Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Endonucleolytic RNA cleavage by a eukaryotic exosome


The exosome is a major eukaryotic nuclease located in both the nucleus and the cytoplasm that contributes to the processing, quality control and/or turnover of a large number of cellular RNAs1,2,3,4,5,6. This large macromolecular assembly has been described as a 3′→5′ exonuclease1 and shown to contain a nine-subunit ring structure evolutionarily related to archaeal exosome-like complexes and bacterial polynucleotide phosphorylases. Recent results have shown that, unlike its prokaryotic counterparts, the yeast and human ring structures are catalytically inactive. In contrast, the exonucleolytic activity of the yeast exosome core was shown to be mediated by the RNB domain of the eukaryote-specific Dis3 subunit7,8,9. Here we show, using in vitro assays, that yeast Dis3 has an additional endoribonuclease activity mediated by the PIN domain located at the amino terminus of this multidomain protein. Simultaneous inactivation of the endonucleolytic and exonucleolytic activities of the exosome core generates a synthetic growth phenotype in vivo, supporting a physiological function for the PIN domain. This activity is responsible for the cleavage of some natural exosome substrates, independently of exonucleolytic degradation. In contrast with current models, our results show that eukaryotic exosome cores have both endonucleolytic and exonucleolytic activities, mediated by two distinct domains of the Dis3 subunit. The mode of action of eukaryotic exosome cores in RNA processing and degradation should be reconsidered, taking into account the cooperation between its multiple ribonucleolytic activities.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Prices vary by article type



Prices may be subject to local taxes which are calculated during checkout

Figure 1: Endonucleolytic activity of the Dis3 PIN domain in vitro.
Figure 2: Synthetic cell-growth phenotypes of PIN mutants.
Figure 3: Dis3 PIN domain mediates cleavage of natural exosome substrates in vivo.


  1. Mitchell, P. et al. The exosome: a conserved eukaryotic RNA processing complex containing multiple 3′→5′ exoribonucleases. Cell 91, 457–466 (1997)

    Article  CAS  PubMed  Google Scholar 

  2. Allmang, C. et al. Functions of the exosome in rRNA, snoRNA and snRNA synthesis. EMBO J. 18, 5399–5410 (1999)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Anderson, J. S. & Parker, R. P. 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)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  5. Wyers, F. et al. Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell 121, 725–737 (2005)

    Article  CAS  PubMed  Google Scholar 

  6. Lebreton, A. & Séraphin, B. Exosome-mediated quality control: Substrate recruitment and molecular activity. Biochim. Biophys. Acta 1779, 558–565 (2008)

    Article  CAS  PubMed  Google Scholar 

  7. Dziembowski, A., Lorentzen, E., Conti, E. & Séraphin, B. A single subunit, Dis3, is essentially responsible for yeast exosome core activity. Nature Struct. Mol. Biol. 14, 15–22 (2007)

    Article  CAS  Google Scholar 

  8. Liu, Q., Greimann, J. C. & Lima, C. D. Reconstitution, activities, and structure of the eukaryotic RNA exosome. Erratum. Cell 131, 188–189 (2007)

    Article  CAS  Google Scholar 

  9. Liu, Q., Greimann, J. C. & Lima, C. D. Reconstitution, activities, and structure of the eukaryotic RNA exosome. Cell 127, 1223–1237 (2006)

    Article  CAS  PubMed  Google Scholar 

  10. Hernandez, H. et al. Subunit architecture of multimeric complexes isolated directly from cells. EMBO Rep. 7, 605–610 (2006)

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Frazao, C. et al. Unravelling the dynamics of RNA degradation by ribonuclease II and its RNA-bound complex. Nature 443, 110–114 (2006)

    Article  ADS  CAS  PubMed  Google Scholar 

  12. Lorentzen, E. et al. Structure of the active subunit of the yeast exosome core, Rrp44: diverse modes of substrate recruitment in the RNase II nuclease family. Mol. Cell 29, 717–728 (2008)

    Article  CAS  PubMed  Google Scholar 

  13. Zuo, Y. et al. Structural basis for processivity and single-strand specificity of RNase II. Mol. Cell 24, 149–156 (2006)

    Article  CAS  PubMed  Google Scholar 

  14. Allmang, C. et al. The yeast exosome and human PM-Scl are related complexes of 3′→5′ exonucleases. Genes Dev. 13, 2148–2158 (1999)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Arcus, V. L. et al. Distant structural homology leads to the functional characterization of an archaeal PIN domain as an exonuclease. J. Biol. Chem. 279, 16471–16478 (2004)

