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Cell_Biology_Alberts. a patient of recurrent stomach ulcers. Remarkably, H. pylori is able to persist for life as a commensal in most humans. One way in which it survives in the stomach is by producing the enzyme urease, which converts urea to ammonia that neutralizes the acid in its immediate vicinity. The bacterium also uses its flagellum for chemotactic motility, allowing it to seek out the more neutral pH near the surface of gastric epithelial cells. H. pylori virulence proteins that target both epithelial and immune cells help H. pylori persist in the stomach, but they can also induce chronic inflammation, alteration in host gene expression, changes in cell proliferation and apoptosis, and disruption of cell–cell junctions, all of which are predisposing factors for stomach cancer.


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Cell_Biology_Alberts. Extracellular pathogens can cause serious disease without entering host cells. Bordetella pertussis, the bacterium that causes whooping cough, for example, colonizes the respiratory epithelium and circumvents the normal mechanism that Figure 23–15 Pathogenic E. coli in the infected bladder of a mouse.


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Cell_Biology_Alberts. (A) Scanning electron micrograph of uropathogenic E. coli, a common cause of bladder and kidney infections. The bacteria are attached to the surface of epithelial cells lining the infected bladder. (B) A closeup view of one of the bacteria showing the pili on its surface. (C) An E. coli pilus has adaptor proteins on its tip that bind to glycolipids on the surface of kidney cells. (A, from G.E. Soto and S.J. Hultgren, J. Bacteriol. 181:1059–1071, 1999. With permission from the American Society for Microbiology; B, courtesy of D.G. Thanassi and S.J. Hultgren, Methods 20:111–126, 2000. With permission from Academic Press.) (A) P P P Tir injected Tir inserts and folds in plasma membrane HOST CELL type III secretion system enteropathogenic E. coli outer membrane inner membrane intimin intimin actin flaments pedestal phosphorylated Tir host proteins that promote actin polymerization clears the respiratory tract by expressing adhesins that bind ciliated epithelial cells. The adherent


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Cell_Biology_Alberts. actin flaments pedestal phosphorylated Tir host proteins that promote actin polymerization clears the respiratory tract by expressing adhesins that bind ciliated epithelial cells. The adherent bacteria produce toxins that eventually kill the ciliated cells, compromising the host’s ability to clear the infection. The most familiar of these is pertussis toxin, which, like the cholera toxin discused above, has an A subunit that ADP-ribosylates the α subunit of the G protein Gi, inhibiting the G protein from suppressing the activity of the host cell’s adenylyl cyclase, thereby increasing the production of cyclic AMP (see Figure 23–6). This toxin also interferes with the chemotactic pathway that neutrophils use to seek out and destroy invading bacteria (see Figures 16–3 and 16–86). B. pertussis colonization of the respiratory tract causes severe coughing, which helps spread the infection.


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Cell_Biology_Alberts. Not all extracellular pathogens that colonize an epithelium exert their effect through toxins. Enteropathogenic E. coli (EPEC), which causes diarrhea in young children, uses a type III secretion system (see Figure 23–7) to deliver its own special receptor protein (called Tir) into the plasma membrane of a host intestinal epithelial cell (Figure 23–16). The extracellular domain of Tir binds to the bacterial surface protein intimin, triggering actin polymerization in the host cell that results in the formation of a unique cell-surface protrusion called a pedestal; this pushes the tightly adherent bacteria up about 10 μm from the host-cell membrane, thereby promoting bacterial movement along the cell surface. A similar strategy is used by vaccinia virus (the virus that was used as a vaccine to eradicate smallpox) to form mobile pedestals, which promote spread of the virus from cell to cell. The study of how EPEC and vaccinia virus promote actin polymerization has been of major importance


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Cell_Biology_Alberts. eradicate smallpox) to form mobile pedestals, which promote spread of the virus from cell to cell. The study of how EPEC and vaccinia virus promote actin polymerization has been of major importance in understanding how intracellular signaling pathways regulate the cytoskeleton in normal, uninfected cells (discussed in Chapter 16). Although pedestal formation promotes the spread of these pathogens, the sympoms of EPEC infection (severe diarrhea) are caused by the loss of absorptive microvilli and disruption of signaling pathways in epithelial cells, which are triggered by Tir and other effector proteins.


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Cell_Biology_Alberts. Many pathogens have to enter host cells to cause disease. These intracellular pathogens include all viruses and many bacteria and protozoa. Each of these has a preferred niche for replication and survival within host cells. Bacteria and protozoa replicate either in the cytosol or within a membrane-enclosed compartment. While most RNA viruses replicate within the cytosol, most DNA viruses replicate in the nucleus. Life inside a host cell has several advantages. The pathogens are not accessible to antibodies, nor are they easy targets for phagocytic cells (discussed in Chapter 24); furthermore, intracellular bacteria and protozoa are bathed in a rich source of nutrients, and viruses have access to the host cell’s biosynthetic


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Cell_Biology_Alberts. Figure 23–16 Interaction of enteropathogenic E. coli (ePeC) with host intestinal epithelial cells. (A) When EPEC contacts an epithelial cell in the lining of the human gut, it delivers a bacterial protein called Tir into the host cell through a type III secretion system. Tir then inserts into the plasma membrane of the host cell, where it functions as a receptor for the bacterial adhesin protein intimin. Next, a host-cell protein tyrosine kinase phosphorylates the intracellular domain of Tir on tyrosines. Phosphorylated Tir recruits host-cell proteins (including an adaptor protein, a WASp protein, and the Arp 2/3 complex) that trigger actin polymerization (see Figure 16–16). Consequently, a branched network of actin filaments assembles underneath the bacterium, forming an actin pedestal (Movie 23.4). (B) EPEC on a pedestal. In this fluorescence micrograph, the DNA of the EPEC and host cell is labeled in blue, Tir protein is labeled in green, and host-cell actin filaments are labeled


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Cell_Biology_Alberts. (Movie 23.4). (B) EPEC on a pedestal. In this fluorescence micrograph, the DNA of the EPEC and host cell is labeled in blue, Tir protein is labeled in green, and host-cell actin filaments are labeled in red. The inset shows a close-up view of the two upper bacteria on pedestals. (B, from


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Cell_Biology_Alberts. D. Goosney et al., Annu. Rev. Cell Dev. Biol. 16:173–189, 2000. With permission from Annual Reviews.) machinery for their reproduction. This lifestyle, however, requires that the pathogen have mechanisms for entering host cells, for finding a suitable subcellular niche where it can replicate, and for exiting from the infected cell to spread the infection. Below we consider some of the myriad ways that individual intracellular pathogens exploit and modify host cell biology to satisfy these requirements. Viruses Bind to Virus Receptors at the Host Cell Surface The first step for any intracellular pathogen is to bind to the surface of the host target cell. Viruses accomplish this by the binding of viral surface proteins to virus receptors displayed on the host cell. The first virus receptor identified was an


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Cell_Biology_Alberts. E. coli surface protein that is recognized by the bacteriophage lambda; the protein normally functions to transport the sugar maltose from outside the bacterium to the inside where it is used as an energy source. Receptors need not be proteins, however: an envelope protein of herpes simplex virus, for example, binds to heparan sulfate proteoglycans (discussed in Chapter 19) on the surface of certain vertebrate host cells, and simian virus 40 (SV40) binds to a glycolipid. The specificity of virus-receptor interactions often serves as a barrier preventing the spread of a virus from one species to another. Acquiring the ability to bind to a new receptor often requires multiple changes in a virus, but it can be crucial in allowing the cross-species transmission that can result in new disease outbreaks.


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Cell_Biology_Alberts. Viruses that infect animal cells generally exploit cell-surface receptor molecules that are either ubiquitous (such as the sialic-acid-containing oligosaccharides used by the influenza virus) or found uniquely on those cell types in which the virus replicates (such as the neuron-specific proteins used by rabies virus). Although a virus usually uses a single type of host-cell receptor, some viruses use more than one type. An important example is HIV-1, which requires two types of receptors to enter a host cell. Its primary receptor is CD4, a cell-surface protein on helper T cells and macrophages that is involved in immune recognition (discussed in Chapter 24). It also requires a co-receptor, which is either CCR5 (a receptor for β-chemokines) or CXCR4 (a receptor for α-chemokines), depending on the particular variant of the virus; macrophages are susceptible only to HIV variants that use CCR5 for entry, whereas helper T cells are most efficiently infected by variants that use CXCR4


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Cell_Biology_Alberts. on the particular variant of the virus; macrophages are susceptible only to HIV variants that use CCR5 for entry, whereas helper T cells are most efficiently infected by variants that use CXCR4 (Figure 23–17). The viruses that are found within the first few months after HIV infection almost invariably use CCR5, which explains why individuals that carry a defective CCR5 gene are less susceptible to HIV infection. In the later stages of infection, viruses often either switch to use CXCR4 or adapt to use both co-receptors through the accumulation of mutations; in this way, the virus can change the cell types it infects as the disease progresses. It may seem paradoxical that viruses would infect immune cells, as we might expect that virus binding would trigger an immune response; but invasion of an immune cell can be a useful way for a virus to weaken the immune response and travel around the body to infect other immune cells.


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Cell_Biology_Alberts. °-chemokine ˜-chemokine (Sdf1) (Rantes, Mip1°, or Mip1˜) Figure 23–17 Receptor and co-receptors for HIV. All strains of HIV require the CD4 protein as a primary receptor. Early in an infection, most of the viruses use CCR5 as a co-receptor, allowing them to infect macrophages and their precursors, monocytes. As the infection progresses, mutant variants arise that now use CXCR4 as a co-receptor, enabling them to infect helper T cells efficiently. The natural ligand for the chemokine receptors (Sdf1 for CXCR4; Rantes, Mip1α, or Mip1β for CCR5) blocks co-receptor function and prevents viral invasion. Viruses Enter Host Cells by Membrane Fusion, Pore Formation, or Membrane Disruption


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Cell_Biology_Alberts. After recognition and attachment to the host cell surface, the virus must enter the cell to replicate. Some enveloped viruses enter the host cell by fusing their envelope membrane with the plasma membrane. Most viruses, whether enveloped or nonenveloped, activate signaling pathways in the cell that induce endocytosis, commonly via clathrin-coated pits (see Figure 13–7), leading to internalization into endosomes. Large viruses that do not fit into clathrin-coated vesicles, such as poxviruses, often enter cells by macropinocytosis, a process by which membrane ruffles fold over and entrap fluid into macropinosomes (see Figure 13–50). Once inside endosomes, fusion of the viral envelope occurs from the lumenal side of the endosome membrane. The mechanism of membrane fusion mediated by viral spike glycoproteins has similarities with SNARE-mediated membrane fusion during normal vesicular trafficking (discussed in Chapter 13).


