Post-proteasomal antigen processing for major histocompatibility complex class I presentation

Peptides presented by major histocompatibility complex class I molecules are derived mainly from cytosolic oligopeptides generated by proteasomes during the degradation of intracellular proteins. Proteasomal cleavages generate the final C terminus of these epitopes. Although proteasomes may produce mature epitopes that are eight to ten residues in length, they more often generate N-extended precursors that are too long to bind to major histocompatibility complex class I molecules. Such precursors are trimmed in the cytosol or in the endoplasmic reticulum by aminopeptidases that generate the N terminus of the presented epitope. Peptidases can also destroy epitopes by trimming peptides to below the size needed for presentation. In the cytosol, endopeptidases, especially thimet oligopeptidase, and aminopeptidases degrade many proteasomal products, thereby limiting the supply of many antigenic peptides. Thus, the extent of antigen presentation depends on the balance between several proteolytic processes that may generate or destroy epitopes.     

Proteolysis and class I major histocompatibility complex antigen presentation

Summary: The class I major histocompatibility complex (MHC class 1) presents 8–10 residue peptides to cytotoxic T lymphocytes. Most of these antigenic peptides are generated during protein degradation in the cytoplasm and are then transported into the endoplasmic reticulum by the transporter associated with antigen processing (TAP), Several lines of evidence have indicated that the proteasome is the major proteolytic activity responsible for generation of antigenic peptides—probably most conclusive has been the finding that specific inhibitors of die proteasome block antigen presentation. However, other proteases (e.g. the signal peptidase) may also generate some epitopes, particularly those on certain MHC class I alleles. The proteasome is responsible for generating the precise C termini of many presented peptides, and appears to be the only activity in ceils that can make this cleavage. In contrast, aminopeptidases in the cytoplasm and endoplasmic reticulum can trim the N terminus of extended peptides to their proper size. Interestingly, the cellular content of proteases involved in the production and destruction of antigenic peptides is modified by inter-feron-γ (IFN-γ) treatment of cells, IFN-γ indicates the expression of three new proteasome β submits that are preferentially incorporated into new proteasomes and alter their pattern of peptidase activities. These changes are likely to enhance the yield of peptides with C termini appropriate for MHC binding and have been shown to enhance the presentation of at least some antigens. IFN-γ also upregulates leucine aminopeptidase, which should promote the removal of N-terminal flanking residues of antigenic peptides. Also, this cytokine downregulates the expression of a metallo-proteinase, thimet oligopeptidase that actively destroys many antigenic peptides. Thus, IFN-γ appears to increase the supply of peptides by stimulating their generation and decreasing their destruction. The specificity and content of these various proteases should determine the amount of peptides available for antigen presentation. Also, the efficiency with which a peptide is presented is determined by the protein's half life (e.g. its ubiquitination rate) and the sequences flanking antigenic peptides, which influence the rates of proteolytic cleavage and destruction.     

Major histocompatibility complex class I-restricted antigen processing and presentation

Major histocompatibility complex (MHC) class I molecules present antigenic peptides to CD8-expressing cytotoxic T lymphocytes (CTLs). This antigen recognition system is critically important for immune surveillance against viruses and tumors. Most class I-binding peptides are generated in the cytosol, as side products from the degradation of misfolded proteins by proteasomes. A subset of the resulting peptides are translocated across the endoplasmic reticulum (ER) membrane by a dedicated peptide transporter, and these peptides are then loaded onto peptide-receptive class I molecules in the ER. The stable assembly of class I molecules with peptides is controlled by a variety of accessory proteins, including chaperones with general housekeeping functions and factors with dedicated roles in class I assembly. Peptide-filled class I molecules are then delivered to the cell surface for recognition by CTLs. This highly regulated process permits the host to rapidly counter invading pathogens with strong and sustained CTL responses and, at the same time, avoid misguided attacks. Here, how the class I antigen processing machinery accomplishes this daunting task is reviewed.     

The seven dirty little secrets of major histocompatibility complex class I antigen processing

Summary: Every field has its dirty little secrets (DLSs): assumptions based on flimsy evidence, findings that directly contradict prevailing models or so beg comprehension that they cannot even seed reasonable alternative hypotheses. Although our natural tendency is to hug these DLSs, they should be exposed, for it is these gaps in our understanding that point to the path to enlightenment. Here, I discuss some of the DLSs of major histocompatibility complex class I antigen processing.     

