RNA virus evasion of nonsense-mediated decay.
RNA virus evasion of nonsense-mediated decay.
复制标题
DOI：
10.1371/journal.ppat.1007459
复制
发表时间：
2018-11
期刊：
影响因子：
6.7
通讯作者：
Simon AE
中科院分区：
文献类型：
--
作者：
May JP;Yuan X;Sawicki E;Simon AE
无义介导的衰变（NMD）是一种宿主RNA控制途径，它可以去除由于突变或剪接缺陷引起的过早终止密码子（ptc）而产生的具有长3 '非翻译区（utr）的异常转录本。为了最大限度地发挥编码潜力，RNA病毒通常含有内部定位的停止密码子，这些密码子也应该是NMD的主要目标。利用基于农业浸润的NMD检测方法，我们在本烟中鉴定出萝卜皱缩病毒（TCV）卡莫病毒基因组中具有NMD抗性的两个片段。TCV p28终止密码子下游的核糖体读出结构稳定了nmd敏感报告基因，来自伞状病毒豌豆生长花叶病毒的移框元件也稳定了nmd敏感报告基因。此外，TCV 3 ' UTR起始处的51-nt非结构化区（USR）插入到不相关的nmd敏感3 ' UTR中时，nmd抗性增加3倍。尽管在类似区域中没有序列相似性，但其他几个卡莫病毒3 ' utr也根据结构的不同赋予了不同程度的NMD抗性。相反，这些区域在nmd靶向停止密码子之后显示出明显缺乏RNA结构。通过将USR中的19个嘧啶转化为嘌呤，nmd抗性仅略有降低，但当在USR下游引入2-nt突变时，抗性被消除，该突变通过形成稳定的发夹大大增加了USR中的二级结构。同样的2-nt突变也增强了独立于基因组RNA表达的亚基因组RNA的NMD易感性。大多数卡莫病毒在其3′UTR的5′端保守缺乏RNA结构，这可能有助于增强亚基因组RNA的稳定性，从而增加编码衣壳蛋白的表达，该蛋白也具有RNA沉默抑制因子的功能。这些结果表明，TCV基因组具有固有的nmd抗性特征，这些策略可能在RNA病毒和具有长3 ' utr的nmd抗性宿主mrna中广泛存在。无义介导的衰变（NMD）在保持宿主转录组的完整性方面起着关键作用。携带过早终止密码子（ptc）的RNA转录本受到NMD的影响，因为它们可以导致与许多遗传疾病和癌症相关的截短有害蛋白质的表达。已知长3 ' utr促进NMD，但许多天然包含长3 ' utr的转录本受到保护。除了结合多嘧啶束结合蛋白1的终止密码子下游的序列外，这种保护的性质和可能的共性尚不清楚。多顺反电子RNA病毒基因组中的天然终止密码子与ptc相似，因此这些病毒必须发展出对抗NMD的手段来维持基因组的稳定性。我们发现紧凑的、正义的芜菁皱缩病毒通过几种策略逃避NMD，包括在外壳蛋白（CP）终止密码子的下游有一个非结构化的RNA区域。CP在病毒生命周期中是一种重要的蛋白质，因为CP是抑制宿主抗病毒RNA沉默和形成病毒粒子所必需的。我们提供的证据表明，当这个51-nt非结构化序列位于停止密码子的下游时，可以保护NMD敏感模板免受NMD的侵害。与真正的UPF1靶点（NMD敏感）相比，在一组bb6000个人类NMD抗性转录本中，停止密码子后面的非结构区域富集了4倍以上，这表明这可能是一种广泛传播的策略，可以保护其他易感转录本免受NMD的影响。
Nonsense-mediated decay (NMD) is a host RNA control pathway that removes aberrant transcripts with long 3’ untranslated regions (UTRs) due to premature termination codons (PTCs) that arise through mutation or defective splicing. To maximize coding potential, RNA viruses often contain internally located stop codons that should also be prime targets for NMD. Using an agroinfiltration-based NMD assay in Nicotiana benthamiana, we identified two segments conferring NMD-resistance in the carmovirus Turnip crinkle virus (TCV) genome. The ribosome readthrough structure just downstream of the TCV p28 termination codon stabilized an NMD-sensitive reporter as did a frameshifting element from umbravirus Pea enation mosaic virus. In addition, a 51-nt unstructured region (USR) at the beginning of the TCV 3’ UTR increased NMD-resistance 3-fold when inserted into an unrelated NMD-sensitive 3’ UTR. Several additional carmovirus 3’ UTRs also conferred varying levels of NMD resistance depending on the construct despite no sequence similarity in the analogous region. Instead, these regions displayed a marked lack of RNA structure immediately following the NMD-targeted stop codon. NMD-resistance was only slightly reduced by conversion of 19 pyrimidines in the USR to purines, but resistance was abolished when a 2-nt mutation was introduced downstream of the USR that substantially increased the secondary structure in the USR through formation of a stable hairpin. The same 2-nt mutation also enhanced the NMD susceptibility of a subgenomic RNA expressed independently of the genomic RNA. The conserved lack of RNA structure among most carmoviruses at the 5’ end of their 3’ UTR could serve to enhance subgenomic RNA stability, which would increase expression of the encoded capsid protein that also functions as the RNA silencing suppressor. These results demonstrate that the TCV genome has features that are inherently NMD-resistant and these strategies could be widespread among RNA viruses and NMD-resistant host mRNAs with long 3’ UTRs. Nonsense-mediated decay (NMD) serves a critical role in preserving the integrity of the host transcriptome. RNA transcripts bearing premature termination codons (PTCs) are subject to NMD as they can lead to expression of truncated, deleterious proteins that are associated with many genetic diseases and cancer. Long 3’ UTRs are known to promote NMD, but many transcripts that naturally contain long 3’ UTRs are protected. The nature and possible commonality of this protection is not known aside from sequences just downstream from termination codons that bind polypyrimidine tract binding protein 1. Natural stop codons in the genomes of multicistronic RNA viruses would resemble PTCs and thus these viruses must have developed the means to combat NMD to maintain genome stability. We show that the compact, positive-sense Turnip crinkle virus evades NMD by several strategies including having an unstructured region of RNA immediately downstream of the coat protein (CP) termination codon. CP is a critical protein in the virus lifecycle since CP is required to both inhibit host antiviral RNA silencing and form virions. We provide evidence that this 51-nt unstructured sequence can protect NMD-sensitive templates from NMD when placed just downstream of stop codons. Unstructured regions following stop codons were over 4-fold enriched in a set of >6000 human NMD-resistant transcripts versus bona fide UPF1 targets (NMD-sensitive), suggesting this may be a wide-spread strategy for protecting otherwise susceptible transcripts from NMD.
登录
查看更多内容
影响因子：
4.6
作者：
Causier B;Li Z;De Smet R;Lloyd JPB;Van de Peer Y;Davies B
通讯作者：
Davies B
影响因子：
64.5
作者：
Hogg JR;Goff SP
通讯作者：
Goff SP
影响因子：
7
作者：
Imamachi N;Salam KA;Suzuki Y;Akimitsu N
通讯作者：
Akimitsu N
影响因子：
16.8
作者：
Bühler, M;Steiner, S;Mühlemann, O
通讯作者：
Mühlemann, O
影响因子：
64.8
作者：
Amrani, N;Ganesan, R;Jacobson, A
通讯作者：
Jacobson, A