The genome sequence of Atlantic cod reveals a unique immune system

Atlantic cod (Gadus morhua) is a large, cold-adapted teleost that sustains long-standing commercial fisheries and incipient aquaculture. Here we present the genome sequence of Atlantic cod, showing evidence for complex thermal adaptations in its haemoglobin gene cluster and an unusual immune architecture compared to other sequenced vertebrates. The genome assembly was obtained exclusively by 454 sequencing of shotgun and paired-end libraries, and automated annotation identified 22,154 genes. The major histocompatibility complex (MHC)?II is a conserved feature of the adaptive immune system of jawed vertebrates, but we show that Atlantic cod has lost the genes for MHC?II, CD4 and invariant chain (Ii) that are essential for the function of this pathway. Nevertheless, Atlantic cod is not exceptionally susceptible to disease under natural conditions. We find a highly expanded number of MHC?I genes and a unique composition of its Toll-like receptor (TLR) families. This indicates how the Atlantic cod immune system has evolved compensatory mechanisms in both adaptive and innate immunity in the absence of MHC?II. These observations affect fundamental assumptions about the evolution of the adaptive immune system and its components in vertebrates.     

Protochordate amphioxus is an emerging model organism for comparative immunology

Protochordate amphioxus is an extant invertebrate regarded quite recently as a basal chordate. It has a vertebrate-like body plan including a circulation system with an organization similar to that of vertebrates. However, amphioxus is less complex than vertebrates for having a genome uncomplicated by extensive genomic duplication, and lacking lymphoid organs and free circulating blood cells. Recent studies on immunity have demonstrated the presence in amphioxus of both the constituent elements of key molecules involved in adaptive immunity such as proto-major histocompatibility complex (proto-MHC), V region-containing chitin-binding protein (VCBP) and V and C domain-bearing protein (VCP), and the complement system operating via the alternative and lectin pathways resembling those seen in vertebrates. In addition, the acute phase response profile in amphioxus has been shown to be similar to that observed in vertebrates. These findings together with the relative structural and genomic simplicity make amphioxus an ideal organism for gaining insights into the origin and evolution of the vertebrate immune system, especially adaptive immunity, and the composition and mechanisms of the vertebrate innate immunity.     

Licensing of natural killer cells by host major histocompatibility complex class I molecules

Self versus non-self discrimination is a central theme in biology from plants to vertebrates, and is particularly relevant for lymphocytes that express receptors capable of recognizing self-tissues and foreign invaders. Comprising the third largest lymphocyte population, natural killer (NK) cells recognize and kill cellular targets and produce pro-inflammatory cytokines. These potentially self-destructive effector functions can be controlled by inhibitory receptors for the polymorphic major histocompatibility complex (MHC) class I molecules that are ubiquitously expressed on target cells. However, inhibitory receptors are not uniformly expressed on NK cells, and are germline-encoded by a set of polymorphic genes that segregate independently from MHC genes. Therefore, how NK-cell self-tolerance arises in vivo is poorly understood. Here we demonstrate that NK cells acquire functional competence through 'licensing' by self-MHC molecules. Licensing involves a positive role for MHC-specific inhibitory receptors and requires the cytoplasmic inhibitory motif originally identified in effector responses. This process results in two types of self-tolerant NK cells--licensed or unlicensed--and may provide new insights for exploiting NK cells in immunotherapy. This self-tolerance mechanism may be more broadly applicable within the vertebrate immune system because related germline-encoded inhibitory receptors are widely expressed on other immune cells.     

