鲤科鱼类SP1密码子的偏好性与进化

Codon preference and evolutionary analysis of SP1 in Cyprinidae

摘要:

目的 特异性蛋白1 (SP1)是Sp/KLF蛋白家族成员之一，是最早被发现的转录因子，参与基因的转录调控。本研究目的是为了解鲤科鱼类 SP 1在进化过程中形成的密码子使用模式及其与不同物种之间的亲缘关系，为实现鲤科鱼类异源高效表达提供理论依据。方法 本研究运用Codon W、Clustal X、MEGA 4.0及SPSS 软件，对 4种鲤科鱼类与其他10个不同物种的 SP 1序列进行密码子偏好性和进化分析。结果 4种鲤科鱼类 SP 1编码亮氨酸和异亮氨酸时分别对CUG和AUC密码子具有较强的偏好性。14个物种 SP 1的ENC平均值为50.57，CAI值介于0.184~0.379，均远小于1，表明该基因密码子偏好性较弱。4个鲤科鱼类 SP 1均表现出相似的密码子偏好性。ENC-plot分析发现 SP 1密码子偏好性主要受自然选择的影响。基于 SP 1序列的系统进化分析与相对同义密码子使用度 RSCU聚类分析结果差异较小。大肠杆菌是草鱼 SP 1最佳的外源表达系统，模式动物斑马鱼、小鼠均可作为草鱼 SP 1的遗传转化受体。结论 CUG和AUC为4个鲤科鱼类 SP 1 最优密码子，物种之间密码子偏好性存在差异，自然选择是导致14个物种 SP 1密码子偏好性的主要影响因素。本研究为鲤科鱼类SP1的分类、演化与表达提供了理论依据。

Abstract:

Specificity Protein 1 (SP1), a member of the Sp/KLF protein family, is one of the earliest identified transcription factors and participates in the transcriptional regulation of many genes. This study aimed to explore the codon usage pattern in evolution process and the phylogenetic relationship among different species of SP1 and also provide references for its high heterologous expression. The software such as Codon W, Clustal X, MEGA 4.0, and SPSS were used to analyze the codon bias and evolutionary of SP1 of 4 cyprinidae fish species and 10 other species. The results showed that the Cyprinidae fish SP1 hithly preferred the codons of CUG and AUC. The mean of an effective number of codons (ENC) of SP1 was 50.57 and the value of the codon adaptation index (CAI) was between 0.184 and 0.379, which was far less than 1. The above two indexes illustrated that SP1 in different species showed codon bias. Moreover, the SP1 of four cyprinid fish showed similar codon preference. The ENC-plot analysis revealed that natural selection was the main reason for the SP1 codon usage bias. In cluster analysis, there was little difference between the phylogenetic analysis based on the CDS sequences of SP1 and the clustering analysis based on RSCU. Escherichia coli was the most suitable heterologous expression system for Ctenopharyngodon idella SP1，and the model animals Danio rerio and Mus musculus could both be used as genetic transformation receptors for C. idella SP1. This study showed that CUG and AUC were the optimal codons of SP1 in 4 cyprinids, there were differences in codon preference between species, and natural selection was the main influencing factor leading to SP1 codon preference in the 14 species. This study provides a theoretical basis for the classification, evolution and expression of Cyprinidae SP1.