Ⅰ型脊髓灰质炎病毒基因密码子使用偏好性分析

Analysis of genetic codon usage bias in poliovirus type Ⅰ

目的 分析Ⅰ型脊髓灰质炎病毒(简称脊灰病毒)基因密码子使用偏好性。方法 从NCBI基因数据库(GenBank)检索并筛选出40条Ⅰ型脊灰病毒株的基因信息,计算其相对同义密码子使用度(RSCU)值、有效密码子数(ENc)值。将Ⅰ型脊灰病毒基因中碱基C和G位于第三位的密码子占所有密码子的百分比[(C+G)3%]与ENc值进行关联性分析,绘制散点图,并与(C+G)3%标准曲线进行比较。采用主成分分析法对Ⅰ型脊灰病毒基因密码子的RSCU值进行分析,并利用分析获得的主因子绘制散点图,观察不同时间和地域的Ⅰ型脊灰病毒基因密码子使用偏好性。结果 Ⅰ型脊灰病毒基因密码子AGA、AGG、CCA、UCA和GUG的RSCU值均≥1.5,密码子GCG、CGA、CGG、CGC、UCG和ACG的RSCU值均≤0.5。Ⅰ型脊灰病毒的ENc平均值为53.633。40株Ⅰ型脊灰病毒毒株均位于(C+G)3%标准曲线以下。2009年之前分离出来的毒株均位于图的下方,2009年之后分离于不同国家或地区的毒株分别聚集于图的一处。结论 Ⅰ型脊灰病毒在AGA、AGG、CCA、UCA、GUG等密码子的使用上偏好性较强,在GCG、CGA、CGG、CGC、UCG、ACG等密码子的使用上偏好性较弱。Ⅰ型脊灰病毒在密码子使用偏好性上处于较弱水平。自然选择在Ⅰ型脊灰病毒基因密码子使用偏好性上起主要作用,不同时间和地域的Ⅰ型脊灰病毒基因密码子使用模式差异较大。

Objective To analyze the genetic codon usage bias in poliovirus type Ⅰ. Methods The relative synonymous codon usage (RSCU) values and effective number of codon (ENC) values were used to investigate the codon usage patterns of 40 poliovirus typeⅠ, which were screened out from Genbank. The predicted values of ENC and the G and C content of the third codon position [(G+C)3%)] were computed, and we plotted the scatter chart. Principal component analysis (PCA) was carried out to analyze the major trend in codon usage pattern in different ORFs of 40 typeⅠpoliovirus genomes, based on the RSCU values. Results RSCU values of the codon AGA, AGG, CCA, UCA, and GUG of 40 poliovirus typeⅠwere greater than or equal to 1.5;RSCU values of the codon GCG, CGA, CGG, CGC, UCG, and ACG were equal or lesser than 0.5. The values of ENC among these poliovirus typeⅠ were similar, with a mean value of 53.633 , meanwhile, all of the spots lay below the expected curve. Strains isolated before 2009 were all located at the bottom of the figure, but these strains isolated from different area after 2009 were obviously different. Conclusions Poliovirus type I has strong preference in codon usage of AGA, AGG, CCA, UCA, GUG, and weak preference in codon usage of GCG, CGA, CGG, CGC, UCG and ACG. The extent of codon preference in poliovirus typeⅠgenomes is less biased (mean ENC>40) and keeps at a stable level. Natural selection is the main factor that determines codon usage bias, rather than mutational pressure. Finally, the codon usage of these strains isolated from different time or area is significantly different.