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Cell_Biology_Alberts. Figure 22–40 Production and pluripotency of eS cells. eS cells are derived from the inner cell mass (iCm) of the early embryo. the iCm cells are transferred to a culture dish containing an appropriate medium, where they become converted to eS cells and can be kept proliferating indefinitely without differentiating. the eS cells can be taken at any time—after genetic manipulation, if desired—and injected back into the inner cell mass of another early embryo. there they take part in formation of a well-formed chimeric animal that is a mixture of ordinary and eS-derived cells. the eS-derived cells can differentiate into any of the cell types in the body, including germ cells from which a new generation of mice can be produced. these next-generation progeny are no longer chimeric, but consist of cells that all inherit half their genes from the cultured eS cell line.


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Cell_Biology_Alberts. blastocyst develops in (blastocyst) clump of ES cells injected cells become foster mother into a healthy injected into incorporated in inner chimeric mouse; the ES cells may recipient blastocyst cell mass of host blastocyst contribute to any tissue cells. Grown in culture, these can be manipulated, by suitable choice of culture conditions, to give rise to large quantities of almost any type of differentiated cell, opening the way to important practical applications. Before discussing them, however, we consider the underlying biology. a Core Set of transcription Regulators defines and maintains the eS Cell State What is it that gives ES cells and related types of pluripotent stem cells their extraordinary capabilities? What can they tell us about the fundamental mechanisms underlying stemness, cell differentiation, and the stability of the differentiated state?


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Cell_Biology_Alberts. For some attributes, the answer is simple. For example, an essential feature of ES cells is that they must avoid senescence. As discussed in Chapter 17, this is the fate of fibroblasts and many other types of somatic cells: they are limited in the number of times they will divide, in part at least because they lack telomerase activity, with the result that their telomeres become progressively eroded in each division cycle, leading eventually to cell-cycle arrest. ES cells, by contrast, express high levels of active telomerase, allowing them to escape senescence and continue dividing indefinitely. This is a property shared with other, more specialized types of stem cells, such as those of the adult intestine, which similarly can carry on dividing for hundreds or thousands of cycles.


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Cell_Biology_Alberts. The deeper problem is to explain how the whole complex pattern of gene expression in an ES cell is organized and maintained. As a first step, one can look for genes expressed specifically in ES cells or in the corresponding pluripotent cells of the early embryo. This approach identifies a relatively small number of candidate ES-critical genes; that is, genes that seem to be essential in one way or another for the peculiar character of ES cells. A gene called Oct4, for example, is exclusively expressed in ES cells and in related classes of cells in the intact organism—specifically, in the germ-cell lineage and in the inner cell mass and its precursors. Oct4 codes for a transcription regulator. When it is lost from ES cells, they lose their ES cell character; and when it is missing in an embryo, the cells that should specialize as inner cell mass are diverted into an extraembryonic pathway of differentiation and their development is aborted.


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Cell_Biology_Alberts. Fibroblasts Can be Reprogrammed to Create induced pluripotent Stem Cells (ipS Cells)


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Cell_Biology_Alberts. In Chapter 7, we saw that fibroblasts and some other cell types can be driven to switch their character and differentiate as muscle cells if the master muscle-specific transcription regulator MyoD is artificially expressed in them. Could the same technique be used to convert adult cell types into ES cells, through forced expression of factors such as Oct4? This question was tackled by transfecting fibroblasts with retroviral vectors carrying genes that one might hope to have such an effect. A total of 24 candidate ES-critical genes were tested in this way. None of them was able by itself to cause the conversion; but in certain combinations they could do so. In 2006, the first breakthrough experiments whittled down the requirement to a core set of four factors, all of them transcription regulators: Oct4, Sox2, Klf4, and Myc, known as the OSKM factors for short. When coexpressed, these could reprogram mouse fibroblasts, permanently converting them into cells closely similar to ES cells


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Cell_Biology_Alberts. Oct4, Sox2, Klf4, and Myc, known as the OSKM factors for short. When coexpressed, these could reprogram mouse fibroblasts, permanently converting them into cells closely similar to ES cells (Figure 22–41). ES-like cells created in this way are called induced pluripotent stem cells, or iPS cells. Like ES cells, iPS cells can continue dividing indefinitely in culture, and when incorporated into a mouse blastocyst they can participate in creation of a perfectly formed chimeric animal. In this animal, they can contribute to the development of any tissue and can turn into any differentiated cell type, including functional germ cells from which a new generation of mice can be raised (see Figure 22–40).


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Cell_Biology_Alberts. iPS cells can now be derived from adult human cells and from various other differentiated cell types besides fibroblasts. Numerous methods can be used to drive up regulation of up regulation ofembryonic stem cell proliferationcell genes down regulation of loosening of differentiation genes chromatin structure


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Cell_Biology_Alberts. Figure 22–41 Reprogramming fibroblasts to IPS cells with the OSKM factors. as indicated, the master gene regulator proteins oct4, Sox2, and klf4 (oSk) induce both their own and each other's synthesis (gray shading). this generates a self-sustaining feedback loop that helps to maintain cells in an embryonic stem cell-like state, even after all of the experimentally added oSkm initiators have been removed. myc overexpression speeds up early stages of the reprogramming process through the mechanisms shown (see Figure 17–61). Stable reprogramming also involves the permanently induced expression of the Nanog gene, which produces an additional master transcription regulator. (adapted from


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Cell_Biology_Alberts. J. kim et al., Cell 132:1049–1061, 2008.) expression of the transforming OSKM factors, including methods that leave no trace of foreign DNA in the reprogrammed cell. Variations of the original cocktail of transcription regulators can drive the conversion, with different specialized cell types having somewhat different requirements. Myc overexpression, for example, turns out not to be absolutely necessary, although it enhances the efficiency of the process. And differentiated cell types may express some of the required factors as part of their normal phenotype. For example, cells of the dermal papilla of hair follicles already express Sox2, Klf4, and Myc; to convert them into iPS cells, it is enough to force them artificially to express Oct4. Oct4, indeed, seems to have a central role and to be generally indispensable for the creation of iPS cells. Reprogramming involves a massive upheaval of the Gene Control System


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Cell_Biology_Alberts. Reprogramming involves a massive upheaval of the Gene Control System Converting a differentiated cell into an iPS cell is not like flicking a switch on some predictable, precisely engineered piece of machinery. Only a few of the cells that receive the OSKM factors will actually become iPS cells—one in several thousand in the original experiments, and still only a small minority with more recent, improved techniques. In fact, the success of the original experiments depended on clever selection to pick out those few cells where the conversion had occurred (Figure 22–42).


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Cell_Biology_Alberts. Conversion to an iPS character by the OSKM factors is not only inefficient but also slow: fibroblasts take ten days or more from introduction of the conversion factors before they begin to express markers of the iPS state. This suggests that the transformation involves a long cascade of changes. These changes are being extensively studied, and they affect both the expression of individual genes and the state of the chromatin. The results of one such study are outlined in Figure 22–43. The process begins with a Myc-induced cell proliferation and loosening of chromatin structure that promotes the binding of the other three master regulators to many hundreds of different sites in the genome. At a large proportion of these sites, Oct4, Sox2, and Klf4 all bind in concert. The binding sites include the endogenous Oct4, Sox2, and Klf4 genes themselves, which eventually creates the types of positive feedback loops just described that makes expression of these genes self-sustaining (see Figure


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Cell_Biology_Alberts. the endogenous Oct4, Sox2, and Klf4 genes themselves, which eventually creates the types of positive feedback loops just described that makes expression of these genes self-sustaining (see Figure 22–41). But self-induction of Oct4, Sox2, and Klf4 is only a small part of the transformation that occurs. The three core factors activate some target genes and repress others, producing a cascade of effects that reorganize the gene control system globally and at every level, changing the patterns of histone modification, DNA methylation, and chromatin compaction, as well as the expression of innumerable proteins and noncoding RNAs. By the end of this complex process, the resulting iPS cell is no longer dependent on the artificially generated factors that triggered the change: it has settled into a stable, self-sustaining state of coordinated gene expression, making its own Oct4, Sox2, Klf4, and Myc (and all the other essential ingredients of a pluripotent stem cell) from its own endogenous


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Cell_Biology_Alberts. a stable, self-sustaining state of coordinated gene expression, making its own Oct4, Sox2, Klf4, and Myc (and all the other essential ingredients of a pluripotent stem cell) from its own endogenous copies of the genes.


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Cell_Biology_Alberts. factors O, S, K and M cell state unchanged, resistance gene not expressed Fbx15 G418-resistance gene iPS cell survives promoter rare change of state to iPS character, resistance gene expressed


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Cell_Biology_Alberts. Figure 22–42 A strategy used to select cells that have converted to an iPS character. the experiment makes use of a gene (Fbx15) that is present in all cells but is normally expressed only in eS and early embryonic cells (although not required for their survival). a fibroblast cell line is genetically engineered to contain a gene that produces an enzyme that degrades G418 under the control of the Fbx15 regulatory sequence. G418 is an aminoglycoside antibiotic that blocks protein synthesis in both bacteria and eukaryotic cells. when the oSkm factors are artificially expressed in this cell line, a small proportion of the cells undergo a change of state and activate the Fbx15 regulatory sequence, driving expression of the G418-resistance gene. when G418 is added to the culture medium, these are the only cells that survive and proliferate. when tested, they turn out to have an ipS character.


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Cell_Biology_Alberts. ~99% of cells transcription wave 2 ~<1% of cells become IPS cells an experimental manipulation of Factors that modify Chromatin Can increase Reprogramming efficiencies The low efficiency and slow rate of conversion suggest that there is some barrier blocking the switch from the differentiated state to the iPS state in these experiments, and that overcoming this barrier is a difficult process that involves a large element of chance. Likewise, the outcome is variable, with significant differences between the individual lines of transformed cells that are generated, even when the initial differentiated cells are genetically and phenotypically identical. Only some of the candidate iPS lines pass all the tests of pluripotency. At a molecular level, there are differences even among the fully validated iPS cells: although they share many features, they vary in details of their gene expression patterns and, for example, in their patterns of DNA methylation.


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Cell_Biology_Alberts. Overcoming these difficulties will be critical for improving our understanding of how cell specialization is controlled and organized in multicellular organisms; it should also facilitate many medical advances. Thus, intensive research is being carried out on the reprogramming process. One approach aims at obtaining a much clearer picture of the role that chromatin structures play in gene regulation in eukaryotes.


