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Science 326 (5957): 1235-1240

Copyright © 2009 by the American Association for the Advancement of Science

Proteome Organization in a Genome-Reduced Bacterium

Sebastian Kühner,1,* Vera van Noort,1,* Matthew J. Betts,1 Alejandra Leo-Macias,1 Claire Batisse,1 Michaela Rode,1 Takuji Yamada,1 Tobias Maier,2 Samuel Bader,1 Pedro Beltran-Alvarez,1 Daniel Castaño-Diez,1 Wei-Hua Chen,1 Damien Devos,1 Marc Güell,2 Tomas Norambuena,3 Ines Racke,1 Vladimir Rybin,1 Alexander Schmidt,4 Eva Yus,2 Ruedi Aebersold,4 Richard Herrmann,5 Bettina Böttcher,1,{dagger} Achilleas S. Frangakis,1 Robert B. Russell,1 Luis Serrano,2,6 Peer Bork,1,{ddagger} Anne-Claude Gavin1,{ddagger}

Abstract: The genome of Mycoplasma pneumoniae is among the smallest found in self-replicating organisms. To study the basic principles of bacterial proteome organization, we used tandem affinity purification–mass spectrometry (TAP-MS) in a proteome-wide screen. The analysis revealed 62 homomultimeric and 116 heteromultimeric soluble protein complexes, of which the majority are novel. About a third of the heteromultimeric complexes show higher levels of proteome organization, including assembly into larger, multiprotein complex entities, suggesting sequential steps in biological processes, and extensive sharing of components, implying protein multifunctionality. Incorporation of structural models for 484 proteins, single-particle electron microscopy, and cellular electron tomograms provided supporting structural details for this proteome organization. The data set provides a blueprint of the minimal cellular machinery required for life.

1 European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.
2 Centro Regulacion Genomica–Universidad Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain.
3 Pontificia Universidad Catolica de Chile, Alameda 340, Santiago, Chile.
4 ETH (Eidgenössische Technische Hochschule) Zürich, Wolfgang-Pauli-Strasse 16, 8093 Zürich, Switzerland; Faculty of Science, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland, and Institute for Systems Biology, Seattle, WA 98013, USA.
5 ZMBH (Zentrum für Molekulare Biologie der Universität Heidelberg), Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
6 ICREA (Institució Catalana de Recerca i Estudis Avançats), 08010 Barcelona, Spain.

* These authors contributed equally to this work.

{dagger} Present address: University of Edinburgh, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR.

{ddagger} To whom correspondence should be addressed. E-mail: gavin{at}embl.de (A.-C.G.); bork{at}embl.de (P.B.)

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