Antigen Processing


Antigen presentation is an important mechanism by which the immune system recognises infection and maintains self‐tolerance. In order to effectively present antigens to T lymphocytes, intracellular enzymes degrade antigenic macromolecules into short fragments, which then bind major histocompatibility complex class I and class II molecules, or alternatively nonpolymorphic major histocompatibility complex class Ib molecules. This process of fragmentation is known as antigen processing and is shaped by the specificity of the enzymes involved as well as the intracellular compartments where processing takes place. Key players in antigen processing include cytoplasmic enzymes such as the proteasome and calpain, as well as cysteine cathepsins, aspartyl proteases, NADPH oxidase and GILT, which all reside in acidic vacuolar compartments. The trafficking of antigens to different intracellular compartments influences the sequence of processing and the selection of antigenic epitopes, which are displayed on the cell surface to promote immune activation or tolerance.

Key Concepts

  • Trafficking of antigens into proper compartments affects the degradation and availability of epitopes for both MHC‐I and MHC‐II presentation.
  • Proteasome activity affects MHC‐I peptide generation and endogenous cytoplasmic peptide generation for MHC‐II.
  • ROS production by NADPH oxidase can affect MHC‐I cross‐presentation and MHC‐II presentation.
  • Cathepsin activity, which is regulated by endosomal pH, generates peptides for MHC‐I cross‐presentation and MHC‐II presentation.
  • The reduction of disulphide bonds by GILT affects availability of epitopes for MHC‐II presentation.
  • While homologous to MHC‐I, nonclassical MHC‐Ib acquire antigens processed in acidic compartments much like MHC‐II.

Keywords: MHC‐I; MHC‐II; CD1; antigen trafficking; antigen processing; antigen presentation

Figure 1. The proteasome. The proteasome is an enzyme complex located in the cytosol that is involved in multiple cellular processes including the production of peptide ligands for MHC‐I. (a) The 20S proteasome consists of four stacked rings. The outer two rings consist of seven α subunits, while the inner two rings consist of seven β subunits. The catalytic subunits are β1, β2 and β5. (b) The 20S proteasome can associate with two 19S regulatory complexes to form the 26S proteasome. Protein substrates are preferentially targeted to the 26S proteasome by polyubiquitination. (c) The cytokine IFN‐γ induces the expression of the alternative β subunits LMP‐2, MECL‐1 and LMP‐7, which can replace β1, β2 and β5, respectively. The resultant structure is known as the immunoproteasome. This structure generates an increased number of peptides capable of binding MHC‐I. IFN‐γ can also induce the expression of another regulatory subunit (PA28 or 11S), which can replace the 19S regulatory subunits, thus further diversifying the repertoire of epitopes available for MHC‐I binding.
Figure 2. MHC‐I antigen presentation pathways. Before being loaded onto MHC‐I, endogenous antigens are degraded into peptides by the proteasome. These peptides are then translocated from the cytoplasm into the ER by TAP. In the ER, MHC‐I fold and associate with tapasin, which links MHC‐I with TAP. Tapasin and chaperones together with MHC‐I form the peptide‐loading complex (PLC), which facilitates peptide binding to receptive MHC‐I. Within the ER, peptides can be further trimmed at the N‐terminus by ERAPs. Peptide:MHC‐I complexes are then shuttled through the Golgi to the cell surface where they interact with CD8+ T cells. MHC‐I can also associate with peptides derived from exogenous antigens in a process known as cross‐presentation. Processing of exogenous antigens for cross‐presentation can take place in phagosomes or within the cytoplasm.
Figure 3. NADPH oxidase activity modulates antigen processing. (a) The NADPH oxidase enzyme complex assembles on the phagosome membrane in dendritic cells, and loss of NADPH oxidase activity results in increased proteolysis of phagocytosed antigens. Some studies have shown that this increase in antigen proteolysis is associated with an increase in phagosome acidification, while others suggest that it is associated with increased levels of cysteine cathepsin activity, independent of pH. Nonetheless, this increase in antigen proteolysis results in the destruction of MHC‐I epitopes and less efficient cross‐presentation. (b) NADPH oxidase activity has also been shown to modulate MHC‐II antigen presentation; however, the location of the enzyme complex in relation to MHC‐II antigen processing is not clear. Lack of NADPH oxidase activity has been associated with the increased cleavage of specific MHC‐II epitopes owing to increased cysteine cathepsin activity and the preferential presentation of membrane‐associated antigens. Overall, lack of NADPH oxidase activity results in an altered repertoire of MHC‐II epitopes.
Figure 4. MHC‐II antigen presentation pathways. Exogenous antigens are internalised via clathrin‐mediated endocytosis and subsequently delivered to the endosomal–lysosomal network for processing by proteases, reductases and potentially other enzymatic and nonenzymatic processes. Endogenous antigens can also enter this network through macroautophagy (MA) and chaperone‐mediated autophagy (CMA). Processing reactions within the endosomal–lysosomal network give rise to antigenic peptides or epitopes, which can intersect MHC‐II molecules in route to the cell surface. Newly synthesised MHC‐II assemble and associate with the chaperone Ii in the ER. The MHC‐II:Ii complexes are then sorted through the Golgi and into the endosomal–lysosomal network. Lysosomal proteases sequentially cleave Ii, leaving the Ii fragment CLIP in the MHC‐II peptide‐binding groove. HLA‐DM catalyses the removal of CLIP and facilitates binding of antigenic peptides. MHC‐II:peptide complexes are then shuttled to the surface to be displayed for recognition by CD4+ T cells.


