Microsites for immunoglobulin switch recombination breakpoints from Xenopus to mammals

102

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 C ), 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 C , that shares features with the C␦ gene in fish and mammals. The latter gene contains eight constant-region-encoding exons and, unlike the chimeric splicing of CH1 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 V H-DH-JH-C -C␦-C -C -C 3 organization, suggesting that the mammalian and amphibian Ig heavy-chain loci share a common ancestor.amphibians ͉ antibody evolution

Section: Identification Of the Genomic Sequence Encoding Igm ( ) Igxmentioning

confidence: 57%

Identification of IgF, a hinge-region-containing Ig class, and IgD inXenopus tropicalis

Zhao

Pan‐Hammarström

et al. 2006

102

“…Previous reports have indicated that CSR breakpoints appear to be located in the proximity of transition points from singlestranded to double-stranded regions in predicted stem-loop structures in S regions (32,38,39). These observations led to a hypothesis that secondary structures transiently formed by the denaturation of S regions during transcription (germline transcription) might be a recognition target of CSR recombinase.…”

Section: Inversion-type Class-switch Substrates and Their Activities Inmentioning

confidence: 98%

Variable deletion and duplication at recombination junction ends: Implication for staggered double-strand cleavage in class-switch recombination

Chen

Kinoshita²,

Honjo³

2001

Immunoglobulin class-switch recombination (CSR) gives rise to looped-out circular DNA of a cleaved S segment, which is lost eventually after cell divisions. To understand the molecular mechanism of S region cleavage during CSR, we constructed artificial CSR substrates in which inversion-type CSR takes place to retain the cleaved S segment. Sequencing analyses of recombinant clones of these substrates revealed that varying degrees of deletions and duplications exist at CSR breakpoints, suggesting the involvement of staggered cleavage of the S region in CSR. In addition, mutations frequently found near junctions showed a similar profile of base replacement to Ig somatic hypermutation. These findings suggest that single-strand tails of staggered cleavage may be repaired by error-prone DNA synthesis. N ewly generated B cells expressing IgM and IgD migrate to peripheral lymphoid organs where they are activated by encounters with antigens, resulting in the clonal expansion of antigenspecific B cells. Activated B cell clones secrete not only IgM but also other isotypes of Ig molecules without altering the antigen specificity. This phenomenon, termed class switching, is mediated by DNA recombination in the Ig heavy (H) chain constant (C) region locus, which results in expression of a new transcription unit containing the same productively rearranged variable region (V H ) gene with a downstream C H gene other than C .Class-switch recombination (CSR) from IgM to another isotype takes place anywhere in several-kilobase G-rich regions, termed switch (S) regions, which are located 5Ј to each set of C H exons and consist of tandemly repetitive short sequences with many palindromes (1-9). CSR is accompanied by a looping-out deletion of intervening DNA sequences (10-12). Only limited sequence homology is found near the site of recombination between S and other S sequences (13-15). Because the junctions of CSR are scattered over the S regions and in some instances in proximity to but outside the S regions, CSR is a region-specific recombination event.It has been well established that the ability of a given cytokine to determine the target specificity of CSR is correlated with transcription induction (germline transcription) from a specific intron promoter located immediately upstream of each S region (16). The germline transcription is believed to regulate chromatin opening (accessibility) of the target S region to determine the isotype specificity of CSR (17, 18). Efficiency of CSR seems to be correlated quantitatively with the activity of germline transcription (19). In addition, subsequent splicing of the CSR germline transcripts seems important for CSR (20,21), but the exact role of germline transcripts per se in CSR remains to be elucidated.Previously, we described an artificial CSR substrate in which each of two S regions was directed by a different constitutive promoter, and transcripts were spliced (22). This study demonstrated that the isotype specificity of CSR was not determined by the nucleotide sequences of S regio...

“…''Resting'' B cells with surface expression of IgM are found in discrete splenic follicles, which are surrounded by a relatively diffuse T cell zone. Amphibia is the oldest class of vertebrates having the Ig isotype switch (18), and previous work definitively has shown an exchange from one C region to another by means of a deletional mechanism (19,20). The order of the H-chain genes, however, has not been established.…”

mentioning

confidence: 99%

IgD, like IgM, is a primordial immunoglobulin class perpetuated in most jawed vertebrates

Ohta

Flajnik²

2006

194

138

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 (␦) from the amphibian Xenopus tropicalis during examination of the IgH locus. The Xenopus ␦ 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 mouse͞human. Unexpectedly, Xenopus IgD is orthologous to IgW, an Ig isotype found only in cartilaginous fish and lungfish, demonstrating that IgD͞W, like IgM, was present in the ancestor of all living jawed vertebrates. In striking contrast to IgM, IgD͞W is evolutionarily labile, showing many duplications͞deletions 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 IgD͞W 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.evolution ͉ immune system S ince the pioneering work of comparative immunologists in the 1960s, IgM has been the Ig isotype believed to be primordial and most stable in vertebrate evolution (1). Despite differences in the degree of polymerization of the secretory form in different vertebrate groups (1, 2) and a major splice variant of the transmembrane (TM) form in teleost fish (3), IgM is renowned for its molecular, biochemical, and functional stability. Present in all living jawed vertebrates, IgM is the first isotype to be expressed both in ontogeny and during humoral adaptive immune responses and is found as the major TM receptor on the surface of both conventional and ''innate'' B cells (4).By contrast, IgD has remained an enigmatic isotype since its discovery long ago (5). Like IgM, IgD is expressed as a TM receptor on B cells of mouse and human, generated as a result of alternative splicing of pre-mRNA containing the transcribed variable (V) region and the IgM and IgD heavy (H) chain constant (C) regions ( and ␦, respectively). Because of its spotty presence in mammals and absence in birds, IgD was assumed to be a recently evolved isotype (6). However, the discovery of an isotype in ray-finned bony fish with sequence similarity to IgD (7) and its presence in some mammals previously believed to lack IgD (8) have greatly modified our view of Ig isotype evolution and suggested it may have arisen much earlier.A similarly strange phylogenetic jump surrounds the isotype IgW, which was discovered first in skates (9, 10) and later in sharks (11,12). The secreted version of the IgW H chain ( ) is present in long and short forms in all elasmobranchs tested to date, and the TM form is al...