    Article  CAS  PubMed  Google Scholar 

  16. Glavan, F., Behm-Ansmant, I., Izaurralde, E. & Conti, E. Structures of the PIN domains of SMG6 and SMG5 reveal a nuclease within the mRNA surveillance complex. EMBO J. 25, 5117–5125 (2006)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Belli, G. et al. An activator/repressor dual system allows tight tetracycline-regulated gene expression in budding yeast. Nucleic Acids Res. 26, 942–947 (1998)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Couttet, P. et al. Messenger RNA deadenylylation precedes decapping in mammalian cells. Proc. Natl Acad. Sci. USA 94, 5628–5633 (1997)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  19. Mandl, C. W., Heinz, F. X., Puchhammer-Stockl, E. & Kunz, C. Sequencing the termini of capped viral RNA by 5′-3′ ligation and PCR. Biotechniques 10, 484–486 (1991)

    CAS  PubMed  Google Scholar 

  20. Kadaba, S. et al. Nuclear surveillance and degradation of hypomodified initiator tRNAMet in S. cerevisiae . Genes Dev. 18, 1227–1240 (2004)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. LaCava, J. et al. RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell 121, 713–724 (2005)

    Article  CAS  PubMed  Google Scholar 

  22. Vanacova, S. et al. A new yeast poly(A) polymerase complex involved in RNA quality control. PLoS Biol. 3, e189 (2005)

    Article  PubMed  Google Scholar 

  23. Carpousis, A. J. The RNA degradosome of Escherichia coli: an mRNA-degrading machine assembled on RNase E. Annu. Rev. Microbiol. 61, 71–87 (2007)

    Article  CAS  PubMed  Google Scholar 

  24. Eberle, A. B., Lykke-Andersen, S., Mühlemann, O. & Jensen, T. H. SMG6 promotes endonucleolytic cleavage of nonsense mRNA in human cells. Nature Struct. Mol. Biol. (in the press)

  25. Schaeffer, D. et al. The exosome contains domains with specific endoribonuclease, exoribonuclease and cytoplasmic mRNA decay activities. Nature Struct. Mol. Biol. (in the press)

  26. Bonneaud, N. et al. A family of low and high copy replicative, integrative and single-stranded S. cerevisiae/E. coli shuttle vectors. Yeast 7, 609–615 (1991)

    Article  CAS  PubMed  Google Scholar 

  27. Rigaut, G. et al. A generic protein purification method for protein complex characterization and proteome exploration. Nature Biotechnol. 17, 1030–1032 (1999)

    Article  CAS  Google Scholar 

  28. Daugeron, M. C., Mauxion, F. & Séraphin, B. The yeast POP2 gene encodes a nuclease involved in mRNA deadenylation. Nucleic Acids Res. 29, 2448–2455 (2001)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Saveanu, C. et al. Nog2p, a putative GTPase associated with pre-60S subunits and required for late 60S maturation steps. EMBO J. 20, 6475–6484 (2001)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references


We thank E. Conti and J. Basquin for providing the Dis3 PIN domain expression construct and 6×His-SUMO protease, and E. Conti, E. Lorentzen, J. Kufel and members of our groups for insightful discussions. This work was supported by La Ligue contre le Cancer (Équipe Labellisée 2008), Agence Nationale de la Recherche project CUTs, CNRS, ESF RNA Quality program (project EUxosome) and the FP6 EU grant 3D repertoire, and an EMBO installation grant. R.T. is the recipient of the Stipend for Young Researchers from the Foundation for Polish Science and was supported through a Faculty of Biology, University of Warsaw intramural grant.

Author Contributions R.T. expressed and purified the recombinant proteins and performed all the in vitro experiments under the supervision of A.D. A.L. performed all in vivo experiments under the supervision of B.S. All authors discussed the results and wrote the paper.

Author information

Authors and Affiliations


Corresponding authors

Correspondence to Andrzej Dziembowski or Bertrand Séraphin.

Supplementary information

Supplementary Information

This file contains Supplementary Figures S1-S9 with Legends and Supplementary Tables S1-S3. (PDF 1653 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Lebreton, A., Tomecki, R., Dziembowski, A. et al. Endonucleolytic RNA cleavage by a eukaryotic exosome. Nature 456, 993–996 (2008).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing