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.

  • Letter
  • Published:

Conformational variations in an infectious protein determine prion strain differences

Nature volume 428, pages 323–328 (2004)Cite this article

Abstract

A remarkable feature of prion biology is the strain phenomenon wherein prion particles apparently composed of the same protein lead to phenotypically distinct transmissible states1,2,3,4. To reconcile the existence of strains with the ‘protein-only’ hypothesis of prion transmission, it has been proposed that a single protein can misfold into multiple distinct infectious forms, one for each different strain1,2,3,5. Several studies have found correlations between strain phenotypes and conformations of prion particles6,7,8,9,10; however, whether such differences cause or are simply a secondary manifestation of prion strains remains unclear, largely due to the difficulty of creating infectious material from pure protein3,5. Here we report a high-efficiency protocol for infecting yeast with the [PSI+] prion using amyloids composed of a recombinant Sup35 fragment (Sup-NM). Using thermal stability and electron paramagnetic resonance spectroscopy, we demonstrate that Sup-NM amyloids formed at different temperatures adopt distinct, stably propagating conformations. Infection of yeast with these different amyloid conformations leads to different [PSI+] strains. These results establish that Sup-NM adopts an infectious conformation before entering the cell—fulfilling a key prediction of the prion hypothesis5—and directly demonstrate that differences in the conformation of the infectious protein determine prion strain variation.

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: Induction of the [PSI+] prion by in-vitro-converted Sup-NM amyloid fibres.
Figure 2: Generation of multiple [PSI+] strains by Sup-NM amyloid fibres converted in vitro.
Figure 3: Different conformations of Sup-NM amyloid fibres are formed at different temperatures.
Figure 4: Induction of distinct [PSI+] strains by Sup-NM amyloid fibres formed at different temperatures.

Similar content being viewed by others

References

  1. Prusiner, S. B., Scott, M. R., DeArmond, S. J. & Cohen, F. E. Prion protein biology. Cell 93, 337–348 (1998)

    Article  CAS  PubMed  Google Scholar 

  2. Collinge, J. Prion diseases of humans and animals: their causes and molecular basis. Annu. Rev. Neurosci. 24, 519–550 (2001)

    Article  CAS  PubMed  Google Scholar 

  3. Aguzzi, A. & Haass, C. Games played by rogue proteins in prion disorders and Alzheimer's disease. Science 302, 814–818 (2003)

    Article  ADS  CAS  PubMed  Google Scholar 

  4. Chien, P., Weissman, J. S. & Depace, A. H. Emerging principles of conformation-based prion inheritance. Annu. Rev. Biochem. (in the press)

  5. Liebman, S. Progress toward an ultimate proof of the prion hypothesis. Proc. Natl Acad. Sci. USA 99, 9098–9100 (2002)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  6. Bessen, R. A. et al. Non-genetic propagation of strain-specific properties of scrapie prion protein. Nature 375, 698–700 (1995)

    Article  ADS  CAS  PubMed  Google Scholar 

  7. Telling, G. C. et al. Evidence for the conformation of the pathologic isoform of the prion protein enciphering and propagating prion diversity. Science 274, 2079–2082 (1996)

    Article  ADS  CAS  PubMed  Google Scholar 

  8. Peretz, D. et al. A change in the conformation of prions accompanies the emergence of a new prion strain. Neuron 34, 921–932 (2002)

    Article  CAS  PubMed  Google Scholar 

  9. Chien, P. & Weissman, J. S. Conformational diversity in a yeast prion dictates its seeding specificity. Nature 410, 223–227 (2001)

    Article  ADS  CAS  PubMed  Google Scholar 

  10. Chien, P., DePace, A. H., Collins, S. & Weissman, J. S. Generation of prion transmission barriers by mutational control of amyloid conformations. Nature 424, 948–951 (2003)

    Article  ADS  CAS  PubMed  Google Scholar 

  11. Uptain, S. M. & Lindquist, S. Prions as protein-based genetic elements. Annu. Rev. Microbiol. 56, 703–741 (2002)

    Article  CAS  PubMed  Google Scholar 

  12. Glover, J. R. et al. Self-seeded fibers formed by Sup35, the protein determinant of [PSI+], a heritable prion-like factor of S. cerevisiae. Cell 89, 811–819 (1997)

    Article  CAS  PubMed  Google Scholar 

  13. King, C. Y. et al. Prion-inducing domain 2–114 of yeast Sup35 protein transforms in vitro into amyloid-like filaments. Proc. Natl Acad. Sci. USA 94, 6618–6622 (1997)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  14. Derkatch, I. L., Chernoff, Y. O., Kushnirov, V. V., Inge-Vechtomov, S. G. & Liebman, S. W. Genesis and variability of [PSI+] prion factors in Saccharomyces cerevisiae. Genetics 144, 1375–1386 (1996)

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Kushnirov, V. V., Kryndushkin, D. S., Boguta, M., Smirnov, V. N. & Ter-Avanesyan, M. D. Chaperones that cure yeast artificial [PSI+] and their prion-specific effects. Curr. Biol. 10, 1443–1446 (2000)

    Article  CAS  PubMed  Google Scholar 

  16. Zhou, P. et al. The yeast non-Mendelian factor [ETA+] is a variant of [PSI+], a prion-like form of release factor eRF3. EMBO J. 18, 1182–1191 (1999)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Kochneva-Pervukhova, N. V. et al. [PSI+] prion generation in yeast: characterization of the ‘strain’ difference. Yeast 18, 489–497 (2001)

