拉沙病毒密码子偏性分析  

Analysis of codon bias in Lassa virus

作　　者：李志豪 尚方建 孟余 刘奇 王聪 Li Zhihao;Shang Fangjian;Meng Yu;Liu Qi;Wang Cong(Integrated Laboratory of Pathogen Biology,School of Basic Medical Science,Dali University,Dali 671000,China)

机构地区：[1]大理大学基础医学院病原生物学综合实验室,671000

出　　处：《国际病毒学杂志》2022年第3期210-215,共6页International Journal of Virology

基　　金：国家自然科学基金项目(81660337,81703573)。

摘　　要：目的研究拉沙病毒(Lassa virus,LASV)密码子使用偏性及其偏性形成的影响因素,比较LASV和几种表达系统密码子使用频率,为LASV重组亚单位疫苗、mRNA疫苗、DNA疫苗等基因工程疫苗的制备筛选出最优外源表达系统。方法使用Excel 2007、EMBOSS、CondonW1.4.2、SigmaPlot 14.0、SPSS 22.0等软件分析LASV核心蛋白(nucleoprotein,N)、包膜糖蛋白(envelope glycoproteins,G)、锌结合蛋白(zinc-binding protein,Z)、RNA聚合酶(RNA polymerase,L)蛋白共446条基因序列的密码子偏性及其影响因素,并将LASV密码子使用模式与几种不同表达系统进行比较。结果LASV的各蛋白编码序列的各位置GC含量存在较大差异,各蛋白平均GC3含量为42.29%~59.47%,ENC均值41.73~52.81,除Z蛋白密码子偏性较强外,N、G、L三种蛋白密码子偏性较弱。4种蛋白RSCU>1的密码子共108个,约占45.76%,其中以A/U结尾占63.9%,GUU、GUG、UCU、UCA、CCU、ACA、GCU、GCA、AGA、AGG为LASV多数蛋白的高频密码子,GCA、AGA为4种蛋白共有的高频密码子。ENC-Plot、中性分析、PR2绘图分析显示,LASV的各蛋白密码子使用偏性受到不同因素影响,其主要因素是自然选择,突变是次要原因。对比分析提示人和酵母菌是LASV较合适的外源表达系统。结论LASV 4种蛋白偏向使用A/U结尾的密码子,目前自然选择是其偏性的主要影响因素,与常用表达系统密码子偏性比较分析提示人和酵母菌是LASV疫苗制备的最优外源表达。Objective To study the codon usage bias in Lassa virus(LASV)and the influencing factors of the bias and to compare the codon frequencies in LASV and several other expression systems,so as to screen the optimal in vitro expression system for the preparation of LASV genetic engineering vaccines,including recombinant sub-unit vaccine,mRNA vaccine and DNA vaccine.Methods The codon bias and the influencing factors of 446 gene sequences of nucleoprotein(N),envelope glycoproteins(G),zinc-binding protein(Z)and RNA polymerase(L)of LASV were analyzed by software such as Excel 2007,EMBOSS,CondonW 1.4.2,SigmaPlot 14.0 and SPSS 22.0.The codon usage patterns of LASV in several different expression systems were also compared.Results There were significant differences in GC content at each position of each protein coding sequence of LASV.The average GC3 contents of all proteins ranged from 42.29% to 59.47%,and the average ENC values of the proteins ranged from 41.73 to 52.81.Except for the Z protein,the codon bias of the three proteins,N,G and L proteins were relatively weak.There are 108 codons with RSCU>1,accounting for 45.76%.For these codons,63.9% was end with A/U.The high-frequency codons of most proteins in LASV were GUU,GUG,UCU,UCA,CCU,ACA,GCU,GCA,AGA and AGG.The common high-frequency codons of all four proteins were GCA and AGA.As indicated by ENC-plot,neutral analysis and PR2-plot analysis,the codon usage bias of each protein in LASV was affected by different factors,and the main factor was natural selection followed by mutations.Comparative analysis showed that human and yeast in vitro expression systems were more suitable for LASV.Conclusions The four proteins of LASV tended to use codons ending in A/U.Natural selection was presently the main influencing factor of the bias.The comparison analysis of codon bias with commonly used expression systems suggested that human and yeast were the optimal exogenous expression for LASV vaccine preparation.

关 键 词：拉沙病毒 密码子偏性 高频密码子 外源表达 

分 类 号：R373[医药卫生—病原生物学]