Abstract: [objective] To bioinformatically characterize the E3 ubiquitin ligase genes in zebrafish and to analyze their mRNA expression profile. [Method] The cDNA sequences analysis, protein secondary structure and structural domain prediction, amino acid sequences homology alignment and phylogenetic tree establishment of E3 ubiquitin ligase genes were carried out with bioinformatical methods. The mRNA expression pattern of the target genes in zebrafish was assessed by using whole mount in situ hybridization. [Result] Six E3 ubiquitin ligase genes were found in NCBI GenBank, including TRIM54, TRIM55a, TRIM55b, TRIM63a, TRIM63b and TRIM101. There are high homologies between these genes. The secondary structure of E3 ubiquitin ligases was mainly composed of alpha helix and random coil. The conserved structural domains were RING zinc finger, B-box zinc finger and coiled coils. Phylogenetic tree analysis showed the E3 ubiquitin ligase genes were divided into four groups TRIM54 gene of different species belonged to one branch; TRIM55 were grouped together, nearing the branch of TRIM101; TRIM63 made up the fourth branch. The mRNA expression of these genes was detected in sarcomeres of zebrafish 24 h after fertilization. TRIM55a, TRIM63a and TRIM101 showed a stronger expression than the other TRIM genes did. These TRIM genes might play essential role in muscular development and function in zebrafish. [Conclusion] The E3 ubiquitin ligase genes had high conservation and their mRNA were specifically expressed in sarcomeres in zebrafish. This study provides a theoretical basis for exploring the roles of E3 ubiquitin ligase genes in fish muscle and an important guidance for fish production.

Key words: zebrafish, E3 ubiquitin ligase, bioinformatics, mRNA expression