BioE3 identifies specific substrates of ubiquitin E3 ligases

Barroso-Gomila, O.; Merino-Cacho, L.; Muratore, V.; Perez, C.; Taibi, V.; Maspero, E.; ... ; Sutherland, J.D. (2023)

Article / Letter to editor

Hundreds of E3 ligases play a critical role in recognizing specific substrates for modification by ubiquitin (Ub). Separating genuine targets of E3s from E3-interactors remains a challenge. We present BioE3, a powerful approach for matching substrates to Ub E3 ligases of interest. Using BirA-E3 ligase fusions and bioUb, site-specific biotinylation of Ub-modified substrates of particular E3s facilitates proteomic identification. We show that BioE3 identifies both known and new targets of two RING-type E3 ligases: RNF4 (DNA damage response, PML bodies), and MIB1 (endocytosis, autophagy, centrosome dynamics). Versatile BioE3 identifies targets of an organelle-specific E3 (MARCH5) and a relatively uncharacterized E3 (RNF214). Furthermore, BioE3 works with NEDD4, a HECT-type E3, identifying new targets linked to vesicular trafficking. BioE3 detects altered specificity in response to chemicals, opening avenues for targeted protein degradation, and may be applicable for other Ub-likes (UbLs, e.g., SUMO) and E3 types. BioE3 applications shed light on cellular regulation by the complex UbL network.

• All authors: Barroso-Gomila, O.; Merino-Cacho, L.; Muratore, V.; Perez, C.; Taibi, V.; Maspero, E.; Azkargorta, M.; Iloro, I.; Trulsson, F.; Vertegaal, A.C.O.; Mayor, U.; Elortza, F.; Polo, S.; Barrio, R.; Sutherland, J.D.
• Date: 2023-11-23
• Journal: Nature Communications
• Volume: 14
• Issue: 1
• DOI: doi:10.1038/s41467-023-43326-8
• Link: https://www.nature.com/articles/s41467-023-43326-8