The Rate-Limiting Step in Yeast PGK1 mRNA Degradation Is an Endonucleolytic Cleavage in the 3′-Terminal Part of the Coding Region

References

• Atwater, J. Α., R. Wisdom, and I. M. Verma. 1990. Regulated mRNA stability. Annu. Rev. Genet. 24:519–541.
   PubMed Web of Science ®Google Scholar
• Barker, G. F., and K. Beemon. 1991. Nonsense codons within the Rous sarcoma virus gag gene decrease the stability of unspliced viral RNA. Mol. Cell. Biol. 11:2760–2768.
   PubMedGoogle Scholar
• Baserga, S. J., and E. J. Benz, Jr. 1988. Nonsense mutations in the human β-globin gene affect mRNA metabolism. Proc. Natl. Acad. Sci. USA 85:2056–2060.
   PubMed Web of Science ®Google Scholar
• Belasco, J. G., and C. F. Higgins. 1988. Mechanisms of mRNA decay in bacteria: a perspective. Gene 72:15–23.
   PubMed Web of Science ®Google Scholar
• Bernstein, P., S. W. Peltz, and J. Ross. 1989. The poly(A)-poly(A)-binding protein complex is a major determinant of mRNA stability in vitro. Mol. Cell. Biol. 9:659–670.
   PubMed Web of Science ®Google Scholar
• Binder, R., S.-P. L. Hwang, R. Ratnasabapathy, and D. L. Williams. 1989. Degradation of apolipoprotein II mRNA occurs via endonucleolytic cleavage at 5′-AAU-375′-UAA-3′ elements in single-stranded loop domains of the 3′-noncoding region. J. Biol. Chem. 264:16910–16918.
   PubMed Web of Science ®Google Scholar
• Bohjanen, P. R., B. Petryniak, C. H. June, C. B. Thompson, and T. Lindsten. 1991. An inducible cytoplasmic factor (AU-B) binds selectively to AUUUA multimers in the 3′ untranslated region of lymphokine messenger RNA. Mol. Cell. Biol. 11:3288–3295.
   PubMed Web of Science ®Google Scholar
• Bouvet, P., J. Paris, M. Philippe, and Η. Β. Osborne. 1991. Degradation of a developmentally regulated mRNA in Xenopus embryos is controlled by the 3′ region and requires the translation of another maternal mRNA. Mol. Cell. Biol. 11:3115–3124.
   PubMedGoogle Scholar
• Brawerman, G. 1989. mRNA decay: finding the right targets. Cell 57:9–10.
   PubMed Web of Science ®Google Scholar
• Brewer, G. 1991. An A+U-rich element RNA-binding factor regulates c-myc messenger RNA stability in vitro. Mol. Cell. Biol. 11:2460–2466.
   PubMed Web of Science ®Google Scholar
• Brewer, G., and J. Ross. 1989. Regulation of c-myc mRNA stability in vitro by a labile destabilizer with an essential nucleic acid component. Mol. Cell. Biol. 9:1996–2006.
   PubMed Web of Science ®Google Scholar
• Brown, A. J. P. 1989. Messenger RNA stability in yeast. Yeast 5:239–257.
   PubMedGoogle Scholar
• Caput, D., B. Beutler, K. Hartog, R. Thayer, S. Brown-Shimmer, and A. Cerami. 1986. Identification of a common nucleotide sequence in the 3′-untranslated region of mRNA molecules specifying inflammatory mediators. Proc. Natl. Acad. Sci. USA 83:1670–1674.
   PubMed Web of Science ®Google Scholar
• Casey, J. L., D. M. Koeller, V. C. Ramin, R. D. Klausner, and J. B. Harford. 1989. Iron regulation of transferrin receptor mRNA requires iron-responsive elements and a rapid turnover determinant in the 3′ untranslated region of the mRNA. EMBO J. 8:3693–3699.
   PubMed Web of Science ®Google Scholar
• Gay, D. Α., S. S. Sisodia, and D. W. Cleveland. 1989. Autoregulatory control of β-tubulin mRNA stability is linked to translation elongation. Proc. Natl. Acad. Sci. USA 86:5763–5767.
   PubMedGoogle Scholar
• Gozalbo, D., and S. Hohmann. 1990. Nonsense suppressors partially revert the decrease of the mRNA level of a nonsense mutant allele in yeast. Curr. Genet. 17:77–79.
   PubMedGoogle Scholar
• Graves, R. Α., Ν. Β. Pandey, Ν. Chodchoy, and W. F. Marzluff. 1987. Translation is required for histone mRNA degradation. Cell 48:615–626.
