Optimising methods for the preservation, capture and identification of ubiquitin chains and ubiquitylated proteins by immunoblotting

Biochemical and Biophysical Research Communications

Volumn 466, Issue 1, 2015, Pages 1-14

  Emmerich, Christoph H ^a   Cohen, Philip ^a  

^a UNIVERSITY OF DUNDEE   (United Kingdom)

Author keywords

Deubiquitylase; Immunoblotting; Ubiquitin; Ubiquitin chain topology; Ubiquitin binding domain

Indexed keywords

UBIQUITIN; DEUBIQUITINASE; UBIQUITINATED PROTEIN;

ARTICLE; IMMUNOBLOTTING; IMMUNOPRECIPITATION; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN LOCALIZATION; QUALITY CONTROL; SIGNAL TRANSDUCTION; STOICHIOMETRY; UBIQUITINATION; ANIMAL; GENETICS; HUMAN; METABOLISM; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROCEDURES; UPREGULATION;

ANIMALS; ELECTROPHORESIS, POLYACRYLAMIDE GEL; HUMANS; IMMUNOBLOTTING; IMMUNOPRECIPITATION; UBIQUITIN; UBIQUITIN-SPECIFIC PROTEASES; UBIQUITINATED PROTEINS; UBIQUITINATION; UP-REGULATION;

EID: 84941942168     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2015.08.109     Document Type: Short Survey

References (58)

