BioID-based identification of SKP Cullin F-box (SCF)(beta-TrCP1/2) E3 ligase substrates

The identification of ubiquitin E3 ligase substrates has been challenging, due in part to low-affinity, transient interactions, the rapid degradation of targets and the inability to identify proteins from poorly soluble cellular compartments. SCF beta-TrCP1 and SCF beta-TrCP2 are well-studied ubiquitin E3 ligases that target substrates for proteasomal degradation, and play important roles in Wnt, Hippo, and NF kappa B signaling. Combining 26S proteasome inhibitor (MG132) treatment with proximity-dependent biotin labeling (BioID) and semiquantitative mass spectrometry, here we identify SCF beta-TrCP1/2 interacting partners. Based on their enrichment in the presence of MG132, our data identify over 50 new putative SCF beta-TrCP1/2 substrates. We validate 12 of these new substrates and reveal previously unsuspected roles for beta-TrCP in the maintenance of nuclear membrane integrity, processing (P)body turnover and translational control. Together, our data suggest that beta-TrCP is an important hub in the cellular stress response. The technique presented here represents a complementary approach to more standard IP-MS methods and should be broadly applicable for the identification of substrates for many ubiquitin E3 ligases