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

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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Figure 1: Hbs1 structure representation.
Figure 2: SAXS analysis of the Dom34–Hbs1dN134 complex.
Figure 3: Effects of Hbs1 and Dom34 mutations on NGD.
Figure 4: Effects of Hbs1 and Dom34 mutants on 18S NRD and growth in ribosomal protein deletion context.

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References

  1. Doma, M.K. & Parker, R. RNA quality control in eukaryotes. Cell 131, 660–668 (2007).

    Article  CAS  Google Scholar 

  2. Isken, O. & Maquat, L.E. Quality control of eukaryotic mRNA: safeguarding cells from abnormal mRNA function. Genes Dev. 21, 1833–1856 (2007).

    Article  CAS  Google Scholar 

  3. Amrani, N., Sachs, M.S. & Jacobson, A. Early nonsense: mRNA decay solves a translational problem. Nat. Rev. Mol. Cell Biol. 7, 415–425 (2006).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  5. van Hoof, A., Frischmeyer, P.A., Dietz, H.C. & Parker, R. Exosome-mediated recognition and degradation of mRNAs lacking a termination codon. Science 295, 2262–2264 (2002).

    Article  CAS  Google Scholar 

  6. Doma, M.K. & Parker, R. Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongation. Nature 440, 561–564 (2006).

    Article  CAS  Google Scholar 

  7. Gandhi, R., Manzoor, M. & Hudak, K.A. 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).

    Article  CAS  Google Scholar 

  8. LaRiviere, F.J., Cole, S.E., Ferullo, D.J. & Moore, M.J. A late-acting quality control process for mature eukaryotic rRNAs. Mol. Cell 24, 619–626 (2006).

    Article  CAS  Google Scholar 

  9. Cole, S.E., LaRiviere, F.J., Merrikh, C.N. & Moore, M.J. A convergence of rRNA and mRNA quality control pathways revealed by mechanistic analysis of nonfunctional rRNA decay. Mol. Cell 34, 440–450 (2009).

    Article  CAS  Google Scholar 

  10. Soudet, J., Gelugne, J.P., Belhabich-Baumas, K., Caizergues-Ferrer, M. & Mougin, A. Immature small ribosomal subunits can engage in translation initiation in Saccharomyces cerevisiae. EMBO J. 29, 80–92 (2010).

    Article  CAS  Google Scholar 

  11. Carr-Schmid, A., Pfund, C., Craig, E.A. & Kinzy, T.G. Novel G-protein complex whose requirement is linked to the translational status of the cell. Mol. Cell. Biol. 22, 2564–2574 (2002).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Eberhart, C.G. & Wasserman, S.A. 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).

    CAS  PubMed  Google Scholar 

  15. Xi, R., Doan, C., Liu, D. & Xie, T. Pelota controls self-renewal of germline stem cells by repressing a Bam-independent differentiation pathway. Development 132, 5365–5374 (2005).

    Article  CAS  Google Scholar 

  16. Graille, M., Chaillet, M. & van Tilbeurgh, H. 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).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  19. Atkinson, G.C., Baldauf, S.L. & Hauryliuk, V. Evolution of nonstop, no-go and nonsense-mediated mRNA decay and their termination factor-derived components. BMC Evol. Biol. 8, 290 (2008).

    Article  Google Scholar 

  20. Wallrapp, C. 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).

    Article  CAS  Google Scholar 

  21. Nelson, R.J., Ziegelhoffer, T., Nicolet, C., Werner-Washburne, M. & Craig, E.A. The translation machinery and 70 kd heat shock protein cooperate in protein synthesis. Cell 71, 97–105 (1992).

    Article  CAS  Google Scholar 

  22. Inagaki, Y., Blouin, C., Susko, E. & Roger, A.J. Assessing functional divergence in EF-1α and its paralogs in eukaryotes and archaebacteria. Nucleic Acids Res. 31, 4227–4237 (2003).

    Article  CAS  Google Scholar 

  23. Pisareva, V.P., Pisarev, A.V., Hellen, C.U., Rodnina, M.V. & Pestova, T.V. Kinetic analysis of interaction of eukaryotic release factor 3 with guanine nucleotides. J. Biol. Chem. 281, 40224–40235 (2006).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  25. Vetter, I.R. & Wittinghofer, A. The guanine nucleotide-binding switch in three dimensions. Science 294, 1299–1304 (2001).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  27. Leibundgut, M., Frick, C., Thanbichler, M., Bock, A. & Ban, N. Selenocysteine tRNA-specific elongation factor SelB is a structural chimaera of elongation and initiation factors. EMBO J. 24, 11–22 (2005).

    Article  CAS  Google Scholar 

  28. Song, H., Parsons, M.R., Rowsell, S., Leonard, G. & Phillips, S.E. 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).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  30. Petoukhov, M.V. & Svergun, D.I. Global rigid body modelling of macromolecular complexes against small-angle scattering data. Biophys. J. 89, 1237–1250 (2005).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  34. Alkalaeva, E.Z., Pisarev, A.V., Frolova, L.Y., Kisselev, L.L. & Pestova, T.V. In vitro reconstitution of eukaryotic translation reveals cooperativity between release factors eRF1 and eRF3. Cell 125, 1125–1136 (2006).

    Article  CAS  Google Scholar 

  35. Hauryliuk, V., Zavialov, A., Kisselev, L. & Ehrenberg, M. Class-1 release factor eRF1 promotes GTP binding by class-2 release factor eRF3. Biochimie 88, 747–757 (2006).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  37. Salas-Marco, J. & Bedwell, D.M. GTP hydrolysis by eRF3 facilitates stop codon decoding during eukaryotic translation termination. Mol. Cell. Biol. 24, 7769–7778 (2004).

    Article  CAS  Google Scholar 

  38. Shoemaker, C.J., Eyler, D.E. & Green, R. Dom34:Hbs1 promotes subunit dissociation and peptidyl-tRNA drop-off to initiate no-go decay. Science 330, 369–372 (2010).

    Article  CAS  Google Scholar 

  39. Séraphin, B. 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).

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  41. Prouteau, M., Daugeron, M.C. & Seraphin, B. Regulation of ARE transcript 3′ end processing by the yeast Cth2 mRNA decay factor. EMBO J. 27, 2966–2976 (2008).

    Article  CAS  Google Scholar 

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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.

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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.

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Correspondence to Bertrand Séraphin or Marc Graille.

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van den Elzen, A., Henri, J., Lazar, N. et al. Dissection of Dom34–Hbs1 reveals independent functions in two RNA quality control pathways. Nat Struct Mol Biol 17, 1446–1452 (2010). https://doi.org/10.1038/nsmb.1963

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