Mammalian mitochondrial proteomics: Insights into mitochondrial functions and mitochondria-related diseases

Expert Review of Proteomics

Volumn 7, Issue 3, 2010, Pages 333-345

  Chen, Xiulan ^a,b   Li, Jing ^a,b   Hou, Junjie ^a,b   Xie, Zhensheng ^a   Yang, Fuquan ^a  

^a INSTITUTE OF BIOPHYSICS   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

2 DE; BN PAGE; Comparative mitochondrial proteome; DIGE; ICAT; LC MS MS; Mitochondrial proteome; Mitochondrial related diseases; SILAC

Indexed keywords

MITOCHONDRIAL PROTEIN; PROTEOME;

AGING; ALZHEIMER DISEASE; AMYOTROPHIC LATERAL SCLEROSIS; CARDIOVASCULAR DISEASE; COMPLEX FORMATION; DEGENERATIVE DISEASE; DIABETES MELLITUS; DISORDERS OF MITOCHONDRIAL FUNCTIONS; HISTOPATHOLOGY; HUMAN; MEDICAL TECHNOLOGY; MITOCHONDRION; NEOPLASM; NONHUMAN; PARKINSON DISEASE; PATHOGENESIS; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN PHOSPHORYLATION; PROTEOMICS; PURIFICATION; REVIEW;

ANIMALS; DATABASES, PROTEIN; HUMANS; MAMMALS; MITOCHONDRIA; MITOCHONDRIAL DISEASES; PROTEOME; PROTEOMICS;

MAMMALIA;

EID: 77953589749     PISSN: 14789450     EISSN: 17448387     Source Type: Journal    
DOI: 10.1586/epr.10.22     Document Type: Review

References (126)

