Journal
PROTEOMICS
Volume 13, Issue 3-4, Pages 526-537Publisher
WILEY
DOI: 10.1002/pmic.201200244
Keywords
Cell biology; Deubiquitylating; Diglycine; Post-translational modification; Proteasome; Ubiquitin
Funding
- PRIME-XS project [262067]
- European Union
- Netherlands Proteomics Centre, Netherlands Genomics Initiative
- Centre for Biomedical Genetics
- Netherlands Organization for Scientific Research (NWO)
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Ubiquitin (Ub) is a small protein modifier that is covalently attached to the epsilon-amino group of lysine residues of protein substrates, generally targeting them for degradation. Due to the emergence of specific anti-diglycine (-GG) antibodies and the improvement in MS, it is now possible to identify more than 10 000 ubiquitylated sites in a single proteomics study. Besides cataloging ubiquitylated sites, it is equally important to unravel the biological relationship between ubiquitylated substrates and the ubiquitin conjugation machinery. Relevant to this, we discuss the role of affinity purification-MS (AP-MS), in characterizing E3 ligase-substrate complexes. Recently, such strategies have also been adapted to screen for binding partners of both deubiquitylating enzymes (DUBs) and ubiquitin-binding domains (UBDs). The complexity of the ubiquitome is further expanded by the fact that Ub itself can be ubiquitylated at any of its seven lysine residues forming polyubiquitin (polyUb), thus diversifying its lengths and topologies to suit a variety of molecular recognition processes. Therefore, applying MS to study polyUb linkages is also becoming an emerging and important area. Finally, we discuss the future of MS-based proteomics in answering important questions with respect to ubiquitylation.
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