Shotgun proteomics and network analysis of ubiquitin-related proteins from human breast carcinoma epithelial cells

Molecular and Cellular Biochemistry

Volumn 359, Issue 1-2, 2012, Pages 375-384

  Zhou, Jian ^a,b   Bi, Deng ^a   Lin, Yong ^a   Chen, Ping ^a   Wang, Xianchun ^a   Liang, Songping ^a  

^a HUNAN NORMAL UNIVERSITY   (China)

^b CHONGQING MEDICAL UNIVERSITY   (China)

Author keywords

Mass spectrometry; Network analysis; PolyUb affinity purification; SDS PAGE; Ubiquitin

Indexed keywords

POLYUBIQUITIN; UBIQUITIN;

ARTICLE; BREAST CARCINOMA; CARCINOMA CELL; CELL CYCLE; CELL FUNCTION; GENE EXPRESSION; HEAT SHOCK RESPONSE; HUMAN; HUMAN CELL; LIQUID CHROMATOGRAPHY; NETWORK ANALYSIS; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEIN ANALYSIS; PROTEIN INTERACTION; PROTEIN PURIFICATION; PROTEIN TRANSPORT; PROTEOMICS; RNA PROCESSING; RNA TRANSCRIPTION; SHOTGUN PROTEOMICS; TANDEM MASS SPECTROMETRY; TRANSLATION INITIATION; UBIQUITINATION;

BREAST NEOPLASMS; CELL LINE, TUMOR; EPITHELIAL CELLS; FEMALE; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; PROTEASE INHIBITORS; PROTEIN INTERACTION MAPS; PROTEINS; PROTEOMICS; UBIQUITINATION; UBIQUITINS;

EUKARYOTA;

EID: 83555166035     PISSN: 03008177     EISSN: 15734919     Source Type: Journal    
DOI: 10.1007/s11010-011-1031-y     Document Type: Article

References (35)

