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:

The structural basis of yeast prion strain variants

Nature volume 449, pages 233–237 (2007)Cite this article

Abstract

Among the many surprises to arise from studies of prion biology, perhaps the most unexpected is the strain phenomenon whereby a single protein can misfold into structurally distinct, infectious states that cause distinguishable phenotypes1,2,3. Similarly, proteins can adopt a spectrum of conformations in non-infectious diseases of protein folding; some are toxic and others are well tolerated4. However, our understanding of the structural differences underlying prion strains and how these differences alter their physiological impact remains limited. Here we use a combination of solution NMR, amide hydrogen/deuterium (H/D) exchange and mutagenesis to study the structural differences between two strain conformations, termed Sc4 and Sc37 (ref. 5), of the yeast Sup35 prion. We find that these two strains have an overlapping amyloid core spanning most of the Gln/Asn-rich first 40 amino acids that is highly protected from H/D exchange and very sensitive to mutation. These features indicate that the cores are composed of tightly packed β-sheets possibly resembling ‘steric zipper’ structures revealed by X-ray crystallography of Sup35-derived peptides6,7. The stable structure is greatly expanded in the Sc37 conformation to encompass the first 70 amino acids, revealing why this strain shows increased fibre stability and decreased ability to undergo chaperone-mediated replication8. Our findings establish that prion strains involve large-scale conformational differences and provide a structural basis for understanding a broad range of functional studies, including how conformational changes alter the physiological impact of prion strains.

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: Solution NMR of SupNM fibres.
Figure 2: H/D exchange of Sc4 and Sc37 fibres.
Figure 3: Mutational analysis of SupNM fibres.

Similar content being viewed by others

References

  1. Cohen, F. E. & Prusiner, S. B. Pathologic conformations of prion proteins. Annu. Rev. Biochem. 67, 793–819 (1998)

    Article  CAS  Google Scholar 

  2. 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)

    Article  CAS  Google Scholar 

  3. Tuite, M. F. & Cox, B. S. The [PSI+] prion of yeast: a problem of inheritance. Methods 39, 9–22 (2006)

    Article  CAS  Google Scholar 

  4. Chiti, F. & Dobson, C. M. Protein misfolding, functional amyloid, and human disease. Annu. Rev. Biochem. 75, 333–366 (2006)

    Article  CAS  Google Scholar 

  5. Tanaka, M., Chien, P., Naber, N., Cooke, R. & Weissman, J. S. Conformational variations in an infectious protein determine prion strain differences. Nature 428, 323–328 (2004)

    Article  ADS  CAS  Google Scholar 

  6. Nelson, R. et al. Structure of the cross-β spine of amyloid-like fibrils. Nature 435, 773–778 (2005)

    Article  ADS  CAS  Google Scholar 

  7. Sawaya, M. R. et al. Atomic structures of amyloid cross-β spines reveal varied steric zippers. Nature 447, 453–457 (2007)

    Article  ADS  CAS  Google Scholar 

  8. Tanaka, M., Collins, S. R., Toyama, B. H. & Weissman, J. S. The physical basis of how prion conformations determine strain phenotypes. Nature 442, 585–589 (2006)

    Article  ADS  CAS  Google Scholar 

  9. 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  Google Scholar 

  10. 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  Google Scholar 

  11. King, C. Y. & Diaz-Avalos, R. Protein-only transmission of three yeast prion strains. Nature 428, 319–323 (2004)

    Article  ADS  CAS  Google Scholar 

  12. Krishnan, R. & Lindquist, S. L. Structural insights into a yeast prion illuminate nucleation and strain diversity. Nature 435, 765–772 (2005)

    Article  ADS  CAS  Google Scholar 

  13. Shewmaker, F., Wickner, R. B. & Tycko, R. Amyloid of the prion domain of Sup35p has an in-register parallel β-sheet structure. Proc. Natl Acad. Sci. USA 103, 19754–19759 (2006)

    Article  ADS  CAS  Google Scholar 

  14. Liu, J. J., Sondheimer, N. & Lindquist, S. L. Changes in the middle region of Sup35 profoundly alter the nature of epigenetic inheritance for the yeast prion. Proc. Natl Acad. Sci. USA [PSI+]. 99 (suppl. 4). 16446–16453 (2002)

    Article  ADS  CAS  Google Scholar 

  15. Flaux, J., Bertelsen, E. B., Horwich, A. L. & Wuthrich, K. NMR analysis of a 900K GroEL–GroES complex. Nature 418, 207–211 (2002)

    Article  ADS  Google Scholar 

  16. Hoshino, M. et al. Mapping the core of the β2-microglobulin amyloid fibril by H/D exchange. Nature Struct. Biol. 9, 332–336 (2002)

    Article  CAS  Google Scholar 

  17. Yamaguchi, K. et al. Core and heterogeneity of β2-microglobulin amyloid fibrils as revealed by H/D exchange. J. Mol. Biol. 338, 559–571 (2004)

    Article  CAS  Google Scholar 

  18. Ritter, C. et al. Correlation of structural elements and infectivity of the HET-s prion. Nature 435, 844–848 (2005)

    Article  ADS  CAS  Google Scholar 

  19. Luhrs, T. et al. 3D structure of Alzheimer’s amyloid-β(1–42) fibrils. Proc. Natl Acad. Sci. USA 102, 17342–17347 (2005)

