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Comprehensive database of human E3 ubiquitin ligases: application to aquaporin-2 regulation - PubMed

  • ️Fri Jan 01 2016

Comprehensive database of human E3 ubiquitin ligases: application to aquaporin-2 regulation

Barbara Medvar et al. Physiol Genomics. 2016.

Abstract

Aquaporin-2 (AQP2) is regulated in part via vasopressin-mediated changes in protein half-life that are in turn dependent on AQP2 ubiquitination. Here we addressed the question, "What E3 ubiquitin ligase is most likely to be responsible for AQP2 ubiquitination?" using large-scale data integration based on Bayes' rule. The first step was to bioinformatically identify all E3 ligase genes coded by the human genome. The 377 E3 ubiquitin ligases identified in the human genome, consisting predominant of HECT, RING, and U-box proteins, have been used to create a publically accessible and downloadable online database (https://hpcwebapps.cit.nih.gov/ESBL/Database/E3-ligases/). We also curated a second database of E3 ligase accessory proteins that included BTB domain proteins, cullins, SOCS-box proteins, and F-box proteins. Using Bayes' theorem to integrate information from multiple large-scale proteomic and transcriptomic datasets, we ranked these 377 E3 ligases with respect to their probability of interaction with AQP2. Application of Bayes' rule identified the E3 ligases most likely to interact with AQP2 as (in order of probability): NEDD4 and NEDD4L (tied for first), AMFR, STUB1, ITCH, ZFPL1. Significantly, the two E3 ligases tied for top rank have also been studied extensively in the reductionist literature as regulatory proteins in renal tubule epithelia. The concordance of conclusions from reductionist and systems-level data provides strong motivation for further studies of the roles of NEDD4 and NEDD4L in the regulation of AQP2 protein turnover.

Keywords: E3 ubiquitin ligases; aquaporin-2; collecting duct; kidney.

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Figures

Fig. 1.
Fig. 1.

A publicly available webpage was created to provide users with a comprehensive list of E3 ligases in the human genome. Access to this webpage can be found at

https://helixweb.nih.gov/ESBL/Database/E3-ligases/

. All sources that have been used can be found in the first paragraph. There is a link to a separate database of accessory proteins related to E3 ubiquitin ligases, as well as a link to download the data to an Excel file. The data on this webpage can be sorted alphabetically by gene symbol, protein name, class, RefSeq number, or UniProt number.

Fig. 2.
Fig. 2.

E3 ubiquitin ligase transcripts most highly expressed in collecting duct segments and their distribution along renal tubule. Aquaporin-2 (AQP2) is expressed in the connecting tubule (CNT), the cortical collecting duct (CCD), outer medullary collecting duct (OMCD), and the inner medullary collecting duct (IMCD). Only E3 ubiquitin ligases that have a transcript level of 1.0 reads per kilobase of transcript per million mapped reads (RPKM) in all 4 of these segments are shown. RPKM values are from Lee et al. (15).

Fig. 3.
Fig. 3.

The 31 most abundant E3 ubiquitin ligase transcripts in mouse mpkCCD cells. The bars are color-coded to indicate the class of each E3 ligase based on the presence of a U-box, RING, HECT, or zf-C2H2 domain. The transcript values are from the mouse mpkCCD transcriptome identified using Affymetrix expression microarrays (31).

Fig. 4.
Fig. 4.

The 20 most abundant E3 ubiquitin ligase proteins in mouse mpkCCD cells. The ligases are color coded to indicate the class of each E3 ligase based on the presence of a U-box, RING, HECT, or UBR domain. The abundance levels for each E3 ligase was found using the relative protein abundances in mouse mpkCCD cells (30).

Fig. 5.
Fig. 5.

Comparisons of the abundance of AQP2 and E3 ubiquitin ligases in subcellular fractions from mouse mpkCCD cells. A: coclustering of AQP2 and all E3 ubiquitin ligases that were found in the indicated differential centrifugation fractions from mpkCCD cells. AQP2 is the bottom-most protein on the heat-map. B: dot products between the distribution vector for AQP2 and the distribution vector for each E3 ligase found in the mpkCCD subcellular fractions. Only the top 30 are shown.

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