Chapter 6 Post-translational Modifications of Mitochondrial Outer Membrane Proteins

Methods in Enzymology

Volumn 457, Issue B, 2009, Pages 97-115

  Distler, Anne M ^a,b   Kerner, Janos ^a,b   Lee, Kwangwon ^a,b   Hoppel, Charles L ^a,b  

^a CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b CASE WESTERN RESERVE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL PROTEIN; OUTER MEMBRANE PROTEIN; CARNITINE PALMITOYLTRANSFERASE;

ALKYLATION; GEL ELECTROPHORESIS; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NONHUMAN; OUTER MEMBRANE; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN PROCESSING; PROTEOMICS; RAT; REVIEW; TECHNOLOGY; WESTERN BLOTTING; AMINO ACID SEQUENCE; ANIMAL; ARTICLE; CHEMISTRY; HUMAN; ISOLATION AND PURIFICATION; METABOLISM; METHODOLOGY; MITOCHONDRIAL MEMBRANE; MOLECULAR GENETICS;

AMINO ACID SEQUENCE; ANIMALS; CARNITINE O-PALMITOYLTRANSFERASE; ELECTROPHORESIS, POLYACRYLAMIDE GEL; HUMANS; MASS SPECTROMETRY; MITOCHONDRIAL MEMBRANES; MITOCHONDRIAL PROTEINS; MOLECULAR SEQUENCE DATA; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEOMICS;

EID: 65449129608     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(09)05006-X     Document Type: Review

References (57)

