Nonsense mediated RNA decay factor UPF1 is critical for posttranscriptional and translational gene regulation in Arabidopsis. upf1 Arabidopsis

Nonsense mediated RNA decay (NMD) is an evolutionary conserved RNA control mechanism that has also been implicated in the broader regulation of gene expression. Nevertheless, a role for NMD in genome regulation has not been fully assessed, partially because NMD inactivation is lethal in many organisms. Here, we performed in depth comparative analysis of Arabidopsis mutants lacking key proteins involved in different steps of NMD. We observed that UPF3, UPF1, and SMG7 have different impacts on NMD and the Arabidopsis transcriptome, with UPF1 having the biggest effect. De novo Ttranscriptome assembly using a stringent pipeline in UPF1-null plants revealed genome wide changes in alternative splicing, including switches in mRNA variants, suggesting a role for UPF1 in splicing. We further found that UPF1 inactivation leads to translational repression, manifested by a global shift in mRNAs from polysomes to monosomes and a downregulation of genes involved in translation and ribosome biogenesis. Despite this global change, NMD targets and low-expressed mRNAs with short half-lives were enriched in polysomes, indicating that UPF1 specifically suppresses the translation of aberrant RNAs. Particularly striking was an increase in the translation of TIR domain-containing, nucleotide-binding, leucine-rich repeat (TNL) immune receptors. The regulation of TNLs via UPF1/NMD-mediated mRNA stability and translational de-repression offers a dynamic mechanism for the rapid activation of TNLs in response to pathogen attack.

无义介导的RNA降解（Nonsense mediated RNA decay, NMD）是一种进化保守的RNA调控机制，同时参与广泛的基因表达调控过程。然而，NMD在基因组调控中的作用尚未得到充分评估，部分原因在于NMD失活在多数生物中会导致致死表型。本研究针对拟南芥中缺失NMD不同步骤关键蛋白的突变体开展了深入比较分析，发现UPF3、UPF1与SMG7对NMD及拟南芥转录组的影响存在显著差异，其中UPF1的调控效应最为突出。通过在UPF1缺失突变体植株中采用严格分析流程开展从头转录组组装，本研究揭示了全基因组范围内的可变剪接变化，包括mRNA变体的转换，这提示UPF1参与剪接调控。进一步研究表明，UPF1失活会引发翻译抑制，具体表现为mRNA在全局范围内从多核糖体向单核糖体转移，同时参与翻译及核糖体生物发生的基因表达下调。尽管存在上述全局性变化，NMD靶标及半衰期较短的低表达mRNA却在多核糖体中富集，这表明UPF1可特异性抑制异常RNA的翻译过程。尤为引人注目的是，含TIR结构域、核苷酸结合富亮氨酸重复序列免疫受体（TIR domain-containing, nucleotide-binding, leucine-rich repeat, TNL）的翻译水平显著上调。通过UPF1/NMD介导的mRNA稳定性调控及翻译去抑制来调节TNL，为病原体侵染下TNL的快速激活提供了一种动态调控机制。