Where are mhc molecules located on a cell

The diverse responses of T cells are collectively called cell-mediated immune reactions. This is to distinguish them from antibody responses, which, of course, also depend on cells (B cells). Like antibody responses, T cell responses are exquisitely antigen-specific, and they are at least as important as antibodies in defending vertebrates against infection. Indeed, most adaptive immune responses, including antibody responses, require helper T cells for their initiation. Most importantly, unlike B cells, T cells can help eliminate pathogens that reside inside host cells. Much of the rest of this chapter is concerned with how T cells accomplish this feat.

T cell responses differ from B cell responses in at least two crucial ways. First, T cells are activated by foreign antigen to proliferate and differentiate into effector cells only when the antigen is displayed on the surface of antigen-presenting cells in peripheral lymphoid organs. The T cells respond in this manner because the form of antigen they recognize is different from that recognized by B cells. Whereas B cells recognize intact antigen, T cells recognize fragments of protein antigens that have been partly degraded inside the antigen-presenting cell. The peptide fragments are then carried to the surface of the presenting cell on special molecules called MHC proteins, which present the fragments to T cells. The second difference is that, once activated, effector T cells act only at short range, either within a secondary lymphoid organ or after they have migrated into a site of infection. They interact directly with another cell in the body, which they either kill or signal in some way (we shall refer to such cells as target cells). Activated B cells, by contrast, secrete antibodies that can act far away.

There are two main classes of T cells—cytotoxic T cells and helper T cells. Effector cytotoxic T cells directly kill cells that are infected with a virus or some other intracellular pathogen. Effector helper T cells, by contrast, help stimulate the responses of other cells—mainly macrophages, B cells, and cytotoxic T cells.

In this section, we describe these two classes of T cells and their respective functions. We discuss how they recognize foreign antigens on the surface of antigen-presenting cells and target cells and consider the crucial part played by MHC proteins in the recognition process. Finally, we describe how T cells are selected during their development in the thymus to ensure that only cells with potentially useful receptors survive and mature. We begin by considering the nature of the cell-surface receptors that T cells use to recognize antigen.

T Cell Receptors Are Antibodylike Heterodimers

Because T cell responses depend on direct contact with an antigen-presenting cell or a target cell, the antigen receptors made by T cells, unlike antibodies made by B cells, exist only in membrane-bound form and are not secreted. For this reason, T cell receptors were difficult to isolate, and it was not until the 1980s that they were first identified biochemically. On both cytotoxic and helper T cells, the receptors are similar to antibodies. They are composed of two disulfide-linked polypeptide chains (called α and β), each of which contains two Ig-like domains, one variable and one constant (Figure 24-42A). Moreover, the three-dimensional structure of the extracellular part of a T cell receptor has been determined by x-ray diffraction, and it looks very much like one arm of a Y-shaped antibody molecule (Figure 24-42B).

Figure 24-42

A T cell receptor heterodimer. (A) Schematic drawing showing that the receptor is composed of an α and a β polypeptide chain. Each chain is about 280 amino acids long and has a large extracellular part that is folded into two Ig-like domains—one (more...)

The pools of gene segments that encode the α and β chains are located on different chromosomes. Like antibody heavy-chain pools, the T cell receptor pools contain separate V, D, and J gene segments, which are brought together by site-specific recombination during T cell development in the thymus. With one exception, all the mechanisms used by B cells to generate antibody diversity are also used by T cells to generate T cell receptor diversity. Indeed, the same V(D)J recombinase is used, including the RAG proteins discussed earlier. The mechanism that does not operate in T cell receptor diversification is antigen-driven somatic hypermutation. Thus, the affinity of the receptors remains low (Ka ~ 105-107 liters/mole), even late in an immune response. We discuss later how various co-receptors and cell-cell adhesion mechanisms greatly strengthen the binding of a T cell to an antigen-presenting cell or a target cell, helping to compensate for the low affinity of the T cell receptors.

A small minority of T cells, instead of making α and β chains, make a different but related type of receptor heterodimer, composed of γ and δ chains. These cells arise early in development and are found mainly in epithelia (in the skin and gut, for example). Their functions are uncertain, and we shall not discuss them further.

As with antigen receptors on B cells, the T cell receptors are tightly associated in the plasma membrane with a number of invariant membrane-bound proteins that are involved in passing the signal from an antigen-activated receptor to the cell interior. We discuss these proteins in more detail later. First, however, we need to consider how cytotoxic and helper T cells function and the special ways in which they recognize foreign antigen.

Antigen-Presenting Cells Activate T Cells

Before cytotoxic or helper T cells can kill or help their target cells, respectively, they must be activated to proliferate and differentiate into effector cells. This activation occurs in peripheral lymphoid organs on the surface of antigen-presenting cells that display foreign antigen complexed with MHC proteins on their surface.

There are three main types of antigen-presenting cells in peripheral lymphoid organs that can activate T cells—dendritic cells, macrophages, and B cells. The most potent of these are dendritic cells (Figure 24-43), whose only known function is to present foreign antigens to T cells. Immature dendritic cells are located in tissues throughout the body, including the skin, gut, and respiratory tract. When they encounter invading microbes at these sites, they endocytose the pathogens or their products and carry them via the lymph to local lymph nodes or gut-associated lymphoid organs. The encounter with a pathogen induces the dendritic cell to mature from an antigen-capturing cell to an antigen-presenting cell that can activate T cells (see Figure 24-5).

Figure 24-43

Immunofluorescence micrograph of a dendritic cell in culture. These crucial antigen-presenting cells derive their name from their long processes, or “dendrites.” The cell has been labelled with a monoclonal antibody that recognizes a surface (more...)

