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Cell_Biology_Alberts. Figure 24–4 A Toll-like receptor. The structure of human TLr3 is shown (green), with a double-stranded rNA molecule (dsrNA, blue) bound to it. The receptor is a homodimer in the membrane of endosomes. The binding of dsrNA to the two horseshoe-shaped domains on the lumenal endosome membrane side of the endosome brings the two cytosolic domains together, allowing adaptor proteins in the cytosol to assemble into a large signaling complex (not shown). (B) The crystal structure of a lumenal domain of the receptor, which contains 23 conventional leucine-rich repeats, each of which contributes a β strand to the continuous β sheet (red) that lines the concave surface of the structure. (A, adapted from L. Liu et al., Science 320:379–381, 2008. With permission from AAAS; B, adapted from J. choe, M.S. Kelker and I.A. Wilson, Science 309:581–585, 2006; pDB: 1ZIW.) 0.2 mm membrane of Gram-negative bacteria; TLR5 recognizes the protein that forms the bacterial flagellum; and TLR9 recognizes short,


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Cell_Biology_Alberts. Kelker and I.A. Wilson, Science 309:581–585, 2006; pDB: 1ZIW.) 0.2 mm membrane of Gram-negative bacteria; TLR5 recognizes the protein that forms the bacterial flagellum; and TLR9 recognizes short, unmethylated sequences of bacterial, viral, or protozoan DNA, called CpG motifs, which are uncommon in vertebrate DNA.


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Cell_Biology_Alberts. In addition to TLRs, vertebrates use several other families of PRRs to detect pathogens. One is the large family of NOD-like receptors (NLRs). Like TLRs, NLRs have leucine-rich repeat motifs, but they are exclusively cytoplasmic and recognize a distinct set of bacterial molecules. Individuals who are homozygous for a particular mutant allele of the NLR gene NOD2 have a greatly increased risk of developing Crohn’s disease, a chronic inflammatory disease of the small intestine, possibly triggered by a bacterial infection. Another class of PRRs consists of RIG‑like receptors (RLRs), which are members of the RNA helicase family of proteins. They are also exclusively cytoplasmic and detect viral pathogens. A fourth class of PRRs consists of C‑type lectin receptors (CLRs), which are trans-membrane cell-surface proteins that recognize carbohydrates (which is why they are called lectins) on various microbes. Table 24–1 summarizes some PRRs and their ligands and locations in cells.


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Cell_Biology_Alberts. trans-membrane cell-surface proteins that recognize carbohydrates (which is why they are called lectins) on various microbes. Table 24–1 summarizes some PRRs and their ligands and locations in cells. Collectively, these and other PRRs act as an alarm system to alert the innate and adaptive immune systems that an infection is brewing (Movie 24.1).


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Cell_Biology_Alberts. When a cell-surface or intracellular PRR binds a PAMP, it stimulates the cell to secrete a variety of cytokines and other extracellular signal molecules. Some of these inhibit viral replication, but most induce a local inflammatory response that helps eliminate the pathogen, as we now discuss. Activated prrs Trigger an Inflammatory response at Sites of Infection


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Cell_Biology_Alberts. Activated prrs Trigger an Inflammatory response at Sites of Infection When a pathogen invades a tissue, it activates PRRs on or in various cells of the innate immune system, resulting in an inflammatory response at the site of infection. The inflammatory response depends on changes in local blood vessels and is characterized clinically by local pain, redness, heat, and swelling. The blood vessels dilate and become permeable to fluid and proteins, leading to local swelling and an accumulation of blood proteins that aid in defense. At the same time, the endothelial cells lining the local blood vessels are stimulated to express cell adhesion proteins, which promote the attachment and escape of white blood cells or leukocytes (see Figure 19–29B), adding to the local swelling; initially neutrophils escape, followed later by lymphocytes and monocytes (the blood-borne precursors of macrophages).


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Cell_Biology_Alberts. The activation of PRRs results in the production of a large variety of extracellular signal molecules that mediate the inflammatory response at the site of an infection. These include both lipid signal molecules, such as prostaglandins, and protein (or peptide) signal molecules called cytokines. Some of the most important pro-inflammatory cytokines are tumor necrosis factor‑α (TNFα), interferon‑γ (IFNγ), a variety of chemokines (which recruit leukocytes), and various interleukins (ILs) that we discuss later, including IL1, IL6, IL12, and IL17. In addition, a secreted PRR (mannose-binding lectin) activates the complement system when the PRR binds to a pathogen; fragments of complement proteins released during complement activation stimulate an inflammatory response (discussed shortly; see Figure 24–7).


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Cell_Biology_Alberts. When activated by PAMPs, most cell-surface and intracellular PRRs stimulate the production of multiple pro-inflammatory cytokines by activating intracellular signaling pathways that switch on transcription regulators, including NFκB, to induce the transcription of the relevant cytokine genes (see Figure 15–62). Some PRRs, however, can also stimulate pro-inflammatory cytokine production by a different mechanism: when activated, several cytoplasmic NLRs assemble with adaptor proteins and specific protease precursors of the caspase family (discussed in Chapter 18) to form inflammasomes, in which pro-inflammatory cytokines such as IL1 are cleaved from their inactive precursor proteins by activated caspases. These cytokines are then released from the cell by a poorly understood, unconventional secretion pathway. Inflammasomes closely resemble apoptosomes in their assembly and structure, but, in apoptosomes, procaspases are activated to initiate a proteolytic caspase cascade that leads to


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Cell_Biology_Alberts. secretion pathway. Inflammasomes closely resemble apoptosomes in their assembly and structure, but, in apoptosomes, procaspases are activated to initiate a proteolytic caspase cascade that leads to apoptosis (see Figure 18–7).


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Cell_Biology_Alberts. NLR-dependent inflammasome assembly can also be triggered in the absence of infection if cells are damaged or stressed. Such cells produce “danger signals,” such as altered or misplaced self molecules, which can activate the relevant NLRs: the arthritis caused by uric acid crystals formed in the joints of individuals with gout, who have abnormally high uric acid levels in their blood, is a painful example. phagocytic cells Seek, engulf, and Destroy pathogens


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Cell_Biology_Alberts. phagocytic cells Seek, engulf, and Destroy pathogens In all animals, the recognition of a microbial invader is usually quickly followed by its engulfment by a phagocytic cell. Macrophages are long-lived phagocytes that reside in most vertebrate tissues; they are among the first cells to encounter invading microbes, whose PAMPs activate the macrophages to secrete pro-inflammatory signal molecules. Neutrophils are short-lived phagocytes that are abundant in blood but are not present in healthy tissues; they are rapidly recruited to sites of infection by various attractive molecules, including formylmethionine-containing peptides (which are released by microbes but are not made by mammalian cells), chemokines secreted by activated macrophages, and peptide fragments produced from cleaved, activated complement proteins. The recruited neutrophils contribute their own pro-inflammatory cytokines.


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Cell_Biology_Alberts. In addition to their PRRs, macrophages and neutrophils display a variety of cell-surface receptors that recognize fragments of complement proteins or antibodies bound to the surface of a pathogen. The binding of such a pathogen to these receptors leads to its phagocytosis (Figure 24–5) and an attack on the ingested pathogen once inside a phagolysosome. The phagocytes possess an impressive armory of weapons to kill the invader, including enzymes such as lysozyme and acid hydrolases that can degrade the pathogen’s cell wall. The cells assemble NADPH oxidase complexes on the phagolysosomal membrane, where the complexes catalyze the production of highly toxic oxygen-derived compounds, including superoxide (O2–), hydrogen peroxide, and hydroxyl radicals. A transient increase in oxygen consumption by the phagocytic cells, called the respiratory burst, accompanies the production of these toxic compounds. Whereas macrophages generally survive this killing frenzy and live to kill again,


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Cell_Biology_Alberts. by the phagocytic cells, called the respiratory burst, accompanies the production of these toxic compounds. Whereas macrophages generally survive this killing frenzy and live to kill again, neutrophils do not. Dead and dying neutrophils are a major component of the pus that forms in acute bacterially infected wounds; their half-life in the human bloodstream is only a few hours.


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Cell_Biology_Alberts. Figure 24–5 Antibody-activated phagocytosis. electron micrograph of a neutrophil phagocytosing an antibody-coated bacterium, which is in the process of dividing. The process in which antibody (or complement) coating of a pathogen increases the efficiency with which the pathogen is phagocytosed is called opsonization. (courtesy of Dorothy F. Bainton, from r.c. Williams, Jr. and h.h. Fudenberg, phagocytic Mechanisms in health and Disease. New York: Intercontinental Medical Book corporation, 1971.) If a pathogen is too large to be successfully phagocytosed (if it is a large parasite such as a worm, for example), a group of macrophages, neutrophils, or eosinophils (another type of leukocyte) will gather around the invader. They secrete defensins and other damaging agents and release the toxic products of the respiratory burst. This barrage is often sufficient to destroy the pathogen (Figure 24–6).


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Cell_Biology_Alberts. The blood and other extracellular fluids contain numerous proteins with antimicrobial activity, some of which are produced in response to an infection, while others are produced constitutively. The most important of these are components of the complement system, which consists of about thirty interacting soluble proteins that are mainly made continuously by the liver and are inactive until an infection or another trigger activates them. They were originally identified by their ability to amplify and “complement” the action of antibodies made by B cells, but some are also secreted PRRs, which directly recognize PAMPs on microbes.


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Cell_Biology_Alberts. The early complement components consist of three sets of proteins, belonging to three distinct pathways of complement activation—the classical pathway, the lectin pathway, and the alternative pathway. The early components of all three pathways act locally to cleave and activate C3, which is the pivotal complement component (Figure 24–7); individuals with a C3 deficiency are subject to repeated bacterial infections. The early components are proenzymes, which are activated sequentially by proteolytic cleavage. The cleavage of each proenzyme in the series activates the next component to generate a serine protease, which cleaves the next proenzyme in the series, and so on. Since each activated enzyme cleaves many molecules of the next proenzyme in the chain, the activation of the early components consists of an amplifying proteolytic cascade.


