Evidence for quasi-silent germline genes coding for phylogenetically ancient determinants of the rabbit a locus allotypes

An overview of the lagomorph immune system and its genetic diversity

Our knowledge of the lagomorph immune system remains largely based upon studies of the European rabbit (Oryctolagus cuniculus), a major model for studies of immunology. Two important and devastating viral diseases, rabbit hemorrhagic disease and myxomatosis, are affecting European rabbit populations. In this context, we discuss the genetic diversity of the European rabbit immune system and extend to available information about other lagomorphs. Regarding innate immunity, we review the most recent advances in identifying interleukins, chemokines and chemokine receptors, Toll-like receptors, antiviral proteins (RIG-I and Trim5), and the genes encoding fucosyltransferases that are utilized by rabbit hemorrhagic disease virus as a portal for invading host respiratory and gut epithelial cells. Evolutionary studies showed that several genes of innate immunity are evolving by strong natural selection. Studies of the leporid CCR5 gene revealed a very dramatic change unique in mammals at the second extracellular loop of CCR5 resulting from a gene conversion event with the paralogous CCR2. For the adaptive immune system, we review genetic diversity at the loci encoding antibody variable and constant regions, the major histocompatibility complex (RLA) and T cells. Studies of IGHV and IGKC genes expressed in leporids are two of the few examples of trans-species polymorphism observed outside of the major histocompatibility complex. In addition, we review some endogenous viruses of lagomorph genomes, the importance of the European rabbit as a model for human disease studies, and the anticipated role of next-generation sequencing in extending knowledge of lagomorph immune systems and their evolution.

Molecular bases of genetic diversity and evolution of the immunoglobulin heavy chain variable region (IGHV) gene locus in leporids

The rabbit has long been a model for studies of the immune system. Work using rabbits contributed both to the battle against infectious diseases such as rabies and syphilis, and to our knowledge, of antibodies' structure, function, and regulated expression. With the description of rabbit Ig allotypes, the discovery of different gene segments encoding immunoglobulins became possible. This challenged the "one gene-one protein" dogma. The observation that rabbit allotypic specificities of the variable regions were present on IgM and IgG molecules also led to the hypothesis of Ig class switching. Rabbit allotypes contributed to the documentation of phenomena such as allelic exclusion and imbalance in production of allelic gene products. During the last 30 years, the rabbit Ig allotypes revealed a number of unique features, setting them apart from mice, humans, and other mammals. Here, we review the most relevant findings concerning the rabbit IGHV. Among these are the preferential usage of one VH gene in VDJ rearrangements, the existence of trans-species polymorphism in the IGHV locus revealed by serology and confirmed by sequencing IGHV genes in Lepus, the unusually large genetic distances between allelic lineages and the fact that the antibody repertoire is diversified in this species only after birth. The whole genome sequence of a rabbit, plus re-sequencing of additional strains and related genera, will allow further evolutionary investigations of antibody variation. Continued research will help define the roles that genetic, allelic, and population diversity at antibody loci may play in host-parasite interactions.

The evolution of the immunoglobulin heavy chain variable region (IgV H ) in Leporids: an unusual case of transspecies polymorphism

In domestic rabbit (Oryctolagus cuniculus), three serological types have been distinguished at the variable domain of the antibody H chain, the so-called V(H) a allotypes a1, a2, and a3. They correspond to highly divergent allelic lineages of the V(H) 1 gene, which is the gene rabbit utilizes in more than 80% of VDJ rearrangements. The sharing of serological V(H) a markers between rabbit and snowshoe hare (Lepus americanus) has suggested that the large genetic distances between rabbit V(H) 1 alleles (9-14% nucleotide differences) can be explained by unusually long lineage persistence times (transspecies polymorphism). Because this interpretation of the serological data is uncertain, we have determined the nucleotide sequences of V(H) genes expressed in specimens of Lepus species. Two sequence groups were distinguished, one of which occurred only in hare specimen displaying serological motifs of the rabbit V(H) a-a2 allotype. Sequences of this group are part of a monophyletic cluster containing the V(H) 1 sequences of the rabbit a2 allotype. The fact that this "transspecies a2 cluster" did not include genes of other rabbit V(H) a allotypes (a1, a3, and a4) is incompatible with the existence of a common V(H) a ancestor gene within the species, and suggests that the divergence of the V(H) a lineages preceded the Lepus vs Oryctolagus split. The sequence data are furthermore compatible with the hypothesis that the V(H)a polymorphism can be two times older than the divergence time between the Lepus and Oryctolagus lineages, which was estimated at 16-24 million years.

The structural and genetic basis for expression of normal and latent VHa allotypes of the rabbit

The immunoglobulin heavy chain variable regions of the rabbit are unusual in having genetically controlled, serologically detectable alternative forms, the VHa allotypes, as well as minor VH allotypes of the x, y and w groups. New insights into the probable structural basis for the VHa allotypes have come from re-examination of earlier protein sequence data in the light of newly deduced protein sequences derived from sequencing cloned cDNAs and genomic DNAs encoding VH regions. Here we review this sequence information, and define the allotype-correlated differences at seven positions in framework region 1 and 10 positions in framework region 3 that may lead to the serologically detectable allotypic determinants (allotopes). Most alternative amino acids at allotype-correlated positions can be derived from each other by single-base changes. Thus somatic mutations and/or gene conversion-like events must be considered along with other serological and genetic explanations for various reported observations of the production of latent VHa allotypes. The proximity of rabbit VH genes (approximately 3 kb apart) might enhance the likelihood of conversion-like events in both germline and somatic cells.

