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. 2000 Jul;155(3):1045–1054. doi: 10.1093/genetics/155.3.1045

Functional interaction of CCR4-NOT proteins with TATAA-binding protein (TBP) and its associated factors in yeast.

V Badarinarayana 1, Y C Chiang 1, C L Denis 1
PMCID: PMC1461164  PMID: 10880468

Abstract

The CCR4-NOT transcriptional regulatory complex affects expression of a number of genes both positively and negatively. We report here that components of the CCR4-NOT complex functionally and physically interact with TBP and TBP-associated factors. First, mutations in CCR4-NOT components suppressed the his4-912delta insertion in a manner similar to that observed for the defective TBP allele spt15-122. Second, using modified HIS3 promoter derivatives containing specific mutations within the TATA sequence, we found that the NOT proteins were general repressors that disrupt TBP function irrespective of the DNA sequence. Third, increasing the dosage of NOT1 specifically inhibited the ability of spt15-122 to suppress the his4-912delta insertion but did not affect the Spt- phenotype of spt3 or spt10 at this locus. Fourth, spt3, spt8, and spt15-21 alleles (all involved in affecting interaction of SPT3 with TBP) suppressed ccr4 and caf1 defects. Finally, we show that NOT2 and NOT5 can be immunoprecipitated by TBP. NOT5 was subsequently shown to associate with TBP and TAFs and this association was dependent on the integrity of TFIID. These genetic and physical interactions indicate that one role of the CCR4-NOT proteins is to inhibit functional TBP-DNA interactions, perhaps by interacting with and modulating the function of TFIID.

