Proteome survey reveals modularity of the yeast cell machinery

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-Anne Heurtier, Verena Hoffman, Christian Hoefert, Karin Klein, Manuela Hudak, Anne-Marie Michon, Malgorzata Schelder, Markus Schirle, Marita Remor, Tatjana Rudi, Sean Hooper, Andreas Bauer, Tewis Bouwmeester, Georg Casari, Gerard Drewes, Gitte Neubauer, Jens M. Rick, Bernhard Kuster, Peer Bork, Robert B. Russell () and Giulio Superti-Furga ()
Additional contact information
Anne-Claude Gavin: Cellzome AG
Patrick Aloy: EMBL
Paola Grandi: Cellzome AG
Roland Krause: Cellzome AG
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

Nature, 2006, vol. 440, issue 7084, 631-636

Abstract: 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.

Date: 2006
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DOI: 10.1038/nature04532

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