Evolutionary development of the B-cell repertoire

Haplotype exclusion: the unique case presented by multiple immunoglobulin gene loci in cartilaginous fish

Cartilaginous fish represent the most phylogenetically distant species from man in which immunoglobulin and T cell antigen receptor genes have been identified. Immunoglobulin genes in cartilaginous fish are organized in hundreds of clusters, located on different chromosomes and presumably are under independent regulation; large numbers of immunoglobulin gene clusters are germline-joined and thus their expression is not directly dependent on somatic rearrangement. Despite the unusual nature of immunoglobulin gene genetics in these species, preliminary characterization of the transcription products of immunoglobulin loci in single cell isolates is consistent with haplotype exclusion. Certain features of immunoglobulin gene organization and expression in cartilaginous fish are remarkably similar to that of odorant receptors and suggest that at the level of transcriptional regulation, at least two different mechanisms could exist that relate to haplotype exclusion.

Variability of the immunoglobulin light chain in the Siberian sturgeon, Acipenser baeri

All sturgeon VL segments isolated in this study belong to a single family, VLI, which can be divided into two subfamilies. Of the 79 cDNA clones isolated, 76 belong to the larger subfamily, VLIa, and only 3 clones constitute the smaller subfamily, VLIb. To evaluate variability, the Shannon entropy was estimated for each individual amino acid position, and to facilitate comparisons of variability between species the mean entropy of the CDR regions was calculated. In such a comparison, the sturgeon was found to have CDR1 and CDR3 variability approaching those found in mouse and clawed frog, but showed very low variability for CDR2. Amino acid position 50 does however display variability in the range of mouse and clawed frog. It is further confirmed that the sturgeon has numerous J segments, but that the junctional diversity does not contribute greatly to the diversity of the light chain. Comparisons of cDNA clones and a genomic VL segment indicate that the VL undergoes changes, particularly in the CDR regions, in a manner that can be explained by somatic hypermutation and/or gene conversion.

Evolution of antigen binding receptors

This review addresses issues related to the evolution of the complex multigene families of antigen binding receptors that function in adaptive immunity. Advances in molecular genetic technology now permit the study of immunoglobulin (Ig) and T cell receptor (TCR) genes in many species that are not commonly studied yet represent critical branch points in vertebrate phylogeny. Both Ig and TCR genes have been defined in most of the major lineages of jawed vertebrates, including the cartilaginous fishes, which represent the most phylogenetically divergent jawed vertebrate group relative to the mammals. Ig genes in cartilaginous fish are encoded by multiple individual loci that each contain rearranging segmental elements and constant regions. In some loci, segmental elements are joined in the germline, i.e. they do not undergo genetic rearrangement. Other major differences in Ig gene organization and the mechanisms of somatic diversification have occurred throughout vertebrate evolution. However, relating these changes to adaptive immune function in lower vertebrates is challenging. TCR genes exhibit greater sequence diversity in individual segmental elements than is found in Ig genes but have undergone fewer changes in gene organization, isotype diversity, and mechanisms of diversification. As of yet, homologous forms of antigen binding receptors have not been identified in jawless vertebrates; however, acquisition of large amounts of structural data for the antigen binding receptors that are found in a variety of jawed vertebrates has defined shared characteristics that provide unique insight into the distant origins of the rearranging gene systems and their relationships to both adaptive and innate recognition processes.

The signature of somatic hypermutation appears to be written into the germline IgV segment repertoire

We present here a unifying hypothesis for the molecular mechanism of somatic hypermutation and somatic gene conversion in IgV genes involving reverse transcription using RNA templates from the V-gene loci to produce cDNA which undergoes homologous recombination with chromosomal V(D)J DNA. Experimental evidence produced over the last 20 years is essentially consistent with this hypothesis. We also review evidence suggesting that somatically generated IgV sequences from B lymphocytes have been fed back to germline DNA over evolutionary time.