    Article  ADS  CAS  Google Scholar 

  20. Carulla, N. et al. Molecular recycling within amyloid fibrils. Nature 436, 554–558 (2005)

    Article  ADS  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  22. 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 

  23. Ross, E. D., Edskes, H. K., Terry, M. J. & Wickner, R. B. Primary sequence independence for prion formation. Proc. Natl Acad. Sci. USA 102, 12825–12830 (2005)

    Article  ADS  CAS  Google Scholar 

  24. Tessier, P. M. & Lindquist, S. Prion recognition elements govern nucleation, strain specificity and species barriers. Nature 447, 556–561 (2007)

    Article  ADS  CAS  Google Scholar 

  25. 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  Google Scholar 

  26. DePace, A. H., Santoso, A., Hillner, P. & Weissman, J. S. A critical role for amino-terminal glutamine/asparagine repeats in the formation and propagation of a yeast prion. Cell 93, 1241–1252 (1998)

    Article  CAS  Google Scholar 

  27. Osherovich, L. Z., Cox, B. S., Tuite, M. F. & Weissman, J. S. Dissection and design of yeast prions. PLoS Biol. 2, E86 (2004)

    Article  Google Scholar 

  28. Crist, C. G., Nakayashiki, T., Kurahashi, H. & Nakamura, Y. [PHI+], a novel Sup35-prion variant propagated with non-Gln/Asn oligopeptide repeats in the absence of the chaperone protein Hsp104. Genes Cells 8, 603–618 (2003)

    Article  CAS  Google Scholar 

  29. Parham, S. N., Resende, C. G. & Tuite, M. F. Oligopeptide repeats in the yeast protein Sup35p stabilize intermolecular prion interactions. EMBO J. 20, 2111–2119 (2001)

    Article  CAS  Google Scholar 

  30. Shkundina, I. S., Kushnirov, V. V., Tuite, M. F. & Ter-Avanesyan, M. D. The role of the N-terminal oligopeptide repeats of the yeast Sup35 prion protein in propagation and transmission of prion variants. Genetics 172, 827–835 (2006)

    Article  CAS  Google Scholar 

  31. 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  Google Scholar 

  32. Muchmore, D. C., McIntosh, L. P., Russell, C. B., Anderson, D. E. & Dahlquist, F. W. Expression and nitrogen-15 labeling of proteins for proton and nitrogen-15 nuclear magnetic resonance. Methods Enzymol. 177, 44–73 (1989)

    Article  CAS  Google Scholar 

  33. Delaglio, F. et al. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6, 277–293 (1995)

    Article  CAS  Google Scholar 

  34. Goddard, T. D. & Kneller, D. G. SPARKY 3.112, University of California, San Francisco. (2006)

  35. Sattler, M., Schleucher, J. & Griesinger, C. Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients. Prog. Nucl. Magn. Reson. Spectrosc. 34, 93–158 (1999)

    Article  CAS  Google Scholar 

  36. Sun, Z. Y., Frueh, D. P., Selenko, P., Hoch, J. C. & Wagner, G. Fast assignment of 15N-HSQC peaks using high-resolution 3D HNcocaNH experiments with non-uniform sampling. J. Biomol. NMR 33, 43–50 (2005)

    Article  CAS  Google Scholar 

  37. Kraulis, P. J. ANSIG: A program for the assignment of protein 1H 2D NMR spectra by interactive graphics. J. Magn. Reson. 84, 627–633 (1989)

    ADS  CAS  Google Scholar 

Download references

Acknowledgements

We thank M. Tanaka, C. Ritter, M. Hoshino, W. Bermel and R. Riek for experimental advice; and D. Breslow, D. Cameron, S. Collins, V. Denic, K. Filaski, C. Foo, C. Gross, J. Hollien, N. Ingolia, E. Quan, E. Rodriguez and K. Tipton and other members of the Weissman laboratory for helpful discussion and critical reading of the manuscript. This research was funded by the NIH and the Howard Hughes Medical Institute.

Backbone assignments of SupNM have been deposited in the Biological Magnetic Resonance Data Bank, accession number 15379.

Author information

Authors and Affiliations

  1. Department of Cellular and Molecular Pharmacology,, Howard Hughes Medical Institute,

    Brandon H. Toyama & Jonathan S. Weissman

  2. Department of Pharmaceutical Chemistry, University of California San Francisco and California Institute for Quantitative Biomedical Research, San Francisco, California 94158-2542, USA,

    Mark J. S. Kelly & John D. Gross

Authors
  1. Brandon H. Toyama
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mark J. S. Kelly
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. John D. Gross
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. 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

Reprints and permissions information is available at www.nature.com/reprints. The authors declare no competing financial interests.

Supplementary information

Supplementary Figures

This file contains Supplementary Figures S1-S5 with Legends (PDF 1143 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Toyama, B., Kelly, M., Gross, J. et al. The structural basis of yeast prion strain variants. Nature 449, 233–237 (2007). https://doi.org/10.1038/nature06108

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature06108

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