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Cell_Biology_Alberts. From our discussion of nuclear transplantation, one might expect that any reprogramming of a differentiated cell would require a radical and widespread change in the chromatin structure of selected genes. Not only are such changes observed, but a large number of different experiments reveal that the efficiency of the reprogramming process can be substantially increased by altering the activity of proteins that affect chromatin structure. Figure 22–44 categorizes some of the factors that have been shown to enhance the transformation of fibroblasts to iPS cells; those in the top three rows—chromatin remodelers, histone modifying enzymes, and histone variants—are especially well known to have profound effects on the organization of nucleosomes in chromatin (discussed in Chapter 4).


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Cell_Biology_Alberts. We can only touch briefly here on the massive amounts of data that have been accumulating in this exciting research area. The major challenge that remains is to obtain a systems-level model for the complex set of biochemical changes that are involved in reprogramming. For example, which chromatin changes come first, and which then follow? How can these be triggered by the master transcription regulators through their binding to specific DNA sequences, and why do many cells in a population appear resistant to these effects? eS and ipS Cells Can be Guided to Generate Specific adult Cell types and even whole organs We can think of embryonic development in terms of a series of choices presented to cells as they follow a road that leads from the fertilized egg to terminal


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Cell_Biology_Alberts. We can think of embryonic development in terms of a series of choices presented to cells as they follow a road that leads from the fertilized egg to terminal Figure 22–43 A summary of some of the major events that accompany the reprogramming of mouse fibroblasts to iPS cells. by sorting cells at various times after the oSkm induction shown, one can carry out detailed biochemical analyses on the different cell populations shown. this led to the discovery that two major waves of new gene transcription are induced, but that the second wave occurs only in the subset of cells expressing an embryonic marker protein. Some 1500 genes are found to be differentially expressed in these cells, compared to the large majority of cells that fail to progress toward ipS cells. as indicated, major dna methylation changes are observed only after the alteration of chromatin structures.


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Cell_Biology_Alberts. in the first transcription wave, among the genes prominently induced are those for cell proliferation, metabolism, and cytoskeletal organization; in contrast, genes associated with fibroblast development are repressed. in the second transcription wave, genes required for embryonic development and for stem cell maintenance are induced. (adapted from J.m. polo et al., Cell 151:1617–1632, 2012.) specifc miRNAs specifc IncRNAs histone deacetylases specifc histone methyl transferases specifc histone demethylases histone acetyl transferases histone variant H2AZ histone variant macroH2A histone variant H3.3 DNA demethylases differentiation. After their long sojourn in culture, the ES cells or iPS cells and their progeny can still read the signs at each branch in the highway and respond as normal embryonic cells would. If ES or iPS cells are implanted directly into an embryo at a later stage or into an adult tissue, however, they fail to receive the appropriate sequence of cues; their


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Cell_Biology_Alberts. normal embryonic cells would. If ES or iPS cells are implanted directly into an embryo at a later stage or into an adult tissue, however, they fail to receive the appropriate sequence of cues; their differentiation then is not properly controlled, and they will often give rise to a tumor of the type known as a teratoma, containing a mixture of cell types inappropriate to the site in the body.


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Cell_Biology_Alberts. In culture, by exposing the ES or iPS cell to an appropriate sequence of signal proteins and growth factors, delivered with the right timing, it is possible to guide the cell along a pathway that approximates a normal developmental pathway, so as to convert it into one of the standard specialized adult cell types (Figure 22–45 and Movie 22.5). Success requires trial and error, but has now been achieved for many different final specialized states, including neuronal, muscular, and intestinal cell types. In a few cases, it has even been possible, by careful manipulation of the culture conditions, to get ES or iPS cells to interact with one another so as to construct an entire organ, albeit on a small scale (Figure 22–46). retinoic acid insulin, thyroid hormone


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Cell_Biology_Alberts. retinoic acid insulin, thyroid hormone Figure 22–44 Factors that have been observed to enhance reprogramming efficiency. emphasized here are those factors that can alter chromatin states, with those in the top three rows having the most direct effects. an up arrow indicates that reprogramming is increased when the activity of the indicated factor is increased; a down arrow indicates that reprogramming is increased when the activity of the indicated factor is decreased. thus, for example, increased activity of histone acetyl transferases and increased activity of histone deacetylases have opposite effects, as expected from their biochemical activities (see p. 196). Figure 22–45 Production of differentiated cells from eS or iPS cells in culture.


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Cell_Biology_Alberts. these cells can be cultured indefinitely as pluripotent cells when attached as a monolayer to a dish. alternatively they can be detached and allowed to form aggregates called embryoid bodies, which causes the cells to begin to specialize. Cells from embryoid bodies, cultured in media with different factors added, can then be driven to differentiate in various ways. (based on e. Fuchs and J.a. Segre, Cell 100:143–155, 2000. with permission from elsevier.) macrophage colony-interleukin-3, stimulating factor, interleukin-1 macrophage iPS cells (about 1,000 cells) dibutyryl cAMP, retinoic acid smooth muscle cell fbroblast fbroblast fbroblast growth factor 2, growth factor 2, growth epidermal platelet-derived factor growth factor growth factor 1258 Chapter 22: Stem Cells and tissue Renewal aggregate of hollow ball of budding of optic vesicle invaginates cultured ES cells neural cells optic vesicle to form optic cup (B) 100 µm


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Cell_Biology_Alberts. Figure 22–46 Cultured eS cells can give rise to a three-dimensional organ. (a) Remarkably, under appropriate conditions, mouse eS cells in culture can proliferate, differentiate, and interact to form a three-dimensional, eye-like structure, which includes a multilayered retina similar in organization to the one that forms in vivo. (b) Fluorescent micrograph of an optic cup formed by eS cells in culture. the structure includes a developing retina, containing multiple layers of neural cells, which produce a protein (pink) that serves as a marker for retinal tissue. (b, from m. eiraku, n. takata, h. ishibashi et al., Nature 472:51–56, 2011. with permission from macmillan publishers ltd.) Cells of one Specialized type Can be Forced to transdifferentiate directly into another


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Cell_Biology_Alberts. Cells of one Specialized type Can be Forced to transdifferentiate directly into another The route we have just described, from one mode of differentiation to another via conversion to an iPS cell, seems needlessly roundabout. Could we not convert cell type A into cell type B directly, without backtracking to the embryonic-like iPS state? For many years, it has been known that such transdifferentiation can be achieved in a few special cases, such as the conversion of fibroblasts into skeletal muscle cells by forced expression of MyoD (see p. 396). But now, with the insights that have come from the study of ES and iPS cells, ways are being found to bring about such interconversions in a much wider range of cases.


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Cell_Biology_Alberts. An elegant example comes from studies of the heart. By forcing expression of an appropriate combination of factors—not Oct4, Sox2, Klf4, and Myc, but Gata4, Mef2c, and Tbx5—it is possible to convert heart fibroblasts directly into heart muscle cells. This has been done in the living mouse, using retroviral vectors, and the transformation occurs with high efficiency when the vectors carrying the transgenes are injected directly into the heart muscle tissue itself. Although they occupy only a small fraction of the tissue volume, the fibroblasts in the heart outnumber the heart muscle cells, and they survive in large numbers even where the heart muscle cells have died. Thus, in a typical nonfatal heart attack, where heart muscle cells have died for lack of oxygen, the fibroblasts proliferate and make collagenous matrix so as to replace the lost muscle with a fibrous scar. This is a poor sort of repair. By forcing expression of the appropriate factors in the heart, as described above, it


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Cell_Biology_Alberts. and make collagenous matrix so as to replace the lost muscle with a fibrous scar. This is a poor sort of repair. By forcing expression of the appropriate factors in the heart, as described above, it has proved possible, in the mouse at least, to do better than nature and regenerate lost heart muscle by transdifferentiation of heart fibroblasts.


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Cell_Biology_Alberts. We are still a long way from putting this technique into practice as a treatment for heart attacks in humans, but it shows what the future may hold—not only for this medical problem, but for many others. eS and ipS Cells are useful for drug discovery and analysis of disease A large part of the excitement surrounding ES and iPS cells and the technology of transdifferentiation comes from the prospect of using the artificially generated cells for tissue repair. It begins to seem that virtually any type of tissue might be replaceable, allowing treatment of degenerative diseases that have previously had no cure. Research in this area is moving rapidly, but there are many difficulties to be overcome. treatment transplantation of genetically with drugs matched healthy cells


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Cell_Biology_Alberts. treatment transplantation of genetically with drugs matched healthy cells With the advent of iPS cells and direct transdifferentiation, at least one major hurdle has been surmounted, in principle at least: the problem of immune rejection. ES cells, because they are created from early embryos that generally come from unrelated donors, will never be genetically identical to the cells of the patient receiving the transplant. The transplanted cells and their progeny are therefore liable to rejection by the immune system. Both iPS and transdifferentiated cells, in contrast, can be generated from a small sample of the patient’s own tissue and so should escape immune attack when transplanted back into the same individual.


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Cell_Biology_Alberts. Tissue repair by transplantation, however, is not the only application for which ES, iPS, and transdifferentiated cells can be used: there are other ways in which they promise to be more immediately valuable. In particular, they can be used to generate large, homogeneous populations of specialized cells of any chosen type in culture; and these can serve for investigation of disease mechanisms and in the search for new drugs acting on a specific cell type (Figure 22–47).


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Cell_Biology_Alberts. Where a disease has a genetic cause, we can derive iPS cells from sufferers and use these cells to produce the specific cell types that malfunction, to investigate how the malfunction occurs, and to screen for drugs that might help to put it right. Timothy syndrome provides an example. In this rare genetic condition, there is a severe, life-threatening disorder in the rhythm of the heart beat (as well as several other abnormalities), as a result of a mutation in a specific type of Ca2+ channel. To study the underlying pathology, researchers took skin fibroblasts from patients with the disorder, generated iPS cells from the fibroblasts, and drove the iPS cells to differentiate into heart muscle cells. These cells, when compared with heart muscle cells prepared similarly from normal control individuals, showed irregular contractions and abnormal patterns of Ca2+ influx and electrical activity that could be characterized in detail. From this finding, it is a small step to development of


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Cell_Biology_Alberts. individuals, showed irregular contractions and abnormal patterns of Ca2+ influx and electrical activity that could be characterized in detail. From this finding, it is a small step to development of an in vitro assay for drugs that might correct the misbehavior of the heart muscle cells.


