Evolution of immunoglobulin heavy chain variable region genes: a VH family can last for 150-200 million years or longer

The Quest for Antibodies and Other Acquired Immune Receptors: A Historical Perspective

The diversity of antibody molecules has for decades been an unsolved enigma that has attracted wide interest among biologists. Parallel to the accumulation of experimental evidence, progress in antibody research was also driven by the theoretical debate that played a particularly prominent role, at least until the entry of molecular biology into this field of investigation. Several publications have examined this topic from a historical perspective. In this article, we aim to examine the history of research into the mechanisms underlying antibody diversity from a partly new standpoint. In jawed vertebrates (gnathostomes), progressively more distant on the evolutionary scale from humans and mice-in non-model mammals, birds, amphibians, bony and cartilaginous fish-certain mechanisms for the diversity of acquired immunity receptors (B-cell receptors [BCR]/immunoglobulins [Ig] and T-cell receptors [TCR]) have been described that are quite unexpected on the basis of what has emerged from biomedical immunology studies. What is more, in Agnatha vertebrates, in several invertebrate phyla and even in bacteria, forms of adaptive immunity have been discovered, based on the ability to finely tune the host defence response to the infectious threats. These defence systems show some similarities with the acquired immunity of jawed vertebrates, although they are based on mechanisms and receptors totally different from BCR/Ig and TCR. Therefore, our aim is to investigate how the theoretical debate on antibody diversity, which developed in the 20th century, partly anticipated some of the central themes in the current research on adaptive immunity systems discovered in the previously mentioned non-model systems. With this aim, we have reformulated, in the language of modern biology, some of the hypotheses advanced in the first decades of antibody diversity research.

Mystifying Molecular Structure, Expression and Repertoire Diversity of IgM Heavy Chain Genes (Ighμ) in Clarias Catfish and Hybrids: Two Novel Transcripts in Vertebrates

Two novel immunoglobulin heavy chain (Ighμ) transcripts encoding membrane-bound forms of IgM (mIgM) were discovered in bighead catfish, Clarias macrocephalus. The first transcript contains four constant and two transmembrane domains [Cμ1-Cμ2-Cμ3-Cμ4-TM1-TM2] that have never been reported in teleosts, and the second transcript is an unusual mIgM that has never been identified in any vertebrate [Cμ1-(Cδ2-Cδ3-Cδ4-Cδ5)-Cμ2-Cμ3-TM1-TM2]. Fluorescence in situ hybridization (FISH) in bighead catfish, North African catfish (C. gariepinus) and hybrid catfish revealed a single copy of Ighμ in individual parent catfish, while two gene copies were found in diploid hybrid catfish. Intensive sequence analysis demonstrated multiple distinct structural variabilities in the VH domain in Clarias, and hybrid catfish were defined and used to generate diversity with various mechanisms. Expression analysis of Ighμ in Aeromonas hydrophila infection of the head kidney, peripheral blood leukocytes and spleen revealed significantly higher levels in North African catfish and hybrid catfish than in bighead catfish.

Genome complexity in the coelacanth is reflected in its adaptive immune system

We have analyzed the available genome and transcriptome resources from the coelacanth in order to characterize genes involved in adaptive immunity. Two highly distinctive IgW-encoding loci have been identified that exhibit a unique genomic organization, including a multiplicity of tandemly repeated constant region exons. The overall organization of the IgW loci precludes typical heavy chain class switching. A locus encoding IgM could not be identified either computationally or by using several different experimental strategies. Four distinct sets of genes encoding Ig light chains were identified. This includes a variant sigma-type Ig light chain previously identified only in cartilaginous fishes and which is now provisionally denoted sigma-2. Genes encoding α/β and γ/δ T-cell receptors, and CD3, CD4, and CD8 co-receptors also were characterized. Ig heavy chain variable region genes and TCR components are interspersed within the TCR α/δ locus; this organization previously was reported only in tetrapods and raises questions regarding evolution and functional cooption of genes encoding variable regions. The composition, organization and syntenic conservation of the major histocompatibility complex locus have been characterized. We also identified large numbers of genes encoding cytokines and their receptors, and other genes associated with adaptive immunity. In terms of sequence identity and organization, the adaptive immune genes of the coelacanth more closely resemble orthologous genes in tetrapods than those in teleost fishes, consistent with current phylogenomic interpretations. Overall, the work reported described herein highlights the complexity inherent in the coelacanth genome and provides a rich catalog of immune genes for future investigations.

