DataSheet_1_Response of the organellar and nuclear (post)transcriptomes of Arabidopsis to drought.pdf

Plants have evolved sophisticated mechanisms to cope with drought, which involve massive changes in nuclear gene expression. However, little is known about the roles of post-transcriptional processing of nuclear or organellar transcripts and how meaningful these changes are. To address these issues, we used RNA-sequencing after ribosomal RNA depletion to monitor (post)transcriptional changes during different times of drought exposure in Arabidopsis Col-0. Concerning the changes detected in the organellar transcriptomes, chloroplast transcript levels were globally reduced, editing efficiency dropped, but splicing was not affected. Mitochondrial transcripts were slightly elevated, while editing and splicing were unchanged. Conversely, alternative splicing (AS) affected nearly 1,500 genes (9% of expressed nuclear genes). Of these, 42% were regulated solely at the level of AS, representing transcripts that would have gone unnoticed in a microarray-based approach. Moreover, we identified 927 isoform switching events. We provide a table of the most interesting candidates, and as proof of principle, increased drought tolerance of the carbonic anhydrase ca1 and ca2 mutants is shown. In addition, altering the relative contributions of the spliced isoforms could increase drought resistance. For example, our data suggest that the accumulation of a nonfunctional FLM (FLOWERING LOCUS M) isoform and not the ratio of FLM-ß and -δ isoforms may be responsible for the phenotype of early flowering under long-day drought conditions. In sum, our data show that AS enhances proteome diversity to counteract drought stress and represent a valuable resource that will facilitate the development of new strategies to improve plant performance under drought.

植物已演化出复杂的机制以应对干旱，这些机制涉及核基因表达的巨大变化。然而，关于核或细胞器转录本的转录后加工作用及其意义知之甚少。为解决这些问题，我们采用了核糖体RNA耗竭后的RNA测序技术，以监测拟南芥Col-0在不同干旱暴露时期内的（转录）后变化。在检测到的细胞器转录组变化中，叶绿体转录水平普遍降低，编辑效率下降，但拼接未受影响。线粒体转录水平略有升高，而编辑和拼接保持不变。相反，选择性拼接（AS）影响了近1500个基因（表达核基因的9%）。其中，42%仅受选择性拼接水平的调控，代表在基于微阵列的方法中可能被忽视的转录本。此外，我们鉴定了927个异构体切换事件。我们提供了最有趣候选者的表格，并作为原理证明，展示了碳酸酐酶ca1和ca2突变体耐受干旱能力的增强。此外，改变拼接异构体相对贡献的比例可以提高抗旱性。例如，我们的数据表明，非功能FLM（FLOWERING LOCUS M）异构体的积累，而非FLM-β和-δ异构体比例，可能是长日照干旱条件下早花表型的原因。总之，我们的数据显示选择性拼接增强了蛋白质组多样性以对抗干旱胁迫，并代表了一种有价值的资源，将有助于开发提高植物在干旱条件下表现的新策略。