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1 National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States; Biochemistry and Molecular Biology, Indiana University School of Medicine, 1345 W. 16th Street, Indianapolis, 46202-2111, United States
2 Dept. of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States
3 National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
4 Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, United States
5 Indiana Centers for Applied Protein Sciences (INCAPS), Indianapolis, United States; Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, United States
6 Indiana Centers for Applied Protein Sciences (INCAPS), Indianapolis, United States
7 Biochemistry and Molecular Biology, Indiana University School of Medicine, 1345 W. 16th Street, Indianapolis, 46202-2111, United States; Indiana Centers for Applied Protein Sciences (INCAPS), Indianapolis, United States
* To whom correspondence should be addressed. E-mail: balabanr{at}nhlbi.nih.gov.
The functionality of the mitochondrion is primarily determined by nuclear encoded proteins. The mitochondrial functional requirements of different tissues vary from a significant biosynthetic role (liver) to a primarily energy metabolism oriented organelle (heart). The purpose of this study was to compare the proteome from rat brain, liver, heart and kidney mitochondria, in order to provide insight into the extent of heterogeneity and to further characterize the overall mitochondrial proteome. In an accompanying paper the functional consequences and expression patterns within the mitochondria are analyzed. Mitochondria were isolated, solubilized, digested, and subjected to quantitative liquid chromatography mass spectroscopy. Out of the 16950 peptides detected, 8045 proteins were identified. High confidence identification threshold was reached by 1062 which were further analyzed for the purposes of this publication. Confirmation of mitochondrial origin of proteins was determined from the literature or using N-terminal mitochondrial localization signals. Using these criteria, 382 proteins were confirmed to be mitochondrial, 493 couldn't be confirmed to be mitochondrial but are not definitively localized elsewhere in the cell. 144 proteins were assigned to the rat mitochondria proteome for the first time via the N-terminal mitochondrial localization signals. Most notable of these were histone family proteins and several structural proteins including tubulin and intermediate filaments. The mitochondrial proteome from each tissue had very specific characteristics indicative of different functional emphasis. These data confirm the notion that mitochondria are tuned by the nucleus for specific functions in different tissues.
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  J.-Y. Park, P.-y. Wang, T. Matsumoto, H. J. Sung, W. Ma, J. W. Choi, S. A. Anderson, S. C. Leary, R. S. Balaban, J.-G. Kang, et al. p53 Improves Aerobic Exercise Capacity and Augments Skeletal Muscle Mitochondrial DNA Content Circ. Res., September 25, 2009; 105(7): 705 - 712. [Abstract] [Full Text] [PDF]
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 H. Bugger, D. Chen, C. Riehle, J. Soto, H. A. Theobald, X. X. Hu, B. Ganesan, B. C. Weimer, and E. D. Abel Tissue-Specific Remodeling of the Mitochondrial Proteome in Type 1 Diabetic Akita Mice Diabetes, September 1, 2009; 58(9): 1986 - 1997. [Abstract] [Full Text] [PDF]
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 D. T. Johnson, R. A. Harris, S. French, A. Aponte, and R. S. Balaban Proteomic changes associated with diabetes in the BB-DP rat Am J Physiol Endocrinol Metab, March 1, 2009; 296(3): E422 - E432. [Abstract] [Full Text] [PDF]
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 I. Pagel-Langenickel, D. R. Schwartz, R. A. Arena, D. C. Minerbi, D. Thor. Johnson, M. A. Waclawiw, R. O. Cannon III, R. S. Balaban, D. J. Tripodi, and M. N. Sack A discordance in rosiglitazone mediated insulin sensitization and skeletal muscle mitochondrial content/activity in Type 2 diabetes mellitus Am J Physiol Heart Circ Physiol, November 1, 2007; 293(5): H2659 - H2666. [Abstract] [Full Text] [PDF]
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 D. T. Johnson, R. A. Harris, P. V. Blair, and R. S. Balaban Functional consequences of mitochondrial proteome heterogeneity Am J Physiol Cell Physiol, February 1, 2007; 292(2): C698 - C707. [Abstract] [Full Text] [PDF]
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