BioE3 identifies specific substrates of ubiquitin E3 ligases

Orhi Barroso-Gomila, Laura Merino-Cacho, Veronica Muratore, Coralia Perez, Vincenzo Taibi, Elena Maspero, Mikel Azkargorta, Ibon Iloro, Fredrik Trulsson, Alfred C. O. Vertegaal, Ugo Mayor, Felix Elortza, Simona Polo, Rosa Barrio () and James D. Sutherland ()
Additional contact information
Orhi Barroso-Gomila: Bizkaia Technology Park
Laura Merino-Cacho: Bizkaia Technology Park
Veronica Muratore: Bizkaia Technology Park
Coralia Perez: Bizkaia Technology Park
Vincenzo Taibi: The AIRC Institute of Molecular Oncology
Elena Maspero: The AIRC Institute of Molecular Oncology
Mikel Azkargorta: Bizkaia Technology Park
Ibon Iloro: Bizkaia Technology Park
Fredrik Trulsson: Leiden University Medical Center (LUMC)
Alfred C. O. Vertegaal: Leiden University Medical Center (LUMC)
Ugo Mayor: Basque Foundation for Science
Felix Elortza: Bizkaia Technology Park
Simona Polo: The AIRC Institute of Molecular Oncology
Rosa Barrio: Bizkaia Technology Park
James D. Sutherland: Bizkaia Technology Park

Nature Communications, 2023, vol. 14, issue 1, 1-19

Abstract: Abstract 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.

Date: 2023
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DOI: 10.1038/s41467-023-43326-8

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