IBAM, Facultad de Ciencias Agrarias, CONICET, Universidad Nacional de Cuyo, M5528AHB, Chacras de Coria, Argentina.
Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, 5500, Mendoza, Argentina.
Plant Mol Biol. 2018 Jun;97(3):215-231. doi: 10.1007/s11103-018-0734-9. Epub 2018 May 14.
Our understanding of the dynamic and evolution of RNA editing in angiosperms is in part limited by the few editing sites identified to date. This study identified 10,217 editing sites from 17 diverse angiosperms. Our analyses confirmed the universality of certain features of RNA editing, and offer new evidence behind the loss of editing sites in angiosperms. RNA editing is a post-transcriptional process that substitutes cytidines (C) for uridines (U) in organellar transcripts of angiosperms. These substitutions mostly take place in mitochondrial messenger RNAs at specific positions called editing sites. By means of publicly available RNA-seq data, this study identified 10,217 editing sites in mitochondrial protein-coding genes of 17 diverse angiosperms. Even though other types of mismatches were also identified, we did not find evidence of non-canonical editing processes. The results showed an uneven distribution of editing sites among species, genes, and codon positions. The analyses revealed that editing sites were conserved across angiosperms but there were some species-specific sites. Non-synonymous editing sites were particularly highly conserved (~ 80%) across the plant species and were efficiently edited (80% editing extent). In contrast, editing sites at third codon positions were poorly conserved (~ 30%) and only partially edited (~ 40% editing extent). We found that the loss of editing sites along angiosperm evolution is mainly occurring by replacing editing sites with thymidines, instead of a degradation of the editing recognition motif around editing sites. Consecutive and highly conserved editing sites had been replaced by thymidines as result of retroprocessing, by which edited transcripts are reverse transcribed to cDNA and then integrated into the genome by homologous recombination. This phenomenon was more pronounced in eudicots, and in the gene cox1. These results suggest that retroprocessing is a widespread driving force underlying the loss of editing sites in angiosperm mitochondria.
我们对植物有性生殖中 RNA 编辑的动态和演变的了解在一定程度上受到迄今为止发现的少数编辑位点的限制。本研究从 17 种不同的有性生殖植物中鉴定出了 10217 个编辑位点。我们的分析证实了某些 RNA 编辑特征的普遍性，并为有性生殖植物中编辑位点丢失的背后提供了新的证据。RNA 编辑是一种在后转录过程中，细胞器转录本中的胞嘧啶（C）被尿嘧啶（U）取代的过程。这些取代主要发生在特定位置的线粒体信使 RNA 上，这些位置被称为编辑位点。通过使用公开的 RNA-seq 数据，本研究在 17 种不同的有性生殖植物的线粒体蛋白编码基因中鉴定出了 10217 个编辑位点。尽管也发现了其他类型的错配，但我们没有发现非规范编辑过程的证据。结果表明，编辑位点在物种、基因和密码子位置之间的分布不均匀。分析表明，编辑位点在有性生殖植物中是保守的，但也有一些物种特异性的编辑位点。非同义编辑位点在植物物种中高度保守（80%），且编辑效率高（80%的编辑程度）。相比之下，第三密码子位置的编辑位点保守性较差（30%），且仅部分编辑（~40%的编辑程度）。我们发现，随着有性生殖植物的进化，编辑位点的丢失主要是通过用胸腺嘧啶取代编辑位点而不是通过编辑识别模体的降解来实现的。连续且高度保守的编辑位点已被胸腺嘧啶取代，这是由于反转录加工，即编辑后的转录本被反转录成 cDNA，然后通过同源重组整合到基因组中。这种现象在真双子叶植物和 cox1 基因中更为明显。这些结果表明，反转录加工是导致有性生殖植物线粒体编辑位点丢失的一种普遍驱动力。
