. M., Veenhuis M., Goodman J. M. Pmp27 promotes peroxisomal proliferation. J Cell Biol. 1995 Apr;129(2):345–355. doi: 10.1083/jcb.129.2.345. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. McCammon M. T., Veenhuis M., Trapp S. B., Goodman J. M. Association of glyoxylate and beta-oxidation enzymes with peroxisomes of Saccharomyces cerevisiae. J Bacteriol. 1990 Oct;172(10):5816–5827. doi: 10.1128/jb.172.10.5816-5827.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Molkentin J. D., Black B. L., Martin J. F., Olson E. N. Cooperative activation of muscle gene expression by MEF2 and myogenic bHLH proteins. Cell. 1995 Dec 29;83(7):1125–1136. doi: 10.1016/0092-8674(95)90139-6. [DOI] [PubMed] [Google Scholar]
  22. Murre C., Bain G., van Dijk M. A., Engel I., Furnari B. A., Massari M. E., Matthews J. R., Quong M. W., Rivera R. R., Stuiver M. H. Structure and function of helix-loop-helix proteins. Biochim Biophys Acta. 1994 Jun 21;1218(2):129–135. doi: 10.1016/0167-4781(94)90001-9. [DOI] [PubMed] [Google Scholar]
  23. Murre C., McCaw P. S., Baltimore D. A new DNA binding and dimerization motif in immunoglobulin enhancer binding, daughterless, MyoD, and myc proteins. Cell. 1989 Mar 10;56(5):777–783. doi: 10.1016/0092-8674(89)90682-x. [DOI] [PubMed] [Google Scholar]
  24. Murre C., McCaw P. S., Vaessin H., Caudy M., Jan L. Y., Jan Y. N., Cabrera C. V., Buskin J. N., Hauschka S. D., Lassar A. B. Interactions between heterologous helix-loop-helix proteins generate complexes that bind specifically to a common DNA sequence. Cell. 1989 Aug 11;58(3):537–544. doi: 10.1016/0092-8674(89)90434-0. [DOI] [PubMed] [Google Scholar]
  25. Parikh V. S., Morgan M. M., Scott R., Clements L. S., Butow R. A. The mitochondrial genotype can influence nuclear gene expression in yeast. Science. 1987 Jan 30;235(4788):576–580. doi: 10.1126/science.3027892. [DOI] [PubMed] [Google Scholar]
  26. Pollenz R. S., Sattler C. A., Poland A. The aryl hydrocarbon receptor and aryl hydrocarbon receptor nuclear translocator protein show distinct subcellular localizations in Hepa 1c1c7 cells by immunofluorescence microscopy. Mol Pharmacol. 1994 Mar;45(3):428–438. [PubMed] [Google Scholar]
  27. Probst M. R., Reisz-Porszasz S., Agbunag R. V., Ong M. S., Hankinson O. Role of the aryl hydrocarbon receptor nuclear translocator protein in aryl hydrocarbon (dioxin) receptor action. Mol Pharmacol. 1993 Sep;44(3):511–518. [PubMed] [Google Scholar]
  28. Reyes H., Reisz-Porszasz S., Hankinson O. Identification of the Ah receptor nuclear translocator protein (Arnt) as a component of the DNA binding form of the Ah receptor. Science. 1992 May 22;256(5060):1193–1195. doi: 10.1126/science.256.5060.1193. [DOI] [PubMed] [Google Scholar]
  29. Rose M. D., Novick P., Thomas J. H., Botstein D., Fink G. R. A Saccharomyces cerevisiae genomic plasmid bank based on a centromere-containing shuttle vector. Gene. 1987;60(2-3):237–243. doi: 10.1016/0378-1119(87)90232-0. [DOI] [PubMed] [Google Scholar]
  30. Rothermel B. A., Shyjan A. W., Etheredge J. L., Butow R. A. Transactivation by Rtg1p, a basic helix-loop-helix protein that functions in communication between mitochondria and the nucleus in yeast. J Biol Chem. 1995 Dec 8;270(49):29476–29482. doi: 10.1074/jbc.270.49.29476. [DOI] [PubMed] [Google Scholar]
  31. Schmitt M. E., Brown T. A., Trumpower B. L. A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae. Nucleic Acids Res. 1990 May 25;18(10):3091–3092. doi: 10.1093/nar/18.10.3091. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Schreiber-Agus N., Chin L., Chen K., Torres R., Rao G., Guida P., Skoultchi A. I., DePinho R. A. An amino-terminal domain of Mxi1 mediates anti-Myc oncogenic activity and interacts with a homolog of the yeast transcriptional repressor SIN3. Cell. 1995 Mar 10;80(5):777–786. doi: 10.1016/0092-8674(95)90356-9. [DOI] [PubMed] [Google Scholar]
  33. Shyjan A. W., Buttow R. A. Organelle communication: intracellular dialogue. Curr Biol. 1993 Jun 1;3(6):398–400. doi: 10.1016/0960-9822(93)90212-7. [DOI] [PubMed] [Google Scholar]
  34. Skoneczny M., Chełstowska A., Rytka J. Study of the coinduction by fatty acids of catalase A and acyl-CoA oxidase in standard and mutant Saccharomyces cerevisiae strains. Eur J Biochem. 1988 Jun 1;174(2):297–302. doi: 10.1111/j.1432-1033.1988.tb14097.x. [DOI] [PubMed] [Google Scholar]
  35. Tolbert N. E. Metabolic pathways in peroxisomes and glyoxysomes. Annu Rev Biochem. 1981;50:133–157. doi: 10.1146/annurev.bi.50.070181.001025. [DOI] [PubMed] [Google Scholar]
  36. Tontonoz P., Kim J. B., Graves R. A., Spiegelman B. M. ADD1: a novel helix-loop-helix transcription factor associated with adipocyte determination and differentiation. Mol Cell Biol. 1993 Aug;13(8):4753–4759. doi: 10.1128/mcb.13.8.4753. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Veenhuis M., Mateblowski M., Kunau W. H., Harder W. Proliferation of microbodies in Saccharomyces cerevisiae. Yeast. 1987 Jun;3(2):77–84. doi: 10.1002/yea.320030204. [DOI] [PubMed] [Google Scholar]
  38. Whitelaw M., Pongratz I., Wilhelmsson A., Gustafsson J. A., Poellinger L. Ligand-dependent recruitment of the Arnt coregulator determines DNA recognition by the dioxin receptor. Mol Cell Biol. 1993 Apr;13(4):2504–2514. doi: 10.1128/mcb.13.4.2504. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Yokoyama C., Wang X., Briggs M. R., Admon A., Wu J., Hua X., Goldstein J. L., Brown M. S. SREBP-1, a basic-helix-loop-helix-leucine zipper protein that controls transcription of the low density lipoprotein receptor gene. Cell. 1993 Oct 8;75(1):187–197. [PubMed] [Google Scholar]

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

RESOURCES