The whole-organism heavy chain B cell repertoire from Zebrafish self-organizes into distinct network features

BACKGROUND

The adaptive immune system is based on selected populations of molecularly distinct individual B and T cell clones. However, it has not been possible to characterize these clones in a comprehensive and informatics manner to date; attempts have been limited by the number of cells in the adaptive immune system and an inability to quantify them. Recently, using the Zebrafish (ZF) Danio rerio as a model organism and parallel sequencing as the quantifying technology, Weinstein et al. overcame this major hurdle and quantified the entire heavy chain B-cell repertoire in ZF. Here, we present a novel network analysis of the data from the Weinstein group, providing new insights into the network structure of the B-cell repertoire.

RESULTS

Using a collection of computational methods, the IgM sequences from 14 fish were analyzed. This analysis demonstrated that the B-cell repertoire of the ZF is structured along similar lines to those previously detected in limited parts of the human B-cell immune system. The analysis confirms the validity of the global data and the evolutionary placement of the ZF based on known sequence motifs. Recombination events in the repertoire were quantified, and demonstrated a lack of shared recombined V, J groups across fish. Nevertheless, it was demonstrated that a similar network architecture is shared among fish. However, the network analysis identified two distinct populations within the group; these findings are compatible with the occurrence of an immune response in a subset of the fish. The emerging connectivity network was demonstrated and quantified, and mutation drifts within the groups were characterized. Dissection of sequence data revealed common network features of the B-cell repertoire as well as individual differences.

CONCLUSION

The ZF B-cell repertoire reveals an underlying order that is compatible with self-organization representing every portion of the sequence-based network. This pattern varies in individual specimens, perhaps as a response to an immune challenge. However, a sequence-non-specific network that maintains a common architecture of sequence diversity was detected.The common feature among different individuals can be captured by the network architecture and characteristics, rather than specific clones. We believe that further study of the dynamics of this network could provide insight into modes of operation of the immune system.

Two new Ig VH gene families in Oncorhynchus mykiss

Genes encoding the immunoglobulin heavy-chain variable region (Ig VH) in rainbow trout (Oncorhynchus mykiss) have been grouped into 11 families. While obtaining a baseline assessment of the various gene families utilized by trout in the production of secreted antibody, we discovered two new families. These proposed Ig VH families, Families XII and XIII, were rarely observed; only two VH sequence types were detected for each new family, suggesting that they may not be commonly used in response to antigens, or that the captive environment may not lead to typical exposures seen in the wild. Additionally, unlike preceding studies, we found at least one representative gene sequence for each of the 11 reported Ig VH gene families, possibly indicating that the repertoire of trout Ig VH gene families may be more universal among different stocks than previously realized.

Characterization of serum immunoglobulin M of grouper and cDNA cloning of its heavy chain

Immunoglobulin M (IgM) from the whole serum of grouper fish, Epinephelus coioides was purified by affinity chromatography using protein A-Sepharose column. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) under reducing conditions revealed that the relative molecular masses (Mr) of the equimolar heavy and light chains of IgM were 78,000 and 27,000, respectively. The cDNAs encoding IgM heavy chain comprising its variable (VH) and constant (CH) regions have been cloned and sequenced from a grouper kidney cDNA library by antibody screening method. Five VH (130-142 amino acids) and four CH (450-454 amino acids) families were identified. The variable and constant regions were conserved with their putative domains. All the four constant region domains (CH1-CH2-CH3-CH4) contained each three conserved cysteine residues, which are considered to form the inter- and intra-chain disulfide bridges. There were three carbohydrate acceptor sites in the constant region. In general, the pattern of IgM gene organization seems to resemble that of other teleosts. Moreover, the CH genes in grouper IgM occur as multifamily as reported in Atlantic salmon and common carp.

