publication . Article . Other literature type . 2011

A Proteome-wide, Quantitative Survey of In Vivo Ubiquitylation Sites Reveals Widespread Regulatory Roles

Wagner, S. A.; Beli, P.; Weinert, B. T.; Michael Nielsen; Cox, J.; Mann, M.; Choudhary, C.;
Open Access English
  • Published: 01 Sep 2011 Journal: Molecular & Cellular Proteomics : MCP, volume 10, issue 10 (issn: 1535-9476, eissn: 1535-9484, Copyright policy)
  • Publisher: The American Society for Biochemistry and Molecular Biology
Abstract
Ubiquitin is a 76 amino acid long protein that can be conjugated to the e-amino group of lysines in a process termed ubiquitylation or ubiquitination (1, 2). Post-translational modification (PTM)1 of proteins by ubiquitin is a reversible regulatory mechanism that is well conserved in eukaryotic organisms. The role of ubiquitylation is extensively studied in the ubiquitin proteasome system (UPS) where substrate-linked ubiquitin provides a signal for proteasomal degradation of target proteins (3). However, ubiquitylation also plays important roles in many other cellular processes including DNA damage repair, DNA replication, cell surface receptor endocytosis, and ...
Subjects
free text keywords: Research, Proteomics, Ubiquitin, biology.protein, biology, Molecular biology, Proteome, Stable isotope labeling by amino acids in cell culture, Quantitative proteomics, Proteasome, Cullin, NEDD8, Biochemistry
Funded by
EC| PRIME-XS
Project
PRIME-XS
Proteomics Research Infrastructure Maximising knowledge EXchange and access (XS)
  • Funder: European Commission (EC)
  • Project Code: 262067
  • Funding stream: FP7 | SP4 | INFRA
,
EC| SYBOSS
Project
SYBOSS
Systems Biology of Stem Cells and Reprogramming
  • Funder: European Commission (EC)
  • Project Code: 242129
  • Funding stream: FP7 | SP1 | HEALTH
58 references, page 1 of 4

1.Glickman M. H.Ciechanover A. (2002) The ubiquitin-proteasome proteolytic pathway: destruction for the sake of construction. Nat. Rev. 82, 373–428 [OpenAIRE]

2.Weissman A. M. (2001) Themes and variations on ubiquitylation. Mol. Cell Biol. 2, 169–178

3.Hochstrasser M. (1995) Ubiquitin, proteasomes, and the regulation of intracellular protein degradation. Current Opinion Cell Biol. 7, 215–223 7612274 [OpenAIRE] [PubMed]

4.Chen Z. J.Sun L. J. (2009) Nonproteolytic functions of ubiquitin in cell signaling. Mol. Cell 33, 275–286 19217402 [PubMed]

5.Grabbe C.Husnjak K.Dikic I. (2011) The spatial and temporal organization of ubiquitin networks. Nat. Rev. Mol. Cell. Biol. 12, 295–307 21448225 [OpenAIRE] [PubMed]

6.Mukhopadhyay D.Riezman H. (2007) Proteasome-independent functions of ubiquitin in endocytosis and signaling. Science 315, 201–205 17218518 [OpenAIRE] [PubMed]

7.Bingol B.Sheng M. (2011) Deconstruction for reconstruction: the role of proteolysis in neural plasticity and disease. Neuron 69, 22–32 21220096 [OpenAIRE] [PubMed]

8.Hoeller D.Hecker C. M.Dikic I. (2006) Ubiquitin and ubiquitin-like proteins in cancer pathogenesis. Nat. Rev. 6, 776–788 [OpenAIRE]

9.Schwartz A. L.Ciechanover A. (2009) Targeting proteins for destruction by the ubiquitin system: implications for human pathobiology. Ann. Rev. Pharmacol. Toxicol. 49, 73–96 18834306 [PubMed]

10.Bedford L.Lowe J.Dick L. R.Mayer R. J.Brownell J. E. (2011) Ubiquitin-like protein conjugation and the ubiquitin-proteasome system as drug tar gets. Nat. Rev. 10, 29–46 [OpenAIRE]

11.Hoeller D.Dikic I. (2009) Targeting the ubiquitin system in cancer therapy. Nature 458, 438–444 19325623 [OpenAIRE] [PubMed]

12.Choudhary C.Mann M. (2010) Decoding signalling networks by mass spectrometry-based proteomics. Nat. Rev. 11, 427–439

13.Zhang D.Zhang D. E. (2011) Interferon-stimulated gene 15 and the protein ISGylation system. J. Interferon Cytokine Res. 31, 119–130 21190487 [OpenAIRE] [PubMed]

14.Rabut G.Pet er M. (2008) Function and regulation of protein neddylation. ‘Protein modifications: beyond the usual suspects’ review series. EMBO Rep. 9, 969–976 18802447 [OpenAIRE] [PubMed]

