Proteomic identification of protein ubiquitination events

Biotechnology and Genetic Engineering Reviews

Volumn 29, Issue 1, 2013, Pages 73-109

  Xu, Guoqiang ^a,b   Jaffrey, Samie R ^b  

^a MEDICAL COLLEGE OF SOOCHOW UNIVERSITY   (China)

^b WEILL CORNELL MEDICAL COLLEGE   (United States)

Author keywords

Anti diglycyl lysine; Mass spectrometry; Proteomics; Ubiquitin; Ubiquitin remnant profiling

Indexed keywords

AMINO ACIDS; CELL SIGNALING; MOLECULAR BIOLOGY; MONOCLONAL ANTIBODIES; NEURODEGENERATIVE DISEASES;

ANTI-DIGLYCYL LYSINE; CELLS SIGNALING; IDENTIFICATION OF PROTEINS; PROTEOMIC IDENTIFICATION; PROTEOMICS; SIGNALLING PATHWAYS; UBIQUITIN; UBIQUITIN-REMNANT PROFILING; UBIQUITINATION;

MASS SPECTROMETRY;

EPITOPE; LIGASE; LYSINE; MONOCLONAL ANTIBODY; POLYUBIQUITIN; PROTEASOME; PROTEOME; UBIQUITINATED PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; HUMAN; IMMUNOPRECIPITATION; LIQUID CHROMATOGRAPHY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NONHUMAN; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN ISOLATION; PROTEOMICS; REGULATORY MECHANISM; TANDEM MASS SPECTROMETRY; UBIQUITINATION; CHEMISTRY; GENETICS; ISOLATION AND PURIFICATION; MASS SPECTROMETRY; PROTEIN CONFORMATION; PROTEIN PROCESSING; SIGNAL TRANSDUCTION;

EUKARYOTA;

AMINO ACID SEQUENCE; HUMANS; LYSINE; MASS SPECTROMETRY; PROTEIN CONFORMATION; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEOMICS; SIGNAL TRANSDUCTION; UBIQUITINATED PROTEINS; UBIQUITINATION;

EID: 84881141146     PISSN: 02648725     EISSN: None     Source Type: Journal    
DOI: 10.1080/02648725.2013.801232     Document Type: Article

References (135)

