Pervasive Chimerism in the Replication-Associated Proteins of Uncultured Single-Stranded DNA Viruses.
Pervasive Chimerism in the Replication-Associated Proteins of Uncultured Single-Stranded DNA Viruses.
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DOI：
10.3390/v10040187
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发表时间：
2018-04-10
期刊：
影响因子：
--
通讯作者：
Krupovic M
中科院分区：
文献类型：
--
作者：
Kazlauskas D;Varsani A;Krupovic M
大量宏基因组研究发现，循环复制相关蛋白 (Rep) 编码单链 (CRESS) DNA 病毒具有显着的多样性，其中大多数未经培养且未分类。与衣壳蛋白不同，Reps 在不同组的 CRESS DNA 病毒中表现出显着的相似性，并且具有 N 端核酸酶和 C 端解旋酶结构域的保守结构域组织。因此，Rep被广泛用作CRESS DNA病毒多样性的识别、分类和评估的标记。然而，研究表明，在某些病毒中，Rep 核酸酶和解旋酶结构域表现出不一致的进化历史。在这里，我们系统地评估了分类和未分类 CRESS DNA 病毒的两个 Rep 域的共同进化模式。我们的分析表明，杆状DNA病毒科、圆环病毒科、双生病毒科、基因病毒科、纳米病毒科和Smacoviridae科成员编码的Rep在这两个域中表现出很大程度上一致的进化模式。相比之下，在未分类的 CRESS DNA 病毒中，71% 似乎具有嵌合代表。如此大量的嵌合现象表明，未分类的 CRESS DNA 病毒代表了一个动态群体，其中编码核酸酶和解旋酶结构域的基因片段的交换极为常见。此外，嵌合序列的清除发现了六个单系Rep组，它们可能代表了CRESS DNA病毒的新家族。
Numerous metagenomic studies have uncovered a remarkable diversity of circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses, the majority of which are uncultured and unclassified. Unlike capsid proteins, the Reps show significant similarity across different groups of CRESS DNA viruses and have conserved domain organization with the N-terminal nuclease and the C-terminal helicase domain. Consequently, Rep is widely used as a marker for identification, classification and assessment of the diversity of CRESS DNA viruses. However, it has been shown that in certain viruses the Rep nuclease and helicase domains display incongruent evolutionary histories. Here, we systematically evaluated the co-evolutionary patterns of the two Rep domains across classified and unclassified CRESS DNA viruses. Our analysis indicates that the Reps encoded by members of the families Bacilladnaviridae, Circoviridae, Geminiviridae, Genomoviridae, Nanoviridae and Smacoviridae display largely congruent evolutionary patterns in the two domains. By contrast, among the unclassified CRESS DNA viruses, 71% appear to have chimeric Reps. Such massive chimerism suggests that unclassified CRESS DNA viruses represent a dynamic population in which exchange of gene fragments encoding the nuclease and helicase domains is extremely common. Furthermore, purging of the chimeric sequences uncovered six monophyletic Rep groups that may represent new families of CRESS DNA viruses.
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影响因子：
5.5
作者：
Diemer GS;Stedman KM
通讯作者：
Stedman KM
影响因子：
6.4
作者：
Iranzo J;Krupovic M;Koonin EV
通讯作者：
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打破并连接单链的DNA：嗯，核酸内切酶超家族。
DOI：
10.1038/nrmicro3067
发表时间：
2013-08
期刊：
Nature reviews. Microbiology
影响因子：
--
作者：
Chandler M;de la Cruz F;Dyda F;Hickman AB;Moncalian G;Ton-Hoang B
通讯作者：
Ton-Hoang B
DOI：
10.1093/bioinformatics/btp348
发表时间：
2009-08-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Capella-Gutiérrez S;Silla-Martínez JM;Gabaldón T
通讯作者：
Gabaldón T
影响因子：
10.7
作者：
Katoh K;Standley DM
通讯作者：
Standley DM