Allan ER, Tailor P, Balce DR, et al. (2014) NADPH oxidase modifies patterns of MHC class II‐restricted epitopic repertoires through redox control of antigen processing. Journal of Immunology 192: 4989–5001.

Ameglio F, Capobianchi MR, Dolei A and Tosi R (1983) Differential effects of gamma interferon on expression of HLA class II molecules controlled by the DR and DC loci. Infection and Immunity 42: 122–125.

Bakke O and Dobberstein B (1990) MHC class II‐associated invariant chain contains a sorting signal for endosomal compartments. Cell 63: 707–716.

Blum JS, Wearsch PA and Cresswell P (2013) Pathways of antigen processing. Annual Review of Immunology 31: 443–473.

Bourgeois EA, Subramaniam S, Cheng TY, et al. (2015) Bee venom processes human skin lipids for presentation by CD1a. Journal of Experimental Medicine 212: 149–163.

Busch R, Cloutier I, Sekaly RP and Hammerling GJ (1996) Invariant chain protects class II histocompatibility antigens from binding intact polypeptides in the endoplasmic reticulum. EMBO Journal 15: 418–428.

Coux O, Tanaka K and Goldberg AL (1996) Structure and functions of the 20S and 26S proteasomes. Annual Review of Biochemistry 65: 801–847.

Crotzer VL, Matute JD, Arias AA, et al. (2012) Cutting edge: NADPH oxidase modulates MHC class II antigen presentation by B cells. Journal of Immunology 189: 3800–3804.

Denzin LK and Cresswell P (1995) HLA‐DM induces CLIP dissociation from MHC class II alpha beta dimers and facilitates peptide loading. Cell 82: 155–165.

Dongre AR, Kovats S, Deroos P, et al. (2001) In vivo MHC class II presentation of cytosolic proteins revealed by rapid automated tandem mass spectrometry and functional analyses. European Journal of Immunology 31: 1485–1494.

Ferrington DA and Gregerson DS (2012) Immunoproteasomes: structure, function, and antigen presentation. Progress in Molecular Biology and Translational Science 109: 75–112.

Gardiner GJ, Deffit SN, Mcletchie S, et al. (2013) A Role for NADPH Oxidase in Antigen Presentation. Frontiers in Immunology 4: 295.

Gradehandt G and Ruede E (1991) The endo/lysosomal protease cathepsin B is able to process conalbumin fragments for presentation to T cells. Immunology 74: 393–398.

Haque A, Hajiaghamohseni LM, Li P, Toomy K and Blum JS (2007) Invariant chain modulates HLA class II protein recycling and peptide presentation in nonprofessional antigen presenting cells. Cellular Immunology 249: 20–29.

Hastings KT (2013) GILT: Shaping the MHC Class II‐Restricted Peptidome and CD4(+) T Cell‐Mediated Immunity. Frontiers in Immunology 4: 429.

Hattori A and Tsujimoto M (2013) Endoplasmic reticulum aminopeptidases: biochemistry, physiology and pathology. Journal of Biochemistry 154: 219–228.

Hinz A and Tampe R (2012) ABC transporters and immunity: mechanism of self‐defense. Biochemistry 51: 4981–4989.

Hsieh CS, Deroos P, Honey K, Beers C and Rudensky AY (2002) A role for cathepsin L and cathepsin S in peptide generation for MHC class II presentation. Journal of Immunology 168: 2618–2625.

Joffre OP, Segura E, Savina A and Amigorena S (2012) Cross‐presentation by dendritic cells. Nature Reviews Immunology 12: 557–569.

Kang SJ and Cresswell P (2004) Saposins facilitate CD1d‐restricted presentation of an exogenous lipid antigen to T cells. Nature Immunology 5: 175–181.

Kisselev AF and Goldberg AL (2001) Proteasome inhibitors: from research tools to drug candidates. Chemical Biology 8: 739–758.