Mechanisms of major histocompatibility complex class II-restricted processing and presentation of the V antigen of Yersinia pestis

We mapped mouse CD4 T-cell epitopes located in three structurally distinct regions of the V antigen of Yersinia pestis. T-cell hybridomas specific for epitopes from each region were generated to study the mechanisms of processing and presentation of V antigen by bone-marrow-derived macrophages. All three epitopes required uptake and/or processing from V antigen as well as presentation to T cells by newly synthesized major histocompatibility complex (MHC) class II molecules over a time period of 3-4 hr. Sensitivity to inhibitors showed a dependence on low pH and cysteine, serine and metalloproteinase, but not aspartic proteinase, activity. The data indicate that immunodominant epitopes from all three structural regions of V antigen were presented preferentially by the classical MHC class II-restricted presentation pathway. The requirement for processing by the co-ordinated activity of several enzyme families is consistent with the buried location of the epitopes in each region of V antigen. Understanding the structure-function relationship of multiple immunodominant epitopes of candidate subunit vaccines is necessary to inform choice of adjuvants for vaccine delivery. In the case of V antigen, adjuvants designed to target it to lysosomes are likely to induce optimal responses to multiple protective T-cell epitopes.     

The role of H2-O and HLA-DO in major histocompatibility complex class Il-restricted antigen processing and presentation

Summary: The function of major histocompatibility complex (MHC) class II molecules is to sample exogenous antigens for presentation to CD4⁺ T helper cells. After synthesis in the endoplasmic reticulum, class II molecules are directed into the endosomal system by association with the invariant chain (Ii), which is sequentially cleaved, generating class II dimers loaded with Ii-derived peptides (CLIP). These class Il-peptide complexes are physiological substrates for H2-M/HLA-DM, a resident of the endosomal/lysosomal system which facilitates the removal of CLIP from newly synthesised class II αβ dimers. Exchange of CLIP for antigenic class Il-binding peptides is also promoted by the action of H2-M/HLA-DM, resulting in stable peptide-class II complexes that are transported to the cell surface for presentation to CD4⁺ T cells. Recent evidence suggests that this H2-M/HLA-DM-mediated 'peptide editing' is influenced by another MHC class Il-encoded molecule, H2-O/HLA-DO. This non-polymorphic αβ heterodimer is associated with H2-M/HLA-DM during intra-cellular transport and within the endosomal system of B cells, H2-0/HLA-DO alters the peptide exchange function of H2-M/HLA-DM in a pH-dependent manner, so that H2-M/HLA-DM activity is limited to more acidic conditions, corresponding to lysosomal compartments. Indeed, H2-O/HLA-DO may serve to limit the presentation of antigens after fluid phase uptake by B cells, while augmenting presentation of antigens internalised via membrane Ig receptors. Such a mechanism may maintain the fidelity of the B-cell-CD4⁺ T-cell interaction, counteracting self reactivity arising from less stringent lymphocyte activation. Here, data evaluating the role of H2-O/HLA-DO shall be reviewed and its putative function discussed.     

Pleiotropic consequences of metabolic stress for the major histocompatibility complex class II molecule antigen processing and presentation machinery

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TAP-dependent major histocompatibility complex class I presentation of soluble proteins using listeriolysin

Immunization of mice with mixtures of listeriolysin, a pore-forming hemolysin secreted by the pathogenic bacterium Listeria monocytogenes, together with soluble ovalbumin, nucleoprotein of influenza virus, or β-galactosidase of Escherichia coli, resulted in strong cytotoxic CD8 T cell responses to each of the respective passenger proteins in vivo. Also, the concomitant addition of either protein with listeriolysin to target cells elicited efficient sensitization of these cells which could be attributed to the pore-forming activity of listeriolysin. This response was dependent upon a functional TAP transporter and was inhibitable by brefeldin A, indicating the transfer of the soluble proteins into the cytosol and the classical major histocompatibility (MHC) class I presentation pathway. The treatment of target cells with listeriolysin under our experimental conditions did not affect cell viability and the pores generated by listeriolysin treatment were repaired within 60 min. Introduction of soluble proteins into the MHC class I presentation pathway by listeriolysin provides a powerful system to study the cytotoxic response towards intracellular pathogens and would allow for rapid screening of potential antigens in vaccine formulations.     