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Cell_Biology_Alberts. Many of these protein cleavages liberate a biologically active small fragment that can attract neutrophils, plus a membrane-binding larger fragment. The binding of the large fragment to a cell membrane, usually the surface of a pathogen, helps stimulate the next reaction in the sequence. In this way, complement activation is largely kept confined to the cell surface where it began. In particular, the large fragment of C3, called C3b, binds covalently to the surface of the pathogen. Here, it recruits protein fragments produced by cleavage of other early complement components to form proteolytic complexes that catalyze the subsequent steps in the complement cascade. The early events in complement activation have diverse functions: C3b-binding receptors on phagocytic cells enhance the ability of these cells to phagocytose the pathogen, and similar receptors on B cells enhance the


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Cell_Biology_Alberts. Figure 24–6 eosinophils attacking a parasite. phagocytes cannot ingest large parasites such as the schistosome larva shown here. When the larva is coated with antibody or complement components, however, eosinophils (and other leukocytes) can recognize it and collectively kill it by secreting a large variety of toxic molecules. (courtesy of Anthony Butterworth.)


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Cell_Biology_Alberts. Figure 24–7 The principal stages in complement activation by the classical, lectin, and alternative pathways. In all three pathways, the reactions of complement activation usually take place on the surface of an invading microbe, such as a bacterium, and lead to the cleavage of c3 and the various consequences shown. As indicated, the complement proteins c1 to c9, mannose-binding lectin (MBL), MBL-associated serine protease (MASp), and factors B and D are the central components of the complement system. The early components are shown within gray arrows, while the late components are shown within a brown arrow. The functions of the protein fragments produced during complement activation are indicated by the black arrows. The various complement proteins that regulate the system are omitted.


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Cell_Biology_Alberts. ability of these cells to make antibodies against various microbial molecules on C3b-coated pathogens; the smaller fragment of C3 (called C3a), as well as small fragments of C4 and C5, act independently as diffusible signals to promote an inflammatory response by recruiting leukocytes to the site of infection. As indicated in Figure 24–7, antibodies bound to the surface of a pathogen activate the classical pathway. Mannose‑binding lectin, mentioned earlier, is a secreted PRR that initiates the lectin pathway of complement activation when it recognizes bacterial or fungal glycolipids and glycoproteins bearing terminal mannose and fucose sugars in a particular spatial conformation. These initial binding events in the classical and lectin pathways cause the recruitment and activation of the early complement components. Finally, molecules on the surface of pathogens will often directly activate the alternative pathway.


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Cell_Biology_Alberts. Host cells produce various plasma membrane molecules that prevent complement reactions from proceeding on their cell surface. The most important of these is the carbohydrate moiety sialic acid, a common constituent of cell-surface glycoproteins and glycolipids (see Figure 10–16). Because pathogens generally lack sialic acid, they are singled out for complement-mediated destruction, while host cells are spared. Some pathogens, including the bacterium Neisseria gonorrhoeae that causes the sexually transmitted disease gonorrhea, coat themselves with a layer of sialic acid to effectively hide from the complement system.


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Cell_Biology_Alberts. Membrane-immobilized C3b, produced by any of the three pathways, triggers a further cascade of reactions that leads to the assembly of the late complement components to form membrane attack complexes. These protein complexes assemble in the pathogen membrane near the site of C3 activation, forming aqueous pores through the membrane (Figure 24–8). For this reason, and because they perturb the structure of the lipid bilayer in their vicinity, they make the membrane leaky and can, in some cases, cause the microbe to lyse.


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Cell_Biology_Alberts. The self-amplifying, inflammatory, and destructive properties of the complement cascade make it essential that key activated components be rapidly inactivated after they are generated, ensuring that the attack does not spread to nearby host cells. Inactivation is achieved in at least two ways. First, specific inhibitor proteins in the blood or on the surface of host cells terminate the cascade, by either binding or cleaving certain complement components once the components have been activated by proteolytic cleavage. Second, many of the activated components in the cascade are unstable; unless they bind immediately to either the next component in the complement cascade or to a nearby membrane, they rapidly inactivate. Virus-Infected cells Take Drastic Measures to prevent Viral replication


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Cell_Biology_Alberts. Virus-Infected cells Take Drastic Measures to prevent Viral replication Because host-cell ribosomes make a virus’s proteins and host-cell lipids form the membranes of enveloped viruses, PAMPs are generally not present on the surface of viruses. Therefore, the only general way that a host cell PRR can recognize the presence of a virus is to detect unusual elements of the viral genome, such as the


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Cell_Biology_Alberts. Figure 24–8 Assembly of the late complement components to form a membrane attack complex. The cleavage of the early complement components (shown within gray arrows in Figure 24–7) results in the formation of c3bcontaining proteolytic complexes called c5 convertases (not shown). These then cleave the first of the late components, c5, to produce c5a and c5b. As illustrated, c5b rapidly assembles with c6 and c7 to form c567, which then binds firmly via c7 to the membrane. One molecule of c8 binds to the complex to form c5678. The binding of a molecule of c9 to c5678 induces a conformational change in c9 that exposes a hydrophobic region and causes c9 to insert into the lipid bilayer of the target membrane. This starts a chain reaction in which the altered c9 binds a second molecule of c9, which can then bind another molecule of c9, and so on. In this way, a ring of c9 molecules forms a large transmembrane channel in the membrane.


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Cell_Biology_Alberts. double-stranded RNA (dsRNA) that is an intermediate in the life cycle of many viruses and is recognized by several PRRs including the Toll-like receptor TLR3; in addition, DNA virus genomes frequently contain significant amounts of the CpG motifs discussed earlier, which can be recognized by TLR9 (see Table 24–1, p. 1300).


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Cell_Biology_Alberts. Mammalian cells are particularly adept at recognizing the presence of dsRNA, which activates intracellular PRRs that induce the host cell to produce and secrete two antiviral cytokines—interferon-α (IFNα) and interferon-β (IFNβ). These interferons are referred to as type I interferons to distinguish them from IFNγ, which is a type II interferon and has different functions, as we discuss later. Type I interferons act in both an autocrine fashion on the infected cells that produced it and a paracrine fashion on uninfected neighbors. They bind to a common cell-surface receptor, which activates the JAK–STAT intracellular signaling pathway (see Figure 15–56) to stimulate specific gene transcription and thereby the production of more than 300 proteins, including many cytokines, reflecting the complexity of the cell’s acute response to a viral infection.


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Cell_Biology_Alberts. The production of type I interferons appears to be a general response of mammalian cells to a viral infection, and viral components other than dsRNA can trigger it. The type I interferons help block viral replication in multiple ways. They activate a latent ribonuclease that nonspecifically degrades single-stranded RNA. They also indirectly activate a protein kinase that phosphorylates and inactivates the protein synthesis initiation factor eIF2 (discussed in Chapter 6), thereby shutting down most protein synthesis in the infected host cell. Apparently, by destroying most of its own RNA and transiently halting most of its protein synthesis, the host cell inhibits viral replication without killing itself. If these measures fail, the cell takes an even more extreme step to prevent the virus from replicating: it kills itself by undergoing apoptosis, often with the help of immune killer cells, as we discuss next. Natural Killer cells Induce Virus-Infected cells to Kill Themselves


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Cell_Biology_Alberts. Natural Killer cells Induce Virus-Infected cells to Kill Themselves Type I interferons also have less direct ways of blocking viral replication. One of these is to enhance the activity of natural killer cells (NK cells), which are leukocytes related to T and B cells but are part of the innate immune system and are recruited early to sites of inflammation. Like cytotoxic T cells of the adaptive immune system (discussed later), NK cells destroy virus-infected cells by inducing the infected cells to kill themselves by undergoing apoptosis (discussed in Chapter 18). We consider how killer cells induce apoptosis later, when we discuss how cytotoxic T cells do it (see Figure 24–43). Although they kill in the same way, the means by which cytotoxic T cells and NK cells distinguish the surface of virus-infected cells from that of uninfected cells are different (Movie 24.2).


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Cell_Biology_Alberts. Both cytotoxic T cells and NK cells recognize the same special class of cell-surface proteins on a host cell to help determine if the cell is virus-infected, but they use distinct receptors to do so. The special cell-surface proteins recognized are called class I MHC proteins, because they are encoded by genes in the major histocompatibility complex; almost all nucleated cells in vertebrates express these genes, and we discuss them in detail later. Cytotoxic T cells use both T cell receptors (TCRs) and co‑receptors to recognize peptide fragments of viral proteins bound to class I MHC proteins on the surface of virus-infected host cells and then induce the infected cells to kill themselves. By contrast, NK cells have cell-surface inhibitory receptors that monitor the level of class I MHC proteins on the surface of other host cells: the high levels of these MHC proteins normally present on healthy cells engage these receptors and thereby inhibit the killing activity of the NK cells. The


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Cell_Biology_Alberts. on the surface of other host cells: the high levels of these MHC proteins normally present on healthy cells engage these receptors and thereby inhibit the killing activity of the NK cells. The NK cells thus focus primarily on host cells expressing abnormally low levels of class I MHC proteins and induce them to kill themselves; these are mainly virus-infected cells and some cancer cells (Figure 24–9). NK cell killing activity is stimulated when various activating receptors on the NK cell surface recognize specific proteins that are greatly increased on the surface of virus-infected cells and some cancer cells.


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Cell_Biology_Alberts. Figure 24–9 A natural killer (NK) cell attacking a cancer cell. This scanning electron micrograph was taken shortly after the NK cell attached to the cancer cell, but before it induced the cell to die by apoptosis. (courtesy of J.c. hiserodt, in Mechanisms of cytotoxicity by Natural Killer cells [r.B. herberman and D. callewaert, eds.]. New York: Academic press, 1995.)


