Viroid-like colonists of human microbiomes

IF 5.7 1区 化学 Q2 CHEMISTRY, PHYSICAL
Ivan N. Zheludev, Robert C. Edgar, Maria Jose Lopez-Galiano, Marcos de la Peña, Artem Babaian, Ami S. Bhatt, Andrew Z. Fire
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引用次数: 0

Abstract

Here, we describe “obelisks,” a class of heritable RNA elements sharing several properties: (1) apparently circular RNA ∼1 kb genome assemblies, (2) predicted rod-like genome-wide secondary structures, and (3) open reading frames encoding a novel “Oblin” protein superfamily. A subset of obelisks includes a variant hammerhead self-cleaving ribozyme. Obelisks form their own phylogenetic group without detectable similarity to known biological agents. Surveying globally, we identified 29,959 distinct obelisks (clustered at 90% sequence identity) from diverse ecological niches. Obelisks are prevalent in human microbiomes, with detection in ∼7% (29/440) and ∼50% (17/32) of queried stool and oral metatranscriptomes, respectively. We establish Streptococcus sanguinis as a cellular host of a specific obelisk and find that this obelisk’s maintenance is not essential for bacterial growth. Our observations identify obelisks as a class of diverse RNAs of yet-to-be-determined impact that have colonized and gone unnoticed in human and global microbiomes.

Abstract Image

人类微生物群落中的类病毒殖民者
在这里,我们描述了 "obelisks"--一类具有以下共同特性的遗传 RNA 元件:(1)明显的环状 RNA ∼ 1 kb 基因组组装;(2)预测的杆状全基因组二级结构;(3)编码新型 "Oblin "蛋白超家族的开放阅读框。方尖碑的一个子集包括一个变体锤头自裂解核糖酶。方尖碑形成了自己的系统发育群,与已知的生物制剂没有可检测到的相似性。我们在全球范围内进行了调查,从不同的生态位中发现了 29,959 种不同的同源物(序列相似度为 90%)。方尖碑在人类微生物组中非常普遍,在查询的粪便和口腔元转录组中,方尖碑的检出率分别为 7%(29/440)和 50%(17/32)。我们确定血链球菌是一种特定方尖碑的细胞宿主,并发现这种方尖碑的维持并非细菌生长所必需。我们的观察结果表明,方尖碑是一类影响尚待确定的多种 RNA,它们在人类和全球微生物组中定植,却不为人所注意。
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来源期刊
Journal of Chemical Theory and Computation
Journal of Chemical Theory and Computation 化学-物理:原子、分子和化学物理
CiteScore
9.90
自引率
16.40%
发文量
568
审稿时长
1 months
期刊介绍: The Journal of Chemical Theory and Computation invites new and original contributions with the understanding that, if accepted, they will not be published elsewhere. Papers reporting new theories, methodology, and/or important applications in quantum electronic structure, molecular dynamics, and statistical mechanics are appropriate for submission to this Journal. Specific topics include advances in or applications of ab initio quantum mechanics, density functional theory, design and properties of new materials, surface science, Monte Carlo simulations, solvation models, QM/MM calculations, biomolecular structure prediction, and molecular dynamics in the broadest sense including gas-phase dynamics, ab initio dynamics, biomolecular dynamics, and protein folding. The Journal does not consider papers that are straightforward applications of known methods including DFT and molecular dynamics. The Journal favors submissions that include advances in theory or methodology with applications to compelling problems.
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