1. D Mukhopadhyay H Riezman 2007 Proteasome-independent functions of ubiquitin in endocytosis and signaling Science 315 201 205 17218518 10.1126/science.1127085 1:CAS:528:DC%2BD2sXivFOisw%3D%3D (Pubitemid 46166358)
2. A Ciechanover 1998 The ubiquitin-proteasome pathway: on protein death and cell life EMBO J 17 7151 7160 9857172 10.1093/emboj/17.24.7151 1:CAS:528:DyaK1MXktl2hsQ%3D%3D (Pubitemid 29002684)
3. J Spence RR Gali G Dittmar F Sherman M Karin D Finley 2000 Cell cycle-regulated modification of the ribosome by a variant multiubiquitin chain Cell 102 67 76 10929714 10.1016/S0092-8674(00)00011-8 1:CAS:528: DC%2BD3cXkvFCrtrw%3D
4. RM Hofmann CM Pickart 1999 Noncanonical MMS2-encoded ubiquitin- conjugating enzyme functions in assembly of novel polyubiquitin chains for DNA repair Cell 96 645 653 10089880 10.1016/S0092-8674(00)80575-9 1:CAS:528:DyaK1MXitVChsrk%3D (Pubitemid 29122807)
5. L Sun ZJ Chen 2004 The novel functions of ubiquitination in signaling Curr Opin Cell Biol 16 119 126 15196553 10.1016/j.ceb.2004.02.005 1:CAS:528:DC%2BD2cXjslWktLg%3D (Pubitemid 38757287)
6. MH Glickman A Ciechanover 2002 The ubiquitin-proteasome proteolytic pathway: destruction for the sake of construction Physiol Rev 82 373 428 11917093 1:CAS:528:DC%2BD38XjtFOnsL4%3D (Pubitemid 34654457)
7. J Peng D Schwartz JE Elias CC Thoreen D Cheng G Marsischky J Roelofs D Finley SP Gygi 2003 A proteomics approach to understanding protein ubiquitination Nat Biotechnol 21 921 926 12872131 10.1038/nbt849 1:CAS:528:DC%2BD3sXlvVKgur0%3D (Pubitemid 36936199)
8. R Maor A Jones TS Nühse DJ Studholme SC Peck K Shirasu 2007 Multidimensional protein identification technology (MudPIT) analysis of ubiquitinated proteins in plants Mol Cell Proteomics 6 601 610 17272265 10.1074/mcp.M600408-MCP200 1:CAS:528:DC%2BD2sXksVKgtbs%3D (Pubitemid 46630093)
9. C Manzano Z Abraham G López-Torrejón JC Del Pozo 2008 Identification of ubiquitinated proteins in Arabidopsis Plant Mol Biol 68 145 158 18535787 10.1007/s11103-008-9358-9 1:CAS:528:DC%2BD1cXptVGltb8%3D
10. J Vasilescu JC Smith M Ethier D Figeys 2005 Proteomic analysis of ubiquitinated proteins from human MCF-7 breast cancer cells by immunoaffinity purification and mass spectrometry J Proteome Res 4 2192 2200 16335966 10.1021/pr050265i 1:CAS:528:DC%2BD2MXhtFegs7vF (Pubitemid 41814287)
11. J Vasilescu DR Zweitzig NJ Denis JC Smith M Ethier DS Haines D Figeys 2007 The proteomic reactor facilitates the analysis of affinity-purified proteins by mass spectrometry: application for identifying ubiquitinated proteins in human cells J Proteome Res 6 298 305 17203973 10.1021/pr060438j 1:CAS:528:DC%2BD28XhtlSrsrbI (Pubitemid 46173681)
12. M Matsumoto S Hatakeyama K Oyamada Y Oda T Nishimura KI Nakayama 2005 Large-scale analysis of the human ubiquitin-related proteome Proteomics 5 4145 4151 16196087 10.1002/pmic.200401280 1:CAS:528:DC%2BD2MXht1Grtb3P (Pubitemid 41626082)
13. E Durr J Yu KM Krasinska LA Carver JR Yates JE Testa P Oh JE Schnitzer 2004 Direct proteomic mapping of the lung microvascular endothelial cell surface in vivo and in cell culture Nat Biotechnol 22 985 992 15258593 10.1038/nbt993 1:CAS:528:DC%2BD2cXmtFWrurc%3D (Pubitemid 39014475)
14. JE Elias SP Gygi 2007 Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry Nat Methods 4 207 214 17327847 10.1038/nmeth1019 1:CAS:528:DC%2BD2sXitFChtrs%3D (Pubitemid 46358868)
15. J Zhou J Xiong J Li S Huang H Zhang Q He Y Lin P Chen X Wang S Liang 2010 Gel absorption-based sample preparation for the analysis of membrane proteome by mass spectrometry Anal Biochem 40 204 210 10.1016/j.ab.2010.05.013
16. E Fuchs K Weber 1994 Intermediate filaments: Structure, dynamics, function and disease Annu Rev Biochen 63 345 382 10.1146/annurev.bi.63.070194. 002021 1:CAS:528:DyaK2cXksl2ksL0%3D
17. I Nakamichi S Hatakeyama KI Nakayama 2002 Formation of Mallory body-like inclusions and cell death induced by deregulated expression of keratin 18 Mol Biol Cell 13 3441 3451 12388748 10.1091/mbc.01-10-0510 1:CAS:528: DC%2BD38XotFyrsrk%3D (Pubitemid 35191366)
18. K Zatloukal C Stumptner A Fuchsbichler P Fickert C Lackner M Trauner H Denk 2004 The keratin cytoskeleton in liver diseases J Pathol 204 367 376 15495250 10.1002/path.1649 1:CAS:528:DC%2BD2cXhtVCgsrrP (Pubitemid 39468148)
