The ancient Virus World and evolution of cells.
The ancient Virus World and evolution of cells.
复制标题
古老的病毒世界和细胞的进化。
DOI：
10.1186/1745-6150-1-29
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发表时间：
2006-09-19
期刊：
影响因子：
5.5
通讯作者：
Dolja, Valerian V.
中科院分区：
文献类型：
--
作者：
Koonin, Eugene V.;Senkevich, Tatiana G.;Dolja, Valerian V.
病毒和细胞生命形式基因组学的最新进展极大地激发了人们对病毒起源和进化的兴趣，并首次为数据驱动的病毒最深根源探索提供了机会。在这里，我们简要回顾了目前的病毒进化的观点，并提出了一个新的，连贯的情况下，似乎是最好的兼容比较基因组数据和自然的细胞进化模型，从独立的考虑，似乎是最吝啬的现有的。编码参与病毒复制和形态发生的关键蛋白以及二十面体病毒体的主要衣壳蛋白的几个基因被许多组的RNA和DNA病毒共享，但在细胞生命形式中缺失。基于这一关键观察和不同病毒之间广泛遗传交换的数据，我们提出了古代病毒世界的概念。病毒世界被解释为病毒基因的独特组成部分，在整个生命历史中不断保持其身份。在这个概念下，病毒和相关自私因子的主要谱系来自原始遗传元件的原始库，细胞和病毒基因的祖先。因此，尽管在进化的后期阶段发生了大量的基因交换和获得，但大多数（如果不是全部的话）现代病毒和其他自私的媒介被推断为是从属于原始基因库的元素中进化而来的。在这个池中，RNA病毒将首先进化，然后是逆转录病毒和DNA病毒。病毒世界的概念是基于早期进化的模型，即大量遗传多样性的出现早于成熟细胞的出现，从而允许在进化的早期阶段进行广泛的基因混合。我们概述了一个方案的起源的主要类别的病毒结合一个特定的模型下，原始的基因库居住在一个网络的无机隔间的细胞前进化。有些矛盾的是，在这种情况下，我们推测，自私的遗传元件祖先的病毒进化之前，典型的细胞，成为细胞内的寄生虫一旦细菌和古细菌到达现场。对过度攻击性的寄生虫的选择会杀死宿主的遗传元件集合，这将导致温和病毒样因子和原始防御机制的早期进化，可能是基于RNA干扰原理。真核细胞的出现被解释为病毒进化的第二个熔炉，真核病毒的主要群体起源于来自各种噬菌体、古细菌病毒、质粒和进化中的真核基因组的基因的广泛重组。同样，这一愿景是基于真核细胞出现的特定模型，在该模型下，古细菌共生是真核发生的起点，这一情景似乎与数据最相符。病毒复制和结构的几个核心基因的存在，被广泛的病毒所共享，但在细胞基因组中缺失（病毒标志基因），这表明了古代病毒世界的模型，从生命进化的前细胞阶段到今天，病毒特异性基因的流动不间断。这一概念与细胞进化的两个关键理论紧密相关：存在一个复杂的、细胞前的、区室化的但广泛混合和重组的基因库，以及真核细胞通过古细菌融合的起源。病毒世界的概念和这些细胞进化过程中主要转变的模型为生命历史的连贯图景提供了补充。W.福特杜利特尔，J.彼得Gogarten，和Arcady Mushegian。
Recent advances in genomics of viruses and cellular life forms have greatly stimulated interest in the origins and evolution of viruses and, for the first time, offer an opportunity for a data-driven exploration of the deepest roots of viruses. Here we briefly review the current views of virus evolution and propose a new, coherent scenario that appears to be best compatible with comparative-genomic data and is naturally linked to models of cellular evolution that, from independent considerations, seem to be the most parsimonious among the existing ones. Several genes coding for key proteins involved in viral replication and morphogenesis as well as the major capsid protein of icosahedral virions are shared by many groups of RNA and DNA viruses but are missing in cellular life forms. On the basis of this key observation and the data on extensive genetic exchange between diverse viruses, we propose the concept of the ancient virus world. The virus world is construed as a distinct contingent of viral genes that continuously retained its identity throughout the entire history of life. Under this concept, the principal lineages of viruses and related selfish agents emerged from the primordial pool of primitive genetic elements, the ancestors of both cellular and viral genes. Thus, notwithstanding the numerous gene exchanges and acquisitions attributed to later stages of evolution, most, if not all, modern viruses and other selfish agents are inferred to descend from elements that belonged to the primordial genetic pool. In this pool, RNA viruses would evolve first, followed by retroid elements, and DNA viruses. The Virus World concept is predicated on a model of early evolution whereby emergence of substantial genetic diversity antedates the advent of full-fledged cells, allowing for extensive gene mixing at this early stage of evolution. We outline a scenario of the origin of the main classes of viruses in conjunction with a specific model of precellular evolution under which the primordial gene pool dwelled in a network of inorganic compartments. Somewhat paradoxically, under this scenario, we surmise that selfish genetic elements ancestral to viruses evolved prior to typical cells, to become intracellular parasites once bacteria and archaea arrived at the scene. Selection against excessively aggressive parasites that would kill off the host ensembles of genetic elements would lead to early evolution of temperate virus-like agents and primitive defense mechanisms, possibly, based on the RNA interference principle. The emergence of the eukaryotic cell is construed as the second melting pot of virus evolution from which the major groups of eukaryotic viruses originated as a result of extensive recombination of genes from various bacteriophages, archaeal viruses, plasmids, and the evolving eukaryotic genomes. Again, this vision is predicated on a specific model of the emergence of eukaryotic cell under which archaeo-bacterial symbiosis was the starting point of eukaryogenesis, a scenario that appears to be best compatible with the data. The existence of several genes that are central to virus replication and structure, are shared by a broad variety of viruses but are missing from cellular genomes (virus hallmark genes) suggests the model of an ancient virus world, a flow of virus-specific genes that went uninterrupted from the precellular stage of life's evolution to this day. This concept is tightly linked to two key conjectures on evolution of cells: existence of a complex, precellular, compartmentalized but extensively mixing and recombining pool of genes, and origin of the eukaryotic cell by archaeo-bacterial fusion. The virus world concept and these models of major transitions in the evolution of cells provide complementary pieces of an emerging coherent picture of life's history. W. Ford Doolittle, J. Peter Gogarten, and Arcady Mushegian.
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