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Cell_Biology_Alberts. The reason that class I MHC protein levels are often low on virus-infected cells is that many viruses have developed a variety of mechanisms to inhibit the expression of these proteins on the surface of the host cells they infect, in order to avoid detection by cytotoxic T cells: some viruses encode proteins that block class I MHC gene transcription; others block the intracellular assembly of pep-tide–MHC complexes; still others block the transport of these complexes to the cell surface. By evading recognition by cytotoxic T cells in these ways, however, a virus incurs the wrath of NK cells, which recognize the infected cells as being different—both because the infected cells express little class I MHC protein and because they express large amounts of other surface proteins that are recognized by the activating receptors on the NK cells (Figure 24–10). Dendritic cells provide the Link Between the Innate and Adaptive Immune Systems


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Cell_Biology_Alberts. Dendritic cells provide the Link Between the Innate and Adaptive Immune Systems Dendritic cells are crucially important components of the innate immune system. They are a heterogeneous class of cells that are widely distributed in the tissues and organs of vertebrates. They express a large variety of PRRs, which enable dendritic cells to recognize and phagocytose invading pathogens and their products and to become activated in the process. The activated dendritic cells cleave the proteins of the pathogen into peptide fragments, which bind to newly synthesized MHC proteins, which then carry the fragments to the dendritic cell surface. The activated cells then migrate to a nearby lymphoid organ such as a lymph node (also called a lymph gland), where they present the peptide–MHC complexes to T cells of the adaptive immune system, activating the T cells to join in the battle against the specific pathogen (Figure 24–11).


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Cell_Biology_Alberts. In addition to the complexes of MHC proteins and microbial peptides displayed on their cell surface, activated dendritic cells also display cell-surface co‑stimulatory proteins that help activate T cells (see Figure 24–11). As we discuss later, the activated dendritic cells also secrete a variety of cytokines that influence the type of response that the T cells make, ensuring that it is appropriate to fight the particular pathogen. In these ways, dendritic cells serve as crucial links between the innate immune system, which provides a rapid first line of defense against invading pathogens, and the adaptive immune system, which mounts slower but more powerful and highly specific responses to attack an invader, as we now discuss. All multicellular organisms possess innate immune defenses against invading pathogens; these defenses include physical and chemical barriers and various defensive cell responses. In vertebrates, these innate defense responses can also


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Cell_Biology_Alberts. Figure 24–10 How an NK cell recognizes its target. An NK cell preferentially attacks infected host cells and cancer cells because these cells have on their surface both activating proteins and, in some cases, abnormally low levels of class I Mhc proteins. (A) The high levels of class I Mhc proteins found on normal host cells activate inhibitory receptors on the NK cell that suppress the killing activity of the NK cell. (B) In contrast, the activating proteins on infected cells and cancer cells bind to activating receptors on the NK cell and stimulate the killing activity of the cell.


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Cell_Biology_Alberts. Figure 24–11 Dendritic cells as functional links between the innate and adaptive immune systems. Dendritic cells pick up invading microbes or their products at the site of an infection. The microbial pAMps activate the dendritic cells to express co-stimulatory proteins and increased amounts of Mhc proteins on their surface and to migrate via lymphatic vessels to a nearby lymph node. In the lymph node, the activated dendritic cells activate T cells that express appropriate receptors for the co-stimulatory proteins and the microbial peptides bound to Mhc proteins on the dendritic cell surface. The activated T cells proliferate, and some of their progeny migrate to the original site of infection, where they help eliminate the microbes, either by activating local macrophages or by killing infected host cells (not shown). In addition, some of the activated T cells help stimulate specific B cells in the lymph node to secrete antibodies against the microbe (not shown).


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Cell_Biology_Alberts. A crucial feature of dendritic cell activation is that the pathogen provides an individual dendritic cell with both the peptides for presentation to T cells and the pAMp signals that activate the dendritic cell to express co-stimulatory proteins. In this way, the individual dendritic cell has all it needs to activate specific T cells that recognize the peptide–Mhc complexes on its surface (Movie 24.3).


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Cell_Biology_Alberts. recruit specific and more powerful adaptive immune responses to help fight the infection. Innate immune responses rely on the ability of host cells to recognize characteristic features of microbial molecules called pathogen‑associated molecular patterns, or PAMPs, which can be associated with a pathogen’s proteins, lipids, sugars, or nucleic acids. PAMPs are mainly recognized by pattern recognition receptors (PRRs), including the Toll‑like receptors (TLRs) found on or in both plant and animal cells. In vertebrates, some PRRs are secreted and can activate complement when they bind microbial PAMPs. The complement system, which can also be activated by antimicrobial antibodies bound to pathogens, consists of a group of blood proteins that are activated in sequence to help fight infections, by disrupting the pathogen's membrane, stimulating an inflammatory response, or targeting the microbe for phagocytosis—mainly by macrophages and neutrophils. The phagocytes use a combination of


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Cell_Biology_Alberts. by disrupting the pathogen's membrane, stimulating an inflammatory response, or targeting the microbe for phagocytosis—mainly by macrophages and neutrophils. The phagocytes use a combination of degradative enzymes, antimicrobial peptides, and oxygen‑derived toxic molecules to kill invading pathogens; in addition, they secrete various signal molecules that help trigger an inflammatory response.


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Cell_Biology_Alberts. Cells infected by a virus produce and secrete type I interferons (IFNα and IFNβ), which induce a complex set of host‑cell responses that inhibit viral replication. The interferons also enhance the killing activity of natural killer (NK) cells. An NK cell kills infected host cells because they express large amounts of surface proteins that activate the NK cell; the killing is especially efficient when infected cells express reduced amounts of class I MHC proteins, which, when present in normal amounts on a host cell surface inhibit the killing activity of NK cells.


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Cell_Biology_Alberts. Dendritic cells of the innate immune system functionally link innate immune responses to adaptive immune responses. The cells become activated when their PRRs pick up microbes and their products at sites of infection and phagocytose them. The activated cells cleave the microbial proteins into peptide fragments, which bind to newly made MHC proteins, which transport the fragments to the cell surface. The activated dendritic cells then carry the peptide–MHC complexes to a lymph organ, where they activate appropriate T cells to make specific adaptive immune responses against the microbes. OVerVIeW OF The ADApTIVe IMMUNe SYSTeM


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Cell_Biology_Alberts. A dramatic “big bang” in immune defense mechanisms occurred when jawed vertebrates evolved and acquired an adaptive immune system. This sophisticated defense system depends on B and T lymphocytes (B and T cells), which, during their development, rearrange particular DNA sequences in various combinations so that, together, the cells can produce an almost limitless variety of B and T cell receptors and antibodies. Collectively, these proteins can bind to essentially any molecule, including small chemicals, carbohydrates, lipids, and proteins; individually, they can distinguish between molecules that are very similar—such as between two proteins that differ in only a single amino acid, or between two optical isomers of the same small molecule. By this strategy, the adaptive immune system can recognize and respond specifically to any pathogen, including new mutant forms. However, because the genetic rearrangement process produces both receptors that can bind to self molecules as well as


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Cell_Biology_Alberts. recognize and respond specifically to any pathogen, including new mutant forms. However, because the genetic rearrangement process produces both receptors that can bind to self molecules as well as receptors that can bind to foreign molecules, vertebrates have had to evolve special mechanisms to ensure that B and T cells do not react against the host’s own molecules and cells—a process called immunological self‑tolerance.


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Cell_Biology_Alberts. Moreover, many harmless foreign substances enter the body, for example, as food or inhaled material, and it would be pointless and potentially dangerous to mount adaptive immune responses against them. Such inappropriate responses are normally avoided because innate immune responses are required to call adaptive immune responses into play and do so only when the innate cells’ PRRs recognize microbial PAMPs, as we discussed earlier. One can trick the adaptive immune system into responding to a harmless foreign molecule, such as a foreign protein, by co-injecting a molecule (often of microbial origin) called an adjuvant, which activates PRRs. This trick is called immunization and is the basis of vaccination. Any substance capable of stimulating B or T cells to make a specific adaptive immune response against it is referred to as an antigen (antibody generator).


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Cell_Biology_Alberts. There are two broad classes of adaptive immune responses—antibody responses and T‑cell‑mediated immune responses, and most pathogens induce both classes of responses. In antibody responses, B cells are activated to secrete antibodies, which are proteins that circulate in the bloodstream and permeate the other body fluids, where they can bind specifically to the foreign antigen that stimulated their production (see Figure 24–2). Binding of antibody neutralizes extracellular viruses and microbial toxins (such as tetanus toxin or cholera toxin) by blocking their ability to bind to receptors on host cells. Antibody binding also marks invading pathogens for destruction, both by making it easier for phagocytes of the innate immune system to ingest and destroy them and by activating the complement system.


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Cell_Biology_Alberts. In T-cell-mediated immune responses, T cells recognize foreign antigens that are bound to MHC proteins on the surface of host cells such as dendritic cells, which are specialized for presenting antigen to T cells and are therefore referred to as professional antigen‑presenting cells (APCs). Because MHC proteins carry fragments of pathogen proteins from inside a host cell to the cell surface, T cells can detect pathogens hiding inside a host cell and either kill the infected cell (see Figure 24–2) or stimulate phagocytes or B cells to help eliminate the pathogens. In this section, we discuss the origins and general properties of B and T cells. In later sections, we consider the specific properties and functions of these cells. B cells Develop in the Bone Marrow, T cells in the Thymus


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Cell_Biology_Alberts. B cells Develop in the Bone Marrow, T cells in the Thymus There are about 2 × 1012 lymphocytes in the human body, making the immune system comparable in cell mass to the liver or the brain. They occur in large numbers in the blood and lymph (the colorless fluid in the lymphatic vessels, which connect the lymph nodes in the body to each other and to the bloodstream). They are also concentrated in lymphoid organs, such as the thymus, lymph nodes, and spleen (Figure 24–12), and many are also found in other organs, including skin, lung, and gut.


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Cell_Biology_Alberts. T cells and B cells derive their names from the organs in which they develop: T cells develop in the thymus, and B cells, in adult mammals, develop in the bone marrow. Both types of cells develop from lymphoid progenitor cells that are produced from multipotent hematopoietic stem cells, which are found mainly in the bone marrow (Figure 24–13). The hematopoietic stem cells give rise to more than just lymphocytes: as discussed in Chapter 22, they produce all of the cells of the Figure 24–12 Human lymphoid organs.


