Quantitative and qualitative 2D electrophoretic analysis of differentially expressed mitochondrial proteins from five mouse organs

Proteomics

Volumn 13, Issue 1, 2013, Pages 179-195

  Techritz, Sandra ^a   Lützkendorf, Susanne ^a   Bazant, Esther ^a   Becker, Silke ^a   Klose, Joachim ^a   Schuelke, Markus ^a  

^a CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

Author keywords

Biomedicine; Mass spectrometry; Mitochondrial proteome; Posttranslational modification; Tissue expression; Two dimensional gel electrophoresis

Indexed keywords

ALCOHOL DEHYDROGENASE; ALDEHYDE DEHYDROGENASE ISOENZYME 2; ATP SYNTHASE ALPHA CHAIN; CARBAMOYL PHOSPHATE SYNTHASE; CARRIER PROTEIN; CATALASE; CYCLOPHILIN A; GREEN FLUORESCENT PROTEIN; ISOCITRATE DEHYDROGENASE; ISOCITRATE DEHYDROGENASE ALPHA SUBUNIT; MITOCHONDRIAL PROTEIN; OXIDOREDUCTASE; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATE SYNTHASE; QUINONE OXIDOREDUCTASE; UNCLASSIFIED DRUG; UPF0317 PROTEIN;

ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; DENSITOMETRY; ELECTROSPRAY MASS SPECTROMETRY; FEMALE; GENETIC CONSERVATION; GENETIC TRANSFECTION; LIQUID CHROMATOGRAPHY; MITOCHONDRIAL RESPIRATION; MITOCHONDRION; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS; TANDEM MASS SPECTROMETRY; TWO DIMENSIONAL ELECTROPHORESIS;

ANIMALS; BRAIN; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; GENE EXPRESSION; KIDNEY; MICE; MITOCHONDRIA, HEART; MITOCHONDRIA, LIVER; MITOCHONDRIA, MUSCLE; MITOCHONDRIAL PROTEINS; TISSUE DISTRIBUTION;

EID: 84872423749     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201100539     Document Type: Article

References (54)