Antigen-presenting cells display three types of protein molecules on their surface that have a role in activating a T cell to become an effector cell: (1) MHC proteins, which present foreign antigen to the T cell receptor, (2) costimulatory proteins, which bind to complementary receptors on the T cell surface, and (3) cell-cell adhesion molecules, which enable a T cell to bind to the antigen-presenting cell for long enough to become activated (Figure 24-44).

Figure 24-44

Three types of proteins on the surface of an antigen-presenting cell involved in activating a T cell. The invariant polypeptide chains that are stably associated with the T cell receptor are not shown.

Before discussing the role of MHC proteins in presenting antigen to T cells, we consider the functions of the two major classes of T cells.

Effector Cytotoxic T Cells Induce Infected Target Cells to Kill Themselves

Cytotoxic T cells provide protection against intracellular pathogens such as viruses and some bacteria and parasites that multiply in the host-cell cytoplasm, where they are sheltered from attack by antibodies. They provide this protection by killing the infected cell before the microbes can proliferate and escape from the infected cell to infect neighboring cells.

Once a cytotoxic T cell has been activated by an infected antigen-presenting cell to become an effector cell, it can kill any target cell infected with the same pathogen. When the effector T cell recognizes a microbial antigen on the surface of an infected target cell, it focuses its secretory apparatus on the target. We can observe this behavior by studying effector T cells bound to their targets: when labeled with anti-tubulin antibodies, the T cell centrosome is seen to be oriented toward the point of contact with the target cell (Figure 24-45). Moreover, antibody labeling shows that talin and other proteins that help link cell-surface receptors to cortical actin filaments are concentrated in the cortex of the T cell at the contact site. The aggregation of T cell receptors at the contact site apparently leads to a local alteration in the actin filaments in the cell cortex. A microtubule-dependent mechanism then moves the centrosome and its associated Golgi apparatus toward the contact site, focusing the killing machinery on the target cell. A similar cytoskeletal polarization is seen when an effector helper T cell interacts functionally with a target cell.

Figure 24-45

Effector cytotoxic T cells killing target cells in culture. (A) Electron micrograph showing an effector cytotoxic T cell binding to the target cell. The cytotoxic T cells were obtained from mice immunized with the target cells, which are foreign tumor (more...)

Once bound to its target cell, a cytotoxic T cell can employ at least two strategies to kill the target, both of which operate by inducing the target cell to kill itself by undergoing apoptosis (discussed in Chapter 17). In killing an infected target cell, the cytotoxic T cell usually releases a pore-forming protein called perforin, which is homologous to the complement component C9 (see Figure 25-42) and polymerizes in the target cell plasma membrane to form transmembrane channels. Perforin is stored in secretory vesicles of the cytotoxic T cell and is released by local exocytosis at the point of contact with the target cell. The secretory vesicles also contain serine proteases, which are thought to enter the target cell cytosol through the perforin channels. One of the proteases, called granzyme B, cleaves, and thereby activates, one or more members of the caspase family of proteases that mediate apoptosis. These caspases then activate other caspases, producing a proteolytic cascade that helps kill the cell (discussed in Chapter 17) (Figure 24-46A). Mice in which the perforin gene is inactivated cannot generate microbe-specific cytotoxic T cells and show increased susceptibility to certain viral and intracellular bacterial infections.

Figure 24-46

Two strategies by which effector cytotoxic T cells kill their target cells. (A) The cytotoxic T cell (TC) releases perforin and proteolytic enzymes onto the surface of an infected target cell by localized exocytosis. The high concentration of Ca2+ in (more...)

In the second killing strategy, the cytotoxic T cell also activates a death-inducing caspase cascade in the target cell but does it less directly. A homotrimeric protein on the cytotoxic T cell surface called Fas ligand binds to transmembrane receptor proteins on the target cell called Fas. The binding alters the Fas proteins so that their clustered cytosolic tails recruit procaspase-8 into the complex via an adaptor protein. The recruited procaspase-8 molecules cross-cleave and activate each other to begin the caspase cascade that leads to apoptosis (Figure 24-46B). Cytotoxic T cells apparently use this killing strategy to help contain an immune response once it is well underway, by killing excessive effector lymphocytes, especially effector T cells: if the gene encoding either Fas or Fas ligand is inactivated by mutation, effector lymphocytes accumulate in vast numbers in the spleen and lymph nodes, which become enormously enlarged.

Effector Helper T Cells Help Activate Macrophages, B Cells, and Cytotoxic T Cells

In contrast to cytotoxic T cells, helper T cells are crucial for defense against both extracellular and intracellular pathogens. They help stimulate B cells to make antibodies that help inactivate or eliminate extracellular pathogens and their toxic products. They activate macrophages to destroy any intracellular pathogen multiplying within the macrophage's phagosomes, and they help activate cytotoxic T cells to kill infected target cells.

Once a helper T cell has been activated by an antigen-presenting cell to become an effector cell, it can then help activate other cells. It does this both by secreting a variety of cytokines and by displaying costimulatory proteins on its surface. When activated by an antigen-presenting cell, a naïve helper T cell can differentiate into either of two distinct types of effector helper cell, called TH1 and TH2. TH1 cells mainly help activate macrophages and cytotoxic T cells, whereas TH2 cells mainly help activate B cells (Figure 24-47). As we discuss later, the nature of the invading pathogen and the types of innate immune responses it elicits largely determine which type of helper T cell develops. This, in turn, determines the nature of the adaptive immune responses mobilized to fight the invaders.