Endolysosomal processing of exogenous antigen into major histocompatibility complex class I-binding peptides

An alternative endolysosomal pathway has recently been suggested for the processing of MHC-I-binding peptides, and peptide/MHC-I complexes have been demonstrated in this compartment. However, it remains unclear where in the antigen-presenting cells such peptides are processed, in the endolysosomes themselves or in the proteasomal complex. Here, we have investigated this using monoclonal antibodies specific for the immunodominant SIINFEKL/Kb complex (25-D1) or for the carbohydrate part of Db- or Kb-binding glycopeptides in combination with inhibitors for classical and endolysosomal MHC-I-processing pathways. Alternative processing was detected in both wt and TAP1(-/-) immature DC (iDC) as the expression of SIINFEKL/Kb complexes on the surface of OVA-treated cells in the presence of Brefeldin A (BFA) or lactacystin and their absence in the presence of the lysosomotropic amines ammonium chloride, chloroquine and methylamine. Internalized Db- and Kb-binding glycopeptides, detected with high specificity using an anti-galabiose (Gal2) monoclonal antibody, were found to appear on the cell surface of BFA-treated cells after intracellular MHC-I-binding. Peptide exchange in Kb was demonstrated as the gradual appearance of SIINFEKL/Kb complexes on BFA-treated cells which earlier had been saturated with another Kb-binding peptide. Our data support the presence of a fully functional endolysosomal processing pathway in iDC guided by the chaperone function of MHC-I molecules.     

Trypanosoma cruzi-infected macrophages are defective in major histocompatibility complex class II antigen presentation

Trypanosoma cruzi, the intracellular protozoan parasite that causes Chagas' disease, interferes with the host immune response to establish a persistent infection. In this report, we demonstrate that macrophages infected with T. cruzi are unable to effectively present antigens to CD4 T cells. The interference is due to defective antigen-presenting cell (APC) function, as antigen-independent stimulation of the T cell in the presence of infected macrophages is not affected. The defect is distal to antigen processing and is not due to decreased major histocompatibility complex (MHC) class II expression, decreased viability, defective peptide loading in the infected macrophages, nor absence of CD28 co-stimulation. There was a role for gp39:CD40 co-stimulation during antigen presentation to the T cells we studied, but the expression of CD40 on T. cruzi-infected macrophages was not decreased. Antigen-specific adhesion between macrophages and T cells was reduced by infection. Equivalent levels of the adhesion molecules lymphocyte function-associated antigen-1, intercellular adhesion molecule-1, vascular cell adhesion molecule-1 or very late antigen-4 are found on infected and uninfected APC, suggesting that reduced expression of these adhesion molecules was not responsible for the defect in antigen-specific adhesion. The defective T cell:macrophage adhesion may be due to the reduced expression of other adhesion molecules or other changes in the cell induced by infection. Interfering with MHC class II antigen presentation in infected macrophages may help T. cruzi to blunt the immune response by the host.     

Virus infection blocks the processing and presentation of exogenous antigen with the major histocompatibility complex class II molecules.

Helper T cell recognition of antigen requires that antigen be processed and presented by class II expressing antigen-presenting cells (APC). Many antigens presented by the immune system are part of infectious organisms, for example, bacteria and viruses, which themselves may affect APC function. Here we show that infection of B cell lines as APC with viruses of two different families, namely, influenza A or vaccinia, completely block processing and presentation of an exogenous globular protein antigen pigeon cytochrome c. The block appears to be primarily within the processing pathway, as virus infection has little effect on the presentation of an antigenic peptide of pigeon cytochrome c which does not require processing. It is likely that several steps in the processing pathway are affected. Only live infectious virus, not UV-inactivated virus blocks APC function, indicating that there is no competition of viral particles with cytochrome c for the class II processing machinery. As compared to uninfected cells, virus-infected cells internalize less antigen bound to surface Ig but degrade a similar portion of that which enters the cell. Virus infection results in reduced protein synthesis in APC which may also be a factor in decreasing APC function. Significantly, we show that the processing of a high affinity evolutionary variant of cytochrome c from Drosophila melanogaster is reduced less by virus infection as compared to c. Such knowledge may guide the selection of antigenic epitopes in vaccine design.     

Trypanosoma cruzi infection does not impair major histocompatibility complex class I presentation of antigen to cytotoxic T lymphocytes

