The Natural History Museum of Denmark, University of Copenhagen, Sølvgade 83 Opg, S, DK-1307 Copenhagen C, Denmark.
BMC Evol Biol. 2010 Nov 11;10:349. doi: 10.1186/1471-2148-10-349.
RNA editing is a post-transcriptional process that, in seed plants, involves a cytosine to uracil change in messenger RNA, causing the translated protein to differ from that predicted by the DNA sequence. RNA editing occurs extensively in plant mitochondria, but large differences in editing frequencies are found in some groups. The underlying processes responsible for the distribution of edited sites are largely unknown, but gene function, substitution rate, and gene conversion have been proposed to influence editing frequencies.
We studied five mitochondrial genes in the monocot order Alismatales, all showing marked differences in editing frequencies among taxa. A general tendency to lose edited sites was observed in all taxa, but this tendency was particularly strong in two clades, with most of the edited sites lost in parallel in two different areas of the phylogeny. This pattern is observed in at least four of the five genes analyzed. Except in the groups that show an unusually low editing frequency, the rate of C-to-T changes in edited sites was not significantly higher that in non-edited 3rd codon positions. This may indicate that selection is not actively removing edited sites in nine of the 12 families of the core Alismatales. In all genes but ccmB, a significant correlation was found between frequency of change in edited sites and synonymous substitution rate. In general, taxa with higher substitution rates tend to have fewer edited sites, as indicated by the phylogenetically independent correlation analyses. The elimination of edited sites in groups that lack or have reduced levels of editing could be a result of gene conversion involving a cDNA copy (retroprocessing). If so, this phenomenon could be relatively common in the Alismatales, and may have affected some groups recurrently. Indirect evidence of retroprocessing without a necessary correlation with substitution rate was found mostly in families Alismataceae and Hydrocharitaceae (e.g., groups that suffered a rapid elimination of all their edited sites, without a change in substitution rate).
The effects of substitution rate, selection, and/or gene conversion on the dynamics of edited sites in plant mitochondria remain poorly understood. Although we found an inverse correlation between substitution rate and editing frequency, this correlation is partially obscured by gene retroprocessing in lineages that have lost most of their edited sites. The presence of processed paralogs in plant mitochondria deserves further study, since most evidence of their occurrence is circumstantial.
RNA 编辑是一种转录后过程，在种子植物中，涉及信使 RNA 中的胞嘧啶到尿嘧啶的变化，导致翻译的蛋白质与 DNA 序列预测的蛋白质不同。RNA 编辑在植物线粒体中广泛发生，但在一些群体中发现编辑频率存在很大差异。负责编辑位点分布的基础过程在很大程度上是未知的，但基因功能、替代率和基因转换已被提议影响编辑频率。
我们研究了单子叶植物目泽泻目中的五个线粒体基因，所有这些基因在分类群中都显示出明显不同的编辑频率。在所有分类群中观察到失去编辑位点的一般趋势，但在两个进化枝中这种趋势特别强烈，在两个不同的进化枝区域中，大多数编辑位点同时丢失。这种模式在至少四个分析的基因中观察到。除了在显示异常低编辑频率的组中，编辑位点的 C 到 T 变化率没有明显高于非编辑的第三密码子位置。这可能表明在核心泽泻目中的 12 个科中的 9 个中，选择并没有积极地去除编辑位点。除了 ccmB 基因外，在编辑位点变化频率和同义替代率之间发现了显著相关性。一般来说，替代率较高的分类群具有较少的编辑位点，这是通过系统发育独立相关性分析得出的。在缺乏或减少编辑水平的组中消除编辑位点可能是涉及 cDNA 拷贝（ retroprocessing ）的基因转换的结果。如果是这样，这种现象在泽泻目中可能相对普遍，并且可能反复影响一些群体。在没有替代率必要相关性的情况下发现 retroprocessing 的间接证据主要在泽泻科和水鳖科（例如，经历了所有编辑位点快速消除而没有替代率变化的组）。
替代率、选择和/或基因转换对植物线粒体中编辑位点动态的影响仍知之甚少。尽管我们发现替代率和编辑频率之间存在负相关，但在失去大部分编辑位点的进化枝中，这种相关性部分被基因 retroprocessing 掩盖。植物线粒体中加工的旁系同源物的存在值得进一步研究，因为它们发生的大多数证据都是间接的。