Figure 24-47

Differentiation of naïve helper T cells into either TH1 or TH2 effector helper cells in a peripheral lymphoid organ. The antigen-presenting cell and the characteristics of the pathogen that activated it mainly determine which type of effector (more...)

Before discussing how helper T cells function to activate macrophages, cytotoxic T cells, or B cells, we need to consider the crucial role of MHC proteins in T cell responses.

T Cells Recognize Foreign Peptides Bound to MHC Proteins

As discussed earlier, both cytotoxic T cells and helper T cells are initially activated in peripheral lymphoid organs by recognizing foreign antigen on the surface of an antigen-presenting cell, usually a dendritic cell. The antigen is in the form of peptide fragments that are generated by the degradation of foreign protein antigens inside the antigen-presenting cell. The recognition process depends on the presence in the antigen-presenting cell of MHC proteins, which bind these fragments, carry them to the cell surface, and present them there, along with a co-stimulatory signal, to the T cells. Once activated, effector T cells then recognize the same peptide-MHC complex on the surface of the target cell they influence, which may be a B cell, a cytotoxic T cell, or an infected macrophage in the case of a helper T cell, or a virus-infected cell in the case of a cytotoxic T cell.

MHC proteins are encoded by a large complex of genes called the major histocompatibility complex (MHC). There are two main structurally and functionally distinct classes of MHC proteins: class I MHC proteins, which present foreign peptides to cytotoxic T cells, and class II MHC proteins, which present foreign peptides to helper cells (Figure 24-48).

Figure 24-48

Recognition by T cells of foreign peptides bound to MHC proteins. Cytotoxic T cells recognize foreign peptides in association with class I MHC proteins, whereas helper T cells recognize foreign peptides in association with class II MHC proteins. In both (more...)

Before examining the different mechanisms by which protein antigens are processed for display to the two main classes of T cells, we must look more closely at the MHC proteins themselves, which have such an important role in T cell function.

MHC Proteins Were Identified in Transplantation Reactions Before Their Functions Were Known

MHC proteins were initially identified as the main antigens recognized in transplantation reactions. When organ grafts are exchanged between adult individuals, either of the same species (allografts) or of different species (xenografts), they are usually rejected. In the 1950s, skin grafting experiments between different strains of mice demonstrated that graft rejection is an adaptive immune response to the foreign antigens on the surface of the grafted cells. Rejection is mediated mainly by T cells, which react against genetically “foreign” versions of cell-surface proteins called histocompatibility molecules (from the Greek word histos, meaning “tissue”). The MHC proteins encoded by the clustered genes of the major histocompatibility complex (MHC) are by far the most important of these. MHC proteins are expressed on the cells of all higher vertebrates. They were first demonstrated in mice, where they are called H-2 antigens (histocompatibility-2 antigens). In humans they are called HLA antigens (human-leucocyte-associated antigens) because they were first demonstrated on leucocytes (white blood cells).

Three remarkable properties of MHC proteins baffled immunologists for a long time. First, MHC proteins are overwhelmingly the preferred antigens recognized in T-cell-mediated transplantation reactions. Second, an unusually large fraction of T cells are able to recognize foreign MHC proteins: whereas fewer than 0.001% of an individual's T cells respond to a typical viral antigen, more than 0.1% of them respond to a single foreign MHC antigen. Third, some of the genes that code for MHC proteins are the most polymorphic known in higher vertebrates. That is, within a species, there is an extraordinarily large number of alleles (alternative forms of the same gene) present (in some cases more than 200), without any one allele predominating. As each individual has at least 12 genes encoding MHC proteins (see later), it is very rare for two unrelated individuals to have an identical set of MHC proteins. This makes it very difficult to match donor and recipient for organ transplantation unless they are closely related.

Of course, a vertebrate does not need to protect itself against invasion by foreign vertebrate cells. So the apparent obsession of its T cells with foreign MHC proteins and the extreme polymorphism of these molecules were a great puzzle. The puzzle was solved only after it was discovered that (1) MHC proteins bind fragments of foreign proteins and display them on the surface of host cells for T cells to recognize, and (2) T cells respond to foreign MHC proteins in the same way they respond to self MHC proteins that have foreign antigen bound to them.

Class I and Class II MHC Proteins Are Structurally Similar Heterodimers

Class I and class II MHC proteins have very similar overall structures. They are both transmembrane heterodimers with extracellular N-terminal domains that bind antigen for presentation to T cells.

Class I MHC proteins consist of a transmembrane α chain, which is encoded by a class I MHC gene, and a small extracellular protein called β2-microglobulin (Figure 24-49A). The β2-microglobulin does not span the membrane and is encoded by a gene that does not lie in the MHC gene cluster. The α chain is folded into three extracellular globular domains (α1, α2, α3), and the α3 domain and the β2-microglobulin, which are closest to the membrane, are both similar to an Ig domain. The two N-terminal domains of the α chain, which are farthest from the membrane, contain the polymorphic (variable) amino acids that are recognized by T cells in transplantation reactions. These domains bind a peptide and present it to cytotoxic T cells.

Figure 24-49

Class I and class II MHC proteins. (A) The α chain of the class I molecule has three extracellular domains, α1, α2 and α3, encoded by separate exons. It is noncovalently associated with a smaller polypeptide chain, β (more...)

Like class I MHC proteins, class II MHC proteinsare heterodimers with two conserved Ig-like domains close to the membrane and two polymorphic (variable) N-terminal domains farthest from the membrane. In these proteins, however, both chains (α and β) are encoded by genes within the MHC, and both span the membrane (Figure 24-49B). The two polymorphic domains bind a peptide and present it to helper T cells.

