Abstract
The impact of mitochondria on several fundamental cellular processes is reflected in their involvement in the pathophysiology of common diseases such as Parkinson’s disease, diabetes, and obesity and a wide range of monogenic disorders primarily associated with energy impairment or metabolic diseases. The importance of mitochondria is also reflected by the steep increase of proteins, which has been localized to this organelle. In yeast, more than 500 of the expected 700–800 mitochondrial proteins are already annotated. In the mammalian species, the expected numbers are estimated to be in the range of 1500–2000 proteins, and the currently annotated entries reach almost 700. In addition to the studies dealing with single proteins, there are many high-throughput approaches that improve the description of the mitochondrial proteome. They include computational predictions of signaling sequences, proteome mapping, mutant screening, expression profiling, protein-protein interaction, and cellular sublocalization studies. The MitoP2 database (http://www.mitop2.de/) was established to structure, explore, and customize the available data on mitochondrial proteins, functions, and diseases. MitoP2 provides a comprehensive picture of the mitochondrial proteome by focusing on (1) the orthology between species, including Saccharomyces cerevisiae, mouse, humans, and Arabidopsis thaliana; (2) the definition of mitochondrial reference sets in these species; (3) the integration of data predictive for mitochondrial localization or function stemming from genomewide approaches; (4) the allocation of a gateway for functional data from model systems and genetics of mitochondriopathies; and (5) the calculation of a combined score for each protein summarizing the indirect evidence for a mitochondrial localization. All data are accessible via search tools and linked to the original data source. By providing an overview of functional annotations from different databases, the MitoP2 database lends itself to genetic investigations of human mitochondriopathies.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Prokisch, H., Scharfe, C., Camp, D. G., 2nd, et al. (2004). Integrative analysis of the mitochondrial proteome in yeast. PLoS Biol. 2, e160.
Huh, W. K., Falvo, J. V., Gerke, L. C., et al. (2003) Global analysis of protein localization in budding yeast. Nature 425, 686–691.
Kumar, A., Cheung, K. H., Tosches, N., et al. (2002) The TRIPLES database: a community resource for yeast molecular biology. Nucleic Acids Res. 30, 73–75.
Andreoli, C., Prokisch, H., Hortnagel, K., et al. (2004) MitoP2, an integrated database on mitochondrial proteins in yeast and man. Nucleic Acids Res. 32, D459–D462.
Elpeleg, O., Miller, C., Hershkovitz, E., et al. (2005) Deficiency of the ADP-forming succinyl-CoA synthase activity is associated with encephalomyopathy and mitochondrial DNA depletion. Am. J. Hum. Genet. 76, 1081–1086.
Cherry, J. M., Ball, C., Weng, S., et al. (1997) Genetic and physical maps of Saccharomyces cerevisiae. Nature 387, 67–73.
Ruepp, A., Zollner, A., Maier, D., et al. (2004) The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res. 32, 5539–5545.
Dimmer, K. S., Fritz, S., Fuchs, F., et al. (2002) Genetic basis of mitochondrial function and morphology in Saccharomyces cerevisiae. Mol. Biol. Cell. 13, 847–853.
Steinmetz, L. M., Scharfe, C., Deutschbauer, A. M., et al. (2002) Systematic screen for human disease genes in yeast. Nat. Genet. 31, 400–404.
DeRisi, J. L., Iyer, V. R., and Brown, P. O. (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278, 680–686.
Lascaris, R., Bussemaker, H. J., Boorsma, A., et al. (2003) Hap4p overexpressionin glucose-grown Saccharomyces cerevisiae induces cells to enter a novel metabolic state. Genome Biol. 4, R3.
Pflieger, D., Le Caer, J. P., Lemaire, C., Bernard, B. A., Dujardin, G., and Rossier, J. (2002) Systematic identification of mitochondrial proteins by LC-MS/MS. Anal.Chem. 74, 2400–2406.
Sickmann, A., Reinders, J., Wagner, Y., et al. (2003) The proteome of Saccharomyces cerevisiae mitochondria. Proc. Natl. Acad. Sci. USA 100, 13,207–13,212.