1. Ahmed, N., Zeng, M., Sinha, I., Polin, L., Wei, W. Z., Rathinam, C., Venuprasad, K. (2011). The E3 ligase Itch and deubiquitinase Cyld act together to regulate Tak1 and inflammation. Nature Immunology, 12, 1176-1183.
2. Amerik, A. Y., & Hochstrasser, M. (2004). Mechanism and function of deubiquitinating enzymes. Biochimica et Biophysica Acta, 1695, 189-207. (Pubitemid 39574973)
3. Andrews, P. S., Schneider, S., Yang, E., Michaels, M., Chen, H., Tang, J., & Emkey, R. (2009). Identification of substrates of SMURF1 ubiquitin ligase activity utilizing protein microarrays. Assay and Drug Development Technologies, 8, 471-487.
4. Argenzio, E., Bange, T., Oldrini, B., Bianchi, F., Peesari, R., Mari, S., Polo, S. (2011). Proteomic snapshot of the EGF-induced ubiquitin network. Molecular Systems Biology, 7, article number 462, 1-15.
5. Arif, M., Senapati, P., Shandilya, J., & Kundu, T. K. (2010). Protein lysine acetylation in cellular function and its role in cancer manifestation. Biochimica et Biophysica Acta, 1799, 702-716.
6. Baboshina, O. V., & Haas, A. L. (1996). Novel multiubiquitin chain linkages catalyzed by the conjugating enzymes E2EPF and RAD6 are recognized by 26 S proteasome subunit 5. Journal of Biological Chemistry, 271, 2823-2831.
7. Beckett, D., Kovaleva, E., & Schatz, P. J. (1999). A minimal peptide substrate in biotin holoenzyme synthetase-catalyzed biotinylation. Protein Science, 8, 921-929. (Pubitemid 29165423)
8. Behrends, C., & Harper, J. W. (2011). Constructing and decoding unconventional ubiquitin chains. Nature Structural and Molecular Biology, 18, 520-528.
9. Bhat, K. P., Truax, A. D., & Greer, S. F. (2010). Phosphorylation and ubiquitination of degron proximal residues are essential for class II transactivator (CIITA) transactivation and major histocompatibility class II expression. Journal of Biological Chemistry, 285, 25893-25903.
10. Breitschopf, K., Bengal, E., Ziv, T., Admon, A., & Ciechanover, A. (1998). A novel site for ubiquitination: The N-terminal residue, and not internal lysines of MyoD, is essential for conjugation and degradation of the protein. EMBO Journal, 17, 5964-5973. (Pubitemid 28474790)
11. Burande, C. F., Heuze, M. L., Lamsoul, I., Monsarrat, B., Uttenweiler-Joseph, S., & Lutz, P. G. (2009). A label-free quantitative proteomics strategy to identify E3 ubiquitin ligase substrates targeted to proteasome degradation. Molecular and Cellular Proteomics, 8, 1719-1727.
12. Bustos, D., Bakalarski, C. E., Yang, Y., Peng, J., & Kirkpatrick, D. S. (2012). Characterizing ubiquitination sites by peptide based immunoaffinity enrichment. Molecular and Cellular Proteomics, 11, 1529-1540.
13. Cadwell, K., & Coscoy, L. (2005). Ubiquitination on nonlysine residues by a viral E3 ubiquitin ligase. Science, 309, 127-130. (Pubitemid 40934990)
14. Carrington, J. C., Cary, S. M., Parks, T. D., & Dougherty, W. G. (1989). A second proteinase encoded by a plant potyvirus genome. EMBO Journal, 8, 365-370.
15. Choudhary, C., Kumar, C., Gnad, F., Gnad, F., Nielsen, M. L., Rehman, M., Walther, T. C.,Mann, M. (2009). Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science, 325, 834-840.
16. Cole, G. M., & Timiras, P. S. (1987). Ubiquitin-protein conjugates in Alzheimer's lesions. Neuroscience Letters, 79, 207-212. (Pubitemid 17144471)
17. Cooper, H. J., Heath, J. K., Jaffray, E., Hay, R. T., Lam, T. T., & Marshall, A. G. (2004). Identification of sites of ubiquitination in proteins: A Fourier transform ion cyclotron resonance mass spectrometry approach. Analytical Chemistry, 76, 6982-6988. (Pubitemid 39610471)
18. Cotter, R. J., Iltchenko, S., Wang, D., & Gundry, R. (2005). Tandem time-of-flight (TOF/TOF) mass spectrometry and proteomics. Journal of the Mass Spectrometry Society of Japan, 53, 7-17.
19. Coulombe, P., Rodier, G., Bonneil, E., Thibault, P., & Meloche, S. (2004). N-terminal ubiquitination of extracellular signal-regulated kinase 3 and p21 directs their degradation by the proteasome. Molecular and Cellular Biology, 24, 6140-6150. (Pubitemid 38891117)
20. Cronan, J. E.Jr. (1990). Biotination of proteins in vivo. A post-translational modification to label, purify, and study proteins. Journal of Biological Chemistry, 265, 10327-10333.
