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

Abstract

The "canonical" proteasomal degradation signal is a substrateanchored polyubiquitin chain. However, a handful of proteins were shown to be targeted following monoubiquitination. In this study, we established-in both human and yeast cells-a systematic approach for the identification of monoubiquitination-dependent proteasomal substrates. The cellular wild-type polymerizable ubiquitin was replaced with ubiquitin that cannot form chains. Using proteomic analysis, we screened for substrates that are nevertheless degraded under these conditions compared with those that are stabilized, and therefore require polyubiquitination for their degradation. For randomly sampled representative substrates, we confirmed that their cellular stability is in agreement with our screening prediction. Importantly, the two groups display unique features: monoubiquitinated substrates are smaller than the polyubiquitinated ones, are enriched in specific pathways, and, in humans, are structurally less disordered. We suggest that monoubiquitination-dependent degradation is more widespread than assumed previously, and plays key roles in various cellular processes. monoubiquitination | 26S proteasome | protein degradation | ubiquitin replacement

Monoubiquitination in proteasomal degradation

“…In both humans and yeast, shorter proteins (<150 amino acids) were more likely to undergo monoubiquitination, confirming the earlier observations by the Ciechanover group (15,19). Braten et al (18) suggest that monoubiquitination may provide a weaker targeting signal to the proteasomes, which is sufficient for degradation of smaller proteins. Because longer proteins were associated with either monoubiquitination or polyubiquitination, properties such as structural disorder are among factors that may govern their recognition by proteasomes.…”

“…Protein structural disorder (i.e., disordered regions that lack a defined tertiary structure) has previously been proposed to be a determinant of protein ubiquitination and proteasomal recognition (20)(21)(22); the Braten et al (18) study provides new data to support this. Proteins of higher organisms often contain large regions that become intrinsically disordered upon posttranslational modification or association with other proteins; such regions can also oscillate between ordered and disordered forms.…”

“…The classification of proteins as monoubiquitin-and polyubiquitin-dependent proteasome substrates was based on the ratio of signal intensity between wild-type and lysineless ubiquitin. Braten et al (18) note that a subset of proteins classified as monoubiquitinated is expected to include proteins harboring multiple monoubiquitinated moieties conjugated to multiple different lysines. Multiple ubiquitin molecules spread across a single protein were shown to provide a degradation signal that can at times mimic polyubiquitination (12).…”

“…1). This unexpected observation led Braten et al (18) to suggest that monoubiquitination is much more common in human cells than in yeast. One explanation for this difference might be the greater structural diversity of monoubiquitinated proteins in human cells (see below).…”

“…The analysis by Braten et al (18) suggests that, although structural disorder is seen in both monoubiquitinated and polyubiquitinated proteins in yeast, it is largely confined to polyubiquitinated proteins in humans. Consistent with the notion that polyubiquitination provides a stronger signal, structurally disordered proteins may benefit from the extended ubiquitination chains.…”