Ubiquitin‐like domains can target to the proteasome but proteolysis requires a disordered region

Abstract

Ubiquitin and some of its homologues target proteins to the proteasome for degradation. Other ubiquitin-like domains are involved in cellular processes unrelated to the proteasome, and proteins containing these domains remain stable in the cell. We find that the 10 yeast ubiquitin-like domains tested bind to the proteasome, and that all 11 identified domains can target proteins for degradation. Their apparent proteasome affinities are not directly related to their stabilities or functions. That is, ubiquitinlike domains in proteins not part of the ubiquitin proteasome system may bind the proteasome more tightly than domains in proteins that are bona fide components. We propose that proteins with ubiquitin-like domains have properties other than proteasome binding that confer stability. We show that one of these properties is the absence of accessible disordered regions that allow the proteasome to initiate degradation. In support of this model, we find that Mdy2 is degraded in yeast when a disordered region in the protein becomes exposed and that the attachment of a disordered region to Ubp6 leads to its degradation.

Mouse Mammary Tumor Virus Signal Peptide Uses a Novel p97-Dependent and Derlin-Independent Retrotranslocation Mechanism To Escape Proteasomal Degradation

“…To test whether the proteasome is able to recognize and degrade the lysine-rich MMTV-encoded SP when targeted for destruction, we engineered a UbL from Rad23 at the N terminus of Escherichia coli dihydrofolate reductase (DHFR) to allow proteasome binding as previously described (49, 50, 52) (UbL-DHFR, Fig. 5A).…”

“…Prototypical proteasome substrates have been studied in both yeast and mammalian cells (48–52). These experiments indicate that polyubiquitin chains are recognized by the proteasome, but that an unstructured region is needed to allow the proteasome to engage its substrate and initiate degradation (48, 49).…”

Meddling with Fate: The Proteasomal Deubiquitinating Enzymes

“…However, the Ubp6 UBL binding site in Rpn1 (T2) is distinct from the site that binds ubiquitin and the shuttling ubiquitin receptors (T1) [17]. The two sites are adjacent but there is little or no competition between Ubp6 and the shuttling ubiquitin receptors [17,43,44]. …”

Toward mechanistic models for genotype–phenotype correlations in phenylketonuria using protein stability calculations

“…Exactly how the PQC system is able to discern misfolded from native proteins remains incompletely understood (Geffen et al, 2016), but is likely to involve recognition of exposed hydrophobic regions in misfolded proteins (Arndt, Rogon, & Hohfeld, 2007;Hartl, Bracher, & Hayer-Hartl, 2011;Kriegenburg et al, 2012). In addition, for efficient degradation it is often required that the substrate proteins display small flexible or disordered regions (Guharoy, Bhowmick, & Tompa, 2016;van der Lee et al, 2014;Yu, Kago, Yellman, & Matouschek, 2016). Recently, the degree of structural destabilization was shown to correlate with the rate of degradation for the cancer-associated mismatch-repair protein MSH2 , such that highly destabilizing protein variants are more rapidly degraded than slightly destabilized variants.…”