21. Danielsen, J. M., Sylvestersen, K. B., Bekker-Jensen, S., Szklarczyk, D., Poulsen, J. W., Horn, H., Nielsen, M. L. (2011). Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. Molecular and Cellular Proteomics, 10, M110 003590.
22. Deng, L., Wang, C., Spencer, E., Yang, L., Braun, A., You, J., Chen, Z. J. (2000). Activation of the kB kinase complex by TRAF6 requires a dimeric ubiquitin-conjugating enzyme complex and a unique polyubiquitin chain. Cell, 103, 351-361.
23. Denis, N. J., Vasilescu, J., Lambert, J. P., Smith, J. C., & Figeys, D. (2007). Tryptic digestion of ubiquitin standards reveals an improved strategy for identifying ubiquitinated proteins by mass spectrometry. Proteomics, 7, 868-874. (Pubitemid 46506734)
24. Emanuele, M. J., Elia, A. E., Xu, Q., Thoma, C. R., Izhar, L., Leng, Y., Elledge, S. J. (2011). Global identification of modular cullin-RING ligase substrates. Cell, 147, 459-474.
25. Escribano, M. J. (1974). Antibodies of restricted heterogeneity obtained in rabbits immunized with tetraglycine peptide conjugated to an autologous carrier. European Journal of Immunology, 4, 793-798.
26. Franco, M., Seyfried, N. T., Brand, A. H., Peng, J., & Mayor, U. (2010). A novel strategy to isolate ubiquitin conjugates reveals wide role for ubiquitination during neural development. Molecular and Cellular Proteomics, 10, M110 002188.
27. Fujimuro, M., Sawada, H., & Yokosawa, H. (1994). Production and characterization of monoclonal antibodies specific to multi-ubiquitin chains of polyubiquitinated proteins. FEBS Letters, 349, 173-180. (Pubitemid 24263257)
28. Fujimuro, M., Sawada, H., & Yokosawa, H. (1997). Dynamics of ubiquitin conjugation during heat-shock response revealed by using a monoclonal antibody specific to multi-ubiquitin chains. European Journal of Biochemistry, 249, 427-433. (Pubitemid 27455783)
29. Gerlach, B., Cordier, S. M., Schmukle, A. C., Emmerich, C. H., Rieser, E., Haas, T. L., Walczak, H. (2011). Linear ubiquitination prevents inflammation and regulates immune signalling. Nature, 471, 591-596.
30. Giasson, B. I., & Lee, V. M. (2003). Are ubiquitination pathways central to Parkinson's disease? Cell, 114, 1-8. (Pubitemid 36859837)
31. Goldknopf, I. L., & Busch, H. (1975). Remarkable similarities of peptide fingerprints of histone 2A and nonhistone chromosomal protein A24. Biochemical and Biophysical Research Communications, 65, 951-960.
32. Goldknopf, I. L., & Busch, H. (1977). Isopeptide linkage between nonhistone and histone 2A polypeptides of chromosomal conjugate-protein A24. Proceedings of the National Academy of Sciences of the United States of America, 74, 864-868. (Pubitemid 8068703)
33. Goldknopf, I. L., Taylor, C. W., Baum, R. M., Yeoman, L. C., Olson, M. O., Prestayko, A. W., Busch, H. (1975). Isolation and characterization of protein A24, a 'histone-like' non-histone chromosomal protein. Journal of Biological Chemistry, 250, 7182-7187.
34. Gregori, L., Poosch, M. S., Cousins, G., & Chau, V. (1990). A uniform isopeptide-linked multiubiquitin chain is sufficient to target substrate for degradation in ubiquitin-mediated proteolysis. Journal of Biological Chemistry, 265, 8354-8357.
35. Gross, E., & Witkop, B. (1962). Nonenzymatic cleavage of peptide bonds: The methionine residues in bovine pancreatic ribonuclease. Journal of Biological Chemistry, 237, 1856-1860.
36. Gupta, R., Kus, B., Fladd, C., Wasmuth, J., Tonikian, R., Sidhu, S., Rotin, D. (2007). Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast. Molecular Systems Biology, 3, article number 116, 1-12.
37. Haas, A. L., & Bright, P. M. (1985). The immunochemical detection and quantitation of intracellular ubiquitin-protein conjugates. Journal of Biological Chemistry, 260, 12464-12473. (Pubitemid 16233446)
38. Haglund, K., & Dikic, I. (2005). Ubiquitylation and cell signaling. EMBO Journal, 24, 3353-3359. (Pubitemid 41486773)
39. Harper, J. W. (2002). A phosphorylation-driven ubiquitination switch for cell-cycle control. Trends in Cell Biology, 12, 104-107. (Pubitemid 34164644)
