Genomic organization and transcription of the medaka and zebrafish cellular retinol-binding protein (rbp) genes

Abstract

In this study, we examined the evolutionary trajectories and the common ancestor of medaka rbp genes by comparing them to the well-studied rbp/RBP genes from zebrafish and other vertebrates. We describe here gene structure, sequence identity, phylogenetic analysis and conserved gene synteny of medaka rbp genes and their putative proteins as well as the tissue-specific distribution of rbp transcripts in adult medaka and zebrafish. Medaka rbp genes consist of four exons separated by three introns that encode putative polypeptides of 134–138 amino acids, a genomic organization characteristic of rbp genes. Medaka Rbp sequences share highest sequence identity and similarity with their orthologs in vertebrates, and form a distinct clade with them in phylogenetic analysis. Conserved gene synteny was evident among medaka, zebrafish and human rbp/RBP genes, which provides compelling evidence that the medaka rbp1, rbp2a, rbp2b, rbp5, rbp7a and rbp7b genes arose from a common ancestor of vertebrates. Moreover, the duplicated rbp2 and rbp7 genes most likely exist owing to a whole-genome duplication (WGD) event specific to the teleost fish lineage. Selection pressure and the nonparametric relative rate test of the medaka and zebrafish duplicated rbp2 and rbp7 genes suggest that these duplicated genes are subjected to purifying selection and one paralog might have evolved at an accelerated rate compared to its sister duplicate since the WGD. The steady-state levels of medaka and zebrafish rbp1, rbp2a, rbp2b and rbp5 transcripts in various tissues suggest that medaka rbp1, rbp2a and rbp2b genes have retained the regulatory elements of an ancestral RBP1 and RBP2 genes, and the medaka rbp5 gene has acquired new function. Furthermore, the tissue-specific regulations of rbp7a and rbp7b genes have diverged markedly in medaka and zebrafish since the teleost-specific WGD.