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Originally published as MBC in Press, 10.1091/mbc.E05-08-0740 on January 11, 2006

Vol. 17, Issue 3, 1436-1450, March 2006

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Proteomic Analysis of the Yeast Mitochondrial Outer Membrane Reveals Accumulation of a Subclass of PreproteinsFormula

Rene P. Zahedi *, Albert Sickmann *, Andreas M. Boehm *, Christiane Winkler *, Nicole Zufall {dagger}, Birgit Schönfisch {dagger}, Bernard Guiard {ddagger}, Nikolaus Pfanner {dagger}, and Chris Meisinger {dagger}

* Rudolf-Virchow-Center for Experimental Biomedicine, Universität Würzburg, D-97078 Würzburg, Germany; {dagger} Institut für Biochemie und Molekularbiologie, Universität Freiburg, D-79104 Freiburg, Germany; and {ddagger} Centre de Génétique Moléculaire, Laboratoire propre du CNRS, F-91190 Gif-sur-Yvette, France

Submitted August 9, 2005; Revised December 21, 2005; Accepted January 3, 2006
Monitoring Editor: Benjamin Glick

Mitochondria consist of four compartments–outer membrane, intermembrane space, inner membrane, and matrix—with crucial but distinct functions for numerous cellular processes. A comprehensive characterization of the proteome of an individual mitochondrial compartment has not been reported so far. We used a eukaryotic model organism, the yeast Saccharomyces cerevisiae, to determine the proteome of highly purified mitochondrial outer membranes. We obtained a coverage of ~85% based on the known outer membrane proteins. The proteome represents a rich source for the analysis of new functions of the outer membrane, including the yeast homologue (Hfd1/Ymr110c) of the human protein causing Sjögren–Larsson syndrome. Surprisingly, a subclass of proteins known to reside in internal mitochondrial compartments were found in the outer membrane proteome. These seemingly mislocalized proteins included most top scorers of a recent genome-wide analysis for mRNAs that were targeted to mitochondria and coded for proteins of prokaryotic origin. Together with the enrichment of the precursor form of a matrix protein in the outer membrane, we conclude that the mitochondrial outer membrane not only contains resident proteins but also accumulates a conserved subclass of preproteins destined for internal mitochondrial compartments.

This article was published online ahead of print in MBC in Press (http://www.molbiolcell.org/cgi/doi/10.1091/mbc.E05–08–0740) on January 11, 2005.

Abbreviations used: ACN, acetonitrile; BAC, benzyldimethyl-n-hexadecylammonium chloride; FA, formic acid; F1beta, F0F1-ATPase subunit beta; HA, hemagglutinin; MALDI, matrix-assisted laser desorption ionization; MLR, mitochondrial localization of mRNA; MS/MS, tandem mass spectrometry; SAM, sorting and assembly machinery; SCX, strong cation exchange; TIM, translocase of inner mitochondrial membrane; TOF, time of flight; TOM, translocase of outer mitochondrial membrane.

Formula The online version of this article contains supplemental material at MBC Online (http://www.molbiolcell.org).

Address correspondence to: Albert Sickmann (albert.sickmann{at}virchow.uni-wuerzburg.de) or Chris Meisinger (christof.meisinger{at}biochemie.uni-freiburg.de).




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