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Dissection of Dom34–Hbs1 reveals independent functions in two RNA quality control pathways

Nature Structural & Molecular Biology volume 17, pages 14461452 (2010) | Download Citation

Abstract

Eukaryotic cells have several quality control pathways that rely on translation to detect and degrade defective RNAs. Dom34 and Hbs1 are two proteins that are related to translation termination factors and are involved in no-go decay (NGD) and nonfunctional 18S ribosomal RNA (rRNA) decay (18S NRD) pathways that eliminate RNAs that cause strong ribosomal stalls. Here we present the structure of Hbs1 with and without GDP and a low-resolution model of the Dom34–Hbs1 complex. This complex mimics complexes of the elongation factor and transfer RNA or of the translation termination factors eRF1 and eRF3, supporting the idea that it binds to the ribosomal A-site. We show that nucleotide binding by Hbs1 is essential for NGD and 18S NRD. Mutations in Hbs1 that disrupted the interaction between Dom34 and Hbs1 strongly impaired NGD but had almost no effect on 18S NRD. Hence, NGD and 18S NRD could be genetically uncoupled, suggesting that mRNA and rRNA in a stalled translation complex may not always be degraded simultaneously.

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References

  1. 1.

    & RNA quality control in eukaryotes. Cell 131, 660–668 (2007).

  2. 2.

    & Quality control of eukaryotic mRNA: safeguarding cells from abnormal mRNA function. Genes Dev. 21, 1833–1856 (2007).

  3. 3.

    , & Early nonsense: mRNA decay solves a translational problem. Nat. Rev. Mol. Cell Biol. 7, 415–425 (2006).

  4. 4.

    et al. An mRNA surveillance mechanism that eliminates transcripts lacking termination codons. Science 295, 2258–2261 (2002).

  5. 5.

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

  6. 6.

    & Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongation. Nature 440, 561–564 (2006).

  7. 7.

    , & Depurination of Brome mosaic virus RNA3 in vivo results in translation-dependent accelerated degradation of the viral RNA. J. Biol. Chem. 283, 32218–32228 (2008).

  8. 8.

    , , & A late-acting quality control process for mature eukaryotic rRNAs. Mol. Cell 24, 619–626 (2006).

  9. 9.

    , , & A convergence of rRNA and mRNA quality control pathways revealed by mechanistic analysis of nonfunctional rRNA decay. Mol. Cell 34, 440–450 (2009).

  10. 10.

    , , , & Immature small ribosomal subunits can engage in translation initiation in Saccharomyces cerevisiae. EMBO J. 29, 80–92 (2010).

  11. 11.

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

  12. 12.

    et al. Disruption of the pelota gene causes early embryonic lethality and defects in cell cycle progression. Mol. Cell. Biol. 23, 1470–1476 (2003).

  13. 13.

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

  14. 14.

    & The pelota locus encodes a protein required for meiotic cell division: an analysis of G2/M arrest in Drosophila spermatogenesis. Development 121, 3477–3486 (1995).

  15. 15.

    , , & Pelota controls self-renewal of germline stem cells by repressing a Bam-independent differentiation pathway. Development 132, 5365–5374 (2005).

  16. 16.

    , & Structure of yeast Dom34: a protein related to translation termination factor Erf1 and involved in No-Go decay. J. Biol. Chem. 283, 7145–7154 (2008).

  17. 17.

    et al. Structural and functional insights into Dom34, a key component of No-Go mRNA decay. Mol. Cell 27, 938–950 (2007).

  18. 18.

    et al. Analysis of Dom34 and its function in no-go decay. Mol. Biol. Cell 20, 3025–3032 (2009).

  19. 19.

    , & Evolution of nonstop, no-go and nonsense-mediated mRNA decay and their termination factor-derived components. BMC Evol. Biol. 8, 290 (2008).

  20. 20.

    et al. The product of the mammalian orthologue of the Saccharomyces cerevisiae HBS1 gene is phylogenetically related to eukaryotic release factor 3 (eRF3) but does not carry eRF3-like activity. FEBS Lett. 440, 387–392 (1998).

  21. 21.

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

  22. 22.

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

  23. 23.

    , , , & Kinetic analysis of interaction of eukaryotic release factor 3 with guanine nucleotides. J. Biol. Chem. 281, 40224–40235 (2006).

  24. 24.

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

  25. 25.

    & The guanine nucleotide-binding switch in three dimensions. Science 294, 1299–1304 (2001).

  26. 26.

    et al. Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog. Science 270, 1464–1472 (1995).

  27. 27.

    , , , & Selenocysteine tRNA-specific elongation factor SelB is a structural chimaera of elongation and initiation factors. EMBO J. 24, 11–22 (2005).

  28. 28.

    , , , & Crystal structure of intact elongation factor EF-Tu from Escherichia coli in GDP conformation at 2.05 A resolution. J. Mol. Biol. 285, 1245–1256 (1999).

