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

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.

[1]  M. Mann,et al.  Mass spectrometry–based proteomics turns quantitative , 2005, Nature chemical biology.

[2]  Lei Zhang,et al.  A Comparative Proteomic Strategy for Subcellular Proteome Research , 2005, Molecular & Cellular Proteomics.

[3]  Eoin Fahy,et al.  MITOPRED: a genome-scale method for prediction of nucleus-encoded mitochondrial proteins , 2004, Bioinform..

[4]  Eoin Fahy,et al.  MITOPRED: a web server for the prediction of mitochondrial proteins , 2004, Nucleic Acids Res..

[5]  M. Mann,et al.  Trypsin Cleaves Exclusively C-terminal to Arginine and Lysine Residues*S , 2004, Molecular & Cellular Proteomics.

[6]  Waltraud X. Schulze,et al.  A Novel Proteomic Screen for Peptide-Protein Interactions* , 2004, Journal of Biological Chemistry.

[7]  M. Novotny,et al.  Fast proteolytic digestion coupled with organelle enrichment for proteomic analysis of rat liver. , 2004, Journal of proteome research.

[8]  M. Mann,et al.  Proteomic characterization of the human centrosome by protein correlation profiling , 2003, Nature.

[9]  Marjan S. Bolouri,et al.  Integrated Analysis of Protein Composition, Tissue Diversity, and Gene Regulation in Mouse Mitochondria , 2003, Cell.

[10]  Albert Sickmann,et al.  The proteome of Saccharomyces cerevisiae mitochondria , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[11]  M. Mann,et al.  Unbiased quantitative proteomics of lipid rafts reveals high specificity for signaling factors , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[12]  May D. Wang,et al.  GoMiner: a resource for biological interpretation of genomic and proteomic data , 2003, Genome Biology.

[13]  Blagoy Blagoev,et al.  A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling , 2003, Nature Biotechnology.

[14]  Bradford W. Gibson,et al.  Characterization of the human heart mitochondrial proteome , 2003, Nature Biotechnology.

[15]  M. Mann,et al.  Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. , 2003, Analytical chemistry.

[16]  T G Frey,et al.  The internal structure of mitochondria. , 2000, Trends in biochemical sciences.

[17]  R. Capaldi The changing face of mitochondrial research. , 2000, Trends in biochemical sciences.

[18]  C. Mannella Introduction: Our Changing Views of Mitochondria , 2000, Journal of bioenergetics and biomembranes.

[19]  S. Merchant,et al.  How membrane proteins travel across the mitochondrial intermembrane space. , 1999, Trends in biochemical sciences.

[20]  R. Carey,et al.  Molecular cloning of KS, a novel rat gene expressed exclusively in the kidney. , 1998, Kidney international.

[21]  F. Ichas,et al.  Regulation of the Permeability Transition Pore in Skeletal Muscle Mitochondria , 1998, The Journal of Biological Chemistry.

[22]  W. Neupert,et al.  Mechanisms of protein import into mitochondria. , 1996, Cell structure and function.

[23]  G. Daum,et al.  Mrs5p, an Essential Protein of the Mitochondrial Intermembrane Space, Affects Protein Import into Yeast Mitochondria* , 1996, The Journal of Biological Chemistry.

[24]  A. Shevchenko,et al.  Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. , 1996, Analytical chemistry.

[25]  D. Linder,et al.  Species-specific expression of cytochrome c oxidase isozymes. , 1995, Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology.

[26]  C. Ragan,et al.  Transmembrane organization of mitochondrial NADH dehydrogenase as revealed by radiochemical labelling and cross-linking. , 1988, The Biochemical journal.

[27]  P. Roepstorff,et al.  Proposal for a common nomenclature for sequence ions in mass spectra of peptides. , 1984, Biomedical mass spectrometry.

[28]  J. Mickelson,et al.  Purification of skeletal-muscle mitochondria by density-gradient centrifugation with Percoll. , 1980, Analytical biochemistry.

[29]  A. Knowles,et al.  The subunit structure of beef heart mitochondrial adenosine triphosphatase. Isolation procedures. , 1972, The Journal of biological chemistry.

[30]  L. Ernster,et al.  AN ELECTRON-TRANSPORT SYSTEM ASSOCIATED WITH THE OUTER MEMBRANE OF LIVER MITOCHONDRIA , 1967, The Journal of cell biology.

[31]  Thomas Meitinger,et al.  MitoP2, an integrated database on mitochondrial proteins in yeast and man , 2004, Nucleic Acids Res..

[32]  C. Li,et al.  Feature extraction and normalization algorithms for high‐density oligonucleotide gene expression array data , 2001, Journal of cellular biochemistry. Supplement.

[33]  K. Nakai,et al.  PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. , 1999, Trends in biochemical sciences.

[34]  С.,et al.  The Cell , 1997, Nature Medicine.

[35]  R. Capaldi,et al.  Mammalian cytochrome-c oxidase: characterization of enzyme and immunological detection of subunits in tissue extracts and whole cells. , 1995, Methods in enzymology.

[36]  M. Wilson,et al.  Mitochondria: a practical approach. , 1987 .