Skip to main content
NCBI home page
The EMBO Journal logoLink to The EMBO Journal
. 1995 Aug 15;14(16):4022–4030. doi: 10.1002/j.1460-2075.1995.tb00073.x

Identification of the cis-elements mediating the autogenous control of ribosomal protein L2 mRNA stability in yeast.

C Presutti 1, T Villa 1, D Hall 1, C Pertica 1, I Bozzoni 1
PMCID: PMC394480  PMID: 7664741

Abstract

The ribosomal protein L2 (rpL2) of Saccharomyces cerevisiae regulates the accumulation of its own mRNA by a feedback mechanism. An RNA sequence is responsible for this control, initially characterized as a 360 nucleotide-long region, localized at the 5' end of the transcript. This region, fused to an unrelated coding sequence, is able to down-regulate the accumulation of the chimeric transcript when increased levels of rpL2 are induced in the cell. The target regulatory region also responds to regulation when inserted inside an intron, demonstrating that the control process can take place inside the nucleus. Deletion analysis from the 5' and 3' borders have restricted the responsive region to approximately 200 nt. The insertion of a poly-G cassette downstream of the regulatory region allowed the identification of truncated 3' cut-off poly(A)+ RNA molecules. The parallel identification of cut-off molecules containing the 5' portion of the transcript allowed us to deduce that the truncated products originate by endonucleolytic cleavage. Altogether, these results are consistent with a mechanism by which the presence of excess amounts of rpL2 in the cell triggers its own mRNA to a degradative pathway; this involves an initial endonucleolytic cleavage that is followed by exonucleolytic trimming. Such a regulatory mechanism shows interesting analogies with the translational regulation of r-proteins in Escherichia coli.

Full text

PDF
4022

Images in this article

4023Image
on p.4023
4024Image
on p.4024
4025Image
on p.4025
4026Image
on p.4026
4028Image
on p.4028