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Cell_Biology_Alberts. Enveloped viruses regulate fusion both to ensure that they fuse only with the appropriate host cell membrane and to prevent fusion with one another. For viruses such as HIV-1 that fuse at neutral pH with the plasma membrane (Figure 23–18A), binding to receptors or co-receptors usually triggers a conformational change in a viral envelope protein that exposes a normally buried fusion peptide (see Figure 13–21). Other enveloped viruses, such as influenza A virus, only fuse with a host cell membrane after endocytosis (Figure 23–18B); in this case, it is frequently the acid environment in the late endosome that triggers the conformational change in a viral surface protein that exposes the fusion peptide. The H+ (B) acidifcation, fusion, uncoating fusion with membrane after endocytosis endosomal membrane disruption pore formation(C) (D) endocytosis endocytosis early endosome lysis uncoating, pore formation DNA enters nucleus Figure 23–18 Four virus entry strategies.


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Cell_Biology_Alberts. (A) Some enveloped viruses, such as HIV, fuse directly with the host-cell plasma membrane to release their RNA genome (blue) and capsid proteins (brown) into the cytosol. (B) Other enveloped viruses, such as influenza virus, first bind to cell-surface receptors, triggering receptor-mediated endocytosis; when the endosome acidifies, the virus envelope fuses with the endosomal membrane, releasing the viral RNA genome (blue) and capsid proteins (brown) into the cytosol. (C) Poliovirus, a nonenveloped virus, induces receptor-mediated endocytosis, and then forms a pore in the endosomal membrane to extrude its RNA genome (blue) into the cytosol. (D) Adenovirus, another nonenveloped virus, uses a more complicated strategy: it induces receptor-mediated endocytosis and then disrupts the endosomal membrane, releasing the capsid and its DNA genome into the cytosol; the trimmed-down virus eventually docks onto a nuclear pore and releases its DNA (red) directly into the nucleus (Movie 23.5).


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Cell_Biology_Alberts. pumped into the early endosome also has another effect; it enters the influenza virion through an ion channel in the viral envelope and triggers changes in the viral capsid. These priming steps allow the capsids to disassemble once released into the cytosol after virus fusion with the late endosomal membrane.


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Cell_Biology_Alberts. Nonenveloped viruses use different strategies to enter host cells—strategies that do not rely on membrane fusion. Poliovirus, which causes poliomyelitis, binds to a cell-surface receptor, triggering both receptor-mediated endocytosis (see Figure 13–52) and a conformational change in the viral particle. The conformational change exposes a hydrophobic projection on one of the capsid proteins, which inserts into the endosomal membrane to form a pore. The viral RNA genome then enters the cytosol through the pore, leaving the capsid in the endosome (Figure 23–18C). Other nonenveloped viruses such as adenovirus disrupt the endosomal membrane after they are taken up by receptor-mediated endocytosis. One of the proteins released from the capsid lyses the endosomal membrane, releasing the remainder of the virus into the cytosol. During endosomal trafficking and subsequent transport within the cytosol, adenoviruses undergo multiple uncoating steps, which sequentially remove structural proteins


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Cell_Biology_Alberts. of the virus into the cytosol. During endosomal trafficking and subsequent transport within the cytosol, adenoviruses undergo multiple uncoating steps, which sequentially remove structural proteins and ready the virus particles to release their DNA into the nucleus through nuclear pore complexes (Figure 23–18D).


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Cell_Biology_Alberts. Bacteria are much larger than viruses—too large to be taken up either through pores or by receptor-mediated endocytosis. Instead, they enter host cells by phagocytosis, which is a normal function of phagocytes such as neutrophils, macrophages, and dendritic cells (discussed in Chapter 24). These phagocytes patrol the tissues of the body and ingest and destroy microbes; however, some intracellular bacterial pathogens such as M. tuberculosis use this to their advantage and have evolved to survive and multiply inside macrophages. Some bacterial pathogens can invade host cells that are normally nonphagocytic. One way they do so is by expressing an invasion protein that binds with high affinity to a host-cell receptor, which is often a cell–cell or cell–matrix adhesion protein (discussed in Chapter 19). For example, Yersinia pseudotuberculosis (a bacterium that causes diarrhea and is a close relative of the plague bacterium


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Cell_Biology_Alberts. Y. pestis) expresses a protein called invasin that has an RGD motif that is similar to fibronectin’s and likewise is recognized by host-cell β1 integrins (see Figure 19–55). Listeria monocytogenes, which causes a rare but serious form of food poisoning, invades host cells by expressing a protein that binds to the cell–cell adhesion protein E-cadherin (see Figure 19–6). For both these bacterial species, binding of the bacterial invasion proteins to the host cell adhesion proteins stimulates signaling through members of the Rho family of small GTPases (discussed in Chapter 16). This in turn activates proteins in the WASp family and the Arp 2/3 complex, leading to actin polymerization at the site of bacterial attachment. Actin polymerization, together with the assembly of a clathrin coat (see Figure 13–6), drives the advancement of the host cell’s plasma membrane over the adhesive surface of the microbe, resulting in the phagocytosis of the bacterium—a process known as the zipper


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Cell_Biology_Alberts. (see Figure 13–6), drives the advancement of the host cell’s plasma membrane over the adhesive surface of the microbe, resulting in the phagocytosis of the bacterium—a process known as the zipper mechanism of invasion (Figure 23–19A).


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Cell_Biology_Alberts. A second pathway by which bacteria can invade nonphagocytic cells is known as the trigger mechanism (Figure 23–19B). It is used by various pathogens that cause food poisoning, including Salmonella enterica, and it is initiated when the bacterium injects a set of effector molecules into the host-cell cytosol through a type III secretion system (see Figure 23–7). Some of these effector molecules activate Rho family proteins, which in turn stimulate actin polymerization, as just discussed. Other bacterial effector proteins interact with host-cell cytoskeletal elements more directly, nucleating and stabilizing actin filaments and causing the rearrangement of actin cross-linking proteins. The overall effect is to cause the formation of localized ruffles on the surface of the host cell (Figure 23–19C and D), which fold over and engulf the bacteria by a process that resembles macropinocytosis. The appearance of cells being invaded by use of the trigger mechanism invasin receptors type III


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Cell_Biology_Alberts. 23–19C and D), which fold over and engulf the bacteria by a process that resembles macropinocytosis. The appearance of cells being invaded by use of the trigger mechanism invasin receptors type III secretioninvasin (integrins, cadherins) apparatus is similar to the ruffling induced by some extracellular growth factors, suggesting that the bacteria exploit normal intracellular signaling pathways.


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Cell_Biology_Alberts. The uptake of viruses and bacteria into host cells is carried out largely by the host, with the pathogen being a relatively passive participant. In contrast, intracellular eukaryotic parasites, which are typically much larger than other types of intracellular pathogens, invade host cells through a variety of complex pathways that usually require energy expenditure by the parasite.


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Cell_Biology_Alberts. Toxoplasma gondii,a cat parasite that also causes occasional serious human infections, is an example. When this protozoan contacts a host cell, it protrudes an unusual microtubule-based structure called a conoid, which facilitates entry into the host cell (Figure 23–20). The energy for invasion seems to come from actin polymerization in the parasite rather than host cytoskeleton, and invasion also requires at least one unusual parasite myosin motor protein (Class XIV; see Figure 16–40). At the point of contact, the parasite discharges effector proteins from secretory organelles into the host cell, and these proteins target various host pathways to enable invasion, to block an innate immune response, and promote survival. As the parasite moves into the host cell, a membrane derived from the host-cell plasma membrane surrounds it. Remarkably, the parasite removes host transmembrane proteins from the surrounding membrane as it forms, so that the parasite is protected in a


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Cell_Biology_Alberts. derived from the host-cell plasma membrane surrounds it. Remarkably, the parasite removes host transmembrane proteins from the surrounding membrane as it forms, so that the parasite is protected in a membrane-enclosed compartment that does not fuse with lysosomes and does not participate in host-cell membrane trafficking processes (see Figure 23–20). The specialized membrane is selectively porous: it allows the parasite to take up small metabolic intermediates and nutrients from the host cell’s cytosol but excludes macromolecules. Malaria parasites invade human red blood cells using a similar mechanism.


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Cell_Biology_Alberts. Figure 23–19 Mechanisms used by bacteria to induce phagocytosis by host cells that are normally nonphagocytic. In the zipper mechanism, bacteria express an invasion protein that binds with high affinity to a host-cell receptor, which is often a cell–cell or cell–matrix adhesion protein. (B) In the trigger mechanism, bacteria inject a set of effector molecules into the host-cell cytosol through a type III secretion system called SPI1 (Salmonella pathogenicity island 1), inducing membrane ruffling. Both the zipper and trigger mechanisms cause the polymerization of actin at the site of bacterial attachment by activating Rho family small GTPases and the Arp 2/3 complex. (C) A scanning electron micrograph showing a very early stage of Salmonella enterica invasion by the trigger mechanism. Bacteria (pseudocolored yellow) are shown surrounded by a small membrane ruffle.


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Cell_Biology_Alberts. Fluorescence micrograph showing that the large ruffles that engulf the Salmonella bacteria are actin-rich. The bacteria are labeled in green and actin filaments in red; because of the color overlap, the bacteria appear yellow. (C, from Rocky Mountain Laboratories, NIAID, NIH; D, from J.E. Galán, Annu. Rev. Cell Dev. Biol. 17:53–86, 2001. With permission from Annual Reviews.)


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Cell_Biology_Alberts. J.E. Galán, Annu. Rev. Cell Dev. Biol. 17:53–86, 2001. With permission from Annual Reviews.) The protozoan Trypanosoma cruzi, which causes Chagas disease, in Mexico and Central and South America, uses two alternative invasion strategies. In a lysosome-dependent pathway, the parasite attaches to host cell-surface receptors, inducing a local increase in Ca2+ in the host cell’s cytosol. The Ca2+ signal recruits lysosomes to the site of parasite attachment, and the lysosomes fuse with the host cell’s plasma membrane, allowing the parasites rapid access to the lysosomal compartment (Figure 23–21). In a lysosome-independent pathway, the parasite penetrates the host-cell plasma membrane by inducing the membrane to invaginate, without the recruitment of lysosomes. 1. ATTACHMENT TO HOST 2. Ca2+ SIGNAL 3. FUSION OF LYSOSOMES CELL-SURFACE RECEPTORS RECRUITS LYSOSOMES WITH PLASMA MEMBRANE Figure 23–20 The life cycle of the intracellular parasite Toxoplasma gondii.


