Proteins in the cytosol are tagged for degradation via the ubiquitin–proteasome system (UPS). This begins with the attachment of a chain of several ubiquitin molecules to the target protein, a process called ubiquitination. First, a lysine residue on the targeted protein is chemically linked to the glycine at the carboxy terminus of one ubiquitin molecule. Ubiquitin chains are then formed by linking the lysine at residue 48 (K48) of the first ubiquitin to the carboxy-terminal glycine of a second ubiquitin, and so on until at least 4 ubiquitin molecules are bound. This K48-linked type of ubiquitin chain is recognized by the 19S cap of the proteasome, which then unfolds the tagged protein so that it can be introduced into the proteasome’s catalytic core. There the protein chain is degraded with a general lack of sequence specificity into short peptides, which are subsequently released into the cytosol. The general degradative functions of the proteasome have been co-opted for antigen presentation, so that MHC molecules have evolved to work with the peptides that the proteasome can produce.
Various lines of evidence implicate the proteasome in the production of peptide ligands for MHC class I molecules. Experimentally tagging proteins with ubiquitin results in more efficient presentation of their peptides by MHC class I molecules, and inhibitors of the proteolytic activity of the proteasome inhibit antigen presentation by MHC class I molecules. Whether the proteasome is the only cytosolic protease capable of generating peptides for transport into the endoplasmic reticulum is not known.
The constitutive β1, β2, and β5 subunits of the catalytic chamber are sometimes replaced by three alternative catalytic subunits that are induced by interferons. These induced subunits are called β1i (or LMP2), β2i (or MECL-1), and β5i (or LMP7). Both β1i and β5i are encoded by the PSMB9 and PSMB8 genes, which are located in the MHC locus, whereas β2i is encoded by PSMB10 outside the MHC locus. Thus, the proteasome can exist both as both a constitutive proteasome present in all cells and as the immunoproteasome, which is present in cells stimulated with interferons. MHC class I proteins are also induced by interferons. The replacement of the β subunits by their interferon-inducible counterparts alters the enzymatic specificity of the proteasome such that there is increased cleavage of polypeptides after hydrophobic residues, and decreased cleavage after acidic residues. This produces peptides with carboxy-terminal residues that are preferred anchor residues for binding to most MHC class I molecules (see Chapter 4) and are also the preferred structures for transport by TAP.
Another substitution for a β subunit in the catalytic chamber has been found to occur in cells in the thymus. Epithelial cells of the thymic cortex (cTECs) express a unique β subunit, called β5t, that is encoded by PSMB11. In cTECs, β5t becomes a component of the proteasome in association with β1i and β2i, and this specialized type of proteasome is called the thymoproteasome. Mice lacking expression of β5t have reduced numbers of CD8 T cells, indicating that the peptide:MHC complexes produced by the thymoproteasome are important in CD8 T-cell development in the thymus.