Clades of huge phages from across Earth's ecosystems
Clades of huge phages from across Earth's ecosystems
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DOI：
10.1038/s41586-020-2007-4
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发表时间：
2020-02-12
期刊：
影响因子：
64.8
通讯作者：
Banfield, Jillian F.
中科院分区：
文献类型：
--
作者：
Al-Shayeb, Basem;Sachdeva, Rohan;Banfield, Jillian F.
噬菌体通常具有小的基因组（1），并依赖于其细菌宿主进行复制（2）。在这里，我们对来自不同生态系统的DNA进行了测序，发现了数百个长度超过200 kb的噬菌体基因组，其中包括735 kb的基因组，据我们所知，这是迄今为止描述的最大的噬菌体基因组。35个基因组被手动管理完成（圆形和无间隙）。扩展的遗传库包括多样的和以前未描述的CRISPR-Cas系统、转移RNA（tRNA）、tRNA合成酶、tRNA修饰酶、转录起始和延伸因子以及核糖体蛋白。CRISPR-Cas系统具有沉默宿主转录因子和翻译基因的能力，可能作为更大的相互作用网络的一部分，该网络拦截翻译以将生物合成重定向到噬菌体编码的功能。此外，一些细菌可能会重新利用细菌CRISPR-Cas系统来消除竞争性细菌。我们从人类和其他动物微生物组以及海洋，湖泊，沉积物，土壤和建筑环境中遗传地定义了巨大微生物的主要分支。我们的结论是，巨大的细菌的大基因库存反映了一种保守的生物学策略，并且细菌分布在广泛的细菌宿主范围和地球的生态系统中。对从地球生态系统中采样的巨大细菌的主要分支的基因组分析表明，它们具有多样化的基因库存，包括各种CRISPR-Cas系统和防御相关基因。
Bacteriophages typically have small genomes(1) and depend on their bacterial hosts for replication(2). Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems.Genomic analyses of major clades of huge phages sampled from across Earth's ecosystems show that they have diverse genetic inventories, including a variety of CRISPR-Cas systems and translation-relevant genes.