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Cell_Biology_Alberts. Figure 23–20 The life cycle of the intracellular parasite Toxoplasma gondii. After attachment to a host cell, T. gondii uses its conoid to inject effector proteins that facilitate invasion. As the host cell’s plasma membrane invaginates to surround the parasite, it somehow removes the normal host-cell membrane proteins, so that the compartment (shown in red) does not fuse with lysosomes. After several rounds of replication, the parasite causes the compartment to break down and the host cell to lyse, releasing the progeny parasites to infect other host cells (Movie 23.6). Light micrograph of T. gondii replicating within a membrane-enclosed compartment (a vacuole) in a cultured cell. (B, courtesy of Manuel Camps and John Boothroyd.) HOST CYTOSOL TrypanosomacruziCa2+ Ca2+ compartment derived from lysosomal membranelysosomes lysosomes early endosome 5. SECRETION OF PORE-FORMING PROTEIN REPLICATION 4. INVASION 6. LYSIS OF SURROUNDING MEMBRANE, RELEASE OF PATHOGEN INTO CYTOSOL


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Cell_Biology_Alberts. Figure 23–21 The two alternative strategies that Trypanosoma cruzi uses to invade host cells. In the lysosome-dependent pathway (left), T. cruzi recruits host-cell lysosomes to its site of attachment to the host cell. The lysosomes fuse with the invaginating plasma membrane to create an intracellular compartment constructed almost entirely of lysosomal membrane. After a brief stay in the compartment, the parasite secretes a pore-forming protein that disrupts the surrounding membrane, thereby allowing the parasite to escape into the host-cell cytosol and proliferate. In the lysosome-independent pathway (right), the parasite induces the host plasma membrane to invaginate and pinch off without recruiting lysosomes; then lysosomes fuse with the endosome prior to the parasite’s escape into the cytosol.


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Cell_Biology_Alberts. Figure 23–22 Choices that an intracellular pathogen faces. After entry into a host cell, generally through phagocytosis into a membrane-enclosed compartment, intracellular pathogens can use one of three strategies to survive and replicate. Pathogens that follow strategy (1) include all viruses, Trypanosoma cruzi, Listeria monocytogenes, and Shigella flexneri. Those that follow strategy (2) include Mycobacterium tuberculosis and Legionella pneumophila. Those that follow strategy (3) include Salmonella enterica, Coxiella burnetii, and Leishmania. Some Intracellular Pathogens Escape from the Phagosome into the Cytosol


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Cell_Biology_Alberts. Some Intracellular Pathogens Escape from the Phagosome into the Cytosol The intracellular parasites just discussed raise a general problem that faces all intracellular pathogens, including viruses, bacteria, and eukaryotic parasites: they must find a cell compartment in which they can replicate. After their endocytosis by a host cell, they usually find themselves in an endosomal compartment, which normally would fuse with lysosomes to form a phagolysosome—a dangerous place for pathogens. To survive, pathogens use a variety of strategies. Some escape from the endosomal compartment before such fusion. Others remain in the endosomal compartments but modify it so that it no longer fuses with lysosomes. Still others have evolved to weather the harsh conditions in the phagolysosome (Figure 23–22).


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Cell_Biology_Alberts. Trypanosoma cruzi uses the escape route by secreting a pore-forming toxin that lyses the lysosome membrane, releasing the parasite into the host cell’s cytosol (see Figure 23–21). The bacterium Listeria monocytogenes uses a similar strategy. Following phagocytosis by the zipper mechanism, it secretes a protein called listeriolysin O, which disrupts the phagosomal membrane, releasing the bacteria into the cytosol (Figure 23–23). Many Pathogens Alter Membrane Traffic in the Host Cell to Survive and Replicate The survival and reproduction of many intracellular pathogens requires that they modify membrane (vesicular) traffic in the host cell. They may, for example, prevent the normal fusing of endosomes with lysosomes, or adapt themselves to 1 2 uptake by zipper mechanism 3 listeriolysin secretion 4 listeriolysin-mediated membrane disruption 5 bacterial release and replication 6 secreted listeriolysin now destroyed in host proteasomes phagosome proteasome pH <6.0 pH >6.0


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Cell_Biology_Alberts. Figure 23–23 escape of Listeria monocytogenes by selective destruction of the phagosomal membrane. The bacterium attaches to E-cadherin on the surface of host epithelial cells and induces its own uptake by the zipper mechanism (see Figure 23–19A). Within the phagosome, the bacterium secretes the protein listeriolysin O, which is activated at pH <6 and forms oligomers in the phagosome membrane, thereby creating large pores and eventually disrupting the membrane. Once in the host-cell cytosol, the bacteria begin to replicate and continue to secrete listeriolysin O; because the pH in the cytosol is >6, however, the listeriolysin O there is inactive and is also rapidly degraded by proteasomes. Thus, the host cell’s plasma membrane remains intact. resist the lysosome’s antimicrobial armaments. Intracellular pathogens must also provide a pathway for importing nutrients from the host cytosol into their compartment of choice.


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Cell_Biology_Alberts. Different pathogens have distinct strategies for altering membrane traffic in the host cell (Figure 23–24). M. tuberculosis prevents the early endosome that contains the bacteria from maturing, so the endosome never acidifies or acquires the other characteristics of a late endosome or lysosome. This strategy requires the activity of its type VII secretion system, as well as mycobacterial lipid products that mimic host lipids and influence vesicular traffic. Phagosomes containing Salmonella enterica, in contrast, acidify and acquire markers of late endosomes and lysosomes, but the bacteria slow the process of phagosomal maturation. They do so by injecting effector proteins through a second type III secretion system. These effectors activate host kinesin motor proteins to pull membrane tubules outward from the phagosome along cytoplasmic microtubules, forming a specialized compartment called the Salmonella-containing vacuole (Figure 23–25).


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Cell_Biology_Alberts. Other bacteria seem to find shelter in intracellular compartments that are distinct from those of the usual endocytic system. One example is Legionella pneumophila, which was first recognized as a human pathogen in 1976, when it was found to be the cause of a type of pneumonia known as Legionnaire’s disease. L. pneumophila is normally a parasite of freshwater amoebae, but it is commonly


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Cell_Biology_Alberts. L. pneumophila is normally a parasite of freshwater amoebae, but it is commonly Figure 23–24 Modifications of membrane traffic in host cells by bacterial pathogens. Intracellular bacterial pathogens, including Mycobacterium tuberculosis, Salmonella enterica, and Legionella pneumophila, all replicate in membrane-enclosed compartments, but the compartments differ. M. tuberculosis remains in a compartment that has early endosomal markers and continues to communicate with the plasma membrane via transport vesicles. S. enterica replicates in a compartment that has late endosomal markers and does not communicate with the plasma membrane. L. pneumophila replicates in an unusual compartment that is wrapped in rough endoplasmic reticulum (ER) membrane and communicates with the ER via transport vesicles. TGN, trans Golgi network.


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Cell_Biology_Alberts. Figure 23–25 Salmonella enterica residing in a modified phagosomal compartment called the Salmonella-containing vacuole. These bacteria invade the host cell using an SPI1 type III secretion system to inject effector proteins that induce the trigger mechanism of microbe entry illustrated in Figure 23–19B. Following its engulfment into a phagosome, the bacterium inactivates its SPI1 type III secretion system and activates its SPI2 type III secretion system to inject different effector proteins, which remodel the phagosome into the specialized Salmonella-containing vacuole. One of the injected effector proteins activates host kinesin motor proteins to pull membrane tubules outward toward the plus ends of the microtubules (see Figure 16–42). (B) Fluorescence micrograph showing S. enterica in a Salmonella-containing vacuole. The bacteria are stained green, the microtubules red, and the nucleus blue. (B, courtesy of Stephane Meresse.) blocking of type IV secretion 0.5 µm


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Cell_Biology_Alberts. Figure 23–26 Legionella pneumophila residing in a compartment with characteristics similar to those of the rough endoplasmic reticulum (eR). (A) Electron micrograph showing the unusual coiled structure that the Legionella pneumophila bacterium induces on the surface of a phagocyte during the invasion process. Some other pathogens, including the bacterium Borrelia burgdorferi, which causes Lyme disease, the eukaryotic pathogen Leishmania, and the yeast Candida albicans, can also invade cells using this type of coiling phagocytosis. (B) Following invasion, L. pneumophila uses its type IV secretion system to secrete effector proteins that block phagosome–endosome fusion and phagosome maturation. It also secretes effector proteins that promote the fusion of the phagosome with ER-derived vesicles, thereby creating a Legionella-containing vacuole with characteristics similar to the rough ER. (A, from M.A. Horwitz, Cell 36:27–33, 1984. With permission from Elsevier.) spread to humans by


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Cell_Biology_Alberts. thereby creating a Legionella-containing vacuole with characteristics similar to the rough ER. (A, from M.A. Horwitz, Cell 36:27–33, 1984. With permission from Elsevier.) spread to humans by central air-conditioning systems, which harbor infected amoebae and produce microdroplets of water that are easily inhaled. Once in the lung, the bacteria are engulfed by macrophages by an unusual process called coiling phagocytosis (Figure 23–26A). L. pneumophila uses a type IV secretion system to inject effector proteins into the phagocyte that modulate the activity of proteins that regulate vesicular traffic, including SNARE proteins and Rab and Arf family small GTPases (discussed in Chapter 13). The effector proteins thereby prevent the phagosome from fusing with endosomes and promote its fusion with vesicles derived from the endoplasmic reticulum, converting the phagosome into a compartment that resembles the rough endoplasmic reticulum (Figure 23–26B).


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Cell_Biology_Alberts. Viruses can also alter membrane traffic in the host cell. Enveloped viruses make use of host cell membranes to acquire their own envelope membrane. In the simplest cases, virally encoded glycoproteins are inserted into the endoplasmic reticulum membrane and follow the secretory pathway through the Golgi apparatus to the plasma membrane; the viral capsid proteins and genome assemble into nucleocapsids, which acquire their envelope as they bud off from the plasma membrane (see Figure 23–12). This mechanism is used by many enveloped viruses including HIV-1. Other enveloped viruses such as herpesviruses and vaccinia virus acquire their lipid envelopes in more complex ways (Figure 23–27). Viruses and Bacteria Use the Host-Cell Cytoskeleton for Intracellular Movement


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Cell_Biology_Alberts. Viruses and Bacteria Use the Host-Cell Cytoskeleton for Intracellular Movement As mentioned earlier, many pathogens escape into the cytosol rather than remaining in a membrane-enclosed compartment. The cytosol of mammalian cells is extremely viscous, as it is crowded with protein complexes, organelles, and cytoskeletal filaments, all of which inhibit the diffusion of particles the size of a bacterium or a viral nucleocapsid. Thus, to reach a particular region of the host cell a pathogen must be actively moved there. As with transport of intracellular organelles, pathogens generally use the host cell’s cytoskeleton for their active movement. nucleus Golgi WRAPPING (?) (B)


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Cell_Biology_Alberts. Several bacteria that replicate in the host cell’s cytosol have adopted a remarkable mechanism that depends on actin polymerization for movement. These bacteria include the human pathogens Listeria monocytogenes, Shigella flexneri, Rickettsia rickettsii (which causes Rocky Mountain spotted fever), and Burkholderia pseudomallei (which causes melioidosis, a disease characterized by severe respiratory symptoms). Baculovirus, an insect virus, also uses this mechanism for intracellular movement. All of these pathogens induce the nucleation and assembly of host-cell actin filaments at one pole of the bacterium or virus. The growing filaments generate force and push the pathogens through the cytosol at rates of up to 1 μm/sec (Figure 23–28). New filaments form at the rear of each pathogen and are left behind like a rocket trail as the microbe advances; the filaments depolymerize within a minute or so as they encounter depolymerizing factors in the cytosol. For L. monocytogenes and S.