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Cell_Biology_Alberts. This approach to drug discovery—where iPS cells are prepared from the individual patient, differentiated into the relevant cell type, and used to test candidate drugs in vitro—would seem to represent a huge advance on the slow, costly traditional methods that involve administration of test compounds to large numbers of people. Figure 22–47 Use of iPS cells for drug discovery and for analysis and treatment of genetic disease. the left side of the diagram shows how differentiated cells that are generated from ipS cells derived from a patient with a genetic disease can be used for analysis of the disease mechanism and for discovery of therapeutic drugs. the right side of the diagram shows how the genetic defect might be repaired in the ipS cells, which could then be induced to differentiate in an appropriate way and grafted back into the patient without danger of immune rejection. (based on d.a. Robinton and G.Q. daley, Nature 481:295–305, 2012).


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Cell_Biology_Alberts. In the adult mammalian body, the various types of stem cells are highly specialized, each giving rise to a limited range of differentiated cell types. Cells become restricted size? how do the cells in each tissue to specific pathways of differentiation during embryonic development. One way know when to terminate their growth to force a return to a pluripotent or totipotent state is by nuclear transplantation: and division, so as to limit the size of the nucleus of a differentiated cell can be injected into an enucleated oocyte, whose an organ or tissue appropriately? cytoplasm reprograms the genome back to an approximation of an early embryonic state. This allows production of an entire new individual. The reversion of the • what is the fundamental molecular genome to this state involves radical, genome-wide changes in chromatin structure difference that distinguishes a stem and DNA methylation. cell?


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Cell_Biology_Alberts. Remarkably, cells taken from the inner cell mass of an early mammalian embryo • how is the correct balance between can be propagated in culture indefinitely in a pluripotent state. When transplanted stem cells, progenitor cells, and back into a host early embryo, these embryonic stem (ES) cells can contribute cells to any tissue, including the germ line. ES cells have been invaluable for genetic engi tissue or organ? neering in mice. Cells with similar properties, called induced pluripotent stem cells (iPS cells), can be generated from adult differentiated cells such as fibroblasts by • what role does chromatin structure forced expression of a cocktail of key transcription regulators. A similar method play in cell memory and in cell reprogramming?


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Cell_Biology_Alberts. can be used to reprogram adult cells directly from one specialized state to another. In principle, iPS cells generated from cells biopsied from an adult human patient • how are molecules inherited could be used for tissue repair in that same individual, avoiding the problem of asymmetrically during cell division? immune rejection. More immediately, they provide a source of specialized cells that can be used to analyze in vitro the effects of mutations affecting human cells and for • how do germ cells avoid aging? screening for drugs for treatment of genetic diseases. Which statements are true? explain why or why not. 22–1 In the small intestine, stem cells in the crypts divide asymmetrically to maintain the population of cells that make up the villi; after each division, one daughter remains a stem cell and the other begins to divide rapidly to produce differentiated progeny. 22–2 Stem cells, being stem cells, are by definition the same in all tissues.


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Cell_Biology_Alberts. 22–2 Stem cells, being stem cells, are by definition the same in all tissues. 22–3 Every tissue that can be renewed is renewed from a tissue-specific population of stem cells. 22–4 Disturbance of the balance in the activities of osteoblasts and osteoclasts in favor of osteoclasts can give rise to the condition known as osteoporosis, the brittle-bone syndrome of the elderly. Discuss the following problems.


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Cell_Biology_Alberts. Discuss the following problems. 22–5 In the 1950s, scientists fed 3H-thymidine to rats to label cells that were synthesizing DNA, and then followed the fates of labeled cells for periods of up to a year. They found three patterns of cell labeling in different tissues. Cells in some tissues such as neurons in the central nervous system and the retina did not get labeled. Muscle, kidney, and liver, by contrast, each showed a small number of labeled cells that retained their label, apparently without further division or loss. Finally, cells such as those in the squamous epithelia of the tongue and esophagus were labeled in fairly large numbers, with radioactive pairs of nuclei visible in 12 hours; however, the labeled cells disappeared over time. Which of these three patterns of labeling would you expect to see if the labeled cells were generated by stem cells? Explain your answer.


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Cell_Biology_Alberts. 22–6 At any given time, intestinal crypts of mice comprise about 15 stem cells and 10 Paneth cells. After cell division, which occurs about once a day, the daughter cells remain stem cells only if they maintain contact with a Paneth cell. This constant competition for Paneth-cell contact raises the possibility that crypts might become monoclonal over time; that is, the crypt cells at one point in time might derive from only 1 of the 15 stem cells that existed at some earlier time. To test this possibility, you use the so-called confetti marker that upon activation expresses any one of three fluorescent proteins in the stem cells of the crypt. You then examine crypts at various times to determine whether they contain cells with multiple colors or only one color (Figure Q22–1). Do the crypts become monoclonal over time or not? How can you tell?


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Cell_Biology_Alberts. 22–7 The origin of new β cells of the pancreas—from stem cells or from preexisting β cells—was not resolved until a decade ago, when the technique of lineage tracing was used to decide the issue. Using transgenic mice that expressed a tamoxifen-activated form of Cre recombinase under the control of the insulin promoter, which is active only in β cells, investigators could remove an inhibitory segment of DNA and thereby allow expression of human placental alkaline phosphatase (HPAP), which can be detected by histochemical staining. After a pulse of tamoxifen that converted about 30% of β cells in young mice to microvilli 22–8 One of the earliest assays for hematopoietic stem cells made use of their ability to form colonies in the spleens of heavily irradiated mice. By varying the amounts


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Cell_Biology_Alberts. Figure Q22–1 Fluorescent cells in crypts in mouse intestines at various times after activation of expression of fluorescent proteins (problem 22–6). the images are taken in the xz plane, which cuts through multiple crypts, as indicated in the schematic drawing. Roughly 50 crypts are visible in each section. Dotted white circles identify some individual crypts. Scale bars are 100 μm. (adapted from h.J. Snippert et al., Cell 143:134–144, 2010. with permission from elsevier.) cells that express HPAP, the investigators followed the percentage of labeled β cells for a year, during which time the total number of β cells in the pancreas increased by 6.5fold. How do you suppose the percentage of β cells would change over time if new β cells were derived from stem cells? What if new β cells were derived from preexisting β cells? Which hypothesis do the results in Figure Q22–2 support?


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Cell_Biology_Alberts. of transplanted bone marrow cells, investigators showed that the number of spleen colonies varied linearly with dose and that the curve passed through the origin, suggesting that single cells were capable of forming individual colonies. However, because colony formation was rare relative to the numbers of transplanted cells, it was possible that undispersed clumps of two or more cells were the actual initiators. A classic paper resolved this issue by exploiting rare, cytologically visible genome rearrangements generated by irradiation. Recipient mice were first irradiated to deplete bone marrow cells, and then they were irradiated a second time after transplantation to generate rare genome rearrangements in the transplanted cell population. Spleen colonies were then screened to find ones that carried genome rearrangements. How do you suppose this experiment distinguishes between colonization by single cells versus cellular aggregates?


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Cell_Biology_Alberts. 22–9 It is possible to purify hematopoietic stem cells using a combination of antibodies directed against cellsurface targets. By removing cells that expressed surface markers characteristic of specific lineages such as B cells, granulocytes, myelomonocytic cells, and T cells, investigators generated a population of cells enriched for stem cells. They further enriched this population for putative stem cells by positively selecting for cells that expressed suspected stem-cell surface markers. Spleen colony formation in irradiated mice by these putative stem cells and the unfractionated bone marrow cells is shown in Figure Q22–3. Given that only about 1 in 10 cells lodges in the spleen, do these results support the idea that the enriched population consists mostly of hematopoietic stem cells? What additional information would you need to have to feel confident that the enriched cells are true stem cells? What proportion of bone marrow cells are hematopoietic stem cells?


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Cell_Biology_Alberts. 22–10 Generation of induced pluripotent stem (iPS) cells was first accomplished using retroviral vectors to carry the OSKM (Oct4, Sox2, Klf4, and Myc) set of transcription regulators into cells. The efficiency of fibroblast reprogramming was typically low (0.01%), in part because large numbers of retroviruses must integrate to bring about reprogramming and each integration event carries with it the risk of inappropriately disrupting or activating a critical gene. In what other ways, or other forms, do you suppose you might deliver the OSKM transcription regulators so as to avoid these problems? percent of ˜ cellsexpressing HPAP number of colonies cells (problem 22–9).


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Cell_Biology_Alberts. percent of ˜ cellsexpressing HPAP number of colonies cells (problem 22–9). Figure Q22–2 percentage of labeled β cells in pancreatic islets of mice at different ages (problem 22–7). all mice were injected with a pulse of tamoxifen at 6 to 8 weeks of age and then stained for human placental 1 alkaline phosphatase (hpap) at various times afterward. error bars 101 102 103 104 105 106 represent standard deviations. number of cells injected Fawcett dw & Jensh R (2002) bloom and Fawcett’s Concise histology, 2nd ed. new york/london: arnold. Gurdon Jb & melton da (2008) nuclear reprogramming in cells. Science 322, 1811–1815. li l & Xie t (2005) Stem cell niche: structure and function. Annu. Rev. Cell Dev. Biol. 21, 605–631. losick vp, morris lX, Fox dt & Spradling a (2011) Drosophila stem cell niches: a decade of discovery suggests a unified view of stem cell regulation. Dev. Cell 21, 159–171.


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Cell_Biology_Alberts. losick vp, morris lX, Fox dt & Spradling a (2011) Drosophila stem cell niches: a decade of discovery suggests a unified view of stem cell regulation. Dev. Cell 21, 159–171. young b, woodford p & o’dowd G (2014) wheater’s Functional histology: a text and Colour atlas, 6th ed. edinburgh: Churchill livingstone/elsevier. barker n, van es Jh, kuipers J et al. (2007) identification of stem cells in small intestine and colon by marker gene Lgr5. Nature 449, 1003–1007. blanpain C & Fuchs e (2014) plasticity of epithelial stem cells in tissue regeneration. Science 344, 1242281. Crosnier C, Stamataki d & lewis J (2006) organizing cell renewal in the intestine: stem cells, signals and combinatorial control. Nat. Rev. Genet. 7, 349–359. Sato t, van es Jh, Snippert hJ et al. (2011) paneth cells constitute the niche for lgr5 stem cells in intestinal crypts. Nature 469, 415–418.


