Virus Evolution Through Horizontal Gene Transfer

通过水平基因转移的病毒进化

• 批准号: 10415466
• 负责人: Stephen Goldstein
• 金额: $ 0.25万
• 依托单位: UNIVERSITY OF UTAH
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-08-24 至 2024-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10415466
• 关键词: Antiviral Agents; Archaea; Archaeal Genes; Automobile Driving; Bacteria; Bacterial Genes; Biochemistry; Cell Culture Techniques; Cells; Complement; Complementary DNA; Complex; Computational Technique; Computer Analysis; Cytoplasm; DNA Sequence; DNA Transposable Elements; DNA Viruses; Data; Distal; Ecosystem; Ectopic Expression; Engineering; Environment; Eukaryota; Evolution; Family; Frequencies; Genes; Genetic; Genetic Materials; Genetic Variation; Genome; Growth; Homologous Gene; Horizontal Gene Transfer; Immune; Immune response; Immunofluorescence Immunologic; In Vitro; Insertional Mutagenesis; L1 Elements; Life; Mammalian Cell; Maps; Mediating; Messenger RNA; Microbe; Modeling; Modernization; Molecular Biology; Molecular Computations; Movement; Organism; Phosphorylation Site; Phylogenetic Analysis; Play; Population; Poxviridae; Process; Protein Inhibition; Proteins; Pseudogenes; RNA-Directed DNA Polymerase; Recording of previous events; Regulation; Retrotransposition; Retrotransposon; Role; Serial Passage; Shapes; Source; Structure; System; Taxonomy; Testing; Training; Vaccinia Virus Study; Vaccinia virus; Vertebrates; Viral; Viral Genes; Viral Genome; Virus; Virus Diseases; Virus Replication; Work; Yeasts; co-infection; genetic element; genetic information; improved; inhibitor/antagonist; insight; melting; nanopore; next generation sequencing; novel; post-doctoral training; pressure; protein kinase R; protein kinase inhibitor; recombinant virus; theories; viral fitness; virology; yeast protein

Project Summary Horizontal gene transfer (HGT) is a well characterized phenomenon driving the evolution and genetic diversity of bacteria but its underlying mechanisms and consequences in the context of viral evolution are far less well- understood. Poxviruses and other large DNA viruses encode numerous genes of clear cellular origin. I aim to investigate how they get there and evolve following their acquisition. We have demonstrated that LINE-1 (L1) retrotransposons play a key role in the transfer of cellular genes into poxvirus genomes but do not yet understand the dynamics of how this occurs without inducing catastrophic insertional mutagenesis. How newly acquired genes evolve proviral functions and avoid deletion due to functional redundancy with their cellular ancestor. The central hypothesis of this proposal is that L1 insertions into poxvirus genomes are enriched in distal regions of the genome, avoiding disruption of essential core genes, where they can evolve to benefit the virus. I will focus on two major outstanding questions emerging from this hypothesis. In Aim 1 I will characterize the interaction between virus replication and cellular L1 machinery. This will comprise spatially defining the interaction within the cytoplasm, understanding if and how L1 activity impacts viral replication, and comprehensively characterizing the frequency and distribution of L1-mediated insertions into the viral genome. To do so I will use a combination of experimental and computational techniques spanning molecular biology, biochemistry, genetics, and next-generation sequencing. In Aim 2 I will seek to elucidate the origin and evolution of poxvirus K3L, a host-derived inhibitor of the antiviral effector PKR. K3L is a structural homolog of vertebrate eIF2 that competitively inhibits PKR-induced translational shutoff. Compared to eIF2 K3L is dramatically truncated and lacks a phosphorylation site, and so cannot mediate the antiviral functions downstream of PKR. Despite this homology, computational and phylogenetic analysis suggests K3L is most closely related to the aIF2 protein of methanogenic archaea and may not have been acquired from the host cell of an ancestral poxvirus but rather from microbes occupying similar or overlapping ecological space. Since my original submission, I have generated new preliminary data that M. fervens aIF2 inhibits vertebrate PKR, giving experimental support to my computational work. I will confirm and expand on these results in mammalian cell culture, and use experimental evolution to model the adaptation of newly acquired viral genes. The recent identification of archaeal-origin genes in other DNA viruses, provides further support for my hypothesis, but K3L would be the first known example in viruses of multicellular eukaryotes. A picture is emerging of viruses as melting pots in nodes of diverse genetic exchange and my proposed studies will illuminate mechanisms of transfer and the participation of a new family of viruses in these exchanges. These studies will advance our understanding of the process of viral co-option of cellular genes as well as explore unexpected mechanisms underlying the genetic diversity of viruses and the ecological spaces they occupy.

项目概要 水平基因转移（HGT）是一种驱动进化和遗传多样性的明显现象 但其在病毒进化背景下的潜在机制和后果却远没有那么清楚—— 明白了。痘病毒和其他大型 DNA 病毒编码许多具有明确细胞起源的基因。我的目标是 调查他们如何实现这一目标并在收购后如何发展。我们已经证明了 LINE-1 (L1) 逆转录转座子在将细胞基因转移到痘病毒基因组中发挥着关键作用，但尚未发挥作用 了解在不引起灾难性插入突变的情况下如何发生这种情况的动态。多么新近 获得的基因进化出原病毒功能并避免由于其细胞的功能冗余而被删除 祖先。该提议的中心假设是痘病毒基因组中的 L1 插入富含 基因组的远端区域，避免破坏重要的核心基因，在那里它们可以进化以造福于 病毒。我将重点讨论该假设中出现的两个主要悬而未决的问题。在目标 1 中我会 表征病毒复制和细胞 L1 机制之间的相互作用。这将包括空间上 定义细胞质内的相互作用，了解 L1 活性是否以及如何影响病毒复制，以及 全面表征 L1 介导的病毒基因组插入的频率和分布。 为此，我将结合分子生物学的实验和计算技术， 生物化学、遗传学和下一代测序。在目标 2 中，我将寻求阐明起源和 痘病毒 K3L 的进化，一种宿主衍生的抗病毒效应物 PKR 抑制剂。 K3L 是以下结构的同系物 脊椎动物 eIF2 竞争性抑制 PKR 诱导的翻译关闭。与 eIF2 K3L 相比 显着截短并且缺乏磷酸化位点，因此不能介导抗病毒功能 PKR 的下游。尽管存在这种同源性，但计算和系统发育分析表明 K3L 是最重要的 与产甲烷古菌的 aIF2α 蛋白密切相关，可能不是从宿主获得的 细胞是祖先痘病毒的细胞，而不是来自占据相似或重叠生态空间的微生物。自从 在我最初提交的材料中，我生成了新的初步数据，表明 M. fervens aIF2 抑制脊椎动物 PKR， 为我的计算工作提供实验支持。我将确认并扩展这些结果 哺乳动物细胞培养，并使用实验进化来模拟新获得的病毒基因的适应。 最近在其他 DNA 病毒中鉴定出古菌起源基因，为我的观点提供了进一步的支持。 假说，但 K3L 将是多细胞真核生物病毒中第一个已知的例子。一张图片是 病毒作为不同基因交换节点中的熔炉的出现，我提出的研究将 阐明新病毒家族在这些交换中的转移机制和参与。这些 研究将增进我们对细胞基因的病毒共同选择过程的理解，并探索 病毒遗传多样性及其占据的生态空间背后的意想不到的机制。