IZMB – Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, 53115 Bonn, Germany.
J Mol Evol. 2012 Feb;74(1-2):37-51. doi: 10.1007/s00239-012-9486-3.
RNA editing in mitochondria and chloroplasts of land plants alters transcript sequences by site-specific conversions of cytidines into uridines. RNA editing frequencies vary extremely between land plant clades, ranging from zero in some liverworts to more than 2,000 sites in lycophytes. Unique pentatricopeptide repeat (PPR) proteins with variable domain extension (E/E+/DYW) have recently been identified as specific editing site recognition factors in model plants. The distinctive functions of these PPR protein domain additions have remained unclear, although deaminase function has been proposed for the DYW domain. To shed light on diversity of RNA editing and DYW proteins at the origin of land plant evolution, we investigated editing patterns of the mitochondrial nad5, nad4, and nad2 genes in a wide sampling of more than 100 liverworts and mosses using the recently developed PREPACT program (www.prepact.de) and exemplarily confirmed predicted RNA editing sites in selected taxa. Extreme variability in RNA editing frequency is seen both in liverworts and mosses. Only few editings exist in the liverwort Lejeunea cavifolia or the moss Pogonatum urnigerum whereas up to 20% of cytidines are edited in the liverwort Haplomitrium mnioides or the moss Takakia lepidozioides. Interestingly, the latter are taxa that branch very early within their respective clades. Amplicons targeting the E/E+/DYW domains and subsequent random clone sequencing show DYW domains among bryophytes to be highly conserved in comparison with their angiosperm counterparts and to correlate well with RNA editing frequencies regarding their diversities. We propose that DYW proteins are the key players of RNA editing at the origin of land plants.
真核生物线粒体和叶绿体中的 RNA 编辑通过特定位置的胞嘧啶向尿嘧啶的转换来改变转录本序列。不同陆地植物类群的 RNA 编辑频率差异极大，从某些苔藓植物的零编辑到石松类植物的 2000 多个编辑位点。最近在模式植物中鉴定出具有可变结构域延伸（E/E+/DYW）的独特五肽重复（PPR）蛋白作为特定编辑位点识别因子。尽管已提出 DYW 结构域具有脱氨酶功能，但这些 PPR 蛋白结构域添加的独特功能仍不清楚。为了阐明陆地植物进化起源处的 RNA 编辑和 DYW 蛋白多样性，我们利用最近开发的 PREPACT 程序（www.prepact.de），对 100 多种苔藓植物和藓类植物的线粒体 nad5、nad4 和 nad2 基因进行了广泛的编辑模式研究，并在选定的分类群中对预测的 RNA 编辑位点进行了实例验证。在苔藓植物和藓类植物中均观察到 RNA 编辑频率的极大变异性。在 Lejeunea cavifolia 或 Pogonatum urnigerum 等苔藓植物中，只有少数几个编辑点存在，而在 Haplomitrium mnioides 或 Takakia lepidozioides 等苔藓植物中，高达 20%的胞嘧啶被编辑。有趣的是，后两种是各自类群中分支非常早的分类群。针对 E/E+/DYW 结构域的扩增子和随后的随机克隆测序显示，与被子植物相比，苔藓植物中的 DYW 结构域高度保守，并且与 RNA 编辑频率及其多样性密切相关。我们提出 DYW 蛋白是陆地植物起源处 RNA 编辑的关键因子。
