乙型肝炎病毒密码子偏好性及影响因素分析

Codon usage bias of the hepatitis B virus and factors influencing it

目的分析乙型肝炎病毒(HBV)B、C基因型密码子使用偏好性及其影响因素,探讨HBV密码子使用模式与宿主、病毒进化的关系。方法从GenBank数据库中收集47株HBV的全基因组序列,利用EMBOSS、SPSS24.0、MEGAX等软件对其密码子偏好性进行统计分析。结果HBV各蛋白编码序列的ENC值为56.37-58.74,CAI值为0.678-0.697,GC3含量为0.474-0.506。RSCU>1的密码子共27个,主要以U/C结尾。高频使用密码子为UCU、CCU和AGC,低频使用密码子为CUA、CCG、CGA、ACG和UCG。ENC绘图显示47株病毒均位于预期曲线之下。中性绘图分析表明GC12与GC3无显著相关性(R2=0.005,P<0.01)。PR2绘图显示第三位碱基T和C含量较高。对应分析显示这些病毒的密码子偏好性受碱基组成影响的可能性较小。利用CAI值和卡方检验的方法确定GAC和GAA为上述毒株的最优密码子。密码子使用频率比值表明B、C基因型与人类的密码子偏好性相近,而聚合酶(P)、表面(S)基因与人类的密码子偏好性存在一定的差异,以P基因差异更大。系统发生分析显示,HBV毒株分类的进化越相近,其密码子偏好性越相似。结论B、C基因型HBV偏爱使用U/C结尾的密码子,其密码子偏好性主要受到自然选择的影响。结合密码子偏好性与密码子优化可能有助于理解HBV进化过程和对最适宿主的选择机制。

Objective To analyze the codon usage bias of the B and C genotypes of the hepatitis B virus(HBV)and factors influencing it and to further explore its relationship to the evolution of HBV.Methods Forty-seven full-length genomes of HBV were obtained from GenBank,and the codon usage bias and factors influencing it were evaluated using the relative synonymous codon usage(RSCU),codon adaptation index(CAI),effective number of codons(ENC),and GC calculated using EMBOSS and CodonW.SPSS24.0 and MEGAX were used for statistical and phylogenetic analysis,respectively.The best codon was determined using aχ2 test(Chi-square test)based on the CAI.Results For the coding sequence of HBV,ENC ranged from 56.37 to 58.74,CAI ranged from 0.678 to 0.697,and GC3 content ranged from 0.474 to 0.506.Twenty-seven codons of HBV with a RSCU value larger than one mainly ended with U/C.The high-frequency codons were UCU,CCU,and AGC while the low-frequency codons were CUA,CCG,CGA,ACG,and UCG.ENC plots indicated that all 47 isolates were below the expected curve.A neutrality plot analysis revealed no significant correlation between GC12 and GC3(R2=0.005,P<0.01).A PR2 bias-plot analysis revealed a high T and C content.Correspondence analysis suggested that overall nucleotide composition slightly affected the codon usage bias within the B and C genotypes of HBV in the current dataset.GAC and GAA were the optimal codons of the above strains based on the CAI value and a chi-square test.A comparative analysis of the relative frequency of codon usage revealed a high frequency of codon usage(84.75%)in HBV genotypes B and C similar to the codon preference in human beings.This was true for the whole genome.The P gene of HBV genotypes B and C displayed the greatest dissimilarity(40.68%),followed by the S gene(28.81%).Phylogenetic analysis indicated that HBV isolates with a similar codon preference were clustered closer together on the phylogenetic tree.Conclusion The HBV genotypes B and C examined in this study tend to have a codon ending with U or C.The codon preference is mainly affected by natural selection rather than base composition.The combination of codon preference and codon optimization may help to understand the evolutionary process of HBV and the mechanism by which it selects its.