Protein repertoire of double-stranded DNA bacteriophages
Protein repertoire of double-stranded DNA bacteriophages
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DOI：
10.1016/j.virusres.2006.01.015
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发表时间：
2006-04-01
期刊：
影响因子：
5
通讯作者：
Mushegian, A
中科院分区：
文献类型：
--
作者：
Liu, J;Glazko, G;Mushegian, A
噬菌体基因组的快速进化和噬菌体间频繁的基因交换所产生的噬菌体基因集的复杂性和多样性，阻碍了破译单个噬菌体蛋白之间的进化关系和重建导致已知噬菌体的完整进化事件的努力。为了开始揭开噬菌体的自然历史，我们建立了噬菌体直系组(POGS)，这是一个噬菌体蛋白家族的自然系统，包括164个双链DNA噬菌体全基因组序列中的6378个基因。噬菌体前体体具有很高的POG覆盖率：平均每个噬菌体基因组中有39个基因属于POG，接近大多数噬菌体所有基因的一半。与噬菌体在水平基因转移中的作用的概念一致，我们看到了许多噬菌体与其微生物宿主之间可能的基因交换。同时，约80%的POG是高度特异的噬菌体基因组，在微生物基因组中并不常见，这表明噬菌体基因集具有很大的一致性和很大的进化独立性。有关同源基因的信息对于已知噬菌体的进化分类和祖先噬菌体基因组的重建是必不可少的。(C)2006爱思唯尔B.V.保留所有权利。
The complexity and diversity of phage gene sets, which are produced by rapid evolution of phage genomes and rampant gene exchanges among phages, hamper the efforts to decipher the evolutionary relationships between individual phage proteins and reconstruct the complete set of evolutionary events leading to the known phages. To start unraveling the natural history of phages, we built the phage orthologous groups (POGs), a natural system of phage protein families that includes 6378 genes from 164 complete genome sequences of double-stranded DNA bacteriophages. Phage proleomes have high POG coverage: on average, 39 genes per phage genome belong to POGs, which is close to half of all genes in most phages. In an agreement with the notion of phage role in horizontal gene transfer, we see many cases of likely gene exchange between phages and their microbial hosts. At the same time, about 80% of all POGs are highly specific to phage genomes and are not commonly found in microbial genomes, indicating coherence and large degree of evolutionary independence of phage gene sets. The information on orthologous genes is essential for evolutionary classification of known bacteriophages and for reconstruction of ancestral phage genomes. (c) 2006 Elsevier B.V. All rights reserved.