Protein abundance changes and ubiquitylation targets identified upon inhibition of the proteasome with Syringolin A

The numerous roles of the ubiquitin proteasome system (UPS) in cellular control have triggered interest in the identification of these ubiquitylation targets and their sites of ubiquitylation. For the identification of ubiquitylated proteins we employed affinity enrichment using an ubiquitin binding domains (UBAs). A change in the experimental set-up allowed for the identification of proteins that so far have been refractory to identification. We also investigated the changes in protein abundance upon interfering with the UPS by inhibition of the proteasome with the specific inhibitor Syringolin A and using a mutant overexpressing ubiquitin that cannot form K48-linked polyubiquitin chains.