1. Scaglia, F., Towbin, J. A., Craigen, W. J., Belmont, J. W. et al., Clinical spectrum, morbidity, and mortality in 113 pediatric patients with mitochondrial disease. Pediatrics 2004, 114, 925-931.
2. Harris, M. A., Clark, J., Ireland, A., Lomax, J. et al., The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 2004, 32, D258-D261.
3. Bender, A., Krishnan, K. J., Morris, C. M., Taylor, G. A. et al., High levels of mitochondrial DNA deletions in substantia nigra neurons in aging and Parkinson disease. Nat. Genet. 2006, 38, 515-517.
4. Pagliarini, D. J., Calvo, S. E., Chang, B., Sheth, S. A. et al., A mitochondrial protein compendium elucidates complex I disease biology. Cell 2008, 134, 112-123.
5. Hao, H. X., Rutter, J., Revealing human disease genes through analysis of the yeast mitochondrial proteome. Cell Cycle 2009, 8, 4007-4008.
6. Mootha, V. K., Bunkenborg, J., Olsen, J. V., Hjerrild, M. et al., Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria. Cell 2003, 115, 629-640.
7. Reifschneider, N. H., Goto, S., Nakamoto, H., Takahashi, R. et al., Defining the mitochondrial proteomes from five rat organs in a physiologically significant context using 2D blue-native/SDS-PAGE. J. Proteome Res. 2006, 5, 1117-1132.
8. Haack, T. B., Danhauser, K., Haberberger, B., Hoser, J. et al., Exome sequencing identifies ACAD9 mutations as a cause of complex I deficiency. Nat. Genet. 2010, 42, 1131-1134.
9. Xie, J., Techritz, S., Haebel, S., Horn, A. et al., A two-dimensional electrophoretic map of human mitochondrial proteins from immortalized lymphoblastoid cell lines: a prerequisite to study mitochondrial disorders in patients. Proteomics 2005, 5, 2981-2999.
10. Schluter, H., Apweiler, R., Holzhutter, H. G., Jungblut, P. R., Finding one's way in proteomics: a protein species nomenclature. Chem. Cent. J. 2009, 3, 11.
11. Gianazza, E., Vergani, L., Wait, R., Brizio, C. et al., Coordinated and reversible reduction of enzymes involved in terminal oxidative metabolism in skeletal muscle mitochondria from a riboflavin-responsive, multiple acyl-CoA dehydrogenase deficiency patient. Electrophoresis 2006, 27, 1182-1198.
12. Lagranha, C. J., Deschamps, A., Aponte, A., Steenbergen, C. et al., Sex differences in the phosphorylation of mitochondrial proteins result in reduced production of reactive oxygen species and cardioprotection in females. Circ. Res. 2010, 106, 1681-1691.
13. Yan, L., Ge, H., Li, H., Lieber, S. C. et al., Gender-specific proteomic alterations in glycolytic and mitochondrial pathways in aging monkey hearts. J. Mol. Cell Cardiol. 2004, 37, 921-929.
14. Zemojtel, T., Kolanczyk, M., Kossler, N., Stricker, S. et al., Mammalian mitochondrial nitric oxide synthase: characterization of a novel candidate. FEBS Lett. 2006, 580, 455-462.
15. Heukeshoven, J., Dernick, R., Improved silver staining procedure for fast staining in PhastSystem Development Unit. I. Staining of sodium dodecyl sulfate gels. Electrophoresis 1988, 9, 28-32.
16. Gygi, S. P., Rochon, Y., Franza, B. R., Aebersold, R., Correlation between protein and mRNA abundance in yeast. Mol. Cell Biol. 1999, 19, 1720-1730.
17. Kaindl, A. M., Zabel, C., Stefovska, V., Lehnert, R. et al., Subacute proteome changes following traumatic injury of the developing brain: implications for a dysregulation of neuronal migration and neurite arborization. Proteomics Clin. Appl. 2007, 1, 640-649.
18. Sokal, R. R., Michener, C. D., A statistical method for evaluating systematic relationships. Univ. Kans Sci. Bull. 1958, 38, 1409-1438.
19. Yeung, K. Y., Ruzzo, W. L., Principal component analysis for clustering gene expression data. Bioinformatics 2001, 17, 763-774.
20. Guenther, U. P., Varon, R., Schlicke, M., Dutrannoy, V. et al., Clinical and mutational profile in spinal muscular atrophy with respiratory distress (SMARD): defining novel phenotypes through hierarchical cluster analysis. Hum. Mutat. 2007, 28, 808-815.
21. Forner, F., Foster, L. J., Campanaro, S., Valle, G. et al., Quantitative proteomic comparison of rat mitochondria from muscle, heart, and liver. Mol. Cell Proteomics 2006, 5, 608-619.
22. Damerval, C., Quantification of silver-stained proteins resolved by two-dimensional electrophoresis: genetic variability as related to abundance and solubility in two maize lines. Electrophoresis 1994, 15, 1573-1579.
23. Corthals, G. L., Wasinger, V. C., Hochstrasser, D. F., Sanchez, J. C., The dynamic range of protein expression: a challenge for proteomic research. Electrophoresis 2000, 21, 1104-1115.
24. Mortensen, P., Gouw, J. W., Olsen, J. V., Ong, S. E. et al., MSQuant, an open source platform for mass spectrometry-based quantitative proteomics. J. Proteome Res. 2010, 9, 393-403.
25. Tran, J. C., Zamdborg, L., Ahlf, D. R., Lee, J. E. et al., Mapping intact protein isoforms in discovery mode using top-down proteomics. Nature 2011, 480, 254-258.
26. Mi, J., Kirchner, E., Cristobal, S., Quantitative proteomic comparison of mouse peroxisomes from liver and kidney. Proteomics 2007, 7, 1916-1928.