1. Duchen MR. Mitochondria in health and disease: perspectives on a new mitochondrial biology. Mol. Aspects Med. 25(4), 365-451 (2004).
2. Lowell BB, Shulman GI. Mitochondrial dysfunction and Type 2 diabetes. Science 307(5708), 384-387 (2005).
3. Wallace DC. Mitochondrial diseases in man and mouse. Science 283(5407), 1482-1488 (1999).
4. Da Cruz S, Parone PA, Martinou JC. Building the mitochondrial proteome. Expert Rev. Proteomics 2(4), 541-551 (2005).
5. Reichert AS, Neupert W. Mitochondriomics or what makes us breathe. Trends Genet. 20(11), 555-562 (2004).
6. Rabilloud T, Kieffer S, Procaccio V et al. Two-dimensional electrophoresis of human placental mitochondria and protein identification by mass spectrometry: toward a human mitochondrial proteome. Electrophoresis 19(6), 1006-1014 (1998).
7. Pagliarini DJ, Calvo SE, Chang B et al. A mitochondrial protein compendium elucidates complex I disease biology. Cell 134(1), 112-123 (2008).
8. Li J, Cai T, Wu P et al. Proteomic analysis of mitochondria from Caenorhabditis elegans. Proteomics 9(19), 4539-4553 (2009).
9. Taylor SW, Fahy E, Zhang B et al. Characterization of the human heart mitochondrial proteome. Nat. Biotechnol. 21(3), 281-286 (2003).
10. Rezaul K, Wu L, Mayya V, Hwang SI, Han D. A systematic characterization of mitochondrial proteome from human T leukemia cells. Mol. Cell. Proteomics 4(2), 169-181 (2005).
11. Zischka H, Weber G, Weber PJ et al. Improved proteome analysis of Saccharomyces cerevisiae mitochondria by free-flow electrophoresis. Proteomics 3(6), 906-916 (2003).
12. Hartwig S, Feckler C, Lehr S et al. A critical comparison between two classical and a kit-based method for mitochondria isolation. Proteomics 9(11), 3209-3214 (2009).
13. O'Farrell PH. High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem. 250(10), 4007-4021 (1975).
14. Kane LA, Yung CK, Agnetti G, Neverova I, Van Eyk JE. Optimization of paper bridge loading for 2-DE analysis in the basic pH region: application to the mitochondrial subproteome. Proteomics 6(21), 5683-5687 (2006).
15. Taylor SW, Warnock DE, Glenn GM et al. An alternative strategy to determine the mitochondrial proteome using sucrose gradient fractionation and 1D PAGE on highly purified human heart mitochondria. J. Proteome Res. 1(5), 451-458 (2002).
16. Schagger H, von Jagow G. Blue native electrophoresis for isolation of membrane protein complexes in enzymatically active form. Anal. Biochem. 199(2), 223-231 (1991).
17. Washburn MP, Wolters D, Yates JR 3rd. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19(3), 242-247 (2001). (Pubitemid 32220565)
18. Ong SE, Blagoev B, Kratchmarova I et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 1(5), 376-386 (2002).
19. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17(10), 994-999 (1999).
20. Ross PL, Huang YN, Marchese JN et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 3(12), 1154-1169 (2004).
21. Miyagi M, Rao KC. Proteolytic 18O-labeling strategies for quantitative proteomics. Mass Spectrom. Rev. 26(1), 121-136 (2007).
22. Ono M, Shitashige M, Honda K et al. Label-free quantitative proteomics using large peptide data sets generated by nanoflow liquid chromatography and mass spectrometry. Mol. Cell. Proteomics 5(7), 1338-1347 (2006).
23. Gilchrist A, Au CE, Hiding J et al. Quantitative proteomics analysis of the secretory pathway. Cell 127(6), 1265-1281 (2006).
24. Bantscheff M, Schirle M, Sweetman G, Rick J, Kuster B. Quantitative mass spectrometry in proteomics: a critical review. Anal. Bioanal. Chem. 389(4), 1017-1031 (2007).
25. Bugger H, Chen D, Riehle C et al. Tissue-specific remodeling of the mitochondrial proteome in Type 1 diabetic akita mice. Diabetes 58(9), 1986-1997 (2009).