1. Bagshaw R.D., Mahuran D.J., and Callahan J.W. A proteomics analysis of lysosomal integral-membrane proteins reveals the diverse composition of the organelle. Mol. Cell Proteomics 4 (2005) 133-143
2. Barnouin K. Two-dimensional gel electrophoresis for analysis of protein complexes. Methods Mol. Biol. 261 (2004) 479-498
3. Bell A.W., Ward M.A., Blackstock W.P., Freeman H.N., Choudhary J.S., Lewis A.P., Chotai D., Fazel A., Gashue J.N., Paiement J., Palcy S., Chevet E., et al. Proteomics characterization of abundant Golgi membrane proteins. J. Biol. Chem. 276 (2001) 5152-5165
4. Benz R. Permeation of hydrophilic solutes through mitochondrial outer membranes: Review on mitochondrial porins. Biochim. Biophys. Acta 1197 (1994) 167-196
5. Bernardi P. Mitochondrial transport of cations: Channels, exchangers, and permeability transition. Physiol. Rev. 79 (1999) 1127-1155
6. Bionda C., Portoukalian J., Schmitt D., Rodriguez-Lafrasse C., and Ardail D. Subcellular compartmentalization of ceramide metabolism: MAM (mitochondria-associated membrane) and/or mitochondria?. Biochem. J. 382 (2004) 527-533
7. Braun R.J., Kinkl N., Beer M., and Ueffing M. Two-dimensional electrophoresis of membrane proteins. Anal. Bioanal. Chem. 389 (2007) 1033-1045
8. Bruserud O., Stapnes C., Tronstad K.J., Ryningen A., Anensen N., and Gjertsen B.T. Protein lysine acetylation in normal and leukaemic haematopoiesis: HDACs as possible therapeutic targets in adult AML. Expert Opin. Ther. Targets 10 (2006) 51-68
9. Buhler S., Michels J., Wendt S., Rück A., Brdiczka D., Welte W., and Przybylski M. Mass spectrometric mapping of ion channel proteins (porins) and identification of their supramolecular membrane assembly. Proteins 30 Suppl 2 (1998) 63-73
10. Caesar R., Warringer J., and Blomberg A. Physiological importance and identification of novel targets for the N-terminal acetyltransferase NatB. Eukaryot. Cell 5 (2006) 368-378
11. Cheng E.H.-Y., Sheiko T., Fisher J.K., Craigen W.J., and Korsmeyer S.J. VDAC2 inhibits BAK activation and mitochondrial apoptosis. Science 301 (2003) 513-517
12. Crouser E.D., Julian M.W., Huff J.E., Mandich D.V., and Green-Church K.B. A proteomic analysis of liver mitochondria during acute endotoxemia. Intensive Care Med. 32 (2006) 1252-1262
13. Da Cruz S., and Martinou J.C. Purification and proteomic analysis of the mouse liver mitochondrial inner membrane. Methods Mol. Biol. 432 (2008) 101-116
14. Da Cruz S., Xenarios I., Langridge J., Vilbois F., Parone P.A., and Martinou J.C. Proteomic analysis of the mouse liver mitochondrial inner membrane. J. Biol. Chem. 278 (2003) 41566-41571
15. Distler A.M., Kerner J., and Hoppel C.L. Post-translational modifications of rat liver mitochondrial outer membrane proteins identified by mass spectrometry. Biochim. Biophys. Acta 1774 (2007) 628-636
16. Distler A.M., Kerner J., and Hoppel C.L. Proteomics of mitochondrial inner and outer membranes. Proteomics 8 (2008) 4066-4082
17. Distler A.M., Kerner J., Peterman S.M., and Hoppel C.L. A targeted proteomic approach for the analysis of rat liver mitochondrial outer membrane proteins with extensive sequence coverage. Anal. Biochem. 356 (2006) 18-29
18. Ficarro S.B., McCleland M.L., Stukenberg P.T., Burke D.J., Ross M.M., Shabanowitz J., Hunt D.F., and White F.M. Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat. Biotech. 20 (2002) 301-305
19. Green D.R., and Kroemer G. The pathophysiology of mitochondrial cell death. Science 305 (2004) 626-629
20. Green D.R., and Reed J.C. Mitochondria and apoptosis. Science 281 (1998) 1309-1312
21. Hellman U., Wernstedt C., Gonez J., and Heldin C.H. Improvement of an "In-Gel" digestion procedure for the micropreparation of internal protein fragments for amino acids sequencing. Anal. Biochem. 224 (1995) 451-455
22. Hoppel C.L., DiMarco J.P., and Tandler B. Riboflavin and rat hepatic cell structure and function: Mitochondrial oxidative metabolism in deficiency states. J. Biol. Chem. 254 (1979) 4164-4170
23. Hoppel C., Kerner J., Turkaly P., Minkler P., and Tandler B. Isolation of hepatic mitochondrial contact sites: Previously unrecognized inner membrane components. Anal. Biochem. 302 (2002) 60-69
24. Hoppel C., Kerner J., Turkaly P., and Tandler B. Rat liver mitochondrial contact sites and carnitine palmitoyltransferase-I. Arch. Biochem. Biophys. 392 (2001) 321-325
25. Hoppel C.L., Kerner J., Turkaly P., Turkaly J., and Tandler B. The malonyl-CoA-sensitive form of carnitine palmitoyltransferase is not localized exclusively in the outer membrane of rat liver mitochondria. J. Biol. Chem. 273 (1998) 23495-23503
26. Issaq H., and Veenstra T. Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE): Advances and perspectives. Biotechniques 44 (2008) 697-700
27. Kerner J., Distler A.M., Minkler P., Parland W., Peterman S.M., and Hoppel C.L. Phosphorylation of rat liver mitochondrial carnitinepalmitoyltransferase-I: Effect on the kinetic properties of the enzyme. J. Biol. Chem. 279 (2004) 41104-41113
28. Kim S.C., Sprung R., Chen Y., Xu Y., Ball H., Pei J., Cheng T., Kho Y., Xiao H., Xiao L., Grishin N.V., White M., et al. Substrate and functional diversity of lysine acetylation revealed by a proteomics survey. Mol. Cell 23 (2006) 607-618
29. Klemm C., Otto S., Wolf C., Haseloff R.F., Beyermann M., and Krause E. Evaluation of the titanium dioxide approach for MS analysis of phosphopeptides. J. Mass Spectrom. 41 (2006) 1623-1632
