马丘波病毒的密码子偏爱性分析  

Analysis on codon usage bias in Machupo virus

作　　者：张曼琳 刘贞麟 李健晴 尹锦熠 王聪 Zhang Manlin;Liu Zhenlin;Li Jianqing;Yin Jinyi;Wang Cong(Integrated Laboratory of Pathogenic Biology,School of Basical Medical Science,Dali University,Dali 671000,China)

机构地区：[1]大理大学基础医学院,671000

出　　处：《国际病毒学杂志》2025年第1期36-40,共5页International Journal of Virology

基　　金：国家自然科学基金(82360727);云南省地方高校联合专项(202101BA070001-114)。

摘　　要：目的对马丘波病毒(machupo virus,MACV)的四种结构蛋白的密码子的偏爱性进行分析,了解其偏爱性的主要影响因素,筛选最适合的MACV的外源性表达系统,为疫苗与抗体的制备提供参考及理论依据。方法使用Condon W软件对从NCBI数据库中筛选下载的MACV的四种表面结构蛋白的基因编码序列(codingDNA sequence,CDS)共150条并进行整理分析,使用Excel、SPSS 26.0、SigmaPlot 14.0、Graphpad Prism 9.5进行数据整理及绘图。结果四种结构蛋白的有效密码子数(effective number of codon,ENC)范围为46.32~49.79,数值更接近61,说明密码子偏爱性使用较弱。相同密码子使用程度分析(Relative synonymous codon usage,RSCU)中AGA、UGU、CCA、AGU、UCA、UCU、ACA、GUG、GUU为共有RSCU>1的序列,多以A\\U结尾。ENC-plot、中性绘图及奇偶校检规则分析(parity rule 2,PR2)表明MACV密码子偏爱性受到压力突变、自然选择和其他因素的影响,自然选择是主要的影响因素。将MACV与人类、酵母菌和大肠杆菌的密码子使用频率进行对比,发现与人类的密码子使用频率最接近。结论本研究发现MACV的密码子偏爱性分析中高频密码子多以A\\U结尾,在众多影响因素中自然选择是关键因素。Objective To analyze the codon usage bias in four structural proteins of Machupo virus(MACV),understand the main influencing factors of the bias and screen the most suitable exogenous expression system for MACV,so as to provide reference and theoretical basis for the preparation of vaccines and antibodies.MethodsA total of 150 coding DNA sequences(CDS)of the four surface structural proteins of MACV were screened and downloaded from NCBI database and were analyzed by Condon W.The data were further collated and mapped by Excel,SPSS26.0,Sigmaplot14.0 and Graphpad prism 9.5 software.ResultsThe effective number of codon(ENC)of the four MACV structural proteins ranged from 46.32 to 49.79 and was closer to 61,indicating that the codon usage bias of the four proteins was weak.In relative synonymous codon usage(RSCU)analysis,AGA,UGU,CCA,AGU,UCA,UCU,ACA,GUG and GUU were the codon sequences with common RSCU>1 and mostly ended with A\\U.The result of ENC-plot,neutral mapping and PR2 plot analysis showed that the formation of MACV codon usage bias was affected by stress mutation,natural selection and other factors,but natural selection was the main factor.Comparing to the codon usage frequences of human,yeast and Escherichia coli,MACV was the closest to human.ConclusionsThe codon usage bias analysis of MACV in this study found that most of the high-frequency codons usually ended with A\\U,and natural selection is the key influencing factor among many influencing factors.

关 键 词：马丘波病毒 密码子 密码子偏爱性 自然选择 突变选择 

分 类 号：TP3[自动化与计算机技术—计算机科学与技术]