Immunoglobulin κ light-chain diversity in rabbit is based on the 3′ length heterogeneity of germ-line variable genes

Antibody diversity is generated by the combinatorial association of multiple distinct genetic segments (variable (V), joining (J) and diversity (D) light (L) and heavy (H) chains - V_L, J_L and V_H, D, J_H) and amplified somatically by three or four different mechanisms^1-6. The κ system in mouse and human consists of 50-100 V_κ segments associated with a cluster of four or five functional J_κ segments, located 2.5 kilobases (kb) 5′ to a single C_κ gene^7-10. The third hypervariable region (CDR3), which is part of the antibody combining site, is usually nine amino acids long in human and mouse κ chains. It is encoded by the last seven codons of the V_κ segment and the first two of the J _κ segment, one codon sometimes being added or deleted between V and J by junctional variation². In the rabbit, the C _κ1 gene which encodes the major isotype^11-14, is associated with a cluster of five J_κ segments, only one of which seems to be functional¹¹, thus significantly decreasing the combinatorial potential. However, amino acid sequence comparison has revealed extensive heterogeneity in the length of rabbit CDR3 (ref. 15), suggesting the existence of a D segment analogous to that in the heavy-chain system. We show here that rabbit V_κ genes have several additional nucleotides at their 3′ ends. Thus, even with a single functional J_κ segment, high CDR3 diversity can be generated based on the length heterogeneity of V_κ germ-line segments and their greater length, which might leave scope for an increased junctional deletion.