Major source of antigenic peptides for the MHC class I pathway is produced during the pioneer round of mRNA translation

Abstract

The MHC class I antigen presentation pathway allows the immune system to distinguish between self and nonself. Despite extensive research on the processing of antigenic peptides, little is known about their origin. Here, we show that mRNAs carrying premature stop codons that prevent the production of full-length proteins via the nonsense-mediated decay pathway still produce a majority of peptide substrates for the MHC class I pathway by a noncanonical mRNA translation process. Blocking the interaction of the translation initiation factor eIF4E with the cap structure suppresses the synthesis of full-length proteins but has only a limited effect on the production of antigenic peptides. These results reveal an essential cell biological function for a class of translation products derived during the pioneer round of mRNA translation and will have important implications for understanding how the immune system detects cells harboring pathogens and generates tolerance.MHC class I-restricted antigen presentation | pioneer round of translation

Translation of pre-spliced RNAs in the nuclear compartment generates peptides for the MHC class I pathway

“…This idea is consistent with the observation that introducing a silent point mutation in codon 39 (CUC to CUG) upstream of the MBP(79-87) epitope in the MBP mRNA led to a 30% increase in antigen presentation (8). Exchanging the SL8 peptide for the MBP peptide and using a T-cell hybridoma specific for this epitope (15) resulted in a similar production of antigenic peptide substrates from intron and exon sequences, demonstrating that presentation of epitopes derived from introns is not restricted to the epitope or to a certain class I molecule (Fig.…”

“…Nuclear RNA was purified with the RNeasy Mini Kit (Qiagen). Reverse transcription was carried out as described previously (8). Primers are listed in SI Materials and Methods.…”

“…The detection of peptides on MHC class I molecules is highly sensitive, with only a few peptide-MHC class I complexes required to activate specific T cells, and thus can serve to detect rare peptide products derived from noncanonical translation during the mRNA maturation process (8). We aimed to take advantage of this property to identify the early ribosomal scanning event that give rise to peptide products.…”

“…However, despite the key role of antigen presentation on MHC class I molecules in immune surveillance, the source of peptides for the MHC class I pathway is not yet known. Accumulating evidence indicates that the processing of alternative peptide substrates plays a major role, and that degradation products derived from full-length proteins have limited access to the MHC class I pathway (8)(9)(10). We recently demonstrated that pioneer translation products (PTPs) that form antigenic peptide substrates for the MHC class I pathway are produced by a translation event that is distinct from the canonical event giving rise to full-length proteins and does not require the cap-binding translation factor eIF4E, and also that mRNAs that have stopped producing peptides substrates for the MHC class I pathway still produce full-length proteins (8).…”

eIF4AIII enhances translation of nuclear cap-binding complex–bound mRNAs by promoting disruption of secondary structures in 5′UTR

“…The above view, however, was recently challenged by two reports showing that NMD occurs in the cytoplasm, regardless of whether the CBC or eIF4E drives the first round of translation (12,13). In addition, several recent studies revealed that translation of CBC-bound mRNAs may occur multiple times (3,(14)(15)(16) and that, more intriguingly, the translation of replication-dependent histone mRNAs mainly occurs on CBCbound mRNA (15). Therefore, for simplicity and clarity, we will hereafter refer to the two types of translation as CBC-dependent translation (CT), which takes place on CBC-bound mRNA, and…”