Specific features of immunoglobulin VH genes of the Antarctic teleost Trematomus bernacchii.
The somatic recombination of different germline-encoded gene segments constitutes a principal source of antibody diversity. In order to investigate the diversity in recombined gene segments encoding the immunoglobulin heavy chain of the Antarctic teleost Trematomus bernacchii, a VH library was constructed by 5'-RACE (rapid amplification of cDNA ends) using RNA isolated from the spleen of an individual specimen. Analysis of cDNA sequences of 45 rearranged VH/D/JH segments revealed specific features, such as: high number of repeats, up to 8 bp long, and palindromic sequences, especially in CDRs (complementary determining regions); occurrence of the RGYW consensus, known as mutational hot spot, higher than in other species. Sixty-four percent of single base substitutions was found within this motif. In addition, the usage of serine codons showed a clear bias for AGY in CDRs, particularly in CDR2, and for TCN in FRs (framework regions). In CDRs, the frequency of non-synonymous changes was higher than that of synonymous changes. Diversity generated by insertions/deletions occurred more often than in other species; inserted bases were often repeats of adjacent bases. In particular the CDR2 showed the highest length variability as compared to other species. Alignment of VH sequences indicated that also the gene conversion mechanism may contribute to generating diversity. These data indicate a CDR mutability higher than in other species and provide some insights into the hypermutational events that may also occur in teleosts.
D000818:Animals; D000864:Antarctic Regions; D001483:Base Sequence; D018076:DNA, Complementary / Q000737:chemistry / Q000235:genetics; D015321:Gene Rearrangement; D005803:Genes, Immunoglobulin / Q000235:genetics; D007143:Immunoglobulin Heavy Chains / Q000235:genetics*; D007135:Immunoglobulin Variable Region / Q000235:genetics*; D008969:Molecular Sequence Data; D010473:Perciformes / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid
D018076:DNA, Complementary; D007143:Immunoglobulin Heavy Chains; D007135:Immunoglobulin Variable Region