Molecular and functional diversity of organelle RNA editing mediated by RNA recognition motif-containing protein ORRM4 in tomato
Molecular and functional diversity of organelle RNA editing mediated by RNA recognition motif-containing protein ORRM4 in tomato
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番茄中RNA识别基序蛋白ORRM4介导的细胞器RNA编辑的分子和功能多样性
DOI：
10.1111/nph.16714
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发表时间：
2020
期刊：
影响因子：
9.4
通讯作者：
Zhu Hongliang
中科院分区：
文献类型：
--
作者：
Yang Yongfang;Liu Xiuying;Wang Keru;Li Jinyan;Zhu Guoning;Ren Shuang;Deng Zhiping;Zhu Benzhong;Fu Daqi;Qu Guiqin;Luo Yunbo;Zhu Hongliang
植物细胞器RNA编辑是一种独特的转录后RNA修饰，对植物发育至关重要。我们先前已经证明，RNA编辑因子SLORRM4是番茄(Solanum Lycopsicum)线粒体功能和果实成熟所必需的。然而，关于SlORRM4介导的RNA编辑的全面图谱还很缺乏。我们观察到SlORRM4同时针对叶绿体和线粒体，其敲除导致叶片淡绿色和果实成熟延迟。通过高通量测序，我们鉴定出了由SlORRM4控制的12个叶绿体编辑位点和336个线粒体编辑位点，分别占叶片叶绿体和果实线粒体的23%和61%。对天然RNA免疫沉淀测序的分析表明，SlORRM4与31个RNA靶点结合，其中19个靶点含有SLORRM4依赖的编辑位点。对推测的SlORRM4相互作用蛋白的大规模分析确定了SlRIP1b，一种RIP/Morf蛋白。此外，功能鉴定表明SlRIP1b与番茄果实成熟有关。我们的结果表明，SlRM4与RNA靶标结合，并与SlRIP1b相互作用，广泛影响番茄细胞器中的RNA编辑。这些结果为深入了解高等植物中RNA编辑因子的分子和功能多样性提供了依据。
Plant organellar RNA editing is a distinct type of post‐transcriptional RNA modification that is critical for plant development. We showed previously that the RNA editing factor SlORRM4 is required for mitochondrial function and fruit ripening in tomato (Solanum lycopersicum). However, a comprehensive atlas of the RNA editing mediated by SlORRM4 is lacking.We observed that SlORRM4 is targeted to both chloroplasts and mitochondria, and its knockout results in pale‐green leaves and delayed fruit ripening. Using high‐throughput sequencing, we identified 12 chloroplast editing sites and 336 mitochondrial editing sites controlled by SlORRM4, accounting for 23% of chloroplast sites in leaves and 61% of mitochondrial sites in fruits, respectively.Analysis of native RNA immunoprecipitation sequencing revealed that SlORRM4 binds to 31 RNA targets; 19 of these targets contain SlORRM4‐dependent editing sites. Large‐scale analysis of putative SlORRM4‐interacting proteins identified SlRIP1b, a RIP/MORF protein. Moreover, functional characterization demonstrated that SlRIP1b is involved in tomato fruit ripening.Our results indicate that SlORRM4 binds to RNA targets and interacts with SlRIP1b to broadly affect RNA editing in tomato organelles. These results provide insights into the molecular and functional diversity of RNA editing factors in higher plants.