In silico characterization of bHLH transcription factor genes in the genome of rainbow trout (Oncorhynchus mykiss)

Abstract

The significance of seafood in nutrition has started to be better understood after the changein the understanding of nutrition in the world. One of the most common species cultivated inthe world is rainbow trout (Oncorhynchus mykiss) from the origin of North America.Transcription factors are a group of proteins containing different functional components forthe accomplishment of various activities. The basic helix (bHLH) domain is a highly preservedamino acid motif that characterizes a family of transcription factors. The bHLH gene family inthe rainbow trout (Oncorhynchus mykiss) genome has been identified in the current study forthe first-time using bioinformatics tools. According to the results, 441 bHLH genes (OmybHLH)were identified in the rainbow trout genome and the physicochemical properties of thoseproteins were determined. The highest number of the genes was in 7th chromosome of rainbowtrout with 29 OmybHLH genes. 38 of OmybHLH genes had no intronic regions. OmybHLHproteins were divided into 4 main groups in the phylogenetic tree consistent with their motifcontent. The common biological function of OmybHLH proteins was the regulation ofbiological processes. The mode of action of OmybHLH proteins was binding activity. TheOmybHLH gene family in the rainbow trout and the bHLH gene family in the Atlantic salmon(SsabHLH) had 95 orthologous gene relationships and average separation times of thoseorthologous genes were found to be 298 million years ago (MYA). Almost all the OmybHLHprotein family members have dominated by the α-helix motif which is a stable conformation.Identification of the bHLH proteins and evaluation of their properties in rainbow trout canopen new perspectives for aquaculture applications and fish culture to get better yield usinggenetic data.