科学家发现并定义了巨大噬菌体的进化分支
2020-02-14   阅读:336   来源:自然

美国加州大学伯克利分校Jillian F. Banfield小组取得一项新突破。他们探究了地球生态系统中巨大噬菌体的进化分支。该研究于2020年2月12日在线发表在国际学术期刊《自然》上。

研究人员对来自不同生态系统的DNA进行了测序,发现了数百个基因组长度超过200千碱基(kb)的噬菌体,其中包括一个基因组长度达735 kb的噬菌体,据研究人员介绍,这是迄今为止发现的基因组最大的噬菌体。研究人员人工整理了35个基因组,使其完整(圆形且无缺口)。这些发现扩展了包括各种以前未知的CRISPR-Cas系统、转运RNA(tRNA)、tRNA合成酶、tRNA修饰酶、翻译起始和延伸因子以及核糖体蛋白在内的遗传库。噬菌体CRISPR–Cas系统具有沉默宿主转录因子和翻译基因的能力,这可能是作为大相互作用网络的一部分,该相互作用网络阻断翻译从而将生物合成重定向至噬菌体编码功能。此外,某些噬菌体可能会重新利用细菌的CRISPR-Cas系统来消除竞争性噬菌体。研究人员在系统生物学上定义了这些巨大噬菌体的进化分支从而将其与人类和其他动物微生物群以及海洋、湖泊、沉积物、土壤和建筑环境中的噬菌体区分开来。该研究发现,巨大噬菌体的大基因组反映了保守的生物学特点,并且这些噬菌体分布在广泛的细菌宿主和整个地球生态系统中。

据了解,噬菌体通常具有较小的基因组,并依赖于其细菌宿主进行复制。

附:英文原文

Title: Clades of huge phages from across Earth’s ecosystems

Author: Basem Al-Shayeb, Rohan Sachdeva, Lin-Xing Chen, Fred Ward, Patrick Munk, Audra Devoto, Cindy J. Castelle, Matthew R. Olm, Keith Bouma-Gregson, Yuki Amano, Christine He, Raphal Mheust, Brandon Brooks, Alex Thomas, Adi Lavy, Paula Matheus-Carnevali, Christine Sun, Daniela S. A. Goltsman, Mikayla A. Borton, Allison Sharrar, Alexander L. Jaffe, Tara C. Nelson, Rose Kantor, Ray Keren, Katherine R. Lane, Ibrahim F. Farag, Shufei Lei, Kari Finstad, Ronald Amundson, Karthik Anantharaman, Jinglie Zhou, Alexander J. Probst, Mary E. Power, Susannah G. Tringe, Wen-Jun Li, Kelly Wrighton, Sue Harrison, Michael Morowitz, David A. Relman, Jennifer A. Doudna, Anne-Catherine Lehours, Lesley Warren, Jamie H. D. Cate, Joanne M. Santini, Jillian F. Banfield

Issue&Volume: 2020-02-12

Abstract: Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. 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.

DOI: 10.1038/s41586-020-2007-4

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