Improved Computational Target Site Prediction for Pentatricopeptide Repeat RNA Editing Factors

Pentatricopeptide repeat (PPR) proteins with an E domain have been identified as specific factors for C to U RNA editing in plant organelles. These PPR proteins bind to a unique sequence motif 5′ of their target editing sites. Recently, involvement of a combinatorial amino acid code in the P (normal length) and S type (short) PPR domains in sequence specific RNA binding was reported. PPR proteins involved in RNA editing, however, contain not only P and S motifs but also their long variants L (long) and L2 (long2) and the S2 (short2) motifs. We now find that inclusion of these motifs improves the prediction of RNA editing target sites. Previously overlooked RNA editing target sites are suggested from the PPR motif structures of known E-class PPR proteins and are experimentally verified. RNA editing target sites are assigned for the novel PPR protein MEF32 (mitochondrial editing factor 32) and are confirmed in the cDNA.

带有E结构域的五肽重复（Pentatricopeptide repeat, PPR）蛋白已被证实为植物细胞器中C到U RNA编辑的特异性因子。这类PPR蛋白会结合其靶编辑位点5'端的独特序列基序。近期有研究表明，P（正常长度型）与S型（短型）PPR结构域内的组合氨基酸密码参与了序列特异性RNA结合过程。然而，参与RNA编辑的PPR蛋白不仅含有P和S基序，还包含其长变体L（长型）、L2（长型2）以及S2（短型2）基序。本研究发现，纳入上述基序可提升RNA编辑靶位点的预测精度。研究人员从已知E类PPR蛋白的PPR基序结构中，发掘出此前被忽视的RNA编辑靶位点，并通过实验进行了验证。此外，本研究为新型PPR蛋白MEF32（线粒体编辑因子32, mitochondrial editing factor 32）标注了RNA编辑靶位点，并在互补DNA（complementary DNA, cDNA）中得到了确认。