40. Hashizume, R., Fukuda, M., Maeda, I., Nishikawa, H., Oyake, D., Yabuki, Y.,Ohta, T. (2001). The RING heterodimer BRCA1-BARD1 is a ubiquitin ligase inactivated by a breast cancer-derived mutation. Journal of Biological Chemistry, 276, 14537-14540.
41. Herrmann, J., Ciechanover, A., Lerman, L. O., & Lerman, A. (2004). The ubiquitin-proteasome system in cardiovascular diseases-A hypothesis extended. Cardiovascular Research, 61, 11-21. (Pubitemid 38056676)
42. Hershko, A., & Ciechanover, A. (1998). The ubiquitin system. Annual Review of Biochemistry, 67, 425-479. (Pubitemid 28411135)
43. Hicke, L. (1999). Gettin' down with ubiquitin: Turning off cell-surface receptors, transporters and channels. Trends in Cell Biology, 9, 107-112. (Pubitemid 29151787)
44. Hjerpe, R., Aillet, F., Lopitz-Otsoa, F., Lang, V., England, P., & Rodriguez, M. S. (2009). Efficient protection and isolation of ubiquitylated proteins using tandem ubiquitin-binding entities. EMBO Reports, 10, 1250-1258.
45. Hjerpe, R., & Rodriguez, M. S. (2008). Efficient approaches for characterizing ubiquitinated proteins. Biochemical Society Transactions, 36, 823-827.
46. Hoege, C., Pfander, B., Moldovan, G. L., Pyrowolakis, G., & Jentsch, S. (2002). RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO. Nature, 419, 135-141. (Pubitemid 35025438)
47. Hoeller, D., & Dikic, I. (2009). Targeting the ubiquitin system in cancer therapy. Nature, 458, 438-444.
48. Hoeller, D., Hecker, C. M., & Dikic, I. (2006). Ubiquitin and ubiquitin-like proteins in cancer pathogenesis. Nature Reviews Cancer, 6, 776-788. (Pubitemid 44450466)
49. Hor, S., Ziv, T., Admon, A., & Lehner, P. J. (2009). Stable isotope labeling by amino acids in cell culture and differential plasma membrane proteome quantitation identify new substrates for the MARCH9 transmembrane E3 ligase. Molecular and Cellular Proteomics, 8, 1959-1971.
50. Hori, T., Osaka, F., Chiba, T., Miyamoto, C., Okabayashi, K., Shimbara, N., Tanaka, K. (1999). Covalent modification of all members of human cullin family proteins by NEDD8. Oncogene, 18, 6829-6834.
51. Hou, D., Cenciarelli, C., Jensen, J. P., Nguygen, H. B., & Weissman, A. M. (1994). Activationdependent ubiquitination of a T cell antigen receptor subunit on multiple intracellular lysines. Journal of Biological Chemistry, 269, 14244-14247. (Pubitemid 24191185)
52. Huang, F., Kirkpatrick, D., Jiang, X., Gygi, S., & Sorkin, A. (2006). Differential regulation of EGF receptor internalization and degradation by multiubiquitination within the kinase domain. Molecular Cell, 21, 737-748. (Pubitemid 43376125)
53. Hunt, L. T., & Dayhoff, M. O. (1977). Amino-terminal sequence identity of ubiquitin and the nonhistone component of nuclear protein A24. Biochemical and Biophysical Research Communications, 74, 650-655. (Pubitemid 8022254)
54. Hurley, J. H., Lee, S., & Prag, G. (2006). Ubiquitin-binding domains. Biochemical Journal, 399, 361-372. (Pubitemid 44672627)
55. Iyer, A., Fairlie, D. P., & Brown, L. (2011). Lysine acetylation in obesity, diabetes and metabolic disease. Immunology and Cell Biology, 90, 39-46.
56. Jadhav, T., & Wooten, M. W. (2009). Defining an embedded code for protein ubiquitination. Journal of Proteomics and Bioinformatics, 2, 316-333.
57. Jeon, H. B., Choi, E. S., Yoon, J. H., Hwang, J. H., Chang, J. W., Lee, E. K., Yoo, Y. J. (2007). A proteomics approach to identify the ubiquitinated proteins in mouse heart. Biochemical and Biophysical Research Communications, 357, 731-736. (Pubitemid 46653841)
58. Kim, J. Y., Anderson, E. D., Huynh, W., Dey, A., & Ozato, K. (2011). Proteomic survey of ubiquitin-linked nuclear proteins in interferon-stimulated macrophages. Journal of Interferon and Cytokine Research, 31, 619-628.
59. Kim, W., Bennett, E. J., Huttlin, E. L., Guo, A., Li, J., Possemato, A., Gygi, S. P. (2011). Systematic and quantitative assessment of the ubiquitin-modified proteome. Molecular Cell, 44, 325-340.
60. Kirkpatrick, D. S., Weldon, S. F., Tsaprailis, G., Liebler, D. C., & Gandolfi, A. J. (2005). Proteomic identification of ubiquitinated proteins from human cells expressing His-tagged ubiquitin. Proteomics, 5, 2104-2111. (Pubitemid 40770574)