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Cell_Biology_Alberts. Figure 24–12 Human lymphoid organs. Lymphocytes develop from lymphoid progenitor cells in the thymus and bone marrow (yellow), which are therefore called central (or primary) lymphoid organs. The newly formed lymphocytes migrate from these primary organs to peripheral (or secondary) lymphoid organs, where they can react with foreign antigen. Only some of the peripheral lymphoid organs (blue) and lymphatic vessels (green) are shown; many lymphocytes, for example, are found in the skin and respiratory tract. As we discuss later, the lymphatic vessels ultimately empty into the bloodstream (not shown).


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Cell_Biology_Alberts. Figure 24–13 The development of b and T cells. The central lymphoid organs, where lymphocytes develop from lymphoid progenitor cells, are labeled in yellow boxes. The lymphoid progenitor cells develop from multipotent hematopoietic stem cells in the bone marrow. Some lymphoid progenitor cells develop locally in the bone marrow into immature B cells, while others migrate to the thymus (via the bloodstream) where they develop into thymocytes (developing T cells). Foreign antigens activate B cells and T cells mainly in peripheral lymphoid organs, such as lymph nodes or the spleen. hematopoietic system, including erythrocytes, leukocytes, and platelets (see Figure 22–32).


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Cell_Biology_Alberts. hematopoietic system, including erythrocytes, leukocytes, and platelets (see Figure 22–32). Because they are sites where lymphocytes develop from lymphoid progenitor cells, the thymus and bone marrow are referred to as central (primary) lymphoid organs (see Figure 24–12). As we discuss later, most B and T cells die in the central lymphoid organs soon after they develop, without ever functioning. Others, however, mature and migrate via the blood to the peripheral (secondary) lymphoid organs—mainly the lymph nodes, spleen, and epithelium-associated lymphoid tissues in the gastrointestinal tract, respiratory tract, and skin. It is in these peripheral lymphoid organs that foreign antigens activate B and T cells (see Figure 24–13).


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Cell_Biology_Alberts. B and T cells become morphologically distinguishable from each other only after antigen has activated them: resting B and T cells look very similar, even in an electron microscope (Figure 24–14A). After activation by an antigen, both proliferate and mature into effector cells. Effector B cells secrete antibodies; in their most mature form, called plasma cells, they are filled with an extensive rough endoplasmic reticulum that is busily making antibodies (Figure 24–14B). In contrast, effector T cells (Figure 24–14C) contain very little endoplasmic reticulum and secrete a variety of cytokines rather than antibodies. Whereas B-cell-derived antibodies are widely distributed by the bloodstream, T-cell-derived cytokines mainly act locally on neighboring cells, although some are carried via the blood and act on distant host cells.


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Cell_Biology_Alberts. The most remarkable feature of the adaptive immune system is that it can respond to millions of different foreign antigens in a highly specific way. Human B cells, for example, collectively, can make more than 1012 different antibody molecules that react specifically with the antigen that induced their production. How can B cells and T cells respond specifically to such an enormous diversity of foreign antigens? The answer for both B and T cells is the same. As each lymphocyte develops in a central lymphoid organ, it becomes committed to react with a particular antigen before ever being exposed to the antigen. It expresses this commitment in the form of cell-surface receptors that specifically bind the antigen. When a lymphocyte encounters its antigen in a peripheral lymphoid organ, the binding of the antigen to the receptors (with help from co-stimulatory signals, discussed later) Figure 24–14 electron micrographs of resting and effector lymphocytes.


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Cell_Biology_Alberts. (A) This resting lymphocyte could be either a B cell or a T cell, as these cells are difficult to distinguish morphologically until antigen activates them to become effector cells. (B) An effector B cell (a plasma cell). It is filled with an extensive rough endoplasmic reticulum (er), which is distended with antibody molecules that are secreted in large amounts. (c) An effector T cell, which has relatively little rough er but is filled with free ribosomes; it secretes cytokines, but in relatively small amounts. The three cells are shown at the same magnification. (A, courtesy of Dorothy Zucker-Franklin; B, courtesy of carlo Grossi; A and B, from D. Zucker-Franklin et al., Atlas of Blood cells: Function and pathology, 2nd ed. Milan, Italy: edi. ermes, 1988; c, courtesy of Stefanello de petris.) activates the lymphocyte; this causes the lymphocyte to proliferate, thereby producing many more cells with the same receptor—a process called clonal expansion. The encounter with antigen also


Cell_Biology_Alberts

Cell_Biology_Alberts. activates the lymphocyte; this causes the lymphocyte to proliferate, thereby producing many more cells with the same receptor—a process called clonal expansion. The encounter with antigen also causes some of the cells to differentiate into effector cells. An antigen therefore selectively stimulates those cells that express complementary antigen-specific receptors and are thus already committed to respond to it (Figure 24–15). This arrangement, called clonal selection, provides an explanation for immunological memory, whereby we develop lifelong immunity to many common infectious diseases after our initial exposure to the pathogen—either through natural infection or vaccination.


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Cell_Biology_Alberts. It is easy to demonstrate such immunological memory in experimental animals. If an animal is immunized once with antigen A, an immune response (antibody, T-cell-mediated, or both) can be detected after several days; the response rises rapidly and exponentially, and then, more gradually, declines. This is the characteristic course of a primary immune response, occurring on an animal’s first exposure to an antigen. If, after some weeks, months, or even years have elapsed, the animal is immunized again with antigen A, it will usually produce a secondary immune response that differs from the primary response: the lag period is shorter, because there are now many more preexisting B or T cells (or both) with specificity for antigen A, and the response is greater and more efficient. These differences indicate that the animal has “remembered” its first exposure to antigen A. If the animal is given a different antigen (for example, antigen B) instead of a second immunization with antigen A,


Cell_Biology_Alberts

Cell_Biology_Alberts. indicate that the animal has “remembered” its first exposure to antigen A. If the animal is given a different antigen (for example, antigen B) instead of a second immunization with antigen A, the response is typical of a primary, and not a secondary, immune response. The secondary response therefore reflects antigen-specific immunological memory for antigen A (Figure 24–16).


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Cell_Biology_Alberts. Immunological memory depends on both lymphocyte proliferation and differentiation. In an adult animal, the peripheral lymphoid organs contain a mixture of lymphocytes in at least three stages of maturation: naïve cells, effector cells, and memory cells. When naïve cells encounter their specific foreign antigen for the first time, the antigen stimulates some of them to proliferate and differentiate into effector cells, which then carry out an immune response (effector B cells secrete antibody, whereas effector T cells either kill infected cells or influence the response of other immune cells—by secreting cytokines, for example). Some of the antigen-stimulated naïve cells multiply and differentiate into memory cells, which are more easily and more quickly induced to become effector cells by a later encounter with the same antigen: like naïve cells, when memory cells encounter their antigen, they give rise to either effector cells or more memory cells (Figure 24–17).


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Cell_Biology_Alberts. Figure 24–15 Clonal selection. An antigen activates only those lymphocytes that are already committed to respond to it. The committed cell expresses cell-surface receptors that specifically recognize the antigen. The human adaptive immune system consists of many millions of different T and B lymphocyte clones, with cells within a clone expressing the same unique antigen receptor. Before its first encounter with antigen, a clone would usually contain only one or a small number of cells. A particular antigen may activate hundreds of different clones, each expressing a different antigen receptor that binds either a different part of the antigen or the same part with a different binding affinity. Although only B cells are shown here, T cells are selected in a similar way. Note that the antigen receptors on the B cells labeled β in this diagram have the same antigen-binding site as the antibodies secreted by the effector Bβ cells. As we discuss later, B cells require co-stimulatory


Cell_Biology_Alberts

Cell_Biology_Alberts. antigen receptors on the B cells labeled β in this diagram have the same antigen-binding site as the antibodies secreted by the effector Bβ cells. As we discuss later, B cells require co-stimulatory signals from T cells to become activated by antigen to proliferate and differentiate into antibody-secreting cells (not shown).


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Cell_Biology_Alberts. antibodies in blood(arbitrary units, Iog scale) frst immunization second immunization with antigen A with antigen A frst immunization with antigen B Thus, during the primary response, clonal expansion and differentiation of antigen-stimulated naïve cells creates many memory cells, which are able to respond to the same antigen more sensitively, rapidly, and effectively. And, unlike most effector cells, which die within days or weeks, memory cells can persist for the lifetime of the animal, even in the absence of their specific antigen, thereby providing lifelong immunological memory. Although most effector B and T cells die after an immune response is over, some survive as effector cells and help provide long-term protection against the pathogen. A small proportion of the plasma cells produced in a primary B cell response, for example, can survive for many months or years in the bone marrow, where they continue to secrete their specific antibodies into the bloodstream.


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Cell_Biology_Alberts. Pathogens generally enter the body through an epithelial surface, usually through the skin, gut, or respiratory tract. To induce an adaptive immune response, microbes or their products must travel from these entry points to a peripheral lymphoid organ, such as a lymph node or the spleen, which are the sites where lymphocytes are activated (see Figure 24–11). The route and destination depend on the site of entry. Lymphatic vessels carry antigens that enter through the skin or respiratory tract to local lymph nodes; antigens that enter through the gut end up in gut-associated peripheral lymphoid organs such as Peyer’s patches; and the spleen filters out antigens that enter the blood (see Figure 24–12). As discussed earlier (see Figure 24–11), in many cases, activated dendritic cells will carry the antigen from the site of infection to the peripheral lymphoid organ, where they play a crucial part in activating T cells, as we discuss later.


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Cell_Biology_Alberts. But only a tiny fraction of naïve B and T cells can recognize a particular microbial antigen in a peripheral lymphoid organ, a reasonable estimate being between 1/10,000 and 1/1,000,000 of each class of lymphocyte, depending on the antigen. How do these rare cells find an antigen-presenting cell displaying their specific antigen? The answer is that the lymphocytes continuously recirculate between one peripheral lymphoid organ and another via the lymph and blood. In a lymph node, for example, lymphocytes continually leave the bloodstream by squeezing out between specialized endothelial cells lining small veins called postcapillary Figure 24–17 A model for the cellular basis of immunological memory.


