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Originally published In Press as doi:10.1074/mcp.M500298-MCP200 on January 14, 2006.
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Molecular & Cellular Proteomics 5:608-619, 2006.
© 2006 by The American Society for Biochemistry and Molecular Biology, Inc.

Research

Quantitative Proteomic Comparison of Rat Mitochondria from Muscle, Heart, and Liver *,S

Francesca Forner{ddagger},§,¶, Leonard J. Foster||, Stefano Campanaro{ddagger}, Giorgio Valle{ddagger},** and Matthias Mann§,{ddagger}{ddagger}

From the {ddagger} Centro Ricerche Interdipartimentale Biotecnologie Innovative (CRIBI), University of Padua, V.le Colombo 3, I-35121 Padua, Italy, || Centre for Proteomics, Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada, and § Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany

Mitochondria, through oxidative phosphorylation, are the primary source of energy production in all tissues under aerobic conditions. Although critical to life, energy production is not the only function of mitochondria, and the composition of this organelle is tailored to meet the specific needs of each cell type. As an organelle, the mitochondrion has been a popular subject for proteomic analysis, but quantitative proteomic methods have yet to be applied to tease apart subtle differences among mitochondria from different tissues or muscle types. Here we used mass spectrometry-based proteomics to analyze mitochondrial proteins extracted from rat skeletal muscle, heart, and liver tissues. Based on 689 proteins identified with high confidence, mitochondria from the different tissues are qualitatively quite similar. However, striking differences emerged from the quantitative comparison of protein abundance between the tissues. Furthermore we applied similar methods to analyze mitochondrial matrix and intermembrane space proteins extracted from the same mitochondrial source, providing evidence for the submitochondrial localization of a number of proteins in skeletal muscle and liver. Several proteins not previously thought to reside in mitochondria were identified, and their presence in this organelle was confirmed by protein correlation profiling. Hierarchical clustering of microarray expression data provided further evidence that some of the novel mitochondrial candidates identified in the proteomic survey might be associated with mitochondria. These data reveal several important distinctions between mitochondrial and submitochondrial proteomes from skeletal muscle, heart, and liver tissue sources. Indeed approximately one-third of the proteins identified in the soluble fractions are associated predominantly to one of the three tissues, indicating a tissue-dependent regulation of mitochondrial proteins. Furthermore a small percentage of the mitochondrial proteome is unique to each tissue.

** To whom correspondence may be addressed. E-mail: giorgio.valle{at}unipd.it


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