Letter | Published:

Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongation

Nature volume 440, pages 561564 (23 March 2006) | Download Citation

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Abstract

A fundamental aspect of the biogenesis and function of eukaryotic messenger RNA is the quality control systems that recognize and degrade non-functional mRNAs. Eukaryotic mRNAs where translation termination occurs too soon (nonsense-mediated decay)1 or fails to occur (non-stop decay)2 are rapidly degraded. We show that yeast mRNAs with stalls in translation elongation are recognized and targeted for endonucleolytic cleavage, referred to as ‘no-go decay’. The cleavage triggered by no-go decay is dependent on translation and involves Dom34p and Hbs1p. Dom34p and Hbs1p are similar to the translation termination factors eRF1 and eRF3 (refs 3, 4), indicating that these proteins might function in recognizing the stalled ribosome and triggering endonucleolytic cleavage. No-go decay provides a mechanism for clearing the cell of stalled translation elongation complexes, which could occur as a result of damaged mRNAs or ribosomes, or as a mechanism of post-transcriptional control.

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References

  1. 1.

    Nonsense-mediated mRNA decay: splicing, translation and mRNP dynamics. Nature Rev. Mol. Cell Biol. 5, 89–99 (2004)

  2. 2.

    , , & Exosome-mediated recognition and degradation of mRNAs lacking a termination codon. Science 295, 2262–2264 (2002)

  3. 3.

    & Yeast dom34 mutants are defective in multiple developmental pathways and exhibit decreased levels of polyribosomes. Genetics 149, 45–56 (1998)

  4. 4.

    , , & Assessing functional divergence in EF-1alpha and its paralogs in eukaryotes and archaebacteria. Nucleic Acids Res. 31, 4227–4237 (2003)

  5. 5.

    et al. Translation termination factor eRF3 mediates mRNA decay through the regulation of deadenylation. J. Biol. Chem. 278, 38287–38291 (2003)

  6. 6.

    & A turnover pathway for both stable and unstable mRNAs in yeast: evidence for a requirement for deadenylation. Genes Dev. 7, 1632–1643 (1993)

  7. 7.

    & Eukaryotic mRNA decapping. Annu. Rev. Biochem. 73, 861–890 (2004)

  8. 8.

    & The DCP2 protein is required for mRNA decapping in Saccharomyces cerevisiae and contains a functional MutT motif. EMBO J. 18, 5411–5422 (1999)

  9. 9.

    , , & Function of the ski4p (Csl4p) and Ski7p proteins in 3′-to-5′ degradation of mRNA. Mol. Cell. Biol. 20, 8230–8243 (2000)

  10. 10.

    & The 3′ to 5′ degradation of yeast mRNAs is a general mechanism for mRNA turnover that requires the SKI2 DEVH box protein and 3′ to 5′ exonucleases of the exosome complex. EMBO J. 17, 1497–1506 (1998)

  11. 11.

    , & Turnover mechanisms of the stable yeast PGK1 mRNA. Mol. Cell. Biol. 15, 2145–2156 (1995)

  12. 12.

    & Premature translational termination triggers mRNA decapping. Nature 370, 578–581 (1994)

  13. 13.

    , & Eukaryotic release factors (eRFs) history. Biol. Cell. 95, 195–209 (2003)

  14. 14.

    , , , & The translation machinery and 70 kd heat shock protein cooperate in protein synthesis. Cell 71, 97–105 (1992)

  15. 15.

    , , & Novel G-protein complex whose requirement is linked to the translational status of the cell. Mol. Cell. Biol. 22, 2564–2574 (2002)

  16. 16.

    et al. Crystal structure and functional analysis of the eukaryotic class II release factor eRF3 from S. pombe. Mol. Cell 14, 233–245 (2004)

  17. 17.

    Conserved functions of yeast genes support the Duplication, Degeneration and Complementation model for gene duplication. Genetics 171, 1455–1461 (2005)

  18. 18.

    et al. Evidence for autoregulation of cystathionine gamma-synthase mRNA stability in Arabidopsis. Science 286, 1371–1374 (1999)

  19. 19.

    & Nonsense-mediated messenger RNA decay is initiated by endonucleolytic cleavage in Drosophila. Nature 429, 575–578 (2004)

  20. 20.

    et al. Nascent peptide-mediated translation elongation arrest coupled with mRNA degradation in the CGS1 gene of Arabidopsis. Genes Dev. 19, 1799–1810 (2005)

  21. 21.

    , , , & Ribosome stalling during translation elongation induces cleavage of mRNA being translated in Escherichia coli. J. Biol. Chem. 279, 15368–15375 (2004)

  22. 22.

    , , , & Nascent-peptide-mediated ribosome stalling at a stop codon induces mRNA cleavage resulting in nonstop mRNA that is recognized by tmRNA. RNA 10, 378–386 (2004)

  23. 23.

    & Cleavage of the A site mRNA codon during ribosome pausing provides a mechanism for translational quality control. Mol. Cell 12, 903–911 (2003)

  24. 24.

    & A salvage pathway for protein structures: tmRNA and trans-translation. Annu. Rev. Microbiol. 57, 101–123 (2003)

  25. 25.

    & An in vivo dual-luciferase assay system for studying translational recoding in the yeast Saccharomyces cerevisiae. RNA 9, 1019–1024 (2003)

  26. 26.

    Constraints on reinitiation of translation in mammals. Nucleic Acids Res. 29, 5226–5232 (2001)

  27. 27.

    , & Codon usage determines translation rate in Escherichia coli. J. Mol. Biol. 207, 365–377 (1989)

  28. 28.

    , & Proline residues at the C terminus of nascent chains induce SsrA tagging during translation termination. J. Biol. Chem. 277, 33825–33832 (2002)

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Acknowledgements

We thank P. Farabaugh for the pJD375 plasmid; A. van Hoof for strains; and members of the Parker laboratory, especially K. Baker and C. Decker, for discussions. This study was supported by funds from the Howard Hughes Medical Institute and the National Institutes of Health.

Author information

Affiliations

  1. Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA

    • Meenakshi K. Doma
    •  & Roy Parker

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Competing interests

Reprints and permissions information is available at npg.nature.com/reprintsandpermissions. The authors declare no competing financial interests.

Corresponding author

Correspondence to Roy Parker.

Supplementary information

Word documents

  1. 1.

    Supplementary Notes

    This file contains the Supplementary Methods, Supplementary Discussion and the Supplementary Figure Legends.

PDF files

  1. 1.

    Supplementary Figure 1

    This figure shows that the PGK1 mRNA with ribosomal stall site is destabilized independent of the major mRNA decay pathways in yeast.

  2. 2.

    Supplementary Figure 2

    This figure shows that 5′ and 3′ fragments accumulate specifically in ski7δ and xrn1δ strains.

  3. 3.

    Supplementary Figure 3

    This figure shows that No-Go decay triggers endonucleolytic cleavage in the vicinity of the stall site.

  4. 4.

    Supplementary Figure 4

    This figure shows the precursor relationship of full length and mRNA decay fragment.

  5. 5.

    Supplementary Figure 5

    This figure shows that No-Go decay is independent of deadenylation.

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DOI

https://doi.org/10.1038/nature04530

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