The presence of Ig-like domains in class I and class II proteins suggests that MHC proteins and antibodies have a common evolutionary history. The locations of the genes that encode class I and class II MHC proteins in humans are shown in Figure 24-50, where we illustrate how an individual can make six types of class I MHC proteins and more than six types of class II proteins.

Figure 24-50

Human MHC genes. This simplified schematic drawing shows the location of the genes that encode the transmembrane subunits of class I (light green) and class II (dark green) MHC proteins. The genes shown encode three types of class I proteins (HLA-A, HLA-B, (more...)

In addition to the classic class I MHC proteins, there are many nonclassical class I MHC proteins, which form dimers with β2-microglobulin. These proteins are not polymorphic, but some of them present specific microbial antigens, including some lipids and glycolipids, to T cells. The functions of most of them, however, are unknown.

An MHC Protein Binds a Peptide and Interacts with a T Cell Receptor

Any individual can make only a small number of different MHC proteins, which together must be able to present peptide fragments from almost any foreign protein to T cells. Thus, unlike an antibody molecule, each MHC protein has to be able to bind a very large number of different peptides. The structural basis for this versatility has emerged from x-ray crystallographic analyses of MHC proteins.

As shown in Figure 24-51A, a class I MHC protein has a single peptide-binding site located at one end of the molecule, facing away from the plasma membrane. This site consists of a deep groove between two long α helices; the groove narrows at both ends so that it is only large enough to accommodate an extended peptide about 8–10 amino acids long. In fact, when a class I MHC protein was first analyzed by x-ray crystallography in 1987, this groove contained bound peptides that had co-crystallized with the MHC protein (Figure 24-51B), suggesting that once a peptide binds to this site it does not normally dissociate.

Figure 24-51

The three-dimensional structure of a human class I MHC protein as determined by x-ray diffraction analysis of crystals of the extracellular part of the molecule. The extracellular part of the protein was cleaved from the transmembrane segment by the proteolytic (more...)

A typical peptide binds in the groove of a class I MHC protein in an extended conformation, with its terminal amino group bound to an invariant pocket at one end of the groove and its terminal carboxyl group bound to an invariant pocket at the other end of the groove. Other amino acids (called “anchor amino acids”) in the peptide bind to “specificity pockets” in the groove formed by polymorphic portions of the MHC protein (Figure 24-52). The side chains of other amino acids of the peptide point outward, in a position to be recognized by receptors on cytotoxic T cells. Because the conserved pockets at the ends of the binding groove recognize features of the peptide backbone that are common to all peptides, each allelic form of a class I MHC protein can bind a large variety of peptides of diverse sequence. At the same time, the differing specificity pockets along the groove, which bind particular amino acid side chains of the peptide, ensure that each allelic form binds and presents a distinct characteristic set of peptides. Thus, the six types of class I MHC proteins in an individual can present a broad range of foreign peptides to the cytotoxic T cells, but in each individual they do so in slightly different ways.

Figure 24-52

A peptide bound in the groove of a class I MHC protein. (A) Schematic drawing of a top view of the groove. The peptide backbone is shown as a string of red balls, each of which represents one of the nine amino acids of the peptide. The terminal amino (more...)

Class II MHC proteins have a three-dimensional structure that is very similar to that of class I proteins, but their antigen-binding groove does not narrow at the ends, so it can accommodate longer peptides, which are usually 13–17 amino acids long. Moreover, the peptide is not bound at its ends. It is held in the groove by parts of its peptide backbone that bind to invariant pockets formed by conserved amino acids that line all class II MHC peptide-binding grooves, as well as by the side chains of anchor amino acids that bind to variable specificity pockets in the groove (Figure 24-53). A class II MHC binding groove can accommodate a more heterogeneous set of peptides than can a class I MHC groove. Thus, although an individual makes only a small number of types of class II proteins, each with its own unique peptide-binding groove, together these proteins can bind and present an enormous variety of foreign peptides to helper T cells, which have a crucial role in almost all adaptive immune responses.

Figure 24-53

A peptide bound in the groove of a class II MHC protein. (A) Schematic drawing similar to that shown in Figure 24-52A. Note that the ends of the peptide are not tightly bound and extend beyond the cleft. The peptide is held in the groove by interactions (more...)

The way in which the T cell receptor recognizes a peptide fragment bound to an MHC protein is revealed by x-ray crystallographic analyses of complexes formed between a soluble receptor and a soluble MHC protein with peptide in its binding groove. (The soluble proteins for these experiments are produced by recombinant DNA technology.) In each case studied, the T cell receptor fits diagonally across the peptide-binding groove and binds through its Vα and Vβ hypervariable loops to both the walls of the groove and the peptide (Figure 24-54). Soluble MHC-peptide complexes are now widely used to detect T cells with a particular specificity; they are usually cross-linked into tetramers to increase their avidity for T cell receptors.

Figure 24-54

The interaction of a T cell receptor with a viral peptide bound to a class I MHC protein. (A) Schematic view of the hypervariable loops of the Vα and Vβ domains of the T cell receptor interacting with the peptide and the walls of the peptide-binding (more...)

MHC Proteins Help Direct T Cells to Their Appropriate Targets

Class I MHC proteins are expressed on virtually all nucleated cells. This is presumably because effector cytotoxic T cells must be able to focus on and kill any cell in the body that happens to become infected with an intracellular microbe such as a virus. Class II proteins, by contrast, are normally confined largely to cells that take up foreign antigens from the extracellular fluid and interact with helper T cells. These include dendritic cells, which initially activate helper T cells, as well as the targets of effector helper T cells, such as macrophages and B cells. Because dendritic cells express both class I and class II MHC proteins, they can activate both cytotoxic and helper T cells.

