Key Laboratory of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China.
RNA. 2023 Feb;29(2):141-152. doi: 10.1261/rna.079450.122.
The adaptiveness of nonsynonymous RNA editing (recoding) could be conferred by the flexibility of the temporal-spatially controllable proteomic diversity, or by its restorative effect which fixes unfavorable genomic mutations at the RNA level. These two complementary hypotheses, namely, the diversifying hypothesis and the restorative hypothesis, have distinct predictions on the landscape of RNA editing sites. We collected the chloroplast C-to-U RNA editomes of 21 vascular plants (11 angiosperms, four gymnosperms, and six ferns) from a previous study, aiming to testify whether the plant editomes typically conform to the restorative hypothesis. All predictions made by the restorative hypothesis are verified: (i) nonsynonymous editing sites are more frequent and have higher editing levels than synonymous sites; (ii) nonsynonymous editing levels are extremely high and show weak tissue-specificity in plants; (iii) on the inferred genomic sites with recent T-to-C mutations, nonsynonymous sites but not synonymous sites are compensated by C-to-U RNA editing. In conclusion, nonsynonymous C-to-U RNA editing in plants is adaptive due to its restorative effects. The recoding levels are high and are constantly required across the whole plant so that the recoding events could perfectly mimic DNA mutations. The evolutionary significance of plant RNA editing is systematically demonstrated at the genome-wide level.
非 synonymous RNA 编辑（重编码）的适应性可能是由时空可控的蛋白质组多样性的灵活性赋予的，或者是由其修复作用赋予的，这种修复作用可以在 RNA 水平上修复不利的基因组突变。这两个互补的假说，即多样化假说和修复假说，对 RNA 编辑位点的景观有不同的预测。我们从前一项研究中收集了 21 种维管植物（11 种被子植物、4 种裸子植物和 6 种蕨类植物）的叶绿体 C-to-U RNA 编辑组，旨在验证植物编辑组是否通常符合修复假说。修复假说的所有预测都得到了验证：（i）非 synonymous 编辑位点比同义位点更频繁且编辑水平更高；（ii）非同义编辑水平极高，在植物中表现出弱的组织特异性；（iii）在最近发生 T-to-C 突变的推断基因组位点上，非同义位点而非同义位点通过 C-to-U RNA 编辑得到补偿。总之，植物中非同义 C-to-U RNA 编辑是适应性的，因为它具有修复作用。重编码水平很高，在整个植物中都不断需要，以便重编码事件可以完美地模拟 DNA 突变。植物 RNA 编辑的进化意义在全基因组水平上得到了系统的证明。
