Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, New York 14627-0216, USA.
RNA. 2011 Jun;17(6):991-1011. doi: 10.1261/rna.2619511. Epub 2011 May 2.
Influenza A is a negative sense RNA virus of significant public health concern. While much is understood about the life cycle of the virus, knowledge of RNA secondary structure in influenza A virus is sparse. Predictions of RNA secondary structure can focus experimental efforts. The present study analyzes coding regions of the eight viral genome segments in both the (+) and (-) sense RNA for conserved secondary structure. The predictions are based on identifying regions of unusual thermodynamic stabilities and are correlated with studies of suppression of synonymous codon usage (SSCU). The results indicate that secondary structure is favored in the (+) sense influenza RNA. Twenty regions with putative conserved RNA structure have been identified, including two previously described structured regions. Of these predictions, eight have high thermodynamic stability and SSCU, with five of these corresponding to current annotations (e.g., splice sites), while the remaining 12 are predicted by the thermodynamics alone. Secondary structures with high conservation of base-pairing are proposed within the five regions having known function. A combination of thermodynamics, amino acid and nucleotide sequence comparisons along with SSCU was essential for revealing potential secondary structures.
甲型流感是一种具有重要公共卫生意义的负义 RNA 病毒。尽管人们对病毒的生命周期有了很多了解，但对甲型流感病毒 RNA 的二级结构知之甚少。RNA 二级结构的预测可以集中实验工作。本研究分析了正、负义 RNA 中八个病毒基因组片段的编码区的保守二级结构。这些预测是基于识别异常热力学稳定性区域，并与抑制同义密码子使用（SSCU）的研究相关联。结果表明，二级结构在正义流感 RNA 中受到青睐。已经确定了 20 个具有潜在保守 RNA 结构的区域，包括两个先前描述的结构化区域。在这些预测中，有 8 个具有高热力学稳定性和 SSCU，其中 5 个与当前注释（例如剪接位点）相对应，而其余 12 个则仅由热力学预测。在具有已知功能的五个区域内提出了具有碱基配对高度保守的二级结构。热力学、氨基酸和核苷酸序列比较以及 SSCU 的组合对于揭示潜在的二级结构至关重要。