A trans-acting class II regulatory gene unlinked to the MHC controls expression of HLA class II genes

Class II (or Ia) antigens are highly polymorphic surface molecules which are essential for the cellular interactions involved in the immune response. In man, these antigens are encoded by a complex multigene family which is located in the major histocompatibility complex (MHC) and which comprises up to 12 distinct alpha- and beta-chain genes, coding for the HLA-DR, -DQ and -DP antigens. One form of congenital severe combined immunodeficiency (SCID) in man, which is generally lethal, is characterized by an absence of HLA-DR histocompatibility antigens on peripheral blood lymphocytes (HLA class II-deficient SCID). In these patients, as reported here, we have observed an absence of messenger RNA for the alpha- and beta-chains of HLA-DR, -DQ and -DP, indicating a global defect in the expression of all class II genes. Moreover, the lack of expression of HLA class II mRNAs could not be corrected by gamma-interferon, an inducer of class II gene expression in normal cells. Family studies have established that the genetic defect does not segregate with the MHC. We conclude, therefore, that the expression of the entire family of class II genes is normally controlled by a trans-acting class II regulatory gene which is unlinked to the MHC and which is affected in the patients. This gene controls a function or a product necessary for the action of gamma-interferon on class II genes.     

Germ-line transmission of a disrupted beta 2-microglobulin gene produced by homologous recombination in embryonic stem cells

Major histocompatibility complex (MHC) class I molecules are integral membrane proteins present on virtually all vertebrate cells and consist of a heterodimer between the highly polymorphic alpha-chain and the beta 2-microglobulin (beta 2-m) protein of relative molecular mass 12,000 (ref. 1). These cell-surface molecules play a pivotal part in the recognition of antigens, the cytotoxic response of T cells, and the induction of self tolerance. It is possible, however, that the function of MHC class I molecules is not restricted to the immune system, but extends to a wide variety of biological reactions including cell-cell interactions. For example, MHC class I molecules seem to be associated with various cell-surface proteins, including the receptors for insulin, epidermal growth factor, luteinizing hormone and the beta-adrenergic receptor. In mice, class I molecules are secreted in the urine and act as highly specific olfactory cues which influence mating preference. The beta 2-m protein has also been identified as the smaller component of the Fc receptor in neonatal intestinal cells, and it has been suggested that the protein induces collagenase in fibroblasts. Cells lacking beta 2-m are deficient in the expression of MHC class I molecules, indicating that the association with beta 2-m is crucial for the transport of MHC class I molecules to the cell surface. The most direct means of unravelling the many biological functions of beta 2-m is to create a mutant mouse with a defective beta 2-m gene. We have now used the technique of homologous recombination to disrupt the beta 2-m gene. We report here that introduction of a targeting vector into embryonic stem cells resulted in beta 2-m gene disruption with high frequency. Chimaeric mice derived from blastocysts injected with mutant embryonic stem cell clones transmit the mutant allele to their offspring.     

H-2-linked low-molecular weight polypeptide antigens assemble into an unusual macromolecular complex

The major histocompatibility complex (MHC) is a cluster of tightly linked genes whose products are of central importance in the functioning of the immune system. Class I and II MHC antigens are integral membrane proteins which regulate cell-surface interactions between T cells and their targets, while class III antigens are components of the complement system of serum proteins. All available evidence indicates that the structure and function of the MHC and its gene products are highly conserved among species (for review, see ref.5). We recently reported the existence in murine cells of a fourth class of MHC-linked polypeptides which are biochemically and genetically distinct from previously identified MHC gene products: BALB.B anti-BALB/c (anti-H-2d) antiserum immunoprecipitates a set of 16 cytoplasmic low-molecular weight polypeptides (LMP) from BALB/c spleen cells and from the WEHI-3 cell line. The production of these peptides is coordinately regulated (by immune interferon) with the production of the class I and II MHC antigens, suggesting that they too are functionally relevant to the immune system. We demonstrate here that these 16 polypeptides are associated with one another in vivo as a very large (580,000-molecular weight, Mr) noncovalent complex. The unusual nature of this complex has allowed the non-immunochemical identification of similar complexes from (serologically negative) H-2b murine cells and from a human cell line. Thus, LMP antigens display two properties in common with other MHC antigens: they are both polymorphic and genetically conserved across species.     

