1. Genetics and Genomics

Genetic profiling of protein burden and nuclear export overload

  1. Reiko Kintaka
  2. Koji Makanae
  3. Shotaro Namba
  4. Hisaaki Kato
  5. Keiji Kito
  6. Shinsuke Ohnuki
  7. Yoshikazu Ohya
  8. Brenda J Andrews
  9. Charles Boone
  10. Hisao Moriya  Is a corresponding author
  1. University of Toronto, Canada
  2. Okayama University, Japan
  3. Meiji University, Japan
  4. University of Tokyo, Japan
https://doi.org/10.7554/eLife.54080
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Cite this article
  1. Reiko Kintaka
  2. Koji Makanae
  3. Shotaro Namba
  4. Hisaaki Kato
  5. Keiji Kito
  6. Shinsuke Ohnuki
  7. Yoshikazu Ohya
  8. Brenda J Andrews
  9. Charles Boone
  10. Hisao Moriya
(2020)
Genetic profiling of protein burden and nuclear export overload
eLife 9:e54080.
https://doi.org/10.7554/eLife.54080
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Abstract

Overproduction (op) of proteins triggers cellular defects. One of the consequences of overproduction is the protein burden/cost, which is produced by an overloading of the protein synthesis process. However, the physiology of cells under a protein burden is not well characterized. We performed genetic profiling of protein burden by systematic analysis of genetic interactions between GFP-op, surveying both deletion and temperature-sensitive mutants in budding yeast. We also performed genetic profiling in cells with overproduction of triple-GFP (tGFP), and the nuclear export signal-containing tGFP (NES-tGFP). The mutants specifically interacted with GFP-op were suggestive of unexpected connections between actin-related processes like polarization and the protein burden, which was supported by morphological analysis. The tGFP-op interactions suggested that this protein probe overloads the proteasome, whereas those that interacted with NES-tGFP involved genes encoding components of the nuclear export process, providing a resource for further analysis of the protein burden and nuclear export overload.

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All data generated or analysed during this study are included in the manuscript and supporting files.

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Author details

  1. Reiko Kintaka

    Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.

  2. Koji Makanae

    Research Core for Interdisciplinary Sciences, Okayama University, Kita-ku, Okayama, Japan
    Competing interests
    The authors declare that no competing interests exist.

  3. Shotaro Namba

    Matching Program Course, Okayama University, Okayama, Japan
    Competing interests
    The authors declare that no competing interests exist.

  4. Hisaaki Kato

    Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
    Competing interests
    The authors declare that no competing interests exist.

  5. Keiji Kito

    Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
    Competing interests
    The authors declare that no competing interests exist.

  6. Shinsuke Ohnuki

    Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
    Competing interests
    The authors declare that no competing interests exist.

  7. Yoshikazu Ohya

    Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0837-1239

  8. Brenda J Andrews

    Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.

  9. Charles Boone

    Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.

  10. Hisao Moriya

    Research Core for Interdisciplinary Sciences, Okayama University, Kita-ku, Okayama, Japan
    For correspondence
    hisaom@cc.okayama-u.ac.jp
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7638-3640

Funding

Japan Society for the Promotion of Science (17H03618)

  • Hisao Moriya

Japan Society for the Promotion of Science (15KK0258)

  • Hisao Moriya

Japan Society for the Promotion of Science (18K19300)

  • Hisao Moriya

Japan Society for the Promotion of Science (20H03242)

  • Hisao Moriya

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

© 2020, Kintaka et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Reiko Kintaka
  2. Koji Makanae
  3. Shotaro Namba
  4. Hisaaki Kato
  5. Keiji Kito
  6. Shinsuke Ohnuki
  7. Yoshikazu Ohya
  8. Brenda J Andrews
  9. Charles Boone
  10. Hisao Moriya
(2020)
Genetic profiling of protein burden and nuclear export overload
eLife 9:e54080.
https://doi.org/10.7554/eLife.54080

Share this article

https://doi.org/10.7554/eLife.54080

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Further reading

    1. Computational and Systems Biology
    2. Genetics and Genomics

    Hsp70-associated chaperones have a critical role in buffering protein production costs

    Zoltán Farkas, Dorottya Kalapis ... Csaba Pál
    Research Article

    Proteins are necessary for cellular growth. Concurrently, however, protein production has high energetic demands associated with transcription and translation. Here, we propose that activity of molecular chaperones shape protein burden, that is the fitness costs associated with expression of unneeded proteins. To test this hypothesis, we performed a genome-wide genetic interaction screen in baker's yeast. Impairment of transcription, translation, and protein folding rendered cells hypersensitive to protein burden. Specifically, deletion of specific regulators of the Hsp70-associated chaperone network increased protein burden. In agreement with expectation, temperature stress, increased mistranslation and a chemical misfolding agent all substantially enhanced protein burden. Finally, unneeded protein perturbed interactions between key components of the Hsp70-Hsp90 network involved in folding of native proteins. We conclude that specific chaperones contribute to protein burden. Our work indicates that by minimizing the damaging impact of gratuitous protein overproduction, chaperones enable tolerance to massive changes in genomic expression.