Virus Evolution Through Horizontal Gene Transfer

通过水平基因转移的病毒进化

• 批准号: 10157165
• 负责人: Stephen Goldstein
• 金额: $ 6.64万
• 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: 2021-06-01 至 2024-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10157165
• 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 the participation of a new family of viruses in these ecological spaces. 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.

项目摘要 水平基因转移（HGT）是一种驱动进化和遗传多样性的现象。 细菌的基本机制和后果，在病毒进化的背景下远不那么好 理解齿。痘病毒和其他大型DNA病毒编码了许多清晰细胞来源的基因。我的目标 调查他们如何到达那里并在收购之后发展。我们已经证明了LINE-1（L1） 逆转录座子在细胞基因转移到痘病毒基因组中起关键作用，但尚未 了解没有诱发灾难性插入诱变的动力学。多么新 获得的基因进化临时功能，并避免由于其细胞功能冗余而导致缺失 祖先。该提议的核心假设是，L1插入痘病毒基因组富含 基因组的远端区域，避免了基本核心基因的破坏，它们可以进化以使其受益 病毒。我将重点介绍这一假设提出的两个主要问题。在目标1中我会 表征病毒复制与细胞L1机械之间的相互作用。这将在空间上完成 定义细胞质内的相互作用，了解L1活性是否影响病毒复制，以及 全面表征L1介导的插入到病毒基因组中的频率和分布。 为此，我将使用跨越分子生物学的实验和计算技术的组合， 生物化学，遗传学和下一代测序。在AIM 2中，我将寻求阐明起源和 Poxvirus K3L的进化，抗病毒效应子PKR的宿主抑制剂。 K3L是 竞争性抑制PKR诱导的翻译关闭的脊椎动物EIF2。与EIF2K3L相比 急剧截短，缺乏磷酸化位点，因此无法介导抗病毒功能 PKR的下游。尽管有这种同源性，但计算和系统发育分析表明K3L最多 与甲烷古细菌的AIF2蛋白密切相关，可能没有从宿主那里获得 祖先痘病毒的细胞，而不是占据相似或重叠的生态空间的微生物。自从 我的原始提交，我生成了新的初步数据，M。FervensAIF2抑制了脊椎动物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病毒中对古细原基因的鉴定，为我提供了进一步的支持 假设，但K3L将是多细胞真核生物病毒的第一个已知例子。图片是 在潜水员遗传交换的节点和我提出的研究中，病毒的出现为熔炉 阐明了新的病毒家族在这些生态空间中的参与。这些研究将进步 我们对细胞基因病毒配置过程的理解以及探索意外的 病毒及其占据生态空间的遗传多样性的机制。