Abstract
The mRNA poly(A) tail serves different purposes, including the facilitation of nuclear export, mRNA stabilization, efficient translation, and, finally, specific degradation. The posttranscriptional addition of a poly(A) tail depends on sequence motifs in the 3' untranslated region (3' UTR) of the mRNA and a complex trans-acting protein machinery. In this study, we have replaced the 3' UTR of the yeast TRP4 gene with sequences encoding a hammerhead ribozyme that efficiently cleaves itself in vivo. Expression of the TRP4-ribozyme allele resulted in the accumulation of a nonpolyadenylated mRNA. Cells expressing the TRP4-ribozyme mRNA showed a reduced growth rate due to a reduction in Trp4p enzyme activity. The reduction in enzyme activity was not caused by inefficient mRNA export from the nucleus or mRNA destabilization. Rather, analyses of mRNA association with polyribosomes indicate that translation of the ribozyme-containing mRNA is impaired. This translational defect allows sufficient synthesis of Trp4p to support growth of trp4 cells, but is, nevertheless, of such magnitude as to activate the general control network of amino acid biosynthesis.
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- Birikh K. R., Heaton P. A., Eckstein F. The structure, function and application of the hammerhead ribozyme. Eur J Biochem. 1997 Apr 1;245(1):1–16. doi: 10.1111/j.1432-1033.1997.t01-3-00001.x. [DOI] [PubMed] [Google Scholar]
- Brown C. E., Sachs A. B. Poly(A) tail length control in Saccharomyces cerevisiae occurs by message-specific deadenylation. Mol Cell Biol. 1998 Nov;18(11):6548–6559. doi: 10.1128/mcb.18.11.6548. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Caponigro G., Parker R. Mechanisms and control of mRNA turnover in Saccharomyces cerevisiae. Microbiol Rev. 1996 Mar;60(1):233–249. doi: 10.1128/mr.60.1.233-249.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Caponigro G., Parker R. Multiple functions for the poly(A)-binding protein in mRNA decapping and deadenylation in yeast. Genes Dev. 1995 Oct 1;9(19):2421–2432. doi: 10.1101/gad.9.19.2421. [DOI] [PubMed] [Google Scholar]
- Cech T. R. Self-splicing of group I introns. Annu Rev Biochem. 1990;59:543–568. doi: 10.1146/annurev.bi.59.070190.002551. [DOI] [PubMed] [Google Scholar]
- Chen C. Y., Xu N., Shyu A. B. mRNA decay mediated by two distinct AU-rich elements from c-fos and granulocyte-macrophage colony-stimulating factor transcripts: different deadenylation kinetics and uncoupling from translation. Mol Cell Biol. 1995 Oct;15(10):5777–5788. doi: 10.1128/mcb.15.10.5777. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Cross F. R., Tinkelenberg A. H. A potential positive feedback loop controlling CLN1 and CLN2 gene expression at the start of the yeast cell cycle. Cell. 1991 May 31;65(5):875–883. doi: 10.1016/0092-8674(91)90394-e. [DOI] [PubMed] [Google Scholar]
- 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]
- Donahue C. P., Fedor M. J. Kinetics of hairpin ribozyme cleavage in yeast. RNA. 1997 Sep;3(9):961–973. [PMC free article] [PubMed] [Google Scholar]
- Düvel K., Egli C. M., Braus G. H. A single point mutation in the yeast TRP4 gene affects efficiency of mRNA 3' end processing and alters selection of the poly(A) site. Nucleic Acids Res. 1999 Mar 1;27(5):1289–1295. doi: 10.1093/nar/27.5.1289. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Eckner R., Ellmeier W., Birnstiel M. L. Mature mRNA 3' end formation stimulates RNA export from the nucleus. EMBO J. 1991 Nov;10(11):3513–3522. doi: 10.1002/j.1460-2075.1991.tb04915.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Egli C. M., Braus G. H. Uncoupling of mRNA 3' cleavage and polyadenylation by expression of a hammerhead ribozyme in yeast. J Biol Chem. 1994 Nov 4;269(44):27378–27383. [PubMed] [Google Scholar]
