MHC Molecules, Antigen Processing and Presentation

Major Histocompatibility Complex (MHC) molecules characteristics

  • The Major Histocompatibility complex is a genetic locus that encodes the glycoprotein molecules (transplantation antigens) which are responsible for tissue rejection of grafts between genetically unidentical individuals.
  • It is also the molecule that binds the peptide antigens processed by Antigen-presenting Cells and presents them to T-cells, hence they are responsible for antigen recognition by the T-cell receptors.
  • Unlike the B-cell receptors that directly interact with the antigens, the T-cell receptors have an intertwined relationship with the MHC molecule, in that T-cell receptors can only receive and bind processed antigens in form of peptides that are bound to the MHC molecule, and therefore, T-cell receptors are specific for MHC molecules.
  • In humans, the Major Histocompatibility complex is known as Human Leukocyte Antigen (HLA). There are three common MHC molecules i.e class I, class II, and class III MHC proteins.
  • The genes of the MHC exhibit genetic variability; and the MHC  has several genes for each class hence it is polygenic.
  • The MHC is also polymorphic, meaning a large number of alleles exist in the population for each of the genes.
  • Therefore, a large number of alleles exist in the population for each of the genes. Each individual inherits a restricted set of alleles from his or her parent. Sets of MHC genes tend to be inherited as a block or haplotype. There are relatively infrequent cross-over events at this locus.
  • The structure of the MHC class I have two domains that are distant from each other, made up of two parallel α helices on top of a platform that is created by a β-pleated sheet. The general structure looks like a cleft whose sides are formed by the α helices and the floor is β-sheet.
  • Generally, the MHC molecules have a broad specificity for peptide antigens and many different peptides can be presented by any given MHC allele binding a single peptide at a time.
  • The α helices forming the binding clefts are the site of the amino acid residues that are polymorphic (varying allelic forms) in MHC proteins, meaning that different alleles can bind and present different peptide antigens. For all these reasons, MHC polymorphism has a major effect on antigen recognition.
  • The function of T-cells on interaction with the MHC molecules reveals that the peptide antigens associated with class I MHC molecules are recognized by CD8+ cytotoxic T-lymphocytes (Tc cells) and MHC class-II associated with peptide antigens that are recognized by CD4+ Helper T-cells (Th cells).

Major Histocompatibility class I (MHC class I)

  • This is the first class of the MHC molecule that encodes the glycoproteins that are expressed on the surface of nearly all nucleated cells.
  • Their major function is to present antigen processed peptides to the T-cytotoxic cells by the cytosolic pathway.
  • In humans, the MHC class I protein is encoded by the HLA-A, -B, and -C genes.
  • This class of the MHC class I is made up of two chains i.e a transmembrane glycoprotein with a molecular weight of 45,000, which is noncovalently associated with a non–MHC-encoded polypeptide of molecular weight of 12,000 that is known as β2-microglobulin.
  • Class I molecules are to be found on virtually all nucleated cells in the body except on cells in the retina and brain.

Major Histocompatibility Class II (MHC class II)

  • The class II MHC genes encode glycoproteins expressed primarily on antigen-presenting cells (macrophages, dendritic cells, and B cells), where they present processed antigenic peptides to TH cells.
  • The class II proteins are encoded by the HLA-D region and the HLA-D regions have three families, DP-, DQ-, and DR-encoded molecules.
  • This class retains control of immune responsiveness and the different allelic forms of these genes confer differences in the ability to mount an immune response against a given antigen.
  • The HLA-D locus-encoded proteins are made up of two noncovalently associates transmembrane glycoproteins with a molecular weight of 33,000 and 29,000 respectively.
  • They have a restricted tissue distribution and they are chiefly found on macrophages, dendritic cells, B-cells, and other antigen-presenting cells. They are also expressed on other cells such as endothelial cells and/or epithelial cells is induced by IFN-γ

Major Histocompatibility Class III (MHC Class III)

  • Class III MHC genes encode for various secreted proteins that have immune functions, including the component of the complement system and molecules that are involved in inflammation such as cytokines.

Antigen Processing and Presentation

  • The recognition of proteins antigens by T-lymphocytes required that the antigens be processes by Antigen-presenting Cells, then displayed within the cleft of the MHC molecules on the membrane of the cell.
  • This involves the degradation of the protein antigens into peptides, a process known as antigen processing.
  • When the antigen has been processed and degraded into peptides, it then associates with MHC molecules within the cell cytoplasm forming a peptide-MHC complex. This complex is then transported to the membrane, where it is displayed by a process of antigen presentation.
  • The MHC Class I and class II MHC molecules associate with peptides that have been processed in different intracellular compartments.
  • The Class I MHC molecules bind peptides derived from endogenous antigens that have been processed within the cytoplasm of the cell such as tumor proteins, bacterial proteins, or viral proteins, or cellular proteins, and processed within the cytosolic pathway.
  • Class II MHC molecules bind peptides derived from exogenous antigens that are internalized by phagocytosis or endocytosis and processed within the endocytic pathway.

