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| martin poenie: Again Inlay refers to ITAMs in a tunicate gene. This is a reference to a protein called A74 that has no similarity to any other known protein. So what are ITAMs? ITAMs are an arrangement of two tyrosines in a peptide with a certain spacing between them. Tyrosines are widely used in cell signaling. When phosphorylated, they can become ligands for proteins with SH2 domains. What makes ITAMs special is that there are proteins such as ZAP70 that contain dual SH2 domains and bind to the ITAM phosphorylated tyrosines as a unit. At present, no such protein has been identified in tunicates. The ITAM motif is based on four residues. It is possible that these are ordinary SH2 binding sites and that no dual SH2 domain-containing will be found. Until and unless one does find such a protein this is not a compelling argument. If proteins with these dual SH2 domains are found in tunicates, then it becomes a good argument. rafe: i'm not an expert on signal transduction, but it seems pretty clear that A74 is involved in immune-related signal transduction, and that tyrosine phosphorylation of the ITAM is part of it. as for the SH2-containing proteins, i should point out that homologues for syk and ZAP70 have been discovered in organisms as distant as hydra [1], and as similar (to tunicates) as sea urchin [2]. additionally, a CD45 homologue, which can augment signaling through ITAMs, was found in hagfish [3]. so while we don't have a tunicate syk-family homologue, many of the other pieces are already in place. it's not unreasonable to think that the downstream targets of A74 will be identified soon, i guess we can reserve judgement til then. do you think it will be homologous to syk/ZAP70? references [1] Steele RE, Stover NA, Sakaguchi M. Appearance and disappearance of Syk family protein-tyrosine kinase genes during metazoan evolution. Gene. 1999 Oct 18;239(1):91-7. [2] Sakuma M, Onodera H, Suyemitsu T, Yamasu K. The protein tyrosine kinases of the sea urchin Anthocidaris crassispina. Zoolog Sci. 1997 Dec;14(6):941-6. [3]Nagata T, Suzuki T, Ohta Y, Flajnik MF, Kasahara M. The leukocyte common antigen (CD45) of the Pacific hagfish, Eptatretus stoutii: implications for the primordial function of CD45. Immunogenetics. 2002 Jul;54(4):286-91. |
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| here's a run down of the general details of this model 1. the RAG genes and RSSs were originally a transposon, and the RAG proteins had transposase activity. 2. a gene existed in the ancestor to the jawed vertebrates that encoded a receptor with at least one immunoglobulin domain 3. this gene was only expressed in a somatic lineage, like hemocytes 4. the receptor could activate a pathway somehow involved in immune-related function 5. the RAG transposon integrated into the receptor near the binding site-coding region. 6. once inserted, the transposase would be under the receptor's transcriptional control. 7. the RAG's ability to reassemble the receptor gene once activated was sloppy, and made slight sequence changes upon reassembly. 8. those changes were beneficial to the host and the evidence supporting it: 1. there seems to be ample evidence suggesting that the RAG genes were once transposases, do you dispute this? the fact that they have transposase activity (in vitro) basically says it all. 2. the immunoglobulin domain is well-represented in nearly all organisms (even prokaryotes, i think). because its structure is so stable, a large portion of cell-surface molecules possess it, even some related to immunity (outside of the jawed vertebrates). however, no direct homologue to the antibody proteins have been found. so here is a prediction of the model: a non-rearranging receptor with an immunoglobulin domain existed in the ancestor to the jawed vertebrates. of course, this ancestral gene may no longer exist, but if it is ever discovered, that would fill in a major hole. 3. a lot of genes have tissue specific expression. as for the extant antibody genes, they are heavily regulated by enhancers (because of the need to prevent premature recombination, or recombination on both alleles). there's no reason to think that the enhancer wasn't there in the ancestral receptor (such as, if it was located between the V and J segments). 4. see 2. 5. this is the only step that appeals to chance. as yersinia said, there could have been many integrations by transposons (our genome is littered with remnants of retrotransposons). all it takes is one to be beneficial, and it will become fixed into the population. 6. a common molecular technique is transgenics, where whole genes are inserted into the chromosome randomly. one of the main problems with this approach is the lack of consistency in transgene expression. this is because the transgene becomes subject to the local transcription control. unless the transgene has a really powerful promoter, it's uncertain whether or not it will be expressed correctly. 7. the current mechanism of RAG-mediated recombination is sloppy. one of the reason is through the generation of hairpin loops at the two exposed ends. this is intrinsic to the activity of the RAG and is common to transposases (in fact, this is one of the observations that led scientists into thinking the RAGs were originally transposons). 8. here the evidence may never be to your satisfaction, but it's very reasonable to suppose that a high rate of mutation would benefit immune receptors. why do you think new flu vaccines come out every season? because the influenza's receptors can mutate very rapidly to avoid host recognition. furthermore, they don't need to mutate drastically and change the total structure of their receptors, only just enough to hamper the host's receptor's binding ability. if during tthe lifetime of the first RAG-integrated organism, one of the thousands to millions of hemocytes alive at the time form a receptor beneficial to the host, this will increase the host's chances for survival and the nature will have something to select upon. maybe this requires more evidence to convince you, but is it really that unreasonable? |
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| a couple of interesting papers on the immune system have popped up recently: 1. Mayer WE, Uinuk-Ool T, Tichy H, Gartland LA, Klein J, Cooper MD. Isolation and characterization of lymphocyte-like cells from a lamprey. Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):14350-5. this paper presents evidence for the existence of lymphocytes (cells intimately involved in the adaptive immune response) in lampreys, which don't have an adaptive immune system. previously, one could have argued that rearranging antigen receptors and lymphocytes were irreducible. now it doesn't look like that is the case. 2. Uinuk-Ool T, Mayer WE, Sato A, Dongak R, Cooper MD, Klein J. Lamprey lymphocyte-like cells express homologs of genes involved in immunologically relevant activities of mammalian lymphocytes. Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):14356-61. this article, the complement to the previous article, shows that the lamprey lymphocytes express genes similar to ones expressed in mammalian lymphocytes. these genes are also involved in the adaptive immune response in mammals, so it's strange that they are present in lamprey. incidently, both these articles are freely accessible online. 3. Dodds AW. Which came first, the lectin/classical pathway or the alternative pathway of complement? Immunobiology. 2002 Sep;205(4-5):340-54. this article provides a model for the evolution of the complement system. if paul wants to call the author's model "storytelling", he's free to do so, but now it's not just some random internet poster's idea. i won't quote his model (it spans 2 pages), but he does say this about the model: "the scheme outlined in figures 5 and 6 involves a stepwise increase in effectiveness of the system, each step giving benefit to the species involved." since the time this thread began, probably a dozen articles have been published that support the notion that the immune system evolved. has ID advanced in any way since then? |