26. Lefort N, Yi Z, Bowen B et al. Proteome profile of functional mitochondria from human skeletal muscle using one-dimensional gel electrophoresis and HPLC-ESI-MS/MS. J. Proteomics 72(6), 1046-1060 (2009).
27. Fountoulakis M, Berndt P, Langen H, Suter L. The rat liver mitochondrial proteins. Electrophoresis 23(2), 311-328 (2002).
28. Forner F, Foster LJ, Campanaro S, Valle G, Mann M. Quantitative proteomic comparison of rat mitochondria from muscle, heart and liver. Mol. Cell. Proteomics 5(4), 608-619 (2006).
29. Zhang J, Li X, Mueller M et al. Systematic characterization of the murine mitochondrial proteome using functionally validated cardiac mitochondria. Proteomics 8(8), 1564-1575 (2008).
30. Prokisch H, Scharfe C, Camp DG et al. Integrative analysis of the mitochondrial proteome in yeast. PLoS Biol. 2(6), e160 (2004).
31. Sickmann A, Reinders J, Wagner Y et al. The proteome of Saccharomyces cerevisiae mitochondria. Proc. Natl Acad. Sci. USA 100(23), 13207-13212 (2003).
32. Fountoulakis M, Schlaeger EJ. The mitochondrial proteins of the neuroblastoma cell line IMR-32. Electrophoresis 24(1-2), 260-275 (2003).
33. Gaucher SP, Taylor SW, Fahy E et al. Expanded coverage of the human heart mitochondrial proteome using multidimensional liquid chromatography coupled with tandem mass spectrometry. J. Proteome Res. 3(3), 495-505 (2004).
34. Forner F, Kumar C, Luber CA, Fromme T, Klingenspor M, Mann M. Proteome differences between brown and white fat mitochondria reveal specialized metabolic functions. Cell. Metab. 10(4), 324-335 (2009).
35. Mootha VK, Bunkenborg J, Olsen JV et al. Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria. Cell 115(5), 629-640 (2003).
36. Johnson DT, Harris RA, French S et al. Tissue heterogeneity of the mammalian mitochondrial proteome. Am. J. Physiol. Cell. Physiol. 292(2), C689-C697 (2007).
37. Emanuelsson O, Nielsen H, Brunak S, von Heijne G. Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J. Mol. Biol. 300(4), 1005-1016 (2000).
38. Claros MG, Vincens P. Computational method to predict mitochondrially imported proteins and their targeting sequences. Eur. J. Biochem. 241(3), 779-786 (1996).
39. Small I, Peeters N, Legeai F, Lurin C. Predotar: a tool for rapidly screening proteomes for N-terminal targeting sequences. Proteomics 4(6), 1581-1590 (2004).
40. Hua S, Sun Z. Support vector machine approach for protein subcellular localization prediction. Bioinformatics 17(8), 721-728 (2001).
41. Emanuelsson O, von Heijne G. Prediction of organellar targeting signals. Biochim. Biophys. Acta 1541(1-2), 114-119 (2001).
42. Nakai K, Horton P. PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem. Sci. 24(1), 34-36 (1999).
43. Jiang XS, Dai J, Sheng QH et al. A comparative proteomic strategy for subcellular proteome research: ICAT approach coupled with bioinformatics prediction to ascertain rat liver mitochondrial proteins and indication of mitochondrial localization for catalase. Mol. Cell. Proteomics 4(1), 12-34 (2005).
44. Distler AM, Kerner J, Hoppel CL. Proteomics of mitochondrial inner and outer membranes. Proteomics 8(19), 4066-4082 (2008).
45. Sottocasa GL, Kuylenstierna B, Ernster L, Bergstrand A. An electron-transport system associated with the outer membrane of liver mitochondria. A biochemical and morphological study. J. Cell. Biol. 32(2), 415-438 (1967).
46. Da Cruz S, Xenarios I, Langridge J, Vilbois F, Parone PA, Martinou JC. Proteomic analysis of the mouse liver mitochondrial inner membrane. J. Biol. Chem. 278(42), 41566-41571 (2003).
