Tripartite degrons confer diversity and specificity on regulated protein degradation in the ubiquitin-proteasome system

Abstract

Specific signals (degrons) regulate protein turnover mediated by the ubiquitin-proteasome system. Here we systematically analyse known degrons and propose a tripartite model comprising the following: (1) a primary degron (peptide motif) that specifies substrate recognition by cognate E3 ubiquitin ligases, (2) secondary site(s) comprising a single or multiple neighbouring ubiquitinated lysine(s) and (3) a structurally disordered segment that initiates substrate unfolding at the 26S proteasome. Primary degron sequences are conserved among orthologues and occur in structurally disordered regions that undergo E3-induced folding-on-binding. Posttranslational modifications can switch primary degrons into E3-binding-competent states, thereby integrating degradation with signalling pathways. Degradation-linked lysines tend to be located within disordered segments that also initiate substrate degradation by effective proteasomal engagement. Many characterized mutations and alternative isoforms with abrogated degron components are implicated in disease. These effects result from increased protein stability and interactome rewiring. The distributed nature of degrons ensures regulation, specificity and combinatorial control of degradation.

Numerous proteins with unique characteristics are degraded by the 26S proteasome following monoubiquitination

“…These differences also have to manifest themselves in the local disorder of the protein chain around the ubiquitinated Lys residues. In general, the sites of posttranslational modifications (PTMs) in proteins tend to exhibit local disorder, as studied in detail for phosphorylation (32) and also ubiquitination (28). In our entire dataset, the lysines that are the sites of ubiquitination tend to be locally disordered, but even more importantly, they show a highly characteristic difference between the two species.…”

“…S3), and if we assume that a single ubiquitin moiety is a weaker signal for degradation than polyubiquitin. As suggested, local structural disorder is involved in various steps of the UPS cascade, from recognition motifs of E3 ligases through local disorder of ubiquitination sites to an LDR initiation site of substrate unfolding (28)(29)(30).…”

“…Intrinsically disordered protein regions lack a welldefined tertiary structure, yet they fulfill important functional roles linked with their highly flexible and adaptable structure (25)(26)(27). Structural disorder correlates with all three elements of degradation signals: location of the ubiquitin ligase recognition motif on substrates, the Lys residue(s) to which ubiquitin is attached, and a nearby long disordered region (LDR) (a region of at least 30 consecutive disordered residues) that initiates the unfolding of the substrate engaged with the proteasome (15,(28)(29)(30). Structural disorder may also be required for ubiquitin conjugation itself, in two different ways.…”

“…The distinction between the signaling strength and functionality of monoubiquitin and polyubiquitin chains in yeast and human cells is also reflected in characteristic differences in the proximity of LDRs to Ubsites, which might be the sites of initiation of proteasomal degradation (28)(29)(30). The need of such assistance for monoubiquitination sites in yeast is apparent from the larger proportion of such sites that are close to an LDR (Fig.…”

Recognition of substrate degrons by E3 ubiquitin ligases and modulation by small-molecule mimicry strategies

“…3 The large number of E3 ligases (> 600) encoded in the human genome [70] and the diversity and specificity of degron recognition motifs (reviewed recently in ref. [71]) provide numerous opportunities for PROTAC drug development. To date, only a handful of E3 ligases (including CRBN, VHL, MDM2 and IAP, Table 1) have been effectively hijacked by all small-molecules PROTACs using the respective E3 ligands.…”