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United States Department of Agriculture

Agricultural Research Service

Title: The Nucleotide Targets of Somatic Mutation and the Role of Selection in Immunoglobulin Heavy Chains of a Teleost Fish

item Yang, F
item Waldbieser, Geoffrey - Geoff
item Lobb, C

Submitted to: Journal of Immunology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/10/2005
Publication Date: 2/1/2006
Citation: Yang, F., Waldbieser, G.C., Lobb, C. 2006. The Nucleotide Targets of Somatic Mutation and the Role of Selection in Immunoglobulin Heavy Chains of a Teleost Fish. Journal of Immunology 176:1655-1667.

Interpretive Summary: Losses to infectious disease are a major cause of losses in farmed catfish. In order to better understand mechanisms of disease resistance in catfish, molecular genetic techniques were used to investigate the basis for spontaneous rates of genetic variation in a gene critical for production of antibodies. The results showed DNA sequence variations in the catfish immunoglobin heavy chain gene were restricted to certain DNA sequence motifs and fewer in scope to known motifs in mammals. This research furthered the understanding of how catfish white blood cells can produce a large variety of antibodies through DNA sequence variation.

Technical Abstract: Sequence analysis of H chain cDNA derived from the spleen of an individual catfish has shown that somatic mutation occurs within both the VH- and JH-encoded regions. Somatic mutation preferentially targets G and C nucleotides with approximately balanced frequencies, resulting in the predominant accumulation of G-to-A and C-to-T substitutions that parallel the activation-induced cytidine deaminase nucleotide exchanges known in mammals. The overall mutation rate of A nucleotides is not significantly different from that expected by sequence-insensitive mutations, and a significant bias exists against mutations occurring in T. Targeting of mutations is dependent upon the sequence of neighboring nucleotides, allowing statistically significant hotspot motifs to be identified. Dinucleotide, trinucleotide, and RGYW analyses showed that mutational targets in catfish are restricted when compared with the spectrum of targets known in mammals. The preferential targets for G and C mutation are the central GC positions in both AGCT and AGCA. The WA motif, recognized as a mammalian hotspot for A mutations, was not a significant target for catfish mutations. The only significant target for A mutations was the terminal position in AGCA. Lastly, comparisons of mutations located in framework region and CDR codons coupled with multinomial distribution studies found no substantial evidence in either independent or clonally related VDJ rearrangements to indicate that somatic mutation coevolved with mechanisms that select B cells based upon nonsynonymous mutations within CDR-encoded regions. These results suggest that the principal role of somatic mutation early in phylogeny was to diversify the repertoire by targeting hotspot motifs preferentially located within CDR-encoded regions.

Last Modified: 10/19/2017
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