47. Da Cruz S, Martinou JC. Purification and proteomic analysis of the mouse liver mitochondrial inner membrane. Methods Mol. Biol. 432, 101-116 (2008).
48. McDonald T, Sheng S, Stanley B et al. Expanding the subproteome of the inner mitochondria using protein separation technologies: one- and two-dimensional liquid chromatography and two-dimensional gel electrophoresis. Mol. Cell. Proteomics 5(12), 2392-2411 (2006).
49. Distler AM, Kerner J, Peterman SM, Hoppel CL. A targeted proteomic approach for the analysis of rat liver mitochondrial outer membrane proteins with extensive sequence coverage. Anal. Biochem. 356(1), 18-29 (2006).
50. Zahedi RP, Sickmann A, Boehm AM et al. Proteomic analysis of the yeast mitochondrial outer membrane reveals accumulation of a subclass of preproteins. Mol. Biol. Cell. 17(3), 1436-1450 (2006).
51. Suzuki T, Terasaki M, Takemoto-Hori C et al. Proteomic analysis of the mammalian mitochondrial ribosome. Identification of protein components in the 28S small subunit. J. Biol. Chem. 276(35), 33181-33195 (2001).
52. Koc EC, Burkhart W, Blackburn K, Koc H, Moseley A, Spremulli LL. Identification of four proteins from the small subunit of the mammalian mitochondrial ribosome using a proteomics approach. Protein Sci. 10(3), 471-481 (2001). (Pubitemid 32221138)
53. Koc EC, Burkhart W, Blackburn K, Moseley A, Koc H, Spremulli LL. A proteomics approach to the identification of mammalian mitochondrial small subunit ribosomal proteins. J. Biol. Chem. 275(42), 32585-32591 (2000).
54. Suzuki T, Terasaki M, Takemoto-Hori C et al. Structural compensation for the deficit of rRNA with proteins in the mammalian mitochondrial ribosome. Systematic analysis of protein components of the large ribosomal subunit from mammalian mitochondria. J. Biol. Chem. 276(24), 21724-21736 (2001).
55. Brookes PS, Pinner A, Ramachandran A et al. High throughput two-dimensional blue-native electrophoresis: a tool for functional proteomics of mitochondria and signaling complexes. Proteomics 2(8), 969-977 (2002).
56. Reifschneider NH, Goto S, Nakamoto H et al. Defining the mitochondrial proteomes from five rat organs in a physiologically significant context using 2D blue-native/SDS-PAGE. J. Proteome Res. 5(5), 1117-1132 (2006).
57. Devreese B, Vanrobaeys F, Smet J, Van Beeumen J, Van Coster R. Mass spectrometric identification of mitochondrial oxidative phosphorylation subunits separated by two-dimensional blue-native polyacrylamide gel electrophoresis. Electrophoresis 23(15), 2525-2533 (2002).
58. Meyer B, Wittig I, Trifilieff E, Karas M, Schagger H. Identification of two proteins associated with mammalian ATP synthase. Mol. Cell. Proteomics 6(10), 1690-1699 (2007).
59. Nakamura Y, Suzuki H, Sakaguchi M, Mihara K. Targeting and assembly of rat mitochondrial translocase of outer membrane 22 (TOM22) into the TOM complex. J. Biol. Chem. 279(20), 21223-21232 (2004).
60. Faye A, Esnous C, Price NT, Onfray MA, Girard J, Prip-Buus C. Rat liver carnitine palmitoyltransferase 1 forms an oligomeric complex within the outer mitochondrial membrane. J. Biol. Chem. 282(37), 26908-26916 (2007).
61. Lopez-Campistrous A, Hao L, Xiang W et al. Mitochondrial dysfunction in the hypertensive rat brain: respiratory complexes exhibit assembly defects in hypertension. Hypertension 51(2), 412-419 (2008).
62. Schilling B, Murray J, Yoo CB et al. Proteomic analysis of succinate dehydrogenase and ubiquinol-cytochrome c reductase (complex II and III) isolated by immunoprecipitation from bovine and mouse heart mitochondria. Biochim. Biophys. Acta 1762(2), 213-222 (2006).