1. A. Ciehanover, Y. Hod, and A. Hershko A heat-stable polypeptide component of an ATP-dependent proteolytic system from reticulocytes Biochem. Biophys. Res. Commun. 81 4 1978 1100 1105
2. Y. Kulathu, and D. Komander Atypical ubiquitylation - the unexplored world of polyubiquitin beyond Lys48 and Lys63 linkages Nat. Rev. Mol. Cell Biol. 13 8 2012 508 523
3. J. Lopez-Mosqueda, and I. Dikic Deciphering functions of branched ubiquitin chains Cell 157 4 2014 767 769
4. C.H. Emmerich, and et al. Activation of the canonical IKK complex by K63/M1-linked hybrid ubiquitin chains Proc. Natl. Acad. Sci. U. S. A. 110 38 2013 15247 15252
5. Y.A. Kristariyanto, and et al. K29-selective ubiquitin binding domain reveals structural basis of specificity and heterotypic nature of K29 polyubiquitin Mol. Cell 58 1 2015 83 94
6. H.J. Meyer, and M. Rape Enhanced protein degradation by branched ubiquitin chains Cell 157 4 2014 910 921
7. M.L. Nielsen, and et al. Iodoacetamide-induced artifact mimics ubiquitination in mass spectrometry Nat. Methods 5 6 2008 459 460
8. A. Borodovsky, and et al. A novel active site-directed probe specific for deubiquitylating enzymes reveals proteasome association of USP14 EMBO J. 20 18 2001 5187 5196
9. P. Xu, and et al. Quantitative proteomics reveals the function of unconventional ubiquitin chains in proteasomal degradation Cell 137 1 2009 133 145
10. A.F. Kisselev, W.A. van der Linden, and H.S. Overkleeft Proteasome inhibitors: an expanding army attacking a unique target Chem. Biol. 19 1 2012 99 115
11. H.C. Drexler Activation of the cell death program by inhibition of proteasome function Proc. Natl. Acad. Sci. U. S. A. 94 3 1997 855 860
12. K. Newton, and et al. Using linkage-specific monoclonal antibodies to analyze cellular ubiquitylation Methods Mol. Biol. 832 2012 185 196
13. P.S. Swerdlow, D. Finley, and A. Varshavsky Enhancement of immunoblot sensitivity by heating of hydrated filters Anal. Biochem. 156 1 1986 147 153
14. M. Fujimuro, H. Sawada, and H. Yokosawa Production and characterization of monoclonal antibodies specific to multi-ubiquitin chains of polyubiquitinated proteins FEBS Lett. 349 2 1994 173 180
15. M.L. Matsumoto, and et al. Engineering and structural characterization of a linear polyubiquitin-specific antibody J. Mol. Biol. 418 3-4 2012 134 144
16. M.L. Matsumoto, and et al. K11-linked polyubiquitination in cell cycle control revealed by a K11 linkage-specific antibody Mol. Cell 39 3 2010 477 484
17. K. Newton, and et al. Ubiquitin chain editing revealed by polyubiquitin linkage-specific antibodies Cell 134 4 2008 668 678
18. D. Komander, and et al. Molecular discrimination of structurally equivalent Lys 63-linked and linear polyubiquitin chains EMBO Rep. 10 5 2009 466 473
19. K. Husnjak, and I. Dikic Ubiquitin-binding proteins: decoders of ubiquitin-mediated cellular functions Annu. Rev. Biochem. 81 2012 291 322
20. D. Scott, and et al. Ubiquitin-binding domains: mechanisms of ubiquitin recognition and use as tools to investigate ubiquitin-modified proteomes Proteomics 15 5-6 2015 844 861
21. Y.C. Lo, and et al. Structural basis for recognition of diubiquitins by NEMO Mol. Cell 33 5 2009 602 615
22. S. Rahighi, and et al. Specific recognition of linear ubiquitin chains by NEMO is important for NF-kappaB activation Cell 136 6 2009 1098 1109
23. M. Vincendeau, D. Krappmann, and K. Hadian In Vitro detection of NEMO-ubiquitin binding using DELFIA and microscale thermophoresis assays Methods Mol. Biol. 1280 2015 311 320
24. C.K. Ea, and et al. Activation of IKK by TNFalpha requires site-specific ubiquitination of RIP1 and polyubiquitin binding by NEMO Mol. Cell 22 2 2006 245 257
25. C.J. Wu, and et al. Sensing of Lys 63-linked polyubiquitination by NEMO is a key event in NF-kappaB activation [corrected] Nat. Cell Biol. 8 4 2006 398 406
26. Y. Kulathu, and et al. Two-sided ubiquitin binding explains specificity of the TAB2 NZF domain Nat. Struct. Mol. Biol. 16 12 2009 1328 1330
27. Y. Sato, and et al. Structural basis for specific recognition of Lys 63-linked polyubiquitin chains by NZF domains of TAB2 and TAB3 EMBO J. 28 24 2009 3903 3909
28. R. Hjerpe, and et al. Efficient protection and isolation of ubiquitylated proteins using tandem ubiquitin-binding entities EMBO Rep. 10 11 2009 1250 1258
29. M.D. Wilson, and et al. MultiDsk: a ubiquitin-specific affinity resin PLoS One 7 10 2012 e46398