Trypanosoma cruzi (T. cruzi), the etiological agent of Chagas' disease, lives free within the cytoplasm of infected host cells. This intracellular niche suggests that parasite antigens may be processed and presented on major histocompatibility complex (MHC) class I molecules for recognition by CD8⁺ T cells. However, the parasite persists indefinitely in the mammalian host, indicating its success at evading immune clearance. It has been shown that T. cruzi interferes with processing and presentation of antigenic peptides in the MHC class II pathway. This investigation sought to determine whether interference in MHC class I processing and presentation occurs with T. cruzi infection. Surface expression of MHC class I molecules was found to be unaffected or up-regulated by T. cruzi infection in vitro. A model system employing a β-galactosidase (β-gal)-specific murine cytotoxic T lymphocyte (CTL) line (0805B) showed: (i) in vitro infection of mouse peritoneal macrophages or J774 cells with T. cruzi did not inhibit MHC class I presentation of exogenous peptide (a nine-amino acid epitope of β-gal) to the CTL line, (ii) in vitro infection of a β-gal-expressing 3T3 cell line (LZEJ) with T. cruzi did not inhibit MHC class I presentation of the endogenous protein to the CTL line and (iii) mouse renal adenocarcinoma cells infected with T. cruzi and subsequently infected with adenovirus expressing β-gal were able to present antigen to the β-gal-specific CTL line. These findings indicate that the failure of the immune response to clear T. cruzi does not result from global interference by the parasite with MHC class I processing and presentation. Parasites engineered to express β-gal were unable to sensitize infected antigen-presenting cells in vitro to lysis by the CTL 0805B line. This was probably due to the intracellular localization of the β-gal within the parasite and its inaccessibility to the host cell cytoplasm.     

Peptide transporter-independent,stress protein-mediated endosomal processing of endogenous protein antigens for major histocompatibility complex class I presentation

The peptide transporter-defective cell line RMA-S expressing the wild-type simian virus 40 large T antigen (wtT-Ag) from a transfected gene did not present two well-defined, H-2 class I (D^b)-restricted epitopes of T-Ag to cytotoxic T lymphocytes (CTL). Hence, “endogenous” processing and presentation of the wtT-Ag depended on a functional peptide transporter heterodimer. In contrast, both T-Ag epitopes were efficiently presented to CTL by transfected RMA-S cells expressing a truncated, cytoplasmic T-Ag variant (cT-Ag) or a karyophilic, amino-terminal 272-amino acid T-Ag fragment. Transporter-independent “endogenous” processing of mutant T-Ag molecules correlated with their association with the constitutively expressed heat shock protein 73 (hsp 73). Class I-restricted presentation of both epitopes processed from these hsp73-associated protein antigens was sensitive to NH₄Cl and chloroquine. These data indicate that selected intracellular proteins access an alternative, hsp73-mediated pathway for class I-restricted presentation that operates independent of peptide transporters in an endosomal compartment.     

Proteolytic processing of peptides in the lumen of the endoplasmic reticulum for antigen presentation by major histocompatibility class I

We have tested the hypothesis that MHC class I molecules are actively involved as protease in the production of natural MHC class I ligands. First, the structure of a class I molecule was analyzed for homology with catalytic sites of known proteases. While several clusters of amino acids in the restriction element resembled protease active sites, structural discrepancies and the influence of nearby residues suggest that these sites are unlikely to have protease activity. Second, we have tested the presentation of viral cytotoxic T cell determinants with affinity for the same restriction element (H-2K(d) or K(k)), when targeted as tandem peptides into the endoplasmic reticulum. Peptide transporter-defective cells were used to exclude cleavage of the tandem peptides by cytosolic proteases. Cleavage by signal peptidase of the tandem peptides was ascertained. The C-terminal peptides in the tandem arrays were almost exclusively presented, suggesting that an aminopeptidase in the endoplasmic reticulum degraded the N-terminally positioned peptides. This result is inconsistent with an MHC class I-catalyzed cleavage following binding of longer peptides in the cleft of the restriction elements. Finally, we conclusively show that an aminopeptidase in the endoplasmic reticulum is also involved in antigen presentation in cells with a functional peptide transporter.     

Role of the major histocompatibility complex class II transmembrane region in antigen presentation and intracellular trafficking

While a sorting signal in the cytoplasmic tail of the major histocompatibility complex (MHC) class II molecules is known to influence their endocytic transport, potential effects of the transmembrane (TM) domain of the MHC class II molecules on endocytic transport remain unclear. We have examined the role of the TM domain by comparing antigen-presenting functions of the wildtype (WT) I-Ab and mutant (MT) I-Ab molecule substituted in the beta-chain TM with alpha chain TM. A20 cells transfected with WT I-Ab were able to present antigen (hen egg lysozyme) better to some hybridomas, while those transfected with MT I-Ab consistently outperformed WT for other hybridomas recognizing different epitopes. This difference in antigen processing and presentation is not caused by the differences in H-2M (DM) requirement or association with Ii. The time required for processing of specific epitopes appears to be different, suggesting sequential involvement of various endocytic compartments in the antigen processing. Although both WT and MT molecules were found in the early endocytic (transferrin receptor-rich) compartments, MT molecules accumulated in these compartments in higher quantities for longer time periods. Similarly, the MT molecule is retained for a longer time period than WT in late endocytic (LAMP-1 associated) compartments. Together, our data indicate an important role of the TM domain of the MHC class II molecules in the intracellular trafficking and, consequently, antigen processing and presentation.     