61. Kitada, T., Asakawa, S., Hattori, N., Matsumine, H., Yamamura, Y., Minoshima, S., Shimizu, N. (1998). Mutations in the parkin gene cause autosomal recessive juvenile parkinsonism. Nature, 392, 605-608. (Pubitemid 28207717)
62. Kong, S. K., & Chock, P. B. (1992). Protein ubiquitination is regulated by phosphorylation. An in vitro study. Journal of Biological Chemistry, 267, 14189-14192.
63. Kundrat, L., & Regan, L. (2010). Identification of residues on Hsp70 and Hsp90 ubiquitinated by the cochaperone CHIP. Journal of Molecular Biology, 395, 587-594.
64. Lee, J. S., Hong, U. S., Lee, T. H., Yoon, S. K., & Yoon, J. B. (2004). Mass spectrometric analysis of tumor necrosis factor receptor-associated factor 1 ubiquitination mediated by cellular inhibitor of apoptosis 2. Proteomics, 4, 3376-3382. (Pubitemid 39525286)
65. Lee, K. A., Hammerle, L. P., Andrews, P. S., Stokes, M. P., Mustelin, T., Silva, J. C., Doedens, J. R. (2011). Ubiquitin ligase substrate identification through quantitative proteomics at both the protein and peptide levels. Journal of Biological Chemistry, 286, 41530-41538.
66. Lee, S., Tsai, Y. C., Mattera, R., Smith, W. J., Kostelansky, M. S., Weissman, A. M., Hurley, J. H. (2006). Structural basis for ubiquitin recognition and autoubiquitination by Rabex-5. Nature Structural and Molecular Biology, 13, 264-271. (Pubitemid 43348513)
67. Li, R. F., Shang, Y., Liu, D., Ren, Z. S., Chang, Z., & Sui, S. F. (2007). Differential ubiquitination of Smad1 mediated by CHIP: Implications in the regulation of the bone morphogenetic protein signaling pathway. Journal of Molecular Biology, 374, 777-790. (Pubitemid 350018776)
68. Loch, C. M., Eddins, M. J., & Strickler, J. E. (2011). Protein microarrays for the identification of praja1 e3 ubiquitin ligase substrates. Cell Biochemistry and Biophysics, 60, 127-135.
69. Lu, J. Y., Lin, Y. Y., Qian, J., Tao, S. C., Zhu, J., Pickart, C., & Zhu, H. (2008). Functional dissection of a HECT ubiquitin E3 ligase. Molecular and Cellular Proteomics, 7, 35-45. (Pubitemid 351248232)
70. Lucking, C. B., Durr, A., Bonifati, V., Vaughan, J., De Michele, G., Gasser, T., Brice, A. (2000). Association between early-onset Parkinson's disease and mutations in the parkin gene. New England Journal of Medicine, 342, 1560-1567. (Pubitemid 30340501)
71. Maine, G. N., Gluck, N., Zaidi, I. W., & Burstein, E. (2009). Bimolecular affinity purification (BAP): Tandem affinity purification using two protein baits. Cold Spring Harbor Protocols, 11, . doi:10.1101/pdb.prot5318.
72. Mann, M., & Jensen, O. N. (2003). Proteomic analysis of post-translational modifications. Nature Biotechnology, 21, 255-261. (Pubitemid 36314808)
73. Maor, R., Jones, A., Nuhse, T. S., Studholme, D. J., Peck, S. C., Shirasu, K. (2007). Multidimensional protein identification technology (MudPIT) analysis of ubiquitinated proteins in plants. Molecular and Cellular Proteomics, 6, 601-610. (Pubitemid 46630093)
74. Marotti, L. A.Jr., Newitt, R., Wang, Y., Aebersold, R., Dohlman, H. G. (2002). Direct identification of a G protein ubiquitination site by mass spectrometry. Biochemistry, 41, 5067-5074. (Pubitemid 34411660)
75. Matsumoto, M., Hatakeyama, S., Oyamada, K., Oda, Y., Nishimura, T., & Nakayama, K. I. (2005). Large-scale analysis of the human ubiquitin-related proteome. Proteomics, 5, 4145-4151. (Pubitemid 41626082)
76. Matsumoto, M. L., Wickliffe, K. E., Dong, K. C., Yu, C., Bosanac, I., Bustos, D., Dixit, V. M. (2010). K11-linked polyubiquitination in cell cycle control revealed by a K11 linkage-specific antibody. Molecular Cell, 39, 477-484.
77. Meierhofer, D., Wang, X., Huang, L., & Kaiser, P. (2008). Quantitative analysis of global ubiquitination in HeLa cells by mass spectrometry. Journal of Proteome Research, 7, 4566-4576.
78. Miranda, M., & Sorkin, A. (2007). Regulation of receptors and transporters by ubiquitination: New insights into surprisingly similar mechanisms. Molecular Interventions, 7, 157-167. (Pubitemid 47026726)
79. Moren, A., Hellman, U., Inada, Y., Imamura, T., Heldin, C. H., & Moustakas, A. (2003). Differential ubiquitination defines the functional status of the tumor suppressor Smad4. Journal of Biological Chemistry, 278, 33571-33582. (Pubitemid 37055811)
