UbiBrowser 2.0: a comprehensive resource for proteome-wide known and predicted ubiquitin ligase/deubiquitinase-substrate interactions in eukaryotic species

Abstract

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.

Figure 1.

Overview of UbiBrowser 2.0, a comprehensive resource for proteome-wide known and predicted ESIs/DSIs in eukaryotic species. First, known ESIs/DSIs were manually curated from literature. Then, proteome-wide ESIs/DSIs in human were predicted by our published protocol for UbiBrowser 1.0 (11). The ‘interolog’-based approach was employed to transfer ESIs/DSIs from human to 38 non-human species (24). ESI: E3–substrate interaction; DSI: deubiquitinase–substrate interaction; API: application programming interface; ‘interolog’: a conserved interaction between a pair of proteins which are interacting orthologs in another species.

Figure 2.

Data statistics of UbiBrowser 2.0. (A) Known ESIs/DSIs comparison between UbiBrowser 2.0 and other databases. (B) Number of known ESIs/DSIs across multiple organisms. (C) Number of high confidence predicted ESIs/DSIs in 39 organisms. (D) Coverage of E3s/DUBs in high confidence predicted ESIs/DSIs against all genome-encoded E3s/DUBs across 39 organisms. (E) Family distribution (18) of E3s/DUBs in high confidence predicted ESIs/DSIs across 39 organisms. From outside to inside, circles corresponding to 39 organisms in alphabetical order. (F) Gene Ontology biological process (19) analysis for high confidence substrates predicted by E3s/DUBs across D. melanogaster, D. rerio, G. gallus, P. troglodytes, S. scrofa, S. cerevisiae, M. musculus and H. sapiens (from outside to inside).

Figure 3.

Derivation of human proteome-wide predicted deubiquitinase–substrate interaction. (A) Protocol of naïve Bayesian classifier to predict human deubiquitinase–substrate interaction (DSI) prediction (11). Based on the golden standard dataset (GSD) constructed by manual curation, four supporting biological evidences were identified and their reliability was assessed by likelihood ratio. For each potential DSI, the likelihood ratio from individual evidence will be integrated into a composite likelihood ratio (LR_comp) and transformed into a final confidence score. (B, C) Performance of the model evaluated by five-fold cross-validation and independent test set validation. Each point on ROC curves of assessment models corresponds to sensitivity and specificity against a particular likelihood ratio cutoff. TPR (true positive rate, sensitivity) and FPR (false positive rate, 1 – specificity) were computed during two assessment procedures: the five-fold cross-validation (B) and independent test set validation (C).

Figure 4.

Transferring of ubiquitin ligase/deubiquitinase–substrate interactions from human to non-human species. (A) Homologous mapping and confidence scoring scheme (please refer to text for details). (B) Number of overlapping interactions between the predicted and manually curated interactions in non-human species (observed overlapping links versus random expectation). The p value was obtained by the binomial test (one-sided). ESI: E3–substrate interaction; DSI: deubiquitinase–substrate interaction.

Figure 5.

A screenshot of the redesigned UbiBrowser 2.0 interface. (A) Three ‘Search’ pages with the added options for ‘process’ and ‘species’. Users can specify the prediction process as ‘Ubiquitination’ or ‘Deubiquitination’, and designate whether the query protein is ‘Ubiquitin ligase (E3)’, ‘Deubiquitinase (DUB)’ or ‘Substrate’. The current version of UbiBrowser supports queries in 39 organisms. (B) ‘Browse’ page for known (left panel) and predicted (right panel) E3/DUB-substrate interactions across 39 organisms. (C) Network view for the retrieved known and predicted ESIs/DSIs. Red node: known interactor; blue node: predicted interactor. (D) Network view for the retrieved predicted ESIs/DSIs (confidence mode). Node size and edge width are positively proportional to the confidence score. The inset is the evidence mode, where various coloured edges between the central node and the surrounding nodes represent different types of supporting evidence. (E) Supporting literature information page for the known ESIs/DSIs, with the entries of E3/DUB and substrate in abstract texts are highlighted in colour. (F) Supporting evidence page for the predicted ESIs/DSIs. Clicking on each red node for known interactor in the network view (C) will pop up the corresponding supporting literature information (E); meanwhile, the blue nodes for predicted interactors in the network view (C and D) can lead to the supporting evidences page (F). ESI: E3–substrate interaction; DSI: deubiquitinase–substrate interaction.

Figure 6.

Use cases for UbiBrowser 2.0: exploration of the E3 ligase and deubiquitinase determining the bidirectional regulation of disease signaling cascades proteins. Confidence scores on graph were assigned by UbiBrowser 2.0. (A) WWP1-EGFR-STAMBP. MAPK signaling was predicted to be regulated by the axis of WWP1-EGFR-STAMBP, which was validated by (30) and (31). (B) NEDD4-TBK1-CYLD. NEDD4 and CYLD were validated to catalyze ploy-ubiquitination of TBK1 and negatively regulate type I IFN signaling (32,33), while CYLD was observed to remove Lys 63-linked polyubiquitin from TBK1 (33). (C) HECW1-SMAD4-USP4. For SMAD4, the predicted E3 HECW1 was validated to promote the metastasis of non-small cell lung cancer cells through mediating the ubiquitination of SMAD4 (34), while the predicted DUB USP4 to inhibit SMAD4 monoubiquitination and to promote activin and BMP signaling (35). Ub: ubiquitin.