Endoplasmic Reticulum Aminopeptidase Associated with Antigen Processing Defines the Composition and Structure of MHC Class I Peptide Repertoire in Normal and Virus-Infected Cells

Abstract

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.

Critical Role of Endoplasmic Reticulum Aminopeptidase 1 in Determining the Length and Sequence of Peptides Bound and Presented by HLA–B27

“…Interestingly, although ERAP1 trims peptides from the N-terminus, these longer peptides found were predominantly C-terminally extended. This is in apparent contrast to the findings from studies performed in mice, where extended class I MHC peptides caused by ERAAP knockout were found to be mainly N-terminal extensions (13). The likely explanation, supported by our in vitro binding studies, is that N-terminally extended epitopes lacking Arg-2, which is critical for the HLA-B27 binding motif, bind so poorly to HLA-B27 that they are rarely detected.…”

“…Our finding that ERAP1 silencing increases the proportion of longer peptides (11-13 mer) bound to HLA-B27 is consistent with previous data on murine class I MHC (13). We also found that ERAP1 silencing changed the nature of the P1 amino acid of peptides bound to HLA-B27, increasing the abundance of uncharged polar residues (S, Y, and T) while reducing the prevalence of E and R residues.…”

“…Therefore, the peptide repertoire of class I MHC proteins is critical both biochemically and immunologically. Deficiency of ERAP associated with antigen processing (ERAAP) in a murine model (ERAAP Ϫ/Ϫ mice) has been shown to alter the repertoire of peptides bound to H-2D b and H-2K b , and the subsequent immune recognition by cytotoxic T lymphocytes (CTLs) (13). Therefore, ERAP1 likely contributes to the pathogenesis of AS through alteration of the HLA-B27 peptide repertoire.…”

The first step of peptide selection in antigen presentation by MHC class I molecules

“…5). This pattern is similar to that observed in cells where peptide loading is obstructed by tapasin deficiency or where peptide trimming is reduced by inactivation of endoplasmic reticulum aminopeptidase associated with antigen processing (ERAAP) (31,32). These observations hint at temperature-dependent conformational adaptations in the H-2K b peptide-binding groove, following the initial binding event.…”

“…The composition of the peptide-MHC class I repertoire is determined primarily by peptide-binding properties of MHC class I itself, but tapasin and ERAAP further shape the peptide repertoire presented (Fig. 5) (31,32). Of note, Duan et al (35) showed that cancer neopeptides that elicit CD8+ T-cell immunity may reflect the peptide pool detected at 26°C and then expand the MHC class I-associated peptidome considered by the immune system.…”