   PubMed Web of Science ®Google Scholar
• Henderson, E. R., C. C. Hardin, S. K. Walk, I. Tinoco, Jr., and Ε. Η. Blackburn. 1987. Telomeric DNA oligonucleotides form novel intramolecular structures containing guanine-guanine base pairs. Cell 51:899–908.
   PubMed Web of Science ®Google Scholar
• Herrick, D., R. Parker, and A. Jacobson. 1990. Identification of stable and unstable mRNAs in Saccharomyces cerevisiae. Mol. Cell. Biol. 10:2269–2284.
   PubMed Web of Science ®Google Scholar
• Hitzeman, R. Α., F. E. Hagie, J. S. Hayflick, C. Y. Chen, P. H. Seeburg, and R. Derynck. 1982. The primary structure of the Saccharomyces cerevisiae gene for 3-phosphoglycerate kinase. Nucleic Acids Res. 10:7791–7808.
   PubMed Web of Science ®Google Scholar
• Hoekema, Α., R. A. Kastelein, M. Vasser, and H. A. de Boer. 1987. Codon replacement in the PGK1 gene of Saccharomyces cerevisiae: experimental approach to study the role of biased codon usage in gene expression. Mol. Cell. Biol. 7:2914–2924.
   PubMed Web of Science ®Google Scholar
• Hwang, S.-P. L., M. Eisenberg, R. Binder, G. S. Shelness, and D. L. Williams. 1989. Predicted structures of apolipoprotein II mRNA constrained by nuclease and dimethyl sulfate reactivity: stable secondary structures occur predominantly in local domains via intraexonic base pairing. J. Biol. Chem. 264:8410–8418.
   PubMedGoogle Scholar
• Iwai, Y., M. Bickel, D. H. Pluznik, and R. B. Cohen. 1991. Identification of sequences within the murine granulocyte-macrophage colony-stimulating factor messenger RNA 3′-untranslated region that mediate messenger RNA stabilization induced by mitogen treatment of EL-4 thymoma cells. J. Biol. Chem. 266:17959–17965.
   PubMed Web of Science ®Google Scholar
• Jack, H.-M., J. Berg, and M. Wabl. 1989. Translation affects immunoglobulin mRNA stability. Eur. J. Immunol. 19:843–847.
   PubMedGoogle Scholar
• Jones, E. 1976. Proteinase mutants of Saccharomyces cerevisiae. Genetics 85:23–33.
   Google Scholar
• Kabnick, K. S., and D. E. Housman. 1988. Determinants that contribute to cytoplasmic stability of human c-fos and β-globin mRNAs are located at several sites in each mRNA. Mol. Cell. Biol. 8:3244–3250.
   PubMed Web of Science ®Google Scholar
• Kennedy, I. M., J. K. Haddow, and J. B. Clements. 1991. A negative regulatory element in the human papillomavirus type 16 genome acts at the level of late mRNA stability. J. Virol. 65:2093–2097.
   PubMed Web of Science ®Google Scholar
• Koeller, D. M., J. L. Casey, M. W. Hentze, Ε. Μ. Gerhardt, L.-N. L. Chan, R. D. Klausner, and J. B. Harford. 1989. A cytosolic protein binds to structural elements within the iron regulatory region of the transferrin receptor mRNA. Proc. Natl. Acad. Sci. USA 86:3574–3578.
   PubMed Web of Science ®Google Scholar
• Laird-Offringa, Ι. Α., C. L. de Wit, P. Elfferich, and A. J. van der Eb. 1990. Poly(A)-tail shortening is the translation-dependent step in c-myc mRNA degradation. Mol. Cell. Biol. 10:6132–6140.
   PubMedGoogle Scholar
• Lee, S. V., Y. Nakao, and R. M. Bock. 1968. The nucleases of yeast. II. Purification, properties and specificity of an endonuclease from yeast. Biochim. Biophys. Acta 151:126–136.
   PubMedGoogle Scholar
• Leer, R. J., M. M. C. Van Ramsdonk-Duin, M. J. M. Hagendoorn, W. H. Mager, and R. J. Planta. 1984. Structural comparison of yeast ribosomal protein genes. Nucleic Acids Res. 12:6685–6700.
   PubMedGoogle Scholar
• Losson, R., and F. Lacroute. 1979. Interference of nonsense mutations with eukaryotic messenger RNA stability. Proc. Natl. Acad. Sci. USA 76:5134–5137.
   PubMed Web of Science ®Google Scholar
• Matter, J. S. 1989. Identification of an AUUUA-specific messenger RNA binding protein. Science 246:664–666.
