Wang Hongju, Meng Tao, Wei Wenqiang
School of Basic Medical Sciences, Henan University, Kaifeng, 475004, Henan, China.
Huaihe Hospital, Henan University, Kaifeng, 475000, Henan, China.
Genes Genomics. 2018 Jul;40(7):767-780. doi: 10.1007/s13258-018-0689-x. Epub 2018 Apr 6.
The helicase gene of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is not only involved in viral DNA replication, but also plays a role in viral host range. To identify the codon usage bias of helicase of AcMNPV, the codon usage bias of helicase was especially studies in AcMNPV and 41 reference strains of baculoviruses by calculating the codon adaptation index (CAI), effective number of codon (ENc), relative synonymous codon usage (RSCU), and other indices. The helicase of baculovirus is less biased (mean ENc = 50.539 > 40; mean CAI = 0.246). AcMNPV helicase has a strong bias toward the synonymous codons with G and C at the third codon position (GC3s = 53.6%). The plot of GC3s against ENc values revealed that GC compositional constraints are the main factor that determines the codon usage bias of major of helicase. Several indicators supported that the codon usage pattern of helicase is mainly subject to mutation pressure. Analysis of variation in codon usage and amino acid composition indicated AcMNPV helicase shows the significant preference for one or more postulated codons for each amino acid. A cluster analysis based on RSCU values suggested that AcMNPV is evolutionarily closer to members of group I alphabaculovirus. Comparison of the codon usage pattern among E. coli, yeast, mouse, human and AcMNPV showed that yeast is a suitable expression system for AcMNPV helicase. AcMNPV helicase shows weak codon usage bias. This study may help in elucidating the functional mechanism of AcMNPV helicase and the evolution of baculovirus helicases.
苜蓿银纹夜蛾多核衣壳核型多角体病毒（AcMNPV）的解旋酶基因不仅参与病毒DNA复制，还在病毒宿主范围中发挥作用。为了确定AcMNPV解旋酶的密码子使用偏好，通过计算密码子适应指数（CAI）、有效密码子数（ENc）、相对同义密码子使用情况（RSCU）等指标，特别研究了AcMNPV和解旋酶的41种杆状病毒参考毒株中解旋酶的密码子使用偏好。杆状病毒的解旋酶偏好性较低（平均ENc = 50.539 > 40；平均CAI = 0.246）。AcMNPV解旋酶对第三位密码子为G和C的同义密码子有强烈偏好（GC3s = 53.6%）。GC3s与ENc值的关系图显示，GC组成限制是决定解旋酶主要密码子使用偏好的主要因素。几个指标支持解旋酶的密码子使用模式主要受突变压力影响。密码子使用和氨基酸组成的变异分析表明，AcMNPV解旋酶对每种氨基酸的一个或多个假定密码子表现出明显偏好。基于RSCU值的聚类分析表明，AcMNPV在进化上与I组α杆状病毒成员更接近。大肠杆菌、酵母、小鼠、人类和AcMNPV之间密码子使用模式的比较表明，酵母是AcMNPV解旋酶的合适表达系统。AcMNPV解旋酶显示出较弱的密码子使用偏好。本研究可能有助于阐明AcMNPV解旋酶的功能机制以及杆状病毒解旋酶的进化。
