publication . Article . Other literature type . 2010

Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling

Xu, Guoqiang; Paige, Jeremy S; Jaffrey, Samie R;
Open Access
  • Published: 18 Jul 2010 Journal: Nature Biotechnology, volume 28, pages 868-873 (issn: 1087-0156, eissn: 1546-1696, Copyright policy)
  • Publisher: Springer Science and Business Media LLC
Abstract
Protein ubiquitination is a post-translational modification (PTM) that regulates various aspects of protein function by different mechanisms. Global profiling of PTMs usually relies on purification and sequencing of PTM-containing peptides from proteolytic digests. Characterization of ubiquitination has lagged behind that of smaller PTMs, such as phosphorylation and acetylation, largely because of the difficulty of isolating and identifying peptides derived from the ubiquitinated portion of proteins. To address this issue, we have generated a monoclonal antibody that can enrich for peptides containing lysine residues modified by diglycine, an adduct left at site...
Subjects
free text keywords: Biotechnology, Molecular Medicine, Applied Microbiology and Biotechnology, Bioengineering, Biomedical Engineering, Peptide sequence, Lysine, Immunoprecipitation, Tubulin, biology.protein, biology, Molecular biology, Ubiquitin-conjugating enzyme, Biochemistry, Protein ubiquitination, F-box protein, Ubiquitin, Article
Funded by
NIH| Comprehensive profiling of ubiquitination in neurons
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1R21MH086128-01A1
  • Funding stream: NATIONAL INSTITUTE OF MENTAL HEALTH
,
NIH| CANCER PHARMACOLOGY
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5T32CA062948-09
  • Funding stream: NATIONAL CANCER INSTITUTE
49 references, page 1 of 4

Hershko, A, Ciechanover, A. The ubiquitin system. Annu Rev Biochem. 1998; 67: 425-479 [OpenAIRE] [PubMed]

Xu, P, Peng, J. Dissecting the ubiquitin pathway by mass spectrometry. Biochim Biophys Acta. 2006; 1764: 1940-1947 [OpenAIRE] [PubMed]

Ericsson, C, Goldknopf, IL, Daneholt, B. Inhibition of transcription does not affect the total amount of ubiquitinated histone 2A in chromatin. Exp Cell Res. 1986; 167: 127-134 [OpenAIRE] [PubMed]

Galluzzi, L, Paiardini, M, Lecomte, MC, Magnani, M. Identification of the main ubiquitination site in human erythroid alpha-spectrin. FEBS Lett. 2001; 489: 254-258 [OpenAIRE] [PubMed]

Tomlinson, E, Palaniyappan, N, Tooth, D, Layfield, R. Methods for the purification of ubiquitinated proteins. Proteomics. 2007; 7: 1016-1022 [OpenAIRE] [PubMed]

Beers, EP, Callis, J. Utility of polyhistidine-tagged ubiquitin in the purification of ubiquitin-protein conjugates and as an affinity ligand for the purification of ubiquitin-specific hydrolases. J Biol Chem. 1993; 268: 21645-21649 [OpenAIRE] [PubMed]

Peng, J. A proteomics approach to understanding protein ubiquitination. Nat Biotechnol. 2003; 21: 921-926 [PubMed]

Srikumar, T, Jeram, SM, Lam, H, Raught, B. A ubiquitin and ubiquitin-like protein spectral library. Proteomics. ; 10: 337-342 [PubMed]

Hershko, A, Heller, H, Elias, S, Ciechanover, A. Components of ubiquitin-protein ligase system. Resolution, affinity purification, and role in protein breakdown. J Biol Chem. 1983; 258: 8206-8214 [OpenAIRE] [PubMed]

Denis, NJ, Vasilescu, J, Lambert, JP, Smith, JC, Figeys, D. Tryptic digestion of ubiquitin standards reveals an improved strategy for identifying ubiquitinated proteins by mass spectrometry. Proteomics. 2007; 7: 868-874 [OpenAIRE] [PubMed]

Rechsteiner, M. Ubiquitin-mediated pathways for intracellular proteolysis. Annu Rev Cell Biol. 1987; 3: 1-30 [OpenAIRE] [PubMed]

Bonifacino, JS, Weissman, AM. Ubiquitin and the control of protein fate in the secretory and endocytic pathways. Annu Rev Cell Dev Biol. 1998; 14: 19-57 [OpenAIRE] [PubMed]

Kirkpatrick, DS, Denison, C, Gygi, SP. Weighing in on ubiquitin: the expanding role of mass-spectrometry-based proteomics. Nat Cell Biol. 2005; 7: 750-757 [OpenAIRE] [PubMed]

Sun, L, Chen, ZJ. The novel functions of ubiquitination in signaling. Curr Opin Cell Biol. 2004; 16: 119-126 [PubMed]

