从人类肠道宏基因组组装的病毒基因组分析中揭示了具有独特基因组特征的多样化潜在的 CrAss 样噬菌体。

Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features.

机构信息

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA.

Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.

出版信息

Nat Commun. 2021 Feb 16;12(1):1044. doi: 10.1038/s41467-021-21350-w.

Abstract

CrAssphage is the most abundant human-associated virus and the founding member of a large group of bacteriophages, discovered in animal-associated and environmental metagenomes, that infect bacteria of the phylum Bacteroidetes. We analyze 4907 Circular Metagenome Assembled Genomes (cMAGs) of putative viruses from human gut microbiomes and identify nearly 600 genomes of crAss-like phages that account for nearly 87% of the DNA reads mapped to these cMAGs. Phylogenetic analysis of conserved genes demonstrates the monophyly of crAss-like phages, a putative virus order, and of 5 branches, potential families within that order, two of which have not been identified previously. The phage genomes in one of these families are almost twofold larger than the crAssphage genome (145-192 kilobases), with high density of self-splicing introns and inteins. Many crAss-like phages encode suppressor tRNAs that enable read-through of UGA or UAG stop-codons, mostly, in late phage genes. A distinct feature of the crAss-like phages is the recurrent switch of the phage DNA polymerase type between A and B families. Thus, comparative genomic analysis of the expanded assemblage of crAss-like phages reveals aspects of genome architecture and expression as well as phage biology that were not apparent from the previous work on phage genomics.

摘要

CrAssphage 是最丰富的人类相关病毒,也是一个大型噬菌体群的创始成员,这些噬菌体在动物相关和环境宏基因组中被发现,感染拟杆菌门的细菌。我们分析了来自人类肠道微生物组的 4907 个环状宏基因组组装基因组(cMAG),并鉴定出近 600 个 crAss 样噬菌体基因组,这些基因组约占这些 cMAGs 中映射到的 DNA 读数的近 87%。保守基因的系统发育分析表明 crAss 样噬菌体的单系性,这是一种假定的病毒目,以及 5 个分支,该目中的潜在科,其中两个以前没有被识别。这些家族中的一个噬菌体基因组几乎是 crAssphage 基因组的两倍大(145-192 千碱基),具有高度密集的自我剪接内含子和整合酶。许多 crAss 样噬菌体编码抑制 tRNA,使 UGA 或 UAG 终止密码子能够通读,主要是在晚期噬菌体基因中。crAss 样噬菌体的一个显著特征是噬菌体 DNA 聚合酶类型在 A 和 B 家族之间反复切换。因此,对 crAss 样噬菌体的扩展集合进行比较基因组分析揭示了基因组结构和表达以及噬菌体生物学的方面,这些方面在以前的噬菌体基因组学工作中并不明显。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/795f/7886860/ba803528c4ba/41467_2021_21350_Fig1_HTML.jpg

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