A型流感病毒同义密码子的使用偏性对RNA二级结构的影响

Influence of Synonymous Codon Bias on the RNA Secondary Structure in Influenza-A Viruses

以A型流感病毒为研究样本,分析了同义密码子使用偏性对RNA二级结构的影响,为进一步研究同义密码子存在的意义及A型流感病毒RNA特征提供一些理论依据。收集整理了NCBI中收录的全部A型流感病毒的核酸序列信息,计算了每一条核酸序列的RNA二级结构,计算出RNA环结构含量和茎结构含量及折叠自由能。在此基础上,计算了RNA二级结构的柔性。同时,计算了每一条核酸序列的相对同义密码子使用值。由此,建立了A型流感病毒RNA二级结构数据库。分析每条核酸序列的相对同义密码子使用值与RNA的环结构、茎结构及柔性之间的关系。分析结果表明,50%的氨基酸的相对同义密码子使用值与RNA茎结构含量和环结构含量显著相关;60%的氨基酸的相对同义密码子使用值与单位平均折叠自由能显著相关;50%的氨基酸的相对同义密码子使用值与RNA柔性显著相关。进一步分析发现,与茎结构含量和环结构含量都显著相关的密码子,它们的相对同义密码子使用值与两种结构含量的相关性截然相反,而且发现,在所选的参量中,RNA柔性与相对同义密码子使用值显示出更好的相关性。结果证实,对于A型流感病毒,同义密码子的使用偏性对RNA二级结构存在很大的影响。

Influenza-A viruses were selected as samples.Then,the relationship between synonymous codon bias and mRNA secondary structures was analyzed.Our data will provide a theoretical basis for further research on the synonymous codon and RNA properties of the influenza-A virus.Information on the nucleicacid sequence of all influenza-A viruses in the National Center for Biotechnology Information was collected.The secondary structure of each nucleic-acid sequence was predicted.Then,the loop structure,stem structure,and free replicating energy of RNA were calculated.Based on this information,the specific flexibility of RNA was worked out.Simultaneously,the synonymous codon bias in each nucleic-acid sequence was counted.A database on the RNA secondary structure of the influenza-A virus was set up.Then,the relationship between the synonymous codon bias and the content of loop structure,stem structure,and flexibility were analyzed.Codon usage of 50% of amino acids was correlated significantly with the content of stem structure or the content of loop structure.Also,60% of amino acids were correlated significantly with average unit folding free energy.In addition,codon usage of 50% of amino acids was correlated significantly with the specific flexibility of RNA.For codons that were correlated significantly with stem structure and loop structure,the correlation between their usage with two types of structural content was completely contrary.Also,the correlation between specific flexibility with synonymous codon bias was better than that observed for other parameters.These results suggest that synonymous codon usage bias has important influences on RNA secondary structure.