Nolan James M, Petrov Vasiliy, Bertrand Claire, Krisch Henry M, Karam Jim D
Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Dr,, New Orleans, LA 70148, USA.
Virol J. 2006 May 23;3:30. doi: 10.1186/1743-422X-3-30.
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.
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，它们通过介导细菌间的水平基因转移并控制细菌生长，对地球生态和微生物进化产生深远影响。目前仅有有限的噬菌体基因组序列数据，即便如此，这些数据也揭示了其基因序列和基因组中存在着极其丰富的多样性。由于已知的T4样噬菌体完整基因组序列实例很少，所以很难评估这类噬菌体对整体噬菌体多样性的贡献。我们对五个T4样基因组的分析占了GenBank中已知T4样基因组的一半。
在此，我们详细研究了噬菌体T4的五个亲缘种的基因组遗传多样性：大肠杆菌噬菌体RB43、RB49和RB69，杀鲑气单胞菌噬菌体44RR2.8t（或44RR）以及嗜水气单胞菌噬菌体Aeh1。我们的数据确定了这些基因组共有的一组核心保守基因，以及数百个非保守的额外开放阅读框（ORF）。尽管其中一些ORF类似于细菌宿主或其他噬菌体的已知基因，但大多数与数据库中的任何已知序列均无显著相似性。此处分析的五个基因组在基因调控方面均与T4存在相似性。在所有五个基因组中均观察到类似于T4早期和晚期共有启动子的序列基序。相比之下，这些基因组中只有RB69和44RR这两个基因组与T4中期模式启动子序列以及识别这些序列所需的T4 motA基因产物存在相似性。此外，我们观察到每个噬菌体在编码宿主样代谢酶、tRNA种类和归巢内切核酸酶的推定基因的数量和种类上存在差异。
我们的观察结果表明，T4样噬菌体的进化利用了微生物世界中高度分化的基因库。T4样噬菌体含有大量以前未被鉴定的遗传物质。这些基因产生的机制可能与先前提出的其他噬菌体基因组进化机制不同。
