Why do RNA viruses recombine?
Why do RNA viruses recombine?
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DOI：
10.1038/nrmicro2614
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发表时间：
2011-07-04
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--
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中科院分区：
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RNA病毒能够经历两种形式的重组：RNA重组（原则上）可以发生在任何类型的RNA病毒中，以及重配（仅限于具有分段基因组的病毒）。RNA重组的速率在RNA病毒之间有显著差异。一些病毒，特别是那些具有负义单链基因组的病毒，表现出如此低的重组率，以至于它们实际上是克隆的。相比之下，一些正义单链RNA病毒和一些逆转录病毒（如HIV）表现出高重组率，可以超过每个核苷酸测量的突变率。尽管重组通常被认为是有性生殖的一种形式，但很少有证据表明RNA病毒中的重组是作为创造有利基因型或去除有害突变的一种方式而进化的。特别是，重组频率和有害突变的负担之间没有关联。类似地，几乎没有证据表明重组可以被选择作为遗传修复的一种形式。RNA病毒重组率与基因组结构的关系最密切。因此，由于基因组RNA在核糖核蛋白复合物中的限制性缔合以及缺乏用于模板转换的底物，负义单链RNA病毒可以以低速率重组，而一些逆转录病毒快速重组，因为它们的病毒体含有两个基因组拷贝，并且这些拷贝之间的模板转换是病毒复制周期的不可避免的一部分。因此，我们假设RNA病毒中的重组是复制中使用的病毒聚合酶的持续合成能力的机械副产品，并且它随基因组结构而变化。重组可以是RNA病毒的重要进化力量，但不同RNA病毒之间的重组率差异很大。在这篇分析文章中，Simon-Loriere和Holmes描述了RNA病毒的重组机制以及这些机制在病毒进化中的作用。在许多RNA病毒中都会发生变性，并且具有重要的进化意义。然而，重组率在RNA病毒之间变化很大，其范围可以从克隆到高度重组。在这里，我们审查的因素，可能会解释这种变化的重组频率，并表明，很少有证据表明，重组是有利于自然选择，以创造有利的基因型或清除有害的突变，预测如果重组功能作为一种形式的有性生殖。相反，重组率似乎反映了病毒基因组组织的更大规模模式，因此重组可能是作用于病毒生物学其他方面的进化压力的机械副产品。
RNA viruses are able to undergo two forms of recombination: RNA recombination, which (in principle) can occur in any type of RNA virus, and reassortment, which is restricted to those viruses with segmented genomes. Rates of RNA recombination vary markedly among RNA viruses. Some viruses, particularly those with negative-sense single-stranded genomes, exhibit such low rates of recombination that they are effectively clonal. By contrast, some positive-sense single-stranded RNA viruses and some retroviruses such as HIV exhibit high rates of recombination that can exceed the rates of mutation when measured per nucleotide. Although recombination is often argued to represent a form of sexual reproduction, there is little evidence that recombination in RNA viruses evolved as a way of creating advantageous genotypes or removing deleterious mutations. In particular, there is no association between recombination frequency and the burden of a deleterious mutation. Similarly, there is little evidence that recombination could have been selected as a form of genetic repair. The strongest association for rates of recombination in RNA viruses is with genome structure. Hence, negative-sense single-stranded RNA viruses may recombine at low rates because of the restrictive association of genomic RNA in a ribonucleoprotein complex, as well as a lack of substrates for template switching, whereas some retroviruses recombine rapidly because their virions contain two genome copies and template switching between these copies is an inevitable part of the viral replication cycle. We therefore hypothesize that recombination in RNA viruses is a mechanistic by-product of the processivity of the viral polymerase that is used in replication, and that it varies with genome structure. Recombination can be an important evolutionary force for RNA viruses, but the rate of recombination varies greatly between different RNA viruses. In this Analysis article, Simon-Loriere and Holmes describe the mechanisms of recombination for RNA viruses and the role of these mechanisms in viral evolution. Recombination occurs in many RNA viruses and can be of major evolutionary significance. However, rates of recombination vary dramatically among RNA viruses, which can range from clonal to highly recombinogenic. Here, we review the factors that might explain this variation in recombination frequency and show that there is little evidence that recombination is favoured by natural selection to create advantageous genotypes or purge deleterious mutations, as predicted if recombination functions as a form of sexual reproduction. Rather, recombination rates seemingly reflect larger-scale patterns of viral genome organization, such that recombination may be a mechanistic by-product of the evolutionary pressures acting on other aspects of virus biology.
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