埃博拉病毒包膜糖蛋白的密码子偏爱性分析

Analysis of the Codon Bias of Ebolavirus Glycoprotein

目的对从2014年西非埃博拉暴发地区感染者分离的4个埃博拉病毒株基因组包膜糖蛋白编码基因进行密码子偏爱性分析,为埃博拉病毒包膜蛋白基因表达中宿主系统选择和密码子优化提供参考。方法通过Gene Bank搜索近期公布的分离自西非地区的4个埃博拉病毒株全基因组序列,获得编码包膜糖蛋白GP1和GP2的基因序列及蛋白编码序列。采用EMBOSS在线预测埃博拉病毒包膜糖蛋白的密码子偏爱性,并通过与Codon Usage Database中大肠杆菌、酵母及人的密码子使用频率进行比较,筛选最适埃博拉病毒GP蛋白体外表达的宿主物种,并提供相应密码子优化方案。结果埃博拉病毒基因组、GP1和GP2的Nc值均在57左右,CAI值均在0.7左右,表明其密码子偏爱性较均一,且基因的表达水平相对较高;编码GP1蛋白F、H、M、N、W等氨基酸和GP2蛋白D、K、N、Q、Y等氨基酸中不同密码子使用频率有较大差异;GP1和GP2蛋白密码子偏爱性有共同之处也存在明显差异。计算σGP/E.coli、σGP/Yeast、σGP/Human的比值,结果显示GP1中>2.0或<0.5的数量分别为24、20和19个;GP2中的数量分别为26、30和19,表明埃博拉病毒GP1和GP2蛋白与人的密码子使用频率较为接近。结论以密码子偏爱性分析作为辅助手段,分析出此次流行于西非的埃博拉病毒包膜糖蛋白的密码子偏爱性及最适表达物种及密码子优化方案,为体外表达GP1和GP2蛋白,从而研发埃博拉病毒检测试剂、亚单位疫苗及基因工程抗体提供参考。

Objective To provide the reference for the selection of gene expression host system of Ebola virus envelope protein, co- don bias were analyzed according to envelope glycoproteins encoding gene of 4 Ebola virus strains isolated in west Africa in 2014. Methods Envelope glycoprotein GP1 and GP2 Gene sequences and related protein coding sequences were obtained, according to Gene Bank search- ing results of complete genome of 4 Ebola virus strains isolated from west Africa region recently. Envelope glyeoproteins codon RMS values （Nc） and codon adaptation index （CAI） were calculated by EMBOSS the CHIPS and the CAI modules online. The fraction and using fre- quency （frequency） of different codes in same amino acids of GP1 and GP2 were investigated by CUSP module analysis. In addition, the resuhs were compared with the using frequency of E. coli, yeast and human. It will be helpful for selecting the optimal expression host system of Ebola virus envelope protein. Results The Nc value of Ebola virus genome, GP1 and GP2 was around 57, CAI value was a- round 0.7. It showed that the codon preference was uniform, and the gene expression level was relatively high. There was great difference in codon bias of amino acid, such as F, H, M, N, W in GP1 and D, K, N, Q, Y in GP2. The results of δGP/E. coli,δGP/Yeast,crGP/ Human showed that the codon usage frequency of Ebola virus GP1 and GP2 protein was more close to human. Conclusion Codon bias and gene expression host system of Ebola virus （isolated in west Africa in 2014）GP1 and GP2 were analyzed by codon bias analysis as an auxiliary means. This study may help selecting gene expression host system and contributes further to development of subunit vaccine, an- tibody and diagnostic reagents.