19. NO Ku MB Omary 2000 Keratins turn over by ubiquitination in a phosphorylation-modulated fashion J Cell Biol 149 547 552 10791969 10.1083/jcb.149.3.547 1:CAS:528:DC%2BD3cXivFKgurg%3D (Pubitemid 30252389)
20. Y Zhang J Wang Y Yuan W Zhang W Guan Z Wu C Jin H Chen L Zhang X Yang F He 2010 Negative regulation of HDM2 to attenuate p53 degradation by ribosomal protein L26 Nucleic Acids Res 38 6544 6554 20542919 10.1093/nar/gkq536 1:CAS:528:DC%2BC3cXhtlKltLjM
21. C Kraft A Deplazes M Sohrmann M Peter 2008 Mature ribosomes are selectively degraded upon starvation by an autophagy pathway requiring the Ubp3p/Bre5p ubiquitin protease Nat Cell Biol 10 602 610 18391941 10.1038/ncb1723 1:CAS:528:DC%2BD1cXltl2isL4%3D (Pubitemid 351627380)
22. J You M Wang T Aoki TA Tamura CM Pickart 2003 Proteolytic targeting of transcriptional regulator TIP120B by a HECT domain E3 ligase J Biol Chem 278 23369 23375 12692129 10.1074/jbc.M212887200 1:CAS:528:DC%2BD3sXkslygsL4%3D (Pubitemid 36830152)
23. C Gorbea D Taillandier M Rechsteiner 2000 Mapping subunit contacts in the regulatory complex of the 26 S proteasome. S2 and S5b form a tetramer with ATPase subunits S4 and S7 J Biol Chem 275 875 882 10625621 10.1074/jbc.275.2.875 1:CAS:528:DC%2BD3cXntlaqtQ%3D%3D (Pubitemid 30051129)
24. JD Dunbar HY Song D Guo LW Wu DB Donner 1997 Two-hybrid cloning of a gene encoding TNF receptor-associated protein 2, a protein that interacts with the intracellular domain of the type 1 TNF receptor: identity with subunit 2 of the 26S protease J Immunol 158 4252 4259 9126987 1:CAS:528:DyaK2sXivVCls7Y%3D (Pubitemid 127483926)
25. N Mailand S Bekker-Jensen H Faustrup F Melander J Bartek C Lukas J Lukas 2007 RNF8 ubiquitylates histones at DNA double-strand breaks and promotes assembly of repair proteins Cell 131 887 900 18001824 10.1016/j.cell.2007.09.040 1:CAS:528:DC%2BD2sXhsVCntbbF (Pubitemid 350138084)
26. S Bergink FA Salomons D Hoogstraten TA Groothuis H de Waard J Wu L Yuan E Citterio AB Houtsmuller J Neefjes JH Hoeijmakers W Vermeulen NP Dantuma 2006 DNA damage triggers nucleotide excision repair-dependent monoubiquitylation of histone H2A Genes Dev 20 1343 1352 16702407 10.1101/gad.373706 1:CAS:528:DC%2BD28XltVyrur4%3D (Pubitemid 43727594)
27. MS Huen R Grant I Manke K Minn X Yu MB Yaffe J Chen 2007 RNF8 transduces the DNA-damage signal via histone ubiquitylation and checkpoint protein assembly Cell 131 901 914 18001825 10.1016/j.cell.2007.09.041 1:CAS:528: DC%2BD2sXhsVCntbfO (Pubitemid 350138083)
28. D Bonenfant M Coulot H Towbin P Schindler J van Oostrum 2006 Characterization of histone H2A and H2B variants and their post-translational modifications by mass spectrometry Mol Cell Proteomics 5 541 552 16319397 1:CAS:528:DC%2BD28XivVWltbk%3D
29. AL Hitchcock K Auld SP Gygi PA Silver 2003 A subset of membrane-associated proteins is ubiquitinated in response to mutations in the endoplasmic reticulum degradation machinery Proc Natl Acad Sci USA 100 12735 12740 14557538 10.1073/pnas.2135500100 1:CAS:528:DC%2BD3sXoslKntLo%3D (Pubitemid 37339968)
30. H Riezman A Munn MI Geli L Hicke 1996 Actin-, myosin- and ubiquitin-dependent endocytosis Experientia 52 1033 1041 8988243 10.1007/BF01952099 1:STN:280:DyaK2s7ktF2qsQ%3D%3D (Pubitemid 27022811)
31. B Raboy G Sharon HA Parag Y Shochat RG Kulka 1991 Effect of stress on protein degradation: role of the ubiquitin system Acta Biol Hung 42 3 20 1668897 1:STN:280:DyaK3s3gs1Gktg%3D%3D
32. SF Falsone B Gesslbauer A Rek AJ Kungl 2007 A proteomic approach towards the Hsp90-dependent ubiquitinylated proteome Proteomics 7 2375 2383 17623298 10.1002/pmic.200600996 1:CAS:528:DC%2BD2sXos1GhtLY%3D (Pubitemid 47121530)
33. H Wegele L Müller J Buchner 2004 Hsp70 and Hsp90-a relay team for protein folding Rev Physiol Biochem Pharmacol 151 1 44 14740253 10.1007/s10254-003-0021-1 1:CAS:528:DC%2BD2cXotFWqtrg%3D
34. DH Lee AL Goldberg 1998 Proteasome inhibitors: valuable new tools for cell biologists Trends Cell Biol 8 397 403 9789328 10.1016/S0962-8924(98)01346-4 1:CAS:528:DyaK1cXmvFWjtbc%3D (Pubitemid 28458705)
35. M Zhou X Wu HN Ginsberg 1996 Evidence that a rapidly turning over protein, normally degraded by proteasomes, regulates hsp72 gene transcription in HepG2 cells J Biol Chem 271 24769 24775 8798747 10.1074/jbc.271.40.24769 1:CAS:528:DyaK28XmtFegs7Y%3D (Pubitemid 26333223)