Missing Links in the Evolution of Immunoglobulins Provided
by the Xenopus tropicalis Genome Project
Evolutionary biologists have taught that amphibians are the critical vertebrate group in understanding the emergence of tetrapods. Establishing a linkage in the evolution of immunoglobulins (Igs) from fish to mammals has not been an easy task. However, various lower vertebrate genome projects are providing investigators with the material to undertake new studies. Among the various issues are the evolutionary origin of hinge-containing Igs like IgG of mammals and the elusive IgD. The latter has not been found in all mammals in part because it is the least homologous among species of the major isotypes. This initially created problems in generating reliable isotype-specific gene probes and cross-reactive antibodies.
Two reports in July published in the Proc. National Academy of Science describe the presence in Xenopus tropicalis of an IgD sequence homolog containing eight C-region domains that links the IgD of catfish with the IgD of mammals. These studies also review the evolutionary plasticity of the gene encoding IgD (“adaptive immunity’s plaything”) throughout vertebrate evolution and establish a relationship with the orthologous IgW of sharks and lungfish. Both studies show that Xenopus IgD is expressed exclusively in spleen, perhaps similar to expression of mammalian IgD and IgM on naïve B cells. While the eight domain nature of Xenopus IgD resembles the IgD of fish, its transmembrane portion shares homology with mammalian IgD. Thus IgD appears to have evolved through very labile evolution from an IgW-like Ig to the IgD of most mammals. While IgW reached a dead-end, IgD continued to evolve through condensation and evolution of its membrane and perhaps signaling regions to serve as a B lymphocyte antigen receptor. Of course the enigma of why both IgD and IgM are needed as B cells receptors still remains.
The Xenopus tropicalis genome project also provided Zhao et al the opportunity to identify the earliest form of a hinged Ig. The hinge of mammalian IgG is believed to provide flexibility which offers new functional possibilities. In all mammals, the hinge region is the least conserved and considered by some to be the last region to become established in the genome. Zhao and colleagues identified a new Ig isotype (IgF) in Xenopus that represents the earliest example of an Ig with an exon encoding a small hinge.
Both of these studies represent breakthrough science in the field of evolutionary biology. The abstracts of each are provided below. The accomplishments of these groups testify to the value of genome projects in helping to understand comparative and evolutionary immunology. Perhaps the ongoing farm genome projects will provide equally interesting discoveries.
Identification of IgF, a hinge-region-containing Ig class, and IgD in Xenopus tropicalis.
Zhao Y, Pan-Hammarstrom Q, Yu S, Wertz N, Zhang X, Li N, Butler JE, Hammarstrom L.
State Key Laboratory for AgroBiotechnology, China Agricultural University, Beijing 100094, People's Republic of China.
Proceedings of the National Academy of Sciences (USA) 103:12087-12092, 2006
Only three Ig isotypes, IgM, IgX, and IgY, were previously known in amphibians. Here, we describe a heavy-chain isotype in Xenopus tropicalis, IgF (encoded by CΦ), with only two constant region domains. IgF is similar to amphibian IgY in sequence, but the gene contains a hinge exon, making it the earliest example, in evolution, of an Ig isotype with a separately encoded genetic hinge. We also characterized a gene for the heavy chain of IgD, located immediately 3' of Cμ, that shares features with the Cδ gene in fish and mammals. The latter gene contains eight constant-region-encoding exons and, unlike the chimeric splicing of μCH1 onto the IgD heavy chain in teleost fish, it is expressed as a unique IgD heavy chain. The IgH locus of X. tropicalis shows a 5' VH-DH-JH-Cμ-Cδ-Cχ-Cυ-Cφ 3' organization, suggesting that the mammalian and amphibian Ig heavy-chain loci share a common ancestor.
IgD, like IgM, is a primordial immunoglobulin class perpetuated in most jawed vertebrates.
Ohta Y, Flajnik M.
Department of Microbiology and Immunology, University of Maryland, 655 West Baltimore Street, Baltimore, MD 21201, USA. yota@som.umaryland.edu
Proceedings of the National Academy of Sciences (USA) 103:10723-10728, 2006
IgD has remained a mysterious Ig class and a bane to immunology students since its discovery >40 years ago. Its spotty occurrence in mammals and birds and the discovery of an isotype with similarities to IgD in bony fish are perplexing. We have identified IgD heavy (H) chain (δ) from the amphibian Xenopus tropicalis during examination of the IgH locus. The Xenopus delta gene is in the same position, immediately 3' of the IgM gene, as in mammals, and it is expressed only in the spleen at low levels, primarily as a transmembrane receptor by surface IgM(+) cells. Our data suggest that frog IgD is expressed on mature B cells, like in mouse/human. Unexpectedly, Xenopus IgD is orthologous to IgW, an Ig isotype found only in cartilaginous fish and lungfish, demonstrating that IgD/W, like IgM, was present in the ancestor of all living jawed vertebrates. In striking contrast to IgM, IgD/W is evolutionarily labile, showing many duplications/deletions of domains, the presence of multiple splice forms, existence as predominantly a secretory or transmembrane form, or loss of the entire gene in a species-specific manner. Our study suggests that IgD/W has played varied roles in different vertebrate taxa since the inception of the adaptive immune system, and it may have been preserved as a flexible locus over evolutionary time to complement steadfast IgM.
