Age-related subproteomic analysis of mouse liver and kidney peroxisomes

Proteome Science

Volumn 5, Issue , 2007, Pages

  Mi, Jia ^a   Garcia Arcos, Itsaso ^a   Alvarez, Ruben ^b   Cristobal, Susana ^a,b  

^a UPPSALA UNIVERSITY   (Sweden)

^b STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; CELL PROTEIN; ISOPRENOID; MEMBRANE PROTEIN; TRANSCRIPTION FACTOR;

AMINO ACID METABOLISM; ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; CELL AGING; CLUSTER ANALYSIS; DENSITY GRADIENT CENTRIFUGATION; FATTY ACID OXIDATION; KIDNEY CELL; LIVER CELL; MALE; MASS SPECTROMETRY; MOUSE; NONHUMAN; OXIDATION; OXIDATIVE STRESS; PEROXISOME; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEOMICS; QUANTITATIVE ANALYSIS; TWO DIMENSIONAL ELECTROPHORESIS; WESTERN BLOTTING;

MUS;

EID: 39049146505     PISSN: None     EISSN: 14775956     Source Type: Journal    
DOI: 10.1186/1477-5956-5-19     Document Type: Article

References (68)

1. Finkel T, Holbrook NJ: Oxidants, oxidative stress and the biology of ageing. Nature 2000, 408(6809):239-247. 10.1038/35041687 11089981
2. Butterfield DA, Abdul HM, Newman S, Reed T: Redox proteomics in some age-related neurodegenerative disorders or models thereof. NeuroRx 2006, 3:344-357. 10.1016/j.nurx.2006.05.003 16815218
3. Piec I, Listrat A, Alliot J, Chambon C, Taylor RG, Bechet D: Differential proteome analysis of aging in rat skeletal muscle. Faseb J 2005, 19:1143-1145. 15831715
4. Li M, Xiao ZQ, Chen ZC, Li JL, Li C, Zhang PF, Li MY: Proteomic analysis of the aging-related proteins in human normal colon epithelial tissue. J Biochem Mol Biol 2007, 40:72-81. 17244485
5. Poon HF, Vaishnav RA, Getchell TV, Getchell ML, Butterfield DA: Quantitative proteomics analysis of differential protein expression and oxidative modification of specific proteins in the brains of old mice. Neurobiol Aging 2005.
6. Hamacher M, Apweiler R, Arnold G, Becker A, Bluggel M, Carrette O, Colvis C, Dunn MJ, Frohlich T, Fountoulakis M, van Hall A, Herberg F, Ji J, Kretzschmar H, Lewczuk P, Lubec G, Marcus K, Martens L, Palacios Bustamante N, Park YM, Pennington SR, Robben J, Stuhler K, Reidegeld KA, Riederer P, Rossier J, Sanchez JC, Schrader M, Stephan C, Tagle D, Thiele H, Wang J, Wiltfang J, Yoo JS, Zhang C, Klose J, Meyer HE: HUPO Brain Proteome Project: Summary of the pilot phase and introduction of a comprehensive data reprocessing strategy Proteomics 2006, 6:4890-4898. 10.1002/pmic.200600295 16927433
7. Drahos KL, Tran HC, Kiri AN, Lan W, McRorie DK, Horn MJ: Comparison of Golgi apparatus and endoplasmic reticulum proteins from livers of juvenile and aged rats using a novel technique for separation and enrichment of organelles. J Biomol Tech 2005, 16:347-355. 16522856
8. Chang J, Van Remmen H, Cornell J, Richardson A, Ward WF: Comparative proteomics: Characterization of a two-dimensional gel electrophoresis system to study the effect of aging on mitochondrial proteins. Mech Ageing Dev 2003, 124:33-41. 10.1016/S0047-6374(02)00167-7 12618004
9. Kim CH, Park DU, Chung AS, Zou Y, Jung KJ, Sung BK, Yu BP, Chung HY: Proteomic analysis of post-mitochondrial fractions of young and old rat kidney. Exp Gerontol 2004, 39:1155-1168. 10.1016/j.exger.2004.04.003 15288690
