Institut de biologie moléculaire des plantes (IBMP), CNRS, Université de Strasbourg, 67000, Strasbourg, France.
Plateforme Protéomique Strasbourg-Esplanade, CNRS, Université de Strasbourg, 67000, Strasbourg, France.
Plant J. 2018 Oct;96(1):119-132. doi: 10.1111/tpj.14022. Epub 2018 Aug 1.
The RNA helicase UP-FRAMESHIFT (UPF1) is a key factor of nonsense-mediated decay (NMD), a mRNA decay pathway involved in RNA quality control and in the fine-tuning of gene expression. UPF1 recruits UPF2 and UPF3 to constitute the NMD core complex, which is conserved across eukaryotes. No other components of UPF1-containing ribonucleoproteins (RNPs) are known in plants, despite its key role in regulating gene expression. Here, we report the identification of a large set of proteins that co-purify with the Arabidopsis UPF1, either in an RNA-dependent or RNA-independent manner. We found that like UPF1, several of its co-purifying proteins have a dual localization in the cytosol and in P-bodies, which are dynamic structures formed by the condensation of translationally repressed mRNPs. Interestingly, more than half of the proteins of the UPF1 interactome also co-purify with DCP5, a conserved translation repressor also involved in P-body formation. We identified a terminal nucleotidyltransferase, ribonucleases and several RNA helicases among the most significantly enriched proteins co-purifying with both UPF1 and DCP5. Among these, RNA helicases are the homologs of DDX6/Dhh1, known as translation repressors in humans and yeast, respectively. Overall, this study reports a large set of proteins associated with the Arabidopsis UPF1 and DCP5, two components of P-bodies, and reveals an extensive interaction network between RNA degradation and translation repression factors. Using this resource, we identified five hitherto unknown components of P-bodies in plants, pointing out the value of this dataset for the identification of proteins potentially involved in translation repression and/or RNA degradation.
RNA 解旋酶 UP-FRAMESHIFT（UPF1）是无义介导的衰变（NMD）的关键因素，NMD 是一种参与 RNA 质量控制和基因表达精细调控的 mRNA 降解途径。UPF1 招募 UPF2 和 UPF3 构成 NMD 核心复合物，该复合物在真核生物中保守。尽管 UPF1 在调节基因表达中起着关键作用，但在植物中，除了 UPFRAMESHIFT 之外，没有其他 RNA 结合蛋白（RNP）的成分被发现。在这里，我们报告了一组与拟南芥 UPF1 以 RNA 依赖或非依赖的方式共纯化的大量蛋白质的鉴定。我们发现，与 UPF1 一样，其几个共纯化的蛋白质在细胞质和 P 体中具有双重定位，P 体是由翻译抑制的 mRNP 凝聚形成的动态结构。有趣的是，UPF1 相互作用组的一半以上的蛋白质也与 DCP5 共纯化，DCP5 是一种保守的翻译抑制剂，也参与 P 体的形成。我们鉴定了一种末端核苷酸转移酶、核糖核酸酶和几种 RNA 解旋酶，它们是与 UPF1 和 DCP5 共纯化的最显著富集的蛋白质之一。在这些中，RNA 解旋酶是 DDX6/Dhh1 的同源物，分别是人类和酵母中的翻译抑制剂。总的来说，这项研究报告了一组与拟南芥 UPF1 和 DCP5 相关的大量蛋白质，这两种蛋白质是 P 体的组成部分，并揭示了 RNA 降解和翻译抑制因子之间广泛的相互作用网络。利用这一资源，我们鉴定了植物中 P 体的五个以前未知的组成部分，指出了该数据集对于鉴定可能参与翻译抑制和/或 RNA 降解的蛋白质的价值。