Antibody repertoire development in teleosts--a review with emphasis on salmonids and Gadus morhua L

The group of teleosts is highly diverse, comprising more than 23000 extant species. Studies of the teleost antibody repertoire have been conducted in many different species within different orders, though some species and families have been better characterised than others. The Atlantic cod (Gadus morhua L.) and several species within the Salmoninae (e.g. Salmo salar and Oncorynchus mykiss) are among the best-studied teleosts in terms of the antibody repertoire. The estimated size of the repertoire, the organisation of immunoglobulin (IG) gene segments, the expressed IG repertoire, the IgM serum concentration, and the serum antibody responses reveal some fundamental differences between these species. The serum IgM concentration of G. morhua is some ten times higher than that of S. salar, though G. morhua is characterised as a 'low' (or 'non') responder in terms of specific antibody production. In contrast, an antibody response is readily induced in S. salar, although the response is strongly regulated by antigen induced suppression. The IGHD gene of G. morhua has a unique structure, while the IGHM and IGHD genes of S. salar have a characteristic genomic organisation in two parallel loci. In addition, salmonids, express a broad repertoire of IGH and IGI V-region gene segments, while a single V gene family dominates the expressed heavy and light chain repertoire of G. morhua. Little is known about the developing antibody repertoire during ontogeny, in different stages of B-cell maturation, or in separate B-cell subsets. Information on the establishment of the preimmune repertoire, and the possible role of environmental antigens is also sparse.

Substitution patterns in alleles of immunoglobulin V genes in humans and mice

Immunoglobulins (Igs) constitute a subfamily of rapidly evolving proteins. It is postulated that this characteristic is due mainly to the participation of these proteins in highly diverse functions of recognition and defense. Although this vision of rapid evolution in Igs is widely accepted, various studies have demonstrated that diverse and contradictory forces not yet completely understood converge in the evolution of these receptors. In a recent study of the substitution patterns in the alleles that form the human IGHV locus, we found that the variation in genetic and structural information does not occur homogeneously among the different genes, nor among the regions and positions conforming said locus. In view of these results and of the importance of a better understanding of the basic evolutionary process in specific receptors (such as Igs) for both immunology and molecular evolution, it is important to explore the nature of the diversification process in these proteins in detail. In this work, therefore, we analyzed the substitution patterns in all the alleles reported for loci IGKV and IGLV in humans and mice, and we compared the results with those previously observed in the human IGHV locus. We found that the process of evolutionary variation of the Igs reflect the diversity of selective pressures operating on the different loci, genes, sub-regions and positions; for example, diversification through substitution is generally centered on CDRs, but only few positions inside the CDRs were frequently substituted. In spite of this general tendency, it is possible to observe differences in the degree of diversification among loci, families and genes. These tendencies to modify only certain attributes of IGV genes seem to be in agreement with differential strategies associated with the restrictions of the molecular immune recognition mechanism. The complexity of the evolutionary patterns observed in this study leads us to think that the predispositions observed herein may also be due in part to processes of DNA dynamics.

A Highly Conserved Interspecies V H in the Human Genome

Idiotype conservation between human and mouse antibodies has been observed in association with various infectious and autoimmune diseases. We have isolated a human anti-idiotypic antibody to a mouse monoclonal anti-IgE antibody (BSW17) suggesting a conserved interspecies idiotype associated with an anti-IgE response. To find the homologue of BSW17 in the human genome we applied the guided selection strategy. Combining V(H) of BSW17 with a human V(L) repertoire resulted in three light chains. The three V(L) chains were then combined with a human V(H) repertoire resulting in three clones specific for human IgE. Surprisingly, one clone, Hu41, had the same epitope specificity and functional in vitro activity as BSW17 and V(H) complementarity-determining regions identical with that of BSW17. Real-time PCR analysis confirmed the presence of the Hu41 V(H) sequence in the human genome. These data document the first example of the isolation of a human antibody where high sequence similarity to the original murine V(H) sequence is associated with common antigen and epitope specificity.