The immunomodulatory effect of anti-Micrococcus luteus antibodies. I. Effect on in vitro rabbit T cell functions

A range of purified rabbit anti-Micrococcus luteus antibodies (anti-MCAb) were tested for their ability to interfere with a variety of in vitro immune responses. Such antibodies strongly inhibited the secondary IgG antibody response to sheep red blood cells without affecting the IgM response or the proliferative responses to mitogens and antigens. By exposing lymphocyte populations to anti-MCAb, it was found that such reagents exerted a strong mitogenic effect on rabbit T lymphocytes, provided these cells were derived from antigen-activated lymph nodes. This mitogenic effect was also obtained with F(ab')2 fragments of anti-MCAb and with hybridoma-derived anti-MCAb. Collectively, these data indicate that anti-MCAb inhibit the initiation of IgG synthesis possibly through the expansion of immunoregulatory T cell subsets.

The quaternary Gs3 and Gs7 allotypes of the rabbit: generation of the determinants by interspecies molecular hybridization

A number of allotypic markers of the rabbit immunoglobulins are present only on intact immunoglobulin molecules and not on the isolated heavy or light chains. Some of these markers, although determined by the kappa light chain, are limited to a single heavy chain class of Ig. They can be generated by in vitro hybridization of the kappa light chain with the appropriate heavy chain. The quaternary IgG allotypic determinants Gs3 and Gs7 which are determined respectively by the b4.1 and b4.2 allelic variants of the kappa b4 light chain can be generated not only by in vitro hybridization of these light chains with a rabbit gamma chain, but also to a certain extent by their hybridization to gamma chains derived from other species.

Effects of anti-Ig reagents on T cell functions I. Activation of rabbit T cells by anti-allotype antibodies

Rabbit lymphocytes were analyzed by flow microfluorometry, using anti-T cell and anti-Ig reagents. Rabbit T cells and cells expressing surface Ig (B cells) appeared to belong to distinct subpopulations which could be separated on the basis of their selective adherence to nylon wool columns or to anti-Ig-coated dishes. Using flow microfluorometry, no evidence was obtained for the expression of a allotypes (VH framework) on T cells. Separated lymphocyte populations were functionally characterized using an in vitro proliferation assay. B and T cells from rabbit spleen or peripheral blood responded in a differential fashion to B and T cell-specific mitogens and to anti-Ig antibodies. Although such T cells did not respond upon stimulation with anti-Ig antibodies alone, significant proliferation could be induced by simultaneous addition of anti-Ig and T cell growth factor. In addition, activated T cells, derived from lymph nodes of immunized rabbits, generated a proliferative response upon stimulation with anti-Ig reagents alone. The above-mentioned effects on T cells could be obtained using heterologous anti-Ig antibodies or isologous anti-allotype antibodies, directed either against a allotypes (VH framework) or against b allotypes (kappa light chain). Antibodies against the Fc portion of rabbit Ig or against irrelevant allotypic specificities were ineffective in triggering T cells. Fab fragments from anti-allotype antibodies were equally stimulatory for T cells as compared to intact IgG, indicating that cross-linking of Ig-like molecules is not a necessary requirement for anti-Ig-induced T cell activation.

Production of IgG-specific auto-anti-allotypes in b4.2-suppressed rabbits

Rabbits were completely suppressed for kappa chain allotype b4.2, and autoantibodies against b4.1 or b4.2 could be raised in 2 out of 3 animals. The animal immunized with b4.1 produced anti-b4 and anti-Ms3, two activities which have never as yet been found together in one antiserum. Both autoantisera lacked the capacity to bind b4.2-IgM, whereas they precipitated 4.2-IgG very well. In one animal, anti-b4 IgM activity appeared after the sixth immunization, at the age of 14 months. Allotype suppression was maintained in both rabbits till the end of their lives whereas all control animals recovered within 6 months. The autoantisera which were specific for b4 IgG could not induce suppression in vivo. However, specific inhibition of b4 IgG secretion was observed in vitro.