   PubMedGoogle Scholar
• Maniatis, T., E. F. Fritsch, and J. Sambrook. 1982. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
   Google Scholar
• Marzluff, W. F., and Ν. Β. Pandey. 1988. Multiple regulatory steps control histone mRNA concentrations. Trends Biochem. Sci. 13:49–52.
   PubMed Web of Science ®Google Scholar
• Mead, D. J., and S. G. Oliver. 1983. Purification and properties of a double-stranded ribonuclease from the yeast Saccharomyces cerevisiae. Eur. J. Biochem. 137:501–507.
   PubMedGoogle Scholar
• Minvielle-Sebastia, L., B. Winsor, N. Bonneaud, and F. Lacroute. 1991. Mutations in the yeast RNA14 and RNA15 genes result in an abnormal messenger RNA decay rate: sequence analysis reveals an RNA-binding domain in the RNA15 protein. Mol. Cell. Biol. 11:3075–3087.
   PubMedGoogle Scholar
• Müllner, E. W., and L. C. Kühn. 1988. A stem-loop in the 3′ untranslated region mediates iron-dependent regulation of transferrin receptor mRNA stability in the cytoplasm. Cell 53:815–825.
   PubMed Web of Science ®Google Scholar
• Müllner, E. W., B. Neupert, and L. C. Kuhn. 1989. A specific mRNA binding factor regulates the iron-dependent stability of cytoplasmic transferrin receptor mRNA. Cell 58:373–382.
   PubMed Web of Science ®Google Scholar
• Munroe, D., and A. Jacobson. 1990. Tales of poly(A): a review. Gene 91:151–158.
   PubMedGoogle Scholar
• Nonet, M., C. Scafe, J. Sexton, and R. Young. 1987. Eukaryotic RNA polymerase conditional mutant that rapidly ceases mRNA synthesis. Mol. Cell. Biol. 7:1602–1611.
   PubMedGoogle Scholar
• Pandey, N. B., and W. F. Marzluff. 1987. The stem-loop structure at the 3′-end of histone mRNA is necessary and sufficient for regulation of histone mRNA stability. Mol. Cell. Biol. 7:4557–4559.
   PubMed Web of Science ®Google Scholar
• Parker, R., and A. Jacobson. 1990. Translation and a 42-nucleotide segment within the coding region of the mRNA encoded by the MATa1 gene are involved in promoting rapid mRNA decay in yeast. Proc. Natl. Acad. Sci. USA 87:2780–2784.
   PubMed Web of Science ®Google Scholar
• Pelsy, F., and F. Lacroute. 1984. Effect of ochre nonsense mutations on yeast URA1 stability. Curr. Genet. 8:277–282.
   PubMedGoogle Scholar
• Peltz, S. W., and J. Ross. 1987. Autogenous regulation of histone mRNA decay by histone proteins in a cell free system. Mol. Cell. Biol. 7:4345–4356.
   PubMedGoogle Scholar
• Peppel, K., J. M. Vinci, and C. Baglioni. 1991. The AU-rich sequences in the 3′ untranslated region mediate the increased turnover of interferon mRNA induced by glucocorticoids. J. Exp. Med. 173:349–355.
   PubMed Web of Science ®Google Scholar
• Petersen, D. D., S. R. Koch, and D. K. Granner. 1989. 3′ Noncoding region of phosphoenolpyruvate carboxykinase mRNA contains a glucocorticoid-responsive mRNA-stabilizing element. Proc. Natl. Acad. Sci. USA 86:7800–7804.
   PubMedGoogle Scholar
• Ross, J. 1989. The turnover of messenger RNA. Sci. Am. 260:28–35.
   Google Scholar
• Shaw, G., and R. Kamen. 1986. A conserved AU sequence from the 3′-untranslated region of GM-CSF mRNA mediates selective mRNA degradation. Cell 46:659–667.
   PubMed Web of Science ®Google Scholar
• Shyu, A.-B., J. G. Belasco, and Μ. Ε. Greenberg. 1991. Two distinct destabilizing elements in the c-fos message trigger deadenylation as a first step in rapid mRNA decay. Genes Dev. 5:221–231.
   PubMed Web of Science ®Google Scholar
• Soloway, P. D., and T. Shenk. 1990. The adenovirus type 5 I-leader open reading frame functions in cis to reduce the half-life of L1 mRNAs. J. Virol. 64:551–558.
   PubMedGoogle Scholar
• Stevens, A. 1980. Purification and characterization of a Saccharomyces cerevisiae exoribonuclease which yields 5′-mononucleotides by a 5′→3′ mode of hydrolysis. J. Biol. Chem. 255:3080–3085.
