Identification of Novel Positive-Strand RNA Viruses by Metagenomic Analysis of Archaea-Dominated Yellowstone Hot Springs
Identification of Novel Positive-Strand RNA Viruses by Metagenomic Analysis of Archaea-Dominated Yellowstone Hot Springs
复制标题
DOI：
10.1128/jvi.07196-11
复制
发表时间：
2012-05-01
影响因子：
5.4
通讯作者：
Young, Mark
中科院分区：
文献类型：
--
作者：
Bolduc, Benjamin;Shaughnessy, Daniel P.;Young, Mark
目前还没有已知的RNA病毒可以感染红腹果蝇。填补我们对病毒知识的这一空白将增强我们对RNA病毒与细胞生命三个领域之间关系的理解，特别是可以阐明感染真核生物的RNA病毒的巨大多样性的起源。我们在这里描述了新的RNA病毒基因组片段的鉴定，从高温酸性温泉在美国黄石国家公园。这些温泉拥有低复杂性的细胞群落，主要由几种极端嗜热菌所控制。采用病毒宏基因组学方法从直接从温泉样品中分离的病毒群体中组装这些RNA病毒基因组的片段。对这些RNA宏基因组的分析表明，其独特的基因内容通常与细菌和真核生物的已知RNA病毒无关。然而，在两个重叠群中鉴定了RNA依赖性RNA聚合酶（RdRp）基因，这是正链RNA病毒的标志。这些重叠群之一的长度约为5，600个核苷酸，编码一种多聚蛋白，该多聚蛋白还含有与野田病毒、四病毒和双RNA病毒的衣壳蛋白同源的区域。在这些重叠群中编码的RdRps的系统发育分析表明，推定的古细菌病毒形成一个独特的组，是不同于真核生物和细菌的RNA病毒的RdRps。总的来说，我们的研究结果表明存在新的正链RNA病毒，可能在超嗜热古细菌宿主中复制，与感染真核生物的RNA病毒高度不同，甚至与已知的细菌RNA病毒更远。这些正链RNA病毒可能是真核生物RNA病毒的直接祖先。
There are no known RNA viruses that infect Archaea. Filling this gap in our knowledge of viruses will enhance our understanding of the relationships between RNA viruses from the three domains of cellular life and, in particular, could shed light on the origin of the enormous diversity of RNA viruses infecting eukaryotes. We describe here the identification of novel RNA viral genome segments from high-temperature acidic hot springs in Yellowstone National Park in the United States. These hot springs harbor low-complexity cellular communities dominated by several species of hyperthermophilic Archaea. A viral metagenomics approach was taken to assemble segments of these RNA virus genomes from viral populations isolated directly from hot spring samples. Analysis of these RNA metagenomes demonstrated unique gene content that is not generally related to known RNA viruses of Bacteria and Eukarya. However, genes for RNA-dependent RNA polymerase (RdRp), a hallmark of positive-strand RNA viruses, were identified in two contigs. One of these contigs is approximately 5,600 nucleotides in length and encodes a polyprotein that also contains a region homologous to the capsid protein of nodaviruses, tetraviruses, and birnaviruses. Phylogenetic analyses of the RdRps encoded in these contigs indicate that the putative archaeal viruses form a unique group that is distinct from the RdRps of RNA viruses of Eukarya and Bacteria. Collectively, our findings suggest the existence of novel positive-strand RNA viruses that probably replicate in hyperthermophilic archaeal hosts and are highly divergent from RNA viruses that infect eukaryotes and even more distant from known bacterial RNA viruses. These positive-strand RNA viruses might be direct ancestors of RNA viruses of eukaryotes.