It is important that effector cytotoxic T cells focus their attack on cells that make the foreign antigens (such as viral proteins), while helper T cells focus their help mainly on cells that have taken up foreign antigens from the extracellular fluid. Since the former type of target cell is always a menace, while the latter type is essential for the body's immune defenses, it is vitally important that T cells never confuse the two target cells and misdirect their cytotoxic and helper functions. Therefore, in addition to the antigen receptor that recognizes a peptide-MHC complex, each of the two major classes of T cells also expresses a co-receptor that recognizes a separate, invariant part of the appropriate class of MHC protein. These two co-receptors, called CD4 and CD8, help direct helper T cells and cytotoxic T cells, respectively, to their appropriate targets, as we now discuss. The properies of class I and class II MHC proteins are compared in Table 24-2.

Table 24-2

Properties of Human Class I and Class II MHC Proteins.

CD4 and CD8 Co-receptors Bind to Nonvariable Parts of MHC Proteins

The affinity of T cell receptors for peptide-MHC complexes on an antigen-presenting cell or target cell is usually too low to mediate a functional interaction between the two cells by itself. T cells normally require accessory receptors to help stabilize the interaction by increasing the overall strength of the cell-cell adhesion. Unlike T cell receptors or MHC proteins, the accessory receptors do not bind foreign antigens and are invariant.

When accessory receptors also have a direct role in activating the T cell by generating their own intracellular signals, they are called co-receptors. The most important and best understood of the co-receptors on T cells are the CD4 and CD8 proteins, both of which are single-pass transmembrane proteins with extracellular Ig-like domains. Like T cell receptors, they recognize MHC proteins, but, unlike T cell receptors, they bind to nonvariable parts of the protein, far away from the peptide-binding groove. CD4 is expressed on helper T cells and binds to class II MHC proteins, whereas CD8 is expressed on cytotoxic T cells and binds to class I MHC proteins (Figure 24-55). Thus, CD4 and CD8 contribute to T cell recognition by helping to focus the cell on particular MHC proteins, and thus on particular types of cells—helper T cells on dendritic cells, macrophages, and B cells, and cytotoxic cells on any nucleated host cell displaying a foreign peptide on a class I MHC protein. The cytoplasmic tail of these transmembrane proteins is associated with a member of the Src family of cytoplasmic tyrosine protein kinases called Lck, which phosphorylates various intracellular proteins on tyrosines and thereby participates in the activation of the T cell. Antibodies to CD4 and CD8 are widely used as tools to distinguish between the two main classes of T cells, in both humans and experimental animals.

Figure 24-55

CD4 and CD8 co-receptors on the surface of T cells. Cytotoxic T cells (TC) express CD8, which recognizes class I MHC proteins, whereas helper T cells (TH) express CD4, which recognizes class II MHC proteins. Note that the co-receptors bind to the same (more...)

Ironically, the AIDS virus (HIV) makes use of CD4 molecules (as well as chemokine receptors) to enter helper T cells. It is the eventual depletion of helper T cells that renders AIDS patients susceptible to infection by microbes that are not normally dangerous. As a result, most AIDS patients die of infection within several years of the onset of symptoms, unless they are treated with a combination of powerful anti-HIV drugs. HIV also uses CD4 and chemokine receptors to enter macrophages, which also have both of these receptors on their surface.

Before a cytotoxic or helper T cell can recognize a foreign protein, the protein has to be processed inside an antigen-presenting cell or target cell so that it can be displayed as peptide-MHC complexes on the cell surface. We first consider how a virus-infected antigen-presenting cell or target cell processes viral proteins for presentation to a cytotoxic T cell. We then discuss how ingested foreign proteins are processed for presentation to a helper T cell.

Cytotoxic T Cells Recognize Fragments of Foreign Cytosolic Proteins in Association with Class I MHC Proteins

One of the first, and most dramatic, demonstrations that MHC proteins present foreign antigens to T cells came from an experiment performed in the 1970s. It was found that effector cytotoxic T cells from a virus-infected mouse could kill cultured cells infected with the same virus only if these target cells expressed some of the same class I MHC proteins as the infected mouse (Figure 24-56). This experiment demonstrated that the T cells of any individual that recognize a specific antigen do so only when that antigen is associated with the allelic forms of MHC proteins expressed by that individual, a phenomenon known as MHC restriction.

Figure 24-56

The classic experiment showing that an effector cytotoxic T cell recognizes some aspect of the surface of the host target cell in addition to a viral antigen. Mice of strain X are infected with virus A. Seven days later, the spleens of these mice contain (more...)

The chemical nature of the viral antigens recognized by cytotoxic T cells was not discovered for another 10 years. In experiments on cells infected with influenza virus, it was unexpectedly found that some of the effector cytotoxic T cells activated by the virus specifically recognize internal proteins of the virus that would not be accessible in the intact virus particle. Subsequent evidence indicated that the T cells were recognizing degraded fragments of the internal viral proteins that were bound to class I MHC proteins on the infected cell surface. Because a T cell can recognize tiny amounts of antigen (as few as one hundred peptide-MHC complexes), only a small fraction of the fragments generated from viral proteins have to bind to class I MHC proteins and get to the cell surface to attract an attack by an effector cytotoxic T cell.

