Evolutionary Bioinformatics Laboratory, Department of Crop Science, University of Illinois, Urbana, IL 61801, USA.
BMC Evol Biol. 2012 Aug 24;12:156. doi: 10.1186/1471-2148-12-156.
The discovery of giant viruses with genome and physical size comparable to cellular organisms, remnants of protein translation machinery and virus-specific parasites (virophages) have raised intriguing questions about their origin. Evidence advocates for their inclusion into global phylogenomic studies and their consideration as a distinct and ancient form of life.
Here we reconstruct phylogenies describing the evolution of proteomes and protein domain structures of cellular organisms and double-stranded DNA viruses with medium-to-very-large proteomes (giant viruses). Trees of proteomes define viruses as a 'fourth supergroup' along with superkingdoms Archaea, Bacteria, and Eukarya. Trees of domains indicate they have evolved via massive and primordial reductive evolutionary processes. The distribution of domain structures suggests giant viruses harbor a significant number of protein domains including those with no cellular representation. The genomic and structural diversity embedded in the viral proteomes is comparable to the cellular proteomes of organisms with parasitic lifestyles. Since viral domains are widespread among cellular species, we propose that viruses mediate gene transfer between cells and crucially enhance biodiversity.
Results call for a change in the way viruses are perceived. They likely represent a distinct form of life that either predated or coexisted with the last universal common ancestor (LUCA) and constitute a very crucial part of our planet's biosphere.
具有与细胞生物相当的基因组和物理大小的巨型病毒、蛋白质翻译机制的残余物以及病毒特异性寄生虫（噬病毒体）的发现，引发了关于它们起源的有趣问题。有证据表明，应该将它们纳入全球系统基因组学研究，并将其视为一种独特而古老的生命形式。
在这里，我们重建了描述细胞生物和具有中到大基因组（巨型病毒）的双链 DNA 病毒的蛋白质组和蛋白质结构域进化的系统发育树。蛋白质组树将病毒定义为与古菌、细菌和真核生物并列的“第四超级群”。结构域树表明，它们通过大规模的原始还原进化过程进化而来。结构域的分布表明，巨型病毒拥有大量的蛋白质结构域，包括那些没有细胞代表的结构域。病毒蛋白质组中嵌入的基因组和结构多样性与具有寄生生活方式的生物体的细胞蛋白质组相当。由于病毒结构域在细胞物种中广泛存在，我们提出病毒介导细胞之间的基因转移，并极大地增强生物多样性。
结果呼吁改变人们对病毒的看法。它们可能代表一种独特的生命形式，要么早于或与最后一个普遍共同祖先（LUCA）共存，并且构成我们星球生物圈的非常重要的部分。