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| The discovery of a V-like Ig multigene family in the protochordate amphioxus provides new insights into the evolution of the adaptive immune response. Diversity is at the same time the essential product of evolution and the essential substrate on which it must act. Although diversity can be the result of many different pressures and mechanisms, it is particularly evident and rapidly evolving in the responses of hosts to pathogens and parasites. Of the many defense systems described from the simplest single-celled bacteria to the most complicated plants and animals, none has been more intensively studied than the mammalian adaptive immune system. It has only recently become apparent that the adaptive immune system arose in the jawed vertebrates, but little is known about the deeper origins of this system or the relationship with other defense systems in nonvertebrate organisms. In this issue of Nature Immunology, Litman and colleagues describe a set of newly identified sequences from the protochordate amphioxus (Fig. 1), which make up a diversified multigene family and could hold some clues to the emergence of the adaptive immune system. |
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| Urochordates and the origin of natural killer cells: Identification of a CD94/NKR-P1-related receptor in blood cells of Botryllus Konstantin Khalturin *, Matthias Becker *, Baruch Rinkevich , and Thomas C. G. Bosch * *Zoological Institute, Christian Albrechts University Kiel, Olshausenstrasse 40, 24098 Kiel, Germany; and National Institute of Oceanography, Tel Shikmona, P.O. Box 8030, Haifa 31080, Israel Published online before print January 7, 2003 Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0234104100 Transplantation immunity based on the recognition of MHC molecules is well described in vertebrates. Vertebrates, however, do not undergo transplantation reaction naturally. The phylogenetically closest group in which transplantation reactions can occur is the Urochordata. Therefore, these animals occupy a key position for understanding the evolution of the vertebrate immune system. When screening for genes differentially expressed during allorecognition in Botryllus schlosseri, we isolated a gene coding for a type II transmembrane protein with a C-type lectin-binding domain and close similarity to vertebrates CD94 and NKR-P1. Here we show that the gene, BsCD94-1, is differentially regulated during allorecognition and that a subpopulation of blood cells carries the corresponding receptor on its cell surface. Southern blot analysis with DNA from individual colonies and intronless BsCD94-1 probe reveal variation between individuals at the genomic level. CD94 in vertebrates is one of the markers for natural killer cells and binds to MHC class I molecules. Natural killer cells play a major role in recognition and elimination of allogeneic cells. Their evolutionary origin, however, remained unknown. The results presented here indicate that the elaboration of the vertebrate immune system may have its roots in an ancestral population of cells in the urochordate blood. |
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| In vivo transposition mediated by V(D)J recombinase in human T lymphocytes Terri L. Messier, J.Patrick O’Neill, Sai-Mei Hou, Janice A. Nicklas and Barry A. Finette abstract: The rearrangement of immunoglobulin (Ig) and T-cell receptor (TCR) genes in lymphocytes by V(D)J recombinase is essential for immunological diversity in humans. These DNA rearrangements involve cleavage by the RAG1 and RAG2 (RAG1/2) recombinase enzymes at recombination signal sequences (RSS). This reaction generates two products, cleaved signal ends and coding ends. Coding ends are ligated by non-homologous end-joining proteins to form a functional Ig or TCR gene product, while the signal ends form a signal joint. In vitro studies have demonstrated that RAG1/2 are capable of mediating the transposition of cleaved signal ends into non-specific sites of a target DNA molecule. However, to date, in vivo transposition of signal ends has not been demonstrated. We present evidence of in vivo inter-chromosomal transposition in humans mediated by V(D)J recombinase. T-cell isolates were shown to contain TCR(alpha) signal ends from chromosome 14 inserted into the X-linked hypo xanthine–guanine phosphoribosyl transferase locus, resulting in gene inactivation. These findings implicate V(D)J recombinase-mediated transposition as a mutagenic mechanism capable of deleterious genetic rearrangements in humans. |
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Dev Comp Immunol 2003 Apr;27(4):263-71 Workshop report: evolutionary immunobiology--new approaches, new paradigms. Du Pasquier L, Smith LC. [...] 3. The boundary between invertebrates and vertebrates Those working on innate immunity and who are impressed by the efficiency of these defense mechanisms frequently ask, "why did vertebrates acquire an adaptive immune system that was based on somatic rearrangement?" The multiplicity and diversity of the innate systems described above may provide the beginnings of an answer to this question. If an animal like Drosophila, which lives for a relatively short time, requires many germ line encoded innate mechanisms to survive, how many mechanisms will be required for the survival of long lived species? At some point during metazoan evolution, an increase in the number of genes devoted to innate immunity would have been required. Rather than an amplification of genetic material devoted to immune defenses becoming detrimental, the introduction of a somatic mechanism to generate a repertoire of recognition structures resulted in an economy or at least a status quo in the amount of the genome that was devoted to immune responsiveness. At the same time a somatic mechanism providing in fact a `kit' to generate one's repertoire by oneself would probably be favored by species producing few offspring where the value of a single individual would be very important. Therefore it would not be that surprising that phyla other than vertebrates have invented (by means that could be different from those of the vertebrates) a somatic way of increasing the diversity of their receptors (e.g. see the above mentioned possibilities of alternate RNA processing and splicing). Today, one of the striking paradoxes of the evolution of the combinatorial immune system is that RAG homologues appear to be totally lacking in the lower deuterostomes and in all non-deuterostome metazoans. This suggests a rapid evolutionary emergence and phylogenetic restriction for the capacity to generate specific inducible immunity in higher vertebrates. This implies that the introduction of the rearranging machinery occurred in a gene encoding a receptor that was already committed to expression in a lymphocyte-like cell, and perhaps involved in innate immune defense mechanisms. Therefore, to understand this major evolutionary step, a search is under way for the origin of the lymphocyte lineage and for an Ig superfamily (IgSf) gene target which may be similar to a T-cell receptor or an immunoglobulin gene. The animals used in these searches include modern members of classes that preceded the gnathostomes