MitoP2, an Integrated Database on Mitochondrial Proteins in Yeast and Man

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2003 Dec 19

PMID 14681457

Citations 30

Authors

C Andreoli

H Prokisch

K Hortnagel

J C Mueller

M Munsterkotter

C Scharfe

T Meitinger

Affiliations

Soon will be listed here.

Abstract

The aim of the MitoP2 database (http://ihg.gsf.de/mitop2) is to provide a comprehensive list of mitochondrial proteins of yeast and man. Based on the current literature we created an annotated reference set of yeast and human proteins. In addition, data sets relevant to the study of the mitochondrial proteome are integrated and accessible via search tools and links. They include computational predictions of signalling sequences, and summarize results from proteome mapping, mutant screening, expression profiling, protein-protein interaction and cellular sublocalization studies. For each individual approach, specificity and sensitivity for allocating mitochondrial proteins was calculated. By providing the evidence for mitochondrial candidate proteins the MitoP2 database lends itself to the genetic characterization of human mitochondriopathies.

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References

Claros M . MitoProt, a Macintosh application for studying mitochondrial proteins. Comput Appl Biosci. 1995; 11(4):441-7. DOI: 10.1093/bioinformatics/11.4.441. View

von Mering C, Krause R, Snel B, Cornell M, Oliver S, Fields S . Comparative assessment of large-scale data sets of protein-protein interactions. Nature. 2002; 417(6887):399-403. DOI: 10.1038/nature750. View

Pflieger D, Le Caer J, Lemaire C, Bernard B, Dujardin G, Rossier J . Systematic identification of mitochondrial proteins by LC-MS/MS. Anal Chem. 2002; 74(10):2400-6. DOI: 10.1021/ac011295h. View

Andersson S, Zomorodipour A, Andersson J, Sicheritz-Ponten T, Alsmark U, Podowski R . The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature. 1998; 396(6707):133-40. DOI: 10.1038/24094. View

Nakai K, Horton P . PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem Sci. 1999; 24(1):34-6. DOI: 10.1016/s0968-0004(98)01336-x. View

Ashburner M, Ball C, Blake J, Botstein D, Butler H, Cherry J . Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000; 25(1):25-9. PMC: 3037419. DOI: 10.1038/75556. View

Scheffler I . Mitochondria make a come back. Adv Drug Deliv Rev. 2001; 49(1-2):3-26. DOI: 10.1016/s0169-409x(01)00123-5. View

Dimmer K, Fritz S, Fuchs F, Messerschmitt M, Weinbach N, Neupert W . Genetic basis of mitochondrial function and morphology in Saccharomyces cerevisiae. Mol Biol Cell. 2002; 13(3):847-53. PMC: 99603. DOI: 10.1091/mbc.01-12-0588. View

Neupert W . Protein import into mitochondria. Annu Rev Biochem. 1997; 66:863-917. DOI: 10.1146/annurev.biochem.66.1.863. View

10.

Tzagoloff A, Dieckmann C . PET genes of Saccharomyces cerevisiae. Microbiol Rev. 1990; 54(3):211-25. PMC: 372773. DOI: 10.1128/mr.54.3.211-225.1990. View

11.

Boeckmann B, Bairoch A, Apweiler R, Blatter M, Estreicher A, Gasteiger E . The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 2003; 31(1):365-70. PMC: 165542. DOI: 10.1093/nar/gkg095. View

12.

Kogelnik A, Lott M, Brown M, Navathe S, Wallace D . MITOMAP: a human mitochondrial genome database--1998 update. Nucleic Acids Res. 1998; 26(1):112-5. PMC: 147233. DOI: 10.1093/nar/26.1.112. View

13.

Zeviani M, Spinazzola A, Carelli V . Nuclear genes in mitochondrial disorders. Curr Opin Genet Dev. 2003; 13(3):262-70. DOI: 10.1016/s0959-437x(03)00052-2. View

14.

Steinmetz L, Scharfe C, Deutschbauer A, Mokranjac D, Herman Z, Jones T . Systematic screen for human disease genes in yeast. Nat Genet. 2002; 31(4):400-4. DOI: 10.1038/ng929. View

15.

Gilks W, Audit B, De Angelis D, Tsoka S, Ouzounis C . Modeling the percolation of annotation errors in a database of protein sequences. Bioinformatics. 2002; 18(12):1641-9. DOI: 10.1093/bioinformatics/18.12.1641. View

16.

DiMauro S, Schon E . Nuclear power and mitochondrial disease. Nat Genet. 1998; 19(3):214-5. DOI: 10.1038/883. View

17.

Katinka M, Duprat S, Cornillot E, Metenier G, Thomarat F, Prensier G . Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature. 2001; 414(6862):450-3. DOI: 10.1038/35106579. View

18.

Attimonelli M, Altamura N, Benne R, Brennicke A, Cooper J, Delia D . MitBASE : a comprehensive and integrated mitochondrial DNA database. The present status. Nucleic Acids Res. 1999; 28(1):148-52. PMC: 102423. DOI: 10.1093/nar/28.1.148. View

19.

Drawid A, Gerstein M . A Bayesian system integrating expression data with sequence patterns for localizing proteins: comprehensive application to the yeast genome. J Mol Biol. 2000; 301(4):1059-75. DOI: 10.1006/jmbi.2000.3968. View

20.

Scharfe C, Zaccaria P, Hoertnagel K, Jaksch M, Klopstock T, Dembowski M . MITOP, the mitochondrial proteome database: 2000 update. Nucleic Acids Res. 1999; 28(1):155-8. PMC: 102491. DOI: 10.1093/nar/28.1.155. View