Differential retention of duplicated retinoid-binding protein (crabp &rbp) genes in the rainbow trout genome after two whole genome duplications and their responses to dietary canola oil

Abstract

The complexity of retinoid intracellular signaling by lipid-binding proteins is further confounded in salmonids, owing to a whole genome duplication (WGD), followed by a second salmonid-specific WGD. As such, many more cellular retinoic acid-binding protein (crabp)/retinol-binding protein (rbp) genes may exist in salmonids, compared to other vertebrate species. In this study, genomic database searches and phylogenetic analyses identified seven crabp and eight rbp genes in the rainbow trout. A parsimonious explanation for the number of crabp/rbp genes in the rainbow trout genome is duplicated genes were lost from the genome by nonfunctionalization following the salmonid-WGD, and the extant duplicate crabp/rbp genes of the much earlier teleost-WGD have been retained by either sub- or neofunctionalization of tissue-specific regulatory mechanisms. Nutritional regulation of retinoid-binding protein genes in the liver was also determined in the fish fed diets containing various amounts of canola oil (CO) for 12 weeks along with hepatic fatty acid profile, Vitamin A (VitA) level, and growth parameters. The crabp/rbp transcripts were modulated markedly by experimental diets except for rbp2a.1/rbp2a.2 at the end of the trial. This result suggests that rbp2a.1/rbp2a.2 don't exhibit obvious divergence of transcriptional regulatory mechanisms that control their nutritional regulation by dietary CO. Growth parameters didn't differ markedly among dietary treatments. An understanding of VitA homeostasis, especially the regulatory effects of retinoids on transcriptional control of target genes, may have considerable importance to basic fish development, physiology, and aquaculture and this study may lead to future research on molecular VitA metabolism especially in salmonids experienced salmonid-WGD.