Integrative analysis of the ubiquitin proteome isolated using Tandem Ubiquitin Binding Entities (TUBEs)

The successful use of proteasome inhibitors in clinical trials revealed the potential of the Ubiquitin Proteasome System for drug development. Protein remodeling through ubiquitylation is known to regulate the stability and activity of essential cellular factors through largely uncharacterized mechanisms. Here, we used Tandem repeated Ubiquitin Binding Entities (TUBEs) under non-denaturing conditions followed by mass spectrometry analysis to study global ubiquitylation events that may lead to the identification of potential drug targets. Using this approach we identified 643 proteins including known and unknown ubiquitin targets from human breast adenocarcinoma MCF7 cells treated with Adriamycin. Coherent with a global cellular response to this genotoxic insult, cellular factors identified are involved in protein synthesis, cellular transport, RNA post-transcriptional modification and signaling pathways regulating early stress responses. This includes components of large macromolecular complexes such as subunits and regulators of the proteasome, supporting the use of this method to characterize networks of molecular interactions coordinated by ubiquitylation. Further in vitro and in silico analysis confirmed that 84% of the total proteins identified here, are ubiquitylated. More importantly the enrichment of known biomarkers and targets for drug development, underlined the potential of this approach for the identification of this clinically relevant information. This article is part of a Special Issue entitled: Proteomics: The clinical link.

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► We identify ubiquitylated proteins and interacting factors using TUBEs.
► We isolate large macromolecular complexes including components of the proteasome.
► Cellular transport, signalling and scaffolding molecules compose analysed samples.
► This procedure enriches potential biomarkers and proteins used for drug development.