in evolution. Michele Anderson (Pasadena) presented information on transcription factors involved in hematopoiesis and the definition of lymphoid lineages. If diversity was a master theme during this workshop, conservation of patterns was another and not only for the Toll cascade. A good example is the conservation of patterns (in structure, function and pathways) of transcription factors. Anderson discussed her investigations of skates, lampreys, amphioxus and sea urchins, and searches for homologues of transcription factors important in hematopoiesis. She has been monitoring the Ikaros/Aiolos/Helios family, PU.1, and GATA-1/2/3 families of transcription factors, all of which include essential or important factors in lymphoid development. In the clear nose skate (Raja eglanteria, a species that is also suitable for developmental studies), the existence of EBF, GATA3, members of the Ikaros family, and PU.1, are all consistent with the finding of Ig and TCR genes expressed at this level of vertebrate phylogeny. Expression of the transcription factor, Spi-C, appeared to be specific to the spleen and therefore, may be involved with B cell development. It was assumed that multiple members of each transcription factor family found in the elasmobranchs arose by gene duplication from a less complex population of progenitor genes. In invertebrates the number of homologues found so far fits with this hypothesis: fewer in the invertebrates and increased gene family sizes in higher vertebrates. For example, PU.1 and Spi-C are not found in the Drosophila genome, while one member of the PU.1 family is found in the lamprey, even though no classical adaptive immune system has been characterized in this species. Based on the sequence of the lamprey GATA gene, it appears to encode a pre-duplication molecule with GATA 2/3 features. The existence of PU.1 and GATA-1/2/3 family transcription factors in the lamprey, a jawless vertebrate, suggests that the stage was set for lineage-specific expression of certain antigen receptors just prior to the introduction of RAG-1 and RAG-2 in the earliest jawed vertebrates. Anderson stressed the importance of the cis-acting elements that control the expression of the duplicated GATA genes and orient them in different patterns of expression. She also warned us about terminology in this field and about the difficulty of identifying orthologues. The workshop participants discussed and agreed upon the need for a strong gene ontology if highly diverse systems are to be compared fruitfully. Still within the context of transcription factors, Jack Marchalonis (Tucson) described the lamprey vitamin D receptor (VDR), a ligand-specific transcription factor that is a member of the Nuclear Receptor Superfamily (NRS), which has been cloned from `protospleen' cDNA of the larval stage. In mammals, the VDR is a transcription factor that mediates the actions of its ligand, vitamin D, and can promote monocyte/macrophage differentiation and inhibit proliferation and cytokine production by activated T lymphocytes. These functions make the VDR relevant and interesting for innate immunity. Like VDRs of jawed vertebrates, the lamprey molecule consists of two C4-type zinc fingers, and both DNA-binding segments and ligand-binding segments show significant conservation across species. Cladograms of the NRS family, using the ecdysone receptor of insects as an outgroup (a distantly related member of this gene family) indicated that the lamprey VDR clustered unambiguously with the other vertebrate VDRs and constituted the basal member of the group. Marchalonis (Tucson) also commented on the complete characterization of the RAG1/RAG2 gene cluster in the sandbar shark and the evolutionary and functional implications of this analysis. The ancestors of the sharks were apparently the first vertebrates in phylogeny to have acquired RAG genes which have been highly conserved during evolution both in terms of sequence and gene organization. In common with other vertebrate species, the shark RAG2 coding region lacks introns and is closely linked in opposite orientation to the RAG1 gene. The intergenic region (~10 kb) is comparable in length to that of tetrapods. About 40% of the spacer consists of SINE and LINE fragments homologous to those found in other sharks, reptiles and birds. |
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At the heart of it, we are attempting to understand the dynamics of complex systems by comparative methods. For example, are there common threads in the metabolic machinery from one system to another? Clearly there must be, as one of the themes of this conference was the adaptation of pre-existing molecules and metabolic pathways to new functions. Likewise, are there common features of the immune (or other metabolic) system that can be extracted and used to understand more fully the evolution of immunity and organisms? This field has become known as phylogenomics. Further, the response of an organism to environmental change is equivalent in concept to immune responses to invading organisms. Does it really matter whether the environmental challenge is a pathogen or an elevation in temperature? The organism will respond to environmental changes that alter metabolic functions. The application of genomic tools to the study of ecosystems, ecogenomics, is an emerging discipline dedicated to this end and owes much to developments in immunology. We are very familiar with the common features in ecosystems of primary producers, herbivores, carnivores and decomposers which circumscribes the flow of energy and mass through the system. In phylogenetics, there are accepted hierarchies in vertebrate groups, and some invertebrates as well, which are assumed to reflect the ancestor–descendent relationships (i.e. flow of genetic material over time). However, similar unifying principles and classification schemes are completely lacking in studies of cellular mechanisms except where individual components are concerned (e.g. the TCA cycle). Hence, the concepts developed in a systems approach to immune function can cut across a wide range of biological studies and mathematical tools are needed to exploit these data. |
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Vet Immunol Immunopathol 2003 Jan 10;91(1):1-12 TOLL-like receptors linking innate and adaptive immune response. Werling D, Jungi TW. Institute of Veterinary Virology, University of Berne, Langgass-Str. 122, CH-3012 Bern, Switzerland. Invading pathogens are controlled by the innate and adaptive arms of the immune system. Adaptive immunity, which is mediated by B and T lymphocytes, recognises pathogens by rearranged high affinity receptors. However, the establishment of adaptive immunity is often not rapid enough to eradicate microorganisms as it involves cell proliferation, gene activation and protein synthesis. More rapid defense mechanisms are provided by innate immunity, which recognises invading pathogens by germ-line-encoded pattern recognition receptors (PRR). Recent evidence shows that this recognition can mainly be attributed to the family of TOLL-like receptors (TLR). Binding of pathogen-associated molecular patterns (PAMP) to TLR induces the production of reactive oxygen and nitrogen intermediates (ROI and RNI), pro-inflammatory cytokines, and up-regulates expression of co-stimulatory molecules, subsequently initiating the adaptive immunity. In this review, we will summarize the discovery and the critical roles of the TLR family in host defense, briefly allude to signaling mechanisms mediating the response to TLR ligands, and will provide an update on current knowledge regarding the ligand specificity of these receptors and their role in immunity of domestic animals, particularly cattle. |