MHC Class I and II Pathways

A. Cytosolic pathway: Endogenous antigen

  • This is the pathway that processes and presents the endogenous antigen using the Class I MHC molecules.
  • The antigen proteins are degraded intracellularly to short peptides by a cytosolic proteolytic system that is present in all cells. These proteins targeted for proteolysis have a small protein known as ubiquitin attached to them.
  • The ubiquitin-protein conjugate then gets degraded by a multifunctional protease complex known as a proteasome.
  • Each proteasome is a large (26S), cylindrical particle that consists of four rings of protein subunits and a central channel of 10–50 Å diameter.
  • The proteasome can cleave peptide bonds between 2-3 different amino acid combinations in an ATP-dependent process.
  • Degradation of the ubiquitin-protein complex takes place in the central hollow of the proteasome.
  • The peptides are then transported from the cytosol to the rough endoplasmic reticulum. This is enabled by the transporter protein, designated TAP (transporter associated with antigen processing) is a membrane-spanning heterodimer consisting of two proteins: TAP1 and TAP2.
  • The TAP1 and TAP2 proteins each have a domain projecting into the lumen of the Rough endoplasmic reticulum (RER), and an ATP-binding domain that extends into the cytosol.
  • Both TAP1 and TAP2 belong to the family of ATP-binding cassette proteins found in the membranes of many cells, including bacteria.
  • They mediate ATP-dependent transport of amino acids, sugars, ions, and peptides.
  • the peptides that are generated in the cytosol by the proteasome, are translocated into the Rough Endoplasmic Reticulum (RER) by TAP proteins by a process that utilizes hydrolyzed ATP. TAP proteins have a high affinity for peptides sizes of 8-10 amino acids, the optimum length for class I MHC binding.
  • Additionally, TAP proteins favor peptides with hydrophobic or basic carboxyl-terminal amino acids, which is the preferred anchor residue for class I MHC molecule, and therefore, TAP is optimized to transport peptides that will interact with class I MHC molecules.
  • Next, the peptides that are assembled with class I MHC are aided by chaperone molecules that facilitate the folding of polypeptides.
  • The alpha and beta-2-microglobulin components of the class I MHC molecules are synthesized on the polysomes along the rough endoplasmic reticulum. These components are assembled into a stable class I MHC molecules complex that can exit the RER requiring the presence of a peptide in the binding groove of the class molecule.
  • The first chaperone involved is known as calnexin, which is a resident membrane protein of the endoplasmic reticulum. Calnexin associates with the class I α chain and promotes its folding. When the Beta-2-microglobulin binds to the α chain, the calnexin is released, and the class I molecule associates with the chaperone calreticulin and with tapasin.
  • Tapasin is a TAP-associated protein that brings the TAP transporter into proximity with the class I molecule and allows it to acquire an antigenic peptide. The physical association of the α chain-beta-2-microglobulin heterodimer with the TAP protein promotes peptide capture by the class I molecule before the peptides are exposed to the RER.
  • The peptides not bound by class I molecules are rapidly degraded.
  • After binding, the class I molecule displays increased stability and can dissociate from calreticulin and tapasin, exit from the RER, and proceed to the cell surface via the Golgi.
  • An additional chaperone protein, ERp57, associates with calnexin and calreticulin complexes. The precise role of this resident endoplasmic reticulum protein in the class I peptide assembly and loading process has not yet been defined, but it is thought to contribute to the formation of disulfide bonds during the maturation of class I chains.

B. Endocytic Pathway: Exogenous antigen

Antigen-presenting cells can internalize antigen by phagocytosis, endocytosis, or both. Macrophages internalize antigen by both phagocytosis and endocytosis. Most of the other APCs are poorly phagocytic and can only internalize the antigen by pinocytosis or endocytosis, whereas most other APCs are not phagocytic and therefore they internalize the exogenous antigen only by endocytosis of by pinocytosis. B-cells which are also APCs internalizes the antigen effectively by receptor-mediated endocytosis using antigen-specific membrane antibody receptors.

