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

Abstract

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.

Fig. 1

Evolutionary topology reflecting the relationships within the Lagomorpha group based on a molecular super matrix (adapted from Matthee et al., 2004).

Fig. 2

Rabbit IGHV (regions from VH haplotype (a2 F–I)) for which nucleotide sequence is available from sequenced, assembled BAC clones. Depicted are V genes, D and J regions and also Cμ. VH functional genes are represented in white rectangles, VH possible pseudogenes in grey and VH pseudogenes in black, identified according to criteria described in Ros et al. (2004). The D-proximal VH gene, VH1, used in the majority of VDJ rearrangements is indicated. Identified above are the non-overlapping BAC clones 38A2 and 225P18 (GenBank Accession Numbers AY386694 and AY386697), and 219D23 (GenBank Accession Number AY386695). The 3' end of BAC 225P18 overlaps the 5'end of BAC 219D23 (adapted from Ros et al., 2004).

Fig. 3

Amino acid sequences of european rabbit (O. cuniculus) proteins (encoded by VH1a1–a3, VHa4.1–4.2, VHx, VHy, VHz) and hare (VHa2L, VHsLe, VHsLg) VH genes. Germline elements are italicized (Accession numbers: VH1a1-M93171; VH1a2-M93172; VH1a3-M93173; VHx-L03846; VHy-L03890; VHz-AF264469.). VHa4.1–4.2, VHa2L, VHsLe and VHsLg represent consensus protein sequences obtained by Esteves et al., 2004, . Framework regions (FR1, FR2, FR3) and each CDR (CDR1 and CDR2) are defined according to the IMGT numbering system (also shown). CDRs are shaded. The amino acids that are characteristic of a1, a2 and a4 lineages are marked with black, grey and white arrows, respectively. Hallmark rabbit VHa residues are highlighted in bold and underlined. Note that the Lepus VHa2L shares these residues, as well as five of the VH1a2 lineage characteristic amino acids. Dots (.) indicate identity with VH1a1, dashes (−) represent indels and question marks (?) represent ambiguous positions in consensus sequences.

Fig. 4

Geographic distribution of VHa locus allotype frequencies, serologically determined for populations of European wild rabbit (O. cuniculus) from the Iberian Peninsula and France. The subspecies O. c. algirus occupies the Southwestern part of Iberia, which is indicated by A. Rabbits of the Northwestern areas of Iberia and of the rest of Europe (indicated by B) belong to the subspecies O. c. cuniculus. The contact zone between the two subspecies is indicated in gray. The coloring of the disks reflects the relative allele frequencies per locality, analyzed as a two-allele locus with a-blank (white) and a-positive (black) alleles. Locality abbreviations are as follows: prt - Portimão; san - Santarém; alc - Alcochete; ida - Idanha; cab - Cabreira; Ll - Las Lomas; hue - Huelva; don - Doñana; cre - Ciudad Real; inf - Infantado; vv - Vila Viçosa; am - Amoladeras; tol - Toledo; bra - Bragança; tar-Tarragona; alt- Alicante; nav - Navarra; lle - Lerida; per - Perpigan; cam - Camargue; ver - Versailles; arj - Arjuzanx; gra - Grax; hel - Helene.

Fig. 5

Neighbour-joining tree for Oryctolagus cuniculus, Lepus europaeus (Le), and Lepus granatensis (Lg) VH genes, showing the transpecies polymorphism of VHa2. VH genes from human class 3 (VH3) determine the root of the tree. Numbers represent the bootstrap values (BP, in bold), and the confidence probability values (CP, in italics). Expressed VH genes (cDNA) are labeled by black (Le), gray (Lg), and white (O. cuniculus) circles. Germline VHa gene sequences (VH1–VH4) of rabbit allotypes a1, a2, and a3 are marked by black triangles. White squares indicate VHn germline genes. Black squares indicate human VH3 germline genes. “With kind permission from Springer Science+Business Media: Immunogenetics, The evolution of the immunoglobulin heavy chain variable region (IgVH) in leporids: an unusual case of transspecies polymorphism., 57(11), 2005, 874, Esteves PJ, Lanning D, Ferrand N, Knight KL, Zhai SK, van der Loo W, Figure 1.”