I Peptide Repertoire in Normal and the Composition and Structure of MHC Class Associated with Antigen Processing Defines Endoplasmic

The MHC class I (MHC-I) molecules ferry a cargo of peptides to the cell surface as potential ligands for CD8 + cytotoxic T cells. For nearly 20 years, the cargo has been described as a collection of short 8-9 mer peptides, whose length and sequences were believed to be primarily determined by the peptide-binding groove of MHC-I molecules. Yet the mechanisms for producing peptides of such optimal length and composition have remained unclear. In this study, using mass spectrometry, we determined the amino acid sequences of a large number of naturally processed peptides in mice lacking the endoplasmic reticulum aminopeptidase associated with Ag processing (ERAAP). We find that ERAAP-deficiency changed the oeuvre and caused a marked increase in the length of peptides normally presented by MHC-I. Furthermore, we observed similar changes in the length of viral peptides recognized by CD8 + T cells in mouse CMV-infected ERAAP-deficient mice. In these mice, a distinct CD8 + T cell population was elicited with specificity for an N-terminally extended epitope. Thus, the characteristic length, as well as the composition of MHC-I peptide cargo, is determined not only by the MHC-I peptide-binding groove but also by ERAAP proteolysis in the endoplasmic reticulum. P roper control of a viral infection relies on recognition of virus-derived material by cytotoxic CD8 + T cells. The CD8 + T cells scan the cell surface for antigenic peptides presented by MHC class I molecules (pMHC-I) (1, 2). To facilitate immune surveillance, every nucleated cell generates thousands of peptides from self or foreign intracellular proteins. The MHC class I (MHC-I) molecules collect and chaperone the peptide cargo from the endoplasmic reticulum (ER) to the cell surface as potential ligands for the Ag receptors of CD8 + T cells. The peptide cargo for presentation by MHC-I is generated by the Ag-processing pathway (3). The pathway generally begins in the cytoplasm where precursor polypeptides are fragmented by the multicatalytic proteasome and other proteases (4,5). These pro-teolytic intermediates are then transported into the ER by cyto-solic chaperones and the TAP. In the ER, the nascent MHC-I molecules acquire their peptide cargo in the peptide loading complex with the assistance of ER-resident chaperones, thiol re-ductases, and proteases (6–9). The peptide-loaded MHC-I then exit the ER and transit through the Golgi to the cell surface. Thus, the peptide pool available for presentation by MHC-I is subject to modification at various stages of the Ag-processing pathway. …