Kropshofer H, Vogt AB, Moldenhauer G, et al. (1996) Editing of the HLA‐DR‐peptide repertoire by HLA‐DM. EMBO Journal 15: 6144–6154.

Lich JD, Elliott JF and Blum JS (2000) Cytoplasmic processing is a prerequisite for presentation of an endogenous antigen by major histocompatibility complex class II proteins. Journal of Experimental Medicine 191: 1513–1524.

Lich JD, Jayne JA, Zhou D, Elliott JF and Blum JS (2003) Editing of an immunodominant epitope of glutamate decarboxylase by HLA‐DM. Journal of Immunology 171: 853–859.

Maehr R, Hang HC, Mintern JD, et al. (2005) Asparagine endopeptidase is not essential for class II MHC antigen presentation but is required for processing of cathepsin L in mice. Journal of Immunology 174: 7066–7074.

Manoury B, Hewitt EW, Morrice N, et al. (1998) An asparaginyl endopeptidase processes a microbial antigen for class II MHC presentation. Nature 396: 695–699.

Manoury B, Mazzeo D, Li DN, et al. (2003) Asparagine endopeptidase can initiate the removal of the MHC class II invariant chain chaperone. Immunity 18: 489–498.

Mizuochi T, Yee ST, Kasai M, et al. (1994) Both cathepsin B and cathepsin D are necessary for processing of ovalbumin as well as for degradation of class II MHC invariant chain. Immunology Letters 43: 189–193.

Mukherjee P, Dani A, Bhatia S, et al. (2001) Efficient presentation of both cytosolic and endogenous transmembrane protein antigens on MHC class II is dependent on cytoplasmic proteolysis. Journal of Immunology 167: 2632–2641.

Nakagawa T, Roth W, Wong P, et al. (1998) Cathepsin L: critical role in Ii degradation and CD4 T cell selection in the thymus. Science 280: 450–453.

Pickart CM (1997) Targeting of substrates to the 26S proteasome. FASEB Journal 11: 1055–1066.

Riese RJ, Wolf PR, Bromme D, et al. (1996) Essential role for cathepsin S in MHC class II‐associated invariant chain processing and peptide loading. Immunity 4: 357–366.

Roche PA, Marks MS and Cresswell P (1991) Formation of a nine‐subunit complex by HLA class II glycoproteins and the invariant chain. Nature 354: 392–394.

Rodgers JR and Cook RG (2005) MHC class Ib molecules bridge innate and acquired immunity. Nature Reviews Immunology 5: 459–471.

Rosa F, Hatat D, Abadie A, et al. (1983) Differential regulation of HLA‐DR mRNAs and cell surface antigens by interferon. EMBO Journal 2: 1585–1589.

Rybicka JM, Balce DR, Chaudhuri S, Allan ER and Yates RM (2012) Phagosomal proteolysis in dendritic cells is modulated by NADPH oxidase in a pH‐independent manner. EMBO Journal 31: 932–944.

Sadasivan B, Lehner PJ, Ortmann B, Spies T and Cresswell P (1996) Roles for calreticulin and a novel glycoprotein, tapasin, in the interaction of MHC class I molecules with TAP. Immunity 5: 103–114.

Savina A, Jancic C, Hugues S, et al. (2006) NOX2 controls phagosomal pH to regulate antigen processing during crosspresentation by dendritic cells. Cell 126: 205–218.

Sorimachi H, Ishiura S and Suzuki K (1997) Structure and physiological function of calpains. Biochemical Journal 328 (Pt 3): 721–732.

Takahashi T, Yonezawa S, Dehdarani AH and Tang J (1986) Comparative studies of two cathepsin B isozymes from porcine spleen. Isolation, polypeptide chain arrangements, and enzyme specificity. Journal of Biological Chemistry 261: 9368–9374.

Villadangos JA and Ploegh HL (2000) Proteolysis in MHC class II antigen presentation: who's in charge? Immunity 12: 233–239.

Watts C (2004) The exogenous pathway for antigen presentation on major histocompatibility complex class II and CD1 molecules. Nature Immunology 5: 685–692.

Zavasnik‐Bergant T and Turk B (2006) Cysteine cathepsins in the immune response. Tissue Antigens 67: 349–355.

Further Reading

Murphy K, Travers P, Walport M, et al. (2012) Janeway's Immunobiology, 8th edn. London and New York: Current Biology‐Garland Science.

Parham P and Janeway C (2014) The Immune System, 4th edn. London and New York: Current Biology‐Garland Science.

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Gardiner, Gail J, Deffit, Sarah N, and Blum, Janice S(Sep 2015) Antigen Processing. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0001228.pub3]