Primary Structure and Complementarity-Determining Region (CDR) 3 Spectratyping of Rainbow Trout TCR{beta} Transcripts Identify Ten V{beta} Families with V{beta}6 Displaying Unusual CDR2 and Differently Spliced Forms

VDJ rearrangement at the teleost TCR[beta] locus leads to a highly diverse repertoire of junctions for each V[beta]J[beta] combination. From a rainbow trout 5' RACE library of TCR[beta] transcripts, 47 clones encompassing a full V[beta]-D[beta]-J[beta]-C[beta] sequence were selected and analyzed. A similarity analysis of the sequences evidenced 10 V[beta] families, of which 6 were not previously described. Immunoscope and sequence analysis of the V[beta]-D[beta]-J[beta] junctions of the new families confirmed that they create a polyclonal and diverse repertoire. Multiple alignments showed that rainbow trout V[beta]s possess most of the conserved residues typical of V[beta] segments. However, this study revealed a high complementarity-determining region 2 (CDR2) and CDR1 length diversity among rainbow trout V[beta] families, suggesting that the spatial orientation of the TCR could fluctuate in the TCR/peptide /MHC complex, depending on the V[beta] expressed. Among the new V[beta] families, V[beta]6 displayed the strongest deviance from typical hypervariable CDR1 and CDR2 loops, with an unusually short CDR2. Moreover, the V[beta]6 sequence is overall divergent from typical V[beta] sequence, raising the question of its functional relevance. Immunoscope experiments identified a V[beta]6-J[beta]3 junction, which was amplified during the response against viral hemorrhagic septicemia virus, a fish rhabdovirus. V[beta]6 seems therefore to be expressed functionally in a selected TCR. However, the shorter V[beta]6 transcripts produced through an alternative splicing lack the C', C'', D, and E strands of the V[beta] domain and are probably nonfunctional.