MHC class II region encoding proteins related to the multidrug resistance family of transmembrane transporters

The T-cell immune response is directed against antigenic peptide fragments generated in intracellular compartments, the cytosol or the endocytic system. Peptides derived from cytosolic proteins, usually of biosynthetic origin, are presented efficiently to T-cell receptors by major histocompatibility complex (MHC) class I molecules, with which they assemble, probably in the endoplasmic reticulum (ER). In the absence of recognizable N-terminal signal sequences, such cytosolic peptides must be translocated across the ER membrane by a novel mechanism. Genes apparently involved in the normal assembly and transport of class I molecules may themselves be encoded in the MHC. Here we show that one of these, the rat cim gene, maps to a highly polymorphic part of the MHC class II region encoding two novel members of the family of transmembrane transporters related to multidrug resistance. Other members of this family of transporter proteins are known to be capable of transporting proteins and peptides across membranes independently of the classical secretory pathway. Such molecules are credible candidates for peptide pumps that move fragments of antigenic proteins from the cytosol into the ER.     

HBK - SPF 鸭 MHC I 区域微卫星标记分析

摘要: 禽主要组织相容性复合体是一组紧密连锁高度多态的基因群,与免疫反应或敏感性密切相关,鸭 MHC I 区域全长 36. 8 kb,由 TAP1、TAP2 和 5 个 MHC I 拷贝基因( UAA-UEA) 组成。HBK-SPF 鸭是中国农业科学院哈尔滨兽医研究所培育的无特定病原体种鸭,分为 B 和 Q 2 个品系,已封闭繁育了 7 个世代。本文在鸭 MHC I 区域筛选了 4个微卫星位点,通过单链构象多态性分析和聚合酶链式反应直接测序,发现 A 位点具有多态性,为( GT) n 的重复结构,第 6 代 HBK-B 和 HBK-Q 的31 个个体和第 7 代 的140 个个体进行聚合酶链式反应,结果直接测序,在重复结构之前的 108bp 中,发现了 4 种纯合单倍型和 6 种杂合单倍型; B 位点未得到目的产物; C 位点位于 MHC I 拷贝基因UDA 和 UEA 之间,扩增结果与 UAA 和 UBA 之间序列高度同源,无法判断基因型; D 位点表现为单态,为( ATA) 15的固定重复结构。本研究为进一步研究鸭 MHC I 基因结构和建立家系提供了依据。     

A potential donor gene for the bm1 gene conversion event in the C57BL mouse

The mammalian major histocompatibility complex (MHC; H-2 complex in mouse) is a large multigene complex which encodes cell-surface antigens involved in the cellular immune response to foreign antigens. Class I polypeptides expressed at the H-2K and H-2D loci of numerous mouse strains exhibit an unusually high degree of genetic polymorphism, which is assumed to be related to their function as primary recognition elements in the immune response. We suggested that this H-2 polymorphism may arise by gene conversion-like events between non-allelic class I genes. This is supported by our recent comparison of the DNA sequences of the normal H-2Kb gene sequence, from the C57BL/10 mouse, and a mutant form of this gene called H-2Kbm1: the mutant allele differs from the H-2Kb gene in seven bases out of a region of 13 bases in exon 3 of the class I gene (which encodes alpha 2 (C1) the second highly polymorphic protein domain), suggesting that this region of new sequence had been introduced into the H-2Kb sequence following unequal pairing of two class I genes in the genome of the C57BL mouse. Schulze et al. have obtained similar results. Here we report work identifying a potential donor gene in our library of 26 class I genes cloned from the C57BL/10 mouse.     

Immune recognition of a human renal cancer antigen through post-translational protein splicing

Cytotoxic T lymphocytes (CTLs) detect and destroy cells displaying class I molecules of the major histocompatibility complex (MHC) that present oligopeptides derived from aberrant self or foreign proteins. Most class I peptide ligands are created from proteins that are degraded by proteasomes and transported, by the transporter associated with antigen processing, from the cytosol into the endoplasmic reticulum, where peptides bind MHC class I molecules and are conveyed to the cell surface. C2 CTLs, cloned from human CTLs infiltrating a renal cell carcinoma, kill cancer cells overexpressing fibroblast growth factor-5 (FGF-5). Here we show that C2 cells recognize human leukocyte antigen-A3 MHC class I molecules presenting a nine-residue FGF-5 peptide generated by protein splicing. This process, previously described strictly in plants and unicellular organisms, entails post-translational excision of a polypeptide segment followed by ligation of the newly liberated carboxy-terminal and amino-terminal residues. The occurrence of protein splicing in vertebrates has important implications for the complexity of the vertebrate proteome and for the immune recognition of self and foreign peptides.     

