Large-scale analysis of the human ubiquitin-related proteome

Masaki Matsumoto, Shigetsugu Hatakeyama, Koji Oyamada, Yoshiya Oda, Toshihide Nishimura, Keiichi Nakayama

Research output: Contribution to journalArticle

142 Citations (Scopus)

Abstract

Protein ubiquitylation contributes to the regulation of many cellular processes including protein degradation, receptor internalization, and repair of DNA damage. We now present a comprehensive characterization of ubiquitin-conjugated and ubiquitin-associated proteins in human cells. The proteins were purified by immunoaffinity chromatography under denaturing or native conditions. They were then digested with trypsin, and the resulting peptides were analyzed by 2-D LC and MS/MS. A total of 670 distinct proteins were identified; 345 proteins (51%) were classified as Urp-D (ubiquitin-related proteome under the denaturing condition) and comprised ubiquitin-conjugated molecules, whereas 325 proteins (49%) were classified as Urp-N (ubiquitin-related proteome only under the native condition) and included molecules that associated with ubiquitylated proteins. The proportions of proteins in various functional categories differed substantially between Urp-D and Urp-N. Many ribosomal subunits were detected in the Urp-D group of proteins and several of these subunits were directly shown to be ubiquitylated by mass spectrometric analysis, suggesting that ubiquitylation might play an important role in the regulation and/or quality control of ribosomal proteins. Our results demonstrate the potential of proteomics analysis of protein ubiquitylation to provide important insight into the regulation of protein stability and other ubiquitin-related cellular functions.

Original languageEnglish
Pages (from-to)4145-4151
Number of pages7
JournalProteomics
Volume5
Issue number16
DOIs
Publication statusPublished - Nov 1 2005

Fingerprint

Proteome
Ubiquitin
Proteins
Ubiquitination
Ribosome Subunits
Protein Stability
Ribosomal Proteins
Protein Subunits
Molecules
Quality Control
Proteomics
Trypsin
Proteolysis
DNA Damage
Chromatography
Quality control
Repair
Peptides
Cells
Degradation

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

Cite this

Large-scale analysis of the human ubiquitin-related proteome. / Matsumoto, Masaki; Hatakeyama, Shigetsugu; Oyamada, Koji; Oda, Yoshiya; Nishimura, Toshihide; Nakayama, Keiichi.

In: Proteomics, Vol. 5, No. 16, 01.11.2005, p. 4145-4151.

Research output: Contribution to journalArticle

Matsumoto, M, Hatakeyama, S, Oyamada, K, Oda, Y, Nishimura, T & Nakayama, K 2005, 'Large-scale analysis of the human ubiquitin-related proteome', Proteomics, vol. 5, no. 16, pp. 4145-4151. https://doi.org/10.1002/pmic.200401280
Matsumoto, Masaki ; Hatakeyama, Shigetsugu ; Oyamada, Koji ; Oda, Yoshiya ; Nishimura, Toshihide ; Nakayama, Keiichi. / Large-scale analysis of the human ubiquitin-related proteome. In: Proteomics. 2005 ; Vol. 5, No. 16. pp. 4145-4151.
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