The known unknowns of antigen processing and presentation

Abstract

The principal components of both MHC class I and class II antigen processing and presentation pathways are well known. In dendritic cells, these pathways are tightly regulated by Toll-like-receptor signalling and include features, such as cross-presentation, that are not seen in other cell types. However, the exact mechanisms involved in the subcellular trafficking of antigens remain poorly understood and in some cases are controversial. Recent data suggest that diverse cellular machineries, including autophagy, participate in antigen processing and presentation, although their relative contributions remain to be fully elucidated. Here, we highlight some emerging themes of antigen processing and presentation that we think merit further attention.

Figure 1. Six steps for loading and trafficking of MHC class I molecules to the cell surface

Antigen processing and presentation by MHC class I molecules can be divided into six discrete steps. Step 1: acquisition of antigens from proteins with errors (for example, due to premature termination or misincorporation). Step 2: misfolded proteins are tagged with ubiquitin for degradation. Step 3: the proteasome degrades these ubiquitylated proteins into peptides. Step 4: the peptides are delivered to the endoplasmic reticulum (ER) by the transporter associated with antigen processing (TAP) complex. Step 5: peptide is loaded onto nascently formed MHC class I molecules; this process is facilitated by members of the peptide-loading complex, such as tapasin and two ‘housekeeping’ ER proteins, known as calreticulin and ERp57. Step 6: peptide-loaded MHC class I molecules are transported via the Golgi complex to the cell surface. The steps for MHC class II–peptide loading conceptually follow this same path.

Figure 2. Contribution of pathogens and self-peptides to loading of MHC class II in DCs

Following phagocytosis of bacteria, surface-expressed Toll-like receptors (TLRs) become activated and influence the nature of phagosome maturation. Similarly, viruses engage TLRs found in endocytic vesicles that recognize nucleic acids. Following the maturation of phagosomes, these structures fuse with lysosomes to form phagolysosomes. MHC class II molecules that are contained in the lysosomes are loaded with peptide fragments formed by lysosomal proteases. Autophagosomes also fuse with lysosomes and serve as an additional source of peptides, including endogenous peptides, for MHC class II presentation. MHC class II molecules, as well as a host of other lysosomal proteins including tetraspanins, are transported in endolysosomal tubules to the cell surface. Surface MHC class II molecules can be found in microdomains with other co-stimulatory proteins. Phagosomes that contain polystyrene beads, which fail to ligate TLRs, do not mature fully and probably contribute less to the antigen processing pathway for MHC class II molecules.

Figure 3. Additional pathways that may be relevant for antigen processing and presentation by MHC class I molecules in TLR-stimulated DCs

How peptides traffic of peptides to MHC class I molecules during cross-presentation in DCs is unknown. We propose several possibilities that could permit peptides to access MHC class I molecules. Autophagosomes containing both endogenous peptides and pathogen-derived proteins could potentially serve as a source of peptides for the MHC class I pathway. Peptides may transit from the phagosome through leaky membranes, following spontaneous lysis of the phagosomal compartment or by traversing the lipid bilayer. Components of the peptide-loading complex and the endoplasmic reticulum (ER) dislocation machinery may be shuttled from the ER to the phagosome, perhaps involving lipid droplets for transport. Transfer of these components to the phagosome may permit loading of MHC class I molecules with peptides at this site rather than in the ER. Gap junctions may serve as conduits to allow neighbouring cells to donate peptide epitopes for loading of MHC class I molecules. The yeast ERAD protein complex is illustrated in greater detail on the panel below.