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Roth DB. From lymphocytes to sharks: V(D)J recombinase moves to the germline. Genome Biol. 2000;1(2):REVIEWS1014. Review. abstract: The antigen-receptor genes of vertebrates are rearranged by a specialized somatic recombination mechanism in developing lymphocytes - and, unexpectedly, also in the germline of cartilaginous fishes. The recombination system that carries out these DNA rearrangements may thus be a significant evolutionary force, perhaps not limited to rearrangements at antigen-receptor loci. |
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Analysis of the TCR(beta) Variable Gene Repertoire in Chimpanzees: Identification of Functional Homologs to Human Pseudogenes Dirk Meyer-Olson*, Kristen W. Brady*, Jason T. Blackard, Todd M. Allen*, Sabina Islam*, Naglaa H. Shoukry, Kelly Hartman*, Christopher M. Walker and Spyros A. Kalams2 The Journal of Immunology, 2003, 170: 4161-4169. abstract: Chimpanzees are used for a variety of disease models such as hepatitis C virus (HCV) infection, where Ag-specific T cells are thought to be critical for resolution of infection. The variable segments of the TCR(alpha/beta) genes are polymorphic and contain putative binding sites for MHC class I and II molecules. In this study, we performed a comprehensive analysis of genes that comprise the TCR variable gene (TCRBV) repertoire of the common chimpanzee Pan troglodytes. We identified 42 P. troglodytes TCRBV sequences representative of 25 known human TCRBV families. BV5, BV6, and BV7 are multigene TCRBV families in humans and homologs of most family members were found in the chimpanzee TCRBV repertoire. Some of the chimpanzee TCRBV sequences were identical with their human counterparts at the amino acid level. Notably four successfully rearranged TCRBV sequences in the chimpanzees corresponded to human pseudogenes. One of these TCR sequences was used by a cell line directed against a viral CTL epitope in an HCV-infected animal indicating the functionality of this V region in the context of immune defense against pathogens. These data indicate that some TCRBV genes maintained in the chimpanzee have been lost in humans within a brief evolutionary time frame despite remarkable conservation of the chimpanzee and human TCRBV repertoires. Our results predict that the diversity of TCR clonotypes responding to pathogens like HCV will be very similar in both species and will facilitate a molecular dissection of the immune response in chimpanzee models of human diseases. |
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Immunopharmacology 1999 May;42(1-3):107-20 Complement systems in invertebrates. The ancient alternative and lectin pathways. Smith LC, Azumi K, Nonaka M. Department of Biological Sciences and Institute of Biomedical Sciences Graduate Program in Genetics, George Washington University, Washington, DC 20052, USA. The complement system in higher vertebrates is composed of about thirty proteins that function in three activation cascades and converge in a single terminal pathway. It is believed that these cascades, as they function in the higher vertebrates, evolved from a few ancestral genes through a combination of gene duplications and divergences plus pathway duplication (perhaps as a result of genome duplication). Evidence of this evolutionary history is based on sequence analysis of complement components from animals in the vertebrate lineage. There are fewer components and reduced or absent pathways in lower vertebrates compared to mammals. Modern examples of the putatively ancestral complement system have been identified in sea urchins and tunicates, members of the echinoderm phylum and the protochordate subphylum, which are sister groups to the vertebrates. Thus far, this simpler system is composed of homologues of C3, factor B, and mannose binding protein associated serine protease suggesting the presence of simpler alternative and lectin pathways. Additional components are predicted to be present. A complete analysis of this invertebrate defense system, which evolved before the invention of rearranging genes, will provide keys to the primitive beginnings of innate immunity in the deuterostome lineage of animals. |
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Immunobiology 2002 Sep;205(4-5):340-54 Which came first, the lectin/classical pathway or the alternative pathway of complement? Dodds AW. Department of Biochemistry, University of Oxford, UK. al@bioch.ox.ac.uk It is a widely accepted canon of immunology that the alternative pathway is more primitive and hence older in evolutionary terms than the lectin/classical pathway. This idea has been reinforced by the discovery of "C3" and "factor B" proteins in invertebrate species. However, it is clear that the gene duplications which gave rise to C3/C4/C5 and factor B/C2 occurred in the vertebrate lineage. Hence, the naming of the invertebrate proteins may be based on preconceptions rather than on solid structural or functional evidence. Lectins and associated MASP/C1r/C1s-like proteins have been found in invertebrates, while factor D, the defining component of an alternative pathway, has so far been found only in the bony fish and higher species. It is a principle of Darwinian evolution that complex systems develop through small sequential steps. It is possible to imagine such a series of steps for the evolution of a lectin pathway, involving as it does recognition of non-self. It is difficult to see how the alternative pathway, which lacks a recognition molecule, could have evolved without the prior development of control proteins to protect self from attack. |
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Antibodies do not necessarily have single specificities. Indeed, the vast majority of our circulating immunoglobulins (the so-called "natural" antibodies) are low affinity, broad specificity antibodies directed towards common antigens (bacterial wall moieties, for instance). Antibodies become highly specific and gain high affinity only late during an antigen-specific immune response, through a process of mutation/selection called affinity maturation. This however has nothing to do with the VDJ recombination process we are discussing here, which takes place, irrespective of antigen, during B cell differentiation in the bone marrow. "Naive", newly generated B cells, as they emerge from the bone marrow, carry antibodies that are mostly of low affinity. For insatnce, the antibodies produced early during an immune response (which reflect the naive repertoire) bind antigen with a Kd in the 10^-5-10^-6 M range - compared that with the high affinity, "matured" antibodies of late immune responses, which have a Kd of 10^-8-10^-9 M. Most antibodies in the primary repertoire are also not very specific – in fact, polyspecific antibodies abound (which goes along with their low affinity for antigen). As an aside, the vast majority of antibodies in the primary repertoire do not in fact recognize anything at all, and the B cells that make them die after a while without ever seeing any "action" (one of the drawbacks of the darwinian approach of the adaptive immune system – high, widespread wastefulness for rare but exceptional returns). As for innate immunity receptors, again you are mistaken. While some of them do indeed have broad spectrum, many have quite subtle specificities, for instance TLR4 binds very specifically to the lipid A moiety of the very large bacterial lipolysaccharide (LPS) molecules. Their binding constants also actually compare quite well with those of most primary response antibodies (in the 10^-6-10^-7 M range). The fundamental difference between adaptive and innate immunity receptors is in fact neither in their affinity nor in their specificity, but in their logic. The adaptive immune system, using VDJ recombination, can generate an almost infinite variety of specificities, and thanks to clonal selection can pick any extremely rare, low affinity antibody molecule and turn it into close to a “magic bullet” (this however has again nothing to do with VDJ recombination). The innate immune system, on the other hand, can count on only a limited array of receptors, which must focus on a few abundant antigens (sometimes classes of antigens) commonly found on pathogens (often, like LPS, molecules that we ourselves do not produce); moreover, the binding of the ligand has to be good to start with, because these antigens cannot undergo mutation and selection processes. |