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Cell_Biology_Alberts. and are left behind like a rocket trail as the microbe advances; the filaments depolymerize within a minute or so as they encounter depolymerizing factors in the cytosol. For L. monocytogenes and S. flexneri, the moving bacteria collide with the plasma membrane and move outward, inducing the formation of long, thin, host-cell protrusions with the bacteria at their tip. As shown in Figure 23–28, a neighboring cell often engulfs these projections, allowing the bacteria to enter the neighbor’s cytoplasm without exposure to the extracellular environment, thereby avoiding antibodies produced by the host’s adaptive immune system. For B. pseudomallei, movement and collision of the bacteria with the plasma membrane promotes cell–cell fusion, which serves a similar purpose of immune avoidance while allowing continued bacterial replication.


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Cell_Biology_Alberts. Figure 23–27 Complex strategies for viral envelope acquisition. (A) Herpesvirus nucleocapsids assemble in the nucleus and then bud through the inner nuclear membrane into the space between the inner and outer nuclear membranes, acquiring a lipid bilayer membrane coat. The virus particles then apparently lose this coat when they fuse with the endoplasmic reticulum membrane to escape into the cytosol. Subsequently, the nucleocapsids bud into the Golgi apparatus and bud out again on the other side, thereby acquiring two new membrane coats in the process. The virus then buds from the cell surface with a single membrane when its outer membrane fuses with the plasma membrane. (B) Vaccinia virus (which is closely related to the virus that causes smallpox and is used to vaccinate against smallpox) assembles in “replication factories” in the cytosol, far away from the plasma membrane. The immature virion, with one membrane, is then surrounded by two additional membranes, both acquired from the


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Cell_Biology_Alberts. assembles in “replication factories” in the cytosol, far away from the plasma membrane. The immature virion, with one membrane, is then surrounded by two additional membranes, both acquired from the Golgi apparatus by a poorly understood wrapping mechanism, to form the intracellular enveloped virion. After fusion of the outermost membrane with the host-cell plasma membrane, the extracellular enveloped virion is released from the host cell.


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Cell_Biology_Alberts. Figure 23–28 The actin-based movement of bacterial pathogens within and between host cells. (A) Following invasion, bacterial pathogens such as Listeria monocytogenes, Shigella flexneri, Rickettsia rickettsii, and Burkholderia pseudomallei induce the assembly of actin-rich tails in the host-cell cytoplasm, which drives rapid bacterial movement. For most of these pathogens, the moving bacteria collide with the host-cell plasma membrane to form membrane-covered protrusions, which are engulfed by neighboring cells—spreading the infection from cell to cell. In contrast, for B. pseudomallei, collision with the plasma membrane promotes cell–cell fusion, creating a conduit through which bacteria can invade neighboring cells (Movie 23.7). The molecular mechanisms of pathogen-induced actin assembly differ for the different pathogens, suggesting that they evolved independently (Figure 23–29).


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Cell_Biology_Alberts. The molecular mechanisms of pathogen-induced actin assembly differ for the different pathogens, suggesting that they evolved independently (Figure 23–29). L. monocytogenes and baculovirus produce proteins that directly bind to and activate the Arp 2/3 complex to initiate the formation of an actin tail and movement (see Figure 16–16). S. flexneri produces an unrelated surface protein that binds to and activates N-WASp, which then activates the Arp 2/3 complex. Rickettsia species produce a protein that directly polymerizes actin by mimicking the function of host formin proteins (see Figure 16–17).


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Cell_Biology_Alberts. Many viral pathogens rely primarily on microtubule-dependent motor proteins rather than actin polymerization to move within the host-cell cytosol. Viruses that infect neurons, such as the neurotropic alpha herpesviruses, which include the virus that causes chickenpox, provide important examples. The virus enters sensory neurons at the tips of their axons, and microtubule-based retrograde “backward” axonal transport carries the nucleocapsids down the axon to the nucleus. The transport is mediated by attachment of viral capsid proteins to the motor protein dynein (see Figure 16–58). After replication and assembly in the nucleus, the enveloped virions are then carried by antegrade “forward” axonal transport along microtubules to the axon tips, with the transport being mediated by the attachment of a different viral capsid protein to a kinesin motor protein (see Figure 16–56). A large number of viruses associate with either dynein or kinesin motor proteins to move along microtubules at


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Cell_Biology_Alberts. of a different viral capsid protein to a kinesin motor protein (see Figure 16–56). A large number of viruses associate with either dynein or kinesin motor proteins to move along microtubules at some stage in their replication. As microtubules serve as oriented tracks for vesicular transport in eukaryotic cells, it is not surprising that many viruses have independently evolved the ability to exploit them for their own transport.


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Cell_Biology_Alberts. Viruses Can Take Over the Metabolism of the Host Cell Viruses use basic host cell machinery for most aspects of their reproduction: they depend on host-cell ribosomes to produce their proteins, and most use host-cell DNA and RNA polymerases for their own replication and transcription. Many viruses encode proteins that modify the host transcription or translation apparatus to favor the synthesis of viral RNAs and proteins over those of the host cell, shifting the synthetic capacity of the cell toward the production of new virus particles. Poliovirus, for example, encodes a protease that specifically cleaves the TATA-binding component of TFIID (see Figure 6–17), shutting off transcription of most of the host cell’s protein-coding genes. Influenza virus produces a protein that blocks both the splicing and the polyadenylation of host-cell RNA transcripts, preventing their export into the cytosol (see Figure 6–38).


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Cell_Biology_Alberts. Viruses also alter translation by the host. Translation initiation for most host-cell mRNAs depends on recognition of their 5ʹ cap by translation initiation factors (see Figure 6–70). This initiation process is often inhibited during viral infection, so that the host-cell ribosomes can be used more efficiently for the synthesis of viral proteins. Some viral genomes encode endonucleases that cleave off the 5ʹ cap from host-cell mRNAs; some go even further by using the liberated 5ʹ caps as primers to synthesize viral mRNAs, a process called cap snatching. Several other viral RNA genomes encode proteases that cleave certain translation initiation factors; these viruses rely on 5ʹ cap-independent translation of their own RNA, using internal ribosome entry sites (IRESs) (see Figure 7–68).


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Cell_Biology_Alberts. A few DNA viruses use host-cell DNA polymerase to replicate their genome. Unfortunately for these viruses, DNA polymerase is expressed at high levels only during S phase of the cell cycle, and most cells that these viruses infect spend most of their time in G1 phase. Adenovirus has evolved a mechanism to drive the host cell into S phase, so that the cell produces large amounts of active DNA polymerase, which then replicates the viral genome; to accomplish this, the adenovirus genome also encodes proteins that inactivate both Rb (see Figure 17–61) and p53 (see Figure 17–62), two key suppressors of cell-cycle progression. As might be expected for any mechanism that encourages unregulated DNA replication, these viruses can promote, under some circumstances, the development of cancer. Other DNA viruses, including poxviruses and mimivirus, encode their own DNA and RNA polymerases, as well as some transcription regulators, allowing them to bypass usual host pathways and replicate outside


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Cell_Biology_Alberts. DNA viruses, including poxviruses and mimivirus, encode their own DNA and RNA polymerases, as well as some transcription regulators, allowing them to bypass usual host pathways and replicate outside the nucleus.


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Cell_Biology_Alberts. RNA viruses must always encode their own replication proteins because host cells lack polymerase enzymes that use RNA as a template. For RNA viruses with a single-stranded genome, the replication strategy depends on whether the RNA is a positive [+] strand, which contains translatable information like mRNA, or a complementary negative [–] strand. When the RNA is a positive [+] strand, the incoming viral genome is used to produce the viral RNA polymerase and viral proteins; the viral polymerase is then used to replicate the viral RNA and to generate mRNAs for the production of more viral proteins. For viruses with a negative [–] strand RNA genome (such as influenza and measles virus), an RNA polymerase enzyme is packaged as a structural protein of the incoming viral capsids.


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Cell_Biology_Alberts. Retroviruses such as HIV-1, which have a positive [+] strand RNA genome, are a special class of RNA virus because they carry with them a viral reverse transcriptase enzyme. After entry to the host cell, the reverse transcriptase uses the viral RNA genome as a template to synthesize a double-stranded DNA copy of the viral genome, which enters into the nucleus and integrates into the host cell’s chromosomes (see Figure 5–62). It is later transcribed by the cell’s DNA-dependent RNA polymerase to produce viral genomes and proteins.


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Cell_Biology_Alberts. The complexity and specificity of the interplay between pathogens and their host cells might suggest that virulence would be difficult to acquire by random mutation. Yet, new pathogens are constantly emerging, and old pathogens are constantly changing in ways that make familiar infections more difficult to prevent or treat. Pathogens have two advantages that enable them to evolve rapidly. First, they replicate very quickly, providing a great deal of material for natural selection to work with. Whereas humans and chimpanzees have acquired a 2% difference in genome sequences over about 8 million years of divergent evolution, poliovirus Figure 23–29 Molecular mechanisms for actin nucleation by various bacterial pathogens. Listeria monocytogenes and Shigella flexneri induce actin nucleation by recruiting and activating the host Arp 2/3 complex (see Figure 16–16), although each uses a different recruitment strategy:


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Cell_Biology_Alberts. L. monocytogenes expresses a surface protein, ActA, that directly binds to and activates the Arp 2/3 complex; S. flexneri expresses a surface protein, IcsA (unrelated to ActA), that recruits the host protein N-WASp, which in turn recruits the Arp 2/3 complex, along with other host proteins, including WIP (WASp-interacting protein). Rickettsia rickettsii uses an entirely different strategy; it expresses a surface protein, Sca2, that directly nucleates actin polymerization by mimicking the activity of host formin proteins. gene b copied to number of parasites levels of antibodies x1000 VSGb gene c copied to expression site infection manages a 2% change in its genome in 5 days—about the time it takes the virus to pass from the human mouth to the gut. Second, selective pressures act rapidly on this genetic variation. The host’s adaptive immune system and modern microbicidal drugs, both of which destroy pathogens that fail to change, are the main sources of these selective pressures.


