13.6: Protein Turnover in Eukaryotic Cells- Regulating Protein Half-Life

We have already seen that organelles have a finite life span or half-life, defined as the time for half of them to disappear in the absence of new synthesis of new organelles. Recall that lysosomes help to destroy worn-out mitochondria, including their molecular components. Recall also the small RNAs (especially miRNA) that destroy old or damaged cellular RNAs.

As we already know, the steady-state level of any cellular structure or molecule exists when the rate of its manufacture or synthesis is balanced by the rate of its turnover. Of course, steady-state levels of things can change. For example, the level of gene expression (the amount of a final RNA or protein gene product in a cell) can change if rates of transcription, processing, or turnover change. We should also expect the same for the steady-state levels of cellular proteins. Here we consider the factors that govern the half-life of cellular proteins, a property of all cellular molecules and structures. The half-lives of different proteins seem to be inherent in their structure. Thus, some amino acid side chains are more exposed at the surface of the protein and are thus more susceptible to change or damage over time than others. Proteins with fewer “vulnerable” amino acids should have a longer half-life than those with more of them. Proteins damaged by errors of translation, folding, or processing gone awry or just worn out from use or “old age” will be targeted for destruction. The mechanism for detecting and destroying unwanted, old, damaged, or misbegotten proteins involves a 76- amino acid polypeptide called ubiquitin that binds to target proteins and delivers them to a large complex of polypeptides called the proteasome. The pathway to protein destruction is shown below in Figure 13.17. Use the illustration to help you follow the numbered steps in the outline that follows the illustration.

Figure 13.17: In this mechanism, ubiquitins and proteasomes remove or destroy old and damaged proteins in cells and recycle their amino acids.

1. The first step is to activate a ubiquitin. This starts when ATP hydrolysis fuels the binding of ubiquitin to a ubiquitin-activating enzyme.
2. A ubiquitin-conjugating enzyme then replaces the ubiquitin-activation enzyme.
3. The protein destined for destruction replaces the ubiquitin-conjugating enzyme.
4. Several more ubiquitins then bind to this complex.
5. The poly-ubiquinated protein delivers its protein to one of the 19S ‘CAP’ structures of a proteasome.
6. After binding to the proteasome-cap structure of a proteasome, the poly-ubiquinated target proteins dissociate and ubiquitins are released and recycled as the target protein unfolds (powered by ATP hydrolysis) and enters a 20S core proteasome.
7. The target protein is digested to short peptide fragments by proteolytic enzymes in the interior of the proteasome core. The fragments are released from the CAP-complex at the other end of the proteasome and digested down to free amino acids in the cytoplasm.

There is a mind-boggling variety of proteins in a cell—including as many as six hundred different ubiquitin proteins, encoded by as many genes! Presumably, each ubiquitin handles a subclass of proteins based on common features of their structure. The structurally complex 26S proteasome is smaller than a eukaryotic small ribosomal subunit (40S). Nevertheless, it is one of the largest cytoplasmic particles, even without the benefit of any RNA in its structure! To see different animated versions of ubiquitin and proteasome in action, look at Proteasome in Action-1 and Proteasome in Action-2.

For their discovery of the ubiquitin-proteasome system and its proteolytic actions, A. Ciechanover, A. Hershko, and I. Rose shared the 2004 Nobel Prize in Chemistry.