Sulfur is a major component of biological molecules and thus an essential element for plants. Deficiency of sulfate, the main source of sulfur in soils, negatively influences plant growth and crop yield. The effect of sulfate deficiency on plants has been well characterized at the physiological, transcriptomic and metabolomic levels in Arabidopsis thaliana and a limited number of crop plants. However, we still lack a thorough understanding of the molecular mechanisms and regulatory networks underlying sulfate deficiency in most plants. In this work we analyzed the impact of sulfate starvation on the transcriptome of tomato plants to identify regulatory networks and key transcriptional regulators at a temporal and organ scale. Sulfate starvation reduces the growth of roots and leaves which is accompanied by major changes in the organ transcriptome, with the response being temporally earlier in roots than leaves. Comparative analysis showed that a major part of the Arabidopsis and tomato transcriptomic response to sulfate starvation is conserved between these plants and allowed for the identification of processes specifically regulated in tomato at the transcript level, including the control of internal phosphate levels. Integrative gene network analysis uncovered key transcription factors controlling the temporal expression of genes involved in sulfate assimilation, as well as cell cycle, cell division and photosynthesis during sulfate starvation in tomato roots and leaves. Interestingly, one of these transcription factors presents a high identity with SULFUR LIMITATION1, a central component of the sulfate starvation response in Arabidopsis. Together, our results provide the first comprehensive catalog of sulfate-responsive genes in tomato, as well as novel regulatory targets for future functional analyses in tomato and other crops.

中文翻译：

---

器官和时间尺度的转录组分析揭示了控制番茄硫酸盐饥饿反应的基因调控网络。

硫是生物分子的主要成分，因此是植物的必需元素。硫酸盐是土壤中硫的主要来源，缺乏硫酸盐会对植物生长和作物产量产生负面影响。硫酸盐缺乏对植物的影响已在拟南芥和有限数量的农作物的生理、转录组和代谢组水平上得到了很好的表征。然而，我们仍然缺乏对大多数植物硫酸盐缺乏的分子机制和调控网络的透彻了解。在这项工作中，我们分析了硫酸盐饥饿对番茄植株转录组的影响，以在时间和器官尺度上识别调控网络和关键转录调控因子。硫酸盐饥饿会减少根和叶的生长，并伴随着器官转录组的重大变化，根的反应时间早于叶。比较分析表明，拟南芥和番茄对硫酸盐饥饿的转录组反应的主要部分在这些植物之间是保守的，并且允许在转录水平上鉴定番茄中特别调节的过程，包括内部磷酸盐水平的控制。整合基因网络分析揭示了控制番茄根和叶硫酸盐饥饿期间参与硫酸盐同化以及细胞周期、细胞分裂和光合作用的基因的时间表达的关键转录因子。有趣的是，这些转录因子之一与硫限制1（拟南芥硫酸盐饥饿反应的核心成分）具有高度同一性。总之，我们的结果提供了番茄中硫酸盐响应基因的第一个全面目录，以及番茄和其他作物未来功能分析的新调控目标。