Rabbit heavy chain haplotypes--allotypic determinants expressed by VH-CH recombinants

This report summarizes our current understanding of the heavy chain haplotypes found in our laboratories' rabbits. Independently derived data from several laboratories have been synthesizes into a consistent picture of the linked inheritance of allotypic markers found on the different heavy chain classes and subclasses of rabbit immunoglobulins in pedigreed rabbits, including the families of three apparent VH-CH recombinants. In one recombinant, the entire group of CH markers (C mu, C gamma, and C alpha) recombined with the set of VH. Although in the other two recombinants all CH markers may also have recombined as a group, in one of these only IgG and IgA CH genes were informative; in the other recombinant, only the IgG allotypes were informative. Some allotypic determinants found on IgM molecules ("conformational") appear only when a specific variable region allotype (VHa) is combined with a specific mu constant region allotype (C mu). New combinations of VHa and C mu allotypes were generated in two of the genetic recombinants and led to new "conformational" determinants. The gains and losses observed lend support to the hypothesis that the determinants result from conformations generated by the combination of allotype-specific VH and C mu protein sequences. Conceivably, DNA events that join VH to diversity (D)- and joining (J)-coding sequences or mRNA processing events that splice J to C mu could be involved in generating the sequences that form allotype-specific determinants.

The phylogenetic relationships of immunoglobulin allotypes and 7S immunoglobulin isotypes of chickens and other phasianoids (turkey, pheasant, quail)

Pheasants, quail and turkeys from different geographical locations were surveyed for the presence of eight 7S Ig and four IgM chicken allotypes. No IgM and only two 7S Ig allotypes were detected. Chicken 7S Ig allotypic specificity G-1.7 cross-reacted with pheasant and turkey isotypic specificities, and was absent in quail. The other determinant (G-1.9) cross-reacted with an allotype found only in turkeys and golden pheasants. These data suggest that G-1.7 and G-1.9 are probably phylogenetically ancient determinants and that polymorphism of chicken immunoglobulins arose after divergence of chickens from other phasianoid birds. Based on the allotypic and isotypic analysis of the 7S Ig antigenic determinants, turkey 7S Ig was as closely related to chicken 7S Ig as was pheasant 7S Ig. Jungle fowl, the ancestor of chickens, had most of the chicken 7S Ig and IgM allotypes present as polymorphic markers.

Suppression of VH, C gamma and C mu gene products in rabbits by maternal immunization against IgM allotype and detection of somatic recombinant molecules in these animals

Suppression of the mu-chain allotype Ms16 was obtained in young heterozygous Ms16/Ms17 rabbits by immunizing the Ms17 mother against the paternal Ms16 allotype. Examination of the concentration of the VH and CH allotypes of paternal origin (a2,Ms16 and e14) in the offspring, revealed not only Ms16 suppression but also VH and C gamma allotypic suppression. The degree of suppression for the C gamma markers (4-25-fold decrease) was much less than that for the C mu or VH markers (50-150-fold decrease). The excess C gamma marker (e14) was found to be present for the major part on molecules possessing the VH allotype derived from the homologous allelic chromosome. The pattern of persistence of molecules with the suppressed C gamma marker in the serum is consistent with the idea that these molecules arise by somatic recombination and that the gene order is VH, C mu and C gamma.

Phylogeny of the rabbit gamma-chain determinants: a d12-like antigenic determinant in Pronolagus rupestris

A survey for constant region gamma-chain allotypes (de locus) was undertaken in different lagomorph genera. As yet only Pronolagus rupestris, a paleolaginae, showed the presence of a determinant similar to rabbit d12 although it lacked the widespread e15 determinant. All seven individuals possessed the d12 like determinant which was studied by immunodiffusion, haemagglutination inhibition, radiobinding and binding inhibition assays. In addition, a new enzymic method for typing for d12, based on the presence of the asymmetric rabbit hinge carbohydrate linked to the d12 characteristic threonine, is presented. This method suggests, however, that, unlike the d12 rabbit, Pronolagus does not seem to have a majority of IgG molecules with a glycosylated hinge.

Isolation and characterization of IgG molecules expressing latent group b allotypes from pedigreed b4b4 rabbits

Latent group b markers were detected in sera, in IgG preparations, and on isolated L chains from rabbits bred for homozygosity at the b locus. Serologic analysis of sera from an extended family of homozygous b4 rabbits revealed the presence of latent b allotypes in 5 of 37 sera tested. Latent b5 and b9 markers were identified; none of the sera tested contained latent b6. In two instances, the level of latent b9 allotypes was sufficiently high to permit isolation and detailed serologic characterization of the immunoglobulin population bearing this allotype. The fact that latent allotypes were detected in pedigreed homozygous rabbits minimizes the possibility that lymphoid cell chimerism is involved in latent allotype expression. Furthermore, characterization of the b9 IgG population indicates that the latent allotypic determinants do not reside on a subset of molecules with dual allotypic reactivity.

Double line phenotypes in rabbit IgG allotypes and their relation to the cis/trans configuration of the IgG markers

Rabbit antiallotype sera raised against heavy chain markers sometimes show double precipitin lines with all or some of the corresponding antigens (double and single line phenotypes). In a number of cases the double line phenotypes behave as alleles of the single line phenotypes and this feature allows a genetic and immunochemical analysis of these systems. In three cases that have been analysed, the double line phenotype arise when a precipitating a locus allotype and a non-precipitating d or e locus allotype are present on the same molecule (a1 and d14), (a1 and d11), (a3 and d11). This only happens when the corresponding genes are present on the same chromosome (cis configuration) of the diploid pair. These sera are therefore useful for determining directly the genotype of the animals.