Limited diversity of the immunoglobulin heavy chain variable domain of the emerald rockcod Trematomus bernacchii

To investigate the diversity of the immunoglobulin heavy chain variable domain of the cold adapted teleost Trematomus bernacchii, 45 cDNA clones, containing complete or partial sequences of rearranged VH/D/JH segments, were analysed. Clones were isolated from a spleen library constructed by 5' RACE or from an expression library previously constructed and immunoscreened with rabbit anti- T. bernacchii Ig heavy chain antibodies. VH sequences shared, on average, 79.9% nucleotide identity and defined only two gene families referred to as Trbe VH I and Trbe VH II, the latter comprising 89% of the VH sequences analysed in this study. A Southern blot analysis, performed with family specific probes, revealed that there are at least 25 genomic VH genes. A phylogenetic tree showed that Trbe VH I clustered with VH genes belonging to group D and Trbe VH II with those of group C. Four putative distinct D segments were found to contribute to the diversity of CDR3, which showed a high glycine content. The Shannon analysis revealed that FRs are very highly conserved. Of CDRs, CDR2 exhibits a mean entropy value higher than CDR1, contributing to variability in a significant manner. Moreover, eight distinct JH segments were identified. These findings provide several clues suggesting a limited diversity of the VH genes in the Antarctic teleost T. bernacchii.

Status and opportunities for genomics research with rainbow trout

The rainbow trout (Oncorhynchus mykiss) is one of the most widely studied of model fish species. Extensive basic biological information has been collected for this species, which because of their large size relative to other model fish species are particularly suitable for studies requiring ample quantities of specific cells and tissue types. Rainbow trout have been widely utilized for research in carcinogenesis, toxicology, comparative immunology, disease ecology, physiology and nutrition. They are distinctive in having evolved from a relatively recent tetraploid event, resulting in a high incidence of duplicated genes. Natural populations are available and have been well characterized for chromosomal, protein, molecular and quantitative genetic variation. Their ease of culture, and experimental and aquacultural significance has led to the development of clonal lines and the widespread application of transgenic technology to this species. Numerous microsatellites have been isolated and two relatively detailed genetic maps have been developed. Extensive sequencing of expressed sequence tags has begun and four BAC libraries have been developed. The development and analysis of additional genomic sequence data will provide distinctive opportunities to address problems in areas such as evolution of the immune system and duplicate genes.

A model B-cell superantigen and the immunobiology of B lymphocytes

Recent reports have shown that protein A of Staphylococcus aureus (SpA) is a specific toxin for B cells by virtue of specific binding interactions with conserved sites on the V(H) region of the B-cell antigen receptor. The structural basis for these Fab-binding interactions has recently been revealed in crystallographic analyses, which have demonstrated many similarities with the interactions of T-cell superantigens. Investigations of the in vivo response to SpA have illustrated how a B-cell superantigen can be used to provide a window for examining fundamental principles that underlie the immunobiology of B lymphocytes.

Diversity of the immunoglobulin heavy chain in the Atlantic salmon (Salmo salar L.) is contributed by genes from two parallel IgH isoloci

Immunoglobulin heavy chain (IgH) variable (V) region cDNAs from the Atlantic salmon, Salmo salar L., have been isolated and analysed with respect to diversity and transcription of the two parallel IgH isoloci in this species. A total of nine V(H) families were defined according to the 80% identity criterion, of which seven were highly related (>80% identity) to the V(H) families defined in rainbow trout and arctic charr. The variability of the CDR1 and 2 was low, although mutational hot-spot consensus sequences were accumulated in these regions. The CDR3 showed largest variability, expressing at least eight different groups of D motifs diversified by fusion of the D motifs, possible N and P nucleotide insertions and exonuclease activity. Presumably functional transcripts expressing D motifs in all three reading frames were identified for two of the motifs. The cDNAs were mapped to either of the two parallel loci, and sequence analysis revealed that the repertoire of V(H) segments was contributed by transcription of genes from both of the IgH isoloci. Transcription of genes from both isoloci generated no obvious effects on variability in the CDR3 of the Atlantic salmon IgH chains, although one additional J(H)-segment with altered N-terminal was generated by the process of duplication and divergence. Thus, the issue of biological significance of the two IgH isoloci remains unclear.

