CD8 ؉ T cells respond to short peptides bound to MHC class I molecules. Although most antigenic proteins contain many sequences that could bind to MHC class I, few of these peptides actually stimulate CD8 ؉ T cell responses. Moreover, the T cell responses that are generated often follow a very reproducible hierarchy to different peptides for reasons that are poorly understood. We find that the loss of a single enzyme, endoplasmic reticulum aminopeptidase 1 (ERAP1), in the antigen-processing pathway results in a marked shift in the hierarchy of immunodominance in viral infections, even when the responding T cells have the same T cell receptor repertoire. In mice, ERAP1 is the major enzyme that trims precursor peptides in the endoplasmic reticulum and, in this process, can generate or destroy antigenic peptides. Consequently, when ERAP1 is lost, the immune response to some viral peptides is reduced, to others increased, and to yet others unchanged. Therefore, many epitopes must be initially generated as precursors that are normally trimmed by ERAP1 before binding to MHC class I, whereas others are normally degraded by ERAP1 to lengths that are too short to bind to MHC class I. Moreover, peptide trimming and the resulting abundance of peptide-MHC complexes are dominant factors in establishing immunodominance.antigen presentation ͉ antigen processing ͉ peptidases C ells infected with a virus or otherwise producing foreign proteins can be recognized and eliminated by CD8 ϩ T cells. CD8 ϩ T cells recognize their targets through interactions between their T cell receptor (TCR) and MHC class I on the surface of the target cell. MHC class I is composed of a light chain (␤ 2 -microglobulin), a highly polymorphic heavy chain, and a small peptide that is produced by degradation of intracellular proteins.MHC class I alleles bind to peptides with a particular set of anchor residues that fit into pockets in the MHC class I peptide-binding groove. Virus proteomes typically contain many peptides with anchor residues suitable for particular MHC class I alleles, yet immune responses are generally directed toward a very limited number of epitopes. This phenomenon, in which only a few epitopes are functionally immunogenic, is known as immunodominance and is, as yet, incompletely understood (reviewed in ref. 1). Although many explanations for immunodominance have been proposed (1-9), their relative importance is not well established.The generation of most MHC class I epitopes requires proteolysis by proteasomes in the cytosol. Proteasomes can generate either the mature epitope that is ultimately presented by MHC class I molecules or precursors that are extended by several amino acids at the amino terminus. Such N-extended peptides are further processed by aminopeptidases to generate the final presented epitope. Although a number of peptidases have been proposed to play roles in MHC class I antigen presentation, few have been shown to play a major role in antigen presentation in intact cells. In cell lysates, aminopeptidases, includin...

Recent reports concluded that tripeptidyl peptidase (TPPII) is essential for MHC class I Ag presentation and that the proteasome in vivo mainly releases peptides 16 residues or longer that require processing by TPPII. However, we find that eliminating TPPII from human cells using small interfering RNA did not decrease the overall supply of peptides to MHC class I molecules and reduced only modestly the presentation of SIINFEKL from OVA, while treatment with proteasome inhibitors reduced these processes dramatically. Purified TPPII digests peptides from 6 to 30 residues long at similar rates, but eliminating TPPII in cells reduced the processing of long antigenic precursors (14–17 residues) more than short ones (9–12 residues). Therefore, TPPII appears to be the major peptidase capable of processing proteasome products longer than 14 residues. However, proteasomes in vivo (like purified proteasomes) release relatively few such peptides, and these peptides processed by TPPII require further trimming in the endoplasmic reticulum (ER) by ER aminopeptidase 1 for presentation. Taken together, these observations demonstrate that TPPII plays a specialized role in Ag processing and one that is not essential for the generation of most presented peptides. Moreover, these findings reveal that three sequential proteolytic steps (by proteasomes, TPPII, and then ER aminopepsidase 1) are required for the generation of a subset of epitopes.