10. Kiri AN, Tran HC, Drahos KL, Lan W, McRorie DK, Horn MJ: Proteomic changes in bovine heart mitochondria with age: Using a novel technique for organelle separation and enrichment. J Biomol Tech 2005, 16:371-379. 16522859
11. Poon HF, Shepherd HM, Reed TT, Calabrese V, Stella AM, Pennisi G, Cai J, Pierce WM, Klein JB, Butterfield DA: Proteomics analysis provides insight into caloric restriction mediated oxidation and expression of brain proteins associated with age-related impaired cellular processes: Mitochondrial dysfunction, glutamate dysregulation and impaired protein synthesis. Neurobiol Aging 2005.
12. Lee JH, Chung KY, Bang D, Lee KH: Searching for aging-related proteins in human dermal microvascular endothelial cells treated with anti-aging agents. Proteomics 2006, 6:1351-1361. 10.1002/pmic.200500287 16404724
13. Robinson LJ, Karlsson NG, Weiss AS, Packer NH: Proteomic analysis of the genetic premature aging disease Hutchinson Gilford progeria syndrome reveals differential protein expression and glycosylation. J Proteome Res 2003, 2:556-557. 10.1021/pr034035k 14582653
14. Konova E, Baydanoff S, Atanasova M, Velkova A: Age-related changes in the glycation of human aortic elastin. Exp Gerontol 2004, 39:249-254. 10.1016/j.exger.2003.10.003 15036419
15. Gerschman R, Gilbert DL, Nye SW, Dwyer P, Fenn WO: Oxygen poisoning and x-irradiation: A mechanism in common. Science 1954, 119:623-626. 10.1126/ science.119.3097.623 13156638
16. Migliaccio E, GRorgio M, Pelicci PG: Apoptosis and aging: role of p66Shc redox protein. Antioxid Redox Signal 2006, 8:600-608. 10.1089/ ars.2006.8.600 16677103
17. Perichon R, Bourre JM: Peroxisomal beta-oxidation activity and catalase activity during development and aging in mouse liver. Biochimie 1995, 77:288-293. 10.1016/0300-9084(96)88138-7 8589059
18. Semsei I, Rao G, Richardson A: Changes in the expression of superoxide dismutase and catalase as a function of age and dietary restriction. Biochem Biophys Res Commun 1989, 164:620-625. 10.1016/ 0006-291X(89)91505-2 2818581
19. Youssef JA, Badr MZ: Aging and enhanced hepatocarcinogenicity by peroxisome proliferator-activated receptor alpha agonists. Ageing Res Rev 2005, 4:103-118. 10.1016/j.arr.2004.10.002 15619473
20. Legakis JE, Koepke JI, Jedeszko C, Barlaskar F, Terlecky LJ, Edwards HJ, Walton PA, Terlecky SR: Peroxisome senescence in human fibroblasts. Mol Biol Cell 2002, 13:4243-4255. 138630 12475949 10.1091/mbc.E02-06-0322
21. Petriv OI, Rachubinski RA: Lack of peroxisomal catalase causes a progeric phenotype in Caenorhabditis elegans. J Biol Chem 2004, 279:19996-20001. 10.1074/jbc.M400207200 14996832
22. Amelina H, Apraiz I, Sun W, Cristobal S: Proteomics-based method for the assessment of marine pollution using liquid chromatography coupled with two-dimensional electrophoresis. J Proteome Res 2007, 6:2094-2104. 10.1021/pr060689s 17458988
23. Mi J, Kirchner E, Cristobal S: Quantitative proteomic comparison of mouse peroxisomes from liver and kidney. Proteomics 2007, 7:1916-1928. 10.1002/pmic.200600638 17474143