The viral proteins are synthesized in the cytosol of the infected cell. As discussed in Chapter 3, proteolytic degradation in the cytosol is mainly mediated by an ATP- and ubiquitin-dependent mechanism that operates in proteasomes—large proteolytic enzyme complexes constructed from many different protein subunits. Although all proteasomes are probably able to generate peptide fragments that can bind to class I MHC proteins, some proteasomes are thought to be specialized for this purpose, as they contain two subunits that are encoded by genes located within the MHC chromosomal region. Even bacterial proteasomes cut proteins into peptides of about the length that fits into the groove of a class I MHC protein, suggesting that the MHC groove evolved to fit this length of peptide.

How do peptides generated in the cytosol make contact with the peptide-binding groove of class I MHC proteins in the lumen of the endoplasmic reticulum (Figure 24-57)? The answer was discovered through observations on mutant cells in which class I MHC proteins are not expressed at the cell surface but are instead degraded within the cell. The mutant genes in these cells proved to encode subunits of a protein belonging to the family of ABC transporters, which we discuss in Chapter 11. This transporter protein is located in the ER membrane and uses the energy of ATP hydrolysis to pump peptides from the cytosol into the ER lumen. The genes encoding its two subunits are in the MHC chromosomal region, and, if either gene is inactivated by mutation, cells are unable to supply peptides to class I MHC proteins. The class I MHC proteins in such mutant cells are degraded in the cell because peptide binding is normally required for the proper folding of these proteins. Until it binds a peptide, a class I MHC protein remains in the ER, tethered to an ABC transporter by a chaperone protein (Figure 24-58).

Figure 24-57

The peptide-transport problem. How do peptide fragments get from the cytosol, where they are produced, into the ER lumen, where the peptide-binding grooves of class I MHC proteins are located? A special transport process is required.

Figure 24-58

The processing of a viral protein for presentation to cytotoxic T cells. An effector cytotoxic T cell kills a virus-infected cell when it recognizes fragments of viral protein bound to class I MHC proteins on the surface of the infected cell. Not all (more...)

In cells that are not infected, peptide fragments come from the cells' own cytosolic and nuclear proteins that are degraded in the processes of normal protein turnover and quality control mechanisms. (Surprisingly, more than 30% of the proteins made by mammalian cells are apparently faulty and are degraded in proteasomes soon after they are synthesized.) These peptides are pumped into the ER and are carried to the cell surface by class I MHC proteins. They are not antigenic because the cytotoxic T cells that could recognize them have been eliminated or inactivated during T cell development, as we discuss later.

When cytotoxic T cells and some helper T cells are activated by antigen to become effector cells, they secrete the cytokine interferon-γ (IFN-γ), which greatly enhances anti-viral responses. The IFN-γ acts on infected cells in two ways. It blocks viral replication, and it increases the expression of many genes within the MHC chromosomal region. These genes include those that encode class I (and class II) MHC proteins, the two specialized proteasome subunits, and the two subunits of the peptide transporter located in the ER (Figure 24-59). Thus, all of the machinery required for presenting viral antigens to cytotoxic T cells is coordinately called into action by IFN-γ, creating a positive feedback that amplifies the immune response and culminates in the death of the infected cells.

Figure 24-59

Some effects of interferon-γ on infected cells. The activated interferon-γ receptors signal to the nucleus, altering gene transcription, which leads to the effects indicated. The effects shaded in yellow tend to make the infected cell (more...)

Helper T Cells Recognize Fragments of Endocytosed Foreign Protein Associated with Class II MHC Proteins

Unlike cytotoxic T cells, helper T cells do not act directly to kill infected cells so as to eliminate microbes. Instead, they stimulate macrophages to be more effective in destroying intracellular microorganisms, and they help B cells and cytotoxic T cells to respond to microbial antigens.

Like the viral proteins presented to cytotoxic T cells, the proteins presented to helper T cells on antigen-presenting cells or target cells are degraded fragments of foreign proteins. The fragments are bound to class II MHC proteins in much the same way that virus-derived peptides are bound to class I MHC proteins. But both the source of the peptide fragments presented and the route they take to find the MHC proteins are different from those of peptide fragments presented by class I MHC proteins to cytotoxic T cells.

Rather than being derived from foreign protein synthesized in the cytosol of a cell, the foreign peptides presented to helper T cells are derived from endosomes. Some come from extracellular microbes or their products that the antigen-presenting cell has endocytosed and degraded in the acidic environment of its endosomes. Others come from microbes growing within the endocytic compartment of the antigen-presenting cell. These peptides do not have to be pumped across a membrane because they do not originate in the cytosol; they are generated in a compartment that is topologically equivalent to the extracellular space. They never enter the lumen of the ER, where the class II MHC proteins are synthesized and assembled, but instead bind to preassembled class II heterodimers in a special endosomal compartment. Once the peptide has bound, the class II MHC protein alters its conformation, trapping the peptide in the binding groove for presentation at the cell surface to helper T cells.

A newly synthesized class II MHC protein must avoid clogging its binding groove prematurely in the ER lumen with peptides derived from endogenously synthesized proteins. A special polypeptide, called the invariant chain, ensures this by associating with newly synthesized class II MHC heterodimers in the ER. Part of its polypeptide chain lies within the peptide-binding groove of the MHC protein, thereby blocking the groove from binding other peptides in the lumen of the ER. The invariant chain also directs class II MHC proteins from the trans Golgi network to a late endosomal compartment. Here, the invariant chain is cleaved by proteases, leaving only a short fragment bound in the peptide-binding groove of the MHC protein. This fragment is then released (catalyzed by a class II-MHC-like protein called HLA-DM), freeing the MHC protein to bind peptides derived from endocytosed proteins (Figure 24-60). In this way, the functional differences between class I and class II MHC proteins are ensured—the former presenting molecules that come from the cytosol, the latter presenting molecules that come from the endocytic compartment.

