catalyzed peptide splicing.Abbreviations: electron-transfer higher-energy collision dissociation (EThcD); higher-energy collision dissociation (HCD); false discovery rate (FDR); HLA class I (HLA-I); lymphoblastoid cell line (LCL); mass spectrometry (MS); molecular weight (MW); proteasome-catalyzed peptide splicing (PCPS). 2The proteasome generates the epitopes presented on HLA class I molecules that elicit CD8 + T cell responses. While reports of proteasome-generated spliced epitopes exist, they have been regarded as rare events. Here, however, we show that the proteasome-generated spliced peptide pool accounts for one third of the entire HLA class I immunopeptidome in terms of diversity and one fourth in terms of abundance. They also represent a unique set of antigens, possessing particular and distinguishing features. We validated this observation using a range of complementary experimental and bioinformatics approaches, and multiple cell types. The widespread appearance and abundance of proteasome-catalyzed peptide splicing events will inform immunobiology and autoimmunity theories, and may provide a previously untapped source of epitopes for uses in vaccines and cancer immunotherapy.3The presentation of epitopes on the cell surface is a key mechanism by which organisms identify the presence of pathogens, metabolic malfunctioning, or tumors. The HLA class I (HLA-I) immunopeptidome, i.e. the epitopes allocated onto the HLA-I molecules, impinges upon the CD8 + T cell repertoire and the cell-mediated immune response (1). HLA-I immunopeptidomes are usually investigated by sequence identification of peptides eluted from HLA-I molecules using LC-tandem mass spectrometry (MS) (Fig. S1). The key step for the transformation of a protein into HLA-Irestricted epitopes is usually processing by the proteasome (1), which cuts proteins into peptides;alternatively, the proteasome can also cut and paste peptide sequences, thereby releasing peptide antigens that do not correspond to the original protein sequence (2) (Fig. S2). This proteasomecatalyzed peptide splicing (PCPS) has long been considered to occur only very rarely; partly this has been because the screening of the HLA-I immunopeptidome for proteasome-generated spliced peptides was impeded by methodological challenges.To overcome these problems we developed an analytical strategy, which accounts for recent discoveries underpinning the PCPS mechanism, and which can handle the vast proteome-wide human spliced peptide database (Fig. S3). With this strategy we initially analyzed the HLA-I-eluted immunopeptidome of the GR lymphoblastoid cell line (GR-LCL) adopting, for a deeper coverage of the immunopeptidome, a 2D peptide pre-fractionation strategy, followed by a hybrid peptide fragmentation method, electron-transfer higher-energy collision dissociation (EThcD) for peptide identification (3, 4) ( Fig. S1), supplemented by an adapted target-decoy approach (Fig. S4). Our analysis led to the identification of 6592 non-spliced and 3417 spliced 9-12mer peptides ( Table S1)....

Epitopes presented by major histocompatibility complex (MHC) class I molecules are selected by a multi-step process. Here we present the first computational prediction of this process based on in vitro experiments characterizing proteasomal cleavage, transport by the transporter associated with antigen processing (TAP) and MHC class I binding. Our novel prediction method for proteasomal cleavages outperforms existing methods when tested on in vitro cleavage data. The analysis of our predictions for a new dataset consisting of 390 endogenously processed MHC class I ligands from cells with known proteasome composition shows that the immunological advantage of switching from constitutive to immunoproteasomes is mainly to suppress the creation of peptides in the cytosol that TAP cannot transport. Furthermore, we show that proteasomes are unlikely to generate MHC class I ligands with a C-terminal lysine residue, suggesting processing of these ligands by a different protease that may be tripeptidyl-peptidase II (TPPII).

Protein substrates of the proteasome must apparently be unfolded and translocated through a narrow channel to gain access to the proteolytic active sites of the enzyme. Protein folding in vivo is mediated by molecular chaperones. Here, to test for chaperone activity of the proteasome, we assay the reactivation of denatured citrate synthase. Both human and yeast proteasomes stimulate the recovery of the native structure of citrate synthase. We map this chaperone-like activity to the base of the regulatory particle of the proteasome, that is, to the ATPase-containing assembly located at the substrate-entry ports of the channel. Denatured but not native citrate synthase is bound by the base complex. Ubiquitination of citrate synthase is not required for its binding or refolding by the base complex of the proteasome. These data suggest a model in which ubiquitin-protein conjugates are initially tethered to the proteasome by specific recognition of their ubiquitin chains; this step is followed by a nonspecific interaction between the base and the target protein, which promotes substrate unfolding and translocation.