24. Emanuelsson O, Elofsson A, von Heijne G, Cristobal S: In silico prediction of the peroxisomal proteome in fungi, plants and animals. J Mol Biol 2003, 330:443-456. 10.1016/S0022-2836(03)00553-9 12823981
25. Apraiz I, Mi J, Cristobal S: Identification of Proteomic Signatures of Exposure to Marine Pollutants in Mussels (Mytilus edulis). Mol Cell Proteomics 2006, 5:1274-1285. 10.1074/mcp.M500333-MCP200 16603574
26. Mi J, Orbea A, Syme N, Ahmed M, Cajaraville MP, Cristobal S: Peroxisomal proteomics, a new tool for risk assessment of peroxisome proliferating pollutants in the marine environment. Proteomics 2005, 5:3954-3965. 10.1002/pmic.200401243 16130170
27. Mi J, Apraiz I, Cristobal S: Peroxisomal proteomic approach to biomarker discovery in blue mussels (Mytilus edulis) exposed to crude oil. Biomarkers 2007, 12:47-50. 10.1080/13547500600943528 17438653
28. Graham JM: In membrane Protocols Methods in Molecular Biology, Humana Pres, Totowa, NJ, USA Graham JMHJA 1993, 19:1-28. 8220689
29. Clauser KR, Baker P, Burlingame AL: Role of accurate mass measurement (+/ - 10 ppm) in protein identification strategies employing MS or MS/MS and database searching. Anal Chem 1999, 71:2871-2882. 10.1021/ac9810516 10424174
30. Perkins DN, Pappin DJ, Creasy DM, Cottrell JS: Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20:3551-3567. 10.1002/ (SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2 10612281
31. Monnhammer EL, Eddy SR, Birney E, Bateman A, Durbin R: Pfam: multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res 1998, 26:320-322. 147209 9399864 10.1093/nar/26.1.320
32. Nakai K, Kanehisa M: A knowledge base for predicting protein localization sites in eukaryotic cells. Genomics 1992, 14:897-911. 10.1016/S0888-7543(05)80111-9 1478671
33. Neuberger G, Maurer-Stroh S, Eisenhaber B, Hartig A, Eisenhaber F: Prediction of peroxisomal targeting signal 1 containing proteins from amino acid sequence. J Mol Biol 2003, 328:581-592. 10.1016/ S0022-2836(03)00319-X 12706718
34. Moldovan L. Moldovan NI: Oxygen free radicals and redox biology of organelles. Histochem Cell Biol 2004, 122:395-412. 10.1007/ s00418-004-0676-y 15452718
35. Beier K, Volkl A, Fahimi HD: The impact of aging on enzyme proteins of rat liver peroxisomes: Quantitative analysis by immunoblotting and immunoelectron microscopy. Virchows Arch B Cell Pathol Incl Mol Pathol 1993, 63:139-146. 8097070
36. Tsay HJ, Wang P, Wang SL, Ku HH: Age-associated changes of superoxide dismutase and catalase activities in the rat brain. J Biomed Sci 2000, 7:466-474. 10.1007/BF02253362 11060495
37. Lee CK, Weindruch R, Prolla TA: Gene-expression profile of the ageing brain in mice. Nat Genet 2000, 25:294-297. 10.1038/77046 10888876
38. De Broe ME: Tubular regeneration and the role of bone marrow cells: 'stem cell therapy'--a panacea? Nephrol Dial Transplant 2005, 20:2318-2320. 10.1093/ndt/gfi164 16188893
39. Biondo-Simoes Mde L, Matias JE, Montibeller GR, Siqueira LC, Nunes Eda S, Grassi CA: Effect of aging on liver regeneration in rats. Acta Cir Bras 2006, 21:197-202. 16862337
