Transcriptomic analysis of tomato response to sulfate starvation at a temporal and organ scale

Sulfur (S) is a major component of biological molecules and thus an essential element for plants. Although the biochemistry and metabolism of sulfate is well understood, little is known about the regulatory mechanisms underlying plant responses to sulfate starvation, even more so in crop plants such as tomato (Solanum lycopersicum). In this work, we analyzed the impact of sulfate starvation on the transcriptome of tomato plants, in order to identify regulatory networks and key transcriptional regulators that control tomato response to sulfate deprivation at a temporal and organ scale. Sulfate starvation generated major changes in the growth of roots and leaves that were accompanied by major changes in the organ transcriptome, with the response being earlier in roots. Comparative analysis showed that the 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, including the regulation of internal phosphate levels. Tissue-specific integrative gene network analysis uncovered key transcription factors controlling the response of sulfate assimilation genes, as well as cell cycle, cell division and photosynthesis during plant development in roots and leaves. Together, our results provide novel regulatory targets for future functional analyses to advance our understanding of the sulfate starvation response in tomato and in other plants.