Etlinger, JD, Li, SX, Guo, GG, Li, N. Phosphorylation and ubiquitination of the 26S proteasome complex. Enzyme Protein. 1993; 47: 325-329 [PubMed]

49 references, page 1 of 4
Abstract
Protein ubiquitination is a post-translational modification (PTM) that regulates various aspects of protein function by different mechanisms. Global profiling of PTMs usually relies on purification and sequencing of PTM-containing peptides from proteolytic digests. Characterization of ubiquitination has lagged behind that of smaller PTMs, such as phosphorylation and acetylation, largely because of the difficulty of isolating and identifying peptides derived from the ubiquitinated portion of proteins. To address this issue, we have generated a monoclonal antibody that can enrich for peptides containing lysine residues modified by diglycine, an adduct left at site...
Subjects
free text keywords: Biotechnology, Molecular Medicine, Applied Microbiology and Biotechnology, Bioengineering, Biomedical Engineering, Peptide sequence, Lysine, Immunoprecipitation, Tubulin, biology.protein, biology, Molecular biology, Ubiquitin-conjugating enzyme, Biochemistry, Protein ubiquitination, F-box protein, Ubiquitin, Article
Funded by
NIH| Comprehensive profiling of ubiquitination in neurons
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1R21MH086128-01A1
  • Funding stream: NATIONAL INSTITUTE OF MENTAL HEALTH
,
NIH| CANCER PHARMACOLOGY
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5T32CA062948-09
  • Funding stream: NATIONAL CANCER INSTITUTE
49 references, page 1 of 4

Hershko, A, Ciechanover, A. The ubiquitin system. Annu Rev Biochem. 1998; 67: 425-479 [OpenAIRE] [PubMed]

Xu, P, Peng, J. Dissecting the ubiquitin pathway by mass spectrometry. Biochim Biophys Acta. 2006; 1764: 1940-1947 [OpenAIRE] [PubMed]

Ericsson, C, Goldknopf, IL, Daneholt, B. Inhibition of transcription does not affect the total amount of ubiquitinated histone 2A in chromatin. Exp Cell Res. 1986; 167: 127-134 [OpenAIRE] [PubMed]

Galluzzi, L, Paiardini, M, Lecomte, MC, Magnani, M. Identification of the main ubiquitination site in human erythroid alpha-spectrin. FEBS Lett. 2001; 489: 254-258 [OpenAIRE] [PubMed]

Tomlinson, E, Palaniyappan, N, Tooth, D, Layfield, R. Methods for the purification of ubiquitinated proteins. Proteomics. 2007; 7: 1016-1022 [OpenAIRE] [PubMed]

Beers, EP, Callis, J. Utility of polyhistidine-tagged ubiquitin in the purification of ubiquitin-protein conjugates and as an affinity ligand for the purification of ubiquitin-specific hydrolases. J Biol Chem. 1993; 268: 21645-21649 [OpenAIRE] [PubMed]

Peng, J. A proteomics approach to understanding protein ubiquitination. Nat Biotechnol. 2003; 21: 921-926 [PubMed]

Srikumar, T, Jeram, SM, Lam, H, Raught, B. A ubiquitin and ubiquitin-like protein spectral library. Proteomics. ; 10: 337-342 [PubMed]

Hershko, A, Heller, H, Elias, S, Ciechanover, A. Components of ubiquitin-protein ligase system. Resolution, affinity purification, and role in protein breakdown. J Biol Chem. 1983; 258: 8206-8214 [OpenAIRE] [PubMed]

Denis, NJ, Vasilescu, J, Lambert, JP, Smith, JC, Figeys, D. Tryptic digestion of ubiquitin standards reveals an improved strategy for identifying ubiquitinated proteins by mass spectrometry. Proteomics. 2007; 7: 868-874 [OpenAIRE] [PubMed]

Rechsteiner, M. Ubiquitin-mediated pathways for intracellular proteolysis. Annu Rev Cell Biol. 1987; 3: 1-30 [OpenAIRE] [PubMed]

Bonifacino, JS, Weissman, AM. Ubiquitin and the control of protein fate in the secretory and endocytic pathways. Annu Rev Cell Dev Biol. 1998; 14: 19-57 [OpenAIRE] [PubMed]

Kirkpatrick, DS, Denison, C, Gygi, SP. Weighing in on ubiquitin: the expanding role of mass-spectrometry-based proteomics. Nat Cell Biol. 2005; 7: 750-757 [OpenAIRE] [PubMed]

Sun, L, Chen, ZJ. The novel functions of ubiquitination in signaling. Curr Opin Cell Biol. 2004; 16: 119-126 [PubMed]

Etlinger, JD, Li, SX, Guo, GG, Li, N. Phosphorylation and ubiquitination of the 26S proteasome complex. Enzyme Protein. 1993; 47: 325-329 [PubMed]

49 references, page 1 of 4
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