40. Yamaguchi Y Nozawa K Savoysky E Hayakawa N Nimura Y Yoshida S Change in telomerase activity of rat organs during growth and aging Exp Cell Res 1998 242 120 127 10.1006/excr.1998.4102 9665809
41. Michalopoulos GK, DeFrances MC: Liver regeneration Science 1997, 276:60-66. 10.1126/science.276.5309.60 9082986
42. Duffield JS, Park KM, Hsiao LL, Kelley VR, Scadden DT, Ichimura T, Bonventre JV: Restoration of tubular epithelial cells during repair of the postischemic kidney occurs independently of bone marrow-derived stem cells. J Clin Invest 2005, 115:1743-1755. 1159124 16007251 10.1172/ JCI22593
43. Perichon R, Bourre JM: Liver peroxisomal fatty acid oxidizing system during aging in control and clofibrate-treated mice. Biochem Mol Biol Int 1995, 37:475-480. 8595387
44. Moser HW, Moser AO: Peroxisomal disorders: overview. Ann N Y Acad Sci 1996, 804:427-441. 10.1111/j.1749-6632.1996.tb18634.x 8993562
45. Kovacs WJ. Olivier LM. Krisans SK: Central role of peroxisomes in isoprenoid biosynthesis. Prog Lipid Res 2002, 41:369-391. 10.1016/ S0163-7827(02)00002-4 12121718
46. Breitling R, Krisans SK: A second gene for peroxisomal HMG-CoA reductase? A genomic reassessment. J Lipid Res 2002, 43:2031-2036. 10.1194/jlr.R200010-JLR200 12454262
47. Hogenboom S, Tuyp JJ, Espeel M, Koster J, Wanders RJ, Waterham HR: Human mevalonate pyrophosphate decarboxylase is localized in the cytosol. Mol Genet Metab 2004, 81:216-224. 10.1016/j.ymgme.2003.12.001 14972328
48. Hogenboom S, Tuyp JJ, Espeel M, Koster J, Wanders RJ, Waterham HR: Mevalonate kinase is a cytosolic enzyme in humans. J Cell Sci 2004, 117:631-639. 10.1242/jcs.00910 14730012
49. Hogenboom S, Tuyp JJ, Espeel M, Koster J, Wanders RJ, Waterham HR: Phosphomevalonate kinase is a cytosolic protein in humans. J Lipid Res 2004, 45:697-705. 10.1194/jlr.M300373-JLR200 14729858
50. Clizbe DB, Owens ML, Masuda KR, Shackelford JE, Krisans SK: IDI2, a second isopentenyl diphosphate isomerase in mammals. J Biol Chem 2007, 282:6668-6676. 10.1074/jbc.M610922200 17202134
51. Kovacs WJ, Tape KN, Shackelford JE, Duan X, Kasumov T, Kelleher JK, Brunengraber H, Krisans SK: Localization of the pre-squalene segment of the isoprenoid biosynthetic pathway in mammalian peroxisomes. Histochem Cell Biol 2007, 127:273-290. 10.1007/s00418-006-0254-6 17180682
52. Ashmarina LI, Rusnak N, Miziorko HM, Mitchell GA: 3-Hydroxy-3-methylglutaryl-CoA lyase is present in mouse and human liver peroxisomes. J Biol Chem 1994, 269:31929-31932. 7527399
53. Ashmarina LI, Pshezhetsky AV, Branda SS, Isaya G, Mitchell GA: 3-Hydroxy-3-methylglutaryl coenzyme A lyase: Targeting and processing in peroxisomes and mitochondria. J Lipid Res 1999, 40:70-75. 9869651
54. Wang SP, Marth JD. Oligny LL. Vachon M, Robert MF, Ashmarina L, Mitchell GA: 3-Hydroxy-3-methylglutaryl-CoA lyGse (HL): gene targeting causes prenatal lethality in HL-deficient mice. Hum Mol Genet 1998, 7:2057-2062 10.1093/hmg/7.13.2057 9817922
55. Foulon V, Antonenkov VD, Croes K, Waelkens E, Mannaerts GP, Van Veldhoven PP, Casteels M: Purification, molecular cloning, and expression of 2-hydroxyphytanoyl-CoA lyase, a peroxisomal thiamine pyrophosphate-dependent enzyme that catalyzes the carbon-carbon bond cleavage during alpha-oxidation of 3-methyl-branched fatty acids. Proc Natl Acad Sci U S A 1999, 96:10039-10044. 17838 10468558 10.1073/ pnas.96.18.10039