30. Knoblach B., Keller B.O., Gronendyk J., Aldred S., Zheng J., Lemire B.D., Li L., and Michalak M. Erp19 and Erp46, new membrers of the thioredoxin family of endoplasmic reticulum proteins. Mol. Cell. Proteomics 2 (2003) 1104-1119
31. Kweon H.K., and Håkansson K. Selective zirconium dioxide-based enrichment of phosphorylated peptides for mass spectrometric analysis. Anal. Chem. 78 (2006) 1743-1749
32. Linden M., and Karlsson G. Identification of porin as a binding site for MAP2. Biochem. Biophys. Res. Commun. 218 (1996) 833-836
33. MacCoss M.J., McDonald W.H., Saraf A., Sadygov R., Clark J.M., Tasto J.J., Gould K.L., Wolters D., Washburn M., Weiss A., Clark J.I., and Yates III J.R. Shotgun identification of protein modifications from protein complexes and lens tissue. Proc. Natl. Acad. Sci. USA 99 (2002) 7900-7905
34. Marelli M., Smith J.J., Jung S., Yi E., Nesvizhskii A.I., Christmas R.H., Saleem R.A., Tam Y.Y., Fagarasanu A., Goodlett D.R., Aebersold R., Rachubinski R.A., et al. Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane. J. Cell. Biol. 167 (2004) 1099-1112
35. Mootha V.K., Bunkenborg J., Olsen J.V., Hjerrild M., Wisniewski J.R., Stahl E., Bolouri M.S., Ray H.N., Sihag S., Kamal M., Patterson N., Lander E.S., et al. Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria. Cell 115 (2003) 629-640
36. Parsons D.F., Williams G.R., and Chance B. Characteristics of isolated and purified preparations of the outer and inner membranes of mitochondria. Ann. NY Acad. Sci. 137 (1966) 643-666
37. Paumen M.B., Ishida Y., Han H., Muramatsu M., Eguchi Y., Tsujimoto Y., and Honjo T. Direct interaction of the mitochondrial membrane protein carnitine palmitoyltransferase I with Bcl-2. Biochem. Biophys. Res. Commun. 231 (1997) 523-525
38. Perrier J., Durand A.G., Hiardina T., and Puigserver A. Catabolism of intracellular N-terminal acetylated proteins: Involvement of acylpeptide hydrolase and acylase. Biochimie 87 (2005) 673-685
39. Pizzo P., and Pozzan T. Mitochondria-endoplasmic reticulum choreography: Structure and signaling dynamics. Trends Cell Biol. 17 (2007) 512-517
40. Polevoda B., Norbeck J., Takakura H., Blomberg A., and Sherman F. Identification and specificities of N-terminal acetyltransferases from Saccharomyces cerevisiae. EMBO J. 18 (1999) 6155-6168
41. Prokisch H., Scharfe C., Camp D.G., Xiao W., David L., Andreoli C., Monroe M.E., Moore R.J., Gritsenko M.A., Kozany C., Hixson K.K., Mottaz H.M., et al. Integrative analysis of the mitochondrial proteome in yeast. PLoS Biol. 2 (2004) e160
42. Rabilloud T. Two-dimensional gel electrophoresis in proteomics: Old, old fashioned, but it still climbs up the mountains. Proteomics 2 (2002) 3-10
43. Santoni V., Molloy M., and Rabilloud T. Membrane proteins and proteomics: Un amour impossible?. Electrophoresis 21 (2000) 1054-1070
44. Schmitt S., Prokisch H., Schlunck T., Camp D.G., Ahting U., Waizenegger T., Scharfe C., Meitinger T., Imhof A., Neupert W., Oefner P.J., and Rapaport D. Proteome analysis of mitochondrial outer membrane from Neurospora crassa. Proteomics 6 (2006) 72-80
45. Shimizu S., Matsuoka Y., Shinohara Y., Yoneda ., and Tsujimoto Y. Essential role of voltage-dependent anion channel in various forms of apoptosis in mammalian cells. J. Cell Biol. 152 (2001) 237-250
46. Sickmann A., Reinders J., Wagner Y., Joppich C., Zahedi R., Meyer H.E., Schonfisch B., Perschil I., Charcinska A., Guiard B., Rehling P., Pfanner N., et al. The proteome of Saccharomyces cereviase mitochondria. Proc. Natl. Acad. Sci. USA 100 (2003) 13207-13212
47. Spierings D., McStay G., Saleh M., Bender C., Chipuk J., Maurer U., and Green D.R. Connected to death: The (unexpurgated) mitochondrial pathway of apoptosis. Science 310 (2005) 66-67
48. Taylor S.W., Fahy E., Zhang B., Glenn G.M., Warnock D.E., Wiley S., Murphy A.N., Gaucher S.P., Capaldi R.A., Gibson B.W., and Ghosh S.S. Characterization of the human heart mitochondrial proteome. Nat. Biotechnol. 21 (2003) 281-286
49. Taylor R.S., Wu C.C., Hays L.G., Eng J.K., Yates III J.R., and Howell K.E. Proteomics of rat liver Golgi complex: Minor proteins are identified through sequential fractionation. Electrophoresis 21 (2000) 3441-3459
50. Turkaly P., Kerner J., and Hoppel C.L. A 22 kDa polyanion inhibits carnitine-dependent fatty acid oxidation in rat liver mitochondria. FEBS Lett. 460 (1999) 241-245
51. Vavvas D., Apazidis A., Gamble J., Saha A.K., Patel A., Kemp B.E., Witters L.A., and Ruderman N.B. Contraction-induced changes in acetyl-CoA carboxylase and 5′-AMP-activated kinase in skeletal muscle. J. Biol. Chem. 272 (1997) 13255-13261
52. Vyssokikh M., and Brdiczka D. VDAC and peripheral channelling complexes in health and disease. Mol. Cell. Biochem. 256-257 (2004) 117-126
53. Washburn M.P., Wolters D., and Yates III J.R. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotech. 19 (2001) 242-305
54. Wu C.C., MacCoss M.J., Howell K.E., and Yates III J.R. A method for the comprehensive proteomic analysis of membrane proteins. Nat. Biotech. 21 (2003) 532-538
55. Wu C.C., MacCoss M.J., Mardones G., Finnigan C., Mogelsvang S., Yates III J.R., and Howell K.E. Organellar proteomics reveals golgi arginine dimethylation. Mol. Biol. Cell 15 (2004) 2907-2919
56. Yang X.J. Lysine acetylation and the bromodomain: A new partnership for signaling. Bioessays 26 (2004) 1076-1087
57. Zahedi R.P., Sickmann A., Boehm A.M., Winkler C., Zufall N., Schönfisch B., Guiard B., Pfanner N., and Meisinger C. Proteomic analysis of the yeast mitochondrial outer membrane reveals accumulation of a subclass of preproteins. Mol. Biol. Cell 17 (2006) 1436-1450