|本期目录/Table of Contents|

冠状病毒同义密码子使用对mRNA二级结构的影响(PDF)

《内蒙古大学学报(自然科学版)》[ISSN:1000-9035/CN:22-1262/O4]

期数:
2015年06期
页码:
609-618
栏目:
研究论文
出版日期:
2015-11-20

文章信息/Info

Title:
Influence of Synonymous Codon Usage Bias on mRNA Secondary Structure in Coronavirus
作者:
黄俏 李瑞芳 于志芬 李雪
内蒙古师范大学物理与电子信息学院, 呼和浩特 010022
Author(s):
HUANG Qiao LI Rui-fang YU Zhi-fen LI Xue
College of Physics and Electronic Information, Inner Mongolia Normal University, Hohhot 010022, China
关键词:
冠状病毒同义密码子使用度mRNA二级结构折叠自由能mRNA柔性
Keywords:
coronavirussynonymous codon usage biasmRNA secondary structurefolding free energymRNA specific flexibility
分类号:
Q6;Q7
DOI:
-
文献标识码:
-
摘要:
从NCBI中获得了45种冠状病毒的mRNA序列总计416条.分别计算了每条编码序列中相对同义密码子使用度(RSCU),然后预测每条mRNA序列的RNA二级结构,计算相应mRNA茎结构含量、环结构含量、单位平均折叠自由能以及mRNA柔性.由此,建立了冠状病毒mRNA二级结构数据库.在此基础上,分析每条mRNA序列同义密码子使用度与mRNA二级结构之间的相关性.分析结果表明,有90%的氨基酸所对应的密码子使用度与mRNA茎结构含量显著相关;有75%的氨基酸所对应的密码子使用度与mRNA环结构含量显著相关;有90%的氨基酸所对应的密码子使用度与单位平均折叠自由能显著相关;有85%的氨基酸所对应的密码子使用度与mRNA柔性显著相关.进一步分析发现,同时与茎结构含量和环结构含量都显著相关的密码子,它们的使用度与两种结构含量的相关性截然相反,在所选的参量中,柔性与同义密码子使用度显示出更好的相关性.结果证实,冠状病毒同义密码子的使用对mRNA二级结构存在很大的影响.
Abstract:
The information of 416 mRNA sequences about 45 coronaviruses included in the NCBI was collected.For every coronavirus,firstly,the synonymous codon usage bias of the mRNA sequence of each protein was calculated.Then the secondary structure of every mRNA sequence was predicted,and the stem structure,the loop structure,the average folding free energy and the specific flexibility of mRNA were calculated.After this,a database about mRNA secondary structure of coronaviruses was founded.On this basis,the correlation between synonymous codon usage bias and the four kinds of parameters of mRNA secondary structure were analyzed for every mRNA sequence.The results show that,the corresponding codon usage of 90 percent of amino acids is significantly correlated with the content of stem structure;that of 75 percent of amino acids is significantly correlated with the content of loop structure;that of 90 percent of amino acids is significantly correlated with the average unit folding free energy;and that of 85 percent of amino acids is significantly correlated with the mRNA specific flexibility.Further analysis is found,that for the codes of both significantly correlated with stem structure and loop structure,the correlation between their usage with two kinds of structure contents is completely opposite,the correlation between specific flexibility with synonymous codon usage bias is excellent in all parameters.The results indicate that there are important influences of the synonymous codon usage bias on the mRNA secondary structure.

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备注/Memo

备注/Memo:
收稿日期:2015-03-25;改回日期:2015-08-06。
基金项目:内蒙古自治区自然科学基金资助项目(2012MS0115);内蒙古自治区研究生教育创新计划资助项目(S20141013523);内蒙古师范大学研究生科研创新基金资助项目(CXJJS14061)
作者简介:黄俏(1990-),女,辽宁盘锦人,2013级硕士研究生.E-mail:418690539@qq.com.
通讯作者:李瑞芳(1974-),女,内蒙古乌兰察布人,副教授,博士.E-mail:liruifang@imnu.edu.cn.
更新日期/Last Update: 1900-01-01