Virus-host coevolution: common patterns of nucleotide motif usage in Flaviviridae and their hosts.
Virus-host coevolution: common patterns of nucleotide motif usage in Flaviviridae and their hosts.
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DOI：
10.1371/journal.pone.0006282
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发表时间：
2009-07-20
期刊：
影响因子：
3.7
通讯作者：
Franco GR
中科院分区：
文献类型：
--
作者：
Lobo FP;Mota BE;Pena SD;Azevedo V;Macedo AM;Tauch A;Machado CR;Franco GR
病毒与宿主的相互作用是一个持续的共同进化过程，涉及宿主免疫系统和病毒逃逸机制。黄病毒科家族由感染脊椎动物（哺乳动物和鸟类）和/或无脊椎动物（蜱和蚊子）生物的快速进化的RNA病毒组成。这些宿主群体是非常不同的生命形式，它们被很长的进化时间分开，因此谱系特异性抗病毒机制可能已经进化。感染单一宿主谱系的黄病毒科病毒将受到特定宿主诱导的压力，因此被它们选择。在这项工作中，我们比较了黄病毒科病毒及其宿主的基因组进化模式，试图揭示在这种不同的群体中诱导共同特征的共同进化过程。特别是，我们已经分析了二核苷酸和密码子的使用模式的编码区的脊椎动物和无脊椎动物的生物体，以及在黄病毒科病毒，专门感染一个或两个主机类型。两个宿主组具有非常独特的二核苷酸和密码子使用模式。在脊椎动物组中发现明显的CpG代表性不足，可能是由甲基化脱氨基过程引起的，以及显著的TpA降低。无脊椎动物组仅显示TpA频率降低偏倚。黄病毒科病毒以宿主特异性方式模仿宿主核苷酸基序使用。脊椎动物感染的病毒具有CpG和TpA的代表性不足，而昆虫病毒只显示TpA代表性不足的偏见。持续感染哺乳动物或昆虫宿主的单宿主黄病毒科成员（分别为Hepacivirus和仅昆虫黄病毒）被发现与其宿主的密码子使用谱比相关的黄病毒科更相似。我们证明，脊椎动物和蚊子的基因组是非常不同的谱系特异性的限制，和黄病毒科病毒，专门感染这些谱系似乎受到相同的进化压力，形成其主机编码区，证明谱系特异性的病毒和主机组之间的共同进化过程。
Virus-host biological interaction is a continuous coevolutionary process involving both host immune system and viral escape mechanisms. Flaviviridae family is composed of fast evolving RNA viruses that infects vertebrate (mammals and birds) and/or invertebrate (ticks and mosquitoes) organisms. These host groups are very distinct life forms separated by a long evolutionary time, so lineage-specific anti-viral mechanisms are likely to have evolved. Flaviviridae viruses which infect a single host lineage would be subjected to specific host-induced pressures and, therefore, selected by them. In this work we compare the genomic evolutionary patterns of Flaviviridae viruses and their hosts in an attempt to uncover coevolutionary processes inducing common features in such disparate groups. Especially, we have analyzed dinucleotide and codon usage patterns in the coding regions of vertebrate and invertebrate organisms as well as in Flaviviridae viruses which specifically infect one or both host types. The two host groups possess very distinctive dinucleotide and codon usage patterns. A pronounced CpG under-representation was found in the vertebrate group, possibly induced by the methylation-deamination process, as well as a prominent TpA decrease. The invertebrate group displayed only a TpA frequency reduction bias. Flaviviridae viruses mimicked host nucleotide motif usage in a host-specific manner. Vertebrate-infecting viruses possessed under-representation of CpG and TpA, and insect-only viruses displayed only a TpA under-representation bias. Single-host Flaviviridae members which persistently infect mammals or insect hosts (Hepacivirus and insect-only Flavivirus, respectively) were found to posses a codon usage profile more similar to that of their hosts than to related Flaviviridae. We demonstrated that vertebrates and mosquitoes genomes are under very distinct lineage-specific constraints, and Flaviviridae viruses which specifically infect these lineages appear to be subject to the same evolutionary pressures that shaped their host coding regions, evidencing the lineage-specific coevolutionary processes between the viral and host groups.
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影响因子：
3.7
作者：
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通讯作者：
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DOI：
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发表时间：
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期刊：
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