In silico predicted robustness of viroids RNA secondary structures.: I.: The effect of single mutations
In silico predicted robustness of viroids RNA secondary structures.: I.: The effect of single mutations
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DOI：
10.1093/molbev/msl005
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发表时间：
2006-07-01
影响因子：
10.7
通讯作者：
Elena, Santiago F.
中科院分区：
文献类型：
--
作者：
Sanjuan, Rafael;Forment, Javier;Elena, Santiago F.
类病毒是植物亚病毒病原体，其基因组由不编码任何蛋白质的单链共价封闭的小RNA分子构成。尽管基因组简单，但它们能够在易感植物中诱导破坏性症状。29种类病毒中的大多数折叠成棒状或准棒状结构，而少数折叠成分支结构。这些RNA结构的形状可能是类病毒最具特征的特性之一，有时被认为是它们唯一的表型。在这里，我们使用RNA热力学二级结构预测算法来比较所有类病毒物种的突变鲁棒性。在表征每个类病毒物种的结构稳定性和中性邻域的宽度的突变效应的分布的统计特性，我们表现出一种进化趋势，在类病毒辐射增加结构的鲁棒性，支持自适应值的鲁棒性。2个类病毒家族之间的鲁棒性差异可以解释为分支结构比棒状结构更脆弱。我们还表明，基因组冗余可以有助于这些简单的RNA基因组的鲁棒性。
Viroids are plant subviral pathogens whose genomes are constituted by a single-stranded and covalently closed small RNA molecule that does not encode for any protein. Despite this genomic simplicity, they are able of inducing devastating symptoms in susceptible plants. Most of the 29 described viroid species fold into a rodlike or quasi-rodlike structure, whereas a few of them fold as branched structures. The shape of these RNA structures is perhaps one of the most characteristic properties of viroids and sometimes is considered their only phenotype. Here we use RNA thermodynamic secondary structure prediction algorithms to compare the mutational robustness of all viroid species. After characterizing the statistical properties of the distribution of mutational effects on structure stability and the wideness of neutral neighborhood for each viroid species, we show an evolutionary trend toward increased structural robustness during viroid radiation, giving support to the adaptive value of robustness. Differences in robustness among the 2 viroid families can be explained by the larger fragility of branched structures compared with the rodlike ones. We also show that genomic redundancy can contribute to the robustness of these simple RNA genomes.