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J.M. Nickerson, H.S. Chin, V.T. Ciavatta; Evolution of the IRBP Gene . Invest. Ophthalmol. Vis. Sci. 2005;46(13):1749.
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© ARVO (1962-2015); The Authors (2016-present)
Purpose: The IRBP gene has an unusual structure, which provokes interest in the way the present–day gene arose from a simpler ancestral gene implied from an extended family of related enzymes. In mammals, IRBP has 4 Repeats, each Repeat consisting of about 300 amino acids. A function of IRBP, directly or indirectly, is to control the number of rod photoreceptor cells in the retina. To begin to understand how IRBP conducts this function, we sought to examine variability in the gene structure during evolution, thinking that if the gene structure varied widely, then the functional unit within IRBP might correspond to a single Repeat rather than multiple Repeats. Here we ask: 1. Are there the same number of Repeats present in distantly related IRBP genes as those in mammals? 2. Is the present model of IRBP gene evolution consistent with new gene structures? Methods: We employed bioinformatics to analyze recently completed or near–complete genomes of several species including the fish, fugu, tetraodon, and Danio rerio. We also analyzed other vertebrate genomes including chimp, dog, chicken, and Xenopus tropicalis. Reverse–transcriptase PCR was used to verify mRNA expression in selected species. Results: Via bioinformatics, we analyzed long sequences of DNA that extended well beyond the bounds of IRBP gene orthologs. The patterns of exons and introns in each gene ortholog and the Repeat structure of each protein were determined. We report a new gene structure for Takafugu rupries, tetraodon, and Danio rerio. Two of these orthologs differ from the expected gene structure. The sequences include a large first ORF encoding 3 complete Repeats and followed by 2 more Repeats spread across an additional 4 exons and 3 introns. Conclusions: The mammalian IRBP gene structure is tightly conserved in newly analyzed orthologs from rat, chimp, and dog. The chicken and Xenopus Tropicalis genes are very similar in structure with 4 exons and 3 introns placed similarly and 4 Repeats in the protein. The fish gene structures diverge markedly. In some species there was a 2 Repeat protein and a 4 exon–3 intron gene. However, in two species, the 2–Repeat gene is preceeded by an intronless 3–Repeat gene. It remains a possibility that these two genes are, in fact, one large 5–Repeat gene. Thus, the evolutionary history of IRBP is revised.
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