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一种由全球普遍存在的拟杆菌噬菌体编码的产生多样性的反转录元件。

A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage.

机构信息

Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA.

Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA.

出版信息

Microbiome. 2018 Oct 23;6(1):191. doi: 10.1186/s40168-018-0573-6.

Abstract

BACKGROUND

Diversity-generating retroelements (DGRs) are genetic cassettes that selectively mutate target genes to produce hypervariable proteins. First characterized in Bordetella bacteriophage BPP-1, the DGR creates a hypervariable phage tail fiber that enables host tropism switching. Subsequent surveys for DGRs conclude that the majority identified to date are bacterial or archaeal in origin. This work examines bacteriophage and bacterial genomes for novel phage-encoded DGRs.

RESULTS

This survey discovered 92 DGRs that were only found in phages exhibiting a temperate lifestyle. The majority of phage-encoded DGRs were identified as prophages in bacterial hosts from the phyla Bacteroidetes, Proteobacteria, and Firmicutes. Sequence reads from these previously unidentified prophages were present in viral metagenomes (viromes), indicating these prophages can produce functional viruses. Five phages possessed hypervariable proteins with structural similarity to the tail fiber of BPP-1, whereas the functions of the remaining DGR target proteins were unknown. A novel temperate phage that harbors a DGR cassette targeting a protein of unknown function was induced from Bacteroides dorei. This phage, here named Bacteroides dorei Hankyphage, lysogenizes 13 different Bacteroides species and was present in 34% and 21% of whole-community metagenomes and human-associated viromes, respectively.

CONCLUSIONS

Here, the number of known DGR-containing phages is increased from four to 92. All of these phages exhibit a temperate lifestyle, including a cosmopolitan human-associated phage. Targeted hypervariation by temperate phages may be a ubiquitous mechanism underlying phage-bacteria interaction in the human microbiome.

摘要

背景

多样性产生 retroelements(DGRs)是选择性地突变靶基因以产生高变蛋白的遗传盒。最初在博德特氏菌噬菌体 BPP-1 中得到表征,DGR 产生了一个高变的噬菌体尾纤维,使宿主趋向性发生转换。随后对 DGRs 的调查得出结论,迄今为止大多数鉴定的 DGRs 来自细菌或古细菌。这项工作检查了噬菌体和细菌基因组中的新型噬菌体编码的 DGRs。

结果

这项调查发现了 92 个仅在表现为温和生活方式的噬菌体中发现的 DGRs。大多数噬菌体编码的 DGRs 被鉴定为细菌宿主中的原噬菌体,这些细菌宿主来自拟杆菌门、变形菌门和厚壁菌门。这些以前未被识别的原噬菌体的序列读取存在于病毒宏基因组(病毒组)中,表明这些原噬菌体可以产生功能性病毒。五个噬菌体具有与 BPP-1 尾纤维结构相似的高变蛋白,而其余 DGR 靶蛋白的功能未知。一种新型温和噬菌体,含有针对未知功能蛋白的 DGR 盒,从多形拟杆菌中诱导产生。这种噬菌体,在这里命名为多形拟杆菌 Hankyphage,溶原化了 13 种不同的拟杆菌,分别存在于 34%和 21%的全社区宏基因组和人类相关病毒组中。

结论

在这里,已知的含有 DGR 的噬菌体数量从 4 个增加到 92 个。所有这些噬菌体都表现出温和的生活方式,包括一种世界性的人类相关噬菌体。温和噬菌体的靶向高变可能是噬菌体与细菌在人类微生物组中相互作用的一种普遍机制。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/23ab/6199706/e333841b529d/40168_2018_573_Fig1_HTML.jpg

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