80. Mori, S., Claesson-Welsh, L., Okuyama, Y., & Saito, Y. (1995). Ligand-induced polyubiquitination of receptor tyrosine kinases. Biochemical and Biophysical Research Communications, 213, 32-39.
81. Mukhopadhyay, D., & Riezman, H. (2007). Proteasome-independent functions of ubiquitin in endocytosis and signaling. Science, 315, 201-205. (Pubitemid 46166358)
82. Na, C. H., Jones, D. R., Yang, Y., Wang, X., Xu, Y., & Peng, J. (2012). Synaptic protein ubiquitination in rat brain revealed by antibody-based ubiquitome analysis. Journal of Proteome Research, 11, 4722-4732.
83. Newton, K., Matsumoto, M. L., Wertz, I. E., Kirkpatrick, D. S., Lill, J. R., Tan, J., Dixit, V. M. (2008). Ubiquitin chain editing revealed by polyubiquitin linkage-specific antibodies. Cell, 134, 668-678.
84. Nielsen, M. L., Vermeulen, M., Bonaldi, T., Cox, J., Moroder, L., & Mann, M. (2008). Iodoacetamide-induced artifact mimics ubiquitination in mass spectrometry. Nature Methods, 5, 459-460. (Pubitemid 351761746)
85. Ogawa, Y., Ono, T., Wakata, Y., Okawa, K., Tagami, H., & Shibahara, K. I. (2005). Histone variant macroH2A1.2 is mono-ubiquitinated at its histone domain. Biochemical and Biophysical Research Communications, 336, 204-209. (Pubitemid 41253422)
86. Ohno, A., Jee, J., Fujiwara, K., Tenno, T., Goda, N., Tochio, H., Shirakawa, M. (2005). Structure of the UBA domain of Dsk2p in complex with ubiquitin molecular determinants for ubiquitin recognition. Structure, 13, 521-532.
87. Oshikawa, K., Matsumoto, M., Oyamada, K., & Nakayama, K. I. (2012). Proteome-wide identification of ubiquitylation sites by conjugation of engineered lysine-less ubiquitin. Journal of Proteome Research, 11, 796-807.
88. Ota, K., Kito, K., Iemura, S., Natsume, T., & Ito, T. (2008). A parallel affinity purification method for selective isolation of polyubiquitinated proteins. Proteomics, 8, 3004-3007.
89. Penengo, L., Mapelli, M., Murachelli, A. G., Confalonieri, S., Magri, L., Musacchio, A., Schneider, T. R. (2006). Crystal structure of the ubiquitin binding domains of rabex-5 reveals two modes of interaction with ubiquitin. Cell, 124, 1183-1195.
90. Peng, J., & Cheng, D. (2005). Proteomic analysis of ubiquitin conjugates in yeast. Methods in Enzymology, 399, 367-381. (Pubitemid 41772741)
91. Peng, J., Schwartz, D., Elias, J. E., Thoreen, C. C., Cheng, D., Marsischky, G., Gygi, S. P. (2003). A proteomics approach to understanding protein ubiquitination. Nature Biotechnology, 21, 921-926. (Pubitemid 36936199)
92. Pickart, C. M. (2001). Mechanisms underlying ubiquitination. Annual Review of Biochemistry, 70, 503-533. (Pubitemid 32663902)
93. Powell, S. R., Herrmann, J., Lerman, A., Patterson, C., & Wang, X. (2012). The ubiquitin-proteasome system and cardiovascular disease. Progress in Molecular Biology and Translational Science, 109, 295-346.
94. Pramstaller, P. P., Schlossmacher, M. G., Jacques, T. S., Scaravilli, F., Eskelson, C., Pepivani, I., Klein, C. (2005). Lewy body Parkinson's disease in a large pedigree with 77 Parkin mutation carriers. Annals of Neurology, 58, 411-422. (Pubitemid 41266627)
95. Rabut, G., & Peter, M. (2008). Function and regulation of protein neddylation. 'Protein modifications: Beyond the usual suspects' review series. EMBO Reports, 9, 969-976.
96. Ruffner, H., Joazeiro, C. A., Hemmati, D., Hunter, T., & Verma, I. M. (2001). Cancer-predisposing mutations within the RING domain of BRCA1: Loss of ubiquitin protein ligase activity and protection from radiation hypersensitivity. Proceedings of the National Academy of Sciences of the United States of America, 98, 5134-5139. (Pubitemid 32397095)
97. Schmidt, T. G., & Skerra, A. (2007). The Strep-tag system for one-step purification and highaffinity detection or capturing of proteins. Nature Protocols, 2, 1528-1535. (Pubitemid 46952331)
98. Shanklin, J., Jabben, M., & Vierstra, R. D. (1987). Red light-induced formation of ubiquitin-phytochrome conjugates: Identification of possible intermediates of phytochrome degradation. Proceedings of the National Academy of Sciences of the United States of America, 84, 359-363. (Pubitemid 17006194)
