Defining the full complement of substrates for each ubiquitin ligase remains an important challenge. Improvements in mass spectrometry instrumentation and computation and in protein biochemistry methods have resulted in several new methods for ubiquitin ligase substrate identification. Here we used the parallel adapter capture (PAC) proteomics approach to study ␤TrCP2/FBXW11, a substrate adaptor for the SKP1-CUL1-F-box (SCF) E3 ubiquitin ligase complex. The processivity of the ubiquitylation reaction necessitates transient physical interactions between FBXW11 and its substrates, thus making biochemical purification of FBXW11-bound substrates difficult. Using the PAC-based approach, we inhibited the proteasome to "trap" ubiquitylated substrates on the SCF FBXW11 E3 complex. Comparative mass spectrometry analysis of immunopurified FBXW11 protein complexes before and after proteasome inhibition revealed 21 known and 23 putatively novel substrates. In focused studies, we found that SCF FBXW11 bound, polyubiquitylated, and destabilized RAPGEF2, a guanine nucleotide exchange factor that activates the small GTPase RAP1. High RAPGEF2 protein levels promoted cell-cell fusion and, consequently, multinucleation. Surprisingly, this occurred independently of the guanine nucleotide exchange factor (GEF) catalytic activity and of the presence of RAP1. Our data establish new functions for RAPGEF2 that may contribute to aneuploidy in cancer. More broadly, this report supports the continued use of substrate trapping proteomics to comprehensively define targets for E3 ubiquitin ligases. All proteomic data are available via ProteomeXchange with identifier PXD001062. U biquitylation is a posttranslational modification that controls protein-protein interactions, protein subcellular localization, protein-mediated catalysis, and, most famously, protein stability. The enzymology of protein ubiquitylation is now fairly well understood and has been well summarized in several recent reviews (1-3). The last and arguably most important step in the ubiquitylation reaction is carried out by an E3 ubiquitin ligase. These proteins select substrates for ubiquitylation, physically bridge and orient the substrate with ubiquitin, and in some cases, directly catalyze ubiquitin transfer. E3 ligases also provide the cell with a means to dynamically regulate substrate ubiquitylation; the interaction of a substrate protein with its cognate E3 ligase is often influenced by peripheral signals, such as phosphorylation (4). In total, more than 600 distinct E3 ubiquitin ligases have been identified within the human genome (5), the vast majority of which remain unstudied. Current estimates suggest that these ligases target more than 9,000 distinct human proteins for ubiquitylation, or roughly 40% of the protein-coding human genome (6, 7). For most of these proteins, the physiological importance of ubiquitin conjugation is not known. Likewise, paired relationships between specific E3 ligases and substrates are for the most part not known.Until recently, substra...

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Caribbean hair sheep are more resistant to gastrointestinal nematodes than conventional wool breeds, but mechanisms that confer resistance are not fully understood. This study compared immune effector cell populations and antibody concentrations in 12 hair and 12 wool lambs infected with the abomasal parasite Haemonchus contortus and sacrificed at 3 or 27 days post-infection (p.i.) and 14 uninfected animals of each breed. Faecal egg counts were over 2.5-fold higher (P = 0.12) and packed cell volumes approximately 8% lower (P < 0.10) in infected wool lambs. Abomasal lymph nodes were heavier in infected animals (P < 0.05) and infected hair sheep had larger lymph nodes than infected wool sheep (P < 0.05). Tissue eosinophil concentrations were likewise larger (P = 0.07) in hair compared with wool sheep at 3 days p.i. Circulating levels of IgE and IgA in uninfected lambs were higher in hair sheep (P < 0.05) and during infection, hair sheep had higher serum IgA than wool sheep at 3, 5, and 21 days p.i. (P < 0.05). Serum IgE in infected lambs did not differ between breeds, but concentrations of IgE in lymph nodes were higher (P < 0.01) at 27 days p.i. in infected hair sheep.