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. 1996 Nov 15;24(22):4543–4551. doi: 10.1093/nar/24.22.4543

Similar upstream regulatory elements of genes that encode the two largest subunits of RNA polymerase II in Saccharomyces cerevisiae.

D B Jansma 1, J Archambault 1, O Mostachfi 1, J D Friesen 1
PMCID: PMC146278  PMID: 8948647

Abstract

We have determined the location of cis-acting elements that are important for the expression of RPO21 and RPO22, genes that encode the two largest subunits of RNA polymerase II (RNAPII) in Saccharomyces cerevisiae. A series of 5'-end deletions and nucleotide substitutions in the upstream regions of RPO21 and RPO22 were tested for their effect on the expression of lacZ fusions of these genes. Deletion of sequences from -723 to -693 in RPO21, which disrupted two Reb1p-binding sites and an Abf1p-binding site, resulted in a 10-fold decrease in expression. A T-rich region downstream of these sites was also important for expression. Deletion of sequences from -437 to -392 in the RPO22-upstream, which resulted in a 30-fold decrease in expression, indicated that the Reb1p- and Abf1p-binding sites in this region were important for RPO22 expression, as was a T-rich sequence immediately downstream of these sites. The RPO21 and RPO22 upstream regions were capable of interacting in vitro (gel-mobility-shift assays) with Reb1p and Abf1p. The similarities in the type and organization of elements in the upstream regions of RPO21 and RPO22 suggest that expression of these genes may be regulated coordinately.

