影响伪狂犬病病毒同义密码子用法特点的因素分析

为了充分了解伪狂犬病病毒基因组结构和病毒进化机制,计算伪狂犬病病毒各基因(组)Nc值、RSCU值、GC3s含量和双核苷酸组成,分析伪狂犬痛病毒密码子用法特点.采用目前最普遍使用的多变量统计分析方法(对应分析)分析影响伪狂犬病病毒基因组同义密码子用法偏爱性的因素.结果表明:①在GC含量丰富的伪狂犬病病毒基因组中,所有基因都偏爱于以G或C结尾的密码子;②伪狂犬病病毒对CpG、CpC、GpC和GpG 4种双核苷酸具有显著偏爱性,而较少使用ApA、ApT、TpA和TpT 4种双核苷酸;③碱基组成限制、碱基突变压力、翻译选择和基因功能是形成伪狂犬病病毒密码子用法特点的4种因素.伪狂犬病病毒所有基因Nc-GC3s分布图显示有些基因如LLT ORF1、LLT ORF2等的偏向性完全是由于碱基的组成限制.GC3s-GC12s散点图则显示碱基突变和自然选择都是PRV密码子偏向性的形成因素.根据RSCU值进行的对应分析表明伪狂犬病病毒大多数基因密码子用法受基因表达水平和基因功能影响.综上所述,伪狂犬病病毒偏爱于G或C结尾的密码子,且碱基组成限制、碱基突变、翻译选择和基因功能是影响伪狂犬病病毒同义密码子用法特点的主要因素.

Analysis of factors shaping synonymous codon usage in pseudorabies virus

Synonymous codon usage and the main factors shaping codon usage in pseudorabies virus were reported in order to understand the architecture and evolution of pseudorabies virus.Firstly,Nc values,RSCU values,GC3s contents and the dinucleotide composition of pseudorabies virus genes or genome were calculated detailly to study the usage of pseudorabies virus.Secondly,correspondence analysis,a commonly used multivariate statistical approach,was carried out to analyze the factors shaping synonymous codon usage bias of pseudorabies virus genome.The results showed that: i)a stsong synonymous codon usage bias on the codons ending at C or G are observed in all the pseudorabies virus genes;ii) the effect of discrimination against the use of four dinucleotides,namely CpG,CpC,CpC and GpG,is observed in codon usage of pseudorabies virus,while the dinucleotides ApA,ApT,TpA and TpT are rarely used;iii) four factors such as base composition,base mutation,translational selection and funcation of gene contribute to the synonymous codon usage in pseudorabies virus.Nc vs.GC3s plot of all pseudorabies virus genes showed that base composition completely contributed to the variation of some genes such as LLT ORF1 and LLT ORF2,and plot of GC3s-GC12s show that base mutation and translational selection are the the two facors shaping synonymous codon usage bias of pseudorabies virus.Further,plot of the two first axes generated by the correspondence analysis of RSCU values for pseudorabies virus show that the expressional level and funcation of most of the pseudorabies virus genes shape their synonymous codon usage bias.In summary,pseudorabies virus bias on G or C ending codons and compositional biases,mutational bias,translational selection,together with funcation of gene shape the synonymous codon usage of pseudorabies virus.