Ghaemmaghami, S., Huh, W. K., Bower, K., et al. (2003) Global analysis of protein expression in yeast. Nature 425, 737–741.
von Mering, C., Krause, R., Snel, B., et al. (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417, 399–403.
Claros, M. G. (1995) MitoProt, a Macintosh application for studying mitochondrial proteins. Comput. Appl. Biosci. 11, 441–447.
Guda, C., Fahy, E., and Subramaniam, S. (2004) MITOPRED: a genome-scale method for prediction of nucleus-encoded mitochondrial proteins. Bioinformatics 20, 1785–1794.
Nakai, K. and Horton, P. (1999) PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem. Sci. 24, 34–36.
Small, I., Peeters, N., Legeai, F., and Lurin, C. (2004) Predotar: A tool for rapidly screening proteomes for N-terminal targeting sequences. Proteomics 4, 1581–1590.
Altschul, S. F., Madden, T. L., Schaffer, A. A., et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402.
Ashburner, M., Ball, C. A., Blake, J. A., et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 25, 25–29.
Schaefer, A. M., Taylor, R. W., Turnbull, D. M., and Chinnery, P. F. (2004) The epidemiology of mitochondrial disorders—past, present and future. Biochim. Biophys. Acta. 1659, 115–120.
Boeckmann, B., Bairoch, A., Apweiler, R., et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31, 365–370.
Bult, C. J., Blake, J. A., Richardson, J. E., et al. (2004) The Mouse Genome Database (MGD): integrating biology with the genome. Nucleic Acids Res. 32, D476–D481.
Gaucher, S. P., Taylor, S. W., Fahy, E., et al. (2004) Expanded coverage of the human heart mitochondrial proteome using multidimensional liquid chromatography coupled with tandem mass spectrometry. J. Proteome Res. 3, 495–505.
Taylor, S. W., Fahy, E., Zhang, B., et al. (2003) Characterization of the human heart mitochondrial proteome. Nat Biotechnol. 21, 281–286.
Da Cruz, S., Xenarios, I., Langridge, J., Vilbois, F., Parone, P. A., and Martinou, J. C. (2003) Proteomic analysis of the mouse liver mitochondrial inner membrane. J. Biol. Chem. 27, 41,566–41,571.
Mootha, V. K., Bunkenborg, J., Olsen, J. V., et al. (2003) Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria. Cell 115, 629–640.
Ozawa, T., Sako, Y., Sato, M., Kitamura, T., and Umezawa, Y. (2003) A genetic approach to identifying mitochondrial proteins. Nat. Biotechnol. 21, 287–293.
Hamosh, A., Scott, A. F., Amberger, J., Bocchini, C., Valle, D., and McKusick, V. A. (2002) Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 30, 52–55.
Drawid, A. and Gerstein, M. (2000) A Bayesian system integrating expression data with sequence patterns for localizing proteins: comprehensive application to the yeast genome. J. Mol. Biol. 301, 1059–1075.
Marc, P., Margeot, A., Devaux, F., Blugeon, C., Corral-Debrinski, M., and Jacq, C. (2002) Genome-wide analysis of mRNAs targeted to yeast mitochondria. EMBO Rep. 3, 159–164.
Ohlmeier, S., Kastaniotis, A. J., Hiltunen, J. K., and Bergmann, U. (2004) The yeast mitochondrial proteome, a study of fermentative and respiratory growth. J. Biol. Chem. 279, 3956–3979.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2007 Humana Press Inc., Totowa, NJ
About this protocol
Cite this protocol
Prokisch, H., Ahting, U. (2007). MitoP2, an Integrated Database for Mitochondrial Proteins. In: Leister, D., Herrmann, J.M. (eds) Mitochondria. Methods in Molecular Biology™, vol 372. Humana Press. https://doi.org/10.1007/978-1-59745-365-3_39
Download citation
DOI: https://doi.org/10.1007/978-1-59745-365-3_39
Publisher Name: Humana Press
Print ISBN: 978-1-58829-667-2
Online ISBN: 978-1-59745-365-3
eBook Packages: Springer Protocols