Article

Nature 415, 141-147 (10 January 2002) | doi:10.1038/415141a; Received 15 August 2001; Accepted 25 October 2001

Functional organization of the yeast proteome by systematic analysis of protein complexes

Anne-Claude Gavin1, Markus Bösche1, Roland Krause1, Paola Grandi1, Martina Marzioch1, Andreas Bauer1, Jörg Schultz1, Jens M. Rick1, Anne-Marie Michon1, Cristina-Maria Cruciat1, Marita Remor1, Christian Höfert1, Malgorzata Schelder1, Miro Brajenovic1, Heinz Ruffner1, Alejandro Merino1, Karin Klein1, Manuela Hudak1, David Dickson1, Tatjana Rudi1, Volker Gnau1, Angela Bauch1, Sonja Bastuck1, Bettina Huhse1, Christina Leutwein1, Marie-Anne Heurtier1, Richard R. Copley2, Angela Edelmann1, Erich Querfurth1, Vladimir Rybin1, Gerard Drewes1, Manfred Raida1, Tewis Bouwmeester1, Peer Bork2, Bertrand Seraphin2,3, Bernhard Kuster1, Gitte Neubauer1 & Giulio Superti-Furga1,2

  1. Cellzome AG, Meyerhofstrasse 1, 69117 Heidelberg, Germany
  2. European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
  3. CGM-CNRS, 91198 Gif sur Yvette Cedex, France

Correspondence to: Anne-Claude Gavin1Giulio Superti-Furga1,2 Correspondence and requests for materials should be addressed to A.C.G. (e-mail: Email: anne-claude.gavin@cellzome.com) or G.S.F. (Email: giulio.superti-furga@cellzome.com). The data are accessible at http://yeast.cellzome.com.

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Most cellular processes are carried out by multiprotein complexes. The identification and analysis of their components provides insight into how the ensemble of expressed proteins (proteome) is organized into functional units. We used tandem-affinity purification (TAP) and mass spectrometry in a large-scale approach to characterize multiprotein complexes in Saccharomyces cerevisiae. We processed 1,739 genes, including 1,143 human orthologues of relevance to human biology, and purified 589 protein assemblies. Bioinformatic analysis of these assemblies defined 232 distinct multiprotein complexes and proposed new cellular roles for 344 proteins, including 231 proteins with no previous functional annotation. Comparison of yeast and human complexes showed that conservation across species extends from single proteins to their molecular environment. Our analysis provides an outline of the eukaryotic proteome as a network of protein complexes at a level of organization beyond binary interactions. This higher-order map contains fundamental biological information and offers the context for a more reasoned and informed approach to drug discovery.