56. Wilkinson TJ, Hanger HC, George PM, Sainsbury R: Is thiamine deficiency in elderly people related to age or co-morbidity? Age Ageing 2000, 29:111-116. 10.1093/ageing/29.2.111 10791444
57. Yang SY, He XY, Schulz H: 3-Hydroxyacyl-CoA dehydrogenase and short chain 3-hydroxyacyl-CoA dehydrogenase in human health and disease. Febs J 2005, 272:4874-4883. 10.1111/j.1742-4658.2005.04911.x 16176262
58. Oppermann UC, Salim S, Tjernberg LO, Terenius L, Jornvall H: Binding of amyloid beta-peptide to mitochondrial hydroxyacyl-CoA dehydrogenase (ERAB): Regulation of an SDR enzyme activity with implications for apoptosis in Alzheimer's disease. FEBS Lett 1999, 451:238-242. 10.1016/ S0014-5793(99)00586-4 10371197
59. Ghosh MK, Hajra AK: A rapid method for the isolation of peroxisomes from rat liver. Anal Biochem 1986, 159:169-174. 10.1016/0003-2697(86)90323-4 3812996
60. Volkl A, Fahimi HD: Isolation and characterization of peroxisomes from the liver of normal untreated rats. Eur J Biochem 1985, 149:257-265. 10.1111/j.1432-1033.1985.tb08920.x 3996409
61. Bradford MM: A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 1976, 72:248-254. 10.1016/0003-2697(76)90527-3 942051
62. Smith PK, Krohn RI, Hermanson GT, Mallia AK, Gartner FH, Provenzano MD, Fujimoto EK, Goeke NM, Olson BJ, Klenk DC: Measurement of protein using bicinchoninic acid. Anal Biochem 1985, 150:76-85. 10.1016/ 0003-2697(85)90442-7 3843705
63. Neuhoff V, Arold N, Taube D, Ehrhardt W: Improved staining of proteins in polyacrylamide gels including isoelectric focusing gels with clear background at nanogram sensitivity using Coomassie Brilliant Blue G-250 and R-250. Electrophoresis 1988, 9:255-262. 10.1002/elps.1150090603 2466658
64. Peri S, Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK, Surendranath V, Niranjan V, Muthusamy B, Gandhi TK, Gronborg M, Ibarrola N, Deshpande N, Shanker K, Shivashankar HN, Rashmi BP, Ramya MA, Zhao Z, Chandrika KN, Padma N, Harsha HC, Yatish AJ, Kavitha MP, Menezes M, Choudhury DR, Suresh S, Ghosh N, Saravana R, Chandran S, Krishna S, Joy M, Anand SK, Madavan V, Joseph A, Wong GW, Schiemann WP, Constantinescu SN, Huang L, Khosravi-Far R, Steen H, Tewari M, Ghaffari S, Blobe GC, Dang CV, Garcia JG, Pevsner J, Jensen ON, Roepstorff P, Deshpande KS, Chinnaiyan AM, Hamosh A, Chakravarti A, Pandey A: Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res 2003, 13:2363-2371. 403728 14525934 10.1101/gr.1680803
65. Cancio I, Volkl A, Beier K, Fahimi HD, Cajaraville MP: Peroxisomes in molluscs, characterization by subcellular fractionation combined with western blotting, immunohistochemistry, and immunocytochemistry. Histochem Cell Biol 2000, 113:51-60. 10.1007/s004180050007 10664070
66. Information NCB http://www.ncbi.nlm.nih.gov/
67. Ensembl http://www.ensembl.org
68. MaAinescu VD, Kohane IS, Riva A: MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes. BMC Bioinformatics 2005, 6:79. 1131891 15799782 10.1186/1471-2105-6-79