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Protein Degradation and Regulation Ubiquitin/Proteasome Pathway Guo Peng, Luo Tong and Yang Kong 2002.12.16. I. Introduction. This pathway is the major non-lysosomal process responsible for the breakdown of most short and long-lived proteins in mammalian cells.
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This pathway is the major non-lysosomal process responsible for the breakdown of most short and long-lived proteins in mammalian cells.
For example, in skeletal muscle, the system is responsible for the breakdown of the major contractile proteins, actin and myosins.
In addition, the pathway also controls various major biological events: cellcycle progression, oncogenesis, transcriptional control, development and differentiation, signal transduction, receptor down-regulation and antigen processing, via the breakdown of specific proteins.
covalent attachment of a polyubiquitin chain to the substrate;
specific recognition of this signal, and degradation of the tagged protein by the 26S proteasome.
environmental toxins, translation errors and genetic mutations can damage proteins. Misfolded proteins are highly deleterious to the cell because they can form non-physiological interactions with other proteins. Repair proteins called chaperones can, in many instances, restore the native conformation of misfolded proteins. However, if a damaged protein is not repaired, it is degraded in specialized organelles such as the ysosome, and by the ubiquitin/proteasome pathway.
Some proteins are stabilized only when they are bound to their natural partners. This ensures that they are present only at stoichiometric levels. Consequently, the overexpression of specific ribosomal proteins can lead to degradation because of their failure to assemble into the ribosome. Similarly, proteinsthat are mislocalized may be degraded because they are unable to form interactions that normally stabilize them.
Proteins that enter the secretory pathway and fold improperly in the endoplasmic reticulum are transported back to the cytosol where they are recognized and degraded by the ubiquitin/proteasome pathway.
The immune system is a surveillance mechanism that can recognize foreign proteins and degrade them. An essential feature of this system is the ability to distinguish ‘self’ from ‘non-self’. The MHC class I antigen presenting cells display peptide fragments that are derived from the foreign protein, to cytotoxic T cells. The generation of these peptides requires the 26S proteasome.
Many regulators of cell growth and development are highly unstable proteins, whose stability is controlled by the ubiquitin/proteasome pathway. Substrates of this pathway include p53, Rb, cyclins, CDK inhibitors, transcription factors, and signal-transducing molecules. Distinct targeting complexes accomplish the recognition of these proteins.
Proteases are required for the generation of free amino acids from short peptides that are generated by the proteasome and other intracellular proteases. In many microorganisms dipeptidases and other proteases that hydrolyze short amino acid chains are secreted to generate free amino acids that can be readily imported into the cell.The availability of free amino acids and di-peptides can allosterically regulate the activity of a specific E3 protein, which in turn controls the levels of a transcription factor that is required for inducing amino acid biosynthetic pathway genes.
Ubiquitination is an important and widespread post-translational modification of proteins, which resembles phosphorylation.
Very importantly, ubiquitination is not only a degradation signal, but also directs proteins to a variety of fates which include roles in ribosomal function, in DNA repair, in protein translocation, and in modulation of structure or activity of the target proteins.
In order to be efficiently degraded, the substrate must be bound to a polyubiquitin degradation signal that comprises at least four ubiquitin moieties, These signals are usually determined by short regions in the primary sequence of the targeted protein.
The nature of the N-terminal amino acid of a protein (N-end rule) may determine its rate of polyubiquitination and subsequent degradation.
Ubiquitin—mediated degradation of cytosolic and membrane proteins occurs in the cytosol and on the cytosolic face of the ER membranes. Although components of the system have been localized to the nucleus, conjugation and degradation have not been demonstrated in this organelle.
Alternation of E1, E2s and proteasome in their activity will affect many substrates.
Phosphorylation of many substrates is required for their recognition by their E3s. Conversley, similar modification of many other proteins prevents this.
Substrates that require prior phosphorylation include the yeast G1 cyclins（细胞周期蛋白）, Cln2 and Cln3, the yeast cyclin—dependent kinase (CDK) inhibitors, Sic1 and Far1.
Degradation of the proto-oncogene c-mos by the ubiquitin pathway is inhibited by phosphorylation on Ser. Interestingly, activation of c-mos leads to phosphorylation and stabilization of c-fos, another substrate of the ubiquitin pathway.
Regulated degradation of specific classes of substrates could be achieved by modulation of the activity of the ubiquitination machinery. For example, it has been shown recently that degradation of mitotic regulators by the APC（抗原呈递细胞） is regulated by different activators and inhibitors and by phosphorylation
Several viral proteins exploit the ubiquitin system by targeting for degradation cellular substrates which may interfere with propagation of the virus. In some instances, the viral protein functions as a bridging‘ element between the E3 and the substrate, thus conferring recognition in trans. The prototype of such a protein is the high risk HPV oncoprotein(人乳头癌蛋白）E6 which interacts with an E6-AP HECT domain E3, and with the tumor suppressor protein p53. This interaction targets p53 for rapid degradation and, thus, most probably prevents stress signalinduced apoptosis and ensures further replication propagation of the virus . In a different case, the Vpu protein of the HIV-1 virus is recognized by the F-box protein, b-TrCP. Vpu also binds to the CD4 receptor in the ER of Tcells infected by the virus. This leads to ubiquitination and subsequent degradation of CD4 by the SCFb-TrCP complex, thus enabling the virus to escape from immune surveillance.
The presence of either one of two transcription factors, MATa1 and MATa2, determines the mating type of haploid yeast cells. The diploid cell expresses both a1 and a2 that form a heterodimer with distinct DNA-binding specificity. In haploid cells, the two factors are rapidly degraded by the ubiquitin system. Degradation of a2 requires two degradation signals, Deg1 and Deg2. Strikingly, both a1 and a2 are stabilized by heterodimerization.For a2 at least, it has been shown that residues required for interaction with a1 overlap with the Deg1 degradation signal and it is possible that binding of a1interferes with the degradation of a2 by masking the ubiquitin recognition signal.