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Cell_Biology_Alberts. An example of an adaptation to the selective pressure imposed by the adaptive immune system is the phenomenon of antigenic variation. An important adaptive immune response against many pathogens is the host’s production of antibodies that recognize specific molecules (antigens) on the pathogen’s surface (discussed in Chapter 24). Many pathogens have evolved mecanisms that deliberately change these antigens during the course of an infection, enabling them to evade antibodies. Some eukaryotic parasites, for example, undergo programmed rearrangements of the genes encoding their surface antigens. A striking example occurs in Trypanosoma brucei, a protozoan parasite that causes African sleeping sickness and is spread by tsetse flies. (T. brucei is a relative of T. cruzi—see Figure 23–21—but it replicates extracellularly rather than intracellularly.) T. brucei is covered with a single type of glycoprotein, called variant-specific glycoprotein (VSG), which elicits in the host a protective


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Cell_Biology_Alberts. it replicates extracellularly rather than intracellularly.) T. brucei is covered with a single type of glycoprotein, called variant-specific glycoprotein (VSG), which elicits in the host a protective antibody response that rapidly clears most of the parasites. The trypanosome genome, however, contains about 1000 different Vsg genes or pseudogenes, each encoding a VSG with a distinct amino acid sequence. Only one of these genes is expressed at any one time, from one of approximately 20 possible expression sites in the genome. Gene rearrangements that copy different Vsg genes into expression sites repeatedly change the VSG protein displayed on the surface of the pathogen. In this way, a few trypanosomes with an altered VSG escape the initial antibody-mediated clearance, replicate, and cause the disease to recur, leading to a chronic cyclic infection (Figure 23–30).


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Cell_Biology_Alberts. Bacterial pathogens can also rapidly change their surface antigens. As discussed in Chapter 5, Salmonella enterica bacteria switch between expressing either of two versions of the protein flagellin, the structural component of the bacterial flagellum (see Figure 23–3D), in a process called phase variation (see Figure 5–65). Species of the genus Neisseria are also champions at this. These Gram-negative cocci can cause meningitis and sexually transmitted diseases. They undergo genetic recombination very similar to that just described for eukaryotic pathogens, which enables them to vary the pilin protein they use to attach to host cells. By inserting one of the multiple silent copies of variant pilin genes into a single expression locus, they can express many slightly different versions of the protein and repeatedly change the amino acid sequence over time. Neisseria bacteria are


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Cell_Biology_Alberts. Figure 23–30 antigenic variation in trypanosomes. (A) There are about 1000 distinct Vsg genes in Trypanosoma brucei, and they are expressed one at a time from approximately 20 expression sites in the genome. To be expressed, an inactive gene is copied and the copy is moved into an expression site through DNA recombination. Each Vsg gene encodes a different surface protein (antigen). These switching events allow the trypanosome to repeatedly change the surface antigen it expresses. (B) A person infected with trypanosomes expressing VSGa mounts a protective antibody response, which clears most of the parasites expressing this antigen. However, a few of the trypanosomes will have switched to expression of VSGb, which can now proliferate until anti-VSGb antibodies clear them. By that time, however, some parasites will have switched to VSGc, and so the cycle continues.


Cell_Biology_Alberts

Cell_Biology_Alberts. also extremely adept at taking up DNA from their environment by natural transformation and incorporating it into their genomes, further contributing to their extraordinary variability. The end result of this considerable variation is a plethora of different surface compositions with which to bewilder the host adaptive immune system. It is therefore not surprising that it has been difficult to develop an effective vaccine against Neisseria infections, although there are now several that protect against Neisseria meningitidis, a common cause of fatal meningitis.


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Cell_Biology_Alberts. In contrast to the DNA rearrangements in bacteria and parasites, viruses rely on an error-prone replication mechanism for antigenic variation. Retroviral genomes, for example, acquire on average one point mutation every replication cycle, because the viral reverse transcriptase (see Figure 5–62) needed to produce DNA from the viral RNA genome lacks the proofreading activity of DNA polymerases. A typical, untreated HIV infection may eventually produce HIV genomes with every possible point mutation. By a process of mutation and selection within each host, most viruses change over time—from a form that is most efficient at infecting macrophages to one more efficient at infecting T cells, as described earlier (see Figure 23–17). Similarly, once a patient is treated with an antiviral drug, the viral genome can quickly mutate and be selected for its resistance to the drug. Remarkably, only about one-third of the nucleotide positions in the coding sequence of the viral genome are invariant,


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Cell_Biology_Alberts. viral genome can quickly mutate and be selected for its resistance to the drug. Remarkably, only about one-third of the nucleotide positions in the coding sequence of the viral genome are invariant, and nucleotide sequences in some parts of the genome, such as the Env gene (see Figure 7–62), can differ by as much as 30% from one HIV isolate to another. This extraordinary genomic plasticity greatly complicates attempts to develop vaccines against HIV. It has also led to the rapid emergence of new HIV strains. Nucleotide sequence comparisons between various strains of HIV and the very similar simian immunodeficiency virus (SIV) isolated from a variety of monkey species suggest that the most virulent type of HIV, HIV-1, may have jumped from primates to humans multiple independent times, starting as long ago as 1908 (Figure 23–31).


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Cell_Biology_Alberts. Influenza viruses are an important exception to the rule that error-prone replication dominates viral evolution. They are unusual in that their genome consists of several (usually eight) strands of RNA. When two strains of influenza infect the same host, the RNA strands of the two strains can reassort to form a new type of influenza virus. In normal years, influenza is a mild disease in healthy adults, although it can be life-threatening in the very young and very old. Different influenza strains infect fowl such as ducks and chickens, but only a subset of these strains can infect humans, and transmission from fowl to humans is rare. In 1918, however, a particularly virulent variant of avian influenza crossed the species barrier to infect humans, triggering the catastrophic pandemic of 1918 called the Spanish flu, which killed 20–50 million people worldwide. Subsequent influenza pandemics have been triggered by genome reassortment, in which a new RNA segment from an avian form of the


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Cell_Biology_Alberts. called the Spanish flu, which killed 20–50 million people worldwide. Subsequent influenza pandemics have been triggered by genome reassortment, in which a new RNA segment from an avian form of the virus replaced one or more of the viral RNA segments from the human form (Figure 23–32). In 2009, a new H1N1 swine virus emerged that derived genes from pig, avian, and human influenza viruses. Such recombination events allowed the new virus to replicate rapidly and spread through an immunologically naive human population. Generally, within two or three years, the human population develops immunity to a new recombinant strain of virus, and the infection rate drops to a steady-state level. Because the recombination events are unpredictable, it is not possible to know when the next influenza pandemic will occur or how severe it might be.


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Cell_Biology_Alberts. The development of drugs that cure rather than prevent infections has had a major impact on human health. Antibiotics, which are either bactericidal (they kill bacteria) or bacteriostatic (they inhibit bacterial growth without killing), are the most successful class of such drugs. Penicillin was one of the first antibiotics = jumps from monkey and ape to human


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Cell_Biology_Alberts. Figure 23–31 Diversification of HIV-1, HIV-2, and related strains of SIV. HIV comprises different viral families, all descended from SIV (simian immunodeficiency virus). On three separate occasions, SIV was passed from a chimpanzee to a human, resulting in three HIV-1 groups: major (M), outlier (O), and non-M non-O (N). The HIV-1 M group is the most common and is primarily responsible for the global AIDS epidemic. On two separate occasions, SIV was passed from a sooty mangabey monkey to a human, resulting in the two HIV-2 groups. In 2009, a new strain of HIV was discovered that appears to have resulted from SIV passage from a gorilla to a human. 1292 Chapter 23: Pathogens and Infection H2N2 H3N?


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Cell_Biology_Alberts. 1292 Chapter 23: Pathogens and Infection H2N2 H3N? used to treat infections in humans, just in time to prevent tens of thousands of deaths from infected battlefield wounds in World War II. Because bacteria (see Figure 1–17) are not closely related evolutionarily to the eukaryotes they infect, much of their basic machinery for DNA replication and transcription, RNA translation, and metabolism differs from that of their host. These differences enable us to develop antibacterial drugs that exhibit selective toxicity, in that they specifically inhibit these processes in bacteria without disrupting them in the host. Most of the antibiotics that we use to treat bacterial infections are small molecules that inhibit macromolecular synthesis in bacteria by targeting bacterial enzymes that either are distinct from their eukaryotic counterparts or are involved in pathways such as cell wall biosynthesis that are absent in animals (Figure 23–33 and see Table 6–4).


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Cell_Biology_Alberts. However, bacteria continuously evolve and strains resistant to antibiotics rapidly develop, often within a few years of the introduction of a new drug. Similar drug resistance also arises rapidly when treating viral infections with antiviral drugs. The virus population in an HIV-infected person treated with the reverse transcriptase inhibitor AZT, for example, will acquire complete resistance to the drug within a few months. The current protocol for treatment of HIV infections involves the simultaneous use of three drugs, which helps to minimize the acquisition of resistance for any one of them. There are three general strategies by which a pathogen can develop drug resistance: (1) it can alter the molecular target of the drug so that it is no longer sensitive to the drug; (2) it can produce an enzyme that modifies or destroys the drug; or (3) it can prevent the drug’s access to the drug target by, for example, actively pumping the drug out of the pathogen (Figure 23–34).


