Genomic exploration of individual giant ocean viruses
Genomic exploration of individual giant ocean viruses
复制标题
单个巨型海洋病毒的基因组探索
DOI：
10.1038/ismej.2017.61
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发表时间：
2017
期刊：
影响因子：
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通讯作者：
S. Wilhelm
中科院分区：
文献类型：
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作者：
W. H. Wilson;Ilana C. Gilg;M. Moniruzzaman;E. Field;S. Koren;Gary R. Lecleir;Joaquín Martínez Martínez;N. Poulton;B. Swan;R. Stepanauskas;S. Wilhelm
病毒是所有生物系统中的主要病原体。病毒繁殖和下游分析仍然是一个挑战，特别是在海洋中，其中大多数微生物宿主仍然对当前的培养技术不敏感。我们使用一种不依赖培养的方法来分离和测序单个病毒。该方案使用高速荧光激活病毒分选流式细胞术、多重置换扩增（MDA）和下游基因组测序。我们关注的是通过流式细胞术容易区分的“巨型病毒”。从美国缅因州布斯贝港码头外收集的一毫升海水样本中，我们分选出近700个单一病毒颗粒，随后集中对12个进行了详细的基因组分析。鉴定了多种多样的病毒，包括虹彩病毒科、扩展的拟病毒科，甚至还有一种分类学上新颖的（未解决的）巨型病毒。我们发现了一个病毒后半胱天冬酶同源物在我们的一个分类病毒颗粒，并讨论了其在重新布线宿主代谢，以增强感染的影响。此外，我们证明了病毒后半胱氨酸蛋白酶在海洋中广泛存在。我们还发现了一种同时含有逆转录酶和转座酶的病毒;虽然高度推测，但我们认为这种遗传互补可能会使这种病毒利用潜伏期传播机制。单病毒基因组学的应用提供了一个强大的机会，绕过病毒的培养，直接转移到天然存在的病毒的基因组研究，确保序列数据是病毒特异性的，非嵌合的，不含细胞污染。
Viruses are major pathogens in all biological systems. Virus propagation and downstream analysis remains a challenge, particularly in the ocean where the majority of their microbial hosts remain recalcitrant to current culturing techniques. We used a cultivation-independent approach to isolate and sequence individual viruses. The protocol uses high-speed fluorescence-activated virus sorting flow cytometry, multiple displacement amplification (MDA), and downstream genomic sequencing. We focused on ‘giant viruses’ that are readily distinguishable by flow cytometry. From a single-milliliter sample of seawater collected from off the dock at Boothbay Harbor, ME, USA, we sorted almost 700 single virus particles, and subsequently focused on a detailed genome analysis of 12. A wide diversity of viruses was identified that included Iridoviridae, extended Mimiviridae and even a taxonomically novel (unresolved) giant virus. We discovered a viral metacaspase homolog in one of our sorted virus particles and discussed its implications in rewiring host metabolism to enhance infection. In addition, we demonstrated that viral metacaspases are widespread in the ocean. We also discovered a virus that contains both a reverse transcriptase and a transposase; although highly speculative, we suggest such a genetic complement would potentially allow this virus to exploit a latency propagation mechanism. Application of single virus genomics provides a powerful opportunity to circumvent cultivation of viruses, moving directly to genomic investigation of naturally occurring viruses, with the assurance that the sequence data is virus-specific, non-chimeric and contains no cellular contamination.
DOI：
10.1073/pnas.82.20.6955
发表时间：
1985-01-01
影响因子：
11.1
作者：
LANE, DJ;PACE, B;PACE, NR
通讯作者：
PACE, NR
影响因子：
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