Pathways of antigen processing

Abstract

T cell recognition of antigen-presenting cells depends on their expression of a spectrum of peptides bound to major histocompatibility complex class I (MHC-I) and class II (MHC-II) molecules. Conversion of antigens from pathogens or transformed cells into MHC-I- and MHC-II-bound peptides is critical for mounting protective T cell responses, and similar processing of self proteins is necessary to establish and maintain tolerance. Cells use a variety of mechanisms to acquire protein antigens, from translation in the cytosol to variations on the theme of endocytosis, and to degrade them once acquired. In this review, we highlight the aspects of MHC-I and MHC-II biosynthesis and assembly that have evolved to intersect these pathways and sample the peptides that are produced.

Figure 1

Three dimensional structures of MHC-I and MHC-II molecules with peptide ligands. A and B) Structure of the MHC-I molecule (HLA-A2 complexed with residues 58-66 of the influenza matrix protein, (229)). MHC-I heavy chain, blue; β₂m, grey; peptide, red. C and D) Structure of the MHC-II molecule (HLA-DR1 complexed with residues 306-318 of influenza haemagglutinin, (230)). MHC-II α chain, grey; MHC-II β chain, blue; peptide, red. Ribbon diagrams were generated with the Protein Workshop software available from the RSCB Protein Data Bank (http://www.rcsb.org). Highly polymorphic residues of HLA-A (B) and HLA-DR (D) proximal to the peptide binding groove (http://hla.alleles.org) are highlighted in yellow. Note that polymorphism of the MHC-II alpha chains is limited, and they are essentially non-polymorphic for HLA-DR alpha chains.

Figure 2

Trafficking of antigens for processing and presentation with MHC molecules: basic pathways and exceptions to the “rules”. Cytosolic proteins are processed primarily by the action of the proteasome. The short peptides are then transported into the ER by TAP for subsequent assembly with MHC-I molecules. In certain antigen presenting cells, particularly dendritic cells, exogenous proteins can also be fed into this pathway by retrotranslocation from phagosomes, a phenomenon known as cross-presentation. The retrotranslocation channels may be recruited from the ER, where they are used for ER-associated degradation, or ERAD, of misfolded transmembrane or secretory proteins. Exogenous proteins, however, are primarily presented by MHC-II molecules. Antigens are internalized by several pathways, including phagocytosis, macropinocytosis, and endocytosis, and eventually traffic to a mature or late endosomal compartment where they are processed and loaded onto MHC-II molecules. Cytoplasmic/nuclear antigens can also be trafficked into the endosomal network via autophagy for subsequent processing and presentation with MHC-II molecules.

Figure 3

MHC-I biosynthesis and antigenic peptide binding in the ER. Trimming of the N-linked glycan by glucosidases I and II (GlsI/ GlsII) to a single terminal glucose residue (“G”) permits the interaction of the MHC-I heavy chain with lectin-like chaperones at several stages during folding and assembly. The initial folding events involve the chaperone calnexin (CNX) and allow subsequent assembly with β₂m. The empty heterodimer, which is inherently unstable, is then recruited by calreticulin (CRT) via the monoglucosylated N-linked glycan to the PLC. The association of MHC-I/β₂m heterodimers with the PLC both stabilizes the empty MHC-I molecule and maintains the binding groove in a conformation that favors high affinity peptide loading. These functions are mediated by direct interactions between the MHC-I heavy chain and tapasin and are supported by coordinating interactions with CRT and ERp57 in the PLC. MHC-I molecules with suboptimal peptides are substrates for UGT1 which reglucosylates the heavy chain glycan, allowing re-entry of the MHC-I into the PLC and exchange for high affinity peptides. Peptides translocated into the ER by TAP originate primarily from the proteasomal degradation of endogenous proteins or DRiPs. These proteins may arise from the translation of either self or foreign (i.e. viral) RNA or, in the case of cross-presentation, by translocation into the cytosol from endosomes or phagosomes. Many of the peptides that are delivered into the ER are longer than the 8-10 residues preferred by MHC-I molecules and undergo trimming by ER aminopeptidases known as ERAAP/ERAP1 and ERAP2. Finally, high affinity peptides bind preferentially to MHC-I molecules in the PLC by a tapasin-mediated editing process, MHC-I-peptide complexes are released and then transit to the cell surface for T cell recognition by CD8⁺ T cells.

Figure 4

MHC-II biosynthesis and antigenic peptide binding in the endocytic pathway. MHC-II α and β associate with I chain trimers to form nonamers. These complexes transit to mature endosomes either via the TGN or by recycling from the cell surface. Within endosomes, I chain is sequentially proteolyzed to yield the residual I chain fragment, CLIP. Displacement of CLIP from the ligand groove of MHC-II αβ is mediated by DM and blunted by DO. Expression of DO and regulation of DM function involves the assembly of DM-DO complexes in the ER and co-transport to endocytic compartments. Antigens delivered to late endosomes by phagocytosis, pinocytosis, endocytosis, and autophagy, are processed by cathepsins and the thiol oxidoreductase GILT, and acquisition of high affinity peptides by MHC-II is facilitated by DM. The MHC-II-peptide complexes are subsequently transported to the cell surface for T cell recognition by CD4⁺ T cells.