MitoP2: an integrative tool for the analysis of the mitochondrial proteome.
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.
Elstner
Matthias
M
Institute of Human Genetics, Helmholtz Zentrum Munich - German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany.
Andreoli
Christophe
C
Ahting
Uwe
U
Tetko
Igor
I
Klopstock
Thomas
T
Meitinger
Thomas
T
Prokisch
Holger
H
D000818:Animals; D030562:Databases, Protein; D006801:Humans; D020407:Internet / Q000295:instrumentation*; D008928:Mitochondria / Q000737:chemistry* / Q000378:metabolism*; D024101:Mitochondrial Proteins / Q000032:analysis; D020543:Proteome / Q000032:analysis*; D015003:Yeasts
D024101:Mitochondrial Proteins; D020543:Proteome
Bioinformatics. 2001 Aug;17(8):721-8
11524373
Anal Chem. 2002 May 15;74(10):2400-6
12038767
Nature. 2003 Oct 16;425(6959):737-41
14562106
Am J Hum Genet. 2006 Nov;79(5):869-77
17033963
J Mol Biol. 2000 Aug 25;301(4):1059-75
10966805
Nucleic Acids Res. 2008 Jan;36(Database issue):D196-201
18158298
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D514-7
15608251
N Engl J Med. 2003 Jun 26;348(26):2656-68
12826641
J Biol Chem. 2003 Oct 17;278(42):41566-71
12865426
Nat Biotechnol. 2006 Jul;24(7):841-7
16823372
Science. 1997 Oct 24;278(5338):680-6
9381177
Nature. 1997 May 29;387(6632 Suppl):67-73
9169866
PLoS Genet. 2006 Oct 20;2(10):e170
17054397
Nature. 2002 May 23;417(6887):399-403
12000970
Cell. 2008 Jul 11;134(1):112-23
18614015
Nature. 2003 Oct 16;425(6959):686-91
14562095
Nucleic Acids Res. 1998 Jan 1;26(1):73-9
9399804
J Biol Chem. 2004 Feb 6;279(6):3956-79
14597615
Nucleic Acids Res. 2008 Jan;36(Database issue):D724-8
18158299
Nucleic Acids Res. 2004 Oct 14;32(18):5539-45
15486203
PLoS Biol. 2004 Jun;2(6):e160
15208715
Proteomics. 2004 Jun;4(6):1581-90
15174128
Trends Biochem Sci. 1999 Jan;24(1):34-6
10087920
Annu Rev Genet. 2005;39:359-407
16285865
Nat Genet. 2000 May;25(1):25-9
10802651
Ann Neurol. 2008 Jan;63(1):35-9
17886296
Nat Genet. 2006 May;38(5):576-82
16582907
Proteomics. 2003 Feb;3(2):157-67
12601808
Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13207-12
14576278
Mol Biol Cell. 2002 Mar;13(3):847-53
11907266
Cell. 2003 Nov 26;115(5):629-40
14651853
Electrophoresis. 2003 Jan;24(1-2):260-75
12652598
Nature. 2006 Oct 19;443(7113):787-95
17051205
Science. 2005 Jan 21;307(5708):384-7
15662004
Mol Cell Proteomics. 2006 Dec;5(12):2392-411
17000643
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D705-11
16381964
J Proteome Res. 2004 May-Jun;3(3):495-505
15253431
Nat Biotechnol. 2003 Mar;21(3):281-6
12592411
BMC Neurosci. 2007 Aug 16;8:67
17705834
Mol Biol Cell. 2006 Mar;17(3):1436-50
16407407
Nat Genet. 2002 Aug;31(4):400-4
12134146
Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
9254694
Nat Biotechnol. 2003 Mar;21(3):287-93
12577068
Nucleic Acids Res. 2002 Jan 1;30(1):73-5
11752258
J Proteome Res. 2006 Jul;5(7):1543-54
16823961
Genome Biol. 2003;4(1):R3
12537548
Proteomics. 2005 Jul;5(11):2981-99
15986334
Electrophoresis. 2002 Aug;23(15):2525-33
12210211