Systematic Identification of Candidate Substrates of the UCH Family of Deubiquitinases
4 affiliations
- 1Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (EHU), 48940 Leioa, Spain
- 2Department of Communications Engineering, University of the Basque Country (EHU), 48013 Bilbao, Spain
- 3Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (EHU), 01006 Vitoria-Gasteiz, Spain
- 4Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
Abstract
Deubiquitinases (DUBs) of the ubiquitin C-terminal hydrolase (UCH) family play critical roles in regulating ubiquitin-dependent signaling, yet their substrate specificity and functional organization remain incompletely defined. Here, we systematically characterized the ubiquitination landscape associated with UCH family members (UCHL1, UCHL3, UCHL5, and BAP1) using a quantitative proteomics workflow combining siRNA-mediated DUB silencing, bioUb-based enrichment of ubiquitinated proteins, and label-free mass spectrometry. Proteins exhibiting increased ubiquitination following DUB depletion were identified as candidate substrates. Our analysis revealed that UCH family members regulate largely distinct subsets of ubiquitinated proteins, with limited overlap in their candidate profiles despite sharing conserved catalytic domains. In parallel, site-resolved ubiquitinomics identified 851 ubiquitination sites, including 106 not previously reported, expanding the current landscape of experimentally validated ubiquitin-modified lysines. Functionally, substrate networks link individual UCH enzymes to distinct yet partially overlapping cellular processes, including hypoxia signaling, RNA metabolism, vesicle trafficking, apoptosis, and chromatin regulation. Notably, known substrates such as HIF-1α validated the approach, while recurrent detection of key regulators, including MCL1, pointed to convergence at the level of apoptosis control. Together, these findings provide a resource for exploring the distinct and potentially overlapping roles of UCH deubiquitinases within cellular ubiquitin-regulatory networks.
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BibTeX
@article{ramirez2026systematic,
title = {{Systematic Identification of Candidate Substrates of the UCH Family of Deubiquitinases}},
author = {Juanma Ramirez and Gorka Prieto and Erik P. Barrio and Ainhoa Atxa-Espiga and Natalia Presa and Olatz Arteaga-Cabeza and Ugo Mayor and Nerea Osinalde},
journal = {International Journal of Molecular Sciences},
year = {2026},
month = oct,
doi = {10.3390/ijms27209217},
url = {https://www.mdpi.com/1422-0067/27/20/9217},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Systematic Identification of Candidate Substrates of the UCH Family of Deubiquitinases
AU - Juanma Ramirez
AU - Gorka Prieto
AU - Erik P. Barrio
AU - Ainhoa Atxa-Espiga
AU - Natalia Presa
AU - Olatz Arteaga-Cabeza
AU - Ugo Mayor
AU - Nerea Osinalde
PY - 2026
DA - 2026/10/01
JO - International Journal of Molecular Sciences
DO - 10.3390/ijms27209217
UR - https://www.mdpi.com/1422-0067/27/20/9217
AB - Deubiquitinases (DUBs) of the ubiquitin C-terminal hydrolase (UCH) family play critical roles in regulating ubiquitin-dependent signaling, yet their substrate specificity and functional organization remain incompletely defined. Here, we systematically characterized the ubiquitination landscape associated with UCH family members (UCHL1, UCHL3, UCHL5, and BAP1) using a quantitative proteomics workflow combining siRNA-mediated DUB silencing, bioUb-based enrichment of ubiquitinated proteins, and label-free mass spectrometry. Proteins exhibiting increased ubiquitination following DUB depletion were identified as candidate substrates. Our analysis revealed that UCH family members regulate largely distinct subsets of ubiquitinated proteins, with limited overlap in their candidate profiles despite sharing conserved catalytic domains. In parallel, site-resolved ubiquitinomics identified 851 ubiquitination sites, including 106 not previously reported, expanding the current landscape of experimentally validated ubiquitin-modified lysines. Functionally, substrate networks link individual UCH enzymes to distinct yet partially overlapping cellular processes, including hypoxia signaling, RNA metabolism, vesicle trafficking, apoptosis, and chromatin regulation. Notably, known substrates such as HIF-1α validated the approach, while recurrent detection of key regulators, including MCL1, pointed to convergence at the level of apoptosis control. Together, these findings provide a resource for exploring the distinct and potentially overlapping roles of UCH deubiquitinases within cellular ubiquitin-regulatory networks.
SN - 1422-0067
ER -