15.Peng J.Schwartz D.Elias J. E.Thoreen C. C.Cheng D.Marsischky G.Roelofs J.Finley D.Gygi S. P. (2003) A proteomics approach to understanding protein ubiquitination. Nat. Biotechnol. 21, 921–926 12872131 [PubMed]

58 references, page 1 of 4
Abstract
Ubiquitin is a 76 amino acid long protein that can be conjugated to the e-amino group of lysines in a process termed ubiquitylation or ubiquitination (1, 2). Post-translational modification (PTM)1 of proteins by ubiquitin is a reversible regulatory mechanism that is well conserved in eukaryotic organisms. The role of ubiquitylation is extensively studied in the ubiquitin proteasome system (UPS) where substrate-linked ubiquitin provides a signal for proteasomal degradation of target proteins (3). However, ubiquitylation also plays important roles in many other cellular processes including DNA damage repair, DNA replication, cell surface receptor endocytosis, and ...
Subjects
free text keywords: Research, Proteomics, Ubiquitin, biology.protein, biology, Molecular biology, Proteome, Stable isotope labeling by amino acids in cell culture, Quantitative proteomics, Proteasome, Cullin, NEDD8, Biochemistry
Funded by
EC| PRIME-XS
Project
PRIME-XS
Proteomics Research Infrastructure Maximising knowledge EXchange and access (XS)
  • Funder: European Commission (EC)
  • Project Code: 262067
  • Funding stream: FP7 | SP4 | INFRA
,
EC| SYBOSS
Project
SYBOSS
Systems Biology of Stem Cells and Reprogramming
  • Funder: European Commission (EC)
  • Project Code: 242129
  • Funding stream: FP7 | SP1 | HEALTH
58 references, page 1 of 4

1.Glickman M. H.Ciechanover A. (2002) The ubiquitin-proteasome proteolytic pathway: destruction for the sake of construction. Nat. Rev. 82, 373–428 [OpenAIRE]

2.Weissman A. M. (2001) Themes and variations on ubiquitylation. Mol. Cell Biol. 2, 169–178

3.Hochstrasser M. (1995) Ubiquitin, proteasomes, and the regulation of intracellular protein degradation. Current Opinion Cell Biol. 7, 215–223 7612274 [OpenAIRE] [PubMed]

4.Chen Z. J.Sun L. J. (2009) Nonproteolytic functions of ubiquitin in cell signaling. Mol. Cell 33, 275–286 19217402 [PubMed]

5.Grabbe C.Husnjak K.Dikic I. (2011) The spatial and temporal organization of ubiquitin networks. Nat. Rev. Mol. Cell. Biol. 12, 295–307 21448225 [OpenAIRE] [PubMed]

6.Mukhopadhyay D.Riezman H. (2007) Proteasome-independent functions of ubiquitin in endocytosis and signaling. Science 315, 201–205 17218518 [OpenAIRE] [PubMed]

7.Bingol B.Sheng M. (2011) Deconstruction for reconstruction: the role of proteolysis in neural plasticity and disease. Neuron 69, 22–32 21220096 [OpenAIRE] [PubMed]

8.Hoeller D.Hecker C. M.Dikic I. (2006) Ubiquitin and ubiquitin-like proteins in cancer pathogenesis. Nat. Rev. 6, 776–788 [OpenAIRE]

9.Schwartz A. L.Ciechanover A. (2009) Targeting proteins for destruction by the ubiquitin system: implications for human pathobiology. Ann. Rev. Pharmacol. Toxicol. 49, 73–96 18834306 [PubMed]

10.Bedford L.Lowe J.Dick L. R.Mayer R. J.Brownell J. E. (2011) Ubiquitin-like protein conjugation and the ubiquitin-proteasome system as drug tar gets. Nat. Rev. 10, 29–46 [OpenAIRE]

11.Hoeller D.Dikic I. (2009) Targeting the ubiquitin system in cancer therapy. Nature 458, 438–444 19325623 [OpenAIRE] [PubMed]

12.Choudhary C.Mann M. (2010) Decoding signalling networks by mass spectrometry-based proteomics. Nat. Rev. 11, 427–439

13.Zhang D.Zhang D. E. (2011) Interferon-stimulated gene 15 and the protein ISGylation system. J. Interferon Cytokine Res. 31, 119–130 21190487 [OpenAIRE] [PubMed]

14.Rabut G.Pet er M. (2008) Function and regulation of protein neddylation. ‘Protein modifications: beyond the usual suspects’ review series. EMBO Rep. 9, 969–976 18802447 [OpenAIRE] [PubMed]

15.Peng J.Schwartz D.Elias J. E.Thoreen C. C.Cheng D.Marsischky G.Roelofs J.Finley D.Gygi S. P. (2003) A proteomics approach to understanding protein ubiquitination. Nat. Biotechnol. 21, 921–926 12872131 [PubMed]

58 references, page 1 of 4
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