Genetic diversity among five T4-like bacteriophages.
Genetic diversity among five T4-like bacteriophages.
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DOI：
10.1186/1743-422x-3-30
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发表时间：
2006-05-23
期刊：
影响因子：
4.8
通讯作者：
Karam JD
中科院分区：
文献类型：
--
作者：
Nolan JM;Petrov V;Bertrand C;Krisch HM;Karam JD
噬菌体是遗传多样性的重要储存库。作为陆地生物量的主要组成部分之一，它们通过介导细菌之间的水平基因转移，控制细菌的生长，对地球生态和微生物进化产生深远的影响。目前只有有限的基因组序列数据可用于噬菌体，但即使这样也揭示了它们的基因序列和基因组的压倒性多样性。T4类噬菌体对整个噬菌体多样性的贡献很难评估，因为这些噬菌体只有几个完整基因组序列的例子。我们对5个T4样基因组的分析代表了GenBank中已知的T4样基因组的一半。在这里，我们详细地研究了噬菌体T4的五个亲缘关系的基因组的遗传多样性：大肠杆菌噬菌体RB43、RB49和RB69，沙门氏气单胞菌噬菌体44RR2.8t(或44RR)和嗜水气单胞菌噬菌体Aeh1。我们的数据定义了这些基因组共有的一组保守的核心基因，以及数百个非保守的额外开放阅读框架(ORF)。虽然这些开放阅读框中的一些与细菌宿主或其他噬菌体的已知基因相似，但大多数与数据库中的任何已知序列都没有显著的相似性。这里分析的五个基因组在基因调控方面都与T4有相似之处。在所有五个基因组中都观察到了类似T4早期和晚期共识启动子的序列基序。相反，这些基因组中只有两个，RB69和44RR，与T4中间模式启动子序列和识别它们所需的T4MoTA基因产物相似。此外，我们观察到每个噬菌体在编码类宿主代谢酶、tRNA种类和归巢内切酶的假定基因的数量和分类上有所不同。我们的观察表明，T4类噬菌体的进化利用了微生物世界中高度分散的基因库。类似T4的噬菌体含有丰富的遗传物质，这些遗传物质以前从未被鉴定过。这些基因可能产生的机制可能与先前提出的其他噬菌体基因组进化的机制不同。
Bacteriophages are an important repository of genetic diversity. As one of the major constituents of terrestrial biomass, they exert profound effects on the earth's ecology and microbial evolution by mediating horizontal gene transfer between bacteria and controlling their growth. Only limited genomic sequence data are currently available for phages but even this reveals an overwhelming diversity in their gene sequences and genomes. The contribution of the T4-like phages to this overall phage diversity is difficult to assess, since only a few examples of complete genome sequence exist for these phages. Our analysis of five T4-like genomes represents half of the known T4-like genomes in GenBank. Here, we have examined in detail the genetic diversity of the genomes of five relatives of bacteriophage T4: the Escherichia coli phages RB43, RB49 and RB69, the Aeromonas salmonicida phage 44RR2.8t (or 44RR) and the Aeromonas hydrophila phage Aeh1. Our data define a core set of conserved genes common to these genomes as well as hundreds of additional open reading frames (ORFs) that are nonconserved. Although some of these ORFs resemble known genes from bacterial hosts or other phages, most show no significant similarity to any known sequence in the databases. The five genomes analyzed here all have similarities in gene regulation to T4. Sequence motifs resembling T4 early and late consensus promoters were observed in all five genomes. In contrast, only two of these genomes, RB69 and 44RR, showed similarities to T4 middle-mode promoter sequences and to the T4 motA gene product required for their recognition. In addition, we observed that each phage differed in the number and assortment of putative genes encoding host-like metabolic enzymes, tRNA species, and homing endonucleases. Our observations suggest that evolution of the T4-like phages has drawn on a highly diverged pool of genes in the microbial world. The T4-like phages harbour a wealth of genetic material that has not been identified previously. The mechanisms by which these genes may have arisen may differ from those previously proposed for the evolution of other bacteriophage genomes.