IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-33814-8.html
   My bibliography  Save this article

Proteome effects of genome-wide single gene perturbations

Author

Listed:
  • Merve Öztürk

    (Institute of Molecular Biology (IMB))

  • Anja Freiwald

    (Institute of Molecular Biology (IMB))

  • Jasmin Cartano

    (Institute of Molecular Biology (IMB))

  • Ramona Schmitt

    (Institute of Molecular Biology (IMB))

  • Mario Dejung

    (Institute of Molecular Biology (IMB))

  • Katja Luck

    (Institute of Molecular Biology (IMB))

  • Bassem Al-Sady

    (University of California San Francisco)

  • Sigurd Braun

    (Ludwig-Maximilians University of Munich
    Justus-Liebig-University Giessen)

  • Michal Levin

    (Institute of Molecular Biology (IMB))

  • Falk Butter

    (Institute of Molecular Biology (IMB))

Abstract

Protein abundance is controlled at the transcriptional, translational and post-translational levels, and its regulatory principles are starting to emerge. Investigating these principles requires large-scale proteomics data and cannot just be done with transcriptional outcomes that are commonly used as a proxy for protein abundance. Here, we determine proteome changes resulting from the individual knockout of 3308 nonessential genes in the yeast Schizosaccharomyces pombe. We use similarity clustering of global proteome changes to infer gene functionality that can be extended to other species, such as humans or baker’s yeast. Furthermore, we analyze a selected set of deletion mutants by paired transcriptome and proteome measurements and show that upregulation of proteins under stable transcript expression utilizes optimal codons.

Suggested Citation

  • Merve Öztürk & Anja Freiwald & Jasmin Cartano & Ramona Schmitt & Mario Dejung & Katja Luck & Bassem Al-Sady & Sigurd Braun & Michal Levin & Falk Butter, 2022. "Proteome effects of genome-wide single gene perturbations," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-33814-8
    DOI: 10.1038/s41467-022-33814-8
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-33814-8
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-022-33814-8?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Martin Frejno & Chen Meng & Benjamin Ruprecht & Thomas Oellerich & Sebastian Scheich & Karin Kleigrewe & Enken Drecoll & Patroklos Samaras & Alexander Hogrebe & Dominic Helm & Julia Mergner & Jana Zec, 2020. "Proteome activity landscapes of tumor cell lines determine drug responses," Nature Communications, Nature, vol. 11(1), pages 1-12, December.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Valentina Cordo’ & Mariska T. Meijer & Rico Hagelaar & Richard R. Goeij-de Haas & Vera M. Poort & Alex A. Henneman & Sander R. Piersma & Thang V. Pham & Koichi Oshima & Adolfo A. Ferrando & Guido J. R, 2022. "Phosphoproteomic profiling of T cell acute lymphoblastic leukemia reveals targetable kinases and combination treatment strategies," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    2. Florian P. Bayer & Manuel Gander & Bernhard Kuster & Matthew The, 2023. "CurveCurator: a recalibrated F-statistic to assess, classify, and explore significance of dose–response curves," Nature Communications, Nature, vol. 14(1), pages 1-11, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-33814-8. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.