The conversion of exogenous and endogenous proteins into immunogenic peptides recognized by T lymphocytes involves a series of proteolytic and other enzymatic events culminating in the formation of peptides bound to MHC class I or class II molecules. Although the biochemistry of these events has been studied in detail, only in the past few years has similar information begun to emerge describing the cellular context in which these events take place. This review thus concentrates on the properties of antigen-presenting cells, especially those aspects of their overall organization, regulation, and intracellular transport that both facilitate and modulate the processing of protein antigens. Emphasis is placed on dendritic cells and the specializations that help account for their marked efficiency at antigen processing and presentation both in vitro and, importantly, in vivo. How dendritic cells handle antigens is likely to be as important a determinant of immunogenicity and tolerance as is the nature of the antigens themselves.

The bare lymphocyte syndrome (BLS) is a hereditary immunodeficiency resulting from the absence of major histocompatibility complex class II (MHCII) expression. Considering the central role of MHCII molecules in the development and activation of CD4(+) T cells, it is not surprising that the immune system of the patients is severely impaired. BLS is the prototype of a "disease of gene regulation." The affected genes encode RFXANK, RFX5, RFXAP, and CIITA, four regulatory factors that are highly specific and essential for MHCII genes. The first three are subunits of RFX, a trimeric complex that binds to all MHCII promoters. CIITA is a non-DNA-binding coactivator that functions as the master control factor for MHCII expression. The study of RFX and CIITA has made major contributions to our comprehension of the molecular mechanisms controlling MHCII genes and has made this system into a textbook model for the regulation of gene expression.

In this review, we discuss recent data from our laboratory that address two aspects of major histocompatibility complex (MHC) class I-restricted antigen processing. First, we consider the nature of the peptide-loading complex, which is the assembly of proteins in the endoplasmic reticulum (ER) into which newly synthesized MHC class I-beta(2) microglobulin (beta(2)m) heterodimers are incorporated, and the mechanisms involved in MHC class I assembly and peptide loading that are facilitated by the peptide-loading complex. Second, we discuss mechanisms of cross-presentation, the phenomenon whereby extracellular and luminal protein antigens can be processed by antigen-presenting cells, particularly dendritic cells, and presented by MHC class I molecules to CD8(+) T cells. The focus of the discussion is mainly on the human MHC class I system.

MHC class II molecules are pivotal for the adaptive immune system, because they guide the development and activation of CD4+ T helper cells. Fulfilling these functions requires that the genes encoding MHC class II molecules are transcribed according to a strict cell-type-specific and quantitatively modulated pattern. This complex gene-expression profile is controlled almost exclusively by a single master regulatory factor, which is known as the class II transactivator. As we discuss here, differential activation of the three independent promoters that drive expression of the gene encoding the class II transactivator ultimately determines the exquisitely regulated pattern of MHC class II gene expression.

T lymphocytes recognize peptide antigens presented by class I and class II molecules encoded by the major histocompatibility complex (MHC). Classical antigen-presentation studies showed that MHC class I molecules present peptides derived from proteins synthesized within the cell, whereas MHC class II molecules present exogenous proteins captured from the environment. Emerging evidence indicates, however, that dendritic cells have a specialized capacity to process exogenous antigens into the MHC class I pathway. This function, known as cross-presentation, provides the immune system with an important mechanism for generating immunity to viruses and tolerance to self.

Antigen presentation by both classical MHC class II molecules and the non-classical MHC class I-like molecule CD1D requires their entry into the endosomal/lysosomal compartment. Lysosomal cysteine proteases constitute an important subset of the enzymes that are present in this compartment and, here, we discuss the role of these proteases in regulating antigen presentation by both MHC class II and CD1D molecules.

The recent discovery of fusion of endoplasmic reticulum membrane with nascent phagosomes suggests that this peripheral compartment in macrophages and dendritic cells may serve as an organelle optimized for major histocompatibility complex (MHC) class I-restricted cross-presentation of exogenous antigens. The process allows intersection of the endosomal system with the endoplasmic reticulum, the classical site of MHC class I peptide loading, and may reconcile the seemingly conflicting evidence indicating both of these sites are crucial in cross-presentation. Here we discuss the potential mechanisms involved in loading exogenous antigens onto MHC class I molecules and the implications of this new evidence for the in vivo function of dendritic cells.

