A systems-wide screen identifies substrates of the SCF beta TrCP ubiquitin ligase

Cellular proteins are degraded by the ubiquitin-proteasome system ( UPS) in a precise and timely fashion. Such precision is conferred by the high substrate specificity of ubiquitin ligases. Identification of substrates of ubiquitin ligases is crucial not only to unravel the molecular mechanisms by which the UPS controls protein degradation but also for drug discovery purposes because many established UPS substrates are implicated in disease. We developed a combined bioinformatics and affinity purification-mass spectrometry (AP-MS) workflow for the system- wide identification of substrates of SCF beta TrCP, a member of the SCF family of ubiquitin ligases. These ubiquitin ligases are characterized by a multi-subunit architecture typically consisting of the invariable subunits Rbx1, Cul1, and Skp1, and one of 69 F-box proteins. The F-box protein of this member of the family is beta TrCP. SCF beta TrCP binds, through the WD40 repeats of beta TrCP, to the DpSGXX( X) pS diphosphorylated motif in its substrates. We recovered 27 previously reported SCF beta TrCP substrates, of which 22 were verified by two independent statistical protocols, thereby confirming the reliability of this approach. In addition to known substrates, we identified 221 proteins that contained the DpSGXX( X) pS motif and also interacted specifically with the WD40 repeats of beta TrCP. Thus, with SCF beta TrCP, as the example, we showed that integration of structural information, AP-MS, and degron motif mining constitutes an effective method to screen for substrates of ubiquitin ligases