A Mammalian Organelle Map by Protein Correlation Profiling

Cell

Volumn 125, Issue 1, 2006, Pages 187-199

  Foster, Leonard J ^a,b   de Hoog, Carmen L ^a,b   Zhang, Yanling ^c,d   Zhang, Yong ^c,d   Xie, Xiaohui ^e   Mootha, Vamsi K ^e,f   Mann, Matthias ^a,c  

^a UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^c MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

^d Chinese Academy of Sciences and China National Center for Bioinformation   (China)

^e MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^f HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; CELL PROTEIN;

ANALYTIC METHOD; ANIMAL TISSUE; ARTICLE; BIOCHEMISTRY; BIOGENESIS; CELL ORGANELLE; CELLULAR DISTRIBUTION; CONFOCAL MICROSCOPY; CONTROLLED STUDY; CORRELATION ANALYSIS; CYTOLOGY; ENZYME ASSAY; GENE EXPRESSION; GENOMICS; LIVER; MAMMAL; MOUSE; NONHUMAN; PEPTIDE MAPPING; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DETERMINATION; PROTEIN LOCALIZATION; PROTEIN MOTIF; PROTEOMICS; TRANSCRIPTION REGULATION;

MAMMALIA;

EID: 33646473345     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cell.2006.03.022     Document Type: Article

References (43)

