Somatic hypermutation of gamma/delta TCR variable domain genes in Camelus dromedarius

We recently demonstrated for the first time in a mammalian organism (Camelus dromedarius) that somatic hypermutation (SHM) occurs in the variable domain of the productively rearranged T cell receptor gamma (TRG) and delta (TRD) genes. Here we report the mutation profile for each nucleotide, as obtained by the comparison of spleen cDNA sequences of a single animal with the corresponding germline genes. The mutations are very frequent both in TRG and TRD genes, with the significant overrepresentation at the palindromic DGYW/WRCH motifs, indicative of activation-induced cytidine deaminase (AID) targeting and at the WA/TW hotspots suggesting a possible origin due to the mismatch repair (MMR) mechanism known to take place during the second phase of SHM. The analysis of distribution of the mutations showed that CDR3, FR4 and FR1 of the TRG variable domain exhibit a statistically significant higher mutation rate than the other regions, the highest value being of 0.015/bp. There is no difference in the mutation rate between the regions of the TRD variable domain, with the exception of a CDR1 value statistically significant higher than that of FR2 in a V gene. In TRG genes, the comparison of the R/S ratios of CDRs and FRs indicated a statistically appreciable difference (chi-squared, p = 0.0009), suggesting a selection pressure acting on gamma/delta T cells. The analysis of clonal radiation in constructed lineages from cDNA TRD sequences showed that R mutations in FRs appear to be early in the lineage implying that the founder mutations do not ablate the structural integrity of the receptor. By computational analysis, we infer that the non conservative residue variations located in the FR2 of the TRD domain may indeed contribute to the further stabilization of the interaction between the two chains of the gamma/delta heterodimer.