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Cell_Biology_Alberts. Sato t, van es Jh, Snippert hJ et al. (2011) paneth cells constitute the niche for lgr5 stem cells in intestinal crypts. Nature 469, 415–418. Sato t & Clevers h (2013) Growing self-organizing mini-guts from a single intestinal stem cell: mechanism and applications. Science 340, 1190–1194. Stanger bZ, tanaka aJ & melton da (2007) organ size is limited by the number of embryonic progenitor cells in the pancreas but not the liver. Nature 445, 886–891. taub R (2004) liver regeneration: from myth to mechanism. Nat. Rev. Mol. Cell Biol. 5, 836–847. watt Fm & huck wtS (2013) Role of the extracellular matrix in regulating stem cell fate. Nat. Rev. Mol. Cell Biol. 14, 467–473. Fibroblasts and Their Transformations: The Connective-Tissue Cell Family Cooper kl, oh S, Sung y et al. (2013) multiple phases of chondrocyte enlargement underlie differences in skeletal proportions. Nature 495, 375–378.


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Cell_Biology_Alberts. Cooper kl, oh S, Sung y et al. (2013) multiple phases of chondrocyte enlargement underlie differences in skeletal proportions. Nature 495, 375–378. karsenty G & wagner eF (2002) Reaching a genetic and molecular understanding of skeletal development. Dev. Cell 2, 389–406. Rinn Jl, bondre C, Gladstone hb et al. (2006) anatomic demarcation by positional variation in fibroblast gene expression programs. PLoS Genet. 2, e119. Seeman e & delmas pd (2006) bone quality—the material and structural basis of bone strength and fragility. N. Engl. J. Med. 354, 2250–2261. Zelzer e & olsen bR (2003) the genetic basis for skeletal diseases. Nature 423, 343–348. Genesis and Regeneration of Skeletal Muscle bassel-duby R & olson en (2006) Signaling pathways in skeletal muscle remodeling. Annu. Rev. Biochem. 75, 19–37. buckingham m (2006) myogenic progenitor cells and skeletal myogenesis in vertebrates. Curr. Opin. Genet. Dev. 16, 525–532.


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Cell_Biology_Alberts. buckingham m (2006) myogenic progenitor cells and skeletal myogenesis in vertebrates. Curr. Opin. Genet. Dev. 16, 525–532. Collins Ca, olsen i, Zammit pS et al. (2005) Stem cell function, self-renewal, and behavioral heterogeneity of cells from the adult muscle satellite cell niche. Cell 122, 289–301. lee SJ (2004) Regulation of muscle mass by myostatin. Annu. Rev. Cell Dev. Biol. 20, 61–86. weintraub h, davis R, tapscott S et al. (1991) the myod gene family: nodal point during specification of the muscle cell lineage. Science 251, 761–766. blood Vessels, lymphatics, and endothelial Cells Carmeliet p & tessier-lavigne m (2005) Common mechanisms of nerve and blood vessel wiring. Nature 436, 193–200. Folkman J & haudenschild C (1980) angiogenesis in vitro. Nature 288, 551–556. Gerhardt h, Golding m, Fruttiger m et al. (2003) veGF guides angiogenic sprouting utilizing endothelial tip cell filopodia. J. Cell Biol. 161, 1163–1177.


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Cell_Biology_Alberts. Gerhardt h, Golding m, Fruttiger m et al. (2003) veGF guides angiogenic sprouting utilizing endothelial tip cell filopodia. J. Cell Biol. 161, 1163–1177. lawson nd & weinstein bm (2002) In vivo imaging of embryonic vascular development using transgenic zebrafish. Dev. Biol. 248, 307–318. pugh Cw & Ratcliffe pJ (2003) Regulation of angiogenesis by hypoxia: role of the hiF system. Nat. Med. 9, 677–684. tammela t & alitalo k (2010) lymphangiogenesis: molecular mechanisms and future promise. Cell 140, 460–476. A Hierarchical Stem-Cell System: blood Cell Formation orkin Sh & Zon li (2008) hematopoiesis: an evolving paradigm for stem cell biology. Cell 132, 631–644. Shizuru Ja, negrin RS & weissman il (2005) hematopoietic stem and progenitor cells: clinical and preclinical regeneration of the hematolymphoid system. Annu. Rev. Med. 56, 509–538. brockes Jp & kumar a (2008) Comparative aspects of animal regeneration. Annu. Rev. Cell Dev. Biol. 24, 525–549.


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Cell_Biology_Alberts. brockes Jp & kumar a (2008) Comparative aspects of animal regeneration. Annu. Rev. Cell Dev. Biol. 24, 525–549. tanaka em & Reddien pw (2011) the cellular basis for animal regeneration. Dev. Cell 21, 172–185. wagner de, wang ie & Reddien pw (2011) Clonogenic neoblasts are pluripotent adult stem cells that underlie planarian regeneration. Science 332, 811–816. apostolou e & hochedlinger k (2013) Chromatin dynamics during cellular reprogramming. Nature 502, 462–471. egawa n, kitaoka S, tsukita k et al. (2012) drug screening for alS using patient-specific induced pluripotent stem cells. Sci. Transl. Med. 4, 145ra104. eggan k, baldwin k, tackett m et al. (2004) mice cloned from olfactory sensory neurons. Nature 428, 44–49. Fox iJ, daley GQ, Goldman Sa et al. (2014) use of differentiated pluripotent stem cells as replacement therapy for treating disease. Science 345, 1247391.


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Cell_Biology_Alberts. Fox iJ, daley GQ, Goldman Sa et al. (2014) use of differentiated pluripotent stem cells as replacement therapy for treating disease. Science 345, 1247391. inoue h, nagata n, kurokawa h & yamanaka S (2014) ipS cells: a game changer for future medicine. EMBO J. 33, 409–417. kim J, Chu J, Shen X et al. (2008) an extended transcriptional network for pluripotency of embryonic stem cells. Cell 132, 1049–1061. orkin Sh & hochedlinger k (2011) Chromatin connections to pluripotency and cellular reprogramming. Cell 145, 835–850. polo Jm, anderssen e, walsh Rm et al. (2012) a molecular roadmap of reprogramming somatic cells into ipS cells. Cell 151, 1617–1632. Radzisheuskaya a & Silver JCR (2014) do all roads lead to oct4? the emerging concepts of induced pluripotency. Trends Cell Biol. 24, 275–284. Sasai y, eiraku m & Suga h (2012) In vitro organogenesis in three dimensions: self-organising stem cells. Development 139, 4111–4121.


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Cell_Biology_Alberts. Sasai y, eiraku m & Suga h (2012) In vitro organogenesis in three dimensions: self-organising stem cells. Development 139, 4111–4121. Soza-Ried J & Fisher aG (2012) Reprogramming somatic cells towards pluripotency by cellular fusion. Curr. Opin. Genet. Dev. 22, 459–465. takahashi k & yamanaka S (2006) induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663–676. theunissen tw & Jaenisch R (2014) molecular control of induced pluripotency. Cell Stem Cell 14, 720–734. watanabe a, yamada y & yamanaka S (2013) epigenetic regulation in pluripotent stem cells: a key to breaking the epigenetic barrier. Philos. Trans. R. Soc. Lond. B Biol. Sci. 368, 20120292. yamanaka S (2013) the winding road to pluripotency (nobel lecture). Angew. Chem. Int. Ed. Engl. 52, 13900–13909.


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Cell_Biology_Alberts. yamanaka S (2013) the winding road to pluripotency (nobel lecture). Angew. Chem. Int. Ed. Engl. 52, 13900–13909. Infectious diseases currently cause about one-quarter of all human deaths worldwide, more than all forms of cancer combined and second only to cardiovascular diseases. In addition to the continuing heavy burden of ancient diseases such as tuberculosis and malaria, newer infectious diseases continually emerge. The current pandemic (worldwide epidemic) of AIDS (acquired immune deficiency syndrome), was first clinically observed in 1981 and has since caused more than 35 million deaths worldwide. Moreover, some diseases long thought to result from other causes are now recognized to be associated with infections. Most gastric ulcers, for example, are caused not by stress or spicy food, but by infection of the stomach lining by the bacterium Helicobacter pylori.


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Cell_Biology_Alberts. The burden of infectious diseases is not spread equally across the planet. Poorer countries and communities suffer disproportionately, often due to poor public sanitation and health systems. Some infectious diseases, however, occur primarily or exclusively in industrialized communities: Legionnaire’s disease, for example, a bacterial infection of the lungs, commonly spreads through air-conditioning systems. Since the mid-1800s, physicians and scientists have struggled to identify the agents—collectively called pathogens—that are capable of causing infectious diseases. More recently, the advent of microbial genetics and molecular cell biology has greatly enhanced our understanding of the causes and mechanisms of infectious diseases. We now know that pathogens frequently exploit the attributes of their host’s cells in order to infect them. This understanding can give us new insights into normal cell biology, as well as strategies for treating and preventing infectious diseases.


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Cell_Biology_Alberts. Although pathogens are understandably a focus of attention, only a relatively small fraction of the microbial species we encounter are pathogens. Much of the biomass of the Earth is made up of microbes, and they produce everything from the oxygen we breathe to the soil nutrients we use to grow food. Even those species of microbes that colonize the human body do not generally cause disease. The collective of microorganisms that reside in or on an organism is called the microbiota. Many of these microbes have a beneficial effect on the health of the organism, assisting its normal development and physiology. In this chapter, we give an overview of the different kinds of pathogens, as well as those microorganisms that colonize our body without causing trouble. We then discuss the cell biology of infection—the molecular interactions between pathogens and their host. In Chapter 24, we consider how our innate and adaptive immune systems collaborate to defend us against pathogens.


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Cell_Biology_Alberts. We normally think of pathogens as hostile invaders, but a pathogen, like any other organism, is simply exploiting an available niche in which to live and procreate. Living on or in a host organism is a very effective strategy, and it is possible that every organism on Earth is subject to some type of infection (Figure 23–1). A human host is a nutrient-rich, warm, and moist environment, which remains at a uniform temperature and constantly renews itself. It is not surprising that many microorganisms have evolved the ability to survive and reproduce in this desirable niche. In this section, we discuss some of the common features that microorganisms must have in order to colonize the human body or cause disease, and we explore the wide variety of organisms that are known to cause disease. The Human Microbiota Is a Complex Ecological System That Is Important for Our Development and Health


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Cell_Biology_Alberts. The Human Microbiota Is a Complex Ecological System That Is Important for Our Development and Health The human body contains about 1013 human cells, as well as a microbiota consisting of approximately 1014 bacterial, fungal, and protozoan cells, which represent thousands of microbial species—the so-called normal flora. The combined genomes of the various species of the human microbiota, called the microbiome, contain more than 5 × 106 genes—more than 100 times greater than the number of genes in the human genome itself. A consequence of this genomic diversity is that the microbiota expands the range of biochemical and metabolic activities available to the humans.


