A three-stemmed mRNA pseudoknot in the SARS coronavirus frameshift signal.
A three-stemmed mRNA pseudoknot in the SARS coronavirus frameshift signal.
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DOI：
10.1371/journal.pbio.0030172
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发表时间：
2005-06
期刊：
影响因子：
9.8
通讯作者：
Dinman JD
中科院分区：
文献类型：
--
作者：
Plant EP;Pérez-Alvarado GC;Jacobs JL;Mukhopadhyay B;Hennig M;Dinman JD
广泛的核糖核酸病毒利用程序化的−-1核糖体移码来产生病毒融合蛋白。对SARS冠状病毒基因组ORF1a和ORF1b重叠区的检查表明，与所有冠状病毒一样，−1核糖体框架移位可被病毒用来产生融合蛋白。对移码信号的计算分析预测，存在一个包含三个双链RNA茎结构的mRNA假结，而不是两个。系统发育分析表明，GenBank数据库中所有其他冠状病毒的移码信号中潜在的三茎假结节是保守的。虽然三茎结构的存在得到了核酸酶图谱和二维核磁共振研究的支持，但我们的发现表明，茎结构之间的相互作用可能导致A-型RNA的局部扭曲。这些扭曲在茎2和3中预测的A-凸起附近尤其明显。体外和体内移码分析表明，SARS-CoV移码信号在功能上与其他病毒移码信号相似：它在所有标准的检测系统中促进有效的移码，并且对已知影响酵母病毒移码效率的药物和基因突变敏感。诱变研究表明，茎2和茎3的特定序列和结构对于有效的移码都是重要的。我们已经确定了一个新的RNA结构基序，它能够促进有效的程序性核糖体移码。冠状病毒中三茎mRNA假结结构的高度保守性表明这为抗病毒治疗提供了一个新的靶点。在SARS病毒基因组中发现了一个新的结构和保守的元件。该元件对基因表达很重要，可能成为抗病毒药物的有用靶点。
A wide range of RNA viruses use programmed −1 ribosomal frameshifting for the production of viral fusion proteins. Inspection of the overlap regions between ORF1a and ORF1b of the SARS-CoV genome revealed that, similar to all coronaviruses, a programmed −1 ribosomal frameshift could be used by the virus to produce a fusion protein. Computational analyses of the frameshift signal predicted the presence of an mRNA pseudoknot containing three double-stranded RNA stem structures rather than two. Phylogenetic analyses showed the conservation of potential three-stemmed pseudoknots in the frameshift signals of all other coronaviruses in the GenBank database. Though the presence of the three-stemmed structure is supported by nuclease mapping and two-dimensional nuclear magnetic resonance studies, our findings suggest that interactions between the stem structures may result in local distortions in the A-form RNA. These distortions are particularly evident in the vicinity of predicted A-bulges in stems 2 and 3. In vitro and in vivo frameshifting assays showed that the SARS-CoV frameshift signal is functionally similar to other viral frameshift signals: it promotes efficient frameshifting in all of the standard assay systems, and it is sensitive to a drug and a genetic mutation that are known to affect frameshifting efficiency of a yeast virus. Mutagenesis studies reveal that both the specific sequences and structures of stems 2 and 3 are important for efficient frameshifting. We have identified a new RNA structural motif that is capable of promoting efficient programmed ribosomal frameshifting. The high degree of conservation of three-stemmed mRNA pseudoknot structures among the coronaviruses suggests that this presents a novel target for antiviral therapeutics. A new structural and conserved element is identified within the SARS virus genome. The element is important for gene expression, and might be a useful target for antiviral drugs.
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