- Egli C. M., Düvel K., Trabesinger-Rüf N., Irniger S., Braus G. H. Sequence requirements of the bidirectional yeast TRP4 mRNA 3'-end formation signal. Nucleic Acids Res. 1997 Jan 15;25(2):417–422. doi: 10.1093/nar/25.2.417. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Egli C. M., Springer C., Braus G. H. A complex unidirectional signal element mediates GCN4 mRNA 3' end formation in Saccharomyces cerevisiae. Mol Cell Biol. 1995 May;15(5):2466–2473. doi: 10.1128/mcb.15.5.2466. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Frohman M. A., Dush M. K., Martin G. R. Rapid production of full-length cDNAs from rare transcripts: amplification using a single gene-specific oligonucleotide primer. Proc Natl Acad Sci U S A. 1988 Dec;85(23):8998–9002. doi: 10.1073/pnas.85.23.8998. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Furter R., Braus G., Paravicini G., Mösch H. U., Niederberger P., Hütter R. Regulation of the TRP4 gene of Saccharomyces cerevisiae at the transcriptional level and functional analysis of its promotor. Mol Gen Genet. 1988 Jan;211(1):168–175. doi: 10.1007/BF00338409. [DOI] [PubMed] [Google Scholar]
- Furter R., Paravicini G., Aebi M., Braus G., Prantl F., Niederberger P., Hütter R. The TRP4 gene of Saccharomyces cerevisiae: isolation and structural analysis. Nucleic Acids Res. 1986 Aug 26;14(16):6357–6373. doi: 10.1093/nar/14.16.6357. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gallie D. R., Lucas W. J., Walbot V. Visualizing mRNA expression in plant protoplasts: factors influencing efficient mRNA uptake and translation. Plant Cell. 1989 Mar;1(3):301–311. doi: 10.1105/tpc.1.3.301. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gallie D. R. The cap and poly(A) tail function synergistically to regulate mRNA translational efficiency. Genes Dev. 1991 Nov;5(11):2108–2116. doi: 10.1101/gad.5.11.2108. [DOI] [PubMed] [Google Scholar]
- Goffeau A., Barrell B. G., Bussey H., Davis R. W., Dujon B., Feldmann H., Galibert F., Hoheisel J. D., Jacq C., Johnston M. Life with 6000 genes. Science. 1996 Oct 25;274(5287):546, 563-7. doi: 10.1126/science.274.5287.546. [DOI] [PubMed] [Google Scholar]
- Gray N. K., Wickens M. Control of translation initiation in animals. Annu Rev Cell Dev Biol. 1998;14:399–458. doi: 10.1146/annurev.cellbio.14.1.399. [DOI] [PubMed] [Google Scholar]
- Hilleren P., McCarthy T., Rosbash M., Parker R., Jensen T. H. Quality control of mRNA 3'-end processing is linked to the nuclear exosome. Nature. 2001 Oct 4;413(6855):538–542. doi: 10.1038/35097110. [DOI] [PubMed] [Google Scholar]
- Hinnebusch A. G. Translational regulation of yeast GCN4. A window on factors that control initiator-trna binding to the ribosome. J Biol Chem. 1997 Aug 29;272(35):21661–21664. doi: 10.1074/jbc.272.35.21661. [DOI] [PubMed] [Google Scholar]
- Iizuka N., Najita L., Franzusoff A., Sarnow P. Cap-dependent and cap-independent translation by internal initiation of mRNAs in cell extracts prepared from Saccharomyces cerevisiae. Mol Cell Biol. 1994 Nov;14(11):7322–7330. doi: 10.1128/mcb.14.11.7322. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Jacobson A., Peltz S. W. Interrelationships of the pathways of mRNA decay and translation in eukaryotic cells. Annu Rev Biochem. 1996;65:693–739. doi: 10.1146/annurev.bi.65.070196.003401. [DOI] [PubMed] [Google Scholar]
- Keller W., Minvielle-Sebastia L. A comparison of mammalian and yeast pre-mRNA 3'-end processing. Curr Opin Cell Biol. 1997 Jun;9(3):329–336. doi: 10.1016/s0955-0674(97)80004-x. [DOI] [PubMed] [Google Scholar]
- Kessler M. M., Henry M. F., Shen E., Zhao J., Gross S., Silver P. A., Moore C. L. Hrp1, a sequence-specific RNA-binding protein that shuttles between the nucleus and the cytoplasm, is required for mRNA 3'-end formation in yeast. Genes Dev. 1997 Oct 1;11(19):2545–2556. doi: 10.1101/gad.11.19.2545. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Mangus D. A., Jacobson A. Linking mRNA turnover and translation: assessing the polyribosomal association of mRNA decay factors and degradative intermediates. Methods. 1999 Jan;17(1):28–37. doi: 10.1006/meth.1998.0704. [DOI] [PubMed] [Google Scholar]
