Integrative analysis of the ubiquitin proteome isolated using Tandem Ubiquitin Binding Entities (TUBEs)

Journal of Proteomics

Volumn 75, Issue 10, 2012, Pages 2998-3014

  Lopitz Otsoa, Fernando ^a   Rodriguez Suarez, Eva ^a   Aillet, Fabienne ^a   Casado Vela, Juan ^a   Lang, Valérie ^a   Matthiesen, Rune ^b   Elortza, Felix ^a   Rodriguez, Manuel S ^a,c  

^a INSTITUTO DE SALUD CARLOS III   (Spain)

^b UNIVERSITY OF PORTO   (Portugal)

^c UNIVERSITY OF THE BASQUE COUNTRY UPV EHU   (Spain)

Author keywords

Interactome; TUBEs; Ubiquitin proteome; Ubiquitome

Indexed keywords

DOXORUBICIN; PROTEASOME; UBIQUITIN;

ARTICLE; CELL STRAIN MCF 7; CELL TRANSPORT; CELLULAR STRESS RESPONSE; COMPUTER MODEL; CONTROLLED STUDY; DRUG TARGETING; GENOTOXICITY; HUMAN; HUMAN CELL; IN VITRO STUDY; MASS SPECTROMETRY; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN ISOLATION; PROTEIN SYNTHESIS; RNA TRANSCRIPTION; SIGNAL TRANSDUCTION; TANDEM REPEAT; TANDEM UBIQUITIN BINDING ENTITY; UBIQUITINATION;

ADENOCARCINOMA; BREAST NEOPLASMS; CELLS, CULTURED; FEMALE; HUMANS; MASS SPECTROMETRY; MODELS, BIOLOGICAL; PROTEIN BINDING; PROTEIN INTERACTION MAPS; PROTEOME; PROTEOMICS; RECOMBINANT PROTEINS; SYSTEMS INTEGRATION; TANDEM REPEAT SEQUENCES; TUMOR MARKERS, BIOLOGICAL; UBIQUITIN; UBIQUITINATED PROTEINS; UBIQUITINATION;

EID: 84861344026     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2011.12.001     Document Type: Article

References (41)