63. Carroll J, Fearnley IM, Shannon RJ, Hirst J, Walker JE. Analysis of the subunit composition of complex I from bovine heart mitochondria. Mol. Cell. Proteomics 2(2), 117-126 (2003).
64. Schulenberg B, Aggeler R, Beechem JM, Capaldi RA, Patton WF. Analysis of steady-state protein phosphorylation in mitochondria using a novel fluorescent phosphosensor dye. J. Biol. Chem. 278(29), 27251-27255 (2003).
65. Hopper RK, Carroll S, Aponte AM et al. Mitochondrial matrix phosphoproteome: effect of extra mitochondrial calcium. Biochemistry 45(8), 2524-2536 (2006).
66. Lee J, Xu Y, Chen Y et al. Mitochondrial phosphoproteome revealed by an improved IMAC method and MS/MS/ MS. Mol. Cell. Proteomics 6(4), 669-676 (2007).
67. Cui Z, Hou J, Chen X et al. The profile of mitochondrial proteins and their phosphorylation signaling network in INS-1 b cells. J. Proteome Res. DOI: 10.1021/pr100139z (2010) (Epub ahead of print).
68. Pagliarini DJ, Dixon JE. Mitochondrial modulation: reversible phosphorylation takes center stage? Trends Biochem. Sci. 31(1), 26-34 (2006).
69. Horbinski C, Chu CT. Kinase signaling cascades in the mitochondrion: a matter of life or death. Free Radic. Biol. Med. 38(1), 2-11 (2005).
70. Yonekawa H, Akita Y. Protein kinase Ce: the mitochondria-mediated signaling pathway. FEBS J. 275(16), 4005-4013 (2008).
71. Feliciello A, Gottesman ME, Avvedimento EV. cAMP-PKA signaling to the mitochondria: protein scaffolds, mRNA and phosphatases. Cell. Signal. 17(3), 279-287 (2005).
72. Carroll J, Fearnley IM, Skehel JM et al. The post-translational modifications of the nuclear encoded subunits of complex I from bovine heart mitochondria. Mol. Cell. Proteomics 4(5), 693-699 (2005).
73. Murray J, Taylor SW, Zhang B, Ghosh SS, Capaldi RA. Oxidative damage to mitochondrial complex I due to peroxynitrite: identification of reactive tyrosines by mass spectrometry. J. Biol. Chem. 278(39), 37223-37230 (2003).
74. Taylor SW, Fahy E, Murray J, Capaldi RA, Ghosh SS. Oxidative post-translational modification of tryptophan residues in cardiac mitochondrial proteins. J. Biol. Chem. 278(22), 19587-19590 (2003).
75. Hunzinger C, Wozny W, Schwall GP et al. Comparative profiling of the mammalian mitochondrial proteome: multiple aconitase-2 isoforms including N-formylkynurenine modifications as part of a protein biomarker signature for reactive oxidative species. J. Proteome Res. 5(3), 625-633 (2006).
76. Lin TK, Hughes G, Muratovska A et al. Specific modification of mitochondrial protein thiols in response to oxidative stress: a proteomics approach. J. Biol. Chem. 277(19), 17048-17056 (2002).
77. Choksi KB, Papaconstantinou J. Age-related alterations in oxidatively damaged proteins of mouse heart mitochondrial electron transport chain complexes. Free Radic. Biol. Med. 44(10), 1795 - 1805 (2008).
78. Vogtle FN, Wortelkamp S, Zahedi RP et al. Global analysis of the mitochondrial N-proteome identifies a processing peptidase critical for protein stability. Cell 139(2), 428-439 (2009).
79. Gillardon F. Differential mitochondrial protein expression profiling in neurodegenerative diseases. Electrophoresis 27(13), 2814-2818 (2006).
80. Atamna H, Frey WH 2nd. Mechanisms of mitochondrial dysfunction and energy deficiency in Alzheimer's disease. Mitochondrion 7(5), 297-310 (2007).
81. Reddy PH, Beal MF. Are mitochondria critical in the pathogenesis of Alzheimer's disease? Brain Res. Brain Res. Rev. 49(3), 618-632 (2005).
82. Lovell MA, Xiong S, Markesbery WR, Lynn BC. Quantitative proteomic analysis of mitochondria from primary neuron cultures treated with amyloid b peptide. Neurochem. Res. 30(1), 113-122 (2005).
