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
Abstract
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.
Acknowledgements
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.
Affiliations
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
Contributions
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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