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Cell_Biology_Alberts. Figure 24–17 A model for the cellular basis of immunological memory. When stimulated by their specific antigen and co-stimulatory signals, naïve lymphocytes proliferate and differentiate. Most become effector cells, which function and then usually die, while others become memory cells. During a subsequent exposure to the same antigen, the memory cells respond more readily, rapidly, and efficiently than did the naïve cells: they proliferate and give rise to effector cells and to more memory cells. Some memory T cells also develop from a minority of effector T cells (not shown). It is not known how the decision to become an effector cell versus a memory cell is made.


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Cell_Biology_Alberts. Figure 24–16 Immunological memory: primary and secondary antibody responses. The secondary response induced by a second exposure to antigen A is faster and greater than the primary response and is specific for A, indicating that the adaptive immune system has specifically remembered its previous encounter with antigen A. The same type of immunological memory is observed in T-cell-mediated responses (not shown). As we discuss later, the types of antibodies produced in the secondary response are different from those produced in the primary response, and these antibodies bind the antigen more tightly.


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Cell_Biology_Alberts. frst exposure to antigen venules. After percolating through the node, they accumulate in small lymphatic vessels that leave the node and connect with other lymphatic vessels that pass through other lymph nodes downstream (see Figure 24–12). Passing into larger and larger vessels, the lymphocytes eventually enter the main lymphatic vessel (the thoracic duct), which carries them back into the blood (Figure 24–18).


Cell_Biology_Alberts

Cell_Biology_Alberts. The continuous recirculation of a lymphocyte between the blood and lymph ends only if its specific antigen activates it in a peripheral lymphoid organ. In that case, the lymphocyte remains in the peripheral lymphoid organ, where it proliferates and differentiates into either effector cells or memory cells. Many of the effector T cells leave the lymphoid organ via the lymph and migrate through the blood to the site of infection (see Figure 24–11), whereas others stay in the lymphoid organ and help activate (or suppress) other immune cells there. Some effector B cells (plasma cells) remain in the peripheral lymphoid organ and secrete antibodies into the blood for days until they die; others migrate to the bone marrow, where they secrete antibodies into the blood for months or years. The memory T and B cells produced join the recirculating pool of lymphocytes.


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Cell_Biology_Alberts. Lymphocyte recirculation depends on specific interactions between the lymphocyte cell surface and the surface of the endothelial cells lining the blood vessels in the peripheral lymphoid organs. Lymphocytes that enter a lymph node via the blood, for example, adhere weakly to specialized endothelial cells lining the postcapillary venules via homing receptors that belong to the selectin family of cell-surface lectins that bind to specific sugar groups on the endothelial cell surface (see Figure 19–28). The lymphocytes roll slowly along the surface of the endothelial cells until another, much stronger adhesion system, dependent on an integrin protein, is called into play by chemokines secreted by the endothelial cells. Now, the lymphocytes stop rolling, and they crawl out of the blood vessel into the lymph node by using yet another cell adhesion protein called CD31 (Figure 24–19). Although B and T cells initially enter the same region of a lymph node, different chemokines guide them to


Cell_Biology_Alberts

Cell_Biology_Alberts. into the lymph node by using yet another cell adhesion protein called CD31 (Figure 24–19). Although B and T cells initially enter the same region of a lymph node, different chemokines guide them to separate regions of the node—B cells to lymphoid follicles and T cells to the paracortex (Figure 24–20).


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Cell_Biology_Alberts. specialized endothelial cell of postcapillary venule Figure 24–19 Migration of a lymphocyte out of the bloodstream into a lymph node.


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Cell_Biology_Alberts. A circulating lymphocyte adheres weakly to the surface of the specialized endothelial cells lining a postcapillary venule in a lymph node. This initial adhesion is mediated by L-selectin (discussed in chapter 19) on the lymphocyte surface. The adhesion is sufficiently weak to enable the lymphocyte, pushed by the flow of blood, to roll along the surface of the endothelial cells. Stimulated by chemokines secreted by specialized endothelial cells in the node (curved red arrow), the lymphocyte rapidly activates a stronger adhesion system, mediated by an integrin. This strong adhesion enables the cell to stop rolling. The lymphocyte then uses an immunoglobulin-like cell adhesion protein (cD31) to bind to the junctions between adjacent endothelial cells and migrate out of the venule. The subsequent migration of the lymphocyte in the lymph node depends on chemokines produced within the node (straight red arrow). The migration of other types of leukocytes out of the bloodstream into sites of


Cell_Biology_Alberts

Cell_Biology_Alberts. migration of the lymphocyte in the lymph node depends on chemokines produced within the node (straight red arrow). The migration of other types of leukocytes out of the bloodstream into sites of infection occurs in a similar way (see Figure 19–28 and Movie 19.2).


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Cell_Biology_Alberts. Figure 24–18 The path followed by lymphocytes as they continuously recirculate between the lymph and blood. The circulation through a lymph node (yellow) is shown here. Microbial antigens are usually carried into the lymph node by activated dendritic cells (not shown), which enter the node via afferent lymphatic vessels draining an infected tissue (green). B and T cells, by contrast, enter via the blood, migrating out of the bloodstream into the lymph node through postcapillary venules. Unless they encounter their antigen, the B and T cells leave the lymph node via efferent lymphatic vessels, which eventually join the thoracic duct. The thoracic duct empties into a large vein carrying blood to the heart, completing the circulation cycle for T and B cells. A typical circulation cycle for these lymphocytes takes about 12–24 hours.


Cell_Biology_Alberts

Cell_Biology_Alberts. Unless they encounter their antigen, both B and T cells soon leave the lymph node via efferent lymphatic vessels. If they encounter their antigen, however, they are stimulated to display adhesion receptors that trap the cells in the node; the cells accumulate at the junction between the B cell and T cell areas, where the rare antigen-specific B and T cells can interact, leading to their proliferation and differentiation into either effector cells or memory cells. Many of the effector cells leave the node, expressing different chemokine receptors that help guide them to their new destinations—effector plasma B cells to the bone marrow and effector T cells to sites of infection.


Cell_Biology_Alberts

Cell_Biology_Alberts. As discussed earlier, cells of the innate immune system use PRRs to distinguish microbial molecules from self molecules made by the host. The adaptive immune system has the far more difficult recognition task of responding specifically to an almost unlimited number of foreign molecules while not responding to the large number of self molecules. How does it accomplish this feat? It helps that self molecules normally do not induce the innate immune reactions required to activate adaptive immune responses. But even when an infection or tissue injury triggers innate reactions, the vast majority of self molecules normally still fail to induce an adaptive immune response. Why?


Cell_Biology_Alberts

Cell_Biology_Alberts. One important reason is that the adaptive immune system “learns” not to respond to self molecules. Normal mice, for example, cannot mount an immune response against one of their own protein components of the complement system called C5 (see Figure 24–7). However, mutant mice that lack the gene encoding C5 but are otherwise genetically identical to normal mice of the same strain can make a strong immune response to this blood protein when immunized with it. The immunological self-tolerance exhibited by normal mice persists only for as long as the self molecule remains in the body: if a self molecule such as C5 is experimentally removed from an adult mouse, the animal gains the ability to respond to it after a few weeks or months, as new B and T cells develop in the absence of C5. Thus, the adaptive immune system is genetically capable of responding to self molecules, but it learns not to do so.


Cell_Biology_Alberts

Cell_Biology_Alberts. Self-tolerance depends on a number of distinct mechanisms, including the following (Figure 24–21): 1. In receptor editing, developing B cells that recognize self molecules change their antigen receptors so that the cells no longer do so. 2. In clonal deletion, potentially self-reactive B and T cells die by apoptosis when they encounter their particular self molecule.


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Cell_Biology_Alberts. 2. In clonal deletion, potentially self-reactive B and T cells die by apoptosis when they encounter their particular self molecule. Figure 24–20 A simplified drawing of a human lymph node. B cells are primarily clustered in structures called lymphoid follicles, whereas T cells are found mainly in the paracortex. chemokines attract both types of lymphocytes into the lymph node from the blood via postcapillary venules (see Figure 24–19). B and T cells then migrate to their respective areas, attracted by different chemokines. If they do not encounter their specific antigen, both B cells and T cells then enter the medullary sinuses and leave the node via the efferent lymphatic vessel. This vessel ultimately empties into the bloodstream, allowing the lymphocytes to begin another cycle of circulation through a peripheral lymphoid organ (see Figure 24–18). During an infection, proliferation of pathogen-specific B cells produces a germinal center in some lymphoid follicles. 3.


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Cell_Biology_Alberts. 3. In clonal inactivation (also called clonal anergy), self-reactive B and T cells become functionally inactivated when they encounter their self molecule. 4. In clonal suppression, self-reactive regulatory T cells (discussed later) suppress the activity of other types of potentially self-reactive lymphocytes. Some of these mechanisms—especially the first two, receptor editing in B cells and clonal deletion of B and T cells—operate in central lymphoid organs when newly formed self-reactive B and T cells first encounter their self molecules, and they are largely responsible for the process called central tolerance. Clonal inactivation and clonal suppression, by contrast, operate mainly when mature B and T cells encounter their self molecules in peripheral lymphoid organs, and they are largely responsible for the process called peripheral tolerance. Clonal deletion, however, can also operate peripherally, and clonal inactivation can also operate centrally.


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Cell_Biology_Alberts. Why does the binding of a self molecule lead to tolerance rather than activation? The answer is still not completely known. As we discuss later, the activation of a B or T cell by its antigen in a peripheral lymphoid organ requires more than just antigen binding: it requires co-stimulatory signals, which are provided by a helper T cell (discussed later) in the case of a B cell and by an activated dendritic cell in the case of a naïve T cell. The production of such signals is usually triggered by exposure to a pathogen, but a self-reactive lymphocyte normally encounters its self antigen in the absence of such signals. Under these conditions, the lymphocyte will not only fail to be activated, it will often be rendered tolerant—being either killed or inactivated, or actively suppressed by a regulatory T cell (see Figure 24–21). In peripheral lymphoid organs, both T cell tolerance and activation usually occur on the surface of a dendritic cell.