The exogenous pathway for antigen presentation on major histocompatibility complex class II and CD1 molecules

The endosomes and lysosomes of antigen-presenting cells host the processing and assembly reactions that result in the display of peptides on major histocompatibility complex (MHC) class II molecules and lipid-linked products on CD1 molecules. This environment is potentially hostile for T cell epitope and MHC class II survival, and the influence of regulators of protease activity and specialized chaperones that assist MHC class II assembly is crucial. At present, evidence indicates that individual proteases make both constructive and destructive contributions to antigen processing for MHC class II presentation to CD4 T cells. Some features of CD1 antigen capture within the endocytic pathway are also discussed.     

Endosomal processing for antigen presentation mediated by CD1 and Class I major histocompatibility complex: roads to display or destruction

The presentation of antigen in a form that can be recognized by T lymphocytes of the immune system requires antigen processing and association of antigen-derived fragments with molecules encoded by the major histocompatibility complex (MHC) locus or by the CD1 locus. Much emphasis on antigen processing and presentation in the last decades has focused on what we consider ‘conventional routes’ of antigen processing and presentation, whereby extracellular antigens are processed for presentation via Class II MHC complexes and cytosolic antigens are presented as peptide–Class I MHC complexes. We here highlight two other pathways in myeloid dendritic cells, those of lipid antigen presentation in association with CD1 and of peptide cross-presentation via Class I MHC complexes. Some pathogens evade immune recognition through inhibition of antigen presentation of phagosomal origin. Deviations in endosomal antigen processing and presentation are also seen in individuals suffering from glycosphingolipid lysosomal lipid storage diseases. We summarize recent developments in the endosomal antigen processing and presentation pathway, for display as lipid–CD1 complexes to natural killer T cells and as peptide–Class I MHC complexes to CD8 T cells.     

Electroporation of exogenous antigen into the cytosol for antigen processing and class I major histocompatibility complex (MHC) presentation: weak base amines and hypothermia (18 degrees C) inhibit the class I MHC processing pathway.

While endogenous antigens are presented by class I major histocompatibility complex (MHC) molecules, exogenous antigens generally require a means for penetration into the cytosol for processing prior to class I MHC presentation. We have optimized conditions for electroporation as a means to experimentally introduce exogenous antigens into the cytosol, providing a system with a number of advantages for dissecting the class I MHC processing pathway. Presentation was assessed by the response of class I or class II MHC-restricted T hybridoma cells. Essentially instantaneous antigen delivery by electroporation facilitated kinetic analysis of the class I pathway and investigation of the effects of various inhibitors or hypothermic conditions on class I MHC antigen processing. This pathway was inhibited by weak base amines (e.g. chloroquine and NH4Cl), cycloheximide, and hypothermia (18 degrees C, which inhibits certain intracellular vesicular processing pathways). The electroporation technique provides a simple, consistent approach for rapid cytosolic antigen delivery for analysis of class I MHC processing.     

Lipopeptides: a novel antigen repertoire presented by major histocompatibility complex class I molecules

Post‐translationally modified peptides, such as those containing either phosphorylated or O‐glycosylated serine/threonine residues, may be presented to cytotoxic T lymphocytes (CTLs) by MHC class I molecules. Most of these modified peptides are captured in the MHC class I groove in a similar manner to that for unmodified peptides. N‐Myristoylated 5‐mer lipopeptides have recently been identified as a novel chemical class of MHC class I‐presented antigens. The rhesus classical MHC class I allele, Mamu‐B*098, was found to be capable of binding N‐myristoylated lipopeptides and presenting them to CTLs. A high‐resolution X‐ray crystallographic analysis of the Mamu‐B*098:lipopeptide complex revealed that the myristic group as well as conserved C‐terminal serine residue of the lipopeptide ligand functioned as anchors, whereas the short stretch of three amino acid residues located in the middle of the lipopeptides was only exposed externally with the potential to interact directly with specific T‐cell receptors. Therefore, the modes of lipopeptide–ligand interactions with MHC class I and with T‐cell receptors are novel and fundamentally distinct from that for MHC class I‐presented peptides. Another lipopeptide‐presenting MHC class I allele has now been identified, leading us to the prediction that MHC class I molecules may be separated on a functional basis into two groups: one presenting long peptides and the other presenting short lipopeptides. Since the N‐myristoylation of viral proteins is often linked to pathogenesis, CTLs capable of sensing N‐myristoylation may serve to control pathogenic viruses, raising the possibility for the development of a new type of lipopeptide vaccine.