The proteasome and the delicate balance between destruction and rescue

Abstract

The proteasome is a large multiprotein complex that degrades unwanted cellular proteins. The mechanisms that control this protein-eating machine are being uncovered

Figure 1. Structure of an Ubiquitinated Protein

Ubiquitin (light violet) is a small 76 amino acid protein that can be covalently attached to target proteins (green) by specific E3 ubiquitin ligases. Such conjugation takes the form of an isopeptide bond between the carboxyl terminus of ubiquitin (denoted as C) and a lysine amino sidechain (K) on the substrate, or in some cases, conjugation can be via a peptide bond between ubiquitin and the amino terminus of the protein (N). These amide bonds are indicated as blue links. Multiple ubiquitin moieties can link in a similar manner via lysine-48 (K48) to form a polyubiquitin chain. As symbolized, more than one such chain can assemble on a single target. The result is a branched fusion protein with multiple amino termini (seven in the depicted example) coalescing at a single carboxyl terminus. Polyubiquitination in this manner targets proteins to the proteasome, where they are hydrolyzed into short peptides (green stack). Deubiquitinating enzymes can hydrolyze the bond between one ubiquitin moiety and another or between ubiquitin and the target protein.

Figure 2. Deubiquitination versus Proteolysis at the Proteasome

Once recognized and anchored to the proteasome via its polyubiquitin tag (light violet), a substrate (green) can be unraveled, unfolded, and translocated by the 19S regulatory particle (red) into the proteolytic chamber of the 20S core particle (purple), where it is hydrolyzed into short peptides (left). A byproduct of proteolysis is the polyubiquitin anchor (that may still be linked to a residual peptide). Cytoplasmic deubiquitinating enzymes eventually process this chain and recycle ubiquitin. However, the proteasome can also directly deubiquitinate the substrate, with diverse outcomes. For example, the substrate can be “shaved” upon cleavage of the bond to the proximal ubiquitin (right). Without its anchor, the substrate is presumably released and rescued. A distinct deubiquitinating activity is “trimming” or removal of the distal ubiquitin moiety (middle). According to one hypothesis, trimming serves as a timer; extended or difficult-to-process chains allow ample time for substrate unfolding and irreversible proteolysis (left), while short or easy-to-process chains inevitably lead to substrate release and rescue (right). This delicate balance between destruction and rescue is fundamental to proteasome efficiency.