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Cell_Biology_Alberts. Once a pathogen has chanced upon an effective drug-resistance strategy, the newly acquired or mutated genes that confer the resistance are frequently spread throughout the pathogen population by horizontal gene transfer. They may even spread between pathogens of different species. The highly effective but expensive antibiotic vancomycin, for example, is used as a treatment of last resort for many severe, hospital-acquired, Gram-positive bacterial infections that are resistant to most other known antibiotics. Vancomycin prevents one step in bacterial cell wall synthesis—the cross-linking of peptidoglycan chains in the bacterial cell wall (see Figure 23–3B). Resistance can arise if the bacterium synthesizes a cell wall using different subunits that do not bind vancomycin. The most effective form of vancomycin resistance depends on the acquisition of a transposon (see Figure 5–60) containing seven genes, the products of which work together to sense the


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Cell_Biology_Alberts. Figure 23–32 Model for the evolution of pandemic strains of influenza virus by recombination. Influenza A virus is a natural pathogen of birds, particularly waterfowl, and it is always present in wild bird populations. In 1918, a particularly virulent form of the virus crossed the species barrier from birds to humans and caused a devastating worldwide epidemic. This strain was designated H1N1, referring to the specific forms of its main antigens, hemagglutinin (H) and neuraminidase (N). Changes in the virus, rendering it less virulent, and the rise of adaptive immunity in the human population, prevented the pandemic from continuing in subsequent seasons, although H1N1 influenza strains continued to cause serious disease every year in very young and very old people. In 1957, a new pandemic arose when three genes were replaced by equivalent genes from an avian virus (green bars); the new strain (designated H2N2) was not effectively cleared by antibodies in people who had previously


Cell_Biology_Alberts

Cell_Biology_Alberts. arose when three genes were replaced by equivalent genes from an avian virus (green bars); the new strain (designated H2N2) was not effectively cleared by antibodies in people who had previously contracted only H1N1 forms of influenza. In 1968, another pandemic was triggered when two genes were replaced from another avian virus; the new virus was designated H3N2. In 1977, there was a resurgence of H1N1 influenza, which had previously been almost completely replaced by the N2 strains. Molecular sequence information suggests that this minor pandemic may have been caused by an accidental release of an influenza strain that had been held in a laboratory since about 1950. In 2009, a new H1N1 swine virus emerged that had derived five genes from pig influenza viruses, two from avian influenza viruses, and one from a human influenza virus. As indicated, most human influenza today is caused by H1N1 and H3N2 strains.


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Cell_Biology_Alberts. protein synthesis,penicillins 30S ribosome inhibitors protein synthesis,sulfonamides presence of vancomycin, shut down the normal pathway for bacterial cell wall synthesis, and produce a different type of cell wall.


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Cell_Biology_Alberts. Drug-resistance genes acquired by horizontal transfer frequently come from environmental microbial reservoirs. Nearly all antibiotics used to treat bacterial infections today are based on natural products produced by fungi or bacteria. Penicillin, for example, is made by the mold Penicillium, and more than 50% of the antibiotics currently used in the clinic are made by Gram-positive bacteria of the genus Streptomyces, which reside in the soil. It is believed that microorganisms produce antimicrobial compounds, many of which have probably existed on Earth for hundreds of millions of years, as weapons in their competition with other microorganisms in the environment. Surveys of bacteria taken from soil samples that have never been exposed to antibiotic drugs used in modern medicine reveal that the bacteria are typically already resistant to about seven or eight of the antibiotics widely used in clinical practice. When pathogenic microorganisms are faced with the selective pressure


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Cell_Biology_Alberts. that the bacteria are typically already resistant to about seven or eight of the antibiotics widely used in clinical practice. When pathogenic microorganisms are faced with the selective pressure provided by antibiotic treatments, they can apparently draw upon this immense source of genetic material to acquire resistance.


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Cell_Biology_Alberts. Like most other aspects of infectious disease, human behavior has exacerbated the problem of drug resistance. Many patients take antibiotics for symptoms that are typically caused by viruses (flu-like illnesses, colds, sore throats, and earaches) and these drugs have no effects. Persistent and chronic misuse of antibiotics can eventually result in antibiotic-resistant normal flora, which can then transfer the resistance to pathogens. Antibiotics are also misused in agriculture, where they are commonly employed as food additives to promote the growth and health of farm animals. An antibiotic closely related to vancomycin was commonly added to cattle feed in Europe; the resulting resistance in the normal flora of these animals is widely believed to be one of the original sources for vancomycin-resistant bacteria that now threaten the lives of hospitalized patients.


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Cell_Biology_Alberts. Figure 23–33 antibiotic targets. Although there are many antibiotics in clinical use, they have a narrow range of targets, which are highlighted in yellow. A few representative antibiotics in each class are listed. Nearly all antibiotics used to treat human infections fall into one of these categories. The vast majority inhibit either bacterial protein synthesis or bacterial cell wall synthesis.


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Cell_Biology_Alberts. Figure 23–34 Three general mechanisms of antibiotic resistance. (A) A nonresistant wild-type bacterial cell bathed in a drug (red triangles) that binds to and inhibits an essential enzyme (light green) will be killed due to enzyme inhibition. (B) A bacterium that has altered the drug’s target enzyme so that the drug no longer binds to the enzyme will survive and proliferate. In many cases, a single point mutation in the gene encoding the target protein can generate resistance. (C) A bacterium that expresses an enzyme (dark green) that either degrades or covalently modifies the drug will survive and proliferate. Some resistant bacteria, for example, make β-lactamase enzymes, which cleave penicillin and similar molecules. (D) A bacterium that expresses or up-regulates an efflux pump that ejects the drug from the bacterial cytoplasm (using energy derived from either ATP hydrolysis or the electrochemical gradient across the bacterial plasma membrane) will survive and proliferate. Some


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Cell_Biology_Alberts. ejects the drug from the bacterial cytoplasm (using energy derived from either ATP hydrolysis or the electrochemical gradient across the bacterial plasma membrane) will survive and proliferate. Some efflux pumps, such as the TetR efflux pump, are specific for a single drug (in this case, tetracycline), whereas others, called multidrug resistance (MDR) efflux pumps, are capable of exporting a wide variety of structurally dissimilar drugs. Upregulation of an MDR pump can render a bacterium resistant to a very large number of different antibiotics in a single step.


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Cell_Biology_Alberts. Because the acquisition of drug resistance is almost inevitable, it is crucial that we continue to develop innovative treatments for infectious diseases. We must also take additional measures to delay the onset of drug resistance.


Cell_Biology_Alberts

Cell_Biology_Alberts. All pathogens share the ability to interact with host cells in diverse ways that promote the replication and spread of the pathogen. Pathogens often colonize the host by adhering to or invading the epithelial surfaces that line the respiratory, gastrointestinal, and urinary tracts, as well as the other body surfaces in direct contact with the environment. Intracellular pathogens, including all viruses and many bacteria and protozoa, invade host cells by one of several mechanisms. Viruses rely largely on receptor-mediated endocytosis, whereas bacteria exploit cell adhesion and phagocytic pathways; in both cases, the host cell provides the machinery and energy for the invasion. Protozoa, by contrast, employ unique invasion strategies that usually require significant metabolic expense on the part of the invader. Once inside, intracellular pathogens seek out a cell compartment that is favorable for their survival and replication, frequently altering host membrane traffic and exploiting


Cell_Biology_Alberts

Cell_Biology_Alberts. part of the invader. Once inside, intracellular pathogens seek out a cell compartment that is favorable for their survival and replication, frequently altering host membrane traffic and exploiting the host-cell cytoskeleton for intracellular movement. Pathogens evolve rapidly, so that new infectious diseases frequently emerge, and old pathogens acquire new ways to evade


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Cell_Biology_Alberts. What are the genetic and molecular features that differ between pathogens and members of the normal human microbiota? How can our immune system distinguish between the two? To what extent are common host-cell biological pathways and molecules hijacked by diverse microbes? Can host-cell defense molecules be mobilized by drugs to fight infection? our attempts at treatment, prevention, and eradication. Which statements are true? explain why or why not. 23–1 Our adult bodies harbor about 10 times more microbial cells than human cells. 23–2 The microbiomes from healthy humans are all very similar. 23–3 Pathogens must enter host cells to cause disease. 23–4 Viruses replicate their genomes in the nucleus of the host cell. 23–5 You should not take antibiotics for diseases caused by viruses. Discuss the following problems. 23–6 In order to survive and multiply, a successful pathogen must accomplish five tasks. Name them.


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Cell_Biology_Alberts. Discuss the following problems. 23–6 In order to survive and multiply, a successful pathogen must accomplish five tasks. Name them. 23–7 Clostridium difficile infection is the leading cause of hospital-associated gastrointestinal illness. It is typically treated with a course of antibiotics, but the infection recurs in about 20% of cases. C. difficile infections are difficult to eradicate because the bacteria exist in two forms: a replicating, toxin-producing form and a spore form that is resistant to antibiotics. Fecal microbiota transplantation—the transfer of normal gut microbiota from a healthy individual—can resolve >90% of recurrent infections, a much better cure rate than further antibiotic treatment alone. Why do you suppose microbiota transplantation is so effective? 23–8 What are the three general mechanisms for horizontal gene transfer?


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Cell_Biology_Alberts. 23–9 The Gram-negative bacterium Yersinia pestis, the causative agent of the plague, is extremely virulent. Upon infection, Y. pestis injects a set of effector proteins into macrophages that suppresses their phagocytic behavior and also interferes with their innate immune responses. One of the effector proteins, YopJ, acetylates serines and threonines on various MAP kinases, including the MAP kinase kinase kinase TAK1, which controls a key signaling step in the innate immune response pathway. To determine how YopJ interferes with TAK1, you transfect human cells with active YopJ (YopJWT) or inactive YopJ (YopJCA) and with FLAG-tagged active TAK1 (TAK1WT) or inactive TAK1 (TAK1K63W), and assay for total TAK1 and for phosphorylated TAK1, using antibodies against the FLAG tag or against phosphorylated TAK1 (Figure Q23–1). How does YopJ block the TAK1 signaling pathway? How do you suppose the serine/threonine acetylase activity of YopJ might interfere with TAK1 activation?


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Cell_Biology_Alberts. IP: ˜-FLAG-TAK1 IB: ˜-pTAK1 IP: ˜-FLAG-TAK1 –76 IB: ˜-FLAG-TAK1


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Cell_Biology_Alberts. Figure Q23–1 effects of YopJ on TaK1 phosphorylation (Problem 23–9). TaK1 was immunoprecipitated (Ip) using antibodies against the FLaG tag (α-FLaG-TaK1). Total TaK1 in the immunoprecipitation was assayed by immunoblot (IB) using the same antibody. phosphorylated TaK1 was assayed by IB using antibodies specific for phospho-TaK1 (α-pTaK1). a scale of protein molecular mass is shown at right in kilodaltons. (From n. paquette et al., Proc. Natl Acad. Sci. USA 109:12710–12715, 2012. With permission from national academy of sciences.) 23–10 The intracellular bacterial pathogen Salmonella typhimurium, which causes gastroenteritis, injects effector proteins to promote its invasion into nonphagocytic host cells by the trigger mechanism. S. typhimurium first stimulates membrane ruffling to promote invasion, and then suppresses membrane ruffling once invasion is complete. This behavior is mediated in part by injection of two effector proteins: SopE, which promotes membrane ruffling and


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Cell_Biology_Alberts. promote invasion, and then suppresses membrane ruffling once invasion is complete. This behavior is mediated in part by injection of two effector proteins: SopE, which promotes membrane ruffling and invasion, and SptP, which blocks the effects of SopE. Both effector proteins target the monomeric GTPase, Rac, which in its active form promotes membrane ruffling. How do you suppose SopE and SptP affect Rac activity? How do you suppose the effects of SopE and SptP are staggered in time if they are injected simultaneously?


