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Research

Proteomics Characterization of Mouse Kidney Peroxisomes by Tandem Mass Spectrometry and Protein Correlation Profiling^*,S

Sebastian Wiese^,, Thomas Gronemeyer^,, Rob Ofman^¶, Markus Kunze^||, Cláudia P. Grou^**, José A. Almeida^**, Martin Eisenacher, Christian Stephan, Heiko Hayen, Lukas Schollenberger, Thomas Korosec^||, Hans R. Waterham^¶, Wolfgang Schliebs^¶¶, Ralf Erdmann^¶¶, Johannes Berger^||, Helmut E. Meyer, Wilhelm Just, Jorge E. Azevedo^**, Ronald J. A. Wanders^¶ and Bettina Warscheid^,||||

From the Medizinisches Proteom-Center, Ruhr-Universitaet Bochum, Universitaetsstrasse 150, 44780 Bochum, Germany, ^¶ Department of Clinical Chemistry, Academic Medical Center, University of Amsterdam, P. O. Box 22700, 1100 DE Amsterdam, The Netherlands, ^|| Center for Brain Research, Medical University of Vienna, A-1090 Vienna, Austria, ^** Instituto de Biologia Molecular e Celular (IBMC), Rua do Campo Alegre, 823, 4150-180 Porto, Portugal and Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Largo do Prof. Abel Salazar, 2, 4099-003 Porto, Portugal, Institute for Analytical Sciences (ISAS), Bunsen-Kirchhoff-Str. 11, 44139 Dortmund, Germany, Biochemie-Zentrum der Universitaet Heidelberg (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany, and ^¶¶ Abteilung fuer Systembiochemie, Medizinische Fakultaet der Ruhr-Universitaet Bochum, 44780 Bochum, Germany

The peroxisome represents a ubiquitous single membrane-bound key organelle that executes various metabolic pathways such as fatty acid degradation by - and β-oxidation, ether-phospholipid biosynthesis, metabolism of reactive oxygen species, and detoxification of glyoxylate in mammals. To fulfil this vast array of metabolic functions, peroxisomes accommodate 50 different enzymes at least as identified until now. Interest in peroxisomes has been fueled by the discovery of a group of genetic diseases in humans, which are caused by either a defect in peroxisome biogenesis or the deficient activity of a distinct peroxisomal enzyme or transporter. Although this research has greatly improved our understanding of peroxisomes and their role in mammalian metabolism, deeper insight into biochemistry and functions of peroxisomes is required to expand our knowledge of this low abundance but vital organelle. In this work, we used classical subcellular fractionation in combination with MS-based proteomics methodologies to characterize the proteome of mouse kidney peroxisomes. We could identify virtually all known components involved in peroxisomal metabolism and biogenesis. Moreover through protein localization studies by using a quantitative MS screen combined with statistical analyses, we identified 15 new peroxisomal candidates. Of these, we further investigated five candidates by immunocytochemistry, which confirmed their localization in peroxisomes. As a result of this joint effort, we believe to have compiled the so far most comprehensive protein catalogue of mammalian peroxisomes.