Mrázek Jan, Karlin Samuel
Department of Microbiology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.
Proc Natl Acad Sci U S A. 2007 Mar 20;104(12):5127-32. doi: 10.1073/pnas.0700429104. Epub 2007 Mar 9.
More than a dozen large DNA viruses exceeding 240-kb genome size were recently discovered, including the "giant" mimivirus with a 1.2-Mb genome size. The detection of mimivirus and other large viruses has stimulated new analysis and discussion concerning the early evolution of life and the complexity and mechanisms of evolutionary transitions. This paper presents analysis in three contexts. (i) Genome signatures of large viruses tend to deviate from the genome signatures of their hosts, perhaps indicating that the large viruses are lytic in the hosts. (ii) Proteome composition within these viral genomes contrast with cellular organisms; for example, most eukaryotic genomes, with respect to acidic residue usages, select Glu over Asp, but the opposite generally prevails for the large viral genomes preferring Asp more than Glu. In comparing Phe vs. Tyr usage, the viral genomes select mostly Tyr over Phe, whereas in almost all bacterial and eukaryotic genomes, Phe is used more than Tyr. Interpretations of these contrasts are proffered with respect to protein structure and function. (iii) Frequent oligonucleotides and peptides are characterized in the large viral genomes. The frequent words may provide structural flexibility to interact with host proteins.
最近发现了十几种基因组大小超过240 kb的大型DNA病毒，包括基因组大小为1.2 Mb的“巨型” 米米病毒。米米病毒和其他大型病毒的发现激发了关于生命早期进化以及进化转变的复杂性和机制的新分析和讨论。本文从三个方面进行分析。（i）大型病毒的基因组特征往往与其宿主的基因组特征不同，这可能表明大型病毒在宿主中具有裂解性。（ii）这些病毒基因组中的蛋白质组组成与细胞生物形成对比；例如，就酸性残基的使用而言，大多数真核基因组选择谷氨酸而非天冬氨酸，但大型病毒基因组通常相反，更喜欢天冬氨酸而非谷氨酸。在比较苯丙氨酸与酪氨酸的使用时，病毒基因组大多选择酪氨酸而非苯丙氨酸，而在几乎所有细菌和真核基因组中，苯丙氨酸的使用多于酪氨酸。针对这些对比，从蛋白质结构和功能方面进行了解释。（iii）大型病毒基因组中频繁出现的寡核苷酸和肽具有特征性。这些频繁出现的序列可能为与宿主蛋白相互作用提供结构灵活性。