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Cell_Biology_Alberts. The microbiota is usually confined to the skin, mouth, digestive tract, and vagina. With the exception of microbes colonizing the skin, it consists primarily of anaerobic bacteria, with distinct communities of species inhabiting each body part. These communities vary considerably between individual humans, even between close relatives or identical twins. Although the microbiota of an individual is generally consistent over time, it is influenced by a variety of factors, including age, diet, health status, and antibiotic use.


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Cell_Biology_Alberts. There are various ecological relationships that these microbes have with their host. In mutualism, both the microbe and host benefit. The anaerobic bacteria that inhabit our intestines, for example, gain shelter and a nutrient supply but also contribute to the digestion of our food, produce important nutrients for us, and are essential for the normal development of our gastrointestinal tract and innate and adaptive immune systems. In commensalism, the microbe benefits but offers no benefit and causes no harm: for example, we are infected with many viruses that have no noticeable effect on our health. In parasitism, the microbe benefits to the detriment of the host, as is often the case for pathogens.


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Cell_Biology_Alberts. Many infectious diseases are caused by a single pathogen. There is increasing evidence, however, that an imbalance in the community of microbes that constitute the microbiota can contribute to some diseases, including autoimmune and allergic diseases, obesity, inflammatory bowel disease, and diabetes. Remarkably, in such cases of microbiota imbalance (referred to as dysbiosis), the transfer of the microbiota from a healthy individual to someone suffering from the disease can be beneficial and sometimes curative, as in the case of Clostridium difficile colitis caused by overgrowth of the bacterium. Pathogens Interact with Their Hosts in Different Ways If it is normal for us to live with a community of microbes, why are some of them capable of causing us illness or death? Although the ability of a particular Figure 23–1 Parasitism at many levels.


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Cell_Biology_Alberts. If it is normal for us to live with a community of microbes, why are some of them capable of causing us illness or death? Although the ability of a particular Figure 23–1 Parasitism at many levels. Most animals harbor parasites, an example being the blacklegged tick or deer tick (Ixodes scapularis), shown here on a human finger. Although ticks of this species thrive on white-tailed deer and other wild mammals, they can also live on humans.


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Cell_Biology_Alberts. Ticks themselves harbor their own parasites including the bacterium Borrelia burgdorferi, stained here with a vital dye that labels living bacteria green and dead bacteria red. These spiral-shaped bacteria live in deer ticks and can be transmitted to humans during a tick’s blood meal. Borrelia burgdorferi causes Lyme disease, which is characterized by a bull’s-eye-shaped skin rash and fever; if the infection is left untreated, various complications can result, including arthritis and neurological abnormalities. The idea that parasites have their own parasites was noted by Jonathan Swift in 1733: “So, naturalists observe, a flea Has smaller fleas that on him prey; And these have smaller still to bite ‘em; And so proceed ad infinitum.” (A, from Acorn, White-Footed Mice and Tick Cycle Augment Risks of Lyme Disease in 2012. March 14, 2012. Reprinted with permission of Anita Sil; B, courtesy of M.


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Cell_Biology_Alberts. M. Embers.) microorganism to cause disease depends on many factors, it requires that the pathogen possess specialized pathogenic characteristics that allow it to live in humans.


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Cell_Biology_Alberts. Primary pathogens can cause overt disease in most healthy people. Some primary pathogens cause acute, life-threatening epidemic infections and spread rapidly from one sick or dying host to another; historically important examples include the bacterium Vibrio cholerae, which causes cholera, and the variola and influenza viruses, which cause smallpox and flu, respectively. Others may persistently infect a single individual for years without causing overt disease; examples include the bacterium Mycobacterium tuberculosis (which can cause the life-threatening lung infection tuberculosis) and the intestinal worm Ascaris. Although these potential primary pathogens can make some people critically ill, billions of people carry these foreign organisms in an asymptomatic way, often unaware that they are infected. It is sometimes difficult to draw a line between the asymptomatic presence of such pathogens and the normal microbiota. Some microbes of the normal flora can act as opportunistic


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Cell_Biology_Alberts. they are infected. It is sometimes difficult to draw a line between the asymptomatic presence of such pathogens and the normal microbiota. Some microbes of the normal flora can act as opportunistic pathogens, in that they cause disease only if our immune systems are weakened or if they gain access to a normally sterile part of the body.


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Cell_Biology_Alberts. In order to survive and multiply, a successful pathogen must be able to: (1) enter the host (usually by breaking an epithelial barrier); (2) find a nutritionally compatible niche in the host’s body; (3) avoid, subvert, or circumvent the host’s innate and adaptive immune responses; (4) replicate, using host resources; and (5) exit one host and spread to another. Pathogens have evolved various mechanisms that maximally exploit the biology of their host organisms to help accomplish these tasks. For some pathogens, these mechanisms are adapted to a unique host species, whereas for others the mechanisms are sufficiently general to permit invasion, survival, and replication in a wide variety of hosts. Because pathogens have evolved the ability to interface directly with the molecular machinery of host cells, we have learned a great deal about cell biological principles by studying them.


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Cell_Biology_Alberts. Our constant exposure to pathogens has strongly influenced human evolution. In modern times, humans have learned how to limit the ability of pathogens to infect us through improvements in public health measures and childhood nutrition, vaccines, antimicrobial drugs, and routine testing of blood used for transfusions. As we learn more about the mechanisms by which pathogens cause disease (called pathogenesis), our creativity and resourcefullness will continue to serve as an important addition to our immune systems in fighting infectious diseases. Pathogens Can Contribute to Cancer, Cardiovascular Disease, and Other Chronic Illnesses


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Cell_Biology_Alberts. Some viral and bacterial pathogens can cause or contribute to chronic, life-threatening illnesses that are not normally classified as infectious diseases. An important example is cancer. As discussed in Chapter 20, the oncogene concept—that certain altered genes can trigger cell transformation and tumor development— came initially from studies of the Rous sarcoma virus, which causes a form of cancer (sarcomas) in chickens. One of the viral genes encodes an overactive homolog of the host tyrosine kinase Src (see Figure 3–63), which has been implicated in many kinds of cancer. Several human cancers are also known to have a viral origin. Human papillomavirus, for example, which causes genital warts, is responsible for more than 90% of cervical cancers (see Figure 20–40). The recent development of a vaccine against the most abundant cancer-associated strains of human papillomavirus promises to prevent many of these cancers in the future. In other cases, chronic tissue damage caused by


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Cell_Biology_Alberts. of a vaccine against the most abundant cancer-associated strains of human papillomavirus promises to prevent many of these cancers in the future. In other cases, chronic tissue damage caused by infection can increase the likelihood of cancer. Inflammation caused by the stomach-dwelling bacterium H. pylori can be a major contributor to stomach cancer, as well as to gastric ulcers.


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Cell_Biology_Alberts. The major causes of death in wealthy industrialized nations are cardiovascular diseases. They frequently result from atherosclerosis, the accumulation in blood vessel walls of fatty deposits that can block blood flow and cause heart attacks and strokes. A hallmark of early atherosclerosis is the appearance in blood vessel walls of clumps of macrophages called foam cells, which recruit other white blood cells into the forming atherosclerotic plaque. Foam cells in atherosclerotic plaques often contain the bacterial pathogen Chlamydia pneumoniae, which commonly causes pneumonia in humans and is a significant risk factor for atherosclerosis in humans and animal models. Other bacterial species are also implicated in atherosclerosis, including bacteria usually associated with teeth and gums, such as Porphyromonas gingivalis. As we learn more about the interactions between pathogens and the human body, it seems likely that more chronic conditions will be found to have a link to an infectious


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Cell_Biology_Alberts. as Porphyromonas gingivalis. As we learn more about the interactions between pathogens and the human body, it seems likely that more chronic conditions will be found to have a link to an infectious agent.


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Cell_Biology_Alberts. Pathogens Can Be Viruses, Bacteria, or Eukaryotes Many types of pathogens cause disease in humans. The most familiar are viruses and bacteria. Viruses cause diseases ranging from AIDS and smallpox to the common cold. Viruses are essentially fragments of nucleic acid (DNA or RNA) that generally encode a relatively small number of gene products, wrapped in a protective shell of proteins (Figure 23–2A) and (in some cases) an outer membrane envelope (see Figure 5–62). Much larger and more complex than viruses, bacteria are prokaryotic cells, which perform most of their basic metabolic functions themselves, relying on the host primarily for nutrition (Figure 23–2B).


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Cell_Biology_Alberts. Some other infectious agents are eukaryotic organisms. These range from single-celled fungi and protozoa (Figure 23–2C) to large, complex metazoa such as parasitic worms. One of the most common human parasites, shared by about a billion people at present, is the nematode worm Ascaris lumbricoides, which infects the gut (Figure 23–2D). It closely resembles its harmless nematode cousin Caenorhabditis elegans, which is used as a model organism for genetic and developmental biological research (see Figure 1–39). C. elegans, however, is only about 1 mm in length, whereas Ascaris can reach 30 cm. We now introduce the basic features of each of the major types of pathogens, before we examine the mechanisms that pathogens use to infect their hosts. Figure 23–2 Pathogens in many forms. The structure of the protein coat, or capsid, of poliovirus. This virus was once a common cause of paralysis, but the disease (poliomyelitis) has been greatly reduced by widespread vaccination.


