Table_2_Divergence in the Regulation of the Salt Tolerant Response Between Arabidopsis thaliana and Its Halophytic Relative Eutrema salsugineum by mRNA Alternative Polyadenylation.XLSX

Salt tolerance is an important mechanism by which plants can adapt to a saline environment. To understand the process of salt tolerance, we performed global analyses of mRNA alternative polyadenylation (APA), an important regulatory mechanism during eukaryotic gene expression, in Arabidopsis thaliana and its halophytic relative Eutrema salsugineum with regard to their responses to salt stress. Analyses showed that while APA occurs commonly in both Arabidopsis and Eutrema, Eutrema possesses fewer APA genes than Arabidopsis (47% vs. 54%). However, the proportion of APA genes was significantly increased in Arabidopsis under salt stress but not in Eutrema. This indicated that Arabidopsis is more sensitive to salt stress and that Eutrema exhibits an innate response to such conditions. Both species utilized distal poly(A) sites under salt stress; however, only eight genes were found to overlap when their 3′ untranslated region (UTR) lengthen genes were compared, thus revealing their distinct responses to salt stress. In Arabidopsis, genes that use distal poly(A) sites were enriched in response to salt stress. However, in Eutrema, the use of poly(A) sites was less affected and fewer genes were enriched. The transcripts with upregulated poly(A) sites in Arabidopsis showed enriched pathways in plant hormone signal transduction, starch and sucrose metabolism, and fatty acid elongation; in Eutrema, biosynthetic pathways (stilbenoid, diarylheptanoid, and gingerol) and metabolic pathways (arginine and proline) showed enrichment. APA was associated with 42% and 29% of the differentially expressed genes (DE genes) in Arabidopsis and Eutrema experiencing salt stress, respectively. Salt specific poly(A) sites and salt-inducible APA events were identified in both species; notably, some salt tolerance-related genes and transcription factor genes exhibited differential APA patterns, such as CIPK21 and LEA4-5. Our results suggest that adapted species exhibit more orderly response at the RNA maturation step under salt stress, while more salt-specific poly(A) sites were activated in Arabidopsis to cope with salinity conditions. Collectively, our findings not only highlight the importance of APA in the regulation of gene expression in response to salt stress, but also provide a new perspective on how salt-sensitive and salt-tolerant species perform differently under stress conditions through transcriptome diversity.

耐盐性是植物适应盐碱环境的至关重要机制。为了解耐盐性形成过程，本研究对拟南芥（Arabidopsis thaliana）及其耐盐近缘种盐芥（Eutrema salsugineum）在盐胁迫条件下的mRNA选择性多聚腺苷酸化（APA）进行了全局分析，APA是真核生物基因表达过程中的关键调控机制。分析结果显示，尽管APA在拟南芥和盐芥中均普遍存在，但盐芥的APA基因数量少于拟南芥（分别为47%和54%）。然而，在盐胁迫条件下，拟南芥的APA基因比例显著增加，而盐芥则没有显著变化。这表明拟南芥对盐胁迫更为敏感，而盐芥表现出对这种条件的固有响应。两种物种在盐胁迫条件下均利用远端多聚腺苷酸化位点；然而，在比较其3'非翻译区（3′ untranslated region，简称3′UTR）延长基因时，仅发现八个基因重叠，从而揭示了它们对盐胁迫的不同响应。在拟南芥中，利用远端多聚腺苷酸化位点的基因在盐胁迫响应中富集，而在盐芥中，多聚腺苷酸化位点的使用受影响较小，且富集的基因较少。拟南芥中上调的多聚腺苷酸化位点转录本表现出植物激素信号转导、淀粉和蔗糖代谢以及脂肪酸延长的富集途径；在盐芥中，生物合成途径（如 stilbenoid、diarylheptanoid和gingerol）和代谢途径（如精氨酸和脯氨酸）显示出富集。APA与拟南芥和盐芥中盐胁迫相关差异表达基因（DE genes）的42%和29%相关。两种物种均鉴定出盐特异性多聚腺苷酸化位点和盐诱导的APA事件；值得注意的是，一些与耐盐性相关的基因和转录因子基因表现出不同的APA模式，如CIPK21和LEA4-5。我们的结果表明，适应种在盐胁迫条件下表现出更有序的RNA成熟阶段响应，而拟南芥通过激活更多的盐特异性多聚腺苷酸化位点来应对盐碱条件。总之，我们的研究不仅突出了APA在盐胁迫下基因表达调控中的重要性，而且为盐敏感和耐盐物种在胁迫条件下的转录组多样性差异提供了新的视角。