99. Shen, Y., Tolic, N., Xie, F., Zhao, R., Purvine, S. O., Schepmoes, A. A., Smith, R. D. (2011). Effectiveness of CID, HCD, and ETD with FT MS/MS for degradomic-peptidomic analysis: Comparison of peptide identification methods. Journal of Proteome Research, 10, 3929-3943.
100. Shi, Y., Chan, D. W., Jung, S. Y., Malovannaya, A., Wang, Y., & Qin, J. (2011). A data set of human endogenous protein ubiquitination sites. Molecular and Cellular Proteomics, 10, M110 002089.
101. Shimura, H., Hattori, N., Kubo, S., Mizuno, Y., Asakawa, S., Minoshima, S., Suzuki, T. (2000). Familial Parkinson disease gene product, parkin, is a ubiquitin-protein ligase. Nature Genetics, 25, 302-305. (Pubitemid 30437317)
102. Shimura, H., Schlossmacher, M. G., Hattori, N., Frosch, M. P., Trockenbacher, A., Schneider, R., Selkoe, D. J. (2001). Ubiquitination of a new form of a-synuclein by parkin from human brain: Implications for Parkinson's disease. Science, 293, 263-269. (Pubitemid 32694735)
103. Sims, J. J., Scavone, F., Cooper, E. M., Kane, L. A., Youle, R. J., Boeke, J. D., & Cohen, R. E. (2012). Polyubiquitin-sensor proteins reveal localization and linkage-type dependence of cellular ubiquitin signaling. Nature Methods, 9, 303-309.
104. Sliter, D. A., Aguiar, M., Gygi, S. P., & Wojcikiewicz, R. J. (2011). Activated inositol 1,4,5-trisphosphate receptors are modified by homogeneous Lys-48-and Lys-63-linked ubiquitin chains, but only Lys-48-linked chains are required for degradation. Journal of Biological Chemistry, 286, 1074-1082.
105. Sokalingam, S., Raghunathan, G., Soundrarajan, N., & Lee, S. G. (2012). A study on the effect of surface lysine to arginine mutagenesis on protein stability and structure using green fluorescent protein. PLoS One, 7, e40410.
106. Song, M., Hakala, K., Weintraub, S. T., & Shiio, Y. (2011). Quantitative proteomic identification of the BRCA1 ubiquitination substrates. Journal of Proteome Research, 10, 5191-5198.
107. Spataro, V., Norbury, C., & Harris, A. L. (1998). The ubiquitin-proteasome pathway in cancer. British Journal of Cancer, 77, 448-455. (Pubitemid 28044050)
108. Starita, L. M., Lo, R. S., Eng, J. K., von Haller, P. D., & Fields, S. (2012). Sites of ubiquitin attachment in Saccharomyces cerevisiae. Proteomics, 12, 236-240.
109. Tagwerker, C., Flick, K., Cui, M., Guerrero, C., Dou, Y., Auer, B., Kaiser, P. (2006). A tandem affinity tag for two-step purification under fully denaturing conditions: Application in ubiquitin profiling and protein complex identification combined with in vivo cross-linking. Molecular and Cellular Proteomics, 5, 737-748.
110. Takada, K., Hirakawa, T., Yokosawa, H., Okawa, Y., Taguchi, H., & Ohkawa, K. (2001). Isolation of ubiquitin-E2 (ubiquitin-conjugating enzyme) complexes from erythroleukaemia cells using immunoaffinity techniques. Biochemical Journal, 356, 199-206. (Pubitemid 34275721)
111. Takada, K., Nasu, H., Hibi, N., Tsukada, Y., Ohkawa, N., Fujimuro, M., Yokosawa, H. (1995). Immunoassay for the quantification of intracellular multi-ubiquitin chains. European Journal of Biochemistry, 233, 42-47.
112. Tan, F., Lu, L., Cai, Y., Wang, J., Xie, Y., Wang, L., Peng, X. (2008). Proteomic analysis of ubiquitinated proteins in normal hepatocyte cell line Chang liver cells. Proteomics, 8, 2885-2896.
113. Tang, H. Y., & Speicher, D. W. (2004). Identification of alternative products and optimization of 2-nitro-5-thiocyanatobenzoic acid cyanylation and cleavage at cysteine residues. Analytical Biochemistry, 334, 48-61. (Pubitemid 39304074)
114. Tokunaga, F., & Iwai, K. (2012). LUBAC, a novel ubiquitin ligase for linear ubiquitination, is crucial for inflammation and immune responses. Microbes and Infection, 14, 563-572.
115. Treier, M., Staszewski, L. M., & Bohmann, D. (1994). Ubiquitin-dependent c-Jun degradation in vivo is mediated by the d domain. Cell, 78, 787-798. (Pubitemid 24294454)
116. Udeshi, N. D., Mani, D. R., Eisenhaure, T., Mertins, P., Jaffe, J. D., Clauser, K. R., Carr, S. A. (2012). Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. Molecular and Cellular Proteomics, 11, 148-159.
