Conserved Secondary Structures in Viral mRNAs
Conserved Secondary Structures in Viral mRNAs
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DOI：
10.3390/v11050401
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发表时间：
2019-05-01
期刊：
影响因子：
4.7
通讯作者：
Frishman, Dmitrij
中科院分区：
文献类型：
--
作者：
Kiening, Michael;Ochsenreiter, Roman;Frishman, Dmitrij
非翻译区和蛋白质编码区的RNA二级结构已被证明在调节过程和病毒复制周期中发挥重要作用。虽然非编码区的结构已经被广泛研究，但对蛋白质编码mRNAs的结构谱系，特别是对病毒的结构谱系，缺乏全面的概述。大分子的二级结构预测，如长的mRNAs，仍然是一个具有挑战性的任务，因为理论上一个序列可以折叠成的结构的总数随着序列长度呈指数增长。我们将结构预测管道应用于病毒同源基因组，该管道首先识别潜在结构区域的局部边界，然后预测它们的功能重要性。使用这个程序，直系组被分成结构上同质的子组，我们称之为亚VOG。这是第一次汇编病毒编码区潜在功能保守的RNA结构，覆盖了完整的RefSeq病毒数据库。我们能够从以前的研究中恢复结构元素，并发现了各种新的结构区域。亚VOG可通过我们的网络资源RNASIV(病毒中的RNA结构)获得。
RNA secondary structure in untranslated and protein coding regions has been shown to play an important role in regulatory processes and the viral replication cycle. While structures in non-coding regions have been investigated extensively, a thorough overview of the structural repertoire of protein coding mRNAs, especially for viruses, is lacking. Secondary structure prediction of large molecules, such as long mRNAs remains a challenging task, as the contingent of structures a sequence can theoretically fold into grows exponentially with sequence length. We applied a structure prediction pipeline to Viral Orthologous Groups that first identifies the local boundaries of potentially structured regions and subsequently predicts their functional importance. Using this procedure, the orthologous groups were split into structurally homogenous subgroups, which we call subVOGs. This is the first compilation of potentially functional conserved RNA structures in viral coding regions, covering the complete RefSeq viral database. We were able to recover structural elements from previous studies and discovered a variety of novel structured regions. The subVOGs are available through our web resource RNASIV (RNA structure in viruses).