斑马鱼E3泛素连接酶基因的生物信息学分析和mRNA表达

Bioinformatical Analysis and mRNA Expression of E3 Ubiquitin Ligase Genes in Zebrafish

[目的]对斑马鱼E3泛素连接酶基因进行生物信息学分析,并研究其mRNA表达情况。[方法]利用生物信息学方法分析斑马鱼E3泛素连接酶基因的cDNA序列、蛋白质二级结构、结构域、氨基酸序列同源性,并构建进化树;利用整胚原位杂交技术研究目的基因在斑马鱼体内的mRNA表达模式。[结果]在NCBI基因库中找出TRIM54、TRIM55a、TRIM55b、TRIM63a、TRIM63b和TRIM101 6个斑马鱼E3泛素连接酶基因。这些基因之间有较高的同源性,二级结构以α-螺旋和无规卷曲为主,编码的蛋白质均含有3个保守结构域:环锌指、B-box锌指和卷曲螺旋。进化树分析显示,所有基因聚为4组:各物种TRIM54基因聚为一组;各物种TRIM55基因聚为一组,但靠近于斑马鱼TRIM101基因分支;TRIM63基因分为一组。整胚原位杂交结果显示,这些TRIM基因的mRNA均在受精后24 h的斑马鱼的肌节中表达,且TRIM55a、TRIM63a和TRIM101基因表达量较高。这些TRIM基因在肌肉发育和肌肉功能中可能发挥作用。[结论]斑马鱼的6个E3泛素连接酶基因有较高的保守性,其mRNA特异性表达于肌节部位。结果对深入研究这些基因在鱼类肌肉中的作用和指导鱼类生产具有一定的意义。

[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.