Structure and genomic organization of immunoglobulin light chain in the channel catfish. An unusual genomic organizational pattern of segmental genes.

Channel catfish L chain cDNA was obtained through a PCR strategy and used to isolate multiple L chain clones from cDNA and genomic libraries. Sequence analysis of full-length cDNA indicates that the V region is preceded by a leader peptide, and represented by framework and CDR regions. Both VL and CL domains contain the invariant cysteines and tryptophans as well as other phylogenetically conserved L chain residues. The sequence similarity of the catfish L chain with higher vertebrate kappa- and lambda-chains, however, does not readily allow the catfish L chain to be classified. Eight cDNA clones isolated from a cDNA library were shown to represent different processed derivatives of sterile L chain transcripts. These transcripts share a similar upstream sequence region and extend downstream to include a CL or alternatively a JL segment in partial germ-line configuration that has been spliced into a CL. Sequence comparisons indicate that these transcripts represent the product of different L chain loci. Genomic Southern blot analyses with VL and CL probes indicate that there are at least 30 VL segments and at least 15 CL segments. The analysis of 17 genomic L chain clones showed that each hybridized with VL-, JL-, and CL-specific probes. Characterization of the gene segments in three of these clones indicates a previously undescribed pattern of segmental gene organization. Gene segments are found in clusters with VL, JL, and CL segments in each cluster. Within a cluster VL segments reside upstream of single copies of closely linked JL and CL segments. The proximity of VL segments downstream from JL-CL segments suggests that individual clusters may be closely linked. The VL segments are located in opposite transcriptional polarity relative to the JL and CL gene segments, which indicates that VL segments are likely rearranged to JL-CL segments by inversion rather than deletion events.