Figure 24-60

The processing of an extracellular protein antigen for presentation to a helper T cell. The drawing shows a simplified view of how peptide-class-II-MHC complexes are formed in endosomes and delivered to the cell surface. Note that the release of the invariant-chain (more...)

Most of the class I and class II MHC proteins on the surface of a target cell have peptides derived from self proteins in their binding groove. For class I proteins, the fragments derive from degraded cytosolic and nuclear proteins. For class II proteins, they mainly derive from degraded proteins that originate in the plasma membrane or extracellular fluid and are endocytosed. Only a small fraction of the 105 or so class II MHC proteins on the surface of an antigen-presenting cell have foreign peptides bound to them. This is sufficient, however, because only a hundred or so of such molecules are required to stimulate a helper T cell, just as in the case of peptide-class-I-MHC complexes stimulating a cytotoxic T cell.

Potentially Useful T Cells Are Positively Selected in the Thymus

We have seen that T cells recognize antigen in association with self MHC proteins but not in association with foreign MHC proteins (see Figure 24-56): that is, T cells show MHC restriction. This restriction results from a process of positive selection during T cell development in the thymus. In this process, those immature T cells that will be capable of recognizing foreign peptides presented by self MHC proteins are selected to survive, while the remainder, which would be of no use to the animal, undergo apoptosis. Thus, MHC restriction is an acquired property of the immune system that emerges as T cells develop in the thymus.

The most direct way to study the selection process is to follow the fate of a set of developing T cells of known specificity. This can be done by using transgenic mice that express a specific pair of rearranged α and β T cell receptor genes derived from a T cell clone of known antigen and MHC specificity. Such experiments show that the transgenic T cells mature in the thymus and populate the peripheral lymphoid organs only if the transgenic mouse also expresses the same allelic form of MHC protein as is recognized by the transgenic T cell receptor. If the mouse does not express the appropriate MHC protein, the transgenic T cells die in the thymus. Thus, the survival and maturation of a T cell depend on a match between its receptor and the MHC proteins expressed in the thymus. Similar experiments using transgenic mice in which MHC expression is confined to specific cell types in the thymus indicate that it is MHC proteins on epithelial cells in the cortex of the thymus that are responsible for this positive selection process. After positively selected T cells leave the thymus, their continued survival depends on their continual stimulation by self-peptide-MHC complexes; this stimulation is enough to promote cell survival but not enough to activate the T cells to become effector cells.

As part of the positive selection process in the thymus, developing T cells that express receptors recognizing class I MHC proteins are selected to become cytotoxic cells, while T cells that express receptors recognizing class II MHC proteins are selected to become helper cells. Thus, genetically engineered mice that lack cell-surface class I MHC proteins specifically lack cytotoxic T cells, whereas mice that lack class II MHC proteins specifically lack helper T cells. The cells that are undergoing positive selection initially express both CD4 and CD8 co-receptors, and these are required for the selection process: without CD4, helper T cells fail to develop, and without CD8, cytotoxic T cells fail to develop.

Positive selection still leaves a large problem to be solved. If developing T cells with receptors that recognize self peptides associated with self MHC proteins were to mature in the thymus and migrate to peripheral lymphoid tissues, they might wreak havoc. A second, negative selection process in the thymus is required to help avoid this potential disaster.

Many Developing T Cells That Could Be Activated by Self Peptides Are Eliminated in the Thymus

As discussed previously, a fundamental feature of the adaptive immune system is that it can distinguish self from nonself and normally does not react against self molecules. An important mechanism in achieving this state of immunological self tolerance is the deletion in the thymus of developing self-reactive T cells—that is, T cells whose receptors bind strongly enough to the complex of a self peptide and a self MHC protein to become activated. Because, as we discuss later, most B cells require helper T cells to respond to antigen, the elimination of self-reactive helper T cells also helps ensure that self-reactive B cells that escape B cell tolerance induction are harmless.

It is not enough, therefore, for the thymus to select for T cells that recognize self MHC proteins; it must also select against T cells that could be activated by self MHC proteins complexed with self peptides. In other words, it must pick out for survival just those T cells that will be capable of responding to self MHC proteins complexed with foreign peptides, even though these peptides are not present in the developing thymus. It is thought that these T cells bind weakly in the thymus to self MHC proteins that are carrying self peptides mismatched to the T cell receptors. Thus, the required goal can be achieved by (1) ensuring the death of T cells that bind strongly to the self-peptide-MHC complexes in the thymus while (2) promoting the survival of those that bind weakly and (3) permitting the death of those that do not bind at all. Process 2 is the positive selection we have just discussed. Process 1 is called negative selection. In both death processes, the cells that die undergo apoptosis (Figure 24-61).

Figure 24-61

Positive and negative selection in the thymus. Cells with receptors that would enable them to respond to foreign peptides in association with self MHC proteins survive, mature, and migrate to peripheral lymphoid organs. All of the other cells undergo (more...)