83. Gillardon F, Rist W, Kussmaul L et al. Proteomic and functional alterations in brain mitochondria from Tg2576 mice occur before amyloid plaque deposition. Proteomics 7(4), 605-616 (2007).
84. Sultana R, Butterfield DA. Oxidatively modified, mitochondria-relevant brain proteins in subjects with Alzheimer disease and mild cognitive impairment. J. Bioenerg. Biomembr. 41(5), 441-446 (2009).
85. Jin J, Davis J, Zhu D et al. Identification of novel proteins affected by rotenone in mitochondria of dopaminergic cells. BMC Neurosci. 8, 67 (2007).
86. Jin J, Meredith GE, Chen L et al. Quantitative proteomic analysis of mitochondrial proteins: relevance to Lewy body formation and Parkinson's disease. Brain Res. Mol. Brain Res. 134(1), 119-138 (2005).
87. Fukada K, Zhang F, Vien A, Cashman NR, Zhu H. Mitochondrial proteomic analysis of a cell line model of familial amyotrophic lateral sclerosis. Mol. Cell. Proteomics 3(12), 1211-1223 (2004).
88. Verma M, Kagan J, Sidransky D, Srivastava S. Proteomic analysis of cancer-cell mitochondria. Nat. Rev. Cancer 3(10), 789-795 (2003).
89. Kagan J, Srivastava S. Mitochondria as a target for early detection and diagnosis of cancer. Crit. Rev. Clin. Lab. Sci. 42(5-6), 453-472 (2005).
90. Herrmann PC, Gillespie JW, Charboneau L et al. Mitochondrial proteome: altered cytochrome c oxidase subunit levels in prostate cancer. Proteomics 3(9), 1801-1810 (2003).
91. Krieg RC, Knuechel R, Schiffmann E, Liotta LA, Petricoin EF 3rd, Herrmann PC. Mitochondrial proteome: cancer-altered metabolism associated with cytochrome c oxidase subunit level variation. Proteomics 4(9), 2789-2795 (2004).
92. Kim HK, Park WS, Kang SH et al. Mitochondrial alterations in human gastric carcinoma cell line. Am. J. Physiol. Cell. Physiol. 293(2), C761-C771 (2007).
93. Copeland WC, Wachsman JT, Johnson FM, Penta JS. Mitochondrial DNA alterations in cancer. Cancer Invest. 20(4), 557-569 (2002).
94. Sanchez-Cespedes M, Parrella P, Nomoto S et al. Identification of a mononucleotide repeat as a major target for mitochondrial DNA alterations in human tumors. Cancer Res. 61(19), 7015-7019 (2001).
95. Mulder H, Ling C. Mitochondrial dysfunction in pancreatic b-cells in Type 2 diabetes. Mol. Cell. Endocrinol. 297(1-2), 34-40 (2009).
96. Turko IV, Murad F. Quantitative protein profiling in heart mitochondria from diabetic rats. J. Biol. Chem. 278(37), 35844-35849 (2003).
97. Deng WJ, Nie S, Dai J, Wu JR, Zeng R. Proteome, phosphoproteome and hydroxyproteome of liver mitochondria in diabetic rats at early pathogenic stages. Mol. Cell. Proteomics 9(1), 100-116 (2010).
98. Maechler P, Wollheim CB. Mitochondrial function in normal and diabetic b-cells. Nature 414(6865), 807-812 (2001).
99. Hojlund K, Wrzesinski K, Larsen PM et al. Proteome analysis reveals phosphorylation of ATP synthase b-subunit in human skeletal muscle and proteins with potential roles in Type 2 diabetes. J. Biol. Chem. 278(12), 10436-10442 (2003).
100. Kartha GK, Moshal KS, Sen U et al. Renal mitochondrial damage and protein modification in Type-2 diabetes. Acta Diabetol. 45(2), 75-81 (2008).
101. Lambert AJ, Brand MD. Research on mitochondria and aging, 2006-2007. Aging Cell 6(4), 417-420 (2007).
102. Liu Y, He J, Ji S et al. Comparative studies of early liver dysfunction in senescence-accelerated mouse using mitochondrial proteomics approaches. Mol. Cell. Proteomics 7(9), 1737-1747 (2008).
103. Yan L, Ge H, Li H et al. Gender-specific proteomic alterations in glycolytic and mitochondrial pathways in aging monkey hearts. J. Mol. Cell. Cardiol. 37(5), 921-929 (2004).
104. O'Connell K, Ohlendieck K. Proteomic DIGE analysis of the mitochondria-enriched fraction from aged rat skeletal muscle. Proteomics 9(24), 5509-5524 (2009).