Generation of immunoglobulin light chain gene diversity in Raja erinacea is not associated with somatic rearrangement, an exception to a central paradigm of B cell immunity

In all vertebrate species examined to date, rearrangement and somatic modification of gene segmental elements that encode portions of the antigen-combining sites of immunoglobulins are integral components of the generation of antibody diversity. In the phylogenetically primitive cartilaginous fishes, gene segments encoding immunoglobulin heavy and light chain loci are arranged in multiple clusters, in which segmental elements are separated by only 300-400 bp. In some cases, segmental elements are joined in the germline of nonlymphoid cells (joined genes). Both genomic library screening and direct amplification of genomic DNA have been used to characterize at least 89 different type I light chain gene clusters in the skate, Raja. Analyses of predicted nucleotide sequences and predicted peptide structures are consistent with the distribution of genes into different sequence groups. Predicted amino acid sequence differences are preferentially distributed in complementarity-determining versus framework regions, and replacement-type substitutions exceed neutral substitutions. When specific germline sequences are related to the sequences of individual cDNAs, it is apparent that the joined genes are expressed and are potentially somatically mutated. No evidence was found for the presence of any type I light chain gene in Raja that is not germline joined. The type I light chain gene clusters in Raja appear to represent a novel gene system in which combinatorial and junctional diversity are absent.

Development of an immune system

Minimally, an immune response is an induced cellular and/or humoral defense mechanism specific for the challenging agent. The system is a cognitive one inasmuch as a second stimulus with the same antigen can specifically induce either an enhanced response (memory) or diminished response (tolerance). The cells responsible for the initial antigen-specific recognition in higher vertebrates are clonally restricted T and B lymphocytes. Accessory cells are necessary for the processing and presentation of antigen, and physiologic mediators (cytokines) are essential for proliferation, interaction, and regulation of the system. Although it now appears that the recombination mechanisms essential for the anticipatory immune response occurred late in the deuterostome stream leading to vertebrates, molecules required for cell adhesion and regulation are widely spread in phylogeny. Their emergence must have preceded the divergence between ancestral protostomes and deuterostomes. Genetic mechanisms underlying the generation of diversity in the light and heavy chains of antibodies of mammals may be quite distinct in primitive vertebrates, particularly elasmobranchs, the ancestors of which diverged from those of mammals more than 400 million years ago. Despite this, clonal selection of antigen receptors of lymphocytes is most probably universal within the vertebrates. There is no need to force induced recognition in protostomes (e.g. insects) or lower deuterostomes (e.g. echinoderms) into mammalian models of immunity.

Genomic clone for sandbar shark lambda light chain: generation of diversity in the absence of gene rearrangement

While the general structure of immunoglobulin chains has remained relatively unchanged throughout evolution, the organization of the genes encoding these molecules differs substantially. To understand how the rearranging immunoglobulin system arose, it is necessary to examine living representatives of the most early vertebrate phyla. Elasmo-branches, which include the sharks, skates, and rays, are the most primitive phylogenetic class of vertebrates from which immunoglobulin DNA sequences have been obtained. In the sandbar shark (Carcharhinus plumbeus), the genes are arranged in individual clusters in which a single variable (V), joining (J), and constant (C) region gene, along with upstream regulatory elements, span a distance of approximately 4.4 kb or approximately 5.8 kb. We report the complete sequence of a genomic clone encoding sandbar shark lambda light chain. A unique finding of our study is that the V and J genes are fused in the germ line. Three additional clones have been shown by DNA sequencing to also have fused V and J genes. The four clones have complementarity-determining regions 3 of various lengths and amino acid sequence variability similar to the products of rearranged genes. Furthermore, analysis by polymerase chain reaction technology revealed an additional 26 genomic clones demonstrating fusion of the V and J segments. Therefore, VJ fusion is the prominent organizational feature of sandbar shark immunoglobulin light chain genes. This finding raises questions concerning the necessity of recombination to produce an antibody repertoire capable of reacting against a diverse array of antigens.