Heterogeneity of the Epstein-Barr Virus (EBV) Major Internal Repeat Reveals Evolutionary Mechanisms of EBV and a Functional Defect in the Prototype EBV Strain B95-8.
Heterogeneity of the Epstein-Barr Virus (EBV) Major Internal Repeat Reveals Evolutionary Mechanisms of EBV and a Functional Defect in the Prototype EBV Strain B95-8.
复制标题
DOI：
10.1128/jvi.00920-17
复制
发表时间：
2017-12-01
影响因子：
5.4
通讯作者：
White RE
中科院分区：
文献类型：
--
作者：
Ba Abdullah MM;Palermo RD;Palser AL;Grayson NE;Kellam P;Correia S;Szymula A;White RE
爱泼斯坦-巴尔病毒(EBV)是一种普遍存在的人类病原体，可导致几种类型的淋巴瘤和癌症。像其他疱疹病毒一样，EBV通过与宿主的共同进化和病毒株之间的基因交换而多样化。EBV基因组的序列分析异常具有挑战性，因为病毒内有大量和长度的重复区域。在这里，我们描述了EBV大的内部重复序列1(IR1；也称为BamW重复序列)的序列组装和分析，该序列针对70多个菌株。潜伏蛋白EBV核抗原领导蛋白(EBNA-LP)的多样性主要存在于IR1下游的外显子内。超过80%的菌株保留了BWRF1开放阅读框(ORF)的完整性，而截短IR1的缺失总是保留了BWRF1。保守区域包括IR1潜伏期启动子(WP)和BWRF1上游的一个区域和两个区域。IR1在70%的毒株中是异质性的，这种异质性源于毒株之间的序列交换以及自发突变，其中毒株间重组在肿瘤病毒中更为常见。这种遗传交换通常包含1kb的区域，等位基因转换改变了重复序列内小区域的频率，但不是靠近侧翼。这些观察表明，IR1--进而是EBV--通过重组和断点修复而多样化，而IR1的协同进化是由小区域的基因转换驱动的。最后，EBV原型毒株B95-8在一个IR1重复单位内包含四个非共识变异体，包括EBNA-LP基因中的一个终止密码子。修复IR1可提高EBNA-LP水平和B95-8细菌人工染色体(BAC)转化质量。重要性爱泼斯坦-巴尔病毒(EBV)感染了世界上大多数人口，但只在一小部分人中引起疾病。然而，全世界超过1%的癌症可归因于EBV。最近的测序项目调查了病毒多样性，以确定不同的菌株是否有不同的疾病影响，已经排除了重复序列的区域，因为它们在技术上更具挑战性。这里我们分析了EBV(IR1)中最大的重复序列。我们首先描述了IR1中编码的蛋白质序列的变异。在研究每个毒株重复序列的变异时，我们在EBV的主要实验室毒株中发现了一个突变，它会损害病毒的功能，我们认为肿瘤相关病毒可能更有可能包含来自两个毒株的混合DNA。这种混合的模式表明，通过从另一个菌株(或重复单位)复制序列来修复DNA损伤，序列可以在菌株之间(以及重复序列内)传播。
Epstein-Barr virus (EBV) is a ubiquitous pathogen of humans that can cause several types of lymphoma and carcinoma. Like other herpesviruses, EBV has diversified through both coevolution with its host and genetic exchange between virus strains. Sequence analysis of the EBV genome is unusually challenging because of the large number and lengths of repeat regions within the virus. Here we describe the sequence assembly and analysis of the large internal repeat 1 of EBV (IR1; also known as the BamW repeats) for more than 70 strains. The diversity of the latency protein EBV nuclear antigen leader protein (EBNA-LP) resides predominantly within the exons downstream of IR1. The integrity of the putative BWRF1 open reading frame (ORF) is retained in over 80% of strains, and deletions truncating IR1 always spare BWRF1. Conserved regions include the IR1 latency promoter (Wp) and one zone upstream of and two within BWRF1. IR1 is heterogeneous in 70% of strains, and this heterogeneity arises from sequence exchange between strains as well as from spontaneous mutation, with interstrain recombination being more common in tumor-derived viruses. This genetic exchange often incorporates regions of <1 kb, and allelic gene conversion changes the frequency of small regions within the repeat but not close to the flanks. These observations suggest that IR1—and, by extension, EBV—diversifies through both recombination and breakpoint repair, while concerted evolution of IR1 is driven by gene conversion of small regions. Finally, the prototype EBV strain B95-8 contains four nonconsensus variants within a single IR1 repeat unit, including a stop codon in the EBNA-LP gene. Repairing IR1 improves EBNA-LP levels and the quality of transformation by the B95-8 bacterial artificial chromosome (BAC). IMPORTANCE Epstein-Barr virus (EBV) infects the majority of the world population but causes illness in only a small minority of people. Nevertheless, over 1% of cancers worldwide are attributable to EBV. Recent sequencing projects investigating virus diversity to see if different strains have different disease impacts have excluded regions of repeating sequence, as they are more technically challenging. Here we analyze the sequence of the largest repeat in EBV (IR1). We first characterized the variations in protein sequences encoded across IR1. In studying variations within the repeat of each strain, we identified a mutation in the main laboratory strain of EBV that impairs virus function, and we suggest that tumor-associated viruses may be more likely to contain DNA mixed from two strains. The patterns of this mixing suggest that sequences can spread between strains (and also within the repeat) by copying sequence from another strain (or repeat unit) to repair DNA damage.