Genomic organization, expression, and phylogenetic analysis of Ca2+ channel beta4 genes in 13 vertebrate species

The Ca(2+) channel beta-subunits, encoded by CACNB genes 1-4, are membrane-associated guanylate kinase (MAGUK) proteins. As auxiliary subunits of voltage-gated Ca(2+) channels, the beta-subunits facilitate membrane trafficking of the pore-forming alpha1 subunits and regulate voltage-dependent channel gating. In this report, we investigate whether two zebrafish beta4 genes, beta4.1 and beta4.2, have diverged in structure and function over time. Comparative expression analyses indicated that beta4.1 and beta4.2 were expressed in separable domains within the developing brain and other tissues. Alternative splicing in both genes was subject to differential temporal and spatial regulation, with some organs expressing different subsets of beta4.1 and beta4.2 transcript variants. We used several genomic tools to identify and compare predicted cDNAs for eight teleost and five tetrapod beta4 genes. Teleost species had either one or two beta4 paralogs, whereas each tetrapod species contained only one. Teleost beta4.1 and beta4.2 genes had regions of sequence divergence, but compared with tetrapod beta4s, they exhibited similar exon/intron structure, strong conservation of residues involved in alpha1 subunit binding, and similar 5' alternative splicing. Phylogenetic results are consistent with the duplicate teleost beta4 genes resulting from the teleost whole genome duplication. Following duplication, the beta4.1 genes have evolved faster than beta4.2 genes. We identified disproportionately large second and third introns in several beta4 genes, which we propose may provide regulatory elements contributing to their differential tissue expression. In sum, both mRNA expression data and phylogenetic analysis support the evolutionary divergence of beta4.1 and beta4.2 subunit function.