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Cell_Biology_Alberts. The structure of the protein coat, or capsid, of poliovirus. This virus was once a common cause of paralysis, but the disease (poliomyelitis) has been greatly reduced by widespread vaccination. The bacterium Vibrio cholerae, the causative agent of the epidemic, diarrheal disease cholera. (C) The protozoan parasite Trypanosoma brucei (purple) in a field of erythrocytes (red blood cells; pink). This parasite causes African sleeping sickness, a potentially fatal disease of the central nervous system. (D) This clump of Ascaris nematodes was removed from the obstructed intestine of a two-year-old boy. (A, courtesy of Robert Grant, Stephan Crainic, and James M. Hogle; B, photograph courtesy of John Mekalanos; C, CDC, Department of Health and Human Services; D, from J.K. Baird et al., Am. J. Trop. Med. Hyg. 35:314–318, 1986. Photograph by Daniel H. Connor.) lipopolysaccharide (LPS) outer leafet of outer membrane pore protein


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Cell_Biology_Alberts. Figure 23–3 Bacterial shapes and cell-surface structures. (A) Bacteria are traditionally classified by shape. (B and C) They are also classified as Gram positive or Gram negative. (B) Gram-positive bacteria such as Streptococcus and Staphylococcus have a single membrane and a thick cell wall made of cross-linked peptidoglycan. They are called Gram positive because they retain the violet dye used in the Gram-staining procedure. (C) Gram-negative bacteria such as Escherichia coli (E. coli) and Salmonella have two membranes, separated by the periplasm (see Figure 11–17). The peptidoglycan cell wall of these organisms is located in the periplasm and is thinner than in Gram-positive bacteria; they therefore fail to retain the dye in the Gram-staining procedure. The inner membrane of both Gram-positive and Gram-negative bacteria is a phospholipid bilayer. The inner leaflet of the outer membrane of Gram-negativebacteria is also made primarily of phospholipids, whereas the outer leaflet of


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Cell_Biology_Alberts. and Gram-negative bacteria is a phospholipid bilayer. The inner leaflet of the outer membrane of Gram-negativebacteria is also made primarily of phospholipids, whereas the outer leaflet of the outer membrane is composed of a unique glycosylated lipid called lipopolysaccharide (LPS). (D) Cell-surface appendages are important for bacterial behavior. Many bacteria swim using the rotation of helical flagella. The bacterium illustrated has only a single flagellum at one pole; however, many have multiple flagella. Straight pili (also called fimbriae) are used to adhere to various surfaces in the host, as well as to facilitate genetic exchange between bacteria. Some kinds of pili can retract to generate force and thereby help bacteria move along surfaces.


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Cell_Biology_Alberts. Bacteria Are Diverse and Occupy a Remarkable Variety of Ecological Niches


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Cell_Biology_Alberts. Although bacteria generally lack internal membranes, they are highly sophisticated cells whose organization and behaviors have attracted the attention of many scientists. Bacteria are classified broadly by their shape—as rods, spheres (cocci), or spirals (Figure 23–3A)— as well as by their so-called Gram-staining properties, which reflect differences in the structure of the bacterial cell wall. Gram-positive bacteria have a thick layer of peptidoglycan cell wall outside their inner (plasma) membrane (Figure 23–3B), whereas Gram-negative bacteria have a thinner peptidoglycan cell wall. In both cases, the cell wall protects against lysis by osmotic swelling, and it is a target of host antibacterial proteins such as lysozyme and antibiotics such as penicillin. Gram-negative bacteria are also covered outside the cell wall by an outer membrane containing lipopolysaccharide (LPS) (Figure 23–3C). Both peptidoglycan and LPS are unique to bacteria and are recognized as pathogen-associated


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Cell_Biology_Alberts. also covered outside the cell wall by an outer membrane containing lipopolysaccharide (LPS) (Figure 23–3C). Both peptidoglycan and LPS are unique to bacteria and are recognized as pathogen-associated molecular patterns (PAMPs) by the host innate immune system, as discussed in Chapter 24. The surface of bacterial cells can also display an array of appendages, including flagella and pili, which enable bacteria to swim or adhere to desirable surfaces, respectively (Figure 23–3D). Apart from cell shape and structure, differences in ribosomal RNA and genomic DNA sequence are also used for phylogenetic classification. Because bacterial genomes are small—typically between 1,000,000 and 5,000,000 nucleotide pairs (compared to more than 3,000,000,000 for humans)—they are now simple to sequence, making this an important new classification tool.


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Cell_Biology_Alberts. Bacteria also exhibit extraordinary molecular, metabolic, and ecological diversity. At the molecular level, bacteria are far more diverse than eukaryotes, and they can occupy ecological niches having extremes of temperature, salt concentrations, and nutrient limitation. Some bacteria replicate in an environmental reservoir such as water or soil and only cause disease if they happen to encounter a susceptible host; these are called facultative pathogens. Others can only replicate inside the body of their host and are therefore called obligate pathogens. Bacteria also differ in the range of hosts they will infect. Shigella flexneri, for example, which causes epidemic dysentery (bloody diarrhea), will infect only humans and other primates. By contrast, the closely related bacterium Salmonella enterica, which is a common cause of food poisoning in humans, can also infect other vertebrates, including chickens and turtles. A champion generalist is the opportunistic pathogen Pseudomonas


Cell_Biology_Alberts

Cell_Biology_Alberts. enterica, which is a common cause of food poisoning in humans, can also infect other vertebrates, including chickens and turtles. A champion generalist is the opportunistic pathogen Pseudomonas aeruginosa, which can cause disease in a wide variety of plants and animals.


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Cell_Biology_Alberts. Pathogenic bacteria and their closest nonpathogenic relatives often differ in a relatively small number of genes. Genes that contribute to the ability of an organism to cause disease are called virulence genes, and the proteins they encode are called virulence factors. Such virulence genes are often clustered together on the bacterial chromosome; large clusters are called pathogenicity islands. Virulence genes can also be carried on bacteriophages (bacterial viruses) or transposons (see Table 5–4), both of which integrate into the bacterial chromosome, or on extrachromosomal virulence plasmids (Figure 23–4A).


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Cell_Biology_Alberts. Pathogenic bacteria are thought to emerge when groups of virulence genes are transferred together into a previously avirulent bacterium by a process called horizontal gene transfer (to distinguish it from vertical gene transfer from parent to offspring). Horizontal transfer can occur by one of three mechanisms: natural transformation by released naked DNA, transduction by bacteriophages, or sexual exchange by conjugation (Figure 23–4B and Movie 23.1). Sequencing the genomes of large numbers of pathogenic and nonpathogenic bacteria has indicated that horizontal gene transfer has made important contributions to bacterial evolution, enabling species to inhabit new ecological and nutritional niches, as well as to cause disease. Even within a single bacterial species, the amount of chromosomal E. coli Shigella fexneri Salmonella enterica


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Cell_Biology_Alberts. E. coli Shigella fexneri Salmonella enterica Figure 23–4 Genetic differences between pathogenic and nonpathogenic bacteria. (A) Genetic differences between nonpathogenic E. coli and two closely related food-borne pathogens—Shigella flexneri, which causes dysentery, and Salmonella enterica, a common cause of food poisoning. Nonpathogenic E. coli has a single circular chromosome. The chromosome of S. flexneri differs from that of E. coli in a limited number of locations; most of the genes required for pathogenesis (virulence genes) are carried on an extrachromosomal virulence plasmid. The chromosome of S. enterica carries two large inserts (pathogenicity islands) not found in the E. coli chromosome; these inserts each contain many virulence genes.


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Cell_Biology_Alberts. (B) Bacterial pathogens evolve by horizontal gene transfer. This can occur by three mechanisms: natural transformation, in which naked DNA is taken in by competent bacteria; transduction, in which bacterial viruses (bacteriophages) transfer DNA from one bacterium into another; and conjugation, during which plasmid DNA, and even chromosomal DNA, is transferred from a donor to a recipient bacterium. V.cholerae V. cholerae O1 serogroup V. cholerae O1 serogroup Classical V. cholerae O139 serogroup VSP1 VSP2 CTX˜Classical CTX˜El Tor RS1˜O139 antigen SXT 1st through 6th pandemics 7th pandemic V.cholerae variation is astonishing; the genomes of different strains of Escherichia coli can differ by as much as 25%. Such variation has led to the concept that a bacterial species has both a core genome common to all isolates within the species and a larger pan-genome consisting of all genes present in the full spectrum of isolates.


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Cell_Biology_Alberts. Acquisition of genes and gene clusters can drive the rapid evolution of pathogens and turn nonpathogens into pathogens. Consider, for example, Vibrio cholerae—the Gram-negative bacterium that causes the epidemic diarrheal disease cholera. Of the hundreds of strains of Vibrio cholerae, the only ones that cause pandemic human disease are those infected with a mobile bacteriophage (CTXϕ) containing genes encoding the two subunits of the toxin that causes the diarrhea. As summarized in Figure 23–5, seven pandemics of V. cholerae have arisen since 1817. The first six were caused by the periodic reemergence of so-called Classical strains. In addition to the toxin-encoding bacteriophage, these Classical strains shared a similar O1 surface antigen, part of the LPS in the outer membrane (see Figure 23–3C). In 1961, the seventh pandemic began, caused by a new strain named “El Tor,” which arose when an O1-expressing strain acquired two bacteriophages and at least two new pathogenicity islands.


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Cell_Biology_Alberts. 23–3C). In 1961, the seventh pandemic began, caused by a new strain named “El Tor,” which arose when an O1-expressing strain acquired two bacteriophages and at least two new pathogenicity islands. El Tor eventually displaced the Classical strains. In 1992, a new strain emerged in which O1 was replaced with another O-antigen variant called O139, which was not recognized by antibodies present in the blood of survivors of previous cholera epidemics. The O139 strain also contains a transposon-like element that encodes antibiotic resistance. As this example makes clear, the rapid evolution of bacterial pathogens can be likened to an arms race which pits the survival of a bacterium against our immune systems and the tools of modern medicine. Similar struggles for survival take place between all pathogens and humans, and understanding these conflicts provides key insights into the evolution of pathogens and greatly informs us how we treat new outbreaks of infectious diseases.


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Cell_Biology_Alberts. Bacterial Virulence Genes Encode Effector Proteins and Secretion Systems to Deliver Effector Proteins to Host Cells What are the gene products that enable a bacterium to cause disease in a healthy host? For pathogenic bacteria that live outside of host cells, called extracellular Figure 23–5 Comparative-genomicsbased model for the evolution of pathogenic Vibrio cholerae strains.