Characterization of superantigen-induced clonal deletion with a novel clan III-restricted avian monoclonal antibody: exploiting evolutionary distance to create antibodies specific for a conserved VH region surface

Evolution of the Ab system has yielded three clans of VH region genes that are represented in almost every known higher species with an adaptive immune system. These clans are defined by sequence homologies primarily in highly conserved framework (FR) subdomains, which serve a scaffolding function maintaining the conformation of loops responsible for Ag binding. Structural analyses indicate that the VH FR1 and FR3 form a conserved composite exposed surface, which has been implicated in interactions with B cell superantigens. To directly investigate the expression of clan-defined supraclonal sets, we exploited the evolutionary distance of the chicken immune system and the selection power of phage display, to derive Abs diagnostic for clan III Ig. Using a specially tailored immunization and selection strategy, we created recombinant avian single chain Fv Abs specific for the clan III products, including those from the human VH3 family, and the analogous murine 7183, S107, J606, X24, and DNA4 families, and binding was competitive with natural B cell superantigens. The archetype, LJ-26, was demonstrated to recognize a clan-specific surface expressed in diverse mammalian, and also the Xenopus and chicken, immune systems. In flow-cytometric studies with LJ-26, we found that treatment of heterozygous T15i transgenic mice with a model B cell superantigen induced a clan III-restricted clonal deletion. These studies demonstrate the utility of a novel recombinant serologic reagent to study the composition of the B cell compartment and also the consequences of B cell superantigen exposure.

Organization of human and mouse skeletal myosin heavy chain gene clusters is highly conserved

Myosin heavy chains (MyHCs) are highly conserved ubiquitous actin-based motor proteins that drive a wide range of motile processes in eukaryotic cells. MyHC isoforms expressed in skeletal muscles are encoded by a multigene family that is clustered on syntenic regions of human and mouse chromosomes 17 and 11, respectively. In an effort to gain a better understanding of the genomic organization of the skeletal MyHC genes and its effects on the regulation, function, and molecular genetics of this multigene family, we have constructed high-resolution physical maps of both human and mouse loci using PCR-based marker content mapping of P1-artificial chromosome clones. Genes encoding six MyHC isoforms have been mapped with respect to their linear order and transcriptional orientations within a 350-kb region in both human and mouse. These maps reveal that the order, transcriptional orientation, and relative intergenic distances of these genes are remarkably conserved between these species. Unlike many clustered gene families, this order does not reflect the known temporal expression patterns of these genes. However, the conservation of gene organization since the estimated divergence of these species (approximately 75-110 million years ago) suggests that the physical organization of these genes may be significant for their regulation and function.

Antibodies of sharks: revolution and evolution

The combinatorial immune response is restricted to jawed vertebrates with cartilaginous fishes being the lowest extant species to have the mechanism for diversification and an extensive panoply of immunoglobulins, T-cell receptors and MHC products. Here, we review the molecular events of the "big bang" or rapid evolutionary appearance of the functionally complete combinatorial immune system coincident with the appearance of ancestral jawed vertebrates, suggesting that this event was catalyzed by horizontal transfer of DNA processing systems. We analyze the nature and extent of variable and constant domain diversity among the distinct immunoglobulin sets of carcharhine sharks focusing upon the lambda-like light chains and the mu and omega heavy chains. The detection and isolation of natural antibodies from the blood of unimmunized sharks illustrates a surprising range of recognition specificities and the existence of polyspecificity suggests that the antibody-forming system of sharks offers unique opportunities for studies of immunological regulation. Although the homologies between shark and mammalian immunoglobulins are unequivocal, major differences in segmental gene organization present challenges to our understanding of basic immunological phenomena such as clonal restriction.

What brought the adaptive immune system to vertebrates?--The jaw hypothesis and the seahorse

A hypothesis is discussed that the adaptive immune system of vertebrates evolved in the gastrointestinal regions of primitive jawed fish (placoderms) due to increased localized injuries and infections which were inadvertently brought about by the novel jaw structures and the predatory life style. The question whether the modern jawless fish, cyclostomes, have adaptive immunity or not is briefly but critically reviewed. The discovery that the gut-associated immune tissues in mammals constitute the primary immune tissues for the local T cells and that some epithelial gamma delta T cells have a unique propensity is summarized and discussed in relation to the jaw hypothesis. Initial study of the seahorse (Hippocampus) indicates that the gut-associated immune tissues may be absent in this teleost species, suggesting an evolutionary link between the adaptive immune system and the jaw structure or eating habit.