- Miozzari G. F., Niederberger P., Hütter R. Permeabilization of microorganisms by Triton X-100. Anal Biochem. 1978 Oct 1;90(1):220–233. doi: 10.1016/0003-2697(78)90026-x. [DOI] [PubMed] [Google Scholar]
- Moy T. I., Silver P. A. Nuclear export of the small ribosomal subunit requires the ran-GTPase cycle and certain nucleoporins. Genes Dev. 1999 Aug 15;13(16):2118–2133. doi: 10.1101/gad.13.16.2118. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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]
- Munroe D., Jacobson A. mRNA poly(A) tail, a 3' enhancer of translational initiation. Mol Cell Biol. 1990 Jul;10(7):3441–3455. doi: 10.1128/mcb.10.7.3441. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Parker R., Jacobson A. Translation and a 42-nucleotide segment within the coding region of the mRNA encoded by the MAT alpha 1 gene are involved in promoting rapid mRNA decay in yeast. Proc Natl Acad Sci U S A. 1990 Apr;87(7):2780–2784. doi: 10.1073/pnas.87.7.2780. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Preiss T., Hentze M. W. Dual function of the messenger RNA cap structure in poly(A)-tail-promoted translation in yeast. Nature. 1998 Apr 2;392(6675):516–520. doi: 10.1038/33192. [DOI] [PubMed] [Google Scholar]
- Preiss T., Muckenthaler M., Hentze M. W. Poly(A)-tail-promoted translation in yeast: implications for translational control. RNA. 1998 Nov;4(11):1321–1331. doi: 10.1017/s1355838298980669. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Proweller A., Butler S. Efficient translation of poly(A)-deficient mRNAs in Saccharomyces cerevisiae. Genes Dev. 1994 Nov 1;8(21):2629–2640. doi: 10.1101/gad.8.21.2629. [DOI] [PubMed] [Google Scholar]
- Sarkar S., Azad A. K., Hopper A. K. Nuclear tRNA aminoacylation and its role in nuclear export of endogenous tRNAs in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1999 Dec 7;96(25):14366–14371. doi: 10.1073/pnas.96.25.14366. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sikorski R. S., Hieter P. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics. 1989 May;122(1):19–27. doi: 10.1093/genetics/122.1.19. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Simos G., Hurt E. Transfer RNA biogenesis: A visa to leave the nucleus. Curr Biol. 1999 Apr 8;9(7):R238–R241. doi: 10.1016/s0960-9822(99)80152-3. [DOI] [PubMed] [Google Scholar]
- Symons R. H. Small catalytic RNAs. Annu Rev Biochem. 1992;61:641–671. doi: 10.1146/annurev.bi.61.070192.003233. [DOI] [PubMed] [Google Scholar]
- Tanner N. K. Ribozymes: the characteristics and properties of catalytic RNAs. FEMS Microbiol Rev. 1999 Jun;23(3):257–275. doi: 10.1111/j.1574-6976.1999.tb00399.x. [DOI] [PubMed] [Google Scholar]
- Tarun S. Z., Jr, Sachs A. B. A common function for mRNA 5' and 3' ends in translation initiation in yeast. Genes Dev. 1995 Dec 1;9(23):2997–3007. doi: 10.1101/gad.9.23.2997. [DOI] [PubMed] [Google Scholar]
- Tarun S. Z., Jr, Sachs A. B. Association of the yeast poly(A) tail binding protein with translation initiation factor eIF-4G. EMBO J. 1996 Dec 16;15(24):7168–7177. [PMC free article] [PubMed] [Google Scholar]
- Ullman K. S., Powers M. A., Forbes D. J. Nuclear export receptors: from importin to exportin. Cell. 1997 Sep 19;90(6):967–970. doi: 10.1016/s0092-8674(00)80361-x. [DOI] [PubMed] [Google Scholar]
- Wahle E., Rüegsegger U. 3'-End processing of pre-mRNA in eukaryotes. FEMS Microbiol Rev. 1999 Jun;23(3):277–295. doi: 10.1111/j.1574-6976.1999.tb00400.x. [DOI] [PubMed] [Google Scholar]
- Zhao J., Hyman L., Moore C. Formation of mRNA 3' ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis. Microbiol Mol Biol Rev. 1999 Jun;63(2):405–445. doi: 10.1128/mmbr.63.2.405-445.1999. [DOI] [PMC free article] [PubMed] [Google Scholar]