Prangishvili David, Garrett Roger A, Koonin Eugene V
Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur, rue Dr. Roux 25, 75724 Paris Cedex 15, France.
Virus Res. 2006 Apr;117(1):52-67. doi: 10.1016/j.virusres.2006.01.007. Epub 2006 Feb 28.
In terms of virion morphology, the known viruses of archaea fall into two distinct classes: viruses of mesophilic and moderately thermophilic Eueryarchaeota closely resemble head-and-tail bacteriophages whereas viruses of hyperthermophilic Crenarchaeota show a variety of unique morphotypes. In accord with this distinction, the sequenced genomes of euryarchaeal viruses encode many proteins homologous to bacteriophage capsid proteins. In contrast, initial analysis of the crenarchaeal viral genomes revealed no relationships with bacteriophages and, generally, very few proteins with detectable homologs. Here we describe a re-analysis of the proteins encoded by archaeal viruses, with an emphasis on comparative genomics of the unique viruses of Crenarchaeota. Detailed examination of conserved domains and motifs uncovered a significant number of previously unnoticed homologous relationships among the proteins of crenarchaeal viruses and between viral proteins and those from cellular life forms and allowed functional predictions for some of these conserved genes. A small pool of genes is shared by overlapping subsets of crenarchaeal viruses, in a general analogy with the metagenome structure of bacteriophages. The proteins encoded by the genes belonging to this pool include predicted transcription regulators, ATPases implicated in viral DNA replication and packaging, enzymes of DNA precursor metabolism, RNA modification enzymes, and glycosylases. In addition, each of the crenarchaeal viruses encodes several proteins with prokaryotic but not viral homologs, some of which, predictably, seem to have been scavenged from the crenarchaeal hosts, but others might have been acquired from bacteria. We conclude that crenarchaeal viruses are, in general, evolutionarily unrelated to other known viruses and, probably, evolved via independent accretion of genes derived from the hosts and, through more complex routes of horizontal gene transfer, from other prokaryotes.
就病毒粒子形态而言，已知的古菌病毒可分为两个不同类别：嗜温及中度嗜热广古菌门的病毒与有尾噬菌体极为相似，而嗜热泉古菌门的病毒则呈现出多种独特的形态类型。与此分类相符，广古菌病毒的测序基因组编码了许多与噬菌体衣壳蛋白同源的蛋白质。相比之下，对泉古菌病毒基因组的初步分析表明，它们与噬菌体没有关系，并且一般来说，具有可检测同源物的蛋白质很少。在此，我们描述了对古菌病毒编码蛋白质的重新分析，重点是对泉古菌门独特病毒的比较基因组学研究。对保守结构域和基序的详细检查发现，泉古菌病毒蛋白质之间以及病毒蛋白质与细胞生命形式的蛋白质之间存在大量以前未被注意到的同源关系，并对其中一些保守基因进行了功能预测。一小部分基因为泉古菌病毒的重叠子集所共有，这与噬菌体的宏基因组结构大体相似。属于该基因库的基因所编码的蛋白质包括预测的转录调节因子、参与病毒DNA复制和包装的ATP酶、DNA前体代谢酶、RNA修饰酶和糖基化酶。此外，每种泉古菌病毒都编码几种具有原核生物而非病毒同源物的蛋白质，其中一些蛋白质据推测似乎是从古菌宿主中获取的，但其他一些可能是从细菌中获得的。我们得出结论，一般来说，泉古菌病毒在进化上与其他已知病毒无关，可能是通过从宿主衍生的基因独立积累以及通过更复杂的水平基因转移途径从其他原核生物进化而来的。