1. Navon A., Ciechanover A. The 26 S proteasome: from basic mechanisms to drug targeting. J Biol Chem 2009, 284:33713-33718.
2. Ikeda F., Dikic I. Atypical ubiquitin chains: new molecular signals. 'Protein Modifications: Beyond the Usual Suspects' review series. EMBO Rep 2008, 9:536-542.
3. Komander D., Reyes-Turcu F., Licchesi J.D., Odenwaelder P., Wilkinson K.D., Barford D. Molecular discrimination of structurally equivalent Lys 63-linked and linear polyubiquitin chains. EMBO Rep 2009, 10:466-473.
4. Dikic I., Wakatsuki S., Walters K.J. Ubiquitin-binding domains - from structures to functions. Nat Rev Mol Cell Biol 2009, 10:659-671.
5. Nijman S.M., Luna-Vargas M.P., Velds A., Brummelkamp T.R., Dirac A.M., Sixma T.K., et al. A genomic and functional inventory of deubiquitinating enzymes. Cell 2005, 123:773-786.
6. Hjerpe R., Rodriguez M.S. Efficient approaches for characterizing ubiquitinated proteins. Biochem Soc Trans 2008, 36:823-827.
7. Witze E.S., Old W.M., Resing K.A., Ahn N.G. Mapping protein post-translational modifications with mass spectrometry. Nat Methods 2007, 4:798-806.
8. Ziv I., Matiuhin Y., Kirkpatrick D.S., Erpapazoglou Z., Leon S., Pantazopoulou M., et al. A perturbed ubiquitin landscape distinguishes between ubiquitin in trafficking and in proteolysis. Mol Cell Proteomics 2011, M111:009753.
9. Nielsen M.L., Vermeulen M., Bonaldi T., Cox J., Moroder L., Mann M. Iodoacetamide-induced artifact mimics ubiquitination in mass spectrometry. Nat Methods 2008, 5:459-460.
10. Hjerpe R., Aillet F., Lopitz-Otsoa F., Lang V., England P., Rodriguez M.S. Efficient protection and isolation of ubiquitylated proteins using tandem ubiquitin-binding entities. EMBO Rep 2009, 10:1250-1258.
11. Lopitz-Otsoa F., Rodriguez M.S., Aillet F. Properties of natural and artificial proteins displaying multiple ubiquitin-binding domains. Biochem Soc Trans 2010, 38:40-45.
12. Shi Y., Chan D.W., Jung S.Y., Malovannaya A., Wang Y., Qin J. A dataset of human endogenous ubiquitination sites. Mol Cell Proteomics 2011, M110:002089.
13. Ishihama Y., Oda Y., Tabata T., Sato T., Nagasu T., Rappsilber J., et al. Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol Cell Proteomics 2005, 4:1265-1272.
14. Mathivanan S., Pandey A. Human Proteinpedia as a resource for clinical proteomics. Mol Cell Proteomics 2008, 7:2038-2047.
15. Kandasamy K., Keerthikumar S., Goel R., Mathivanan S., Patankar N., Shafreen B., et al. Human Proteinpedia: a unified discovery resource for proteomics research. Nucleic Acids Res 2009, 37:D773-D781.
16. Emanuele M.J., Elia A.E., Xu Q., Thoma C.R., Izhar L., Leng Y., et al. Global identification of modular cullin-RING ligase substrates. Cell 2011, 147:459-474.
17. Wagner S.A., Beli P., Weinert B.T., Nielsen M.L., Cox J., Mann M., et al. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. Mol Cell Proteomics 2011, M111:013284.
18. Kim W., Bennett E.J., Huttlin E.L., Guo A., Li J., Possemato A., et al. Systematic and quantitative assessment of the ubiquitin-modified proteome. Mol Cell 2011, 44:325-340.
19. Ranek M.J., Wang X. Activation of the ubiquitin-proteasome system in doxorubicin cardiomyopathy. Curr Hypertens Rep 2009, 11:389-395.
20. Liu J., Zheng H., Tang M., Ryu Y.C., Wang X. A therapeutic dose of doxorubicin activates ubiquitin-proteasome system-mediated proteolysis by acting on both the ubiquitination apparatus and proteasome. Am J Physiol Heart Circ Physiol 2008, 295:H2541-H2550.
21. Aillet F., Lopitz-Otsoa F., Hjerpe R., Torres-Ramos M., Lang V., Rodríguez M.S. Isolation of ubiquitylated proteins using Tandem Ubiquitin- Binding Entities (TUBEs). Methods Mol Biol 2012, 832:173-183.
22. Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25:25-29.
23. Glickman M.H., Raveh D. Proteasome plasticity. FEBS Lett 2005, 579:3214-3223.
24. Brighouse A., Dacks J.B., Field M.C. Rab protein evolution and the history of the eukaryotic endomembrane system. Cell Mol Life Sci 2010, 67:3449-3465.
25. Obsilova V., Silhan J., Boura E., Teisinger J., Obsil T. 14-3-3 proteins: a family of versatile molecular regulators. Physiol Res 2008, 57(Suppl. 3):S11-S21.
26. Jimeno S., Aguilera A. The THO complex as a key mRNP biogenesis factor in development and cell differentiation. J Biol 2010, 9:6.
27. Geng L., Huntoon C.J., Karnitz L.M. RAD18-mediated ubiquitination of PCNA activates the Fanconi anemia DNA repair network. J Cell Biol 2010, 191:249-257.
28. Parcellier A., Schmitt E., Gurbuxani S., Seigneurin-Berny D., Pance A., Chantome A., et al. HSP27 is a ubiquitin-binding protein involved in I-kappaBalpha proteasomal degradation. Mol Cell Biol 2003, 23:5790-5802.
29. Wisniewski J.R., Zougman A., Kruger S., Mann M. Mass spectrometric mapping of linker histone H1 variants reveals multiple acetylations, methylations, and phosphorylation as well as differences between cell culture and tissue. Mol Cell Proteomics 2007, 6:72-87.
30. Bridges D., Moorhead G.B. 14-3-3 proteins: a number of functions for a numbered protein. Sci STKE 2004, re10.
31. Kannouche P.L., Wing J., Lehmann A.R. Interaction of human DNA polymerase eta with monoubiquitinated PCNA: a possible mechanism for the polymerase switch in response to DNA damage. Mol Cell 2004, 14:491-500.
32. Papouli E., Chen S., Davies A.A., Huttner D., Krejci L., Sung P., et al. Crosstalk between SUMO and ubiquitin on PCNA is mediated by recruitment of the helicase Srs2p. Mol Cell 2005, 19:123-133.
33. Wilkinson K.A., Henley J.M. Mechanisms, regulation and consequences of protein SUMOylation. Biochem J 2010, 428:133-145.
34. Danielsen J.M., Sylvestersen K.B., Bekker-Jensen S., Szklarczyk D., Poulsen J.W., Horn H., et al. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. Mol Cell Proteomics 2011, M110:003590.
35. Urano T., Saito T., Tsukui T., Fujita M., Hosoi T., Muramatsu M., et al. Efp targets 14-3-3 sigma for proteolysis and promotes breast tumour growth. Nature 2002, 417:871-875.
36. Gwizdek C., Hobeika M., Kus B., Ossareh-Nazari B., Dargemont C., Rodriguez M.S. The mRNA nuclear export factor Hpr1 is regulated by Rsp5-mediated ubiquitylation. J Biol Chem 2005, 280:13401-13405.
37. Iglesias N., Tutucci E., Gwizdek C., Vinciguerra P., Von Dach E., Corbett A.H., et al. Ubiquitin-mediated mRNP dynamics and surveillance prior to budding yeast mRNA export. Genes Dev 2010, 24:1927-1938.
38. Yamamoto Y., Hoshino Y., Ito T., Nariai T., Mohri T., Obana M., et al. Atrogin-1 ubiquitin ligase is upregulated by doxorubicin via p38-MAP kinase in cardiac myocytes. Cardiovasc Res 2008, 79:89-96.
39. Gwizdek C., Iglesias N., Rodriguez M.S., Ossareh-Nazari B., Hobeika M., Divita G., et al. Ubiquitin-associated domain of Mex67 synchronizes recruitment of the mRNA export machinery with transcription. Proc Natl Acad Sci U S A 2006, 103:16376-16381.
40. Isasa M., Katz E.J., Kim W., Yugo V., Gonzalez S., Kirkpatrick D.S., et al. Monoubiquitination of RPN10 regulates substrate recruitment to the proteasome. Mol Cell 2010, 38:733-745.
41. Xu G., Paige J.S., Jaffrey S.R. Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling. Nat Biotechnol 2010, 28:868-873.