Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India.
International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
BMC Genomics. 2019 May 16;20(1):382. doi: 10.1186/s12864-019-5731-0.
Several lines of evidence suggest that recombination plays a central role in replication and evolution of herpes simplex virus-1 (HSV-1). G-quadruplex (G4)-motifs have been linked to recombination events in human and microbial genomes, but their role in recombination has not been studied in DNA viruses.
The availability of near full-length sequences from 40 HSV-1 recombinant strains with exact position of the recombination breakpoints provided us with a unique opportunity to investigate the role of G4-motifs in recombination among herpes viruses. We mapped the G4-motifs in the parental and all the 40 recombinant strains. Interestingly, the genome-wide distribution of breakpoints closely mirrors the G4 densities in the HSV-1 genome; regions of the genome with higher G4 densities had higher number of recombination breakpoints. Biophysical characterization of oligonucleotides from a subset of predicted G4-motifs confirmed the formation of G-quadruplex structures. Our analysis also reveals that G4-motifs are enriched in regions flanking the recombination breakpoints. Interestingly, about 11% of breakpoints lie within a G4-motif, making these DNA secondary structures hotspots for recombination in the HSV-1 genome. Breakpoints within G4-motifs predominantly lie within G4-clusters rather than individual G4-motifs. Of note, we identified the terminal guanosine of G4-clusters at the boundaries of the U (unique long) region on either side of the OriL (origin of replication within U) represented the commonest breakpoint among the HSV-1 recombinants.
Our findings suggest a correlation between the HSV-1 recombination landscape and the distribution of G4-motifs and G4-clusters, with possible implications for the evolution of DNA viruses.
有几条证据表明，重组在单纯疱疹病毒 1（HSV-1）的复制和进化中起着核心作用。G-四链体（G4）基序与人类和微生物基因组中的重组事件有关，但它们在 DNA 病毒中的重组作用尚未得到研究。
来自 40 株 HSV-1 重组株的近乎全长序列的可用性，以及重组断点的确切位置，为我们提供了一个独特的机会来研究 G4 基序在疱疹病毒之间重组中的作用。我们绘制了亲本和所有 40 株重组株中的 G4 基序。有趣的是，断点的全基因组分布与 HSV-1 基因组中的 G4 密度非常吻合；基因组中 G4 密度较高的区域具有较高数量的重组断点。对一组预测的 G4 基序的寡核苷酸进行的生物物理特性分析证实了 G-四链体结构的形成。我们的分析还表明，G4 基序在重组断点的侧翼区域富集。有趣的是，大约 11%的断点位于 G4 基序内，这使得这些 DNA 二级结构成为 HSV-1 基因组中重组的热点。G4 基序内的断点主要位于 G4 簇内，而不是单个 G4 基序内。值得注意的是，我们在 OriL（复制起点位于 U 内）两侧 U（独特长）区域边界的 G4 簇的末端鸟嘌呤中发现了 G4 簇，这是 HSV-1 重组体中最常见的断点。
我们的发现表明 HSV-1 重组景观与 G4 基序和 G4 簇的分布之间存在相关性，这可能对 DNA 病毒的进化产生影响。