The humoral response to xenografts is controlled by a restricted repertoire of immunoglobulin VH genes

BACKGROUND

The early phases of the host immune response to xenografts are dominated by anti-donor antibodies. The immunological pathways responsible for mediating the host humoral responses to xenografts are largely unknown, and this report addresses the nature of the immunoglobulin genes controlling the host antibody response to xenografts.

METHODS

cDNA libraries established from rat anti-hamster monoclonal antibodies and splenic lymphocytes from LEW rats rejecting hamster heart xenografts were used to clone, sequence, and identify the immunoglobulin genes responsible for encoding rat xenoantibodies to hamster heart grafts. Libraries for germline variable region heavy chain (VH) genes encoding the anti-hamster xenograft antibodies were established by genomic DNA cloning and analyzed by nucleotide sequencing. The frequency of Ig VH gene usage for controlling the antibody responses to hamster xenografts was examined by colony-filter dot hybridization. The nucleic acid structure of these genes was then compared to their genomic progenitors to identify the number and structural diversity expressed by the Ig VH genes used to mediate the response.

RESULTS

Rat monoclonal antibodies selected for their ability to precipitate the rejection of hamster xenografts exclusively use a closely related group of VH genes. The VH genes used by these antibodies are restricted to a single family of germline genes (VHHAR) for which 15 family members have been identified. The frequency of VHHAR gene usage in splenic IgM-producing B cells from LEW rats rapidly expands from 0.8% in naive animals to 13% in recipients 4 days after xenotransplantation. cDNA libraries expressing VHHAR genes were established from splenic lymphocytes derived from naive or xenograft recipients at 4 and 21 days after transplantation. Examination of 20 cDNA clones revealed that the majority (75%) of these clones express VHHAR genes displaying limited somatic mutation.

CONCLUSIONS

The use of a closely related group of Ig VH genes in a germline configuration to control the early humoral response to xenografts suggests that this response may represent the utilization of a primitive, T cell-independent pathway of antibody production by the graft recipients.

The differences between the structural repertoires of VH germ-line gene segments of mice and humans: implication for the molecular mechanism of the immune response

Although human and murine antibodies are similar when considering their diversification strategies, they differ in the proportion by which kappa and lambda type chains are present in their receptive V, repertoires. It has been shown that this difference implies a divergence in the structural repertoire of the kappa and lambda genes of these species. Nonetheless, the differences in VH have not been systematically studied. In this paper a systematic characterization of the VH structural repertoire of mice is made, so that a comparison with the VH structural repertoire of humans, described in detail elsewhere, could be properly accomplished. Our study shows the structural repertoire of mice to be dominated by canonical structure class 1-2 (approximately 60%), while in humans the dominant one is class 1-3 (approximately 40%). Analysis of the evolutionary relationships between human and mice suggest that this divergence may have a functional meaning. The implications of such findings are discussed.

Molecular origins and evolution of immunoglobulin heavy-chain genes of jawed vertebrates

Cartilaginous fish are the most ancient extant jawed vertebrates possessing bona fide immunoglobulin (Ig) and T-cell receptor molecules. The study of these animals is critical for understanding the origins of the vertebrate immune system. Here, Samuel Schluter, Ralph Bernstein and John Marchalonis review the latest data concerning heavy-chain variable genes and associated isotypes in these animals, and propose a model for the early origins of Igs.

Heavy-chain variable regions in carcharhine sharks: development of a comprehensive model for the evolution of VH domains among the gnathanstomes

We determined the sequence of 18 DNA clones encoding VH regions of sandbar shark and bull shark. All of these sequences exhibit key structural coding features characteristic of known VH genes of higher vertebrates. These VH sequences disclosed considerable diversity, and can be divided into six families according to the criterion of 80% DNA sequence identity. The overlapping of some VH gene clones to two or more families is a particular feature found in carcharhine sharks, which suggests that VH diversification is a continuing process. The basic sequence patterns of heavy-chain V regions found in all representative gnathanstomes and in VH of the shark heavy immunoglobulin IgW provides evidence for selection of canonical residues in all VH structures. Elasmobranch VH sequences can be divided into two classes or clans, one comprising the 'classical' VH set and the other comprising VHS related to those of IgW (V omega). Phylogenetic analyses place the VH cluster as the root of all the classic VHS and indicates that the V omega set is most probably that of the primordial heavy chain.