Skip to main content

Thank you for visiting nature.com. 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.

  • Article
  • Published:

The Machado-Joseph disease deubiquitylase ATX-3 couples longevity and proteostasis

Nature Cell Biology volume 13, pages 273–281 (2011)Cite this article

Abstract

Protein ubiquitylation is a key post-translational control mechanism contributing to different physiological processes, such as signal transduction and ageing. The size and linkage of a ubiquitin chain, which determines whether a substrate is efficiently targeted for proteasomal degradation, is determined by the interplay between ubiquitylation and deubiquitylation. A conserved factor that orchestrates distinct substrate-processing co-regulators in diverse species is the ubiquitin-selective chaperone CDC-48 (also known as p97). Several deubiquitylation enzymes (DUBs) have been shown to interact with CDC-48/p97, but the mechanistic and physiological relevance of these interactions remained elusive. Here we report a synergistic cooperation between CDC-48 and ATX-3 (the Caenorhabditis elegans orthologue of ataxin-3) in ubiquitin-mediated proteolysis and ageing regulation. Surprisingly, worms deficient for both cdc-48.1 and atx-3 demonstrated extended lifespan by up to 50%, mediated through the insulin–insulin-like growth factor 1 (IGF-1) signalling pathway. As lifespan extension specifically depends on the deubiquitylation activity of ATX-3, our findings identify a mechanistic link between protein degradation and longevity through editing of the ubiquitylation status of substrates involved in insulin–IGF-1 signalling.

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

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

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

Figure 1: CDC-48.1 and ATX-3 regulate longevity and stress response.
Figure 2: Lifespan extension of cdc-48.1(tm544); atx-3(gk193) double mutants depends on insulin–IGF-1 signalling.
Figure 3: ERAD is not critical for lifespan extension of cdc-48.1; atx-3 double mutants.
Figure 4: CDC-48.1 and ATX-3 act redundantly in ubiquitin chain editing.
Figure 5: The hydrolase activity of ATX-3 is essential for stress response and longevity.
Figure 6: CDC-48.1, ATX-3 and UFD-2 cooperate throughout ubiquitin chain formation.

Similar content being viewed by others

References

  1. Kerscher, O., Felberbaum, R. & Hochstrasser, M. Modification of proteins by ubiquitin and ubiquitin-like proteins. Annu. Rev. Cell Dev. Biol. 22, 159–180 (2006).

    Article  CAS  PubMed  Google Scholar 

  2. Ciechanover, A., Orian, A. & Schwartz, A. L. Ubiquitin-mediated proteolysis: biological regulation via destruction. Bioessays 22, 442–451 (2000).

    Article  CAS  PubMed  Google Scholar 

  3. Gidalevitz, T., Kikis, E. A. & Morimoto, R. I. A cellular perspective on conformational disease: the role of genetic background and proteostasis networks. Curr. Opin. Struct. Biol. 20, 23–32 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Powers, E. T., Morimoto, R. I., Dillin, A., Kelly, J. W. & Balch, W. E. Biological and chemical approaches to diseases of proteostasis deficiency. Annu. Rev. Biochem. 78, 959–991 (2009).

    Article  CAS  PubMed  Google Scholar 

  5. Vernace, V. A., Schmidt-Glenewinkel, T. & Figueiredo-Pereira, M. E. Aging and regulated protein degradation: who has the UPPer hand? Aging Cell 6, 599–606 (2007).

    Article  CAS  PubMed  Google Scholar 

  6. Tonoki, A. et al. Genetic evidence linking age-dependent attenuation of the 26S proteasome with the aging process. Mol. Cell Biol. 29, 1095–1106 (2009).

    Article  CAS  PubMed  Google Scholar 

  7. Yun, C. et al. Proteasomal adaptation to environmental stress links resistance to proteotoxicity with longevity in Caenorhabditis elegans. Proc. Natl Acad. Sci. USA 105, 7094–7099 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Ghazi, A., Henis-Korenblit, S. & Kenyon, C. Regulation of Caenorhabditis elegans lifespan by a proteasomal E3 ligase complex. Proc. Natl Acad. Sci. USA 104, 5947–5952 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Carrano, A. C., Liu, Z., Dillin, A. & Hunter, T. A conserved ubiquitination pathway determines longevity in response to diet restriction. Nature 460, 396–399 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Mehta, R. et al. Proteasomal regulation of the hypoxic response modulates aging in C. elegans. Science 324, 1196–1198 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Li, W., Gao, B., Lee, S. M., Bennett, K. & Fang, D. RLE-1, an E3 ubiquitin ligase, regulates C. elegans aging by catalyzing DAF-16 polyubiquitination. Dev. Cell 12, 235–246 (2007).