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Selected References

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  1. Adman R., Schultz L. D., Hall B. D. Transcription in yeast: separation and properties of multiple FNA polymerases. Proc Natl Acad Sci U S A. 1972 Jul;69(7):1702–1706. doi: 10.1073/pnas.69.7.1702. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Allison L. A., Moyle M., Shales M., Ingles C. J. Extensive homology among the largest subunits of eukaryotic and prokaryotic RNA polymerases. Cell. 1985 Sep;42(2):599–610. doi: 10.1016/0092-8674(85)90117-5. [DOI] [PubMed] [Google Scholar]
  3. Archambault J., Friesen J. D. Genetics of eukaryotic RNA polymerases I, II, and III. Microbiol Rev. 1993 Sep;57(3):703–724. doi: 10.1128/mr.57.3.703-724.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Archambault J., Jansma D. B., Friesen J. D. Underproduction of the largest subunit of RNA polymerase II causes temperature sensitivity, slow growth, and inositol auxotrophy in Saccharomyces cerevisiae. Genetics. 1996 Mar;142(3):737–747. doi: 10.1093/genetics/142.3.737. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Barettino D., Feigenbutz M., Valcárcel R., Stunnenberg H. G. Improved method for PCR-mediated site-directed mutagenesis. Nucleic Acids Res. 1994 Feb 11;22(3):541–542. doi: 10.1093/nar/22.3.541. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Brindle P. K., Holland J. P., Willett C. E., Innis M. A., Holland M. J. Multiple factors bind the upstream activation sites of the yeast enolase genes ENO1 and ENO2: ABFI protein, like repressor activator protein RAP1, binds cis-acting sequences which modulate repression or activation of transcription. Mol Cell Biol. 1990 Sep;10(9):4872–4885. doi: 10.1128/mcb.10.9.4872. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Buchman A. R., Kimmerly W. J., Rine J., Kornberg R. D. Two DNA-binding factors recognize specific sequences at silencers, upstream activating sequences, autonomously replicating sequences, and telomeres in Saccharomyces cerevisiae. Mol Cell Biol. 1988 Jan;8(1):210–225. doi: 10.1128/mcb.8.1.210. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Buchman A. R., Kornberg R. D. A yeast ARS-binding protein activates transcription synergistically in combination with other weak activating factors. Mol Cell Biol. 1990 Mar;10(3):887–897. doi: 10.1128/mcb.10.3.887. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Carmen A. A., Holland M. J. The upstream repression sequence from the yeast enolase gene ENO1 is a complex regulatory element that binds multiple trans-acting factors including REB1. J Biol Chem. 1994 Apr 1;269(13):9790–9797. [PubMed] [Google Scholar]
  10. Chambers A., Stanway C., Tsang J. S., Henry Y., Kingsman A. J., Kingsman S. M. ARS binding factor 1 binds adjacent to RAP1 at the UASs of the yeast glycolytic genes PGK and PYK1. Nucleic Acids Res. 1990 Sep 25;18(18):5393–5399. doi: 10.1093/nar/18.18.5393. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Chasman D. I., Lue N. F., Buchman A. R., LaPointe J. W., Lorch Y., Kornberg R. D. A yeast protein that influences the chromatin structure of UASG and functions as a powerful auxiliary gene activator. Genes Dev. 1990 Apr;4(4):503–514. doi: 10.1101/gad.4.4.503. [DOI] [PubMed] [Google Scholar]
  12. Della Seta F., Ciafré S. A., Marck C., Santoro B., Presutti C., Sentenac A., Bozzoni I. The ABF1 factor is the transcriptional activator of the L2 ribosomal protein genes in Saccharomyces cerevisiae. Mol Cell Biol. 1990 May;10(5):2437–2441. doi: 10.1128/mcb.10.5.2437. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Della Seta F., Treich I., Buhler J. M., Sentenac A. ABF1 binding sites in yeast RNA polymerase genes. J Biol Chem. 1990 Sep 5;265(25):15168–15175. [PubMed] [Google Scholar]
  14. Dorsman J. C., van Heeswijk W. C., Grivell L. A. Yeast general transcription factor GFI: sequence requirements for binding to DNA and evolutionary conservation. Nucleic Acids Res. 1990 May 11;18(9):2769–2776. doi: 10.1093/nar/18.9.2769. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Fedor M. J., Lue N. F., Kornberg R. D. Statistical positioning of nucleosomes by specific protein-binding to an upstream activating sequence in yeast. J Mol Biol. 1988 Nov 5;204(1):109–127. doi: 10.1016/0022-2836(88)90603-1. [DOI] [PubMed] [Google Scholar]
  16. Fried M., Crothers D. M. Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis. Nucleic Acids Res. 1981 Dec 11;9(23):6505–6525. doi: 10.1093/nar/9.23.6505. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Goel A., Pearlman R. E. Transposable element-mediated enhancement of gene expression in Saccharomyces cerevisiae involves sequence-specific binding of a trans-acting factor. Mol Cell Biol. 1988 Jun;8(6):2572–2580. doi: 10.1128/mcb.8.6.2572. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Gonçalves P. M., Griffioen G., Minnee R., Bosma M., Kraakman L. S., Mager W. H., Planta R. J. Transcription activation of yeast ribosomal protein genes requires additional elements apart from binding sites for Abf1p or Rap1p. Nucleic Acids Res. 1995 May 11;23(9):1475–1480. doi: 10.1093/nar/23.9.1475. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Guarente L., Ptashne M. Fusion of Escherichia coli lacZ to the cytochrome c gene of Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1981 Apr;78(4):2199–2203. doi: 10.1073/pnas.78.4.2199. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Halfter H., Müller U., Winnacker E. L., Gallwitz D. Isolation and DNA-binding characteristics of a protein involved in transcription activation of two divergently transcribed, essential yeast genes. EMBO J. 1989 Oct;8(10):3029–3037. doi: 10.1002/j.1460-2075.1989.tb08453.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Hamil K. G., Nam H. G., Fried H. M. Constitutive transcription of yeast ribosomal protein gene TCM1 is promoted by uncommon cis- and trans-acting elements. Mol Cell Biol. 1988 Oct;8(10):4328–4341. doi: 10.1128/mcb.8.10.4328. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Hill J., Donald K. A., Griffiths D. E., Donald G. DMSO-enhanced whole cell yeast transformation. Nucleic Acids Res. 1991 Oct 25;19(20):5791–5791. doi: 10.1093/nar/19.20.5791. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Holland J. P., Brindle P. K., Holland M. J. Sequences within an upstream activation site in the yeast enolase gene ENO2 modulate repression of ENO2 expression in strains carrying a null mutation in the positive regulatory gene GCR1. Mol Cell Biol. 1990 Sep;10(9):4863–4871. doi: 10.1128/mcb.10.9.4863. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Iyer V., Struhl K. Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure. EMBO J. 1995 Jun 1;14(11):2570–2579. doi: 10.1002/j.1460-2075.1995.tb07255.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Johnston M. A model fungal gene regulatory mechanism: the GAL genes of Saccharomyces cerevisiae. Microbiol Rev. 1987 Dec;51(4):458–476. doi: 10.1128/mr.51.4.458-476.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Kimmerly W., Buchman A., Kornberg R., Rine J. Roles of two DNA-binding factors in replication, segregation and transcriptional repression mediated by a yeast silencer. EMBO J. 1988 Jul;7(7):2241–2253. doi: 10.1002/j.1460-2075.1988.tb03064.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Klein C., Struhl K. Protein kinase A mediates growth-regulated expression of yeast ribosomal protein genes by modulating RAP1 transcriptional activity. Mol Cell Biol. 1994 Mar;14(3):1920–1928. doi: 10.1128/mcb.14.3.1920. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Liaw P. C., Brandl C. J. Defining the sequence specificity of the Saccharomyces cerevisiae DNA binding protein REB1p by selecting binding sites from random-sequence oligonucleotides. Yeast. 1994 Jun;10(6):771–787. doi: 10.1002/yea.320100608. [DOI] [PubMed] [Google Scholar]
  29. McBroom L. D., Sadowski P. D. DNA bending by Saccharomyces cerevisiae ABF1 and its proteolytic fragments. J Biol Chem. 1994 Jun 10;269(23):16461–16468. [PubMed] [Google Scholar]
  30. Morrow B. E., Johnson S. P., Warner J. R. Proteins that bind to the yeast rDNA enhancer. J Biol Chem. 1989 May 25;264(15):9061–9068. [PubMed] [Google Scholar]
  31. Morrow B. E., Ju Q., Warner J. R. A bipartite DNA-binding domain in yeast Reb1p. Mol Cell Biol. 1993 Feb;13(2):1173–1182. doi: 10.1128/mcb.13.2.1173. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Neuman-Silberberg F. S., Bhattacharya S., Broach J. R. Nutrient availability and the RAS/cyclic AMP pathway both induce expression of ribosomal protein genes in Saccharomyces cerevisiae but by different mechanisms. Mol Cell Biol. 1995 Jun;15(6):3187–3196. doi: 10.1128/mcb.15.6.3187. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Nonet M., Scafe C., Sexton J., Young R. Eucaryotic RNA polymerase conditional mutant that rapidly ceases mRNA synthesis. Mol Cell Biol. 1987 May;7(5):1602–1611. doi: 10.1128/mcb.7.5.1602. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Planta R. J., Raué H. A. Control of ribosome biogenesis in yeast. Trends Genet. 1988 Mar;4(3):64–68. doi: 10.1016/0168-9525(88)90042-x. [DOI] [PubMed] [Google Scholar]
  35. Rhode P. R., Elsasser S., Campbell J. L. Role of multifunctional autonomously replicating sequence binding factor 1 in the initiation of DNA replication and transcriptional control in Saccharomyces cerevisiae. Mol Cell Biol. 1992 Mar;12(3):1064–1077. doi: 10.1128/mcb.12.3.1064. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. 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]
  37. Shore D. RAP1: a protean regulator in yeast. Trends Genet. 1994 Nov;10(11):408–412. doi: 10.1016/0168-9525(94)90058-2. [DOI] [PubMed] [Google Scholar]
  38. Silve S., Rhode P. R., Coll B., Campbell J., Poyton R. O. ABF1 is a phosphoprotein and plays a role in carbon source control of COX6 transcription in Saccharomyces cerevisiae. Mol Cell Biol. 1992 Sep;12(9):4197–4208. doi: 10.1128/mcb.12.9.4197. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Struhl K. Molecular mechanisms of transcriptional regulation in yeast. Annu Rev Biochem. 1989;58:1051–1077. doi: 10.1146/annurev.bi.58.070189.005155. [DOI] [PubMed] [Google Scholar]
  40. Sweetser D., Nonet M., Young R. A. Prokaryotic and eukaryotic RNA polymerases have homologous core subunits. Proc Natl Acad Sci U S A. 1987 Mar;84(5):1192–1196. doi: 10.1073/pnas.84.5.1192. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. 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]
  42. Workman J. L., Buchman A. R. Multiple functions of nucleosomes and regulatory factors in transcription. Trends Biochem Sci. 1993 Mar;18(3):90–95. doi: 10.1016/0968-0004(93)90160-o. [DOI] [PubMed] [Google Scholar]
  43. Young R. A. RNA polymerase II. Annu Rev Biochem. 1991;60:689–715. doi: 10.1146/annurev.bi.60.070191.003353. [DOI] [PubMed] [Google Scholar]
  44. Yura T., Ishihama A. Genetics of bacterial RNA polymerases. Annu Rev Genet. 1979;13:59–97. doi: 10.1146/annurev.ge.13.120179.000423. [DOI] [PubMed] [Google Scholar]

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