猪细小病毒NS1基因密码子偏爱性分析

CODON PREFERENCE OF NONSTRUCTURAL PROTEIN NS1 GENE OF PORCINE PARVOVIRUS

为给猪细小病毒(Porcine parvovirus,PPV)主要非结构蛋白(NS1)基因选择良好的宿主表达系统提供参考依据,本研究运用EMBOSS在线分析软件的CHIPS和CUSP程序对PPV NS1基因进行密码子偏爱性分析。结果显示PPV NS1基因的CAI值为0.642,ENC值为39.703,这表明NS1在密码子使用上存在较明显的偏爱性,且第三位核苷酸尤其偏爱A或T;从与PPV NS1基因密码子使用频率比值上看,使用频率差异较大的在大肠杆菌有33个、酵母有26个、人有27个;PPV NS1基因共有71个大肠杆菌稀有密码子,并且还有多个稀有密码子多次串联成簇出现的情况。结果表明酵母等真核生物与其密码子偏爱性较为接近,可作为该基因体外表达宿主的首选。

To provide a host system for optimal expression of major nonstructural protein （NS1） of Porcine parvovirus （PPV）, codon preference was analyzed using CHIPS and CUSP programs of EMBOSS software. The results showed that CAI and ENC values of NS 1 gene were 0.642 and 39.703, indicating a strong bias in codon preference. Sixty-one codons in the predicted polypeptides were used with a strong bias towards A and T at the third codon position. There were obvious differences of 33, 26 and 27 codon frequencies between PPV NS 1 and E.coli, yeast and human, respectively. Furthermore, PPV NS 1 gene possessed total 71 rare codons that were located in E.coli and found serially strung together. The PPV NS1 was the most similar to yeast in codon usage patterns, suggesting that yeast should be preferentially used as the suitable expression system.