Proteomic snapshot of the EGF-induced ubiquitin network

• Published in: Molecular systems biology 2011-01, Vol.7 (1), p.462-n/a
• Main Authors: Bange, Tanja, Mari, Sara, Di Fiore, Pier Paolo, Argenzio, Elisabetta, Polo, Simona, Oldrini, Barbara, Mann, Matthias, Peesari, Raghunath, Bianchi, Fabrizio
• Format: Article
• Language: English
• Subjects: Actin; Amino acids; Amplification; Animals; Blotting, Western; Cancer; Cascades; Cell adhesion; Cell adhesion & migration; Cell culture; Cell Line; Chains; Cluster Analysis; Conjugation; Crosstalk; Deoxyribonucleic acid; DNA; DNA damage; EMBO31; EMBO37; Endocytosis; Enrichment; Enzymes; EphA2 protein; Epidermal growth factor; Epidermal Growth Factor - chemistry; Epidermal Growth Factor - metabolism; Epidermal growth factor receptors; HeLa Cells; Homeostasis; Humans; Internalization; Intracellular; Intracellular signalling; Kinases; Localization; Mass Spectrometry; Mass spectroscopy; Mice; Microscopy, Fluorescence; Molecular chains; Monomers; Network analysis; Networks; Phosphorylation; Phosphotyrosine; Physiology; Protein purification; Protein-tyrosine kinase; Protein-tyrosine kinase receptors; Proteins; Proteome - chemistry; Proteome - metabolism; Proteomics - methods; Purification; Receptor, EphA2 - metabolism; Screens; Signal Transduction; Stable isotopes; Stimulation; Systems Biology - methods; Topology; Transcription; Translation; Tyrosine; Ubiquitin - chemistry; Ubiquitin - metabolism
• ISSN: 1744-4292; 1744-4292
• DOI: 10.1038/msb.2010.118

The activity, localization and fate of many cellular proteins are regulated through ubiquitination, a process whereby one or more ubiquitin (Ub) monomers or chains are covalently attached to target proteins. While Ub‐conjugated and Ub‐associated proteomes have been described, we lack a high‐resolution picture of the dynamics of ubiquitination in response to signaling. In this study, we describe the epidermal growth factor (EGF)‐regulated Ubiproteome, as obtained by two complementary purification strategies coupled to quantitative proteomics. Our results unveil the complex impact of growth factor signaling on Ub‐based intracellular networks to levels that extend well beyond what might have been expected. In addition to endocytic proteins, the EGF‐regulated Ubiproteome includes a large number of signaling proteins, ubiquitinating and deubiquitinating enzymes, transporters and proteins involved in translation and transcription. The Ub‐based signaling network appears to intersect both housekeeping and regulatory circuitries of cellular physiology. Finally, as proof of principle of the biological relevance of the EGF‐Ubiproteome, we demonstrated that EphA2 is a novel, downstream ubiquitinated target of epidermal growth factor receptor (EGFR), critically involved in EGFR biological responses. In this work, the authors report the first proteome‐wide analysis of EGF‐regulated ubiquitination, revealing surprisingly pervasive growth factor‐induced ubiquitination across a broad range of cellular systems and signaling pathways. Synopsis In this work, the authors report the first proteome‐wide analysis of EGF‐regulated ubiquitination, revealing surprisingly pervasive growth factor‐induced ubiquitination across a broad range of cellular systems and signaling pathways. Ubiquitination is a process by which one or more ubiquitin (Ub) monomers or chains are covalently attached to target proteins by E3 ligases. Deubiquitinating enzymes (DUBs) revert Ub conjugation, thus ensuring a dynamic equilibrium between pools of ubiquitinated and deubiquitinated proteins (Amerik and Hochstrasser, 2004 ). Traditionally, ubiquitination has been associated with protein degradation; however, it is now becoming apparent that this post‐translation modification is an important signaling mechanism that can modulate the function, localization and protein/protein interaction abilities of targets (Mukhopadhyay and Riezman, 2007 ; Ravid and Hochstrasser, 2008 ). One of the best‐characterized signal