Selected References

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

  1. Binder R., Horowitz J. A., Basilion J. P., Koeller D. M., Klausner R. D., Harford J. B. Evidence that the pathway of transferrin receptor mRNA degradation involves an endonucleolytic cleavage within the 3' UTR and does not involve poly(A) tail shortening. EMBO J. 1994 Apr 15;13(8):1969–1980. doi: 10.1002/j.1460-2075.1994.tb06466.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Binder R., Hwang S. P., Ratnasabapathy R., Williams D. L. Degradation of apolipoprotein II mRNA occurs via endonucleolytic cleavage at 5'-AAU-3'/5'-UAA-3' elements in single-stranded loop domains of the 3'-noncoding region. J Biol Chem. 1989 Oct 5;264(28):16910–16918. [PubMed] [Google Scholar]
  3. Caffarelli E., Fragapane P., Gehring C., Bozzoni I. The accumulation of mature RNA for the Xenopus laevis ribosomal protein L1 is controlled at the level of splicing and turnover of the precursor RNA. EMBO J. 1987 Nov;6(11):3493–3498. doi: 10.1002/j.1460-2075.1987.tb02674.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Capieaux E., Vignais M. L., Sentenac A., Goffeau A. The yeast H+-ATPase gene is controlled by the promoter binding factor TUF. J Biol Chem. 1989 May 5;264(13):7437–7446. [PubMed] [Google Scholar]
  5. Chang D. D., Sharp P. A. Regulation by HIV Rev depends upon recognition of splice sites. Cell. 1989 Dec 1;59(5):789–795. doi: 10.1016/0092-8674(89)90602-8. [DOI] [PubMed] [Google Scholar]
  6. Cole J. R., Nomura M. Changes in the half-life of ribosomal protein messenger RNA caused by translational repression. J Mol Biol. 1986 Apr 5;188(3):383–392. doi: 10.1016/0022-2836(86)90162-2. [DOI] [PubMed] [Google Scholar]
  7. Dabeva M. D., Post-Beittenmiller M. A., Warner J. R. Autogenous regulation of splicing of the transcript of a yeast ribosomal protein gene. Proc Natl Acad Sci U S A. 1986 Aug;83(16):5854–5857. doi: 10.1073/pnas.83.16.5854. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Decker C. J., Parker R. A turnover pathway for both stable and unstable mRNAs in yeast: evidence for a requirement for deadenylation. Genes Dev. 1993 Aug;7(8):1632–1643. doi: 10.1101/gad.7.8.1632. [DOI] [PubMed] [Google Scholar]
  9. 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]
  10. Dorsman J. C., Doorenbosch M. M., Maurer C. T., de Winde J. H., Mager W. H., Planta R. J., Grivell L. A. An ARS/silencer binding factor also activates two ribosomal protein genes in yeast. Nucleic Acids Res. 1989 Jul 11;17(13):4917–4923. doi: 10.1093/nar/17.13.4917. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Dorsman J. C., van Heeswijk W. C., Grivell L. A. Identification of two factors which bind to the upstream sequences of a number of nuclear genes coding for mitochondrial proteins and to genetic elements important for cell division in yeast. Nucleic Acids Res. 1988 Aug 11;16(15):7287–7301. doi: 10.1093/nar/16.15.7287. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Draper D. E. How do proteins recognize specific RNA sites? New clues from autogenously regulated ribosomal proteins. Trends Biochem Sci. 1989 Aug;14(8):335–338. doi: 10.1016/0968-0004(89)90167-9. [DOI] [PubMed] [Google Scholar]
  13. Eng F. J., Warner J. R. Structural basis for the regulation of splicing of a yeast messenger RNA. Cell. 1991 May 31;65(5):797–804. doi: 10.1016/0092-8674(91)90387-e. [DOI] [PubMed] [Google Scholar]
  14. Faye G., Leung D. W., Tatchell K., Hall B. D., Smith M. Deletion mapping of sequences essential for in vivo transcription of the iso-1-cytochrome c gene. Proc Natl Acad Sci U S A. 1981 Apr;78(4):2258–2262. doi: 10.1073/pnas.78.4.2258. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Fragapane P., Caffarelli E., Lener M., Prislei S., Santoro B., Bozzoni I. Identification of the sequences responsible for the splicing phenotype of the regulatory intron of the L1 ribosomal protein gene of Xenopus laevis. Mol Cell Biol. 1992 Mar;12(3):1117–1125. doi: 10.1128/mcb.12.3.1117. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Gritz L., Abovich N., Teem J. L., Rosbash M. Posttranscriptional regulation and assembly into ribosomes of a Saccharomyces cerevisiae ribosomal protein-beta-galactosidase fusion. Mol Cell Biol. 1985 Dec;5(12):3436–3442. doi: 10.1128/mcb.5.12.3436. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Huet J., Cottrelle P., Cool M., Vignais M. L., Thiele D., Marck C., Buhler J. M., Sentenac A., Fromageot P. A general upstream binding factor for genes of the yeast translational apparatus. EMBO J. 1985 Dec 16;4(13A):3539–3547. doi: 10.1002/j.1460-2075.1985.tb04114.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Ito H., Fukuda Y., Murata K., Kimura A. Transformation of intact yeast cells treated with alkali cations. J Bacteriol. 1983 Jan;153(1):163–168. doi: 10.1128/jb.153.1.163-168.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Kearney K. R., Nomura M. Secondary structure of the autoregulatory mRNA binding site of ribosomal protein L1. Mol Gen Genet. 1987 Nov;210(1):60–68. doi: 10.1007/BF00337759. [DOI] [PubMed] [Google Scholar]
  20. Legrain P., Rosbash M. Some cis- and trans-acting mutants for splicing target pre-mRNA to the cytoplasm. Cell. 1989 May 19;57(4):573–583. doi: 10.1016/0092-8674(89)90127-x. [DOI] [PubMed] [Google Scholar]
