UbiSite approach for comprehensive mapping of lysine and N-terminal ubiquitination sites

Vyacheslav Akimov, Inigo Barrio-Hernandez, Sten V F Hansen, Philip Hallenborg, Anna-Kathrine Pedersen, Dorte B Bekker-Jensen, Michele Puglia, Stine D K Christensen, Jens T Vanselow, Mogens M Nielsen, Irina Kratchmarova, Christian D Kelstrup, Jesper V Olsen, Blagoy Blagoev*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

Ubiquitination is a post-translational modification (PTM) that is essential for balancing numerous physiological processes. To enable delineation of protein ubiquitination at a site-specific level, we generated an antibody, denoted UbiSite, recognizing the C-terminal 13 amino acids of ubiquitin, which remain attached to modified peptides after proteolytic digestion with the endoproteinase LysC. Notably, UbiSite is specific to ubiquitin. Furthermore, besides ubiquitination on lysine residues, protein N-terminal ubiquitination is readily detected as well. By combining UbiSite enrichment with sequential LysC and trypsin digestion and high-accuracy MS, we identified over 63,000 unique ubiquitination sites on 9,200 proteins in two human cell lines. In addition to uncovering widespread involvement of this PTM in all cellular aspects, the analyses reveal an inverse association between protein N-terminal ubiquitination and acetylation, as well as a complete lack of correlation between changes in protein abundance and alterations in ubiquitination sites upon proteasome inhibition.

Original languageEnglish
JournalNature Structural and Molecular Biology
Volume25
Issue number7
Pages (from-to)631-640
ISSN1545-9993
DOIs
Publication statusPublished - 2018

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