A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage
A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage
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DOI：
10.1186/s40168-018-0573-6
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发表时间：
2018-10-23
期刊：
影响因子：
15.5
通讯作者：
Rohwer, Forest
中科院分区：
文献类型：
--
作者：
Benler, Sean;Cobian-Gueemes, Ana Georgina;Rohwer, Forest
背景多样性生成逆转录元件（DGR）是选择性突变靶基因以产生高变蛋白的遗传盒。 DGR 首次在博德特氏菌噬菌体 BPP-1 中得到表征，它产生了一种高度可变的噬菌体尾纤维，可以实现宿主向性切换。随后对 DGR 的调查得出结论，迄今为止发现的大多数 DGR 都是细菌或古菌来源。这项工作检查了噬菌体和细菌基因组中新型噬菌体编码的 DGR。结果这项调查发现了 92 种仅在表现出温和生活方式的噬菌体中发现的 DGR。大多数噬菌体编码的 DGR 被鉴定为来自拟杆菌门、变形菌门和厚壁菌门的细菌宿主中的原噬菌体。这些先前未鉴定的原噬菌体的序列读数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 尾部纤维结构相似的高变蛋白，而其余 DGR 靶蛋白的功能未知。一种新型温带噬菌体是从多雷拟杆菌中诱导产生的，该噬菌体含有针对未知功能蛋白质的 DGR 盒。这种噬菌体在这里被命名为 Bacteroides dorei Hankyphage，可溶源 13 种不同的拟杆菌属物种，并分别存在于整个群落宏基因组和人类相关病毒组的 34% 和 21% 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，包括与人类相关的世界性噬菌体。温带噬菌体的靶向高度变异可能是人类微生物组中噬菌体-细菌相互作用的普遍机制。
BackgroundDiversity-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.ResultsThis 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.ConclusionsHere, 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.