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Short disordered protein segment regulates cross-species transmission of a yeast prion

Nature Chemical Biology volume 16, pages 756–765 (2020)Cite this article

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Abstract

Soluble prion proteins contingently encounter foreign prion aggregates, leading to cross-species prion transmission. However, how its efficiency is regulated by structural fluctuation of the host soluble prion protein remains unsolved. In the present study, through the use of two distantly related yeast prion Sup35 proteins, we found that a specific conformation of a short disordered segment governs interspecies prion transmissibility. Using a multidisciplinary approach including high-resolution NMR and molecular dynamics simulation, we identified critical residues within this segment that allow interspecies prion transmission in vitro and in vivo, by locally altering dynamics and conformation of soluble prion proteins. Remarkably, subtle conformational differences caused by a methylene group between asparagine and glutamine sufficed to change the short segment structure and substantially modulate the cross-seeding activity. Thus, our findings uncover how conformational dynamics of the short segment in the host prion protein impacts cross-species prion transmission. More broadly, our study provides mechanistic insights into cross-seeding between heterologous proteins.

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Fig. 1: A short disordered segment in SC- and KL-Sup35NM monomers exhibits species-specific difference in dynamics and regulates a species-specific seeding activity.
Fig. 2: Substitutions within a short disordered segment in SC-Sup35NM monomer markedly alter its cross-reactivity toward KL-Sup35NM seeds both in vitro and in vivo.
Fig. 3: Altered side-chain contacts within a short disordered segment through substitutions modulate the main-chain conformation of the segment and the cross-reactivity.
Fig. 4: The local main-chain conformation within a short disordered segment can be markedly different through subtle side-chain differences.
Fig. 5: The role of local conformational dynamics in regulating species-specific seeding activity.

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Data availability

The chemical shifts of KL-Sup35NM, 5MT-A, 5MT-B and 4MT-A have been deposited in the Biological Magnetic Resonance Bank under accession nos. 50131, 50132, 50133 and 50134, respectively. Other data and materials are available from the corresponding author upon reasonable request.

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Acknowledgements

We thank N. Takahashi for reagent preparation, H. Chih-Hao Shen for advice on NMR analysis, H. Kurahashi for advice on yeast experiments and the members of Tanaka laboratory for discussion. DNA-sequencing and MS were performed by the RIKEN Center for Brain Science Research Resources Division. Funding was provided by the Grants-in-Aid for Scientific Research (B) (no. 15H04345; to M.T.) from the Ministry of Education, Culture, Sports, Science and Technology, Japan, the Grants-in-Aid for the Research Committee of Prion Disease and Slow Virus Infection (to Y.O., K.K. and M.T.) from the Ministry of Health, Labour and Welfare, Japan. M.T. received funding from the following: the RIKEN Pioneering Project (Cellular Evolution), the RIKEN Aging Project, Takeda Science Foundation, Nakatani Foundation, the Kato Memorial Trust for Nambyo Research and the Mochida Foundation. T.S. was a recipient of the Junior Research Associate fellowship from RIKEN.

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Author notes

  1. These authors contributed equally: Yuji O. Kamatari, Takao Yoda.

Authors and Affiliations

  1. Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan

    Toshinobu Shida & Motomasa Tanaka

  2. Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Wako, Japan

    Toshinobu Shida & Motomasa Tanaka

  3. Life Science Research Center, Gifu University, Gifu, Japan

    Yuji O. Kamatari

  4. United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan

    Yuji O. Kamatari & Kazuo Kuwata

  5. Nagahama Institute of Bio-Science and Technology, Nagahama, Japan

    Takao Yoda

  6. Computational Biophysics Research Team, RIKEN Research Center for Computational Science, Kobe, Japan

    Takao Yoda & Yuji Sugita

  7. Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Sendai, Japan

    Yoshiki Yamaguchi

  8. RIKEN-Max Planck Joint Research Center, Wako, Japan

    Yoshiki Yamaguchi

  9. Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA

    Michael Feig

  10. Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan

    Michael Feig & Yuji Sugita

  11. Graduate School of Science, Kobe University, Kobe, Japan

    Yumiko Ohhashi

  12. Department of Applied Chemistry, Tokyo University of Science, Shinjuku-ku, Tokyo, Japan

    Yumiko Ohhashi

  13. Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan

    Yuji Sugita

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Contributions

T.S. and M.T. designed the experiments. T.S. performed all the experiments. T.S. and M.T. analyzed and discussed the data. T.S. and Y.K. performed NMR data collection. T.S., Y.K., Y.Y., Y.O., K.K. and M.T. analyzed and discussed the data. T.Y. carried out MD simulations. T.Y., T.S., M.F., Y.S. and M.T. analyzed and discussed the data. T.S. and M.T. wrote the manuscript with input from all the authors.

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Correspondence to Motomasa Tanaka.

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Shida, T., Kamatari, Y.O., Yoda, T. et al. Short disordered protein segment regulates cross-species transmission of a yeast prion. Nat Chem Biol 16, 756–765 (2020). https://doi.org/10.1038/s41589-020-0516-y

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