  • When the exogenous antigen is internalized, it is degraded into peptides in the compartments of the endocytic processing pathway.
  • The breaking down of antigens into peptides takes 1-3 hours to transverse the endocytic pathway and appear at the cell surface in the form of a peptide-class II MHC complex.
  • In this pathway, three acidic compartments: early endosome (pH 6.0-6.5), late endosome or endolysosomes (pH 5.0-6.0); and lysosomes (pH 4.5-5.0). The internalized antigen moves from the early to late endosomes and later to the lysosomes where they encounter the hydrolytic enzyme, with a decreasing pH in each compartment.
  • the lysosomes have a unique collection of 40 acid-dependent hydrolases including proteases, nucleases, glycosidases,  lipases, phospholipases, and phosphatases. Within the compartments of the endocytic pathway, the antigen is degraded into oligopeptide made up of 13-18 residues, that bind to class II MHC molecule. The hydrolytic enzymes are active in low Ph, they inhibit antigen processing chemical agents that may increase the compartment pH and that of protease inhibitors.
  • Movement of the peptides from one compartment to the next has been associated with small transport vesicles.
  • After getting to the final compartments, they return to the cell periphery fusing with the plasma membrane, enabling the recycling of surface receptors.
  • The antigen-presenting cells express both MHCI and MHC II molecules, therefore to prevent binding of MHC II to the same set of antigenic peptides as those of class I MHC, some mechanisms must exist to prevent this.
  • When the MHC II has been synthesized within the RER, three pairs of class II chains associate with a preassembled trimer of a protein known as an invariant chain (Ii, CD74). The trimeric protein interacts with the peptide-binding cleft of the class II MHC molecules, preventing any endogenously derived peptides from binding to the cleft while the MHC class II remains within the RER.
  • The invariant chain is also involved in the folding of class II MHC and its chains, the exit from the RER, and routing it to the endocytic processing pathway from the trans-Golgi network into the endocytic vesicles.
  • Secondly, the peptides assemble with class II MHC molecule by displacing CLIP (Class-II associated invariant chain peptide). Most of class II MHC-invariant chain complexes are transported from the RER where they are formed through the Golgi complex and trans-Golgi network, and then through the endocytic pathway, moving from early endosomes to late endosomes then finally to the lysosomes.
  • This increases the proteolytic activity from each compartment to the next.
  • This causes the degradation of the invariant chain gradually, leaving a short fragment of the invariant chain known as the CLIP (Class II-associated invariant chain peptide) that remains bound to the class II molecule after the invariant chain has been cleaved with the endosomal compartment.
  • CLIP occupies the peptide-binding groove of the class II MHC molecule, preventing premature binding of the antigenic peptide. HLA-DM molecule catalyzes the exchange of CLIP with the antigenic peptides. It is found in mammalian cells, mice, and rabbits. HLA-DM is neoclassical and nonpolymorphic.
  • When the HLA-DM and class II CLIP complex react, it facilitates the exchange of CLIP for another peptide but in the presence of HLA-DO, it can bind to HLA-DM reducing the efficiency of the exchange reaction.
  • The HLA-DO which has a similar structure as that of HLA-DM helps to modulate the function of HLA-DM, however, the function is obscure.

Presentation of Non-peptide antigens

  • Nonpeptide antigens are also recognized by the immune system, these are antigens that are derived from infectious agents such as Mycobacterium tuberculosis.
  • These antigens are recognized by T-cell Receptors known as δγ-TCR (T-cell receptor are dimers of αβ and δγ) which are derived from glycolipid of bacterial pathogens such as Mycobacterium tuberculosis.
  • These nonprotein antigens are presented by members of the CD1 family of nonclassical class I molecules.
  • The CD1 family of molecules associates with β2-microglobulin and it has its structure similar to that of MHC I molecules. It has 5 genes that encode for human CD1 molecules (CD1A-E, encoding the gene products CD1a-d, no E has been identified yet. These genes are located on the chromosomes and not on MHC I.
  • They are classified into two groups based on sequence homology. Group 1 includes CD1A, B, C, and E; CD1D is in group 2. All mammalian species have CD1 genes, although the number varies. Rodents have only group 2 CD1 genes, whereas rabbits, like humans, have five genes, including both group 1 and 2 types.
  • The sequence identity of CD1 with classical class I molecules is considerably lower than the identity of the class I molecules with each other. CD1D1 as compared to class I MHC shows that the antigen-binding groove of Cd1d1 is deeper and more voluminous than that of class I MHC molecule.

Clinical Significance of Antigen processing and presentation

  • Sometimes the antigen-presenting cells (APCs) can deliver self-antigens which cause autoimmune diseases. When the self-antigens are presented to the T-cells, it initiates an immune reaction against our own tissues, causing autoimmune disorders such as Graves Disease, rheumatoid arthritis.
  • In Graves’ disease, TSHR (Thyroid-stimulating hormone receptors) acts as the self-antigen, which is presented to T-cells activating B-cells which produce autoantibodies against TSHRs in the thyroid. This leads to the activation of TSHRs causing hyperthyroidism and leading to goiter.

References and Source

  • Immunology by Kuby, 5th Edition
  • Microbiology by Prescott, 5th Edition
  • Lippincott’s Illustration Review in Immunology
  • Comprehensive immunology: Antigens and Immunogens by Frederic C. McDuffie
  • Medical Microbiology by Jawertz, 23rd Edition
  • Immunobiology: The Immune System in Health and Disease. 5th edition: Chapter 3, Antigen Recognition by B-cell and T-cell Receptors
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