  29. 29.

    et al. Structural insights into eRF3 and stop codon recognition by eRF1. Genes Dev. 23, 1106–1118 (2009).

  30. 30.

    & Global rigid body modelling of macromolecular complexes against small-angle scattering data. Biophys. J. 89, 1237–1250 (2005).

  31. 31.

    et al. Structure of the Dom34–Hbs1 complex and implications for no-go decay. Nat. Struct. Mol. Biol. 17, 1233–1240 (2010).

  32. 32.

    et al. Structural basis for mRNA surveillance by archaeal Pelota and GTP-bound EF1α complex. Proc. Natl. Acad. Sci. USA 107, 17575–17579 (2010).

  33. 33.

    et al. Role of the individual domains of translation termination factor eRF1 in GTP binding to eRF3. Proteins 70, 388–393 (2008).

  34. 34.

    , , , & In vitro reconstitution of eukaryotic translation reveals cooperativity between release factors eRF1 and eRF3. Cell 125, 1125–1136 (2006).

  35. 35.

    , , & Class-1 release factor eRF1 promotes GTP binding by class-2 release factor eRF3. Biochimie 88, 747–757 (2006).

  36. 36.

    et al. The role of ABCE1 in eukaryotic posttermination ribosomal recycling. Mol. Cell 37, 196–210 (2010).

  37. 37.

    & GTP hydrolysis by eRF3 facilitates stop codon decoding during eukaryotic translation termination. Mol. Cell. Biol. 24, 7769–7778 (2004).

  38. 38.

    , & Dom34:Hbs1 promotes subunit dissociation and peptidyl-tRNA drop-off to initiate no-go decay. Science 330, 369–372 (2010).

  39. 39.

    Sm and Sm-like proteins belong to a large family: identification of proteins of the U6 as well as the U1, U2, U4 and U5 snRNPs. EMBO J. 14, 2089–2098 (1995).

  40. 40.

    & Eukaryotic Lsm proteins: lessons from bacteria. Nat. Struct. Mol. Biol. 12, 1031–1036 (2005).

  41. 41.

    , & Regulation of ARE transcript 3′ end processing by the yeast Cth2 mRNA decay factor. EMBO J. 27, 2966–2976 (2008).

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Acknowledgements

We thank K. Blondeau, B. Faivre, J. Cicolari, D. Lebert, Y. Billier, B. Bonneau and D. Rentz for technical assistance; M. Moore (U. Mass. Medical School) and R. Parker (University of Arizona) for plasmid gifts; and P. Vachette for discussions. Supported by the Agence Nationale pour la Recherche (ANR-06-BLAN-0075-02 and ANR-07-BLAN-0093), the Association Française contre les Myopathies (AFM), La Ligue contre le Cancer Equipe Labellisée 2008, CNRS, the ESF EUROCORES RNA Quality and the EU '3D-Repertoire' program (LSHG-CT-2005-512028). J.H. and A.M.G.v.d.E. hold predoctoral grants from the Université Paris-Sud 11 and Université de Strasbourg, respectively. M.E.G. is supported by the Spanish Ministry of Science and Innovation. We acknowledge SOLEIL for provision of synchrotron radiation facilities and thank A. Thompson and J. Perez for assistance with beamlines Proxima-1 and SWING, respectively.

Author information

Author notes

    • Antonia M G van den Elzen
    •  & Julien Henri

    These authors contributed equally to this work.

Affiliations

  1. Equipe Labellisée La Ligue, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGMBC), Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR7104, Illkirch, France; Inserm, U964, Illkirch, France; Université de Strasbourg, Strasbourg, France.

    • Antonia M G van den Elzen
    • , María Eugenia Gas
    •  & Bertrand Séraphin
  2. Centre de Génétique Moléculaire (CGM), CNRS FRE3144, Gif-sur-Yvette, France.

    • Antonia M G van den Elzen
    • , María Eugenia Gas
    • , François Lacroute
    •  & Bertrand Séraphin
  3. Institut de Biochimie et Biophysique Moléculaire et Cellulaire (IBBMC), CNRS UMR8619 Bat 430 Université Paris-Sud, Orsay, France.

    • Julien Henri
    • , Noureddine Lazar
    • , Dominique Durand
    • , Magali Nicaise
    • , Herman van Tilbeurgh
    •  & Marc Graille

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Contributions

J.H., A.M.G.v.d.E., M.G. and B.S. designed experiments. J.H., A.M.G.v.d.E., N.L., D.D., F.L., M.N. and M.E.G. performed experiments. J.H., A.M.G.v.d.E., D.D., H.v.T., M.G. and B.S. analyzed data and wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Bertrand Séraphin or Marc Graille.

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    Supplementary Methods, Supplementary Data, Supplementary Table 1 and Supplementary Figures 1–5

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DOI

https://doi.org/10.1038/nsmb.1963

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