Protein Targeting and Degradation:- Protein Degradation Is Mediated by Specialized Systems in All Cell
Protein degradation prevents the buildup of abnormal or unwanted proteins and permits the recycling of amino acids. The half-lives of eukaryotic proteins vary from 30 seconds to many days. Most proteins turn over rapidly relative to the lifetime of a cell, although a few (such as hemoglobin) can last for the life of the cell (about 110 days for an erythrocyte). Rapidly degraded proteins include those that are defective because of incorrectly inserted amino acids or because of damage accumulated during normal functioning. And enzymes that act at key regulatory points in metabolic pathways often turn over rapidly. Defective proteins and those with characteristically short half-lives are generally degraded in both bacterial and eukaryotic cells by selective ATP-dependent cytosolic systems. A second system in vertebrates, operating in lysosomes, recycles the amino acids of mem brane proteins, extracellular proteins, and proteins with characteristically long half-lives. In E. coli, many proteins are degraded by an ATP dependent protease called Lon (the name refers to the “long form” of proteins, observed only when this pro tease is absent). The protease is activated in the presence of defective proteins or those slated for rapid turnover; two ATP molecules are hydrolyzed for every peptide bond cleaved. The precise role of this ATP hydrolysis is not yet clear. Once a protein has been reduced to small inactive peptides, other ATP-independent pro teases complete the degradation process. The ATP-dependent pathway in eukaryotic cells is quite different, involving the protein ubiquitin, which, as its name suggests, occurs throughout the eukaryotic kingdoms. One of the most highly conserved proteins known, ubiquitin (76 amino acid residues) is essentially identical in organisms as different as yeasts and humans. Ubiquitin is covalently linked to proteins slated for destruction via an ATP-dependent pathway involving three separate enzymes (E1, E2, and E3 in Fig. 1).
FIGURE 1 Three-step cascade pathway by which ubiquitin is at tached to a protein. Two different enzyme-ubiquitin intermediates are involved. The free carboxyl group of ubiquitin’s carboxyl-terminal Gly residue is ultimately linked through an amide (isopeptide) bond to an ε-amino group of a Lys residue of the target protein. Additional cycles produce polyubiquitin, a covalent polymer of ubiquitin subunits that targets the attached protein for destruction in eukaryotes.
FIGURE 2Three-dimensional structure of the eukaryotic proteasome. The 26S proteasome is highly conserved in all eukaryotes. The two subassemblies are the 20S core particle and the 19S regulatory particle. (a) (PDB ID 1IRU) The core particle consists of four rings arranged to form a barrel-like structure. Each of the inner rings has seven different β subunits (light blue), three of which have protease activities (dark blue). The outer rings each have seven different sub units (gray). (b) A regulatory particle forms a cap on each end of the core particle. The core particle is colored as in (a). The base and lid segments of each regulatory particle are presented in different shades of red. The regulatory particle unfolds ubiquitinated proteins (blue) and translocates them into the core particle, as shown.
Ubiquitinated proteins are degraded by a large com plex known as the 26S proteasome (Mr 2.5 106) (Fig. 2). The proteasome consists of two copies each of at least 32 different subunits, most of which are highly conserved from yeasts to humans. The protea some contains two main types of subcomplexes, a barrel like core particle and regulatory particles on either end of the barrel. The 20S core particle consists of four rings; the outer rings are formed from seven subunits, and the inner rings from seven β subunits. Three of the seven subunits in each β ring have protease activities, each with different substrate specificities. The stacked rings of the core particle form the barrel-like structure within which target proteins are degraded. The 19S regulatory particle on each end of the core particle contains 18 subunits, including some that recognize and bind to ubiquitinated proteins. Six of the subunits are ATPases that probably function in unfolding the ubiquitinated proteins and translocating the unfolded polypeptide into the core particle for degradation.
Although we do not yet understand all the signals that trigger ubiquitination, one simple signal has been found. For many proteins, the identity of the first residue that remains after removal of the amino-terminal Met residue, and any other posttranslational proteolytic processing of the amino-terminal end, has a profound in fluence on half-life . These amino-terminal signals have been conserved over billions of years of evolution, and are the same in bacterial protein degradation systems and in the human ubiquitination pathway are also being identified. Ubiquitin-dependent proteolysis is as important for the regulation of cellular processes as for the elimination of defective proteins. Many proteins required at only one stage of the eukaryotic cell cycle are rapidly degraded by the ubiquitin-dependent pathway after completing their function. The same pathway also processes and presents class I MHC antigens. Ubiquitin-dependent destruction of cyclin is critical to cell-cycle regulation. The E2 and E3 components of the ubiquitination cascade pathway (Fig. 2) are in fact two large families of proteins. Different E2 and E3 enzymes exhibit different specificities for target proteins and thus regulate different cellular processes. Some E2 and E3 enzymes are highly localized in certain cellular compartments, reflecting a specialized function. Not surprisingly, defects in the ubiquitination pathway have been implicated in a wide range of disease states. An inability to degrade certain proteins that activate cell division (the products of oncogenes) can lead to tumor formation, whereas a too-rapid degradation of proteins that act as tumor suppressors can have the same effect. The ineffective or overly rapid degradation of cellular proteins also appears to play a role in a range of other conditions: renal diseases, asthma, neurodegenerative disorders such as Alzheimer’s and Parkinson’s diseases (associated with the formation of characteristic proteinaceous structures in neurons), cystic fibrosis (caused in some cases by a too rapid degradation of a chloride ion channel, with resultant loss of function), Liddle’s syn drome (in which a sodium channel in the kidney is not degraded, leading to excessive Na absorption and early-onset hypertension)—and many other disorders. Drugs designed to inhibit proteasome function are being developed as potential treatments for some of these conditions. In a changing metabolic environment, protein degradation is as important to a cell’s survival as is protein synthesis, and much remains to be learned about these interesting pathways.