1. Aebersold R., and Mann M. Mass spectrometry-based proteomics. Nature 422 (2003) 198-207
2. Agaton C., Galli J., Hoiden Guthenberg I., Janzon L., Hansson M., Asplund A., Brundell E., Lindberg S., Ruthberg I., Wester K., et al. Affinity proteomics for systematic protein profiling of chromosome 21 gene products in human tissues. Mol. Cell. Proteomics 2 (2003) 405-414
3. Andersen J.S., Lyon C.E., Fox A.H., Leung A.K., Lam Y.W., Steen H., Mann M., and Lamond A.I. Directed proteomic analysis of the human nucleolus. Curr. Biol. 12 (2002) 1-11
4. Andersen J.S., Wilkinson C.J., Mayor T., Mortensen P., Nigg E.A., and Mann M. Proteomic characterization of the human centrosome by protein correlation profiling. Nature 426 (2003) 570-574
5. Andreoli C., Prokisch H., Hortnagel K., Mueller J.C., Munsterkotter M., Scharfe C., and Meitinger T. MitoP2, an integrated database on mitochondrial proteins in yeast and man. Nucleic Acids Res. 32 (2004) D459-D462
6. Azarani A., Boileau G., and Crine P. Recombinant human endothelin-converting enzyme ECE-1b is located in an intracellular compartment when expressed in polarized Madin-Darby canine kidney cells. Biochem. J. 333 (1998) 439-448
7. Boon K., Caron H.N., van Asperen R., Valentijn L., Hermus M.C., van Sluis P., Roobeek I., Weis I., Voute P.A., Schwab M., and Versteeg R. N-myc enhances the expression of a large set of genes functioning in ribosome biogenesis and protein synthesis. EMBO J. 20 (2001) 1383-1393
8. Breuza L., Halbeisen R., Jeno P., Otte S., Barlowe C., Hong W., and Hauri H.P. Proteomics of ERGIC membranes from brefeldin A-treated HepG2 cells identifies ERGIC-32, a new cycling protein that interacts with human Erv46. J. Biol. Chem. 279 (2004) 242-253
9. Cotter D., Guda P., Fahy E., and Subramaniam S. MitoProteome: mitochondrial protein sequence database and annotation system. Nucleic Acids Res. 32 (2004) D463-D467
10. 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
11. Danial N.N., Gramm C.F., Scorrano L., Zhang C.Y., Krauss S., Ranger A.M., Datta S.R., Greenberg M.E., Licklider L.J., Lowell B.B., et al. BAD and glucokinase reside in a mitochondrial complex that integrates glycolysis and apoptosis. Nature 424 (2003) 952-956
12. de Hoog C.L., and Mann M. Proteomics. Annu. Rev. Genomics Hum. Genet. 5 (2004) 267-293
13. Dell'Angelica E.C., Klumperman J., Stoorvogel W., and Bonifacino J.S. Association of the AP-3 adaptor complex with clathrin. Science 280 (1998) 431-434
14. DeRisi J.L., Iyer V.R., and Brown P.O. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278 (1997) 680-686
15. Dunkley T.P., Watson R., Griffin J.L., Dupree P., and Lilley K.S. Localization of organelle proteins by isotope tagging (LOPIT). Mol. Cell Proteomics 3 (2004) 1128-1134
16. Foster L.J., de Hoog C.L., and Mann M. Unbiased quantitative proteomics of lipid rafts reveals high specificity for signaling factors. Proc. Natl. Acad. Sci. USA 100 (2003) 5813-5818
17. Gaucher S.P., Taylor S.W., Fahy E., Zhang B., Warnock D.E., Ghosh S.S., and Gibson B.W. Expanded coverage of the human heart mitochondrial proteome using multidimensional liquid chromatography coupled with tandem mass spectrometry. J. Proteome Res. 3 (2004) 495-505
18. Ghaemmaghami S., Huh W.K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., and Weissman J.S. Global analysis of protein expression in yeast. Nature 425 (2003) 737-741
19. Glaser P., and Boone C. Beyond the genome: from genomics to systems biology. Curr. Opin. Microbiol. 7 (2004) 489-491
20. Hashiramoto M., and James D.E. Characterization of insulin-responsive GLUT4 storage vesicles isolated from 3T3-L1 adipocytes. Mol. Cell. Biol. 20 (2000) 416-427
21. Huh W.K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., and O'Shea E.K. Global analysis of protein localization in budding yeast. Nature 425 (2003) 686-691
22. Jover R., Bort R., Gomez-Lechon M.J., and Castell J.V. Cytochrome P450 regulation by hepatocyte nuclear factor 4 in human hepatocytes: a study using adenovirus-mediated antisense targeting. Hepatology 33 (2001) 668-675
23. Kumar A., Agarwal S., Heyman J.A., Matson S., Heidtman M., Piccirillo S., Umansky L., Drawid A., Jansen R., Liu Y., et al. Subcellular localization of the yeast proteome. Genes Dev. 16 (2002) 707-719
24. Li J.B., Gerdes J.M., Haycraft C.J., Fan Y., Teslovich T.M., May-Simera H., Li H., Blacque O.E., Li L., Leitch C.C., et al. Comparative genomics identifies a flagellar and basal body proteome that includes the BBS5 human disease gene. Cell 117 (2004) 541-552
25. 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., et al. Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria. Cell 115 (2003) 629-640
26. Mootha V.K., Handschin C., Arlow D., Xie X., St Pierre J., Sihag S., Yang W., Altshuler D., Puigserver P., Patterson N., et al. Erralpha and Gabpa/b specify PGC-1alpha-dependent oxidative phosphorylation gene expression that is altered in diabetic muscle. Proc. Natl. Acad. Sci. USA 101 (2004) 6570-6575
27. Mootha V.K., Lepage P., Miller K., Bunkenborg J., Reich M., Hjerrild M., Delmonte T., Villeneuve A., Sladek R., Xu F., et al. Identification of a gene causing human cytochrome c oxidase deficiency by integrative genomics. Proc. Natl. Acad. Sci. USA 100 (2003) 605-610
28. Olsen J.V., Ong S.E., and Mann M. Trypsin cleaves exclusively C-terminal to arginine and lysine residues. Mol. Cell. Proteomics 3 (2004) 608-614
29. Peters J.M., Franke W.W., and Kleinschmidt J.A. Distinct 19 S and 20 S subcomplexes of the 26 S proteasome and their distribution in the nucleus and the cytoplasm. J. Biol. Chem. 269 (1994) 7709-7718
30. Rappsilber, J., Ishihama, Y., Foster, L.J., Mittler, G., and Mann, M. (2003). Approximate relative abundance of proteins within a mixture determined from LC-MS data. In Abstracts of the 51st Conference in Mass Spectrometry and Allied Topics.
31. Reits E.A., Benham A.M., Plougastel B., Neefjes J., and Trowsdale J. Dynamics of proteasome distribution in living cells. EMBO J. 16 (1997) 6087-6094
32. Ross-Macdonald P., Coelho P.S., Roemer T., Agarwal S., Kumar A., Jansen R., Cheung K.H., Sheehan A., Symoniatis D., Umansky L., et al. Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature 402 (1999) 413-418
33. Scarpulla R.C. Nuclear control of respiratory chain expression in mammalian cells. J. Bioenerg. Biomembr. 29 (1997) 109-119
34. Schulze W.X., and Mann M. A novel proteomic screen for peptide-protein interactions. J. Biol. Chem. 279 (2004) 10756-10764
35. Simpson J.C., Wellenreuther R., Poustka A., Pepperkok R., and Wiemann S. Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing. EMBO Rep. 1 (2000) 287-292
36. Su A.I., Cooke M.P., Ching K.A., Hakak Y., Walker J.R., Wiltshire T., Orth A.P., Vega R.G., Sapinoso L.M., Moqrich A., et al. Large-scale analysis of the human and mouse transcriptomes. Proc. Natl. Acad. Sci. USA 99 (2002) 4465-4470
37. Syka J.E., Marto J.A., Bai D.L., Horning S., Senko M.W., Schwartz J.C., Ueberheide B., Garcia B., Busby S., Muratore T., et al. Novel linear quadrupole ion trap/FT mass spectrometer: performance characterization and use in the comparative analysis of histone H3 post-translational modifications. J. Proteome Res. 3 (2004) 621-626
38. Tulp A., Fernandez-Borja M., Verwoerd D., and Neefjes J. High-resolution density gradient electrophoresis of subcellular organelles and proteins under nondenaturing conditions. Electrophoresis 19 (1998) 1288-1293
39. Wiemann S., Arlt D., Huber W., Wellenreuther R., Schleeger S., Mehrle A., Bechtel S., Sauermann M., Korf U., Pepperkok R., et al. From ORFeome to biology: a functional genomics pipeline. Genome Res. 14 (2004) 2136-2144
40. 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
41. Xie X., Lu J., Kulbokas E.J., Golub T.R., Mootha V., Lindblad-Toh K., Lander E.S., and Kellis M. Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature 434 (2005) 338-345
42. Yates III J.R., Gilchrist A., Howell K.E., and Bergeron J.J.M. Proteomics of organelles and large cellular structures. Nat. Rev. Mol. Cell Biol. 6 (2005) 702-714
43. Zhao Y., Zhang W., and Kho Y. Proteomic analysis of integral plasma membrane proteins. Anal. Chem. 76 (2004) 1817-1823