The Immune System

IT WAS A DRAMATIC MOMENT IN THE MOST dramatic confrontation so far between science educators and scientists determined to keep evolution in the classroom and advocates of the quasi-religious theory known as intelligent design (ID). In 2005, Lehigh University biochemist Michael Behe sat on a witness stand in Dover, Pennsylvania, as lawyer Eric Rothschild quizzed him about the claim in Behe’s pro-ID book, Darwin’s Black Box, that “We can look high or we can look low in books or in journals, but the result is the same. The scientific literature has no answers to the question of the origin of the immune system.” When Behe reiterated that belief, Rothschild was ready. He began piling in front of the witness a large stack of recent journal articles, books, and book chapters, all relating research on the evolutionary origins of immunity, and asking Behe several times what he thought about the various publications. The biochemist admitted that he hadn’t read much of the material, but he wouldn’t budge from his position. “So these are not good enough?” Rothschild asked at one point. “They’re wonderful articles. … They simply just don’t address the question that I pose,” Behe responded. The judge, John E. Jones, found Behe’s responses revealing. Behe “was presented with 58 peer-reviewed publications, nine books, and several immunology textbook chapters about the evolution of the immune system;

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a specific pathogen are rallied and then maintained in the body as an immune memory. This “adaptive” arm seemed to have appeared out of nowhere some 450 million years ago and may be the serendipitous outcome of invading DNA introduced by a virus or microbe infecting a fishlike creature. It may seem ironic that an infectious agent endowed vertebrates with the keys to a new microbial defense, but it illustrates that microbes have shaped the evolution of animals for millennia. Indeed, a few researchers now suggest that immune systems evolved as much to manage and exploit benef icial microbes as to fend off nasty ones. “It’s a paradigm shift in immunology,” says Thomas Bosch of Christian Albrechts University Kiel in Germany. Finding proof for such a radical change in thinking will be challenging, but scientists should soon have a more detailed view of immune evolution as they decipher the genomes of more invertebrates and vertebrates and tally up the defensive weapons shared by the various branches of life.

however, he simply insisted that this was still not sufficient evidence of evolution,” the judge wrote in his decision. Jones concluded that ID proponents set “a scientifically unreasonable burden of proof for the theory of evolution.” Score one for evolution, which is now taught without competition from ID in Dover schools. It is fitting that studies of the origins of immunity provided a strong defense for the ideas first set forth by Charles Darwin 150 years ago. Darwin’s elaboration of diversification and natural selection as organizing principles of life inspired early immunologists, helping them see that humans and pathogens are locked in their own survivalof-the-fittest battle. His theory also helped researchers realize that some of our immune defenses depend on a system of diversity coupled with selection among proteins. Darwinian immunology As this newfound evolutionary mindset It was only shortly after On the Origin of shaped immunological thinking near the turn Species was published in 1859 that infectious of the 19th century, researchers also began to diseases were discovered and became a comspeculate about how our complex system of pelling example of a Darwinian struggle— defenses arose. After decades of research, humans pitted against pathogens—notes modern immunologists now think that single- science historian Alfred Tauber of Boston celled organisms must have started by harness- University. To understand that contest, ing toxic peptides and gene-disabling mole- immunology emerged in the late 19th century cules to thwart invading microbes—these as the science of host defense. Soon, scienweapons are still found in the simplest eukary- tists were fighting over the importance of otes and more complex animals. And then two competing defense mechanisms: the when multicellular creatures evolved, they humoral system of antibodies in the blood were able to devote specialized cells to tasks versus mobile amoebalike cells known as such as engulfing bacteria and viruses. phagocytes. German biologist Paul Ehrlich Today, an ancient set of defensive mecha- and others championed the former; Russian nisms based upon protein recepElie Metchnikoff, an embryolotors that recognize common fea- THE YEAR OF gist, lobbied for the latter. tures of dangerous pathogens has Darwin’s ideas permeated become hard-wired into the Metchnikoff’s formulation, says genome of every animal. (Plants Tauber. The Russian maintained have their own, parallel system.) that phagocytes evolved first as Considered the f irst line of nutritive cells—eating and delivdefense in animals, this “innate” ering food to cells in animals immunity involves cells and molwithout a gut—and were eventuecules that rush to the site of an ally enlisted to eat deleterious infection. Comparative studies of bacteria as well. In 1882, he earthworms, sea squirts, sponges, This essay is the fifth observed that phagocytes within a and more suggest that this inflam- in a monthly series. starfish enveloped and digested For more on evolutionary matory response dates back to the topics online, see the foreign bodies, including bacteria. Origins blog at origin of multicellularity. As the field of immunology In what has been called the blogs.sciencemag.org/ matured, it embraced both origins. For more on “big bang of immunology,” most the immune system, Metchnikoff and the humoralists, vertebrates later evolved a second listen to a podcast by as researchers realized that the author John Travis at form of immunity, in which white www.sciencemag.org/ phagocytes complemented the blood cells exquisitely targeted to multimedia/podcast. defense offered by blood factors.

