Ravantti Janne J, Gaidelyte Ausra, Bamford Dennis H, Bamford Jaana K H
Department of Computer Science, P.O. Box 26, (Teollisuuskatu 23), 00014 University of Helsinki, Helsinki, Finland.
Virology. 2003 Sep 1;313(2):401-14. doi: 10.1016/s0042-6822(03)00295-2.
Extra- and intracellular viruses in the biosphere outnumber their cellular hosts by at least one order of magnitude. How is this enormous domain of viruses organized? Sampling of the virosphere has been scarce and focused on viruses infecting humans, cultivated plants, and animals as well as those infecting well-studied bacteria. It has been relatively easy to cluster closely related viruses based on their genome sequences. However, it has been impossible to establish long-range evolutionary relationships as sequence homology diminishes. Recent advances in the evaluation of virus architecture by high-resolution structural analysis and elucidation of viral functions have allowed new opportunities for establishment of possible long-range phylogenic relationships-virus lineages. Here, we use a genomic approach to investigate a proposed virus lineage formed by bacteriophage PRD1, infecting gram-negative bacteria, and human adenovirus. The new member of this proposed lineage, bacteriophage Bam35, is morphologically indistinguishable from PRD1. It infects gram-positive hosts that evolutionarily separated from gram-negative bacteria more than one billion years ago. For example, it can be inferred from structural analysis of the coat protein sequence that the fold is very similar to that of PRD1. This and other observations made here support the idea that a common early ancestor for Bam35, PRD1, and adenoviruses existed.
生物圈中的细胞外和细胞内病毒数量至少比其细胞宿主多一个数量级。如此庞大的病毒领域是如何组织的呢?对病毒圈的采样一直很少,且主要集中在感染人类、栽培植物和动物的病毒以及感染经过充分研究的细菌的病毒上。基于病毒的基因组序列,将亲缘关系密切的病毒聚类相对容易。然而,随着序列同源性降低,建立远距离进化关系变得不可能。通过高分辨率结构分析评估病毒结构以及阐明病毒功能方面的最新进展,为建立可能的远距离系统发育关系——病毒谱系提供了新机会。在这里,我们采用基因组学方法来研究一个由感染革兰氏阴性菌的噬菌体PRD1和人类腺病毒构成的假定病毒谱系。这个假定谱系的新成员噬菌体Bam35,在形态上与PRD1无法区分。它感染革兰氏阳性宿主,这些宿主在超过十亿年前就从革兰氏阴性菌中进化分离出来。例如,从衣壳蛋白序列的结构分析可以推断,其折叠方式与PRD1非常相似。本文的这一观察结果及其他观察结果支持了这样一种观点,即Bam35、PRD1和腺病毒存在一个共同的早期祖先。