Parallel global profiling of plant TOR dynamics

TARGET OF RAPAMYCIN (TOR) is a deeply conserved protein kinase thatcoordinates eukaryotic metabolism with nutrient availability. In mammals, TORspecifically promotes translation of ribosomal protein mRNAs when amino acids areavailable to support protein synthesis. The mechanisms controlling translationdownstream from TOR remain contested, however, and are largely unexplored inplants. Here, we took parallel global profiling approaches to define the in planta TOR-regulated transcriptome, translatome, proteome, and phosphoproteome. We found thatTOR regulates ribosome biogenesis in plants at multiple levels, but throughmechanisms that do not directly depend on the canonical 5 oligopyrimidine tract motif(5TOP) found in mammalian ribosomal protein mRNAs. To investigate this further, wefocused on a putative TOR substrate identified in our phosphoproteome: LARP1, aeukaryotic RNA-binding protein that is proposed to mediate TOR translational control of5TOP mRNAs in humans and that has gained increased interest because it associateswith SARS-CoV-2. By conducting parallel global profiling experiments with larp1mutants, we discovered that the TOR-LARP1 signaling axis controls 5TOP mRNAtranslation in plants and defined a set of conserved eukaryotic 5TOP mRNAs thatencode cyclins, importins/karyopherins, translation elongation factors, and TCTP1,among others. We then identified novel, plant-specific 5TOP mRNAs involved in criticalbiological processes, including ribosome biogenesis, chromatin remodeling, and auxinsignaling. Our study illuminates the ancestral roles of the TOR-LARP1-5TOP metabolicregulatory network and provides evolutionary context for ongoing debates about themolecular function of LARP1 in eukaryotic cells.

雷帕霉素靶蛋白（TARGET OF RAPAMYCIN, TOR）是一类高度保守的蛋白激酶，可协调真核生物代谢与营养可利用状态的适配。在哺乳动物中，当氨基酸充足以支持蛋白质合成时，TOR会特异性促进核糖体蛋白mRNA的翻译。然而，调控TOR下游翻译过程的分子机制尚存争议，且在植物中尚未得到充分探索。本研究采用平行全局谱学分析策略，对植物体内TOR调控的转录组、翻译组、蛋白质组及磷酸化蛋白质组进行了系统解析。我们发现，TOR可通过多个层级调控植物的核糖体生物发生，但所依赖的机制并不直接依赖于哺乳动物核糖体蛋白mRNA中存在的经典5'寡嘧啶基序（5'TOP）。为进一步探究该调控机制，我们聚焦于磷酸化蛋白质组中鉴定出的推定TOR底物LARP1——一类真核RNA结合蛋白（RNA-binding protein）。在人类中，LARP1被认为可介导5'TOP mRNA的TOR翻译调控，且因其与新型冠状病毒（SARS-CoV-2）的关联而受到广泛关注。通过对larp1突变体开展平行全局谱学分析实验，我们发现TOR-LARP1信号轴可调控植物中的5'TOP mRNA翻译，并鉴定出一组保守的真核5'TOP mRNA，其编码产物涵盖细胞周期蛋白、输入蛋白/核转运蛋白、翻译延伸因子及TCTP1等。此外，我们还鉴定出参与核糖体生物发生、染色质重塑及生长素信号通路等关键生物学过程的新型植物特异性5'TOP mRNA。本研究阐明了TOR-LARP1-5'TOP代谢调控网络的祖先功能，并为当前关于真核细胞中LARP1分子功能的相关争论提供了进化层面的参考依据。