  21. Lucioli A., Presutti C., Ciafrè S., Caffarelli E., Fragapane P., Bozzoni I. Gene dosage alteration of L2 ribosomal protein genes in Saccharomyces cerevisiae: effects on ribosome synthesis. Mol Cell Biol. 1988 Nov;8(11):4792–4798. doi: 10.1128/mcb.8.11.4792. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Mattheakis L. C., Nomura M. Feedback regulation of the spc operon in Escherichia coli: translational coupling and mRNA processing. J Bacteriol. 1988 Oct;170(10):4484–4492. doi: 10.1128/jb.170.10.4484-4492.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Mattheakis L., Vu L., Sor F., Nomura M. Retroregulation of the synthesis of ribosomal proteins L14 and L24 by feedback repressor S8 in Escherichia coli. Proc Natl Acad Sci U S A. 1989 Jan;86(2):448–452. doi: 10.1073/pnas.86.2.448. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Mattox W., Ryner L., Baker B. S. Autoregulation and multifunctionality among trans-acting factors that regulate alternative pre-mRNA processing. J Biol Chem. 1992 Sep 25;267(27):19023–19026. [PubMed] [Google Scholar]
  25. Muhlrad D., Decker C. J., Parker R. Deadenylation of the unstable mRNA encoded by the yeast MFA2 gene leads to decapping followed by 5'-->3' digestion of the transcript. Genes Dev. 1994 Apr 1;8(7):855–866. doi: 10.1101/gad.8.7.855. [DOI] [PubMed] [Google Scholar]
  26. 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]
  27. Nomura M., Gourse R., Baughman G. Regulation of the synthesis of ribosomes and ribosomal components. Annu Rev Biochem. 1984;53:75–117. doi: 10.1146/annurev.bi.53.070184.000451. [DOI] [PubMed] [Google Scholar]
  28. Peppel K., Baglioni C. Deadenylation and turnover of interferon-beta mRNA. J Biol Chem. 1991 Apr 15;266(11):6663–6666. [PubMed] [Google Scholar]
  29. Peterson M. L., Perry R. P. The regulated production of mu m and mu s mRNA is dependent on the relative efficiencies of mu s poly(A) site usage and the c mu 4-to-M1 splice. Mol Cell Biol. 1989 Feb;9(2):726–738. doi: 10.1128/mcb.9.2.726. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Philippe C., Portier C., Mougel M., Grunberg-Manago M., Ebel J. P., Ehresmann B., Ehresmann C. Target site of Escherichia coli ribosomal protein S15 on its messenger RNA. Conformation and interaction with the protein. J Mol Biol. 1990 Jan 20;211(2):415–426. doi: 10.1016/0022-2836(90)90362-P. [DOI] [PubMed] [Google Scholar]
  31. 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]
  32. Presutti C., Ciafré S. A., Bozzoni I. The ribosomal protein L2 in S. cerevisiae controls the level of accumulation of its own mRNA. EMBO J. 1991 Aug;10(8):2215–2221. doi: 10.1002/j.1460-2075.1991.tb07757.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Presutti C., Lucioli A., Bozzoni I. Ribosomal protein L2 in Saccharomyces cerevisiae is homologous to ribosomal protein L1 in Xenopus laevis. Isolation and characterization of the genes. J Biol Chem. 1988 May 5;263(13):6188–6192. [PubMed] [Google Scholar]
  34. Presutti C., Villa T., Bozzoni I. The primary sequence of the Schizosaccharomyces pombe protein homologous to S.cerevisiae ribosomal protein L2. Nucleic Acids Res. 1993 Aug 11;21(16):3900–3900. doi: 10.1093/nar/21.16.3900. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. 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]
  36. Shyu A. B., Belasco J. G., Greenberg M. E. Two distinct destabilizing elements in the c-fos message trigger deadenylation as a first step in rapid mRNA decay. Genes Dev. 1991 Feb;5(2):221–231. doi: 10.1101/gad.5.2.221. [DOI] [PubMed] [Google Scholar]
  37. Stotz A., Linder P. The ADE2 gene from Saccharomyces cerevisiae: sequence and new vectors. Gene. 1990 Oct 30;95(1):91–98. doi: 10.1016/0378-1119(90)90418-q. [DOI] [PubMed] [Google Scholar]
  38. Stutz F., Rosbash M. A functional interaction between Rev and yeast pre-mRNA is related to splicing complex formation. EMBO J. 1994 Sep 1;13(17):4096–4104. doi: 10.1002/j.1460-2075.1994.tb06727.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Séraphin B., Kretzner L., Rosbash M. A U1 snRNA:pre-mRNA base pairing interaction is required early in yeast spliceosome assembly but does not uniquely define the 5' cleavage site. EMBO J. 1988 Aug;7(8):2533–2538. doi: 10.1002/j.1460-2075.1988.tb03101.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Teem J. L., Rosbash M. Expression of a beta-galactosidase gene containing the ribosomal protein 51 intron is sensitive to the rna2 mutation of yeast. Proc Natl Acad Sci U S A. 1983 Jul;80(14):4403–4407. doi: 10.1073/pnas.80.14.4403. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Tsay Y. F., Thompson J. R., Rotenberg M. O., Larkin J. C., Woolford J. L., Jr Ribosomal protein synthesis is not regulated at the translational level in Saccharomyces cerevisiae: balanced accumulation of ribosomal proteins L16 and rp59 is mediated by turnover of excess protein. Genes Dev. 1988 Jun;2(6):664–676. doi: 10.1101/gad.2.6.664. [DOI] [PubMed] [Google Scholar]
  42. Vilardell J., Warner J. R. Regulation of splicing at an intermediate step in the formation of the spliceosome. Genes Dev. 1994 Jan;8(2):211–220. doi: 10.1101/gad.8.2.211. [DOI] [PubMed] [Google Scholar]
  43. Vreken P., Raué H. A. The rate-limiting step in yeast PGK1 mRNA degradation is an endonucleolytic cleavage in the 3'-terminal part of the coding region. Mol Cell Biol. 1992 Jul;12(7):2986–2996. doi: 10.1128/mcb.12.7.2986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Warner J. R., Mitra G., Schwindinger W. F., Studeny M., Fried H. M. Saccharomyces cerevisiae coordinates accumulation of yeast ribosomal proteins by modulating mRNA splicing, translational initiation, and protein turnover. Mol Cell Biol. 1985 Jun;5(6):1512–1521. doi: 10.1128/mcb.5.6.1512. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Wilson T., Treisman R. Removal of poly(A) and consequent degradation of c-fos mRNA facilitated by 3' AU-rich sequences. Nature. 1988 Nov 24;336(6197):396–399. doi: 10.1038/336396a0. [DOI] [PubMed] [Google Scholar]

Articles from The EMBO Journal are provided here courtesy of Nature Publishing Group

RESOURCES