Tears of the Cheetah
Thomas J. O'Brien
Thomas Dunn Books
O'Brien runs the Laboratory of Genomic Diversity at the NIH, NCI. He is an expert on feline genetics and also discovered the gene that blocks HIV infection. It details the basis for the lack of genetic diversity in the cheetah and its implications in understanding the value of genetic diversity in resistance to disease.
The immunoglobulin heavy-chain locus in zebrafish: Identification and expression of a previously unknown isotype, immunoglobulin Z
Nature Immunology 6: 295-302, 2005
Nadia Danilova, Joroen Bussmann, Kerstin Jekosch and Lisa Steiner
The only immunoglobulin heavy-chain classes known so far in teleosts have been mu and delta. We identify here a previously unknown class, immunoglobulin zeta, expressed in zebrafish and other teleosts. In the zebrafish heavy-chain locus, variable (V) gene segments lie upstream of two tandem diversity, joining and constant (DJC) clusters, resembling the mouse T cell receptor alpha (Tcra) and delta (Tcrd) locus. V genes rearrange to (DJC)(zeta) or to (DJC)(mu) without evidence of switch rearrangement. The zebrafish immunoglobulin zeta gene (ighz) and mouse Tcrd, which are proximal to the V gene array, are expressed earlier in development. In adults, ighz was expressed only in kidney and thymus, which are primary lymphoid organs in teleosts. This additional class adds complexity to the immunoglobulin repertoire and raises questions concerning the evolution of immunoglobulins and the regulation of the differential expression of ighz and ighm.
Antibody repertoire development
Developmental & Comparative Immunology 30:1-247
J. E. Butler (Volume Editor)
The volume contains 15 articles, 12 of which deal with individual species or species groups ranging from sharks to various eutherian mammals. Included are cartilaginous fishes, boney fishes, non-galliform birds, chicken, humans, mice, rabbits, sheep, cattle, horse, camels and swine. Emphasis is on how and where the repertoire is generated. Data on the constant and variable region genes encoding the repertoire and in some cases their genomic organization, are also provided. Provocative contributions by Melvin Cohn and John Marchalonis add flavor to the volume. This volume should serve as a valuable reference in the field of comparative immunology.
First molecular and biochemical analysis of in vivo affinity maturation in an ectothermic vertebrate
Proc. National Academy Sciences (USA) 103:1846-1851
Dooley H, Stanfield RL, Brady RA, Flajnik MF
The cartilaginous fish are the oldest phylogenetic group in which Igs have been found. Sharks produce a unique Ig isotype, IgNAR, a heavy-chain homodimer that does not associate with light chains. Instead, the variable (V) regions of IgNAR bind antigen as soluble single domains. Our group has shown that IgNAR plays an integral part in the humoral response of nurse sharks (Ginglymostoma cirratum) upon antigen challenge. Here, we generated phage-displayed libraries of IgNAR V regions from an immunized animal and found a family of clones derived from the same rearrangement event but differentially mutated during expansion. Because of the cluster organization of shark Ig genes and the paucicopy nature of IgNAR, we were able to construct the putative ancestor of this family. By studying mutations in the context of clone affinities, we found evidence that affinity maturation occurs for this isotype. Subsequently, we were able to identify mutations important in the affinity improvement of this family. Because the family clones were all obtained after immunization, they provide insight into the in vivo maturation mechanisms, in general, and for single-domain antibody fragments.
Veterinary Research
Special Issue on Mucosal Immunity in Domestic Animals
Vol. 32, February 2006
K. Haverson, M. Bailey, B. Charley, eds.
The volume contains ten review articles covering major species of veterinary importance. Topics included are those at the cutting edge of the field and include such issues as: the common mucosal immune system, lymphocyte migration, the avian lung-associated immune system, a comparison of IgA systems among species, intraepithelial lymphocytes and T and B cell repertoires. Reviews can be downloaded from the Veterinary Research website (see links).
Collection, Handling and Analysis of Specimens for Studies of Mucosal Immunity in Large Animals
Mucosal Immunology, Volume 2, Elsevier-Academic Press, 2005
ISBN 0-12-491543-4
J. Mestecky, M.E. Lamm, W. Strober, J. Bienenstock, J.R. McGhee, L. Mayer, eds.
Mucosal Immunology is a two volume compendium of the field with contributions by more than 240 scientists from around the globe. The specific article cited is Appendix III found on pp 1853-1868. It includes contributions from 10 investigators with expertise in different areas of large animal mucosal immunology. The two volume second edition contains a wealth of information for scientists, students and teachers.