When cells are stimulated with pro-inflammatory cytokines, most of their constitutively expressed proteasomes are replaced with immunoproteasomes, which increase the production of peptides for presentation on MHC class I molecules. In addition, cortical thymic epithelial cells selectively express a type of proteasome known as the thymoproteasome that is required for the positive selection of thymocytes. Here, we discuss how these specialized types of proteasome shape the T cell receptor repertoire of cytotoxic T lymphocytes and propose that immunoproteasomes have functions, in addition to antigen processing, that influence cytokine production and T cell differentiation, survival and function. We also discuss how inhibitors of immunoproteasomes can suppress undesired T cell responses in autoimmune diseases.

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.

The transporter associated with antigen processing (TAP) is essential for peptide delivery from the cytosol into the lumen of the endoplasmic reticulum (ER), where these peptides are loaded on major histocompatibility complex (MHC) I molecules. Loaded MHC I leave the ER and display their antigenic cargo on the cell surface to cytotoxic T cells. Subsequently, virus-infected or malignantly transformed cells can be eliminated. Here we discuss the structure, function, and mechanism of TAP as a central part of the peptide-loading complex. Furthermore, aspects of virus and tumor escape strategies are presented.

Ever since the emergence of models for the processing and presentation of antigenic determinants by MHC class II molecules, the main view has been that proteins are unfolded, enzymatically cleaved into peptide lengths of about 12-25 amino acids and then loaded onto MHC class II molecules. There is, however, an alternative model stating that partially intact unfolding antigens are first bound by MHC class II molecules and then trimmed to fragments of a smaller size while remaining bound to the MHC class II molecule. In this analysis, we make the case that a considerable portion of the elutable peptide cargo belongs to this latter class.

Recent advances have shown the crucial role of histone-modifying enzymes in controlling gene activation and repression. This led to the 'histone code' hypothesis, which proposes that combinations of histone modifications work in concert to affect specific gene expression. Mounting evidence suggests that the class II transactivator modulates promoter accessibility by coordinating the recruitment of chromatin modifiers in a time-dependent fashion. MHC-II expression is exquisitely controlled by these highly specific, coordinated and dynamic interactions at the promoter.

Antigen processing and recognition is a key feature of antibacterial immune responses to intracellular bacteria. In contrast to viruses, which are primarily controlled by conventional MHC II- and MHC I-restricted CD4+ or CD8+ T cells, respectively, unconventional T cells participate additionally in antibacterial protection. These unconventional T cells include glycolipid-specific CD1-restricted T cells and phospholigand-specific gammadelta T cells. We are just beginning to understand the broad spectrum of antigen recognition and stimulation of distinct T-cell populations by bacterial pathogens. From the host perspective, a broad spectrum of different T-cell populations that recognize proteins, lipids and carbohydrates strengthens protective immunity. From the perspective of the pathogen, antigen presentation represents a bottleneck that should be exploited for evasion from, or devastation of, acquired immunity. Although several such mechanisms have been described in viral systems, few have thus far been elucidated in bacterial infections.

Antigen-presenting molecules, including MHC I, II and CD1, have central roles in the induction of T cell-mediated immunity against pathogens and tumors and also in the maintenance of tolerance towards self-antigens. The presentation of exogenously derived peptide and lipid antigens to specific T cells by professional antigen-presenting cells (pAPCs) is an essential part of both processes. Exogenous antigen loading takes place mostly within specialized endocytic and phagocytic compartments of pAPCs and targeting of antigen-presenting molecules to these intracellular compartments is mediated by highly conserved cytoplasmic sorting motifs. Recent data have revealed that the cytoplasmic tails of antigen-presenting molecules, by controlling the access of these molecules to exogenously derived antigens, have a crucially important and largely underappreciated role in the generation of tolerance and T-cell mediated immunity.

In this article we review the following important points in the antigen-presenting system: (1) the regulation of the expression of major histocompatibility complex (MHC) molecules, (2) the mechanism of cross-presentation, and (3) the interaction of antigen-presenting cells (APC) and T-cells. 1. The expression of MHC class I or class II molecules is regulated by the interaction of the MHC enhanceosome and the class II transactivator (CIITA). CIITA also regulates the gene expression of plexna-1, which encodes a semaphorin receptor, plexin-A1, that might be involved in the interaction with T-cells through an unknown ligand for plexin-A1. 2. Two pathways, a proteasome/TAP-independent pathway and a proteasome/TAP-dependent pathway, have now been identified in the cross-presentation. In the proteasome/TAP-dependent pathway, the translocon/Sec61 protein channel is an important element for the transport of antigenic peptides in phagosomes to the cytoplasm. 3. The integration of adhesion/costimulatory molecules and peptide-MHC complexes at the surface of APC creates the "immunological synapse" region, which potentiates the efficiency of APC-T-cell interactions. The peptide-MHC complexes preferentially reside in the "raft" structure or associate with tetraspanin family molecules.