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Cell_Biology_Alberts. 23–11 John Snow is widely regarded as the father of modern epidemiology. Most famously, he investigated an outbreak of cholera in London in 1854 that killed more than 600 victims before it was finished. Snow recorded where the victims lived, and plotted the data on a map, along with the locations of the water pumps that served as the source of water for the public (Figure Q23–2). He concluded that the disease was most likely spread in the water, although he could find nothing suspicious-looking in it. His conclusion ran counter to the then-current belief that cholera was from “miasmas” in bad air. Very few believed his theory during the next 50 years, with the “bad air” theory persisting until at least 1901. What do you suppose Snow saw in the data that led him to his conclusion? Why do you think most scientists remained skeptical for so long?


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Cell_Biology_Alberts. Figure Q23–2 a map of where the victims of the 1854 cholera outbreak lived, superimposed on a modern Google map of the area (Problem 23–11). The locations of the victims’ houses are indicated in a gradient of colors from blue (indicating few cases) to orange (indicating many cases). public water pumps are shown as red squares. 23–12 Influenza epidemics account for 250,000 to 500,000 deaths globally each year. These epidemics are markedly seasonal, occurring in temperate climates in the northern and southern hemispheres during their respec Figure Q23–3 seasonal patterns of influenza epidemics (Problem 23–12). Cases of influenza at different times of the year are shown for the northern hemisphere (blue), the southern hemisphere (orange), and the tropics (red).


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Cell_Biology_Alberts. tive winters. By contrast, in the tropics, there is significant influenza activity year round, with a peak in the rainy season (Figure Q23–3). Can you suggest some possible explanations for the patterns of influenza epidemics in temperate zones and the tropics? 23–13 Several negative-strand viruses carry their genome as a set of discrete RNA segments. Examples include influenza virus (eight segments), Rift Valley fever virus (three segments), Hantavirus (three segments), and Lassa virus (two segments), to name a few. Why does segmentation of the genome provide a strong evolutionary advantage for these viruses?


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Cell_Biology_Alberts. 23–14 Avian influenza viruses readily infect birds, but are transmitted to humans very rarely. Similarly, human influenza viruses spread readily to other humans, but have never been detected in birds. The key to this specificity lies in the viral capsid protein, hemagglutinin, which binds to sialic acid residues on cell-surface glycoproteins, triggering virus entry into the cell (Movie 23.8). Hemagglutinin on human viruses recognizes sialic acid in a 2-6 linkage with galactose, whereas avian hemagglutinin recognizes sialic acid in a 2-3 linkage with galactose. Humans make carbohydrate chains that have only the 2-6 linkage between sialic acid and galactose; birds make only the 2-3 linkage; but pigs make carbohydrate chains with both linkages. How does this situation make pigs ideal hosts for generating new strains of human influenza viruses?


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Cell_Biology_Alberts. 23–15 The majority of antibiotics used in the clinic are made as natural products by bacteria. Why do you suppose bacteria make the very agents we use to kill them? 23–16 In the early days of penicillin research, it was discovered that bacteria in the air could destroy the penicillin, a big problem for large-scale production of the drug. How do you suppose this occurs? 23–17 When the Oxford team of Ernst Chain and Norman Heatley had laboriously collected their first two grams of penicillin (probably no more than 2% pure!), Chain injected two normal mice with 1 g each of this preparation, and waited to see what would happen. The mice survived with no apparent ill effects. Their boss, Howard Florey, was furious at what he saw as a waste of good antibiotic. Why was this experiment important? Cossart P, Boquet P, Normark S & Rappuoli R (eds) (2005) Cellular Microbiology, 2nd ed. Washington, DC: ASM Press.


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Cell_Biology_Alberts. Cossart P, Boquet P, Normark S & Rappuoli R (eds) (2005) Cellular Microbiology, 2nd ed. Washington, DC: ASM Press. Engleberg NC, DiRita V & Dermody T (2012) Schaechter’s Mechanisms of Microbial Disease, 5th ed. Philadelphia, PA: Lippincott, Williams & Wilkins.Norkin LA (2010) Virology: Molecular Biology and Pathogenesis. Washington, DC: ASM Press. Wilson BA, Salyers AA, Whitt DD & Winkler ME (2011) Bacterial Pathogenesis: A Molecular Approach, 3rd ed. Washington, DC: ASM Press. Introduction to Pathogens and the Human Microbiota Aly AS, Vaughan AM & Kappe SH (2009) Malaria parasite development in the mosquito and infection of the mammalian host. Annu. Rev. Microbiol. 63, 195–221. Baltimore D (1971) Expression of animal virus genomes. Bacteriol. Rev. 35, 235–241. Clemente JC, Ursell LK, Parfrey LW & Knight R (2012) The impact of the gut microbiota on human health: an integrative view. Cell 148, 1258–1270.


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Cell_Biology_Alberts. Clemente JC, Ursell LK, Parfrey LW & Knight R (2012) The impact of the gut microbiota on human health: an integrative view. Cell 148, 1258–1270. Crick FH & Watson JD (1956) Structure of small viruses. Nature 177, 473–475. Fauci A & Morens DM (2012) The perpetual challenge of infectious diseases. N. Engl. J. Med. 366, 454–461. Frost LS, Leplae R, Summers AO & Toussaint A (2005) Mobile genetic elements: the agents of open source evolution. Nat. Rev. Microbiol. 3, 722–732. Galán JE & Wolf-Watz H (2006) Protein delivery into eukaryotic cells by type III secretion machines. Nature 444, 567–573. Hacker J & Kaper JB (2000) Pathogenicity islands and the evolution of microbes. Annu. Rev. Microbiol. 54, 641–679. Nelson EJ, Harris JB, Morris JG Jr et al. (2009) Cholera transmission: the host, pathogen and bacteriophage dynamic. Nat. Rev. Microbiol. 7, 693–702. Pflughoeft KJ & Versalovic J (2012) Human microbiome in health and disease. Annu. Rev. Pathol. 7, 99–122.


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Cell_Biology_Alberts. Pflughoeft KJ & Versalovic J (2012) Human microbiome in health and disease. Annu. Rev. Pathol. 7, 99–122. Polk DB & Peek RM Jr (2010) Helicobacter pylori: gastric cancer and beyond. Nat. Rev. Cancer 10, 403–414. Poulin R & Morand S (2000) The diversity of parasites. Q. Rev. Biol. 75, 277–293. Rappleye CA & Goldman WE (2006) Defining virulence genes in the dimorphic fungi. Annu. Rev. Microbiol. 60, 281–303. Thomas CM & Nielsen KM (2005) Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat. Rev. Microbiol. 3, 711–721. Votteler J & Sundquist WI (2013) Virus budding and the ESCRT pathway. Cell Host Microbe 14, 232–241. Young JAT & Collier RJ (2007) Anthrax toxin: receptor binding, internalization, pore formation, and translocation. Annu. Rev. Biochem. 76, 243–265. Cell Biology of Infection Alix E, Mukherjee S & Roy CR (2011) Subversion of membrane transport pathways by vacuolar pathogens. J. Cell Biol. 195, 943–952.


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Cell_Biology_Alberts. Cell Biology of Infection Alix E, Mukherjee S & Roy CR (2011) Subversion of membrane transport pathways by vacuolar pathogens. J. Cell Biol. 195, 943–952. Beiting DP & Roos DS (2011) A systems biological view of intracellular pathogens. Immunol. Rev. 240, 117–128. Brandenburg B & Zhuang X (2007) Virus trafficking – learning from single-virus tracking. Nat. Rev. Microbiol. 5, 197–208. Cossart P & Sansonetti PJ (2004) Bacterial invasion: the paradigms of enteroinvasive pathogens. Science 304, 242–248. Daugherty MD & Malik HS (2012) Rules of engagement: molecular insights from host-virus arms races. Annu. Rev. Genet. 46, 677–700. Davies J & Davies D (2010) Origins and evolution of antibiotic resistance. Microbiol. Mol. Biol. Rev. 74, 417–433. Dimitrov DS (2004) Virus entry: molecular mechanisms and biomedical applications. Nat. Rev. Microbiol. 2, 109–122.


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Cell_Biology_Alberts. Dimitrov DS (2004) Virus entry: molecular mechanisms and biomedical applications. Nat. Rev. Microbiol. 2, 109–122. Duffy S, Shackelton LA & Holmes EC (2008) Rates of evolutionary change in viruses: patterns and determinants. Nat. Rev. Genet. 9, 267–276. Forsberg KJ, Reyes A, Wang B et al. (2012) The shared antibiotic resistome of soil bacteria and human pathogens. Science 337, 1107–1111. Ghedin E, Sengamalay NA, Shumway M et al. (2005) Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution. Nature 437, 1162–1166. Goldberg DE, Siliciano RF & Jacobs WR Jr (2012) Outwitting evolution: fighting drug-resistant TB, malaria, and HIV. Cell 148, 1271–1283. Haglund CM & Welch MD (2011) Pathogens and polymers: microbe-host interactions illuminate the cytoskeleton. J. Cell Biol. 195, 7–17. Ham H, Sreelatha A & Orth K (2011) Manipulation of host membranes by bacterial effectors. Nat. Rev. Microbiol. 9, 635–646.


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Cell_Biology_Alberts. Ham H, Sreelatha A & Orth K (2011) Manipulation of host membranes by bacterial effectors. Nat. Rev. Microbiol. 9, 635–646. Hayward RD, Leong JM, Koronakis V & Campellone KG (2006) Exploiting pathogenic Escherichia coli to model transmembrane receptor signalling. Nat. Rev. Microbiol. 4, 358–370. Kenny B, DeVinney R, Stein M et al. (1997) Enteropathogenic E. coli (EPEC) transfers its receptor for intimate adherence into mammalian cells. Cell 91, 511–520. Lusso P (2006) HIV and the chemokine system: 10 years later. EMBO J. 25, 447–456. Medina RA & García-Sastre A (2011) Influenza A viruses: new research developments. Nat. Rev. Microbiol. 9, 590–603. Mengaud J, Ohayon H, Gounon P et al. (1996) E-cadherin is the receptor for internalin, a surface protein required for entry of


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Cell_Biology_Alberts. L. monocytogenes into epithelial cells. Cell 84, 923–932. Mercer J, Schelhaas M & Helenius A (2010) Virus entry by endocytosis. Annu. Rev. Biochem. 79, 803–833. Miller S & Krijnse-Locker J (2008) Modification of intracellular membrane structures for virus replication. Nat. Rev. Microbiol. 6, 363–374. Mullins JI & Jensen MA (2006) Evolutionary dynamics of HIV-1 and the control of AIDS. Curr. Top. Microbiol. Immunol. 299, 171–192. Parrish CR & Kawaoka Y (2005) The origins of new pandemic viruses: the acquisition of new host ranges by canine parvovirus and influenza A viruses. Annu. Rev. Microbiol. 59, 553–586. Pizarro-Cerdá J & Cossart P (2006) Bacterial adhesion and entry into host cells. Cell 124, 715–727. Ray K, Marteyn B, Sansonetti PJ & Tang CM (2009) Life on the inside: the intracellular lifestyle of cytosolic bacteria. Nat. Rev. Microbiol. 7, 333–340. Sibley LD (2011) Invasion and intracellular survival by protozoan parasites. Immunol. Rev. 240, 72–91. Tilney LG & Portnoy DA


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Cell_Biology_Alberts. lifestyle of cytosolic bacteria. Nat. Rev. Microbiol. 7, 333–340. Sibley LD (2011) Invasion and intracellular survival by protozoan parasites. Immunol. Rev. 240, 72–91. Tilney LG & Portnoy DA (1989) Actin filaments and the growth, movement, and spread of the intracellular bacterial parasite, Listeria monocytogenes. J. Cell Biol. 109, 1597–1608. Vink C, Rudenko G & Seifert HS (2012) Microbial antigenic variation mediated by homologous DNA recombination. FEMS Microbiol. Rev. 36, 917–948. Walsh D & Mohr I (2011) Viral subversion of the host protein synthesis machinery. Nat. Rev. Microbiol. 9, 860–875.