    Article  CAS  PubMed  Google Scholar 

  18. Uptain, S. M., Sawicki, G. J., Caughey, B. & Lindquist, S. Strains of [PSI+] are distinguished by their efficiencies of prion-mediated conformational conversion. EMBO J. 20, 6236–6245 (2001)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. King, C. Y. Supporting the structural basis of prion strains: induction and identification of [PSI+] variants. J. Mol. Biol. 307, 1247–1260 (2001)

    Article  CAS  PubMed  Google Scholar 

  20. Sparrer, H. E., Santoso, A., Szoka, F. C. & Weissman, J. S. Evidence for the prion hypothesis: Induction of the yeast [PSI+] factor by in vitro-converted sup35 protein. Science 289, 595–599 (2000)

    Article  ADS  CAS  PubMed  Google Scholar 

  21. Derkatch, I. L., Bradley, M. E., Zhou, P., Chernoff, Y. O. & Liebman, S. W. Genetic and environmental factors affecting the de novo appearance of the [PSI+] prion in Saccharomyces cerevisiae. Genetics 147, 507–519 (1997)

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Maddelein, M.-L., Dos Reis, S., Duvezin-Caubet, S., Coulary-Salin, B. & Saupe, S. J. Amyloid aggregates of the HET-s prion protein are infectious. Proc. Natl Acad. Sci. USA 99, 7402–7407 (2002)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  23. Santoso, A., Chien, P., Osherovich, L. Z. & Weissman, J. S. Molecular basis of a yeast prion species barrier. Cell 100, 277–288 (2000)

    Article  CAS  PubMed  Google Scholar 

  24. Chernoff, Y. O. et al. Evolutionary conservation of prion-forming abilities of the yeast Sup35 protein. Mol. Microbiol. 35, 865–876 (2000)

    Article  CAS  PubMed  Google Scholar 

  25. Kushnirov, V. V., Kochneva-Pervukhova, N. V., Chechenova, M. B., Frolova, N. S. & Ter-Avanesyan, M. D. Prion properties of the Sup35 protein of yeast Pichia methanolica. EMBO J. 19, 324–331 (2000)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Baxa, U., Speransky, V., Steven, A. C. & Wickner, R. B. Mechanism of inactivation on prion conversion of the Saccharomyces cerevisiae Ure2 protein. Proc. Natl Acad. Sci. USA 99, 5253–5260 (2002)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  27. DePace, A. H. & Weissman, J. S. Origins and kinetic consequences of diversity in Sup35 yeast prion fibers. Nature Struct. Biol. 9, 389–396 (2002)

    CAS  PubMed  Google Scholar 

  28. Rice, S. et al. Thermodynamic properties of the kinesin neck-region docking to the catalytic core. Biophys. J. 84, 1844–1854 (2003)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  29. McHaourab, H. S., Lietzow, M. A., Hideg, K. & Hubbell, W. L. Motion of spin-labeled side chains in T4 lysozyme: Correlation with protein structure and dynamics. Biochemistry 35, 7692–7704 (1996)

    Article  CAS  PubMed  Google Scholar 

  30. Sondheimer, N. & Lindquist, S. L. Rnq1: an epigenetic modifier of protein function in yeast. Mol. Cell 5, 163–172 (2000)

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank S. Collins, J. Newman, L. Osherovich, K. Tipton and members of the Weissman laboratory for discussion and reading of the manuscript. M.T. was supported by JSPS postdoctoral fellowships for research abroad. P.C. was supported by National Science Foundation Graduate Fellowships and the ARCS foundation. Funding was also provided by Howard Hughes Medical Instititute, The David and Lucile Packard Foundation and the National Institutes of Health.

Author information

Authors and Affiliations

  1. Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California-San Francisco, San Francisco, California, 94143, USA

    Motomasa Tanaka, Peter Chien & Jonathan S. Weissman

  2. Graduate Group in Biophysics, University of California-San Francisco, San Francisco, California, 94143, USA

    Peter Chien & Jonathan S. Weissman

  3. Department of Biochemistry and Biophysics, University of California-San Francisco, San Francisco, California, 94143, USA

    Nariman Naber & Roger Cooke

Authors
  1. Motomasa Tanaka
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Peter Chien
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Nariman Naber
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Roger Cooke
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jonathan S. Weissman
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jonathan S. Weissman.

Ethics declarations

Competing interests

The authors declare that they have no competing financial interests.

Supplementary information

Supplementary Information

Preparation of lyticase (DOC 5 kb)

Supplementary Figure 1

Effects of proteinase K and deoxyribonuclease I on prion infectivity. (JPG 95 kb)

Supplementary Figure 2

Non-Mendelian inheritance of a [PSI+] strain generated by protein infection. (JPG 78 kb)

Supplementary Figure 3

Sedimentation analysis of strong and weak [PSI+] strains generated by protein infection. (JPG 55 kb)

Supplementary Figure 4

Induction of [PSI+] by over-expression of Sup-NM-GFP in [psi-][PIN+] strain. (JPG 44 kb)

Supplementary Figure 5

Induction of prion state by partially purified prion particles derived from strong and weak [PSI+] strains. (JPG 75 kb)

Supplementary Figure 6

Partial proteolysis of Sup-NM fibres formed at 4, 23, or 37°C. (JPG 51 kb)

Supplementary Figure 7

Curing efficiency of strong and weak [PSI+] strains generated by protein infection, by Hsp104 over-expression. (JPG 45 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Tanaka, M., Chien, P., Naber, N. et al. Conformational variations in an infectious protein determine prion strain differences. Nature 428, 323–328 (2004). https://doi.org/10.1038/nature02392

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature02392

This article is cited by

Comments

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.

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