Somatic diversification of variable lymphocyte receptors in the agnathan sea lamprey

Although jawless vertebrates are apparently capable of adaptive immune responses, they have not been found to possess the recombinatorial antigen receptors shared by all jawed vertebrates. Our search for the phylogenetic roots of adaptive immunity in the lamprey has instead identified a new type of variable lymphocyte receptors (VLRs) composed of highly diverse leucine-rich repeats (LRR) sandwiched between amino- and carboxy-terminal LRRs. An invariant stalk region tethers the VLRs to the cell surface by means of a glycosyl-phosphatidyl-inositol anchor. To generate rearranged VLR genes of the diversity necessary for an anticipatory immune system, the single lamprey VLR locus contains a large bank of diverse LRR cassettes, available for insertion into an incomplete germline VLR gene. Individual lymphocytes express a uniquely rearranged VLR gene in monoallelic fashion. Different evolutionary strategies were thus used to generate highly diverse lymphocyte receptors through rearrangement of LRR modules in agnathans (jawless fish) and of immunoglobulin gene segments in gnathostomes (jawed vertebrates).     

Self-recognition promotes the foreign antigen sensitivity of naive T lymphocytes

Major histocompatibility complex (MHC) class I and II molecules are highly polymorphic proteins that bind and present foreign peptides to the clonally distributed alphabeta receptors (TCR) of T lymphocytes. As a population, the immature T lymphocytes generated in the thymus express a very diverse set of TCR specificities. A process of positive selection filters this broad repertoire to optimize peripheral T cells for antigen recognition in the context of available MHC products. Only those precursor T cells whose TCRs generate an adequate but not excessive signalling response to self-peptides bound to the expressed MHC proteins undergo successful maturation. Here we show that post-thymic self-recognition facilitates the antigen reactivity of mature T cells. Both experimental and physiological interruption of T-cell contact with self-peptide MHC ligands leads to a rapid decline in signalling and response sensitivity to foreign stimuli. Because the adaptive immune system must be recruited early in an infectious process when antigen is limiting, these findings suggest that positive selection ensures predictable T-cell recognition of available self-ligands, which in turn promotes efficient responses to pathogens.     

The origin of MHC class II gene polymorphism within the genus Mus

The I region of the major histocompatibility complex (MHC) of the mouse (H-2) contains a tightly-linked cluster of highly polymorphic genes (class II MHC genes) which control immune responsiveness. Speculation on the origin of this polymorphism, which is believed to be essential for the function of the class II proteins in immune responses to disease, has given rise to two hypotheses. The first is that hypermutational mechanisms (gene conversion or segmental exchange) promote the rapid generation of diversity in MHC genes. The alternative is that polymorphism has arisen from the steady accumulation of mutations over long evolutionary periods, and multiple specific alleles have survived speciation (trans-species evolution). We have looked for evidence of 'segmental exchange' and/or 'trans-species evolution' in the class II genes of the genus Mus by molecular genetic analysis of I-A beta alleles. The results indicate that greater than 90% (28 out of 31) of the alleles examined can be organized into two evolutionary groups both on the basis of restriction site polymorphisms and by the presence or absence of a short interspersed nucleotide element (SINE). Using this SINE sequence as an evolutionary tag, we demonstrate that I-A beta alleles in these two evolutionary groups diverged at least three million years ago and have survived the speciation events leading to several modern Mus species. Nucleotide sequence comparisons of eight Mus m. domesticus I-A beta alleles representing all three evolutionary groups indicate that most of the divergence in exon sequences is due to the steady accumulation of mutations that are maintained independently in the different alleles. But segmental exchanges between alleles from different evolutionary groups have also played a role in the diversification of beta 1 exons.     

