Identification of protein substrates of the Cullin-RING E3 ubiquitin ligase CRL4 through its substrate recognition factors DCAFs

ABSTRACT: Cullin-RING finger Ligases (CRLs) represent the largest family of E3 ubiquitin ligases and are responsible for ubiquitination of ~20% of cellular proteins degraded through the proteasome, catalyzing the transfer of E2-loaded ubiquitin to a substrate. Eight Cullins were described in vertebrates and among them, CUL4 associates with DDB1 acting as an adaptor to form the CUL4-DDB1 ubiquitin ligase complex, involved in protein ubiquitination and regulation of many cellular processes. The specificity of CUL4-DDB1 is mediated by substrate recognition adaptors named DDB1/CUL4 associated factors (DCAFs), which are characterized by the presence of a short structural motif of approximately 40 amino acids terminating in a tryptophan (W)-aspartic acid (D) dipeptide, the WD40 domain. Using different approaches (bioinformatics/structural analyses), independent studies suggested at least 60 different WD40 containing proteins that could act as adaptors for the DDB1/CUL4 complex. In this study, we aimed to validate the DCAFs based on their interaction with DDB1 and to define new partners and potential substrates of each DCAF using affinity purification followed by mass spectrometry. Using BioID and AP-MS approaches, we confirmed seven WDR40 protein that can be considered as DCAF with a high confidence level. Because identification of protein substrates of E3-ubiquitin ligases is not always guaranteed by identifying protein interactions, changes in protein stability and protein degradation was measured by pulse-SILAC to identify the protein substrates targeted for proteasomal degradation by each DCAFs. In conclusion, this work provides new insights into the roles of DCAFs as substrate adaptors for the DDB1-CUL4 complex, identifies the proteins targeting and the cellular processes that are involved.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell

DISEASE(S): Disease Free

SUBMITTER: Dominique Levesque  

LAB HEAD: François-Michel Boisvert

PROVIDER: PXD037482 | Pride | 2023-10-24

REPOSITORIES: Pride