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It can't, anymore that a human system can get a V1 fused to a V2 in its Ig clusters. V segments have RSSs only on their 3', and they all have the same spacers (for steric reasons related to RAG structure, recombination only occurs between RSSs that vave different sized spacers), so that recombination cannot occur. What can occur is a V from one shark cluster recombining with a D in another. |
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But it wouldn't make a difference anyway, because RAG figures out where to cut based on RSS (IS in above diagram), and these sequences would get copied along with the V, D or J segments as they get duplicated [...] |
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| The study of immunoglobulin genes in non-mouse and non-human models has shown that different vertebrate groups have evolved distinct methods of generating antibody diversity. By contrast, the development of T cells in the thymus is quite similar in all of the species that have been examined. The three mechanisms by which B cells uniquely modify their immunoglobulin genes -- somatic hypermutation, gene conversion and class switching -- are increasingly believed to share some fundamental mechanisms, which studies in different vertebrate groups have helped (and will continue to help) to resolve. When these mechanisms are better understood, we should be able to look to the constitutive pathways from which they have evolved and perhaps determine whether the rearrangement of variable, diversity and joining antibody gene segments -- V(D)J recombination -- was superimposed on an existing adaptive immune system. |
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Not moving the goalposts quite yet. From DBB: quote: -------------------------------------------------- In this chapter I have looked at three features of the immune system - clonal selection, antibody diversity, and the complement system - and demonstrated that each individually poses massive challenges to a putative step-by-step evolution. [Niic, for the sake of argument, I'll grant you this one]. But showing that the parts can't be built step by step only tells part of the story, because the parts interact with each other...an animal that has a clonal selection system won't get much benefit out of it if there is no way to generate antibody diversity. A large repertoire of antibodies won't do much good if there is no system to kill invaders. A system to kill invaders won't do much good if there's no way to identify them. At each step we are stopped not only by local system problems, but also by requirements of the integrated system. -------------------------------------------------- |
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Now, let me move from Behe to one of your earlier sources, the recent (but out-of-date) collection of articles by a number of experts in the field, Origin and Evolution of the Vertebrate Immune System (Current Topics in Microbiology and Immunology, 248). "New Approaches Towards an Understanding of Deuterostome Immunity" J. P. Rast et al quote: -------------------------------------------------------------------------------- Both of these attributes, the tendency towards mechanistic novelty and a high rate of sequence evolution, may emerge from the dynamic nature of host-pathogen interactions and thus be a universal characteristic of immune systems. -------------------------------------------------------------------------------- Universal, Niic, universal. Now, I'm not sure if Rast et al are talking about the same thing as Behe exactly, but it would seem to me that the points they are making are very similar. In order for an immune system of any type to work properly, several features need to be present all at once. Why else would the authors be proposing universality for "the tendency towards mechanistic novelty and a high rate of sequence evolution?" |
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Immunol Rev. 2002 Dec;190:161-8. Natural selection and the diversification of vertebrate immune effectors. Hughes AL. The molecules of the vertebrate immune system provide some of the best documented examples of natural selection acting at the molecular level. The major histocompatibility complex (MHC) molecules are a family of highly polymorphic loci whose products present peptides to T cells. Four distinct lines of evidence support the hypothesis that the natural selection acts to maintain MHC polymorphism: (1) evidence from the unusual allelic frequency distribution seen at MHC loci; (2) evidence from the pattern of nucleotide substitution at MHC loci, which shows an enhanced rate of nonsynonymous (amino acid-altering) substitution in the codons encoding the peptide-binding region of the molecules; (3) the existence of long-lasting polymorphisms at certain MHC loci; and (4) the fact that introns at MHC loci are homogenized by recombination and subsequent genetic drift. Certain other immune system gene families provide evidence that natural selection has acted to create diversity among family members. Examples include molecules of the specific immune system (such as immunoglobulin V region genes) and molecules of the innate immune system (such as defensins). |
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It's interesting to me that those few words seem to sum up a major hurdle for the standard Darwinistic explanation of things - if I understand them correctly, they are suggesting that every creature that has, or has ever had, an immune system, has the ability to respond very quickly to the presence of enemy organisms, creating new features or substances on-the-fly so to speak, and to generate a high rate of sequence evolution (are they refering to a high rate of somatic mutations?) in response to the threat. |
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As I keep saying over and over, "the immune system" as a whole is big and ill-defined. -------------------------------------------------------------------------------- Now, do you mean by this that features of the immune system are difficult to explain or describe? [snip quote] Or what? Your comment seems to contradict your basic claim that Dembski and Behe are all wet regarding current research and literature. What is it, exactly, that you mean by your comment? |
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Or do you mean, It's difficult to cram the immune system into the restrictive, overly reductionistic and simplistic non-explanations of classical Darwinian theory? |
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| "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." |
