Antigen presentation. DM exchange mechanism

HLA-DM catalytically enhances peptide dissociation by sensing peptide-MHC class II interactions throughout the peptide-binding cleft

Human leukocyte antigen-DM (HLA-DM) is an integral component of the major histocompatibility complex class II (MHCII) antigen-processing and -presentation pathway. HLA-DM shapes the immune system by differentially catalyzing peptide exchange on MHCII molecules, thereby editing the peptide-MHCII (pMHCII) repertoire by imposing a bias on the foreign and self-derived peptide cargos that are presented on the cell surface for immune surveillance and tolerance induction by CD4⁺ T cells. To better understand DM selectivity, here we developed a real-time fluorescence anisotropy assay to delineate the pMHCII intrinsic stability, DM-binding affinity, and catalytic turnover, independent kinetic parameters of HLA-DM enzymatic activity. We analyzed prominent pMHCII contacts by differentiating the kinetic parameters in pMHCII homologs, observing that peptide interactions throughout the MHCII-binding cleft influence both the rate of peptide dissociation from the DM-pMHCII catalytic complex and the binding affinity of HLA-DM for a pMHCII. We show that the intrinsic stability of a pMHCII linearly correlates with DM catalytic turnover, but is nonlinearly correlated with its binding affinity. Surprisingly, interactions at the peptides N terminus up to and including MHCII position one (P1) anchor affected the catalytic turnover, suggesting that the active DM-pMHCII catalytic complex operates on pMHCII complexes with full peptide occupancy. Furthermore, interactions at the peptide C terminus modulated DM-binding affinity, suggesting distal communication between peptide interactions with the MHCII and the DM-pMHCII binding interface. Our results imply an intimate linkage between the DM-pMHCII interface and peptide-MHCII interactions throughout the peptide-binding cleft.

Binding interactions between peptides and proteins of the class II major histocompatibility complex

The activation of helper T cells by peptides bound to proteins of the class II Major Histocompatibility Complex (MHC II) is pivotal to the initiation of an immune response. The primary functional requirement imposed on MHC II proteins is the ability to efficiently bind thousands of different peptides. Structurally, this is reflected in a unique architecture of binding interactions. The peptide is bound in an extended conformation within a groove on the membrane distal surface of the protein that is lined with several pockets that can accommodate peptide side-chains. Conserved MHC II protein residues also form hydrogen bonds along the length of the peptide main-chain. Here we review recent advances in the study of peptide-MHC II protein reactions that have led to an enhanced understanding of binding energetics. These results demonstrate that peptide-MHC II protein complexes achieve high affinity binding from the array of hydrogen bonds that are energetically segregated from the pocket interactions, which can then add to an intrinsic hydrogen bond-mediated affinity. Thus, MHC II proteins are unlike antibodies, which utilize cooperativity among binding interactions to achieve high affinity and specificity. The significance of these observations is discussed within the context of possible mechanisms for the HLA-DM protein that regulates peptide presentation in vivo and the design of non-peptide molecules that can bind MHC II proteins and act as vaccines or immune modulators.

Peptide binding and antigen presentation by class II histocompatibility glycoproteins

The immune system has evolved complex mechanisms for the recognition and elimination of pathogens. CD4+ helper T lymphocytes play a central role in orchestrating immune responses and their activation is carefully regulated. These cells selectively recognize short peptide antigens stably associated with membrane-bound class II histocompatibility glycoproteins that are selectively expressed in specialized antigen presenting cells. The class II-peptide complexes are generated through a series of events that occur in membrane-bound compartments within antigen presenting cells that, collectively, have become known as the class II antigen processing pathway. In the present paper, our current understanding of this pathway is reviewed with emphasis on mechanisms that regulate peptide binding by class II histocompatibility molecules.

Bacterial modulation of antigen processing and presentation

This review examines the mechanisms by which bacteria influence the antigenic processing of endogenous and exogenous antigens presented by class I, class II, and nonclassical MHC molecules. Consequent effects on presentation of bacterial antigens, the ability of bacteria to evade host defences, and the potential induction of autoimmunity are discussed.

Abundant empty class II MHC molecules on the surface of immature dendritic cells

A monoclonal antibody specific for the empty conformation of class II MHC molecules revealed the presence of abundant empty molecules on the surface of spleen- and bone marrow-derived dendritic cells (DC) among various types of antigen-presenting cells. The empty class II MHC molecules are developmentally regulated and expressed predominantly on immature DC. They can capture peptide antigens directly from the extracellular medium and present bound peptides to antigen-specific T lymphocytes. The ability of the empty cell-surface class II MHC proteins to bind peptides and present them to T cells without intracellular processing can serve to extend the spectrum of antigens able to be presented by DC, consistent with their role as sentinels in the immune system.

