Mower Jeffrey P
Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.
Mol Biol Evol. 2008 Jan;25(1):52-61. doi: 10.1093/molbev/msm226. Epub 2007 Oct 16.
RNA editing is a type of nucleic acid modification found in many eukaryotic lineages. In plants, RNA editing occurs by the site-specific conversion of cytidines to uridines in mitochondrial and plastid transcripts. To quantify the rates of edit site gain and loss in angiosperm mitochondrial genes, a nonreversible maximum likelihood model was developed that treats sites of RNA editing as a fifth nucleotide state. The rate of loss of editing, either by genomic replacement with a thymidine or by loss of recognition by the editing complex, was found to be significantly higher than the rate of gain. Furthermore, the frequency of editing is not at equilibrium in angiosperm mitochondrial sequences; there is a strong tendency for the number of edited sites to decrease over time. These results indicate that selection plays a key role in driving the higher rate of edit site loss relative to gain and suggest that the strength of selection against editing has become increasingly stringent over the course of angiosperm evolution. The model described here should be easily adaptable to other systems that involve nucleic acid modifications.
RNA编辑是在许多真核生物谱系中发现的一种核酸修饰类型。在植物中，RNA编辑通过线粒体和质体转录本中胞嘧啶向尿嘧啶的位点特异性转换而发生。为了量化被子植物线粒体基因中编辑位点获得和丢失的速率，开发了一种不可逆的最大似然模型，该模型将RNA编辑位点视为第五种核苷酸状态。结果发现，无论是通过用胸腺嘧啶进行基因组替换还是通过编辑复合体失去识别，编辑丢失的速率都显著高于获得的速率。此外，在被子植物线粒体序列中，编辑频率并不处于平衡状态；随着时间的推移，编辑位点的数量有强烈的减少趋势。这些结果表明，选择在驱动编辑位点丢失速率高于获得速率方面起着关键作用，并表明在被子植物进化过程中，针对编辑的选择强度变得越来越严格。这里描述的模型应该很容易适用于其他涉及核酸修饰的系统。