Progress in crystallization of major histocompatibility complex class I in vertebrates

The major histocompatibility complex(MHC)of proteins that exists in all vertebrates is encoded by a cluster of genes associated with the immune response and related functions.MHC is divided into MHC I,II,and III;MHC I is involved in antigenic presentation,binding T cell receptors,and leading ultimately to specific cellular immune responses.The complicated functions of MHC I are determined by the nature of the complex.The crystal structure of MHC I has been solved for many animals,revealing the relationship between spatial structure and function.MHC I consists of an a heavy chain and a b2m light chain,both ligated non-covalently to a complex when a peptide is bound to the antigenic-binding groove.The a heavy chain is divided into an extracellular domain,a transmembrane domain,and an intracellular domain.The extracellular domain consists of sub-regions a1,a2,and a3.The a1 and a2 together form the antigenic-binding groove and bind antigenic peptides with 8–10 amino acid residues.MHC I can form a stable spatial structure;however,it should be noted that there are differences in the structure of MHC I among animal species,including anchored amino acids in binding peptides,binding sites,molecular distance,crystallization conditions,etc.Here,progress in determination of the crystal structure of human,mouse,chicken,non-human primate,and swine MHC I is described in detail.     

Organization and evolution of the class I gene family in the major histocompatibility complex of the C57BL/10 mouse

The major histocompatibility complex (MHC) encodes several classes of protein vital to the regulation of the immune response. We have isolated 26 class I genes that map to this region in the C57BL/10 mouse and linked these into three gene clusters. The number of genes differs from the number found in the BALB/c strain and comparison of the organization of the class I genes in these two strains shows conserved regions and polymorphic regions which probably result from deletions, insertions and translocations within the MHC.     

Evolution of the MHC class I genes of a New World primate from ancestral homologues of human non-classical genes

The products of the classical human major histocompatibility complex (MHC) class I genes (HLA-A, -B, -C) are highly polymorphic molecules that bind peptides and present them to T lymphocytes. The non-polymorphic, non-classical MHC class I gene products (HLA-E, -F, -G) are not restricting elements for the majority of T lymphocytes. The evolutionary relationship of the non-classical and classical MHC class I genes is unclear. Here we present the cloning and sequencing of the MHC class I genes of a New World primate, the cotton-top tamarin (Saguinus oedipus). The expressed MHC class I genes of this species are more closely related to the human non-classical HLA-G gene than they are to genes of the human classical HLA-A, -B, and -C loci. These observations imply that classical and non-classical genes do not necessarily constitute mutually exclusive groups over evolutionary time.     

Structural polymorphism of human DR antigens

DR ANTIGENS are polymorphic cell surface molecules whose expression is controlled by a locus closely linked or identical to the D locus of the major histocompatibility complex (MHC) of man (for reviews see refs 1, 2). They are functionally and structurally homologous to the murine la antigens determined by the I-E subregion of the MHC, a region which has been implicated in the genetic control of immune responses(3,4). Both sets of antigens are mainly expressed on cells associated with immune function (for reviews see refs 1, 2, 5), and are involved in mediating T-cell, B-cell and macrophage interactions required for the generation of immune responses(6-9). In addition, both consist of two non-covalently associated polypeptides, designated alpha and beta, with molecular weights of 34,000 and 28,000, respectively(10). The association of some DR antigens with increased susceptibility to certain diseases (for review see ref. 1) and the genetic restrictions imposed on cellular interactions by the HLA-D region(9,11) may represent the effects of structural variability among DR antigens. The aim of the studies reported here was to examine the nature and degree of structural variation among DR antigens isolated from cultured lymphoid B cells with different DR phenotypes. Such information may provide an understanding of the molecular mechanisms by which DR antigens mediate their function.