Trafficking of the Igalpha/Igbeta heterodimer with membrane Ig and bound antigen to the major histocompatibility complex class II peptide-loading compartment

The binding of antigen to the B cell antigen receptor (BCR) initiates two major cellular events. First, upon cross-linking by antigen, the BCR induces signal transduction cascades leading to the transcription of a number of genes associated with B cell activation. Second, the BCR internalizes and delivers antigens to processing compartments, where processed antigenic peptides are loaded onto major histocompatibility complex (MHC) class II molecules for presentation to T helper cells. The BCR consists of membrane Ig (mIg) and Igalpha/Igbeta heterodimer (Igalpha/Igbeta). The Igalpha/Igbeta, the signal transducing component of the BCR, has been indicated to play a role in antigen processing. In order to understand the function of the Igalpha/Igbeta in antigen transport, we studied the intracellular trafficking pathway of the Igalpha/Igbeta. We show that in the absence of antigen binding, the Igalpha/Igbeta constitutively traffics with mIg from the plasma membrane, through the early endosomes, to the MHC class II peptide-loading compartment. Cross-linking the BCR does not alter the trafficking pathway; however, it accelerates the transport of the Igalpha/Igbeta to the MHC class II peptide-loading compartment. This suggests that the Igalpha/Igbeta heterodimer is involved in BCR-mediated antigen transport through the entire antigen transport pathway.

Uveitogenic epitopes of retinal S-antigen are generated in vivo via an alternative antigen-presentation pathway

We have found that different antigen-processing pathways are involved in the induction of experimental autoimmune uveoretinitis (EAU) by the retinal autoantigens S-antigen and interphotoreceptor retinoid-binding protein (IRBP). Although in vitro T-cell proliferative responses to IRBP were completely inhibited in the presence of irreversible cysteine protease inhibitors, no significant reduction of S-antigen proliferative responses was found. Furthermore, acidic proteolysis of S-antigen by the cysteine protease cathepsin B prior to immunization radically reduced pathogenicity (disease severity). In addition, in vitro processing of S-antigen, but not IRBP, was also found to be resistant to the action of cycloheximide and lysosomotropic agents, inhibition of proliferation only occurring after extended exposure of antigen-presenting cells to methyl amine or high concentrations of chloroquine. These data indicate that an alternative pathway of antigen processing exists for S-antigen, which is independent of processing within the normal endolysosomal pathway and that uveitogenic peptides of naturally processed S-antigen bind to major histocompatibility complex class II antigens either at the cell surface or within very early endosomes where cathepsin B is inactive.

Distinct Peptide Loading Pathways for MHC Class II Molecules Associated with Alternative Ii Chain Isoforms

Mutant mouse strains expressing either p31 or p41 Ii chain appear equally competent with respect to their class II functional activities including Ag presentation and CD4+ T cell development. To further explore possibly divergent roles provided by alternative Ii chain isoforms, we compare class II structure and function in double mutants also carrying a null allele at the H2-DM locus. As for DM mutants expressing wild-type Ii chain, AαbAβb dimers present in DM-deficient mice expressing either Ii chain isoform appear equally occupied by class II-associated Ii chain-derived peptides (CLIP). Surprisingly, in functional assays, these novel mouse strains exhibit strikingly different phenotypes. Thus, DM-deficient mice expressing wild-type Ii chain or p31 alone are both severely compromised in their abilities to present peptides. In contrast, double mutants expressing the p41 isoform display markedly enhanced peptide-loading capabilities, approaching those observed for wild-type mice. The present data strengthen evidence for divergent class II presentation pathways and demonstrate for the first time that functionally distinct roles are mediated by alternatively spliced forms of the MHC class II-associated Ii chain in a physiologic setting.

A roadmap for HLA-DR peptide binding specificities

Peptide residue positional environments have previously been defined for class I MHC allelic products. These environments provide a less restrictive description of the traditional peptide binding pockets of class I molecules. When combined with the peptide anchor motifs that have been identified for some class I molecules, predictions as to likely motifs for other MHC molecules, which share the same potential environment can be made. Here, the same approach is used to derive peptide residue positional environments for class II MHC molecules. The environments are used to make predictions as to likely binding motifs for HLA-DR allelic products. The predictions are presented in the form of a Table and shown to have concordance with experimental results.

Lack of association of DMB polymorphism with insulin-dependent diabetes

Considerable evidence exists that the genes coding for the HLA class II DQ molecules in the MHC region are major contributors to genetic susceptibility in insulin-dependent diabetes. Located centromeric to the DQ loci are the genes encoding DMA and DMB, two class II-like molecules which play an essential role in the pathway leading to antigen presentation by HLA class II. In this study we have examined the distribution of the DMB allele and studied HLA DQA1-DQB1-TAP2-DMB haplotypes in 52 IDDM families and 65 un-related controls. DMB allele frequencies in IDDM and control subjects were not significantly different. DMB*0101 was present in 85% of patients vs. 76% of controls, DMB*0102 in 12 vs. 17%, DMB*0103 in 3 vs. 5%, DMB*0104 in 0 vs. 2%. The IDDM-susceptible MHC DQA1-DQB1 haplotypes found by analysis of IDDM families were not associated with specific DMB alleles. We conclude that the described DMB polymorphisms are not associated with IDDM susceptibility and DMB genotyping is unlikely to improve the assessment of genetic risk for IDDM.

