Li Ruifang, Yu Zhifen, Huang Qiao, Guo Chunyang, Li Xue
Bing Du Xue Bao. 2016 Nov;32(6):773-81.
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 nucleic-acid 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.
选取甲型流感病毒作为样本。然后，分析同义密码子偏好与mRNA二级结构之间的关系。我们的数据将为进一步研究甲型流感病毒的同义密码子和RNA特性提供理论依据。收集了美国国立生物技术信息中心中所有甲型流感病毒的核酸序列信息。预测了每个核酸序列的二级结构。然后，计算了RNA的环结构、茎结构和自由复制能量。基于这些信息，得出了RNA的特定柔韧性。同时，统计了每个核酸序列中的同义密码子偏好。建立了甲型流感病毒RNA二级结构的数据库。然后，分析了同义密码子偏好与环结构含量、茎结构含量和柔韧性之间的关系。50%的氨基酸密码子使用与茎结构含量或环结构含量显著相关。此外，60%的氨基酸与平均单位折叠自由能显著相关。另外，50%的氨基酸密码子使用与RNA的特定柔韧性显著相关。对于与茎结构和环结构显著相关的密码子，它们的使用与两种结构含量之间的相关性完全相反。而且，特定柔韧性与同义密码子偏好之间的相关性优于其他参数。这些结果表明，同义密码子使用偏好对RNA二级结构有重要影响。