105. Kim N, Lee Y, Kim H et al. Potential biomarkers for ischemic heart damage identified in mitochondrial proteins by comparative proteomics. Proteomics 6(4), 1237-1249 (2006).
106. Liu XH, Qian LJ, Gong JB, Shen J, Zhang XM, Qian XH. Proteomic analysis of mitochondrial proteins in cardiomyocytes from chronic stressed rat. Proteomics 4(10), 3167-3176 (2004).
107. Smith JR, Matus IR, Beard DA, Greene AS. Differential expression of cardiac mitochondrial proteins. Proteomics 8(3), 446-462 (2008).
108. Fountoulakis M, Soumaka E, Rapti K et al. Alterations in the heart mitochondrial proteome in a desmin null heart failure model. J. Mol. Cell. Cardiol. 38(3), 461-474 (2005).
109. Ruiz-Romero C, Calamia V, Mateos J et al. Mitochondrial dysregulation of osteoarthritic human articular chondrocytes analyzed by proteomics: a decrease in mitochondrial superoxide dismutase points to a redox imbalance. Mol. Cell. Proteomics 8(1), 172-189 (2009).
110. Venkatraman A, Landar A, Davis AJ et al. Modification of the mitochondrial proteome in response to the stress of ethanol-dependent hepatotoxicity. J. Biol. Chem. 279(21), 22092-22101 (2004).
111. Shi L, Wang Y, Tu S et al. The responses of mitochondrial proteome in rat liver to the consumption of moderate ethanol: the possible roles of aldo-keto reductases. J. Proteome Res. 7(8), 3137-3145 (2008).
112. Miller I, Gemeiner M, Gesslbauer B et al. Proteome analysis of rat liver mitochondria reveals a possible compensatory response to endotoxic shock. FEBS Lett. 580(5), 1257-1262 (2006).
113. Detmer SA, Chan DC. Functions and dysfunctions of mitochondrial dynamics. Nat. Rev. Mol. Cell Biol. 8(11), 870-879 (2007).
114. Cotter D, Guda P, Fahy E, Subramaniam S. MitoProteome: mitochondrial protein sequence database and annotation system. Nucleic Acids Res. 32, D463-D467 (2004).
115. Elstner M, Andreoli C, Ahting U et al. MitoP2: an integrative tool for the analysis of the mitochondrial proteome. Mol. Biotechnol. 40(3), 306-315 (2008).
116. Elstner M, Andreoli C, Klopstock T, Meitinger T, Prokisch H. The mitochondrial proteome database: MitoP2. Methods Enzymol. 457, 3-20 (2009).
117. Smith AC, Robinson AJ. MitoMiner: an integrated database for the storage and analysis of mitochondrial proteomics data. Mol. Cell. Proteomics 8(6), 1324-1337 (2009).
118. McDonald TG, Van Eyk JE. Mitochondrial proteomics. Undercover in the lipid bilayer. Basic Res. Cardiol. 98(4), 219-227 (2003).
119. Meisinger C, Sickmann A, Pfanner N. The mitochondrial proteome: from inventory to function. Cell. 134(1), 22-24 (2008).
120. Wilkins M. Proteomics data mining. Expert Rev. Proteomics 6(6), 599-603 (2009).
121. Emanuelsson O, Brunak S, von Heijne G, Nielsen H. Locating proteins in the cell using TargetP, SignalP and related tools. Nat. Protoc. 2(4), 953-971 (2007).
122. Guda C, Fahy E, Subramaniam S. MITOPRED: a genome-scale method for prediction of nucleus-encoded mitochondrial proteins. Bioinformatics 20(11), 1785-1794 (2004).
123. Chou KC, Shen HB. Cell-PLoc: a package of web servers for predicting subcellular localization of proteins in various organisms. Nat. Protoc. 3(2), 153-162 (2008).
124. Ingman M, Gyllensten U. mtDB: Human Mitochondrial Genome Database, a resource for population genetics and medical sciences. Nucleic Acids Res. 34, D749-D751 (2006).
125. Ruiz-Pesini E, Lott MT, Procaccio V et al. An enhanced MITOMAP with a global mtDNA mutational phylogeny. Nucleic Acids Res. 35(Database issue), D823-D828 (2007).
126. Heazlewood JL, Millar AH. AMPDB: the Arabidopsis Mitochondrial Protein Database. Nucleic Acids Res. 33(Database issue), D605-D610 (2005).