Neuman Benjamin W, Smart Alexandria, Gilmer Orian, Smyth Redmond P, Vaas Josef, Böker Nicolai, Samborskiy Dmitry V, Bartenschlager Ralf, Seitz Stefan, Gorbalenya Alexander E, Caliskan Neva, Lauber Chris
Department of Biology, Microbial Pathogenesis and Immunity, Texas A&M University, College Station, TX 77840.
Helmholtz Institute for RNA-Based Infection Research, Helmholtz Centre for Infection Research, Würzburg 97080, Germany.
Proc Natl Acad Sci U S A. 2025 Feb 18;122(7):e2413675122. doi: 10.1073/pnas.2413675122. Epub 2025 Feb 10.
Positive-strand RNA viruses of the order have the largest known RNA genomes of vertebrate and invertebrate viruses with 36.7 and 41.1 kb, respectively. The acquisition of a proofreading exoribonuclease (ExoN) by an ancestral nidovirus enabled crossing of the 20 kb barrier. Other factors constraining genome size variations in nidoviruses remain poorly defined. We assemble 76 genome sequences of invertebrate nidoviruses from >500.000 published transcriptome experiments and triple the number of known nidoviruses with >36 kb genomes, including a 64 kb RNA genome. Many of the identified viral lineages acquired putative enzymatic and other protein domains linked to genome size, host phyla, or virus families. The inserted domains may regulate viral replication and virion formation, or modulate infection otherwise. We classify ExoN-encoding nidoviruses into seven groups and four subgroups, according to canonical and noncanonical modes of viral replicase expression by ribosomes and genomic organization (reModes). The most-represented group employing the canonical reMode comprises invertebrate and vertebrate nidoviruses, including coronaviruses. Six groups with noncanonical reModes include invertebrate nidoviruses with 31-to-64 kb genomes. Among them are viruses with segmented genomes and viruses utilizing dual ribosomal frameshifting that we validate experimentally. Moreover, largest polyprotein length and genome size in nidoviruses show reMode- and host phylum-dependent relationships. We hypothesize that the polyprotein length increase in nidoviruses may be limited by the host-inherent translation fidelity, ultimately setting a nidovirus genome size limit. Thus, expansion of ExoN-encoding RNA virus genomes, the vertebrate/invertebrate host division, the control of viral replicase expression, and translation fidelity are interconnected.
该目正链RNA病毒拥有脊椎动物和无脊椎动物病毒中已知最大的RNA基因组，分别为36.7 kb和41.1 kb。一种祖先尼多病毒获得了一种校对性外切核糖核酸酶（ExoN），从而突破了20 kb的界限。其他限制尼多病毒基因组大小变化的因素仍不清楚。我们从超过50万个已发表的转录组实验中组装了76个无脊椎动物尼多病毒的基因组序列，使已知的基因组大于36 kb的尼多病毒数量增加了两倍，其中包括一个64 kb的RNA基因组。许多已鉴定的病毒谱系获得了与基因组大小、宿主门类或病毒科相关的假定酶和其他蛋白质结构域。插入的结构域可能调节病毒复制和病毒粒子形成，或以其他方式调节感染。我们根据核糖体对病毒复制酶的典型和非典型表达模式以及基因组组织（复制模式），将编码ExoN的尼多病毒分为七组和四个亚组。采用典型复制模式的最具代表性的组包括无脊椎动物和脊椎动物尼多病毒，包括冠状病毒。六个具有非典型复制模式的组包括基因组大小为31至64 kb的无脊椎动物尼多病毒。其中有基因组分段的病毒和利用双核糖体移码的病毒，我们通过实验进行了验证。此外，尼多病毒中最大的多蛋白长度和基因组大小显示出与复制模式和宿主门类相关的关系。我们推测，尼多病毒多蛋白长度的增加可能受到宿主固有翻译保真度的限制，最终设定了尼多病毒基因组大小的限制。因此，编码ExoN的RNA病毒基因组的扩展、脊椎动物/无脊椎动物宿主划分、病毒复制酶表达的控制和翻译保真度是相互关联的。