117. Vasilescu, J., Smith, J. C., Ethier, M., & Figeys, D. (2005). Proteomic analysis of ubiquitinated proteins from human MCF-7 breast cancer cells by immunoaffinity purification and mass spectrometry. Journal of Proteome Research, 4, 2192-2200. (Pubitemid 41814287)
118. Vasilescu, J., Zweitzig, D. R., Denis, N. J., Smith, J. C., Ethier, M., Haines, D. S., & Figeys, D. (2007). The proteomic reactor facilitates the analysis of affinity-purified proteins by mass spectrometry: Application for identifying ubiquitinated proteins in human cells. Journal of Proteome Research, 6, 298-305. (Pubitemid 46173681)
119. Wagner, S. A., Beli, P., Weinert, B. T., Nielsen, M. L., Cox, J., Mann, M., & Choudhary, C. (2011). A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. Molecular and Cellular Proteomics, 10, M111 013284.
120. Walters, K. J., Kleijnen, M. F., Goh, A. M., Wagner, G., & Howley, P. M. (2002). Structural studies of the interaction between ubiquitin family proteins and proteasome subunit S5a. Biochemistry, 41, 1767-1777. (Pubitemid 34132251)
121. Wang, D., Kalume, D., Pickart, C., Pandey, A., & Cotter, R. J. (2006). Identification of protein ubiquitylation by electrospray ionization tandem mass spectrometric analysis of sulfonated tryptic peptides. Analytical Chemistry, 78, 3681-3687. (Pubitemid 43848962)
122. Wang, D., Xu, W., McGrath, S. C., Patterson, C., Neckers, L., & Cotter, R. J. (2005). Direct identification of ubiquitination sites on ubiquitin-conjugated CHIP using MALDI mass spectrometry. Journal of Proteome Research, 4, 1554-1560. (Pubitemid 41464780)
123. Wang, X., Herr, R. A., Chua, W. J., Lybarger, L., Wiertz, E. J., & Hansen, T. H. (2007). Ubiquitination of serine, threonine, or lysine residues on the cytoplasmic tail can induce ERAD of MHC-I by viral E3 ligase mK3. Journal of Cell Biology, 177, 613-624. (Pubitemid 46799833)
124. Wang, X., Herr, R. A., & Hansen, T. H. (2012). Ubiquitination of substrates by esterification. Traffic, 13, 19-24.
125. Warren, M. R., Parker, C. E., Mocanu, V., Klapper, D., & Borchers, C. H. (2005). Electrospray ionization tandem mass spectrometry of model peptides reveals diagnostic fragment ions for protein ubiquitination. Rapid Communications in Mass Spectrometry, 19, 429-437. (Pubitemid 40269526)
126. Wiesner, J., Premsler, T., & Sickmann, A. (2008). Application of electron transfer dissociation (ETD) for the analysis of posttranslational modifications. Proteomics, 8, 4466-4483.
127. Wilkinson, K. D., Tashayev, V. L., O'Connor, L. B., Larsen, C. N., Kasperek, E., & Pickart, C. M. (1995). Metabolism of the polyubiquitin degradation signal: Structure, mechanism, and role of isopeptidase T. Biochemistry, 34, 14535-14546.
128. Xirodimas, D. P. (2008). Novel substrates and functions for the ubiquitin-like molecule NEDD8. Biochemical Society Transactions, 36, 802-806.
129. Xirodimas, D. P., Saville, M. K., Bourdon, J. C., Hay, R. T., & Lane, D. P. (2004). Mdm2-mediated NEDD8 conjugation of p53 inhibits its transcriptional activity. Cell, 118, 83-97. (Pubitemid 38902816)
130. Xirodimas, D. P., Sundqvist, A., Nakamura, A., Shen, L., Botting, C., & Hay, R. T. (2008). Ribosomal proteins are targets for the NEDD8 pathway. EMBO Reports, 9, 280-286. (Pubitemid 351330994)
131. Xu, G., Paige, J. S., & Jaffrey, S. R. (2010). Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling. Nature Biotechnology, 28, 868-873.
132. Xu, P., Duong, D. M., Seyfried, N. T., Xie, Y., Robert, J., Rush, J., Peng, J. (2009). Quantitative proteomics reveals the function of unconventional ubiquitin chains in proteasomal degradation. Cell, 137, 133-145.
133. Yen, H. C., & Elledge, S. J. (2008). Identification of SCF ubiquitin ligase substrates by global protein stability profiling. Science, 322, 923-929.
134. Young, P., Deveraux, Q., Beal, R. E., Pickart, C. M., & Rechsteiner, M. (1998). Characterization of two polyubiquitin binding sites in the 26S protease subunit 5a. Journal of Biological Chemistry, 273, 5461-5467. (Pubitemid 28124009)
135. Zhang, D., & Zhang, D. E. (2011). Interferon-stimulated gene 15 and the protein ISGylation system. Journal of Interferon and Cytokine Research, 31, 119-130.