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Proteome survey reveals modularity of the yeast cell machinery

Author

Listed:
  • Anne-Claude Gavin

    (Cellzome AG
    EMBL)

  • Patrick Aloy

    (EMBL)

  • Paola Grandi

    (Cellzome AG)

  • Roland Krause

    (Cellzome AG
    MPI-MG, MPI-IB, Charité Campus Mitte)

  • Markus Boesche

    (Cellzome AG)

  • Martina Marzioch

    (Cellzome AG)

  • Christina Rau

    (Cellzome AG)

  • Lars Juhl Jensen

    (EMBL)

  • Sonja Bastuck

    (Cellzome AG)

  • Birgit Dümpelfeld

    (Cellzome AG)

  • Angela Edelmann

    (Cellzome AG)

  • Marie-Anne Heurtier

    (Cellzome AG)

  • Verena Hoffman

    (Cellzome AG)

  • Christian Hoefert

    (Cellzome AG)

  • Karin Klein

    (Cellzome AG)

  • Manuela Hudak

    (Cellzome AG)

  • Anne-Marie Michon

    (Cellzome AG)

  • Malgorzata Schelder

    (Cellzome AG)

  • Markus Schirle

    (Cellzome AG)

  • Marita Remor

    (Cellzome AG)

  • Tatjana Rudi

    (Cellzome AG)

  • Sean Hooper

    (EMBL)

  • Andreas Bauer

    (Cellzome AG)

  • Tewis Bouwmeester

    (Cellzome AG)

  • Georg Casari

    (Cellzome AG)

  • Gerard Drewes

    (Cellzome AG)

  • Gitte Neubauer

    (Cellzome AG)

  • Jens M. Rick

    (Cellzome AG)

  • Bernhard Kuster

    (Cellzome AG)

  • Peer Bork

    (EMBL)

  • Robert B. Russell

    (EMBL)

  • Giulio Superti-Furga

    (Cellzome AG
    Center for Molecular Medicine of the Austrian Academy of Sciences)

Abstract

Protein complexes are key molecular entities that integrate multiple gene products to perform cellular functions. Here we report the first genome-wide screen for complexes in an organism, budding yeast, using affinity purification and mass spectrometry. Through systematic tagging of open reading frames (ORFs), the majority of complexes were purified several times, suggesting screen saturation. The richness of the data set enabled a de novo characterization of the composition and organization of the cellular machinery. The ensemble of cellular proteins partitions into 491 complexes, of which 257 are novel, that differentially combine with additional attachment proteins or protein modules to enable a diversification of potential functions. Support for this modular organization of the proteome comes from integration with available data on expression, localization, function, evolutionary conservation, protein structure and binary interactions. This study provides the largest collection of physically determined eukaryotic cellular machines so far and a platform for biological data integration and modelling.

Suggested Citation

  • Anne-Claude Gavin & Patrick Aloy & Paola Grandi & Roland Krause & Markus Boesche & Martina Marzioch & Christina Rau & Lars Juhl Jensen & Sonja Bastuck & Birgit Dümpelfeld & Angela Edelmann & Marie-Ann, 2006. "Proteome survey reveals modularity of the yeast cell machinery," Nature, Nature, vol. 440(7084), pages 631-636, March.
    • Handle: RePEc:nat:nature:v:440:y:2006:i:7084:d:10.1038_nature04532
    DOI: 10.1038/nature04532
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    Cited by:

    1. Bingjie Hao & István A. Kovács, 2023. "A positive statistical benchmark to assess network agreement," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    2. Jie Zhao & Xiujuan Lei & Fang-Xiang Wu, 2017. "Predicting Protein Complexes in Weighted Dynamic PPI Networks Based on ICSC," Complexity, Hindawi, vol. 2017, pages 1-11, August.

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