UbiBrowser 2.0: a comprehensive resource for proteome-wide known and predicted ubiquitin ligase/deubiquitinase–substrate interactions in eukaryotic species
Open accessAbstract
As an important post-translational modification, ubiquitination mediates ∼80% of protein degradation in eukaryotes. The degree of protein ubiquitination is tightly determined by the delicate balance between specific ubiquitin ligase (E3)-mediated ubiquitination and deubiquitinase-mediated deubiquitination. In 2017, we developed UbiBrowser 1.0, which is an integrated database for predicted human proteome-wide E3–substrate interactions. Here, to meet the urgent requirement of proteome-wide E3/deubiquitinase–substrate interactions (ESIs/DSIs) in multiple organisms, we updated UbiBrowser to version 2.0 (http://ubibrowser.ncpsb.org.cn). Using an improved protocol, we collected 4068/967 known ESIs/DSIs by manual curation, and we predicted about 2.2 million highly confident ESIs/DSIs in 39 organisms, with >210-fold increase in total data volume. In addition, we made several new features in the updated version: (i) it allows exploring proteins’ upstream E3 ligases and deubiquitinases simultaneously; (ii) it has significantly increased species coverage; (iii) it presents a uniform confidence scoring system to rank predicted ESIs/DSIs. To facilitate the usage of UbiBrowser 2.0, we also redesigned the web interface for exploring these known and predicted ESIs/DSIs, and added functions of ‘Browse’, ‘Download’ and ‘Application Programming Interface’. We believe that UbiBrowser 2.0, as a discovery tool, will contribute to the study of protein ubiquitination and the development of drug targets for complex diseases.
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FBXW7 is a potential E3 ubiquitin ligase related to PU.1.
“To investigate whether this combination affected PU.1 degradation, we searched for the potential E3 ubiquitin ligases related to PU.1 using UbiBrowser and found FBXW728.”
From Targeting Msx2 as a brake in the fusion fate of osteoclasts and an anabolic therapy in pre-clinical models of osteoporosis (2025) · cites this paper as [28]
The Enhanced User Interface case study shows that UbiBrowser 2.0 can be searched for potential E3 ligases of a protein, supporting the cited method. Our copy does not identify FBXW7 as a potential E3 ligase for PU.1; searches for FBXW7, PU.1, and SPI1 did not find that pairing. The specific finding is presented as the citing authors’ own search result, not a finding reported in this paper. (LLM, conf=0.82)
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- Authors
- Wang, X., Li, Y., He, M., Kong, X., Jiang, P., Liu, X., Diao, L., Zhang, X., Li, H., Ling, X., Xia, S., Liu, Z., Liu, Y., Cui, C.-P., Wang, Y., Tang, L., Zhang, L., He, F., & Li, D.
- Affiliations
- Beijing Proteome Research Center (CN)
- Hebei University (CN)
- Anhui Medical University (CN)
- Beijing Geneworks Technology Co.,Ltd., Beijing 100101, China
- Corresponding author
- Zhang, Lingqiang
- He, Fuchu
- Li, Dong
- ORCID
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2021-10-20
- Volume
- 50
- Issue
- D1
- Pages
- D719-D728
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC8728189
- OpenAlex
- W3205926919
- Cited by
- 260
- References
- 38
- Citations by year
- 2026: 86 · 2025: 67 · 2024: 66 · 2023: 28 · 2022: 11 · 2021: 2
- FWCI
- 9.17
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Funders
- National Natural Science Foundation of China (32088101, 31871341)
- National Key Research and Development Program of China (2020YFE0202200)
- Beijing Talents Foundation
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Degradation and Inhibitors
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- ubiquitin ligase, deubiquitinase, deubiquitination, ubiquitination, post-translational modification, protein degradation, interaction prediction, database curation, confidence scores, eukaryotic proteomes, online databases
- MeSH terms
- Deubiquitinating Enzymes, Eukaryotic Cells, Software, Substrate Specificity, Proteome, Databases, Genetic, Ubiquitin-Protein Ligases
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