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In 1908, the embryologist even shared a this phenomenon, which became known as Nobel Prize with Ehrlich. the generation of diversity, or GOD, problem. A half-century later, another major intelIn the late 1970s, in work that would earn lectual advance within immunology bore the him a Nobel Prize, Susumu Tonegawa of the fingerprints of Darwin. Darwin’s theory of Massachusetts Institute of Technology in evolution held that a large amount of variation Cambridge demonstrated that B cells can exists among individuals in a species and that produce such a vast array of antibodies species can adapt to new circumstances thanks to a complicated process called VDJ because evolution weeds out the less fit, favor- recombination. A maturing B cell starts with ing variants that improve reproduction and sur- dozens to hundreds of three classes of gene vival. Immunologist Frank Macfarlane Burnet segments—the V’s, D’s, and J’s—and as it drew heavily on this concept in developing develops, the cell excises all but one of each his theory about how the body forms its anti- class. The surviving V, D, and J then get bodies, the pathogen-binding molecules secreted by lymphocytes called B cells, according to science historian Arthur Silverstein of Johns Hopkins University School of Medicine in Baltimore, Maryland. While other immunologists focused on how antibodies might evolve to better target a pathogen, undergoing their own kind of natural selection, Burnet proposed that the lymphocyte was the key evolutionary player being selected within the body. Those white blood cells making antibodies that react to the body’s own tissues would be deleted, whereas one whose antibodies recognized a pathogen would survive and indeed be stimulated to expand greatly in number. “It is a Darwinian theory,” notes Tauber. “You have enormous variation and then selection.” This process, what Burnet called clonal selection, lets the body tailor its response to a particular pathogen. Moreover, some of the selected lymphocytes stick around, providing a “memory” that helps the immune system Hungry cells. Elie Metchnikoff drew cells thwart the same invader even consuming bacteria (top), and electron faster if it comes again. microscopes today provide a more modern view of such phagocytosis (bottom).

Understanding the big bang Clonal selection theory didn’t answer all the mysteries about antibody formation. Although Burnet’s idea assumed a large variation in preexisting antibodies, immunologists in the 1960s and ’70s realized that animals could generate distinct antibodies to almost any protein or other molecular feature of a microbe. In fact, the vertebrate immune system could raise antibodies specif ic even to humanmade molecules not found in nature. Given the prevailing dogma that behind every protein there was a specific gene, immunologists were at a loss to explain

stitched together into a DNA sequence that encodes an antibody unique to each mature B cell. (The other key player in the adaptive system, the T cell, also bypasses the one gene–one protein hurdle and similarly recombines gene segments to create distinct cell-surface receptors for pathogens.) The elucidation of VDJ recombination gradually exposed immunology’s big bang, recalls David Schatz of the Yale School of Medicine. By 1990, he and other colleagues then working in David Baltimore’s lab at the

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Whitehead Institute for Biomedical Research in Cambridge had identified two genes essential to VDJ recombination, RAG1 and RAG2 (for recombination-activating genes). Sharks and all the other jawed vertebrates with adaptive immunity have these genes, but all the evidence at the time indicated that hagfish, lampreys, and invertebrates didn’t. So, where did RAG1 and RAG2 come from? Several clues, including that the two genes are located immediately next to each other, prompted Schatz and his colleagues to wonder whether the pair had once been part of a DNA recombination system in fungi or viruses that got incorporated into vertebrates. As immunologists teased out what the proteins encoded by the two did, they realized the molecules are the scissors and knitting needles that cut out all but one V, D, and J and stitch those remaining three gene segments together. In 1995, Craig Thompson, then at the University of Chicago in Illinois, formally proposed that the DNA now encoding RAG1 and RAG2 was once a mobile genetic element called a transposon. Transposons can cut themselves out of one DNA sequence and stick themselves back in another, so immunologists could envision those skills being co-opted to recombine V, D, and J gene segments. In this “transposon hypothesis,” Thompson suggested that at some point after jawed and jawless vertebrates split into two branches, about 450 million years ago, a transposon invaded the former lineage, perhaps brought in by a virus that infected a germ cell. Boom—the enzymes that would ultimately provide adaptive immunity, by creating diverse antibodies and T cell receptors, were now in place and could mutate into that new role. Many research teams began trying to verify the transposon hypothesis. In 1998, for example, Schatz’s team and one led by Martin Gellert of the National Institute of Diabetes and Digestive and Kidney Diseases in Bethesda, Maryland, independently showed that the enzymes encoded by RAG1 and RAG2 could, in addition to cutting out DNA sequences, actually insert one stretch of DNA into another. In a commentary in Nature, immunologist Ronald Plasterk of the Netherlands Cancer Institute in Amsterdam expressed the awe of many at this solid evi-

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CREDITS (TOP TO BOTTOM): E. METCHNIKOFF/IMMUNITÄT BEI INFEKTIONSKRANKHEITEN (VERLAG VON GUSTAV FISCHER, JENA, 1902)/S. H. E. KAUFMAN, MAX PLANCK INSTITUTE FOR INFECTION BIOLOGY, BERLIN; V. BRINKMANN, PLOS PATHOGENS, 1(3), NOVEMBER 2005