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Cell_Biology_Alberts. Welch MD & Way M (2013) Arp2/3-mediated actin-based motility: a tail of pathogen abuse. Cell Host Microbe 14, 242–255. The Innate and Adaptive Immune Systems 24


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Cell_Biology_Alberts. As we discussed in Chapter 23, all living organisms serve as hosts for other species, usually in relationships that are benign or even mutually helpful. But all organisms, and all cells in a multicellular organism, need to defend themselves against infection by harmful invaders, collectively called pathogens, which can be microbes (bacteria, viruses, or fungi), or larger parasites. Even bacteria defend themselves against viruses, using intracellular proteins called restriction factors, which block viral propagation. Invertebrates use a variety of defense strategies, including protective barriers, toxic molecules, restriction factors, and phagocytic cells that ingest and destroy invading pathogens. Vertebrates, too, depend on such innate immune responses, but they can also harness more sophisticated and specific mechanisms, called adaptive immune responses. The innate responses occur first, calling the adaptive immune responses into play if required, in which case, both types of


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Cell_Biology_Alberts. sophisticated and specific mechanisms, called adaptive immune responses. The innate responses occur first, calling the adaptive immune responses into play if required, in which case, both types of responses work together to eliminate the pathogen (Figure 24–1).


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Cell_Biology_Alberts. Whereas innate immune responses are general defense reactions that can involve almost any cell type in an organism, the adaptive immune responses are highly specific to the particular pathogen that induced them and depend on a class of white blood cells (leukocytes) called lymphocytes. There are two major classes of lymphocytes that mount adaptive immune responses—B lymphocytes (B cells), which secrete antibodies that bind specifically to the pathogen, and T lymphocytes (T cells), which can either directly kill cells infected with the pathogen or produce secreted or cell-surface signal proteins that stimulate other host cells to help eliminate the pathogen (Figure 24–2). Unlike innate immune responses, which are generally short-lasting, the adaptive responses provide long-lasting protection: a person who recovers from measles or is vaccinated against it, for example, is protected for life against measles by the adaptive immune system, although not against other common viruses, such as


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Cell_Biology_Alberts. a person who recovers from measles or is vaccinated against it, for example, is protected for life against measles by the adaptive immune system, although not against other common viruses, such as those that cause mumps or chickenpox.


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Cell_Biology_Alberts. Both the innate and adaptive immune systems have evolved sensing mechanisms that enable them to recognize harmful invaders (pathogens) and distinguish them from both the host’s own cells and molecules and harmless or beneficial foreign organisms and their molecules. The innate system relies on sensor proteins that recognize particular types or patterns of molecules that are common to pathogens but are absent or sequestered in the host. The adaptive system, by contrast, uses unique genetic mechanisms to produce a virtually limitless diversity of related proteins—receptors on T and B cells and secreted antibodies—that, between them, can bind almost any foreign molecule. This remarkable strategy enables the adaptive immune system to react specifically against any pathogen, even if the animal never encountered it before. But, it also requires that the system learn not to react against self molecules or harmless foreign ones; if these learning mechanisms fail, harmful autoimmune or


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Cell_Biology_Alberts. animal never encountered it before. But, it also requires that the system learn not to react against self molecules or harmless foreign ones; if these learning mechanisms fail, harmful autoimmune or allergic responses result.


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Cell_Biology_Alberts. In this chapter, we focus on vertebrate immune responses and the features that distinguish them from other kinds of cell responses. We begin with innate immune defenses and then discuss the highly specialized properties of the adaptive immune system. The INNATe IMMUNe SYSTeM OVerVIeW OF The ADApTIVe IMMUNe SYSTeM B ceLLS AND Figure 24–1 Innate and adaptive immune responses. Innate immune responses are activated directly by pathogens and defend all multicellular organisms against infection. In vertebrates, pathogens, together with the innate immune responses they activate, also stimulate adaptive immune responses, which then work together with innate immune responses to help fight the infection. The INNATe IMMUNe SYSTeM


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Cell_Biology_Alberts. The INNATe IMMUNe SYSTeM Adaptive immune responses are slow to develop when a vertebrate first encounters a new pathogen. This is because the specific B cells and T cells that can respond to a particular pathogen are initially few in number and must be stimulated to proliferate and differentiate before they can mount effective adaptive immune responses, which can take days. By contrast, a single bacterium that divides every hour can generate almost twenty million progeny in a single day, producing a full-blown infection. Vertebrates, therefore, rely on their innate immune system to defend them against infection during the first critical hours and days of exposure to a new pathogen. Plants and invertebrates lack adaptive immune systems and therefore rely entirely on innate immunity for protection against pathogens. In this section, we consider some of the strategies the innate immune system uses to recognize pathogens and to provide a first line of defense against them.


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Cell_Biology_Alberts. In this section, we consider some of the strategies the innate immune system uses to recognize pathogens and to provide a first line of defense against them. epithelial Surfaces Serve as Barriers to Infection


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Cell_Biology_Alberts. In vertebrates, the first encounters with infectious organisms are typically at the epithelial surfaces that form the skin and line the respiratory, digestive, urinary, and reproductive tracts. These epithelia provide both physical and chemical barriers to invasion by pathogens: tight junctions between epithelial cells bar entry between the cells, and a variety of substances secreted by the cells discourage the attachment and entry of pathogens. The keratinized epithelial cells of the skin, for example, form a thick physical barrier, and the sebaceous glands in the skin secrete fatty acids and lactic acid, which inhibit bacterial growth. In addition, epithelial cells in all tissues, including those in plants and invertebrates, secrete antimicrobial molecules called defensins. Defensins are positively charged, amphipathic peptides that bind to and disrupt the membranes of many pathogens, including enveloped viruses, bacteria, fungi, and parasites.


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Cell_Biology_Alberts. The epithelial cells that line internal organs such as the respiratory and digestive tracts also secrete slimy mucus, which sticks to the epithelial surface and makes it difficult for pathogens to adhere. The beating of cilia on the surface of the epithelial cells lining the respiratory tract and the peristaltic action of the intestine also discourage the adherence of pathogens. Moreover, as we discuss in Chapter 23, healthy skin and gut are populated by enormous numbers of harmless (and often helpful) commensal microbes, collectively called the normal flora, which compete for nutrients with pathogens; some also produce antimicrobial peptides that actively inhibit pathogen proliferation. pattern recognition receptors (prrs) recognize conserved Features of pathogens


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Cell_Biology_Alberts. pattern recognition receptors (prrs) recognize conserved Features of pathogens Pathogens do occasionally breach the epithelial barricades, in which case underlying, nonepithelial cells of the innate immune system provide the next line of defense. These cells sense the presence of pathogens largely through the use of receptor proteins that recognize microbe-associated molecules that either are not present or are sequestered in the host organism. Because these microbial molecules often occur in repeating patterns, they are called pathogen-associated molecular patterns (PAMPs), even though they are not unique to microbes that can cause disease. PAMPs are present in various microbial molecules, including nucleic acids, lipids, polysaccharides, and proteins.


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Cell_Biology_Alberts. The special receptor proteins that recognize PAMPs are called pattern recognition receptors (PRRs). Some PRRs are transmembrane proteins on the surface of many types of host cells, where they recognize extracellular pathogens; on professional phagocytic cells (phagocytes) such as macrophages and neutrophils (discussed in Chapter 22), they can mediate the uptake of the pathogens into phagosomes, which then fuse with lysosomes, where the pathogens are destroyed. Other PRRs are located intracellularly, where they can detect intracellular pathogens such as viruses; these PRRs are either free in the cytosol or associated with Figure 24–2 The two main classes of adaptive immune responses.


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Cell_Biology_Alberts. Figure 24–2 The two main classes of adaptive immune responses. Lymphocytes carry out both classes of adaptive responses—shown here as responses to a viral infection. In one class, B cells secrete antibodies that specifically bind to and neutralize extracellular viruses, by preventing the viruses from infecting host cells. In the other, T cells mediate the response; in this example, they kill the virus-infected host cells. In both cases, innate immune responses help activate the adaptive immune responses through pathways that are not shown.


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Cell_Biology_Alberts. Figure 24–3 A scanning electron micrograph of a mutant fruit fly that died from a fungal infection. The fly is covered with fungal hyphae, as it lacked a Toll receptor, which helps protect Drosophila from fungal infections. (From B. Lemaitre et al., Cell 86:973–983, 1996.) the membranes of the endolysosomal system (discussed in Chapter 13). Still other PRRs are secreted and bind to the surface of extracellular pathogens, marking them for destruction by either phagocytes or blood proteins that are part of the complement system (discussed later). There Are Multiple classes of prrs


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Cell_Biology_Alberts. There Are Multiple classes of prrs The first PRR identified was the Toll receptor in Drosophila, which was well-known for its role in fly development (see Figure 21–17). It was later discovered to be also required for the production of antimicrobial peptides that protect the fly against fungal infections (Figure 24–3). Toll is a transmembrane glycoprotein with a large extracellular domain that contains a series of leucine-rich repeats. Soon it was discovered that both plants and animals have a variety of Toll-like receptors (TLRs) that function as PRRs in innate immune responses against various pathogens. Mammals make at least 10 different TLRs, each recognizing distinct ligands: TLR3, for example, recognizes double-stranded viral RNA in the endosomal lumen (Figure 24–4); TLR4 recognizes lipopolysaccharide (LPS) on the outer