Identification of Ubiquitin Chain Interacting Proteins
Ubiquitylation, the modification of proteins by ubiquitin (Ub), is one of the most prevalent and versatile post-translational modifications in eukaryotic cells. As Ub also serves as its own substrate, proteins can be modified by numerous different Ub chains, in which the individual moieties are linked via one or several of the seven lysines of Ub. Homogeneous Ub chains, in which the moieties are sequentially linked via the same residue, have been most extensively studied. Yet, due to their restricted availability, the functions of Ub chains linked via K27, K29 or K33 are poorly understood. We have developed an approach that, for the first time, allows the generation of all seven homogeneous Ub chains in large quantities. We show that the chains enable the identification of Ub chain binding proteins by affinity-based proteomics. The potential of our approach is demonstrated by the identification of previously unknown interaction partners of K27-, K29-, and K33-linked Ub chains.
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