    Article  CAS  PubMed  Google Scholar 

  12. Choe, K. P., Przybysz, A. J. & Strange, K. The WD40 repeat protein WDR-23 functions with the CUL4/DDB1 ubiquitin ligase to regulate nuclear abundance and activity of SKN-1 in Caenorhabditis elegans. Mol. Cell Biol. 29, 2704–2715 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Chen, D., Thomas, E. L. & Kapahi, P. HIF-1 modulates dietary restriction-mediated lifespan extension via IRE-1 in Caenorhabditis elegans. PLoS Genet. 5, e1000486 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  14. Jentsch, S. & Rumpf, S. Cdc48 (p97): a “molecular gearbox” in the ubiquitin pathway? Trends Biochem. Sci. 32, 6–11 (2007).

    Article  CAS  PubMed  Google Scholar 

  15. Mouysset, J., Kaehler, C. & Hoppe, T. A conserved role of Caenorhabditis elegans CDC-48 in ER-associated protein degradation. J. Struct. Biol. 156, 41–49 (2006).

    Article  CAS  PubMed  Google Scholar 

  16. Janiesch, P. C. et al. The ubiquitin-selective chaperone CDC-48/p97 links myosin assembly to human myopathy. Nat. Cell Biol. 9, 379–390 (2007).

    Article  CAS  PubMed  Google Scholar 

  17. Hoppe, T. Multiubiquitylation by E4 enzymes: 'one size' doesn't fit all. Trends Biochem. Sci. 30, 183–187 (2005).

    Article  CAS  PubMed  Google Scholar 

  18. Sowa, M. E., Bennett, E. J., Gygi, S. P. & Harper, J. W. Defining the human deubiquitinating enzyme interaction landscape. Cell 138, 389–403 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Winborn, B. J. et al. The deubiquitinating enzyme ataxin-3, a polyglutamine disease protein, edits Lys63 linkages in mixed linkage ubiquitin chains. J. Biol. Chem. 283, 26436–26443 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Todi, S. V. et al. Ubiquitination directly enhances activity of the deubiquitinating enzyme ataxin-3. EMBO J. 28, 372–382 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Kawaguchi, Y. et al. CAG expansions in a novel gene for Machado-Joseph disease at chromosome 14q32.1. Nat. Genet. 8, 221–228 (1994).

    Article  CAS  PubMed  Google Scholar 

  22. Wang, Q., Li, L. & Ye, Y. Regulation of retrotranslocation by p97-associated deubiquitinating enzyme ataxin-3. J. Cell Biol. 174, 963–971 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Boeddrich, A. et al. An arginine/lysine-rich motif is crucial for VCP/p97-mediated modulation of ataxin-3 fibrillogenesis. EMBO J. 25, 1547–1558 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Rodrigues, A. J. et al. ATX-3, CDC-48 and UBXN-5: a new trimolecular complex in Caenorhabditis elegans. Biochem. Biophys. Res. Commun. 386, 575–581 (2009).

    Article  CAS  PubMed  Google Scholar 

  25. Herndon, L. A. et al. Stochastic and genetic factors influence tissue-specific decline in ageing C. elegans. Nature 419, 808–814 (2002).

    Article  CAS  PubMed  Google Scholar 

  26. Hoppe, T. et al. Regulation of the myosin-directed chaperone UNC-45 by a novel E3/E4-multiubiquitylation complex in C. elegans. Cell 118, 337–349 (2004).

    Article  CAS  PubMed  Google Scholar 

  27. Mouysset, J. et al. Cell cycle progression requires the CDC-48UFD-1/NPL-4 complex for efficient DNA replication. Proc. Natl Acad. Sci. USA 105, 12879–12884 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Yamauchi, S., Yamanaka, K. & Ogura, T. Comparative analysis of expression of two p97 homologues in Caenorhabditis elegans. Biochem. Biophys. Res. Commun. 345, 746–753 (2006).