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Selected References

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  1. Arndt K. M., Ricupero S. L., Eisenmann D. M., Winston F. Biochemical and genetic characterization of a yeast TFIID mutant that alters transcription in vivo and DNA binding in vitro. Mol Cell Biol. 1992 May;12(5):2372–2382. doi: 10.1128/mcb.12.5.2372. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Arndt K. M., Wobbe C. R., Ricupero-Hovasse S., Struhl K., Winston F. Equivalent mutations in the two repeats of yeast TATA-binding protein confer distinct TATA recognition specificities. Mol Cell Biol. 1994 Jun;14(6):3719–3728. doi: 10.1128/mcb.14.6.3719. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Auble D. T., Hansen K. E., Mueller C. G., Lane W. S., Thorner J., Hahn S. Mot1, a global repressor of RNA polymerase II transcription, inhibits TBP binding to DNA by an ATP-dependent mechanism. Genes Dev. 1994 Aug 15;8(16):1920–1934. doi: 10.1101/gad.8.16.1920. [DOI] [PubMed] [Google Scholar]
  4. Cade R. M., Errede B. MOT2 encodes a negative regulator of gene expression that affects basal expression of pheromone-responsive genes in Saccharomyces cerevisiae. Mol Cell Biol. 1994 May;14(5):3139–3149. doi: 10.1128/mcb.14.5.3139. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Chen W., Struhl K. Saturation mutagenesis of a yeast his3 "TATA element": genetic evidence for a specific TATA-binding protein. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2691–2695. doi: 10.1073/pnas.85.8.2691. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Chiang Y. C., Komarnitsky P., Chase D., Denis C. L. ADR1 activation domains contact the histone acetyltransferase GCN5 and the core transcriptional factor TFIIB. J Biol Chem. 1996 Dec 13;271(50):32359–32365. doi: 10.1074/jbc.271.50.32359. [DOI] [PubMed] [Google Scholar]
  7. Collart M. A., Struhl K. CDC39, an essential nuclear protein that negatively regulates transcription and differentially affects the constitutive and inducible HIS3 promoters. EMBO J. 1993 Jan;12(1):177–186. doi: 10.1002/j.1460-2075.1993.tb05643.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Collart M. A., Struhl K. NOT1(CDC39), NOT2(CDC36), NOT3, and NOT4 encode a global-negative regulator of transcription that differentially affects TATA-element utilization. Genes Dev. 1994 Mar 1;8(5):525–537. doi: 10.1101/gad.8.5.525. [DOI] [PubMed] [Google Scholar]
  9. Collart M. A. The NOT, SPT3, and MOT1 genes functionally interact to regulate transcription at core promoters. Mol Cell Biol. 1996 Dec;16(12):6668–6676. doi: 10.1128/mcb.16.12.6668. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Denis C. L., Malvar T. The CCR4 gene from Saccharomyces cerevisiae is required for both nonfermentative and spt-mediated gene expression. Genetics. 1990 Feb;124(2):283–291. doi: 10.1093/genetics/124.2.283. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Draper M. P., Liu H. Y., Nelsbach A. H., Mosley S. P., Denis C. L. CCR4 is a glucose-regulated transcription factor whose leucine-rich repeat binds several proteins important for placing CCR4 in its proper promoter context. Mol Cell Biol. 1994 Jul;14(7):4522–4531. doi: 10.1128/mcb.14.7.4522. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Draper M. P., Salvadore C., Denis C. L. Identification of a mouse protein whose homolog in Saccharomyces cerevisiae is a component of the CCR4 transcriptional regulatory complex. Mol Cell Biol. 1995 Jul;15(7):3487–3495. doi: 10.1128/mcb.15.7.3487. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Eisenmann D. M., Arndt K. M., Ricupero S. L., Rooney J. W., Winston F. SPT3 interacts with TFIID to allow normal transcription in Saccharomyces cerevisiae. Genes Dev. 1992 Jul;6(7):1319–1331. doi: 10.1101/gad.6.7.1319. [DOI] [PubMed] [Google Scholar]
  14. Eisenmann D. M., Dollard C., Winston F. SPT15, the gene encoding the yeast TATA binding factor TFIID, is required for normal transcription initiation in vivo. Cell. 1989 Sep 22;58(6):1183–1191. doi: 10.1016/0092-8674(89)90516-3. [DOI] [PubMed] [Google Scholar]
  15. Goppelt A., Meisterernst M. Characterization of the basal inhibitor of class II transcription NC2 from Saccharomyces cerevisiae. Nucleic Acids Res. 1996 Nov 15;24(22):4450–4455. doi: 10.1093/nar/24.22.4450. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Irie K., Yamaguchi K., Kawase K., Matsumoto K. The yeast MOT2 gene encodes a putative zinc finger protein that serves as a global negative regulator affecting expression of several categories of genes, including mating-pheromone-responsive genes. Mol Cell Biol. 1994 May;14(5):3150–3157. doi: 10.1128/mcb.14.5.3150. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Klopotowski T., Wiater A. Synergism of aminotriazole and phosphate on the inhibition of yeast imidazole glycerol phosphate dehydratase. Arch Biochem Biophys. 1965 Dec;112(3):562–566. doi: 10.1016/0003-9861(65)90096-2. [DOI] [PubMed] [Google Scholar]
  18. Komarnitsky P. B., Klebanow E. R., Weil P. A., Denis C. L. ADR1-mediated transcriptional activation requires the presence of an intact TFIID complex. Mol Cell Biol. 1998 Oct;18(10):5861–5867. doi: 10.1128/mcb.18.10.5861. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Lee T. I., Wyrick J. J., Koh S. S., Jennings E. G., Gadbois E. L., Young R. A. Interplay of positive and negative regulators in transcription initiation by RNA polymerase II holoenzyme. Mol Cell Biol. 1998 Aug;18(8):4455–4462. doi: 10.1128/mcb.18.8.4455. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Liu H. Y., Badarinarayana V., Audino D. C., Rappsilber J., Mann M., Denis C. L. The NOT proteins are part of the CCR4 transcriptional complex and affect gene expression both positively and negatively. EMBO J. 1998 Feb 16;17(4):1096–1106. doi: 10.1093/emboj/17.4.1096. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Liu H. Y., Toyn J. H., Chiang Y. C., Draper M. P., Johnston L. H., Denis C. L. DBF2, a cell cycle-regulated protein kinase, is physically and functionally associated with the CCR4 transcriptional regulatory complex. EMBO J. 1997 Sep 1;16(17):5289–5298. doi: 10.1093/emboj/16.17.5289. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Madison J. M., Winston F. Evidence that Spt3 functionally interacts with Mot1, TFIIA, and TATA-binding protein to confer promoter-specific transcriptional control in Saccharomyces cerevisiae. Mol Cell Biol. 1997 Jan;17(1):287–295. doi: 10.1128/mcb.17.1.287. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Mahadevan S., Struhl K. Tc, an unusual promoter element required for constitutive transcription of the yeast HIS3 gene. Mol Cell Biol. 1990 Sep;10(9):4447–4455. doi: 10.1128/mcb.10.9.4447. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Maldonado E., Hampsey M., Reinberg D. Repression: targeting the heart of the matter. Cell. 1999 Nov 24;99(5):455–458. doi: 10.1016/s0092-8674(00)81533-0. [DOI] [PubMed] [Google Scholar]
  25. Malvar T., Biron R. W., Kaback D. B., Denis C. L. The CCR4 protein from Saccharomyces cerevisiae contains a leucine-rich repeat region which is required for its control of ADH2 gene expression. Genetics. 1992 Dec;132(4):951–962. doi: 10.1093/genetics/132.4.951. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. McKenzie E. A., Kent N. A., Dowell S. J., Moreno F., Bird L. E., Mellor J. The centromere and promoter factor, 1, CPF1, of Saccharomyces cerevisiae modulates gene activity through a family of factors including SPT21, RPD1 (SIN3), RPD3 and CCR4. Mol Gen Genet. 1993 Sep;240(3):374–386. doi: 10.1007/BF00280389. [DOI] [PubMed] [Google Scholar]
  27. Moqtaderi Z., Bai Y., Poon D., Weil P. A., Struhl K. TBP-associated factors are not generally required for transcriptional activation in yeast. Nature. 1996 Sep 12;383(6596):188–191. doi: 10.1038/383188a0. [DOI] [PubMed] [Google Scholar]
  28. Ranallo R. T., Struhl K., Stargell L. A. A TATA-binding protein mutant defective for TFIID complex formation in vivo. Mol Cell Biol. 1999 Jun;19(6):3951–3957. doi: 10.1128/mcb.19.6.3951. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Sakai A., Chibazakura T., Shimizu Y., Hishinuma F. Molecular analysis of POP2 gene, a gene required for glucose-derepression of gene expression in Saccharomyces cerevisiae. Nucleic Acids Res. 1992 Dec 11;20(23):6227–6233. doi: 10.1093/nar/20.23.6227. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Schild D. Suppression of a new allele of the yeast RAD52 gene by overexpression of RAD51, mutations in srs2 and ccr4, or mating-type heterozygosity. Genetics. 1995 May;140(1):115–127. doi: 10.1093/genetics/140.1.115. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Struhl K., Davis R. W. Production of a functional eukaryotic enzyme in Escherichia coli: cloning and expression of the yeast structural gene for imidazole-glycerolphosphate dehydratase (his3). Proc Natl Acad Sci U S A. 1977 Dec;74(12):5255–5259. doi: 10.1073/pnas.74.12.5255. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Tabtiang R. K., Herskowitz I. Nuclear proteins Nut1p and Nut2p cooperate to negatively regulate a Swi4p-dependent lacZ reporter gene in Saccharomyces cerevisiae. Mol Cell Biol. 1998 Aug;18(8):4707–4718. doi: 10.1128/mcb.18.8.4707. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. 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]
  34. de Barros Lopes M., Ho J. Y., Reed S. I. Mutations in cell division cycle genes CDC36 and CDC39 activate the Saccharomyces cerevisiae mating pheromone response pathway. Mol Cell Biol. 1990 Jun;10(6):2966–2972. doi: 10.1128/mcb.10.6.2966. [DOI] [PMC free article] [PubMed] [Google Scholar]

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