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Cell_Biology_Alberts. For reasons that are usually unknown, self-tolerance mechanisms sometimes fail, causing T or B cells (or both) to react against the animal’s own molecules. Figure 24–21 Mechanisms of immunological self-tolerance. When a self-reactive immature B cell binds its self molecule in the central lymphoid organ where the cell is produced, it may alter its antigen receptor so that it is no longer self-reactive (cell 1); this process is called receptor editing. Alternatively, when either an immature B or T cell binds its self molecule in a central lymphoid organ, it may die by apoptosis, a process called clonal deletion (cell 2). Because these two forms of tolerance (shown on the left) occur in central lymphoid organs, they are called central tolerance.


Cell_Biology_Alberts

Cell_Biology_Alberts. When a self-reactive naïve B or T cell escapes tolerance in the central lymphoid organ and binds its self molecule in a peripheral lymphoid organ (cell 4), or in another peripheral tissue, it will generally not be activated, because the binding usually occurs in the absence of sufficient co-stimulatory signals; instead, the cell may die by apoptosis (often after a period of proliferation), be inactivated, or be suppressed by a regulatory T cell. These forms of tolerance (shown on the right) are called peripheral tolerance. As discussed later, the cells providing the co-stimulatory signals are T lymphocytes for B cells and usually dendritic cells for T cells (not shown). For T cells at least, both activation and tolerance in a peripheral lymphoid organ usually occurs on the surface of a dendritic cell, although the dendritic cells are different in the two cases.


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Cell_Biology_Alberts. Myasthenia gravis is an example of such an autoimmune disease. Most of the affected individuals make antibodies against the acetylcholine receptors on their own skeletal muscle cells; these receptors are required for the muscle to contract normally in response to nerve stimulation, which releases acetylcholine (see Figure 11–39). The antibodies interfere with the normal functioning of the receptors so that the patients become weak and may die because they cannot breathe. Similarly, in juvenile (type 1) diabetes, adaptive immune reactions against insulin-secreting β cells in the pancreas kill these cells, leading to severe insulin deficiency.


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Cell_Biology_Alberts. Innate immune responses triggered by pathogens at sites of infection help activate adaptive immune responses in peripheral lymphoid organs. The adaptive immune system is composed of many millions of B and T cell clones, with the cells in each clone sharing a unique cell‑surface receptor that enables them to bind a particular pathogen antigen. The binding of antigen to these receptors, with the help of co‑stimulatory signals, stimulates the lymphocyte to proliferate and differentiate into an effector cell that can help eliminate the pathogen. Effector B cells secrete antibodies, which can act over long distances to help eliminate extracellular pathogens and their toxins. Effector T cells, by contrast, produce cell‑surface and secreted co‑stimulatory molecules, which mainly act locally to help other immune cells eliminate the pathogen; in addition, some T cells can induce infected host cells to kill themselves.


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Cell_Biology_Alberts. During a primary adaptive immune response to an antigen, lymphocytes that recognize the antigen proliferate so that there are more of them to respond the next time, during a secondary response to the same antigen; moreover, during a primary response, some lymphocytes differentiate into memory cells, which can respond faster and more efficiently the next time the same pathogen invades. These two mechanisms are largely responsible for immunological memory. Both B and T cells circulate continuously between one peripheral lymphoid organ and another via the blood and lymph; only if they encounter their specific foreign antigen in a peripheral lymphoid organ do they stop migrating, proliferate, and differentiate into effector cells or memory cells. Lymphocytes that would react against self molecules either alter their receptors (in the case of B cells) or are eliminated or inactivated; they can also be suppressed by regulatory T cells. These mechanisms collectively are responsible for


Cell_Biology_Alberts

Cell_Biology_Alberts. molecules either alter their receptors (in the case of B cells) or are eliminated or inactivated; they can also be suppressed by regulatory T cells. These mechanisms collectively are responsible for immunological self‑tolerance, which ensures that the adaptive immune system normally avoids attacking the molecules and cells of the host.


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Cell_Biology_Alberts. Vertebrates inevitably die of infection if they are unable to make antibodies. Antibodies are secreted proteins that defend us against extracellular pathogens in several ways. They bind to viruses and microbial toxins, thereby preventing them from binding to and damaging host cells (see Figure 24–2). When bound to an extracellular pathogen or its products, antibodies also recruit some of the components of the innate immune system, including various types of leukocytes and components of the complement system, which work together to inactivate or eliminate the invaders. Synthesized exclusively by B cells, antibodies are produced in billions of forms, each with a different amino acid sequence. They belong to the class of proteins called immunoglobulins (abbreviated as Igs) and are among the most abundant protein components in the blood. In this section, we discuss the structure and function of immunoglobulins and how they are made in so many different forms.


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Cell_Biology_Alberts. B cells Make Immunoglobulins (Igs) as Both cell-Surface Antigen receptors and Secreted Antibodies The first Igs made by a newly formed B cell are not secreted but are instead inserted into the plasma membrane, where they serve as receptors for antigen. They are called B cell receptors (BCRs), and each B cell has approximately 105 of them in its plasma membrane. Each BCR is stably associated with invariant trans-membrane proteins that activate intracellular signaling pathways when antigen binds to the BCR; we discuss these invariant proteins later, when we consider how B cells are activated with the assistance of helper T cells.


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Cell_Biology_Alberts. Each B cell clone produces a single species of BCR, with a unique antigen-binding site. When an antigen and a helper T cell activate a naïve or a memory B cell, the B cell proliferates and differentiates into an effector cell, which then produces and secretes large amounts of soluble (rather than membrane-bound) Ig. The secreted Ig is now called an antibody, and it has the same unique antigen-binding site as the BCR (Figure 24–22).


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Cell_Biology_Alberts. A typical Ig molecule is bivalent, with two identical antigen-binding sites. It consists of four polypeptide chains—two identical light chains and two identical heavy chains. The N-terminal parts of both light and heavy chains usually cooperate to form the antigen-binding surface, while the more C-terminal parts of the heavy chains form the tail of the Y-shaped protein (Figure 24–23). The tail mediates many of the activities of antibodies, and antibodies with the same antigen-binding sites can have any one of a number of different tail regions, each of which gives the antibody different functional properties, such as the ability to activate complement or to bind to receptor proteins on phagocytic cells that bind a specific type of antibody tail. Mammals Make Five classes of Igs


Cell_Biology_Alberts

Cell_Biology_Alberts. In mammals, there are five major classes of Igs, each of which mediates a characteristic biological response following antigen binding to an antibody: IgA, IgD, IgE, IgG, and IgM, each with its own class of heavy chain—α, δ, ε, γ, and μ, respectively. IgA molecules have α chains, IgG molecules have γ chains, and so on. Moreover, there are four human IgG subclasses (IgG1, IgG2, IgG3, and IgG4), with γ1, γ2, γ3, and γ4 heavy chains, respectively. There are also two IgA subclasses in humans. In addition to the various classes and subclasses of heavy chains, higher vertebrates have two types of light chains, κ and λ, which seem to be functionally indistinguishable. Either type of light chain may be associated with any of the heavy chains, but an individual Ig molecule always contains identical light chains and identical heavy chains: an IgG molecule, for instance, may have either κ or λ light chains, but not one of each. As a result, an Ig’s antigen-binding sites are always identical (see


Cell_Biology_Alberts

Cell_Biology_Alberts. light chains and identical heavy chains: an IgG molecule, for instance, may have either κ or λ light chains, but not one of each. As a result, an Ig’s antigen-binding sites are always identical (see Figure 24–22).


Cell_Biology_Alberts

Cell_Biology_Alberts. The various heavy chains give a distinctive conformation to the tail region of antibodies, so that each class (and subclass) has characteristic properties of its own. IgM is always the first class of Ig that a developing B cell in the bone marrow makes. It forms the BCRs on the surface of immature naïve B cells. After these cells Figure 24–22 The b cell receptors (bCRs) and secreted antibodies made by a b cell clone. The binding of an antigen to Bcrs on either a naïve or memory B cell (together with co-stimulatory signals provided by helper T cells—not shown) activates the cell to proliferate and differentiate into effector B cells. The effector cells produce and secrete antibodies with a unique antigen-binding site, which is the same as that of the cell-surface Bcrs. Because antibodies have two identical antigen-binding sites, they can cross-link antigens, as shown for an antigen with multiple identical antigenic determinants.


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 24–23 A schematic drawing of a bivalent antibody molecule. The two heavy chains each have a hinge region, which, because of its flexibility, improves the efficiency with which the antibody can cross-link antigens (see Figure 24–22). The two heavy chains also form the tail of the antibody, which determines its functional properties. The heavy and light chains are held together by both covalent S–S bonds (red) and noncovalent bonds (not shown).


Cell_Biology_Alberts

Cell_Biology_Alberts. leave the bone marrow, they start to produce IgD BCRs as well, with the same antigen-binding site as the IgM BCRs. These cells are now called mature naïve B cells, as they can now respond to their specific foreign antigen in peripheral lymphoid organs (Figure 24–24). IgM is also the major class of antibody secreted into the blood in the early stages of a primary antibody response on first exposure to an antigen. In its secreted form, IgM is a wheel-like pentamer composed of five four-chain units, giving it a total of 10 antigen-binding sites that allow it to bind strongly to pathogens; in its antigen-bound form, IgM is highly efficient at activating complement, which is important in early antibody responses to pathogens.


Cell_Biology_Alberts

Cell_Biology_Alberts. The major antibody class in the blood is IgG. These antibodies are four-chain monomers (see Figure 24–23), and they are produced in especially large quantities during secondary antibody responses. The tail region of some subclasses of IgG antibodies that are bound to antigen can activate complement and also bind to specific receptors on macrophages and neutrophils. Largely by means of such Fc receptors (so-named because antibody tails are called Fc regions), these phagocytic cells bind, ingest, and destroy infecting microorganisms that have become coated with the IgG antibodies produced in response to the infection; the activated Fc receptors also signal the phagocyte to secrete pro-inflammatory cytokines (Movie 24.4).


