Human cytomegalovirus evades ZAP detection by suppressing CpG dinucleotides in the major immediate early 1 gene
Human cytomegalovirus evades ZAP detection by suppressing CpG dinucleotides in the major immediate early 1 gene
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DOI：
10.1371/journal.ppat.1008844
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发表时间：
2020-09-01
期刊：
影响因子：
6.7
通讯作者：
Grey, Finn
中科院分区：
文献类型：
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作者：
Lin, Yao-Tang;Chiweshe, Stephen;Grey, Finn
脊椎动物的RNA和小DNA病毒的基因组显示出显著的CpG二核苷酸频率抑制。牺牲性增加二核苷酸频率的结果在病毒复制的大幅衰减，这表明这些组成的变化可能有助于识别非自身RNA序列。最近，干扰素诱导蛋白ZAP被鉴定为负责通过直接结合和可能的下游靶向降解来感测病毒RNA中的CpG的宿主因子。使用阵列干扰素刺激的基因表达文库筛选，我们确定ZAPS，及其相关因子TRIM25，作为人巨细胞病毒（HCMV）复制的抑制剂。ZAPS和TRIM25的外源表达显著降低了病毒复制，而敲低导致病毒复制增加。HCMV表现出惊人的CpG代表性的异质性模式，在IE1主要立即早期转录本中特异性抑制CpG基序，这在随后表达的基因中是不存在的。我们证明了抑制IE1基因中的CpG二核苷酸可以逃避ZAP的抑制作用。我们发现，急性病毒复制是互斥的高水平的细胞ZAP，可能解释了较高水平的CpG在病毒基因表达后IE1由于ZAP在感染细胞中的压力损失。最后，我们表明，TRIM25调节在HCMV感染和干扰素诱导过程中ZAP短和长亚型之间的选择性剪接，TRIM25的敲低导致ZAPS降低和相应的ZAPL表达增加。这些结果首次表明，ZAP是一种有效的宿主限制因子，对大的DNA病毒和HCMV逃避ZAP检测通过抑制主要立即早期1转录内的CpG二核苷酸。此外，TRIM25是需要通过调节选择性splicing.Author摘要病毒的进化成功依赖于他们的能力，以规避防御机制的主机，他们感染的干扰素诱导的短亚型的ZAP的有效上调。这些防御机制依赖于宿主区分自我和非自我的能力，从而识别和抑制入侵的病原体，最终目标是遏制或根除感染。病毒基因组的特定核苷酸组成已被认为是宿主防御的潜在靶标。内源性病毒已经进化为反映哺乳动物基因组中CpG基序的表达不足。最近，宿主因子ZAP已显示出识别和抑制具有人工高CpG含量的RNA病毒，证明了一种新的宿主防御机制。在这里，我们表明ZAP可以有效地抑制人巨细胞病毒。反过来，该病毒已经进化为降低感染宿主细胞后立即表达的病毒基因中的CpG水平，从而逃避ZAP识别。这项研究表明，除了靶向RNA病毒外，ZAP还可以靶向大型DNA病毒，反过来，这些病毒已经进化出逃避机制，确保有效复制。
The genomes of RNA and small DNA viruses of vertebrates display significant suppression of CpG dinucleotide frequencies. Artificially increasing dinucleotide frequencies results in substantial attenuation of virus replication, suggesting that these compositional changes may facilitate recognition of non-self RNA sequences. Recently, the interferon inducible protein ZAP, was identified as the host factor responsible for sensing CpG in viral RNA, through direct binding and possibly downstream targeting for degradation. Using an arrayed interferon stimulated gene expression library screen, we identified ZAPS, and its associated factor TRIM25, as inhibitors of human cytomegalovirus (HCMV) replication. Exogenous expression of ZAPS and TRIM25 significantly reduced virus replication while knockdown resulted in increased virus replication. HCMV displays a strikingly heterogeneous pattern of CpG representation with specific suppression of CpG motifs within the IE1 major immediate early transcript which is absent in subsequently expressed genes. We demonstrated that suppression of CpG dinucleotides in the IE1 gene allows evasion of inhibitory effects of ZAP. We show that acute virus replication is mutually exclusive with high levels of cellular ZAP, potentially explaining the higher levels of CpG in viral genes expressed subsequent to IE1 due to the loss of pressure from ZAP in infected cells. Finally, we show that TRIM25 regulates alternative splicing between the ZAP short and long isoforms during HCMV infection and interferon induction, with knockdown of TRIM25 resulting in decreased ZAPS and corresponding increased ZAPL expression. These results demonstrate for the first time that ZAP is a potent host restriction factor against large DNA viruses and that HCMV evades ZAP detection through suppression of CpG dinucleotides within the major immediate early 1 transcript. Furthermore, TRIM25 is required for efficient upregulation of the interferon inducible short isoform of ZAP through regulation of alternative splicing.Author summary The evolutionary success of viruses is dependent on their ability to circumvent defence mechanisms of the hosts they infect. These defence mechanisms rely on the ability of the host to discriminate between self and non-self, allowing identification and inhibition of invading pathogens, with the ultimate goal of containing or eradicating the infection. The specific nucleotide composition of viral genomes has been recognised as a potential target of host defences. Endogenous viruses have evolved to mirror underrepresentation of CpG motifs in mammalian genomes. Recently, the host factor ZAP has been shown to recognise and inhibit RNA viruses with artificially high CpG content, demonstrating a novel host defence mechanism. Here, we show that ZAP can potently inhibit human cytomegalovirus. In turn, the virus has evolved to reduce the levels of CpG in viral genes expressed immediately after infection of host cells, allowing evasion of ZAP recognition. This study demonstrates that in addition to targeting RNA viruses, ZAP can target large DNA viruses and, in turn, these viruses have evolved evasion mechanisms, ensuring efficient replication.