   PubMed Web of Science ®Google Scholar
• Stevens, A. 1985. Pyrimidine-specific cleavage by an endoribonuclease of Saccharomyces cerevisiae. J. Bacteriol. 164:57–62.
   PubMedGoogle Scholar
• Stevens, A. 1986. Novel specificity of an endoribonuclease of yeast. FEBS Lett. 205:210–214.
   PubMedGoogle Scholar
• Stevens, Α., and Μ. Κ. Maupin. 1987. A 5′→3′ exoribonuclease of Saccharomyces cerevisiae: size and novel substrate specificity. Arch. Biochem. Biophys. 252:339–347.
   PubMedGoogle Scholar
• Stoeckle, M. Y., and H. Hanafusa. 1989. Processing of 9E3 mRNA and regulation of its stability in normal and Rous sarcoma virus-transformed cells. Mol. Cell. Biol. 9:4738–4745.
   PubMedGoogle Scholar
• Theil, E. C. 1990. Regulation of ferritin and transferrin receptor mRNAs. J. Biol. Chem. 265:4771–4774.
   PubMed Web of Science ®Google Scholar
• Vakalopoulou, E., J. Schaack, and T. Shenk. 1991. A 32-kilodalton protein binds to AU-rich domains in the 3′ untranslated regions of rapidly degraded mRNAs. Mol. Cell. Biol. 11:3355–3364.
   PubMed Web of Science ®Google Scholar
• Van den Heuvel, J. J., R. J. M. Bergkamp, R. J. Planta, and H. A. Raue. 1989. Effect of deletions in the 5′-noncoding region on the translational efficiency of phosphoglycerate kinase mRNA in yeast. Gene 79:83–95.
   PubMed Web of Science ®Google Scholar
• Van den Heuvel, J. J., R. J. Planta, and H. A. Raue. 1990. Effect of leader primary structure on the translational efficiency of phosphoglycerate kinase mRNA in yeast. Yeast 6:473–482.
   PubMedGoogle Scholar
• Vreken, P., N. Buddelmeijer, and H. A. Raue. Nucleic Acids Res., in press.
   Google Scholar
• Vreken, P., R. van der Veen, V. C. H. F. de Regt, A. L. de Maat, R. J. Planta, and H. A. Raue. 1991. Turnover rate of yeast PGK mRNA can be changed by specific alterations in its trailer structure. Biochimie 73:729–737.
   PubMedGoogle Scholar
• Williamson, J. R., M. K. Raghuraman, and T. R. Cech. 1989. Monovalent cation-induced structure of telomeric DNA: the G-quartet model. Cell 59:871–880.
   PubMed Web of Science ®Google Scholar
• Wisdom, R., and W. Lee. 1991. The protein-coding region of c-myc mRNA contains a sequence that specifies rapid mRNA turnover and induction by protein synthesis inhibitors. Genes Dev. 5:232–243.
   PubMed Web of Science ®Google Scholar
• Xu, H. X., L. Johnson, and M. Grunstein. 1990. Coding and noncoding sequences at the 3′ end of yeast histone H2B mRNA confer cell cycle regulation. Mol. Cell. Biol. 10:2687–2694.
   PubMed Web of Science ®Google Scholar
• Yen, T. J., D. A. Gay, J. S. Pachter, and D. W. Cleveland. 1988. Autoregulated changes in stability of polyribosome-bound β-tubulin mRNAs are specified by the first 13 translated nucleotides. Mol. Cell. Biol. 8:1224–1235.
   PubMed Web of Science ®Google Scholar
• Yen, T. J., P. S. Machlin, and D. W. Cleveland. 1988. Autoregulated instability of β-tubulin mRNAs by recognition of the nascent amino terminus of β-tubulin. Nature (London) 334:580–585.
   PubMed Web of Science ®Google Scholar
• Zimmerman, S. B., G. H. Cohen, and D. R. Davies. 1975. X-ray fiber diffraction and model-building study of polyguanylic acid and polyinosinic acid. J. Mol. Biol. 92:181–192.
   PubMed Web of Science ®Google Scholar
• Zitomer, R. S., D. L. Montgomery, D. L. Nichols, and B. D. Hall. 1979. Transcriptional regulation of the yeast cytochrome c gene. Proc. Natl. Acad. Sci. USA 76:3627–3631.
   PubMed Web of Science ®Google Scholar
• Zucker, M., and P. Stiegler. 1981. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 9:133–148.
   PubMedGoogle Scholar