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dence of the transposon hypothesis. “We may effective as the adaptive arm. After all, about sensors. And plant disease-resistance proteins owe our existence to one transposition event 90% of animal species have no adaptive that recognize bacteria, viruses, and fungi that occurred 450 million years ago,” he wrote. immunity, yet they thrive, with many living include portions that structurally resemble At the Dover trial, much of the research for decades, in a world of microbes. TLRs, hinting that ancestors of these microliterature piled in front of Behe detailed the At the heart of this protection are proteins, bial sensors were on patrol long before plants increasing evidence for this transposon called Toll-like receptors (TLRs), on cells of and animals diverged. hypothesis. Although those papers satisfied the innate immune system. Over the past As additional genomes reveal their secrets, the judge and show why the hypothesis is decade, it has become clear that TLRs are the evolutionary biologists should ultimately sort widely accepted, a major surprise since the long-sought cell-surface receptors that recog- out which creatures have which immune molDover verdict suggests that this ecules. Making sense of that data transposon invasion took place “Whatever the actual evolutionary may demand conceptual breakeven earlier. throughs in understanding the purIn 2006, a team led by Jonathan pathway that led to the very complex pose of our immune defenses. Rast of the University of Toronto in Many immunologists accustomed Canada and Sebastian Fugmann of vertebrate adaptive [immune] system, to studying people, mammals, or the National Institute on Aging in other vertebrates assume that the Bethesda, Maryland, analyzed the it was surely a gradual progression adaptive immune system emerged genome of the purple sea urchin because it allowed these more comand found genes that closely resem- that co-opted many preexisting plex animals to deal with more ble RAG1 and RAG2, the first time immune mechanisms.” complex microbial threats. And they’ve been uncovered in inverteThompson, now scientific director —Jonathan Rast, at the Abramson Family Cancer brates. Their existence in the urchin University of Toronto Research Institute in Philadelphia, suggests that the transposon with these enzymes invaded animals far Pennsylvania, thinks the key advanearlier than had been thought but was lost in nize common microbial features such as bac- tage is that the adaptive response conserves most lineages except for jawed vertebrates, terial wall components or the distinctive DNA scarce resources by quickly fine-tuning the which adapted them to perform VDJ recombi- sequences of a virus. This role could date back otherwise all-out assault mounted by the nation. That’s an easier version of the story for to the earliest multicellular organisms, as innate immune system. “Specificity gives you some immunologists to swallow, as it allows humans and some of the most evolutionarily the advantage of being able to use the least more time for mutations to deactivate the primitive animals share TLRs and the mole- amount of an immune system,” he says. jumping ability of a transposon and convert its cules involved in the TLR signaling cascade. Still, some invertebrate biologists aren’t DNA to a new job. “There was never a big The sea urchin genome revealed more than convinced that their colleagues have nailed bang of immunology,” suggests Bosch. 200 TLR genes, for example, and in 2006, a down the selective advantage of the adaptive Thompson and others aren’t so ready to group headed by Werner E. G. Müller of the immune system. “It’s very hard to say what is defuse the explosive hypothesis, however. University of Mainz in Germany reported that the benefit,” says Bosch. He predicts one The RAG1-RAG2 transposon may sponges also encode these microbial important line of future inquiry in the evoluhave entered sea urchins and vertetionary study of immunology will be how brates independently, they stress. The immune systems have helped organisms role of RAG1 and RAG2 in sea urchins adapt to their specific environments or remains unknown, and Rast agrees that ecological niches. the timing of the transposon invasion Bosch also cites the growing realizaresponsible for adaptive immunity tion that animals harbor within their bodies a won’t be nailed down until more inverteworld of microbes that are crucial to develbrate genomes are deciphered over the opment, nutrition, and more; by some estinext few years. “The basic idea of an immune mates, humans are 90% bacterial cells. ‘big bang’ in the vertebrates has led to a variImmunologists, says Bosch, need to shift ety of oversimplifications and conceptual their thinking “from bacteria make you sick problems,” says Rast. “Whatever the actual to bacteria make you healthy.” Such a shift evolutionary pathway that led to the very may ultimately force a reconsideration of the complex vertebrate adaptive system, it was roots of the immune system. Did the innate surely a gradual progression that co-opted and adaptive arms truly evolve to keep out many preexisting immune mechanisms.” harmful organisms? Or instead, are one or both more like bouncers at a nightclub, First line of defense honed for the more subtle task of allowing Researchers have also made progress underthe right microbes in and kicking the less standing the origins of innate immunity, desirable ones out? If another evolutionencouraged by the recent appreciation that versus-ID trial ever takes place, biologists these defenses can be as sophisticated and addressing this provocative question will no doubt have added to the impressive stack of literature on how our immune Exhibit A. This stack of evolutionary immune system arose. –JOHN TRAVIS research literature was used in the Dover trial.

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