Cell_Biology_Alberts

Cell_Biology_Alberts. The tail region of IgE antibodies binds to another class of Fc receptors on the surface of mast cells in tissues and of basophils in the blood. Because antigen-free IgE antibodies bind with high affinity to such Fc receptors, the antibodies act as antigen receptors on these cells. Antigen binding to the bound antibodies activates the Fc receptors and stimulates the cells to secrete a variety of cytokines and biologically active amines, especially histamine, which causes blood vessels to dilate and become leaky; this helps leukocytes, antibodies, and complement components to enter sites where mast cells have been activated. The release of amines from mast cells and basophils is largely responsible for the symptoms of such allergic reactions as hay fever, asthma, and hives. In addition, mast cells secrete factors that attract and activate leukocytes called eosinophils, which also have Fc receptors that bind IgE molecules and can kill extracellular parasitic worms, especially if the


Cell_Biology_Alberts

Cell_Biology_Alberts. mast cells secrete factors that attract and activate leukocytes called eosinophils, which also have Fc receptors that bind IgE molecules and can kill extracellular parasitic worms, especially if the worms are coated with IgE antibodies (see Figure 24–6).


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Cell_Biology_Alberts. IgA is the principal antibody class in secretions, including saliva, tears, milk, and respiratory and intestinal secretions. Yet another class of Fc receptors, located on the relevant epithelial cells, guides the secretion by binding antigen-free IgA dimers and transporting them across the epithelium. The properties of the various classes of antibodies in humans are summarized in Table 24–2.


Cell_Biology_Alberts

Cell_Biology_Alberts. All classes of Ig can be made in a membrane-bound form, as well as in a soluble, secreted form. The two forms differ only in the C-terminus of their heavy chain. The heavy chains of membrane-bound Ig molecules (BCRs) have a trans-membrane hydrophobic C-terminus, which anchors them in the lipid bilayer of the B cell’s plasma membrane. The heavy chains of secreted antibody molecules, by contrast, have instead a hydrophilic C-terminus, which allows them to escape from the cell. The switch in the character of the Ig molecules made occurs because the activation of B cells by antigen and helper T cells induces a change in the way in which the heavy-chain RNA transcripts are made and processed in the nucleus (see Figure 7–59).


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Cell_Biology_Alberts. Figure 24–24 Stages of b cell development. All of the stages shown occur before the cells bind their specific antigen. The first cells in the B cell lineage that make Ig are called pro-B cells; they make μ heavy chains, which remain in the endoplasmic reticulum until a special type of light chain is made called a surrogate light chain. The surrogate light chains substitute for genuine light chains and assemble with μ chains to form a receptor molecule that inserts into the plasma membrane. The cells are now called pre-B cells. Signaling from this pre-B cell receptor allows the cells to make bona fide light chains, which combine with μ chains to form four-chain IgM molecules that serve as cell-surface Bcrs on immature naïve B cells. After these cells leave the bone marrow, they start to express IgD Bcrs as well, which have the same antigen-binding sites as the IgM Bcrs; it is this mature naïve B cell that reacts with its specific foreign antigen in peripheral lymphoid organs.


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Cell_Biology_Alberts. Ig Light and heavy chains consist of constant and Variable regions Both light and heavy chains have a variable amino acid sequence at their N-terminal ends but a constant sequence at their C-terminal ends. Whereas the constant region and variable region of a light chain are the same size, the constant region of a heavy chain is about three or four times longer, depending on the class (Figure 24–25).


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Cell_Biology_Alberts. The variable regions of the light and heavy chains come together to form the antigen-binding sites, and the variability of their amino acid sequences provides the structural basis for the diversity of these binding sites. The greatest diversity occurs in three small hypervariable regions in the variable regions of both light and heavy chains. Only about 5–10 amino acids in each hypervariable region form the actual antigen-binding site (Figure 24–26). As a result, the size of the antigenic determinant that an Ig molecule recognizes is generally comparably small: it can consist of fewer than 10 amino acids on the surface of a globular protein, for example (see Figure 24–22).


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Cell_Biology_Alberts. Both light and heavy chains are made up of repeating segments—each about 110 amino acids long and each containing one intrachain disulfide bond. Each repeating segment folds independently to form a compact functional unit called an immunoglobulin (Ig) domain. As shown in Figure 24–27A, a light chain consists of one variable (VL) and one constant (CL) domain, whereas a heavy chain has one variable and three or four constant domains: the variable domains of the light and heavy chains pair to form the antigen-binding region. Each Ig domain has a very similar three-dimensional structure, consisting of a sandwich of two β Figure 24–25 Constant and variable regions of Ig chains. The variable regions of the light and heavy chains form the antigen-binding sites, while the constant regions of the heavy chains determine the other biological properties of an Ig protein. The different subclasses of IgG antibodies have different γ-chain constant regions.


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Cell_Biology_Alberts. variable region hypervariable regions Figure 24–26 Ig hypervariable regions. of heavy chain of heavy chain highly schematized drawing of how the three hypervariable regions in each light and heavy chain together form each antigen-binding site of an Ig protein. sheets held together by a disulfide bond; the variable domains are unique in that each has its particular set of hypervariable regions, which are arranged in three hypervariable loops that cluster together at the ends of the variable domains to form the antigen-binding site (Figure 24–27B). Even in the absence of antigen stimulation, a human can probably make more than 1012 different Ig molecules—its preimmune, primary Ig repertoire. The primary repertoire consists of IgM and IgD proteins and is apparently large enough to ensure that there will be an antigen-binding site to fit almost any potential


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Cell_Biology_Alberts. Figure 24–27 Ig domains. (A) The light and heavy chains in an Ig protein are each folded into similar repeating domains. The variable domains (shaded in blue) of the light and heavy chains (VL and Vh) make up the antigen-binding sites, while the constant domains (shaded in gray) of the heavy chains (mainly ch2 and ch3) determine the other biological properties of the protein. The heavy chains of IgM and Ige do not have a hinge region and have an extra constant domain (ch4). hydrophobic interactions between domains on adjacent chains help hold the chains together in the Ig molecule: VL binds to Vh, cL binds to ch1, and so on. (B) X-ray crystallography-based structures of the Ig domains of a light chain (Movie 24.5). Both the variable and constant domains have a similar overall structure, consisting of two β sheets joined by a disulfide bond (red). Note that all the hypervariable regions (black) form loops at the far end of the variable domain, where they come together to form part of


Cell_Biology_Alberts

Cell_Biology_Alberts. consisting of two β sheets joined by a disulfide bond (red). Note that all the hypervariable regions (black) form loops at the far end of the variable domain, where they come together to form part of the antigen-binding site. All Igs are glycosylated on their ch2 domains (not shown); the attached oligosaccharide chains vary from Ig to Ig and can greatly influence the biological properties of the protein, largely by affecting its binding to Fc receptors on immune cells.


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Cell_Biology_Alberts. antigenic determinant, albeit with low affinity—Ka ≈ 105–107 liters/mole. After stimulation by antigen and helper T cells, B cells can switch from making IgM and IgD to making other classes of Ig—a process called class switching. In addition, the binding affinity of these Igs for their antigen progressively increases over time—a process called affinity maturation. Thus, antigen stimulation generates a secondary Ig repertoire, with a greatly increased affinity (Ka up to 1011 liters/mole) and diversity of both Ig classes and antigen-binding sites.


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Cell_Biology_Alberts. How can each of us make so many different Igs? The problem is not quite as formidable as it might first appear. Recall that the variable regions of the Ig light and heavy chains usually combine to form the antigen-binding site. Thus, if we had 1000 genes encoding light chains and 1000 genes encoding heavy chains, we could, in principle, combine their products in 1000 × 1000 different ways to make 106 different antigen-binding sites. Nonetheless, we have evolved special genetic mechanisms to enable our B cells to generate an almost unlimited number of different light and heavy chains in a remarkably economical way. We do so in two steps. First, before antigen stimulation, developing B cells join together separate gene segments in DNA to create the genes that encode the primary repertoire of low-affinity IgM and IgD proteins. Second, after antigen stimulation, the assembled Ig genes can undergo two further changes—mutations that can increase the affinity of their antigen-binding site


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Cell_Biology_Alberts. of low-affinity IgM and IgD proteins. Second, after antigen stimulation, the assembled Ig genes can undergo two further changes—mutations that can increase the affinity of their antigen-binding site and DNA rearrangements that switch the class of Ig made. Together, these changes produce the secondary repertoire of high-affinity IgG, IgE, and IgA proteins.


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Cell_Biology_Alberts. We produce our primary Ig repertoire by joining separate Ig gene segments together during B cell development. Each type of Ig chain—κ light chains, λ light chains, and heavy chains—is encoded by a separate locus on a separate chromosome. Each locus contains a large number of gene segments encoding the V region of an Ig chain, and one or more gene segments encoding the C region. During the development of a B cell in the bone marrow, a complete coding sequence for each of the two Ig chains to be synthesized is assembled by site-specific genetic recombination (discussed in Chapter 5). Once a V-region coding sequence is assembled next to a C-region sequence, it can then be co-transcribed and the resulting RNA transcript processed to produce an mRNA molecule that codes for the complete Ig polypeptide chain.


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Cell_Biology_Alberts. Each light-chain V region, for example, is encoded by a DNA sequence assembled from two gene segments—a long V gene segment and a short joining or J gene segment (Figure 24–28). Each heavy-chain V region is similarly constructed by combining gene segments, but here an additional diversity segment, or D gene segment, is also required (Figure 24–29). In addition to bringing together the separate gene segments of the Ig gene, these rearrangements also activate transcription from the gene promoter through changes in the relative positions of the cis-regulatory DNA sequences acting on the gene. Thus, a complete Ig chain can be synthesized only after the DNA has been rearranged.


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Cell_Biology_Alberts. The large number of inherited V, J, and D gene segments available for encoding Ig chains contributes substantially to Ig diversity, and the combinatorial joining of these segments (called combinatorial diversification) greatly increases this contribution. Any of the 35 or so functional V segments in our κ light-chain locus, for example, can be joined to any of the 5 J segments (see Figure 24–28), so that this locus can encode at least 175 (35 × 5) different κ-chain V regions. Similarly, any of the 40 V segments in the human heavy-chain locus can be joined to any of the 23 or so D segments and to any of the 6 J segments to encode at least 5520 (40 × 23 × 6) different heavy-chain V regions. By this mechanism alone, called V(D)J recombination, a human can produce 295 different VL regions (175 κand 120 λ) and 5520 different VH regions. In principle, these could then be combined to make over 1.5 × 106 (295 × 5520) different antigen-binding sites.