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How did these pre-rearranged genes arise? One possibility is that they are descendants of the ancestral antigen-receptor gene, before integration of the putative transposable element. A second possibility is that these genes arose from RAG-mediated DNA rearrangement events that occurred in the germline, an operation that violates the precept that the RAG recombinase is functional only in developing lymphocytes. A recent paper by Lee et al. [4] addresses these questions by examining immunoglobulin genes in the nurse shark. The nurse shark NS4 immunoglobulin light chain gene family provided very useful information, as there are several highly homologous genes present both in pre-rearranged and unrearranged forms. These features allowed the authors to evaluate sequences in sufficient detail to ascertain whether the genes bear characteristic features of V(D)J recombination or footprints of transposition. Their analysis revealed that the pre-rearranged genes did indeed contain tell-tale signs of coding joints formed by V(D)J recombination, including both N nucleotides and P nucleotides, which strongly suggest a hairpin intermediate. The presence of these features in several junctions suggests several independent germline V(D)J recombination events, although analysis of multiple unrelated individuals suggests that these events are not frequent. Importantly, analysis of the unrearranged NS4 genes failed to detect the target site duplications that are hallmarks of transposon insertions. Thus, while the pre-rearranged NS4 genes appear to have been derived from unrearranged genes by germline V(D)J recombination, there is as yet no evidence to support the hypothesis that the unrearranged genes were derived from the pre-rearranged genes by insertion of a transposable element; this is discussed in a recent review by Lewis and Wu [16]. |
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In this issue, a study by Lee et al. (12) further investigates whether joined genes—later interrupted by a transposon insertion—or unjoined genes—subsequently connected by site-specific recombination—came first in the evolution of the Ig light chain locus in the nurse shark. There is increased interest in this issue, not only because it reveals the ways in which RAG-mediated events have reorganized Ig and TCR loci, but also because RAG-mediated transposition, though demonstrated in a purified in vitro system, has not yet been observed in any in vivo setting. Lee et al. took advantage of the fact that certain Ig light chain genes in two shark species were apparent orthologs. Whereas all of the type III L chain genes in the horned shark were unjoined, the corresponding NS4 genes in the nurse shark occurred in both joined and unjoined form. A key feature of the analysis was that the NS4 genes in the nurse shark were highly homologous to one another, allowing evolutionary relationships to be established with some confidence. In combination, these circumstances enabled the authors to do two things: construct a phylogenetic tree of the NS4 family sequences, and provide through DNA sequence analysis a means to distinguish between the transposon integration and site-specific recombination scenarios. As mentioned above, a sequence that has been interrupted by RAG-mediated transposition is expected to exhibit (relative to the uninterrupted form) a 5-bp target site duplication (or more rarely a 4- or 3-bp duplication; Fig 1 B, wavy lines) on either side of an RSS-bordered insertion (6) (7). A gene that has instead been joined through site-specific recombination is expected to exhibit (relative to the unjoined form) a loss of a small, unfixed number of bp from the ends of the joined coding sequences, along with the acquisition of junctional insertions (of two classes: one random in sequence, and termed an N insertion, another occurring only at ends that escaped trimming, and bearing a palindromic relationship to the cut end, termed a P insert; for a review, see reference 10). The two approaches taken by Lee et al. (12) returned the same answer: the joined NS4 genes arose through site-specific V(D)J recombination and not through germline RAG-mediated transposition. Their phylogenetic analyses indicated that germline joining occurred more than once, and in every case the unjoined form lacked any evidence of the DNA sequence duplications predicted for transposition. Instead joined genes exhibited junctions that appeared to reflect processing accompanying V(D)J recombination: trimming and P nucleotide addition. |
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[Roth 2000] Early on, it was suggested that the V(D)J recombination system might have arisen by the fortuitous integration of a transposable element into an ancestral antigen-receptor gene [14]. This hypothesis was strengthened by the discovery that the RAG genes are tightly linked [7], and by the finding that the RAG proteins can act as a transposase. Thus, a plausible model for the acquisition of the V(D)J recombination system during vertebrate evolution is the integration of a transposable element carrying the linked RAG genes into a primordial antigen-receptor gene in an ancestral jawed vertebrate, approximately 450 million years ago (reviewed in [1,11]). Presumably, this initial integration event created the first rearranging antigen-receptor gene; subsequent gene duplication events then created the multiple immunoglobulin and T-cell receptor loci. |
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[Lewis and Wu 2000] As recently as only a few years ago, any real information bearing on the actual genesis of the V(D)J recombination system seemed to be irretrievably lost. However, as more was learned about the molecular genetic and biochemical properties of the V(D)J recombination proteins, termed recombination activating gene (RAG)-1 and RAG-2, tantalizing suggestions of a transposon origin began to emerge. These clues included the following: first, the fact that the genes encoding RAG-1 and RAG-2, which are unrelated in sequence, are tightly linked, and as such share this property with genes that are known to undergo horizontal transfer (4). Second, the chemical mechanism of the recombination reaction, where DNA strand breakage and rejoining is accomplished through one step transesterification reactions, was like that of several well-described mobile elements (5). Finally, a surprising finding further indicated that RAG-1 and RAG-2 might have once been part of a transposon when two groups independently demonstrated that purified RAG-1 and RAG-2 proteins have a latent ability to carry out the transposition of DNA (6) (7). Why this latter observation was so important is that there was no a priori expectation that a protein that can perform V(D)J recombination through site-specific recognition of recombination signal sequences (RSS) should also be able to transpose RSS-terminated DNA fragments. A quick description of both types of rearrangement is needed to appreciate this point, and will also come to bear later in this commentary. As diagrammed in Fig 1, the transpositional excision and reintegration of DNA (Fig 1 B) is a fairly different transaction from the creation of site-specific connections in V(D)J recombination (Fig 1 A). One difference is in the number and specificity of double strand DNA breaks; transposition not only entails the introduction of breaks at each of two RSS, as in V(D)J recombination, but also requires the generation of a third, non–sequence-specific cut at an undetermined integration site. The signature features of a transposition product versus those arising from site-specific V(D)J recombination are also quite distinct. After transposition, a transposed DNA fragment terminated by the RSS, is flanked by a five-nucleotide repeat created by a staggered cut at the target integration site ((6) (7); Fig 1 B, wavy lines). In contrast, after V(D)J recombination, a signal joint and a coding joint are created. Signal joints are formed from exact RSS fusions, and coding joints from fusions of the associated coding segments. The latter characteristically contain small, irregular nucleotide deletions and insertions, reflecting various processing operations performed on the coding end intermediates as they undergo joining (Fig 1 A). Thus, the unusual in vitro ability of RAG-1 and RAG-2 to do two quite different things, and in particular to transpose DNA, provided strong support for the original speculation that the V(D)J recombination system used to be a transposable element (3). The fact that the once portable genome now serves a different and highly utilitarian role in its new context suggests that the V(D)J recombination system stands as a prime example of the rehabilitation of "selfish DNA" (for a review, see reference (8)). [...]  