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Article

A Proteomic Approach for Systematic Mapping of Substrates of Human Deubiquitinating Enzymes

1
Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
2
Department of Communications Engineering, University of the Basque Country (UPV/EHU), 48013 Bilbao, Spain
3
Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
4
Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
5
Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
6
Proteomics Unit, Spanish National Cancer Research Center (CNIO), 28029 Madrid, Spain
7
Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
8
Proteomics Core Facility-SGIKER, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
9
Functional Proteomics Facility, Centro Nacional de Biotecnología (CNB-CSIC), ProteoRed-ISCIII, 28029 Madrid, Spain
10
Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
*
Author to whom correspondence should be addressed.
Current address: Department of Pediatrics, Yale School of Medicine, New Haven, CT 06510, USA.
Current address: Department of Oncology, Georgetown University, Washington, DC 20007, USA.
Academic Editor: Kwang-Hyun Baek
Int. J. Mol. Sci. 2021, 22(9), 4851; https://doi.org/10.3390/ijms22094851
Received: 13 April 2021 / Revised: 28 April 2021 / Accepted: 29 April 2021 / Published: 3 May 2021
The human genome contains nearly 100 deubiquitinating enzymes (DUBs) responsible for removing ubiquitin moieties from a large variety of substrates. Which DUBs are responsible for targeting which substrates remain mostly unknown. Here we implement the bioUb approach to identify DUB substrates in a systematic manner, combining gene silencing and proteomics analyses. Silencing of individual DUB enzymes is used to reduce their ubiquitin deconjugating activity, leading to an increase of the ubiquitination of their substrates, which can then be isolated and identified. We report here quantitative proteomic data of the putative substrates of 5 human DUBs. Furthermore, we have built a novel interactive database of DUB substrates to provide easy access to our data and collect DUB proteome data from other groups as a reference resource in the DUB substrates research field. View Full-Text
Keywords: ubiquitination; deubiquitinating enzyme; quantitative proteomics; DUBase ubiquitination; deubiquitinating enzyme; quantitative proteomics; DUBase
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MDPI and ACS Style

Ramirez, J.; Prieto, G.; Olazabal-Herrero, A.; Borràs, E.; Fernandez-Vigo, E.; Alduntzin, U.; Osinalde, N.; Beaskoetxea, J.; Lectez, B.; Aloria, K.; Rodriguez, J.A.; Paradela, A.; Sabidó, E.; Muñoz, J.; Corrales, F.; Arizmendi, J.M.; Mayor, U. A Proteomic Approach for Systematic Mapping of Substrates of Human Deubiquitinating Enzymes. Int. J. Mol. Sci. 2021, 22, 4851. https://doi.org/10.3390/ijms22094851

AMA Style

Ramirez J, Prieto G, Olazabal-Herrero A, Borràs E, Fernandez-Vigo E, Alduntzin U, Osinalde N, Beaskoetxea J, Lectez B, Aloria K, Rodriguez JA, Paradela A, Sabidó E, Muñoz J, Corrales F, Arizmendi JM, Mayor U. A Proteomic Approach for Systematic Mapping of Substrates of Human Deubiquitinating Enzymes. International Journal of Molecular Sciences. 2021; 22(9):4851. https://doi.org/10.3390/ijms22094851

Chicago/Turabian Style

Ramirez, Juanma; Prieto, Gorka; Olazabal-Herrero, Anne; Borràs, Eva; Fernandez-Vigo, Elvira; Alduntzin, Unai; Osinalde, Nerea; Beaskoetxea, Javier; Lectez, Benoit; Aloria, Kerman; Rodriguez, Jose A.; Paradela, Alberto; Sabidó, Eduard; Muñoz, Javier; Corrales, Fernando; Arizmendi, Jesus M.; Mayor, Ugo. 2021. "A Proteomic Approach for Systematic Mapping of Substrates of Human Deubiquitinating Enzymes" Int. J. Mol. Sci. 22, no. 9: 4851. https://doi.org/10.3390/ijms22094851

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