Abstract
The ubiquitin-proteasome system targets misfolded proteins for degradation. Since the accumulation of such proteins is potentially harmful for the cell, their prompt removal is important. E3 ubiquitin-protein ligases mediate substrate ubiquitination by bringing together the substrate with an E2 ubiquitin-conjugating enzyme, which transfers ubiquitin to the substrate. For misfolded proteins, substrate recognition is generally delegated to molecular chaperones that subsequently interact with specific E3 ligases. An important exception is San1, a yeast E3 ligase. San1 harbors extensive regions of intrinsic disorder, which provide both conformational flexibility and sites for direct recognition of misfolded targets of vastly different conformations. So far, no mammalian ortholog of San1 is known, nor is it clear whether other E3 ligases utilize disordered regions for substrate recognition. Here, we conduct a bioinformatics analysis to examine >600 human and S. cerevisiae E3 ligases to identify enzymes that are similar to San1 in terms of function and/or mechanism of substrate recognition. An initial sequence-based database search was found to detect candidates primarily based on the homology of their ordered regions, and did not capture the unique disorder patterns that encode the functional mechanism of San1. However, by searching specifically for key features of the San1 sequence, such as long regions of intrinsic disorder embedded with short stretches predicted to be suitable for substrate interaction, we identified several E3 ligases with these characteristics. Our initial analysis revealed that another remarkable trait of San1 is shared with several candidate E3 ligases: long stretches of complete lysine suppression, which in San1 limits auto-ubiquitination. We encode these characteristic features into a San1 similarity-score, and present a set of proteins that are plausible candidates as San1 counterparts in humans. In conclusion, our work indicates that San1 is not a unique case, and that several other yeast and human E3 ligases have sequence properties that may allow them to recognize substrates by a similar mechanism as San1.
Highlights
A coordinated and efficient regulation of protein levels is of crucial importance to all cells, and ubiquitin-mediated proteasomal degradation plays a central role in proteinHow to cite this article Boomsma et al (2016), Bioinformatics analysis identifies several intrinsically disordered human E3 ubiquitinprotein ligases
In a first attempt to identify such a protein, we focused on the unusual Really Interesting New Gene (RING) domain of San1
This procedure detected a number of potential matches, but the hits were predominantly defined by similarities in the ordered regions of San1—primarily the RING domain, and the detected homologues did not generally display the disorder and binding patterns characteristic of San1 (Fig. S1)
Summary
A coordinated and efficient regulation of protein levels is of crucial importance to all cells, and ubiquitin-mediated proteasomal degradation plays a central role in proteinHow to cite this article Boomsma et al (2016), Bioinformatics analysis identifies several intrinsically disordered human E3 ubiquitinprotein ligases. Cellular proteins are targeted for proteasomal degradation by the attachment of multiple moieties of the small regulatory protein ubiquitin, most often to lysine residues, but in some cases to serines, threonines or cysteines (Wang, Herr & Hansen, 2012). This process occurs through the sequential action of a ubiquitin-activating enzyme (a so-called E1 enzyme), a ubiquitin-conjugating enzyme (E2) and a ubiquitin-protein ligase (E3). RING E3 ligases bridge ubiquitin-charged E2s with substrates, which become ubiquitinated Multiple rounds of this process ensure substrate polyubiquitination, a requirement for degradation of most proteasomal substrates (for a recent review of the ubiquitin-proteasome system see Kleiger & Mayor, 2014)
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