Rat T-cell receptor TRAV11 ( Vα14 ) genes: further evidence of extensive multiplicity with homogeneous CDR1 and diversified CDR2 by genomic contig and cDNA analysis

The antigen recognition system of NKT cells acts via an invariant T-cell receptor (TR) which recognizes CD1d and is highly conserved in mice, rats and humans. NKT cells expressing an invariant mouse TR composed of TRAV11-TRAJ18 (formerly Vα14-Jα281) are positively selected by CD1d, and recognize an antigen in context with CD1d. Here we show ten distinct TRAV11 genes (previously designated by us as TRAV14 ) on rat Chromosome 15 (BN/SsNHsd/MCW strain). In the rat TRAV11 genes, the splicing sites, the recombination signal sequences, and the possible promoter regions were well conserved, indicating that they were functional. Predicted protein sequences of rat TRAV11 genes were analyzed, including the three loops (CDR1–3) which connect the β-strands of the domain encoded by the TRA V-REGION and is hypervariable in sequence. The CDR1-IMGT sequence (from 27 to 32; VTPFNN) was conserved among most rat TRAV11 genes. The CDR2-IMGT sequences (from 56 to 61) were grouped into two types: type 1 [L(T/K)NKEE], and type 2 [LAYKKE]. The mRNAs of both types have a different tissue distribution. The CDR3 sequences were short and invariant, the rat TRAV11 genes being preferentially rearranged with rat TRAJ18 (Jα281), with the joint consisting of a single amino acid (A or G). Thus, rats had multiple TRAV11 chains with diversified CDR2-IMGT and homogenous CDR1-IMGT and CDR3-IMGT.