Characterization of ubiquitination dependent dynamics in growth factor receptor signaling by quantitative proteomics

Protein ubiquitination is a dynamic reversible post-translational modification that plays a key role in the regulation of numerous cellular processes including signal transduction, endocytosis, cell cycle control, DNA repair and gene transcription. The conjugation of the small protein ubiquitin or chains of ubiquitin molecules of various types and lengths to targeted proteins is known to alter proteins' lifespan, localization and function and to modulate protein interactions. Despite its central importance in various aspects of cellular life and function there are only a limited number of reports investigating ubiquitination on a proteomic scale, mainly due to the inherited complexity and heterogeneity of ubiquitination. We describe here a quantitative proteomics strategy based on the specificity of ubiquitin binding domains (UBDs) and Stable Isotope Labeling by Amino acids in Cell culture (SILAC) for selectively decoding ubiquitination-driven processes involved in the regulation of cellular signaling networks. We applied this approach to characterize the temporal dynamics of ubiquitination events accompanying epidermal growth factor receptor (EGFR) signal transduction. We used recombinant UBDs derived from endocytic adaptor proteins for specific enrichment of ubiquitinated complexes from the EGFR network and subsequent quantitative analyses by high accuracy mass spectrometry. We show that the strategy is suitable for profiling the dynamics of ubiquitination occurring on individual proteins as well as ubiquitination-dependent events in signaling pathways. In addition to a detailed seven time-point profile of EGFR ubiquitination over 30 minutes of ligand stimulation, our data determined prominent involvement of Lysine-63 ubiquitin branching in EGF signaling. Furthermore, we found two centrosomal proteins, PCM1 and Azi1, to form a multi-protein complex with the ubiquitin E3 ligases MIB1 and WWP2 downstream of the EGFR, thereby revealing possible ubiquitination cross-talk between EGF signaling and centrosomal-dependent rearrangements of the microtubules. This is a general strategy that can be utilized to study the dynamics of other cellular systems and post-translational modifications.