Intact proteins can bind to class II histocompatibility molecules with high affinity

The ability of intact protein antigens to bind to purified class II histocompatibility molecules was investigated. Intact bovine ribonuclease (RNase) inhibited peptide binding to DR1 with a potency similar to that of a high affinity peptide or irreversibly denatured RNase. Similarly, horse myoglobin (Mb) was a potent inhibitor of peptide binding to I-E(k). I-E(k)-Mb complexes were directly visualized as a distinct band with reduced mobility on SDS PAGE. Direct binding experiments with biotin-labeled proteins demonstrated that Mb and RNase bind to class II molecules through the peptide-binding groove with high affinity, and that binding occurs in the absence of detergent. The possibility that HLA-DM can catalyse the binding of intact protein antigens was supported by the observation that DM enhances the binding of biotin-RNase to DR1. Our results provide further support for the hypothesis that intact, partially unfolded protein antigens can act as ligands for initial interaction with class II molecules.

Evolutionary relationship of HLA-DRB genes inferred from intron sequences

The major histocompatibility complex (Mhc) consists of class I and class II genes. In the human Mhc (HLA) class II genes, nine DRB loci have been identified. To elucidate the origin of these duplicated loci and allelic divergences at the most polymorphic DRB1 locus, introns 4 and 5 as well as the 3' untranslated region (altogether approximately 1,000 base pairs) of seven HLA-DRB loci, three HLA-DRB1 alleles, and nine nonhuman primate DRB genes were examined. It is shown that there were two major diversification events in HLA-DRB genes, each involving gene duplications and allelic divergences. Approximately 50 million years (my) ago, DRB1*04 and an ancestor of the DRB1*03 cluster (DRB1*03, DRB1*15, and DRB3) diverged from each other and DRB5, DRB7, DRB8, and an ancestor of the DRB2 cluster (DRB2, DRB4, and DRB6) arose by gene duplication. Later, about 25 my ago, DRB1*15 diverged from DRB1*03, and DRB3 was duplicated from DRB1*03. Then, some 20 my ago, the lineage leading to the DRB2 cluster produced two new loci, DRB4 and DRB6. The DRB1*03 and DRB1*04 allelic lineages are extraordinarily old and have persisted longer than some duplicated genes. The orthologous relationships of DRB genes between human and Old World monkeys are apparent, but those between Catarrhini and New World monkeys are equivocal because of a rather rapid expansion and contraction of primate DRB genes by duplication and deletion.

Immunology and the confocal microscope

The techniques of classical epifluorescence microscopy are already widely used by the immunological community to detect antigens at the cellular level. Coupled with the use of specific inhibitors that affect diverse intracellular events, these techniques have provided valuable information on the mechanisms involved in antigen presentation. The same biological samples can now be examined by confocal microscopy, which has a higher resolution than conventional microscopy and allows one to analyse quantitatively single cross-sections of the sample. The confocal microscope is therefore especially well-suited for studies on intracellular membrane traffic, cell-to-cell interactions, and the distribution of particular antigens and their co-localization with other intracellular markers. This review describes the technique of confocal microscopy and the goals of sample preparation, along with several detailed protocols for fixing and permeabilizing cells and mounting them on microscope slides. Representative examples are cited from studies on the endocytosis of surface receptors, the distribution of adhesion and major histocompatibility complex (MHC) molecules, and the interaction of an intracellular parasite with MHC molecules of the host cell.

Presentation of antigens derived from microorganisms residing in host-cell vacuoles

Antigens presented by major histocompatibility complex molecules have been classified into those presented by 'endogenous' and 'exogenous' pathways. Some microorganisms reside within host-cell vacuoles that appear to avoid both pathways. Novel presentation mechanisms are being unraveled for these microorganisms, and their antigens, rather than being just peptides, can also consist of lipids or DNA fragments.

Class II antigen processing compartments and the function of HLA-DM

The DM alpha and DM beta genes encode a nonpolymorphic, class II-like molecule which functions by an, as yet, undefined mechanism in the assembly of Major Histocompatibility Complex class II-peptide complexes. Indeed, mutant cells which express class II molecules but fail to express DM are unable to process and present native protein antigens. A striking phenotype of the mutation is class II molecules that contain almost exclusively a nested set of invariant chain peptides, termed CLIP, for class II associated Ii peptides, instead of the normal array of endogenously and exogenously derived peptides. Thus, DM appears to be required for the correct assembly of processed antigen-class II complexes. Recently, the subcellular compartments that contain DM and in which functional processed antigen-class II complexes are first formed have been described. Here, the evidence for the function of DM in the antigen-processing compartments is reviewed.