    Article  CAS  PubMed  Google Scholar 

  29. Johnson, T. E. et al. Longevity genes in the nematode Caenorhabditis elegans also mediate increased resistance to stress and prevent disease. J. Inherit. Metab. Dis. 25, 197–206 (2002).

    Article  CAS  PubMed  Google Scholar 

  30. Kimura, K. D., Tissenbaum, H. A., Liu, Y. & Ruvkun, G. daf-2, an insulin receptor-like gene that regulates longevity and diapause in Caenorhabditis elegans. Science 277, 942–946 (1997).

    Article  CAS  PubMed  Google Scholar 

  31. Lin, K., Hsin, H., Libina, N. & Kenyon, C. Regulation of the Caenorhabditis elegans longevity protein DAF-16 by insulin/IGF-1 and germline signaling. Nat. Genet. 28, 139–145 (2001).

    Article  CAS  PubMed  Google Scholar 

  32. Ogg, S. et al. The Fork head transcription factor DAF-16 transduces insulin-like metabolic and longevity signals in C. elegans. Nature 389, 994–999 (1997).

    Article  CAS  PubMed  Google Scholar 

  33. Panowski, S. H., Wolff, S., Aguilaniu, H., Durieux, J. & Dillin, A. PHA-4/Foxa mediates diet-restriction-induced longevity of C. elegans. Nature 447, 550–555 (2007).

    Article  CAS  PubMed  Google Scholar 

  34. Bishop, N. A. & Guarente, L. Two neurons mediate diet-restriction-induced longevity in C. elegans. Nature 447, 545–549 (2007).

    Article  CAS  PubMed  Google Scholar 

  35. Lee, S. S., Kennedy, S., Tolonen, A. C. & Ruvkun, G. DAF-16 target genes that control C. elegans life-span and metabolism. Science 300, 644–647 (2003).

    Article  CAS  PubMed  Google Scholar 

  36. Berdichevsky, A., Viswanathan, M., Horvitz, H. R. & Guarente, L. C. elegans SIR-2.1 interacts with 14-3-3 proteins to activate DAF-16 and extend life span. Cell 125, 1165–1177 (2006).

    Article  CAS  PubMed  Google Scholar 

  37. Apfeld, J. & Kenyon, C. Regulation of lifespan by sensory perception in Caenorhabditis elegans. Nature 402, 804–809 (1999).

    Article  CAS  PubMed  Google Scholar 

  38. Henis-Korenblit, S. et al. Insulin/IGF-1 signaling mutants reprogram ER stress response regulators to promote longevity. Proc. Natl Acad. Sci. USA 107, 9730–9735 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Urano, F. et al. A survival pathway for Caenorhabditis elegans with a blocked unfolded protein response. J. Cell Biol. 158, 639–646 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Johnson, E. S., Ma, P. C., Ota, I. M. & Varshavsky, A. A proteolytic pathway that recognizes ubiquitin as a degradation signal. J. Biol. Chem. 270, 17442–17456 (1995).

    Article  CAS  PubMed  Google Scholar 

  41. Dantuma, N. P., Lindsten, K., Glas, R., Jellne, M. & Masucci, M. G. Short-lived green fluorescent proteins for quantifying ubiquitin/proteasome-dependent proteolysis in living cells. Nat. Biotechnol. 18, 538–543 (2000).

    Article  CAS  PubMed  Google Scholar 

  42. Kulkarni, M. & Smith, H. E. E1 ubiquitin-activating enzyme UBA-1 plays multiple roles throughout C. elegans development. PLoS Genet. 4, e1000131 (2008).

    Article  PubMed  PubMed Central  Google Scholar 

  43. Komander, D. The emerging complexity of protein ubiquitination. Biochem. Soc. Trans. 37, 937–953 (2009).

    Article  CAS  PubMed  Google Scholar 

  44. Koegl, M. et al. A novel ubiquitination factor, E4, is involved in multiubiquitin chain assembly. Cell 96, 635–644 (1999).

    Article  CAS  PubMed  Google Scholar 

  45. Saeki, Y., Tayama, Y., Toh-e, A. & Yokosawa, H. Definitive evidence for Ufd2-catalyzed elongation of the ubiquitin chain through Lys48 linkage. Biochem. Biophys. Res. Commun. 320, 840–845 (2004).