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Cell_Biology_Alberts. Progenitor strains in the wild first acquired the biosynthetic pathway necessary to make the O1 antigen type of carbohydrate chain on the outer-membrane lipopolysaccharide (see Figure 23–3C). Incorporation of the CTXϕ bacteriophage created the Classical pathogenic strains responsible for the first six worldwide epidemics of cholera between 1817 and 1923. Sometime in the twentieth century, an O1 strain in the environment picked up the CTXϕ bacteriophage again, along with an associated bacteriophage RS1ϕ and two pathogenicity islands (VSP1 and VSP2), creating the El Tor strain that emerged as the seventh worldwide pandemic in 1961. In 1992, an El Tor strain was isolated that had picked up a new DNA cassette, enabling it to produce the O139 antigen type of carbohydrate chain rather than the O1 type. This altered the bacterium’s interaction with the human immune system, without diminishing its virulence; this bacterium also picked up a new pathogenicity island (SXT). An electron


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Cell_Biology_Alberts. than the O1 type. This altered the bacterium’s interaction with the human immune system, without diminishing its virulence; this bacterium also picked up a new pathogenicity island (SXT). An electron micrograph of Vibrio cholerae (V. cholerae) is shown in Figure 23–2B.


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Cell_Biology_Alberts. bacterial pathogens, virulence genes often encode secreted toxic proteins (toxins) that interact with host cell structural or signaling proteins to elicit a response that is beneficial to the pathogen. Several of these bacterial toxins are among the most potent of known human poisons. Bacterial toxins are often composed of two protein components—an A subunit with enzymatic activity, and a B subunit that binds to specific receptors on the host cell surface and directs the trafficking of the A subunit to the cytosol by various routes (Figure 23–6). The Vibrio cholerae phage, for example, encodes the two subunits of cholera toxin (Movie 23.2). The A subunit catalyzes the transfer of an ADP-ribose moiety from NAD+ to the trimeric G protein Gs (see Figure 15–23), which activates adenylyl cyclase to make cyclic AMP (see Figure 15–25). ADP-ribosylation prevents inactivation of the G protein and results in the overaccumulation of intracellular cyclic AMP and the release of ions and water into


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Cell_Biology_Alberts. to make cyclic AMP (see Figure 15–25). ADP-ribosylation prevents inactivation of the G protein and results in the overaccumulation of intracellular cyclic AMP and the release of ions and water into the intestinal lumen, leading to the watery diarrhea associated with cholera. The infection then spreads to new hosts via released bacteria, which can contaminate food and water.


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Cell_Biology_Alberts. Some pathogenic bacteria secrete multiple toxins, each of which targets a different signaling pathway in host cells. Anthrax, for example, is an acute infectious disease of sheep, cattle, and occasionally humans. It is caused by contact with spores of the Gram-positive bacterium Bacillus anthracis. Dormant spores can survive in soil for long periods. If inhaled, ingested, or rubbed into breaks in the skin, spores can germinate and the bacteria replicate. The bacteria secrete two toxins with identical B subunits but different A subunits. The B subunits bind to a host cell-surface receptor protein to transfer the two different A subunits into


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Cell_Biology_Alberts. Figure 23–6 Bacterial toxin entry into host cells. Bacterial toxins are often composed of A and B protein subunits. The B (binding) subunit of the toxin interacts with host-cell toxin receptors, enabling endocytosis and intracellular trafficking of B subunit as well as its associated and enzymatically active A subunit(s). In the case of Bacillus anthracis, the B subunit changes conformation in the low pH environment of the endosome to form a pore through which two different A subunits, lethal factor and edema factor, are transported across the membrane of the endosome in an unfolded conformation. In the cases of Vibrio cholerae toxin and Bordetella pertussis toxin, the B and A subunits are transported to the Golgi apparatus and then to the endoplasmic reticulum (ER), where the A subunits are then translocated into the cytosol in an unfolded conformation through a proteintranslocation channel.


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Cell_Biology_Alberts. host cells (see Figure 23–6). The A subunits are called lethal factor and edema factor. The A subunit of edema toxin is an adenylyl cyclase that catalyzes the production of cyclic AMP (see Figure 15–25), leading to an ion imbalance that can cause an accumulation of extracellular fluid (edema) in the skin or lung. The A subunit of lethal toxin is a protease that cleaves several activated members of the mitogen-activated protein kinase kinase (MAP kinase kinase) family (see Figure 15–49), disrupting intracellular signaling and leading to immune cell dysfunction and cell death. Injection of lethal toxin into the bloodstream of an animal causes shock (a large fall in blood pressure) and death.


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Cell_Biology_Alberts. Apart from toxins, bacteria use specialized secretion systems to secrete many other effector proteins that interact with host cells. Gram-negative bacteria have a general secretion system and several classes of accessory secretion systems (types I–VI). A subset of these accessory secretion systems, called contact-dependent secretion systems, is present in many bacteria that contact or live inside host cells. The type III secretion system (Figure 23–7), for example, injects into the host-cell cytoplasm effector proteins that can elicit a variety of host cell responses that enable the bacterium to invade or survive. There is a remarkable degree of structural similarity between the type III syringe and the base of a bacterial flagellum. Because flagella are found in a wider range of bacteria than are type III secretion systems, and the secretion systems appear to be adaptations specific for pathogenesis, it seems likely that the type III secretion systems evolved from flagella. Other


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Cell_Biology_Alberts. than are type III secretion systems, and the secretion systems appear to be adaptations specific for pathogenesis, it seems likely that the type III secretion systems evolved from flagella. Other types of delivery systems used by bacterial pathogens appear to have evolved independently. For example, type IV secretion systems are closely related to the conjugation apparatus that many bacteria use to exchange genetic material.


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Cell_Biology_Alberts. Pathogenic fungi and protozoan parasites are eukaryotes, as are their hosts. Consequently, antifungal and antiparasitic drugs are often less effective and more toxic to the host than are antibiotics that target bacteria. A second characteristic of fungal and parasitic infections that makes them difficult to treat is the tendency of the pathogens to switch among several different forms during their life cycles. A drug that is effective at killing one form can be ineffective at killing another form; therefore the population can survive the treatment.


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Cell_Biology_Alberts. Fungi include both unicellular yeasts (such as Saccharomyces cerevisiae and Schizosaccharomyces pombe, which are used to bake bread and brew beer, and as model organisms for cell biology research) and filamentous, multicellular molds (like those found on moldy fruit or bread). Most of the important pathogenic fungi exhibit dimorphism—the ability to grow in either yeast or mold form. The yeast-to-mold or mold-to-yeast transition is frequently associated with infection.


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Cell_Biology_Alberts. Figure 23–7 Type III secretion systems that can deliver effector proteins into the cytosol of a host cell. (A) Electron micrograph of purified type III secretion systems, each of which consists of over two dozen proteins. (B) The large lower ring is embedded in the bacterial inner membrane, and the smaller upper ring is embedded in the bacterial outer membrane. During infection, docking of the tip of the hollow needle at a host-cell plasma membrane results in the secretion of bacterial translocator proteins (green), which form a pore in the host membrane, through which bacterial effector proteins are then secreted into the host cell. (A, from O. Schraidt et al., PLoS Pathog. 6(4):e1000824, 2010.) in the environment in the host Histoplasma capsulatum, for example, grows as a mold at low temperature in the soil, but it switches to a yeast form when inhaled into the lung, where it can cause the disease histoplasmosis (Figure 23–8).


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Cell_Biology_Alberts. Protozoan parasites are single-celled eukaryotes with more elaborate life cycles than fungi, and they frequently require more than one host. Malaria is the most devastating protozoal disease, infecting more than 200 million people every year and killing upward of 500,000. It is caused by four species of Plasmodium, which are transmitted to humans by the bite of the female Anopheles mosquito. release of infection of red blood cells invasion of gut and growth Figure 23–8 Dimorphism in the pathogenic fungus Histoplasma capsulatum. (A) At low temperature in the soil, H. capsulatum grows as a multicellular filamentous mold consisting of many individual cells connected together. (B) After it is inhaled into the lung of a mammal, the increase in temperature causes a switch to a yeast form consisting of small clumps of round cells. (C) A stained histologic section of a mouse lung infected with


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Cell_Biology_Alberts. H. capsulatum, showing a macrophage containing yeast forms of the pathogen. (A and B, courtesy of Sinem Beyhan and Anita Sil; C, courtesy of Davina Hocking Murray and Anita Sil.) Figure 23–9 The complex life cycle of malaria parasites. (A) The sexual cycle of Plasmodium falciparum requires passage between a human host and an insect host (Movie 23.3). (B)–(D) Blood smears from people with malaria, showing three different forms of the parasite that appear in red blood cells: (B) ring stage; (C) schizont; and (D) gametocyte. (B–D, courtesy of the Centers for Disease Control, Division of Parasitic Diseases, DPDx.)


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Cell_Biology_Alberts. Plasmodium falciparum causes the most serious form of malaria and is the most intensively studied of the malaria-causing parasites. It exists in many distinct forms, and it requires both the human and mosquito hosts to complete its sexual cycle (Figure 23–9). Several of these forms are highly specialized to invade and replicate in specific tissues—the lining of the insect gut, the human liver, and the human red blood cell. Even within a single host cell type, the red blood cell, the Plasmodium parasite undergoes a complex sequence of developmental events, reflected in striking morphological changes (Figure 23–9B–D). All Aspects of Viral Propagation Depend on Host Cell Machinery


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Cell_Biology_Alberts. All Aspects of Viral Propagation Depend on Host Cell Machinery Bacteria, fungal, and protozoan pathogens are living cells themselves. They use their own machinery for DNA replication, transcription, and translation, and, for the most part, they provide their own sources of metabolic energy. Viruses, by contrast, are the ultimate hitchhikers, carrying little more than information in the form of nucleic acid. Most clinically important human viruses have small genomes consisting of double-stranded DNA or single-stranded RNA (Table 23–1), and we now have complete genome sequences of almost all of them.


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Cell_Biology_Alberts. Viral genomes typically encode three types of protein: proteins for replicating the genome, proteins for packaging the genome and delivering it to more host cells, and proteins for modifying the structure or function of the host cell to enhance the replication of the virus (see Figure 7–62). In general, viral replication involves (1) entry into the host cell, (2) disassembly of the infectious virus particle, (3) replication of the viral genome, (4) transcription of viral genes and synthesis of viral proteins, (5) assembly of these viral components into progeny virus particles,


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Cell_Biology_Alberts. Figure 23–10 a simple viral life cycle. The hypothetical simple virus shown here consists of a small double-stranded DNA molecule that codes for only a single viral capsid protein. To reproduce, the viral genome must first enter a host cell, where it is replicated to produce multiple copies, which are transcribed and translated to produce the viral coat protein. The viral genomes can then assemble spontaneously with the coat protein to form a new virus particle, which escapes from the host cell. No known virus is this simple. and (6) release of progeny virions (Figure 23–10). A single virus particle (a virion) that infects a single host cell can produce thousands of progeny.