Figure 2. Postulated intermediates in the molecular evolution of the Ig and TCR loci. (A) One theory is that the event responsible for the existence of the modular recombination units characterizing today's Ig and TCR loci was a singularity that took place early in vertebrate evolution. With the integration of a mobile element, an ancient gene encoding an Ig superfamily domain was split into two parts. The mobile element imported RAG recombinase, its RSS, and possibly other element-related features, into the vertebrate genome. Reassembly of a functional exon required site-specific excision of the introduced mobile element, through a RAG-mediated recombination event targeting the RSS motifs. (B) After the RAG transposon integrated, the interrupted gene was duplicated. It has been suggested by Litman et al. (reference 2) that the presence of clustered arrays of duplicated genes, as found today in sharks, resembles an early locus configuration. On this view, V(D)J recombination activity in germline tissues could have led to the following derived features: (i) joined copies, as seen in cartilaginous fish, arose through a "standard" V(D)J joining event resulting in coding joint formation; (ii) the de novo creation of D segments could have arisen from intercluster recombinations resulting in the formation of signal joints with junctional insertions; (iii) the substitution of a 12-spacer RSS for a 23-spacer RSS or vice versa may have resulted from the "hybrid joint" outcome of germline joining. All of the postulated manipulations are RAG mediated and site specific. Events shown in i and iii are supported by evidence from sharks. MYA, million years ago. |
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| The human complement system is composed of more than 30 serum and cell surface components, and most of these components show a characteristic domain structure, enabling us to trace the evolution of the genes based on their structures. Ongoing genome projects in both vertebrates and invertebrates revealed that most domains used by mammalian complement components are found in both protostomes and deuterostomes. However, the unique combinations of them as found in mammalian complement components are present only in deuterostomes, indicating that the complement system was established in the deuterostome lineage. Unexpectedly, the complement system of an invertebrate deuterostome, ascidian, shows a similar level of complexity as that of mammals. However, phylogenetic analysis suggested that expansion of complement genes by gene duplications occurred independently both in the ascidian and vertebrate lineages. Although most characteristic domain structures of the mammalian complement components are found in ascidians, detailed evolutionary analysis casts doubt on their mutual reactivity. Thus, the vertebrate complement system seems to be established by integrating some independent parts into one reaction system. |
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Same Tools, Different BoxesConvergent evolution plays out in plant and animal innate immunity | By Philip Hunter [picture by] D.F. Dowd As life's diversity demonstrates, nature has a pretty large toolbox for designing adaptations. While in many ways an efficient builder, it often reuses blueprints, even if not starting with the same tools. Analogous wing structures in bird and bat suggest a why-mess-with-success ethos. New World cacti and desert-dwelling Euphorbiaceae in the Old World share protective spines and photosynthesizing stems even though the last common ancestor predates such modifications. Beyond structural adaptations, researchers are investigating convergent evolution at the molecular level, and this may allow for broader comparisons even between plants and animals. Both, of course, share the building blocks and fundamental biochemistry that evolved before the two kingdoms presumably diverged from common single-celled ancestors. But with their radically different cell structures, plants and animals were thought to have pursued largely independent evolutionary routes. Such disparity was reflected in the lack of interaction between the respective research communities. But much is changing, especially with respect to the study of innate immunity, which turns out to involve strikingly similar mechanisms in both plants and animals. One can find resemblances in the receptors that recognize pathogenic components such as lipopolysaccharide; in the signaling systems that initiate responses through kinase cascades; and in the defense mechanisms, including reactive molecules such as nitric oxide, says Jonathan Jones, senior scientist at the Sainsbury Laboratory of the John Innes Centre in Norwich, UK. Moreover, says Jones, autoimmune disorders can develop in plants as well as animals. In many cases, researchers consider plant and animal innate-immunity analogs to have evolved independently, because the underlying genes involved are radically different. Here, convergence is occurring purely at the functional level, according to Daniel Klessig, president and CEO of Boyce Thompson Institute (BTI) for Plant Research in Ithaca, NY. But now, say some, both functional and genetic similarities between plant and animal immunity are leading to cross-pollination between the respective research fields. NOS BY ANY OTHER NAME Functional similarities can exist without accompanying sequence homologies. Klessig offers parallels in nitric oxide production between plants and animals. Nitric oxide is believed to exert direct anti-microbial effects by interfering with protein function and forming cytotoxic oxidants. Klessig's group recently discovered the enzyme responsible for nitric oxide production in plants, a variant of the glycine decarboxylase complex's P protein.1 This plant nitric oxide synthase (NOS) shares biochemical and kinetic features with animal NOSs, says Klessig. [picture by] D.F. Dowd "Like the mammalian NOS, it is induced or activated by infection and has very high specific activity. We have also recently, in collaboration with Greg Martin's group [also at BTI] shown that like in animals, silencing of the plant NOS suppresses disease resistance." Although the animal and plant NOSs are very similar in what they do, not much of the underlying genetic sequence is common. "This suggests they use different chemistry for nitric oxide production," says Klessig. There are some proteins common to plants and animals with considerable sequence homology, but researchers dispute whether many of these evolved purely to serve innate immunity. Some hypothesize that the evolution of mitogen-activated protein kinases (MAPKs) was driven at least partly by the requirements of innate immunity. MAPKs largely regulate mitosis, but they also