MitoP2: an integrative tool for the analysis of the mitochondrial proteome - PubMed (original) (raw)
Review
MitoP2: an integrative tool for the analysis of the mitochondrial proteome
Matthias Elstner et al. Mol Biotechnol. 2008 Nov.
Abstract
Mitochondria are crucial for normal cell metabolism and maintenance. Mitochondrial dysfunction has been implicated in a spectrum of human diseases, ranging from rare monogenic to common multifactorial disorders. Important for the understanding of organelle function is the assignment of its constituents, and although over 1,500 proteins are predicted to be involved in mammalian mitochondrial function, so far only about 900 are assigned to mitochondria with reasonable certainty. Continuing efforts are being taken to obtain a complete inventory of the mitochondrial proteome by single protein studies and high-throughput approaches. To be of best value for the scientific community this data needs to be structured, explored, and customized. For this purpose, the MitoP2 database ( http://www.mitop2.de ) was established and is maintained in order to incorporate such data. The central database contains manually evaluated yeast, mouse, and human reference proteins, which show convincing evidence of a mitochondrial location. In addition, entries from genome-wide approaches that suggest protein localization are integrated and serve to compile a combined score for each candidate, which provides a best estimate of mitochondrial localization. Furthermore, it integrates information on the orthology between species, including Saccharomyces cerevisiae, mouse, human, Arabidopsis thaliana, and Neurospora crassa, thus mutually enhancing evidence across species. In contrast to other known databases, MitoP2 takes into account the reliability by which the protein is estimated as being mitochondrially located, as described herein. Multiple search functions, as well as information on disease causing genes and available mouse models, makes MitoP2 a valuable tool for the genetic investigation of human mitochondrial pathology.
Similar articles
- The mitochondrial proteome database: MitoP2.
Elstner M, Andreoli C, Klopstock T, Meitinger T, Prokisch H. Elstner M, et al. Methods Enzymol. 2009;457:3-20. doi: 10.1016/S0076-6879(09)05001-0. Methods Enzymol. 2009. PMID: 19426859 - MitoP2, an integrated database for mitochondrial proteins.
Prokisch H, Ahting U. Prokisch H, et al. Methods Mol Biol. 2007;372:573-86. doi: 10.1007/978-1-59745-365-3_39. Methods Mol Biol. 2007. PMID: 18314752 - MitoP2: the mitochondrial proteome database--now including mouse data.
Prokisch H, Andreoli C, Ahting U, Heiss K, Ruepp A, Scharfe C, Meitinger T. Prokisch H, et al. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D705-11. doi: 10.1093/nar/gkj127. Nucleic Acids Res. 2006. PMID: 16381964 Free PMC article. - The mitochondrial proteome and human disease.
Calvo SE, Mootha VK. Calvo SE, et al. Annu Rev Genomics Hum Genet. 2010;11:25-44. doi: 10.1146/annurev-genom-082509-141720. Annu Rev Genomics Hum Genet. 2010. PMID: 20690818 Free PMC article. Review. - The proteome of baker's yeast mitochondria.
Gonczarowska-Jorge H, Zahedi RP, Sickmann A. Gonczarowska-Jorge H, et al. Mitochondrion. 2017 Mar;33:15-21. doi: 10.1016/j.mito.2016.08.007. Epub 2016 Aug 14. Mitochondrion. 2017. PMID: 27535110 Review.
Cited by
- Conserved and novel functions for Arabidopsis thaliana MIA40 in assembly of proteins in mitochondria and peroxisomes.
Carrie C, Giraud E, Duncan O, Xu L, Wang Y, Huang S, Clifton R, Murcha M, Filipovska A, Rackham O, Vrielink A, Whelan J. Carrie C, et al. J Biol Chem. 2010 Nov 12;285(46):36138-48. doi: 10.1074/jbc.M110.121202. Epub 2010 Sep 9. J Biol Chem. 2010. PMID: 20829360 Free PMC article. - Genetic diagnosis of Mendelian disorders via RNA sequencing.
Kremer LS, Bader DM, Mertes C, Kopajtich R, Pichler G, Iuso A, Haack TB, Graf E, Schwarzmayr T, Terrile C, Koňaříková E, Repp B, Kastenmüller G, Adamski J, Lichtner P, Leonhardt C, Funalot B, Donati A, Tiranti V, Lombes A, Jardel C, Gläser D, Taylor RW, Ghezzi D, Mayr JA, Rötig A, Freisinger P, Distelmaier F, Strom TM, Meitinger T, Gagneur J, Prokisch H. Kremer LS, et al. Nat Commun. 2017 Jun 12;8:15824. doi: 10.1038/ncomms15824. Nat Commun. 2017. PMID: 28604674 Free PMC article. - A stress-responsive system for mitochondrial protein degradation.
Heo JM, Livnat-Levanon N, Taylor EB, Jones KT, Dephoure N, Ring J, Xie J, Brodsky JL, Madeo F, Gygi SP, Ashrafi K, Glickman MH, Rutter J. Heo JM, et al. Mol Cell. 2010 Nov 12;40(3):465-80. doi: 10.1016/j.molcel.2010.10.021. Mol Cell. 2010. PMID: 21070972 Free PMC article. - MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins.
Calvo SE, Clauser KR, Mootha VK. Calvo SE, et al. Nucleic Acids Res. 2016 Jan 4;44(D1):D1251-7. doi: 10.1093/nar/gkv1003. Epub 2015 Oct 7. Nucleic Acids Res. 2016. PMID: 26450961 Free PMC article. - Deficiency of ECHS1 causes mitochondrial encephalopathy with cardiac involvement.
Haack TB, Jackson CB, Murayama K, Kremer LS, Schaller A, Kotzaeridou U, de Vries MC, Schottmann G, Santra S, Büchner B, Wieland T, Graf E, Freisinger P, Eggimann S, Ohtake A, Okazaki Y, Kohda M, Kishita Y, Tokuzawa Y, Sauer S, Memari Y, Kolb-Kokocinski A, Durbin R, Hasselmann O, Cremer K, Albrecht B, Wieczorek D, Engels H, Hahn D, Zink AM, Alston CL, Taylor RW, Rodenburg RJ, Trollmann R, Sperl W, Strom TM, Hoffmann GF, Mayr JA, Meitinger T, Bolognini R, Schuelke M, Nuoffer JM, Kölker S, Prokisch H, Klopstock T. Haack TB, et al. Ann Clin Transl Neurol. 2015 May;2(5):492-509. doi: 10.1002/acn3.189. Epub 2015 Mar 13. Ann Clin Transl Neurol. 2015. PMID: 26000322 Free PMC article.
References
- Bioinformatics. 2001 Aug;17(8):721-8 - PubMed
- Anal Chem. 2002 May 15;74(10):2400-6 - PubMed
- Nature. 2003 Oct 16;425(6959):737-41 - PubMed
- Am J Hum Genet. 2006 Nov;79(5):869-77 - PubMed
- J Mol Biol. 2000 Aug 25;301(4):1059-75 - PubMed
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Molecular Biology Databases