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BioE3 identifies specific substrates of ubiquitin E3 ligases

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 liga...

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Autores principales: Barroso-Gomila, Orhi, Merino-Cacho, Laura, Muratore, Veronica, Perez, Coralia, Taibi, Vincenzo, Maspero, Elena, Azkargorta, Mikel, Iloro, Ibon, Trulsson, Fredrik, Vertegaal, Alfred C. O., Mayor, Ugo, Elortza, Felix, Polo, Simona, Barrio, Rosa, Sutherland, James D.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10667490/
https://www.ncbi.nlm.nih.gov/pubmed/37996419
http://dx.doi.org/10.1038/s41467-023-43326-8
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author Barroso-Gomila, Orhi
Merino-Cacho, Laura
Muratore, Veronica
Perez, Coralia
Taibi, Vincenzo
Maspero, Elena
Azkargorta, Mikel
Iloro, Ibon
Trulsson, Fredrik
Vertegaal, Alfred C. O.
Mayor, Ugo
Elortza, Felix
Polo, Simona
Barrio, Rosa
Sutherland, James D.
author_facet Barroso-Gomila, Orhi
Merino-Cacho, Laura
Muratore, Veronica
Perez, Coralia
Taibi, Vincenzo
Maspero, Elena
Azkargorta, Mikel
Iloro, Ibon
Trulsson, Fredrik
Vertegaal, Alfred C. O.
Mayor, Ugo
Elortza, Felix
Polo, Simona
Barrio, Rosa
Sutherland, James D.
author_sort Barroso-Gomila, Orhi
collection PubMed
description 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.
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spelling pubmed-106674902023-11-23 BioE3 identifies specific substrates of ubiquitin E3 ligases Barroso-Gomila, Orhi Merino-Cacho, Laura Muratore, Veronica Perez, Coralia Taibi, Vincenzo Maspero, Elena Azkargorta, Mikel Iloro, Ibon Trulsson, Fredrik Vertegaal, Alfred C. O. Mayor, Ugo Elortza, Felix Polo, Simona Barrio, Rosa Sutherland, James D. Nat Commun Article 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. Nature Publishing Group UK 2023-11-23 /pmc/articles/PMC10667490/ /pubmed/37996419 http://dx.doi.org/10.1038/s41467-023-43326-8 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Barroso-Gomila, Orhi
Merino-Cacho, Laura
Muratore, Veronica
Perez, Coralia
Taibi, Vincenzo
Maspero, Elena
Azkargorta, Mikel
Iloro, Ibon
Trulsson, Fredrik
Vertegaal, Alfred C. O.
Mayor, Ugo
Elortza, Felix
Polo, Simona
Barrio, Rosa
Sutherland, James D.
BioE3 identifies specific substrates of ubiquitin E3 ligases
title BioE3 identifies specific substrates of ubiquitin E3 ligases
title_full BioE3 identifies specific substrates of ubiquitin E3 ligases
title_fullStr BioE3 identifies specific substrates of ubiquitin E3 ligases
title_full_unstemmed BioE3 identifies specific substrates of ubiquitin E3 ligases
title_short BioE3 identifies specific substrates of ubiquitin E3 ligases
title_sort bioe3 identifies specific substrates of ubiquitin e3 ligases
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10667490/
https://www.ncbi.nlm.nih.gov/pubmed/37996419
http://dx.doi.org/10.1038/s41467-023-43326-8
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