The most convincing evidence for negative selection derives once again from experiments with transgenic mice. After the introduction of T cell receptor transgenes encoding a receptor that recognizes a male-specific peptide antigen, for example, large numbers of mature T cells expressing the transgenic receptor are found in the thymus and peripheral lymphoid organs of female mice. Very few, however, are found in male mice, where the cells die in the thymus before they have a chance to mature. Like positive selection, negative selection requires the interaction of a T cell receptor and a CD4 or CD8 co-receptor with an appropriate MHC protein. Unlike positive selection, however, which occurs mainly on the surface of thymus epithelial cells, negative selection occurs on the surface of thymus dendritic cells and macrophages, which, as we have seen, function as antigen-presenting cells in peripheral lymphoid organs.

The deletion of self-reactive T cells in the thymus cannot eliminate all potentially self-reactive T cells, as some self molecules are not present in the thymus. Thus, some potentially self-reactive T cells are deleted or functionally inactivated after they leave the thymus, presumably because they recognize self peptides bound to MHC proteins on the surface of dendritic cells that have not been activated by microbes and therefore do not provide a costimulatory signal. As we discuss later, antigen recognition without costimulatory signals can delete or inactivate a T or B cell.

Some potentially self-reactive T cells, however, are not deleted or inactivated. Instead, special regulatory (or suppressor) T cells are thought to keep them from responding to their self antigens by secreting inhibitory cytokines such as TGF-β (discussed in Chapter 15). These self-reactive T cells may sometimes escape from this suppression and cause autoimmune diseases.

The Function of MHC Proteins Explains Their Polymorphism

The role of MHC proteins in binding foreign peptides and presenting them to T cells provides an explanation for the extensive polymorphism of these proteins. In the evolutionary war between pathogenic microbes and the adaptive immune system, microbes tend to change their antigens to avoid associating with MHC proteins. When a microbe succeeds, it is able to sweep through a population as an epidemic. In such circumstances, the few individuals that produce a new MHC protein that can associate with an antigen of the altered microbe have a large selective advantage. In addition, individuals with two different alleles at any given MHC locus (heterozygotes) have a better chance of resisting infection than those with identical alleles at the locus, as they have a greater capacity to present peptides from a wide range of microbes and parasites. Thus, selection will tend to promote and maintain a large diversity of MHC proteins in the population. Strong support for this hypothesis, that infectious diseases have provided the driving force for MHC polymorphism, has come from studies in West Africa. Here, it is found that individuals with a specific MHC allele have a reduced susceptibility to a severe form of malaria. Although the allele is rare elsewhere, it is found in 25% of the West African population where this form of malaria is common.

If greater MHC diversity means greater resistance to infection, why do we each have so few MHC genes encoding these molecules? Why have we not evolved strategies for increasing the diversity of MHC proteins—by alternative RNA splicing, for example, or by the genetic recombination mechanisms used to diversify antibodies and T cell receptors? Presumably, the limits exist because each time a new MHC protein is added to the repertoire, the T cells that recognize self peptides in association with the new MHC protein must be eliminated to maintain self tolerance. The elimination of these T cells would counteract the advantage of adding the new MHC protein. Thus, the number of MHC proteins we express may represent a balance between the advantages of presenting a wide diversity of foreign peptides to T cells against the disadvantages of severely restricting the T cell repertoire during negative selection in the thymus. This explanation is supported by computer modeling studies.

Summary

There are two main functionally distinct classes of T cells: cytotoxic T cells kill infected cells directly by inducing them to undergo apoptosis, while helper T cells help activate B cells to make antibody responses and macrophages to destroy microorganisms that either invaded the macrophage or were ingested by it. Helper T cells also help activate cytotoxic T cells. Both classes of T cells express cell-surface, antibodylike receptors, which are encoded by genes that are assembled from multiple gene segments during T cell development in the thymus. These receptors recognize fragments of foreign proteins that are displayed on the surface of host cells in association with MHC proteins. Both cytotoxic and helper T cells are activated in peripheral lymphoid organs by antigen-presenting cells, which express peptide-MHC complexes, costimulatory proteins, and various cell-cell adhesion molecules on their cell surface.

Class I and class II MHC proteins have crucial roles in presenting foreign protein antigens to cytotoxic and helper T cells, respectively. Whereas class I proteins are expressed on almost all vertebrate cells, class II proteins are normally restricted to those cell types that interact with helper T cells, such as dendritic cells, macrophages, and B lymphocytes. Both classes of MHC proteins have a single peptide-binding groove, which binds small peptide fragments derived from proteins. Each MHC protein can bind a large and characteristic set of peptides, which are produced intracellularly by protein degradation: class I MHC proteins generally bind fragments produced in the cytosol, while class II MHC proteins bind fragments produced in the endocytic compartment. After they have formed inside the target cell, the peptide-MHC complexes are transported to the cell surface. Complexes that contain a peptide derived from a foreign protein are recognized by T cell receptors, which interact with both the peptide and the walls of the peptide-binding groove. T cells also express CD4 or CD8 co-receptors, which recognize nonpolymorphic regions of MHC proteins on the target cell: helper cells express CD4, which recognizes class II MHC proteins, while cytotoxic T cells express CD8, which recognizes class I MHC proteins.

The T cell receptor repertoire is shaped mainly by a combination of positive and negative selection processes that operate during T cell development in the thymus. These processes help to ensure that only T cells with potentially useful receptors survive and mature, while the others die by apoptosis. T cells that will be able to respond to foreign peptides complexed with self MHC proteins are positively selected, while many T cells that could react strongly with self peptides complexed with self MHC proteins are eliminated. T cells with receptors that could react strongly with self antigens not present in the thymus are eliminated, functionally inactivated, or actively kept suppressed after they leave the thymus.

Where is MHC molecule located?

On which cells MHC class I molecules are found?

Where are MHC II molecules found?

Where is the MHC region located quizlet?