    Article  CAS  PubMed  Google Scholar 

  46. Newton, K. et al. Ubiquitin chain editing revealed by polyubiquitin linkage-specific antibodies. Cell 134, 668–678 (2008).

    Article  CAS  PubMed  Google Scholar 

  47. Richly, H. et al. A series of ubiquitin binding factors connects CDC48/p97 to substrate multiubiquitylation and proteasomal targeting. Cell 120, 73–84 (2005).

    Article  CAS  PubMed  Google Scholar 

  48. Zhang, D. et al. Together, Rpn10 and Dsk2 can serve as a polyubiquitin chain-length sensor. Mol. Cell 36, 1018–1033 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Kim, H. T., Kim, K. P., Uchiki, T., Gygi, S. P. & Goldberg, A. L. S5a promotes protein degradation by blocking synthesis of nondegradable forked ubiquitin chains. EMBO J. 28, 1867–1877 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Brenner, S. The genetics of Caenorhabditis elegans. Genetics 77, 71–94 (1974).

    CAS  PubMed  PubMed Central  Google Scholar 

  51. Sambrook, J., Fritsch, E. F. & Maniatis, T. Molecular Cloning: A Laboratory Manual. (Cold Spring Harbour Laboratory Press, 1989).

    Google Scholar 

  52. Praitis, V., Casey, E., Collar, D. & Austin, J. Creation of low-copy integrated transgenic lines in Caenorhabditis elegans. Genetics 157, 1217–1226 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  53. Timmons, L. & Fire, A. Specific interference by ingested dsRNA. Nature 395, 854 (1998).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank Y. Kohara, the Caenorhabditis Genetics Center (funded by the NIH National Center for Research Resources), the Dana-Farber Cancer Institute and Gene service Ltd for antibodies, plasmids, cDNAs and strains and we thank S. Hohenberger for technical help. We also thank A. Antebi, I. Dikic, and B. Schumacher for reading the manuscript. This work is supported by grants of the Deutsche Forschungsgemeinschaft (especially the Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Research Unit FOR885), and the Rubicon European Union Network of Excellence to T.H., and a doctoral fellowship of the Hans & Ilse Breuer Foundation to R.B. T.H. is an EMBO Young Investigator.

Author information

Author notes

  1. Kirsten Kuhlbrodt

    Present address: Present address: QIAGEN Hamburg GmbH, Research & Development, Koenigstraße 4a, 22767 Hamburg, Germany.,

  2. Roja Barikbin

    Present address: Present address: Center of Internal Medicine, Department of Experimental Immunology and Hepatology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany.,

  3. Kirsten Kuhlbrodt, Philipp Christoph Janiesch and Éva Kevei: These authors contributed equally to this work.

Authors and Affiliations

  1. Centre for Molecular Neurobiology (ZMNH), University of Hamburg, Falkenried 94, Hamburg, 20251, Germany

    Kirsten Kuhlbrodt, Philipp Christoph Janiesch & Roja Barikbin

  2. Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Zülpicher Straße 47a, Cologne, 50674, Germany

    Éva Kevei, Alexandra Segref & Thorsten Hoppe

Authors
  1. Kirsten Kuhlbrodt
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Philipp Christoph Janiesch
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Éva Kevei
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Alexandra Segref
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Roja Barikbin
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Thorsten Hoppe
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

E.K., P.C.J., K.K. and R.B. designed, performed and analysed the experiments. E.K., P.C.J. and K.K. contributed most of the results; E.K. performed all final experiments for the revisions. A.S. established the in vivo degradation assay. T.H. conceived the project, supervised the design and data interpretation and wrote the manuscript. All authors discussed the results and commented on the manuscript.

Corresponding author

Correspondence to Thorsten Hoppe.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

Supplementary Information (PDF 1973 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Kuhlbrodt, K., Janiesch, P., Kevei, É. et al. The Machado-Joseph disease deubiquitylase ATX-3 couples longevity and proteostasis. Nat Cell Biol 13, 273–281 (2011). https://doi.org/10.1038/ncb2200

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/ncb2200

This article is cited by

Search

Advanced search

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