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Cell_Biology_Alberts. V(D)J recombination is mediated by an enzyme complex called V(D)J recombinase, which recognizes recombination signal sequences in the DNA that flanks each gene segment to be joined. Although the process ensures that only appropriate gene segments recombine, a variable number of nucleotides are often lost from the ends of the recombining gene segments, and one or more randomly regions of DNA to be joined chosen nucleotides are also inserted. This random loss and gain of nucleotides at joining sites is called junctional diversification, and it enormously increases the diversity of V-region coding sequences created by V(D)J recombination (up to about 108-fold), specifically in the third hypervariable region. This increased diversification comes at a price, however. In many cases, it shifts the reading frame to produce a nonfunctional gene, in which case the developing B cell fails to make a functional Ig molecule and consequently dies in the bone marrow. Once a B cell makes a functional


Cell_Biology_Alberts

Cell_Biology_Alberts. reading frame to produce a nonfunctional gene, in which case the developing B cell fails to make a functional Ig molecule and consequently dies in the bone marrow. Once a B cell makes a functional heavy chain and light chain that form an antigen-binding site, it turns off the V(D)J recombination process, thereby ensuring that the cell makes Ig of only one antigen-binding specificity.


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Cell_Biology_Alberts. B cells making BCRs that bind strongly to self antigens in the bone marrow would be dangerous. Such B cells maintain expression of an active V(D)J recombinase and are activated by such self-binding to undergo a second round of V(D)J recombination in a light-chain locus, thereby changing the specificity of its BCR—the process of receptor editing discussed earlier; self-reactive B cells that fail to change their specificity die by apoptosis, in the process of clonal deletion (see Figure 24–21). As mentioned earlier, with the passage of time following an infection or vaccination, there is usually a progressive increase in the affinity of the antibodies produced against the pathogen. This phenomenon of affinity maturation is due to


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Cell_Biology_Alberts. Figure 24–28 The V–J joining process involved in making a human κ light chain. In the “germ-line” DNA (where the Ig gene segments are not rearranged and are therefore not being expressed), the cluster of five J gene segments is separated from the c-region coding sequence by a short intron and from the 35 or so functional V gene segments by thousands of nucleotide pairs. During the development of a B cell, a randomly chosen V gene segment (V3 in this case) is moved to lie precisely next to one of the J gene segments (J3 in this case). The “extra” J gene segments (J4 and J5) and the intron sequence are transcribed (along with the joined V3 and J3 gene segments and the c-region coding sequence) and then removed by rNA splicing to generate mrNA molecules with contiguous V3, J3, and C sequences, as shown. These mrNAs are then translated into κ light chains. A J gene segment encodes the 15 or so c-terminal amino acids of the V region, and a short sequence containing the V–J segment


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Cell_Biology_Alberts. as shown. These mrNAs are then translated into κ light chains. A J gene segment encodes the 15 or so c-terminal amino acids of the V region, and a short sequence containing the V–J segment junction encodes the third hypervariable region, which is the most variable part of the light-chain V region.


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Cell_Biology_Alberts. Figure 24–29 The human heavy-chain locus. There are 40 V segments, about 23 D segments, 6 J segments, and an ordered cluster of c-region coding sequences, each cluster encoding a different class of heavy chain. The D segment (and part of the J segment) encodes amino acids in the third hypervariable region, which is the most variable part of the heavy-chain V region. The genetic mechanisms involved in producing a heavy chain are the same as those shown in Figure 24–28 for light chains, except that two DNA rearrangement steps are required instead of one: first a D segment joins to a J segment, and then a V segment joins to the rearranged DJ segment. The rearrangements lead to the production of a VDJc mrNA that encodes a complete Ig heavy chain. The figure is not drawn to scale: the total length of the heavy-chain locus is over two megabases. Moreover, a number of details are omitted: for example, the exons encoding each c-region Ig domain and the hinge region (see Figure 24–27) and the


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Cell_Biology_Alberts. of the heavy-chain locus is over two megabases. Moreover, a number of details are omitted: for example, the exons encoding each c-region Ig domain and the hinge region (see Figure 24–27) and the different subclasses of cγ-coding segments are not shown.


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Cell_Biology_Alberts. the accumulation of point mutations in both heavy-chain and light-chain V-region coding sequences. The mutations occur long after the coding regions have been assembled. After B cells have been stimulated by antigen and helper T cells in a peripheral lymphoid organ, some of the activated B cells proliferate rapidly in the lymphoid follicles and form germinal centers (see Figure 24–20). Here, the B cells mutate at the rate of about one mutation per V-region coding sequence per cell generation. Because this is about a million times greater than the spontaneous mutation rate in other genes and occurs in somatic cells rather than germ cells, the process is called somatic hypermutation.


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Cell_Biology_Alberts. Very few of the altered Igs generated by hypermutation will have an increased affinity for the antigen. But, because the same Ig genes produce both BCRs and secreted antibodies, the antigen will stimulate preferentially those few B cells that do make BCRs with increased affinity for the antigen. Clones of these altered B cells will preferentially survive and proliferate, especially as the amount of antigen decreases to very low levels late in the response. Most other B cells in the germinal center will die by apoptosis. Thus, as a result of repeated cycles of somatic hyper-mutation followed by antigen-driven proliferation of selected clones of effector and memory B cells, antibodies of increasingly higher affinity become abundant during an adaptive immune response, providing progressively better protection against the pathogen (Movie 24.6).


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Cell_Biology_Alberts. A breakthrough in understanding the molecular mechanism of somatic hyper-mutation came with the identification of an enzyme that is required for the process. It is called activation-induced deaminase (AID) because it is expressed specifically in activated B cells and deaminates cytosine (C) to uracil (U) during transcription of V-region coding DNA. The deamination produces U:G mismatches in the DNA double helix, and the repair of these mismatches produces various types of mutations, depending on the repair pathway used. Somatic hypermutation affects only actively transcribed DNA, because AID works only on single-stranded DNA (which is transiently exposed during transcription) and because proteins involved in the transcription of V-region coding sequences are required to recruit the AID enzyme. AID is also required for activated B cells to switch from IgM and IgD production to the production of the other classes of Ig, as we now discuss. B cells can Switch the class of Ig They Make


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Cell_Biology_Alberts. After a developing B cell leaves the bone marrow, before it interacts with antigen, it expresses both IgM and IgD BCRs on its surface, both with the same antigen-binding sites (see Figure 24–24). Stimulation by antigen and helper T cells activates many of these mature naïve B cells to become IgM-secreting effector cells, so that IgM antibodies dominate the primary antibody response. Later in the immune response, however, when activated B cells are undergoing somatic hypermutation, the combination of antigen and helper-T-cell-derived cytokines (discussed later) stimulates many of the B cells to switch from making membrane-bound IgM and IgD to making IgG, IgE, or IgA, in the process of class switching. Some of these cells become memory cells that express the corresponding class of Ig as BCRs on their surface, while others become effector cells that secrete the Ig molecules as antibodies. The IgG, IgE, and IgA molecules retain their original antigen-binding site and are collectively


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Cell_Biology_Alberts. BCRs on their surface, while others become effector cells that secrete the Ig molecules as antibodies. The IgG, IgE, and IgA molecules retain their original antigen-binding site and are collectively referred to as secondary classes of Igs, because they are produced only after antigen stimulation, dominate secondary antibody responses, and make up the secondary Ig repertoire.


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Cell_Biology_Alberts. As discussed earlier, the constant region of an Ig heavy chain determines the class of the Ig. Thus, the ability of B cells to switch the class of antibody they make without changing the antigen-binding site implies that the same assembled VH-region coding sequence (which specifies the antigen-binding part of the heavy chain) can sequentially associate with different CH-coding sequences. This has important functional implications. It means that, in an individual animal, a particular antigen-binding site that has been selected by environmental antigens can be distributed among the various classes of antibodies, thereby acquiring the different biological properties of each class. Cµ C° TRANSCRIPTION, RNA SPLICING,5ˆ


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Cell_Biology_Alberts. When a B cell switches from making IgM and IgD to one of the secondary classes of Ig, an irreversible change occurs in the DNA—a process called class switch recombination. It entails the deletion of all the CH-coding sequences between the assembled VDJ-coding sequence and the particular CH-coding sequence that the cell is destined to express. Class switch recombination differs from V(D)J recombination in several ways. (1) It happens after antigen stimulation, mainly in germinal centers, and depends on helper T cells. (2) It uses different recombination signal sequences, called switch sequences, which flank the different CH-coding segments. (3) It involves cutting and joining the switch sequences, which are noncoding sequences, and leaves the assembled VH-region coding sequence unchanged (Figure 24–30). (4) Most importantly, the molecular mechanism is different. It depends on AID, which is also involved in somatic hypermutation, rather than on the V(D)J recombinase. The cytokines that


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Cell_Biology_Alberts. 24–30). (4) Most importantly, the molecular mechanism is different. It depends on AID, which is also involved in somatic hypermutation, rather than on the V(D)J recombinase. The cytokines that activate class switching induce the production of transcription regulators that activate transcription from the relevant switch sequences, allowing the recruitment of AID to these sites.


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Cell_Biology_Alberts. Once bound, AID initiates switch recombination by deaminating some cytosines to uracil in the vicinity of these switch sequences. Excision of these uracils is thought to lead to double-strand breaks in the participating switch regions, which are then joined by a form of nonhomologous end joining (discussed in Chapter 5). Thus, whereas the primary Ig repertoire in humans (and mice) is generated by V(D)J joining mediated by V(D)J recombinase, the secondary antibody repertoire is generated by somatic hypermutation and class switch recombination, both of which are mediated by AID. Figure 24–31 lists the main mechanisms that we have discussed in this chapter that diversify Igs.