30. J.J. Sims, and R.E. Cohen Linkage-specific avidity defines the lysine 63-linked polyubiquitin-binding preference of rap80 Mol. Cell 33 6 2009 775 783
31. M.S. Ritorto, and et al. Screening of DUB activity and specificity by MALDI-TOF mass spectrometry Nat. Commun. 5 2014 4763
32. S. Yamaoka, and et al. Complementation cloning of NEMO, a component of the IkappaB kinase complex essential for NF-kappaB activation Cell 93 7 1998 1231 1240
33. J.J. Sims, and et al. Polyubiquitin-sensor proteins reveal localization and linkage-type dependence of cellular ubiquitin signaling Nat. Methods 9 3 2012 303 309
34. J.J. Sims, and et al. Avid interactions underlie the Lys63-linked polyubiquitin binding specificities observed for UBA domains Nat. Struct. Mol. Biol. 16 8 2009 883 889
35. T.E. Mevissen, and et al. OTU deubiquitinases reveal mechanisms of linkage specificity and enable ubiquitin chain restriction analysis Cell 154 1 2013 169 184
36. F.E. Reyes-Turcu, and et al. The ubiquitin binding domain ZnF UBP recognizes the C-terminal diglycine motif of unanchored ubiquitin Cell 124 6 2006 1197 1208
37. Z.P. Xia, and et al. Direct activation of protein kinases by unanchored polyubiquitin chains Nature 461 7260 2009 114 119
38. K. Keusekotten, and et al. OTULIN antagonizes LUBAC signaling by specifically hydrolyzing Met1-linked polyubiquitin Cell 153 6 2013 1312 1326
39. T. Wang, and et al. Evidence for bidentate substrate binding as the basis for the K48 linkage specificity of otubain 1 J. Mol. Biol. 386 4 2009 1011 1023
40. A. Catic, and et al. Screen for ISG15-crossreactive deubiquitinases PLoS One 2 7 2007 e679
41. B. Nicholson, and et al. Characterization of ubiquitin and ubiquitin-like-protein isopeptidase activities Protein Sci. 17 6 2008 1035 1043
42. L. Gong, and et al. Identification of a novel isopeptidase with dual specificity for ubiquitin- and NEDD8-conjugated proteins J. Biol. Chem. 275 19 2000 14212 14216
43. Y. Ye, and et al. Polyubiquitin binding and cross-reactivity in the USP domain deubiquitinase USP21 EMBO Rep. 12 4 2011 350 357
44. H. Wada, and et al. Cleavage of the C-terminus of NEDD8 by UCH-L3 Biochem. Biophys. Res. Commun. 251 3 1998 688 692
45. T. Gan-Erdene, and et al. Identification and characterization of DEN1, a deneddylase of the ULP family J. Biol. Chem. 278 31 2003 28892 28900
46. K. Wu, and et al. DEN1 is a dual function protease capable of processing the C terminus of Nedd8 and deconjugating hyper-neddylated CUL1 J. Biol. Chem. 278 31 2003 28882 28891
47. F. Aillet, and et al. Heterologous SUMO-2/3-ubiquitin chains optimize IkappaBalpha degradation and NF-kappaB activity PLoS One 7 12 2012 e51672
48. M.H. Tatham, and et al. RNF4 is a poly-SUMO-specific E3 ubiquitin ligase required for arsenic-induced PML degradation Nat. Cell Biol. 10 5 2008 538 546
49. B.K. Fiil, and et al. OTULIN restricts Met1-linked ubiquitination to control innate immune signaling Mol. Cell 50 6 2013 818 830
50. S.E. Kaiser, and et al. Protein standard absolute quantification (PSAQ) method for the measurement of cellular ubiquitin pools Nat. Methods 8 8 2011 691 696
51. B. Stieglitz, and et al. LUBAC synthesizes linear ubiquitin chains via a thioester intermediate EMBO Rep. 13 9 2012 840 846
52. D.S. Kirkpatrick, and et al. Proteomic identification of ubiquitinated proteins from human cells expressing His-tagged ubiquitin Proteomics 5 8 2005 2104 2111
53. V. Akimov, and et al. StUbEx: stable tagged ubiquitin exchange system for the global investigation of cellular ubiquitination J. Proteome Res. 13 9 2014 4192 4204
54. M. Xu, and et al. A ubiquitin replacement strategy in human cells reveals distinct mechanisms of IKK activation by TNFalpha and IL-1beta Mol. Cell 36 2 2009 302 314
55. J.B. Schaefer, and D.O. Morgan Protein-linked ubiquitin chain structure restricts activity of deubiquitinating enzymes J. Biol. Chem. 286 52 2011 45186 45196
56. K.E. Wickliffe, and et al. The mechanism of linkage-specific ubiquitin chain elongation by a single-subunit E2 Cell 144 5 2011 769 781
57. Y. Ye, and et al. Ubiquitin chain conformation regulates recognition and activity of interacting proteins Nature 492 7428 2012 266 270
58. T.T. Yamin, and D.K. Miller The interleukin-1 receptor-associated kinase is degraded by proteasomes following its phosphorylation J. Biol. Chem. 272 34 1997 21540 21547