27. Zhang, H., Fan, X., Bagshaw, R., Mahuran, D. J. et al., Purification and proteomic analysis of lysosomal integral membrane proteins. Methods Mol. Biol. 2008, 432, 229-241.
28. Gelfi, C., Vasso, M., Cerretelli, P., Diversity of human skeletal muscle in health and disease: contribution of proteomics. J. Proteomics 2011, 74, 774-795.
29. Coulonval, K., Bockstaele, L., Paternot, S., Roger, P. P., Phosphorylations of cyclin-dependent kinase 2 revisited using two-dimensional gel electrophoresis. J. Biol. Chem. 2003, 278, 52052-52060.
30. Reinders, J., Wagner, K., Zahedi, R. P., Stojanovski, D. et al., Profiling phosphoproteins of yeast mitochondria reveals a role of phosphorylation in assembly of the ATP synthase. Mol. Cell Proteomics 2007, 6, 1896-1906.
31. Raddatz, K., Albrecht, D., Hochgrafe, F., Hecker, M. et al., A proteome map of murine heart and skeletal muscle. Proteomics 2008, 8, 1885-1897.
32. Nakagawa, T., Shimizu, S., Watanabe, T., Yamaguchi, O. et al., Cyclophilin D-dependent mitochondrial permeability transition regulates some necrotic but not apoptotic cell death. Nature 2005, 434, 652-658.
33. Baines, C. P., Kaiser, R. A., Purcell, N. H., Blair, N. S. et al., Loss of cyclophilin D reveals a critical role for mitochondrial permeability transition in cell death. Nature 2005, 434, 658-662.
34. Cohen-Sfady, M., Nussbaum, G., Pevsner-Fischer, M., Mor, F. et al., Heat shock protein 60 activates B cells via the TLR4-MyD88 pathway. J. Immunol. 2005, 175, 3594-3602.
35. Lehnardt, S., Schott, E., Trimbuch, T., Laubisch, D. et al., A vicious cycle involving release of heat shock protein 60 from injured cells and activation of toll-like receptor 4 mediates neurodegeneration in the CNS. J. Neurosci. 2008, 28, 2320-2331.
36. Rao, P. V., Gonzalez, P., Persson, B., Jornvall, H. et al., Guinea pig and bovine zeta-crystallins have distinct functional characteristics highlighting replacements in otherwise similar structures. Biochemistry 1997, 36, 5353-5362.
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. 2000, 300, 1005-1016.
38. Lopez, L. C., Schuelke, M., Quinzii, C. M., Kanki, T. et al., Leigh syndrome with nephropathy and CoQ10 deficiency due to decaprenyl diphosphate synthase subunit 2 (PDSS2) mutations. Am. J. Hum. Genet. 2006, 79, 1125-1129.
39. Zhou, H. J., Liu, Y. K., Chui, J. F., Sun, Q. L. et al., A glycoproteome database of normal human liver tissue. J. Cancer Res. Clin. Oncol. 2007, 133, 379-387.
40. Guy, H. I., Evans, D. R., Function of the major synthetase subdomains of carbamyl-phosphate synthetase. J. Biol. Chem. 1996, 271, 13762-13769.
41. Bhat, N. K., Avadhani, N. G., The transport and processing of carbamyl phosphate synthetase-I in mouse hepatic mitochondria. Biochem. Biophys. Res. Commun. 1984, 118, 514-522.
42. Huo, R., Zhu, H., Lu, L., Ying, L. et al., Molecular cloning, identification and characteristics of a novel isoform of carbamyl phosphate synthetase I in human testis. J. Biochem. Mol. Biol. 2005, 38, 28-33.
43. Kanemitsu, F., Mizushima, J., Kageoka, T., Okigaki, T. et al., Characterization of two types of mitochondrial creatine kinase isolated from normal human cardiac muscle and brain tissue. Electrophoresis 2000, 21, 266-270.
44. Reinders, J., Zahedi, R. P., Pfanner, N., Meisinger, C. et al., Toward the complete yeast mitochondrial proteome: multidimensional separation techniques for mitochondrial proteomics. J. Proteome Res. 2006, 5, 1543-1554.
45. Impraim, C., Wang, G., Yoshida, A., Structural mutation in a major human aldehyde dehydrogenase gene results in loss of enzyme activity. Am. J. Hum. Genet. 1982, 34, 837-841.
46. Salvi, M., Battaglia, V., Brunati, A. M., La, R. N. et al., Catalase takes part in rat liver mitochondria oxidative stress defense. J. Biol. Chem. 2007, 282, 24407-24415.
47. Jiang, X. S., Dai, J., Sheng, Q. H., Zhang, L. 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 2005, 4, 12-34.
48. Sass, J. O., Fischer, K., Wang, R., Christensen, E. et al., D-glyceric aciduria is caused by genetic deficiency of D-glycerate kinase (GLYCTK). Hum. Mutat. 2010, 31, 1280-1285.
49. Guo, J. H., Hexige, S., Chen, L., Zhou, G. J. et al., Isolation and characterization of the human D-glyceric acidemia related glycerate kinase gene GLYCTK1 and its alternatively splicing variant GLYCTK2. DNA Seq. 2006, 17, 1-7.
50. Allan, D., Lohnes, D., Cloning and developmental expression of mouse aldehyde reductase (AKR1A4). Mech. Dev. 2000, 94, 271-275.
51. Xiang, S., Tong, L., Crystal structures of human and Staphylococcus aureus pyruvate carboxylase and molecular insights into the carboxyltransfer reaction. Nat. Struct. Mol. Biol. 2008, 15, 295-302.
52. Mao, L., Zabel, C., Wacker, M. A., Nebrich, G. et al., Estimation of the mtDNA mutation rate in aging mice by proteome analysis and mathematical modeling. Exp. Gerontol. 2006, 41, 11-24.
53. Zabel, C., Nguyen, H. P., Hin, S. C., Hartl, D. et al., Proteasome and oxidative phoshorylation changes may explain why aging is a risk factor for neurodegenerative disorders. J. Proteomics 2010, 73, 2230-2238.
54. Sahin, E., Depinho, R. A., Axis of ageing: telomeres, p53 and mitochondria. Nat. Rev. Mol. Cell Biol. 2012, 13, 397-404.