CpG and UpA dinucleotides in both coding and non-coding regions of echovirus 7 inhibit replication initiation post-entry.
CpG and UpA dinucleotides in both coding and non-coding regions of echovirus 7 inhibit replication initiation post-entry.
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DOI：
10.7554/elife.29112
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发表时间：
2017-09-29
期刊：
影响因子：
7.7
通讯作者：
Simmonds P
中科院分区：
文献类型：
--
作者：
Fros JJ;Dietrich I;Alshaikhahmed K;Passchier TC;Evans DJ;Simmonds P
大多数脊椎动物和植物RNA和小DNA病毒抑制基因组CpG和UpA二核苷酸频率，显然模仿宿主mRNA组成。通过一种完全未知的机制，增加CpG/UpA二核苷酸的毒性使病毒减弱。在几种细胞类型中使用埃可病毒7（E7）模型，我们表明，在E7复制的限制，增加CpG/UpA二核苷酸突变体病毒进入后立即发生，与传入的病毒粒子未能形成复制复合物。CpG/UpA-高病毒储备物的序列显示没有证据表明增加的突变错误会使它们复制缺陷，这些病毒RNA在细胞质应激颗粒中没有差异隔离，也没有诱导系统性抗病毒状态。重要的是，限制不是通过对翻译效率的影响介导的，因为具有插入非编码区的高CpG/UpA序列的复制子类似地复制缺陷。因此，宿主细胞具有内在的防御途径，其防止具有增加的CpG/UpA频率的病毒复制，而与密码子使用无关。生物以DNA分子或一种称为RNA的相关化学物质的形式储存遗传物质。DNA和RNA都含有被称为碱基的结构单元。有几种不同类型的碱基，它们在DNA或RNA分子中出现的特定顺序编码遗传信息。在RNA中，这些碱基被称为胞嘧啶、鸟嘌呤、腺嘌呤和尿嘧啶（或简称为C、G、A和U）。碱基在DNA和RNA中出现的顺序可能会有很大的偏差。例如，在有骨架的动物（也称为脊椎动物）的RNA中，胞嘧啶之后是鸟嘌呤，尿嘧啶之后是腺嘌呤的出现频率低于数学预测。病毒是一种含有DNA或RNA的颗粒，被蛋白质制成的外壳所包围。它们不能自己繁殖，因此必须侵入宿主生物体的细胞。感染脊椎动物的病毒模仿宿主中的碱基偏好，这一策略可能有助于病毒的遗传物质隐藏在宿主细胞中。先前的实验已经表明，经过改造的病毒更容易被消除，这些病毒具有更多的胞嘧啶，然后是鸟嘌呤，尿嘧啶，然后是腺嘌呤。然而，尚不清楚这是如何运作的。弗罗斯等人研究了一种名为埃可病毒7的病毒在人类和其他几种脊椎动物细胞内繁殖的能力。实验表明，人为增加该病毒中胞嘧啶、鸟嘌呤和尿嘧啶、腺嘌呤的数量，会降低病毒进入宿主细胞后立即繁殖的能力。变化的位置对病毒被抑制的强度没有任何影响。此外，Fros等人证实，这些变化不会影响病毒遗传物质制造繁殖和制造外壳所需蛋白质的能力。这表明宿主特异性地阻止病毒遗传物质被复制，这仅仅是基于病毒遗传物质中碱基的顺序。这些发现提供了证据，证明人类和其他脊椎动物细胞含有识别并快速响应外来遗传物质的因子，这些遗传物质的遗传密码中存在与自身不匹配的偏差。在未来，人工增加病毒基因组中特定碱基序列的频率可以用来设计更有效的疫苗来对抗病毒引起的疾病。
Most vertebrate and plant RNA and small DNA viruses suppress genomic CpG and UpA dinucleotide frequencies, apparently mimicking host mRNA composition. Artificially increasing CpG/UpA dinucleotides attenuates viruses through an entirely unknown mechanism. Using the echovirus 7 (E7) model in several cell types, we show that the restriction in E7 replication in mutants with increased CpG/UpA dinucleotides occurred immediately after viral entry, with incoming virions failing to form replication complexes. Sequences of CpG/UpA-high virus stocks showed no evidence of increased mutational errors that would render them replication defective, these viral RNAs were not differentially sequestered in cytoplasmic stress granules nor did they induce a systemic antiviral state. Importantly, restriction was not mediated through effects on translation efficiency since replicons with high CpG/UpA sequences inserted into a non-coding region were similarly replication defective. Host-cells thus possess intrinsic defence pathways that prevent replication of viruses with increased CpG/UpA frequencies independently of codon usage. Living things store their genetic material as molecules of DNA or a related chemical called RNA. Both DNA and RNA contain building blocks known as bases. There are several different types of bases and the specific order they appear in a DNA or RNA molecule encodes the genetic information. In RNA these bases are known as cytosine, guanine, adenine and uracil (or C, G, A and U for short). The order that bases appear in DNA and RNA can be highly biased. For example, in RNAs from animals with backbones (also known as vertebrates), cytosine followed by guanine and uracil followed by adenine occur less often than mathematics would predict. Viruses are particles that contain DNA or RNA surrounded by a coat made of proteins. They are unable to multiply by themselves and must therefore invade the cells of host organisms. Viruses that infect vertebrates mimic the base biases found in their host, a strategy that likely helps the virus’ genetic material to hide within host cells. Previous experiments have shown that viruses engineered to have more cytosines followed by guanines and uracils followed by adenines were easier to eliminate. However, it is not clear how this worked. Fros et al. investigated the ability of a virus called echovirus 7 to multiply inside the cells of humans and several other vertebrates. The experiments show that artificially increasing the number of cytosines followed by guanines and uracils followed by adenines in this virus reduced the ability of the virus to multiply immediately after the virus had entered the host cell. The location of the changes did not have any effect on how strongly the virus was inhibited. Furthermore, Fros et al. confirmed that these changes did not affect the ability of the virus’ genetic material to make the proteins it needs to multiply and make its coat. This suggests that the host specifically prevents the virus genetic material from being copied, solely based on the order of the bases in the viral genetic material. These findings provide evidence that human and other vertebrate cells contain factors that recognize and rapidly respond to foreign genetic material with biases in their genetic code that do not match their own. In the future, artificially increasing the frequency of specific orders of bases in viral genomes could be used to design more effective vaccines against diseases caused by viruses.