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Cell_Biology_Alberts. and (6) release of progeny virions (Figure 23–10). A single virus particle (a virion) that infects a single host cell can produce thousands of progeny. Virions come in a wide variety of shapes and sizes (Figure 23–11), and although most have relatively small genomes, genome size can vary considerably. The recently discovered giant viruses of amoebae, called pandoraviruses, are the largest known viruses, with 700 nm particles and double-stranded DNA genomes of over 2,000,000 nucleotide pairs. The virions of poxvirus are also large: they are 250–350 nm long and enclose a genome of double-stranded DNA of about 270,000 nucleotide pairs. At the other end of the size scale are the virions of parvovirus, which are less than 30 nm in diameter and have a single-stranded DNA genome of fewer than 5000 nucleotides.


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Cell_Biology_Alberts. Viral genomes are packaged in a protein coat, called a capsid, which in some viruses is further enclosed by a lipid bilayer membrane, or envelope. The capsid is made of one or several proteins, arranged in regular arrays that generally produce structures with either helical symmetry, which results in a cylindrical structure (for example, influenza, measles, and bunyavirus), or icosahedral symmetry (for example, poliovirus and herpesvirus; see Figure 23–11). Some viruses instead produce capsids with more complicated structures (for example, poxviruses). When the capsid is packaged with the viral genome, the structure is called a nucleocapsid. The nucleocapsids of nonenveloped viruses usually leave an infected cell by lysing it. For enveloped viruses, by contrast, the nucleocapsid is enclosed within a lipid bilayer membrane that the virus acquires in the process of budding from the host-cell plasma membrane, which it does without disrupting the membrane or killing the cell (Figure


Cell_Biology_Alberts

Cell_Biology_Alberts. within a lipid bilayer membrane that the virus acquires in the process of budding from the host-cell plasma membrane, which it does without disrupting the membrane or killing the cell (Figure 23–12). Enveloped viruses can cause persistent infections that may last for years, often without noticeable deleterious effects on the host.


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Cell_Biology_Alberts. Because the host cell performs most of the critical steps in viral replication, the identification of effective antiviral drugs that do not harm the host can be difficult. Probably the most effective strategy for containing viral diseases is through vaccinating of potential hosts. Highly successful vaccination programs have effectively poliovirus HIV Figure 23–11 examples of viral infuenza coronavirus rabies virus mumps virus(AIDS virus) virus (common cold) morphology. As shown, both DNA and shape. eliminated smallpox infection from the planet, and the eradication of poliomyelitis is approaching completion (Figure 23–13).


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Cell_Biology_Alberts. Infectious diseases are caused by pathogens, which include viruses, bacteria, and fungi, as well as protozoan and metazoan parasites. All pathogens must have mechanisms for entering their host and for evading immediate destruction by the host. The great majority of bacteria are not pathogenic to humans. Those that are pathogenic produce specific virulence factors that mediate the bacteria’s interactions with the host; these proteins change the behavior of host cells in ways that promote the replication and spread of the bacteria. Eukaryotic pathogens such as fungi and protozoan parasites typically pass through several different forms during the course of infection; the ability to switch among these forms is usually required for these pathogens to survive in a host and cause disease. In some cases, such as malaria, parasites must pass sequentially through several host species to complete their life cycles. Unlike bacteria and eukaryotic parasites, viruses have no metabolism of their


Cell_Biology_Alberts

Cell_Biology_Alberts. some cases, such as malaria, parasites must pass sequentially through several host species to complete their life cycles. Unlike bacteria and eukaryotic parasites, viruses have no metabolism of their own and no intrinsic ability to produce the proteins encoded by their DNA or RNA genomes; they rely on subverting the machinery of the host cell.


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Cell_Biology_Alberts. reported cases of polio per100,000 population Figure 23–12 acquisition of a viral envelope. (A) Electron micrograph of an animal cell from which six copies of an enveloped virus (Semliki forest virus) are budding. (B) Schematic drawing of the envelope assembly and budding processes. The lipid bilayer that surrounds the viral capsid is derived directly from the plasma membrane of the host cell. In contrast, the proteins in this lipid bilayer (shown in green) are encoded by the viral genome. (A, courtesy of M. Olsen and G. Griffith.) Figure 23–13 effective control of a viral disease through vaccination. The graph shows the number of cases of poliomyelitis reported per year in the United States. The arrows indicate the timing of the introduction of the Salk vaccine (inactivated virus given by injection) and the Sabin vaccine (live attenuated virus given orally).


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Cell_Biology_Alberts. The mechanisms through which pathogens cause disease are as diverse as the pathogens themselves. Nonetheless, all pathogens must carry out certain common tasks: they must gain access to the host, reach an appropriate niche, avoid host defenses, replicate, and exit from the infected host to spread to an uninfected one. In this section, we examine the common strategies that many pathogens use to accomplish these tasks. Pathogens Overcome Epithelial Barriers to Infect the Host The first step in infection is for the pathogen to gain access to the host. A thick covering of skin protects most parts of the human body from the environment. The protective boundaries of some other human tissues (eyes, nasal passages, respiratory tract, mouth, digestive tract, urinary tract, and female genital tract) are less robust. In the lungs and small intestine, for example, the barrier is just a single monolayer of epithelial cells. Nonetheless, all these epithelia serve as barriers to infection.


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Cell_Biology_Alberts. Wounds in barrier epithelia allow pathogens direct access to unoccupied niches within otherwise sterile host tissues. This avenue of entry requires little in the way of pathogen specialization, and many members of the normal flora can cause serious illness if they enter through such wounds. Staphylococci from the skin and nose, or Streptococci from the throat and mouth, are two examples of opportunistic bacterial pathogens that are responsible for many serious infections resulting from breaches in epithelial barriers. The recent emergence of bacterial strains of Staphylococcus that are resistant to the antibiotics commonly used for treatment (for example, methicillin-resistant Staphylococcus aureus, or MRSA, which infects up to 50,000,000 people worldwide) is of particular concern. Papillomaviruses, which cause warts and cervical cancer, also take advantage of breaches in epithelial barriers.


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Cell_Biology_Alberts. Primary pathogens, however, need not wait for a wound to gain access to their host. One efficient way for such a pathogen to cross the skin is to catch a ride in the saliva of a biting arthropod. A diverse group of bacteria, viruses, and protozoa has developed the ability to survive in insects and then use them as vectors to spread from one mammalian host to another. As discussed earlier, the Plasmodium protozoan that causes malaria develops through several forms in its life cycle, including some that are specialized for survival in a human and others that are specialized for survival in a mosquito (see Figure 23–9). Viruses that are spread by insect bites cause yellow fever and Dengue fever, as well as many kinds of viral encephalitis (inflammation of the brain). These viruses replicate in both insect cells and mammalian cells, as required for their transmission by an insect vector.


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Cell_Biology_Alberts. The efficient spread of a pathogen via an insect vector requires that an individual insect consumes a blood meal from an infected host and transfers the pathogen to a naive host. In a few striking cases, the pathogen alters the behavior of the insect so that its transmission to a new host is more likely. An example is the bacterium Yersinia pestis, which causes bubonic plague. It multiplies in the flea’s foregut to form aggregated masses that physically block the digestive tract; during each repeated, but futile, attempt at feeding, some of the bacteria in the foregut are flushed into the bite site, thus transmitting plague to a new host (Figure 23–14).


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Cell_Biology_Alberts. Whereas many epithelial barriers such as the skin and the lining of the mouth and large intestine are densely populated by normal flora, others, including the lining of the lower lung and the bladder, are normally kept nearly sterile. How do these epithelia avoid bacterial colonization? A layer of protective mucus covers the respiratory epithelium, and the coordinated beating of cilia sweeps the mucus and trapped bacteria up and out of the lung. The epithelial lining of the bladder and the upper gastrointestinal tract also has a thick layer of mucus, and


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Cell_Biology_Alberts. Figure 23–14 Plague bacteria within a flea. This light micrograph shows the digestive tract dissected from a flea that had dined about two weeks previously on the blood of an animal infected with the plague bacterium, Yersinia pestis. The bacteria multiplied in the flea gut to produce large cohesive aggregates (red arrows); the bacterial mass on the left is occluding the passage between the esophagus and the midgut. This type of blockage prevents a flea from digesting its blood meals, so that hunger causes it to bite repeatedly, disseminating the infection. (From B.J. Hinnebusch, E.R. Fischer and T.G. Schwan, J. Infect. Dis. 178:1406–1415, 1998.) these organs are periodically flushed by urination and by peristalsis, respectively, which washes away most microbes.


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Cell_Biology_Alberts. Pathogenic bacteria and eukaryotic parasites that infect these epithelial surfaces have evolved specific mechanisms for overcoming these protective mechanisms. Those that infect the urinary tract, for example, adhere tightly to the epithelial lining via specific adhesins, which are proteins or protein complexes that recognize and bind to cell-surface molecules on the epithelium. An important group of adhesins in E. coli strains that infect the kidney are components of the pili—surface projections that can be several micrometers long and thus able to span the thickness of the protective mucus layer; at the tip of each pilus is an adhesin protein that binds tightly to the D-galactose–D-galactose disaccharide on glycolipids on the surface of kidney cells (Figure 23–15). Strains of E. coli that infect the bladder rather than the kidney express a second kind of pilus with a different adhesin protein that binds to bladder epithelial cells. It is the specificity of the adhesin proteins on


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Cell_Biology_Alberts. that infect the bladder rather than the kidney express a second kind of pilus with a different adhesin protein that binds to bladder epithelial cells. It is the specificity of the adhesin proteins on the tips of the two types of pili that is responsible for the bacteria’s colonizing of the different parts of the urinary tract.


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Cell_Biology_Alberts. The stomach is an especially hostile environment for pathogens. Besides the thick layer of mucus and peristaltic washing, it is filled with acid (average pH ≈2), which is lethal to almost all bacteria ingested in food. Yet, it is home to a microbiota of hundreds of resident species, including the bacterium H. pylori, which, as we discussed earlier, is the major cause of stomach ulcers and some stomach cancers. The hypothesis that a persistent bacterial infection could cause stomach ulcers was initially met with skepticism. The young Australian doctor who made the initial discovery finally proved the point: he drank a pure culture of H. pylori and developed inflammation of the stomach, which often precedes the development of ulcers. A short course of antibiotics can now effectively cure 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,