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Landscape of submitochondrial protein distribution

F.-Nora Vögtle, Julia M. Burkhart, Humberto Gonczarowska-Jorge, Cansu Kücükköse, Asli Aras Taskin, Dominik Kopczynski, Robert Ahrends, Dirk Mossmann, Albert Sickmann, René P. Zahedi & Chris Meisinger

Nature Communications 8, Article number: 290 (2017)

Mitochondria Proteomics

Received: 02 February 2017 Accepted: 15 June 2017

Published online: 18 August 2017

Source/Fonte: Chris Meisinger


The mitochondrial proteome comprises ~1000 (yeast)–1500 (human) different proteins, which are distributed into four different subcompartments. The sublocalization of these proteins within the organelle in most cases remains poorly defined. Here we describe an integrated approach combining stable isotope labeling, various protein enrichment and extraction strategies and quantitative mass spectrometry to produce a quantitative map of submitochondrial protein distribution in S. cerevisiae. This quantitative landscape enables a proteome-wide classification of 986 proteins into soluble, peripheral, and integral mitochondrial membrane proteins, and the assignment of 818 proteins into the four subcompartments: outer membrane, inner membrane, intermembrane space, or matrix. We also identified 206 proteins that were not previously annotated as localized to mitochondria. Furthermore, the protease Prd1, misannotated as intermembrane space protein, could be re-assigned and characterized as a presequence peptide degrading enzyme in the matrix.


We thank B. Schönfisch, C. Prinz and L. Myketin for expert technical assistance. We thank Dr. J.C. Martinou for the Bax protein. Work included in this study has also been performed in partial fulfillment of the requirements for the doctoral thesis of C.K. This work was supported by the Deutsche Forschungsgemeinschaft, Excellence Initiative of the German Federal & State Governments (EXC 294 BIOSS), the RTG GRK2202 (to C.M.), the Ministerium für Innovation, Wissenschaft und Forschung des Landes Nordrhein-Westfalen (to R.P.Z., J.M.B., and H.G.J.), the Emmy-Noether Programm of the Deutsche Forschungsgemeinschaft to F.N.V. and the CAPES Foundation to H.G.J.

Author information

Author notes

F.-Nora Vögtle and Julia M. Burkhart contributed equally to this work.


Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, 79104, Germany

F.-Nora Vögtle, Cansu Kücükköse, Asli Aras Taskin, Dirk Mossmann & Chris Meisinger

Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V, Dortmund, 44139, Germany

Julia M. Burkhart, Humberto Gonczarowska-Jorge, Dominik Kopczynski, Robert Ahrends, Albert Sickmann & René P. Zahedi

Faculty of Biology, University of Freiburg, Freiburg im Breisgau, 79104, Germany

Cansu Kücükköse

Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, AB24 3FX, UK

Albert Sickmann

Medizinisches Proteom Center, Ruhr Universität Bochum, Bochum, 44801, Germany

Albert Sickmann

BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg im Breisgau, 79104, Germany

Chris Meisinger


F.-N.V., J.M.B., H.G.-J., C.K., A.A.T., and D.M. performed the experiments. D.K. and R.A. performed statistical analysis. F.-N.V., J.M.B., R.P.Z., and C.M. designed experiments, analyzed, and interpreted the data. C.M., F.-N.V., J.M.B., and R.P.Z. developed the project and wrote the manuscript. H.G.-J. and A.S. reviewed and edited the manuscript. C.M. and R.P.Z. coordinated and directed the project. All authors approved the final version of the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to René P. Zahedi or Chris Meisinger.

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