have been implicated in the innate immune response as a signaling intermediary connecting recognition and response mechanisms, with some apparently striking parallels in plants and animals. Interference with MAPK signaling depletes resistance in both plants and animals. But while there is evidence that MAPK signaling has a role in programmed cell death to stop the spread of bacterial or viral infection, the exact nature of the immune responses elicited by the signaling is unknown.2 According to plant immunologist Jeff Dangl at the department of biology, University of North Carolina, Chapel Hill, some sequence homology in the MAPKs would be expected, given that genes encoding for kinase cascades account for about 10% of most eukaryote genomes. MAPKs have been widely available throughout evolution for a variety of signaling functions. "If you're going to do something, you'll pull something out of the toolkit," says Dangl. Here parallel paths to innate immunity modified a common tool developed for other functions. Yet, some aspects of innate immunity require convergence at the molecular level, notably in common pathogen receptors. This can involve direct recognition of factors on the pathogen's surface, or response to pathogen proteins injected into the cell. Pathogens produce proteins that interfere with the host defenses, says Jones. In turn, the host has evolved proteins in an effort to negate the effect of pathogen interference, leading to a long-term molecular arms race. "You've got these layers of yin and yang between the host and the parasite," Jones notes. Some responses are conserved between plants and animals. To grow in any host, flora or fauna, bacteria must identify their environment and then switch on genes to encode the proteins required for replication under those conditions. A primary locus for Gram-negative bacteria is the HRP gene locus, which encodes the Type III machinery that secretes so-called effector proteins directly into the cell. Mary Beth Mudgett,2 assistant professor of biology at Stanford University, focuses on the molecular mechanisms used collectively by Type III effector proteins to suppress host defenses. Mudgett's work is in plants, but a class of Type III effector protein is conserved between the bacteria infecting both plants and animals. The animal-infecting bacteria produce YopJ, but plant-pathogen versions now have been discovered sharing a key, four-amino-acid catalytic site. YopJ and its counterpart operate by cutting a protein involved in the MAPK cascade, blocking the pathway as a result.3 HOMOLOGY IN THE CARDS Significant similarities exist between some plant and animal receptors involved in sensing pathogen surface proteins, Jones says. He cites the case of NB/LRR proteins in plants, which have similar functions and sequences to the CARD4 and CARD15 proteins in animals. These proteins recognize lipopolysaccharides found on the outer membranes of some bacteria, and transduce internal cellular responses.4 The molecular characterization of these proteins has revealed that in plants and animals, similar domains are used in pathogen recognition and response initiation. This has stimulated debate over whether these proteins evolved specifically for disease resistance or whether it is another case of innate immunity reaching into the common toolkit. Whatever the case, the overlap between CARD15 and NB/LRR has had felicitous implications for research into Crohn disease. A mutation in CARD15 increases susceptibility to Crohn, possibly by creating an inflammatory response to benign gut bacteria antigens.4 And the similarity with NB/LRR makes it possible to study gene mutants in plants. Dangl says that the genetics of resistance is easier to study in plants than in animals such as mice. "The plant guys are well ahead of the animal guys in terms of knowing what genes in the host are needed to transduce a signal perceived by these receptors, because it is easier to do experiments to isolate mutants," says Dangl. In other words, the genes involved in signaling the innate response to gut bacteria in humans can be studied to some extent in rapidly growing plants such as Arabidopsis. For this reason, plant work has now been well cited by Crohn disease researchers, according to Dangl. >P> And though there's nothing analogous to Crohn disease, plants can experience autoimmune disorders, such as the so-called paranoid plant syndrome. Paranoid plants include a collection of disease lesion-mimic mutants (Les) in maize that spontaneously form necrotic lesions usually seen in diseased plants. Also, Arabidopsis mutants for MAPK 4 are stunted and display systemic defenses, such as salicylic-acid production, even in the absence of a pathogen.5 Here, the mutation of a negative immune regulator confers resistance to a number of infections. "Defense pathways that are powerful need strong negative regulation, and autoimmune diseases can occur when this negative regulation does not work," says Jones. The existence of autoimmune disease in plants is interesting, but has no significance for human conditions such as arthritis, he says. But the overlap between plant and animal immunity may have potential significance for piecing together the innate system's finer pathways. Dangl concedes that the plant research community, of which he is a part, has been quick to exploit these connections to compete for funding generally destined for animal studies. "The animal guys ignored us," he says. Now they must take notice. Philip Hunter (phunter@phunter.com) is a freelance writer in London. References 1. M.R. Chandok et al., "The pathogen-inducible nitric oxide synthase (iNOS) in plants is a variant of the P protein of the glycine decarboxylase complex," Cell, 113:469-82, 2003. 2. R.A. Alegado et al., "Characterization of mediators of microbial virulence and innate immunity using the Caenorhabditis elegans host-pathogen model," Cell Microbiol, 5:435-44, 2003. 3. A. Hotson et al., "Xanthomonas type III effector XopD targets SUMO-conjugated proteins in plants," Mol Microbiol, 50:377-89, 2003. 4. J.P. Roberts, "An immunological role in the CARDs," The Scientist, 17[20]:29-30, Oct. 20, 2003. 5. M. Petersen et al., "Arabidopsis MAP kinase 4 negatively regulates systemic acquired resistance," Cell, 103:1111-20, 2000. |
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| Simple model organisms that are amenable to comprehensive experimental analysis can be used to elucidate the molecular genetic architecture of complex traits. They can thereby enhance our understanding of these traits in other organisms, including humans. Here, we describe the use of the nematode Caenorhabditis elegans as a tractable model system to study innate immunity. We detail our current understanding of the worm's immune system, which seems to be characterized by four main signaling cascades: a p38 mitogen-activated protein kinase, a transforming growth factor-beta-like, a programed cell death, and an insulin-like receptor pathway. Many details, especially regarding pathogen recognition and immune effectors, are only poorly characterized and clearly warrant further investigation. We additionally speculate on the evolution of the C. elegans immune system, taking into special consideration the relationship between immunity, stress responses and digestion, the diversification of the different parts of the immune system in response to multiple and/or coevolving pathogens, and the trade-off between immunity and host life history traits. Using C. elegans to address these different facets of host-pathogen interactions provides a fresh perspective on our understanding of the structure and complexity of innate immune systems in animals and plants. |