The influence of CpG and UpA dinucleotide frequencies on RNA virus replication and characterization of the innate cellular pathways underlying virus attenuation and enhanced replication
The influence of CpG and UpA dinucleotide frequencies on RNA virus replication and characterization of the innate cellular pathways underlying virus attenuation and enhanced replication
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DOI：
10.1093/nar/gku075
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发表时间：
2014-04-01
影响因子：
14.9
通讯作者：
Simmonds, Peter
中科院分区：
文献类型：
--
作者：
Atkinson, Nicky J.;Witteveldt, Jeroen;Simmonds, Peter
大多数感染哺乳动物和其他脊椎动物的RNA病毒显示CpG和UpA二核苷酸频率的显著抑制。为了研究这一功能，构建了小核糖核酸病毒埃可病毒7（E7）的突变体，其在两个1.1-1.3 Kbase区域中具有改变的CpG和UpA组成。与野生型病毒相比，那些具有增加的CpG和UpA频率的病毒表现出受损的复制动力学和更高的RNA/感染性比率。值得注意的是，去除CpG和UpAs的突变体显示出增强的复制、更大的噬斑和在共感染时迅速胜过野生型病毒。从报告基因中去除CpG和UpAs的荧光素酶表达E7亚基因组复制子显示出100倍的发光。E7和突变体对外源性β-干扰素的敏感性相当，没有证据表明ADAR 1或模式识别受体RIG-I，MDA 5或PKR的差异识别。然而，激酶抑制剂roscovitine和C16部分或完全逆转高CpG和UpA突变体的减毒表型，可能通过抑制目前未表征的模式识别受体，响应RNA组合物。产生具有增强的复制动力学的病毒在疫苗生产和报告基因构建中具有应用。更根本的是，这些发现引入了一种新的进化范式，其中病毒基因组的二核苷酸组成受到独立于编码能力的选择压力，并深刻影响宿主-病原体相互作用。
Most RNA viruses infecting mammals and other vertebrates show profound suppression of CpG and UpA dinucleotide frequencies. To investigate this functionally, mutants of the picornavirus, echovirus 7 (E7), were constructed with altered CpG and UpA compositions in two 1.1-1.3 Kbase regions. Those with increased frequencies of CpG and UpA showed impaired replication kinetics and higher RNA/infectivity ratios compared with wild-type virus. Remarkably, mutants with CpGs and UpAs removed showed enhanced replication, larger plaques and rapidly outcompeted wild-type virus on co-infections. Luciferase-expressing E7 sub-genomic replicons with CpGs and UpAs removed from the reporter gene showed 100-fold greater luminescence. E7 and mutants were equivalently sensitive to exogenously added interferon-beta, showed no evidence for differential recognition by ADAR1 or pattern recognition receptors RIG-I, MDA5 or PKR. However, kinase inhibitors roscovitine and C16 partially or entirely reversed the attenuated phenotype of high CpG and UpA mutants, potentially through inhibition of currently uncharacterized pattern recognition receptors that respond to RNA composition. Generating viruses with enhanced replication kinetics has applications in vaccine production and reporter gene construction. More fundamentally, the findings introduce a new evolutionary paradigm where dinucleotide composition of viral genomes is subjected to selection pressures independently of coding capacity and profoundly influences host-pathogen interactions.