Transcriptome and metabolome analysis of plant sulfate starvation and resupply provides novel information on transcriptional regulation of metabolism associated with sulfur, nitrogen and phosphorus nutritional responses in Arabidopsis.
Transcriptome and metabolome analysis of plant sulfate starvation and resupply provides novel information on transcriptional regulation of metabolism associated with sulfur, nitrogen and phosphorus nutritional responses in Arabidopsis.
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DOI：
10.3389/fpls.2014.00805
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发表时间：
2014
影响因子：
5.6
通讯作者：
Hoefgen R
中科院分区：
文献类型：
--
作者：
Bielecka M;Watanabe M;Morcuende R;Scheible WR;Hawkesford MJ;Hesse H;Hoefgen R
硫是植物生长发育所必需的常量营养素。在系统水平上透彻地了解植物代谢变化的分子基础取决于硫素营养状况，这将促进我们的基本知识，并有助于针对未来作物改良。尽管过去对硫酸盐饥饿诱导的转录反应进行了研究，但对硫代谢调控的了解还很零碎。这项工作的重点是利用组学技术发现转录因子(TF)等调控基因的候选基因。为此，采用了短期硫酸盐饥饿/再供应办法。ATH1基因芯片研究和代谢物测定产生了21个转录因子，它们在转录水平上对硫酸盐饥饿的反应增加了两倍以上。通过对硫酸盐饥饿/再供应和其他营养饥饿(如硝酸盐和磷酸盐)下的反应行为进行分类，可以确定TF基因是针对不同的矿物质营养耗竭而言是特定的还是共同的。将这种共同行为分析扩展到整个转录组数据集，从而能够预测可能的下游基因。此外，结合转录组和代谢组数据，可以确定转录因子和下游反应之间的关系，即生物合成基因的表达变化和随后的代谢反应。详细讨论了硫代葡萄糖苷和多胺生物合成的影响链。从这项研究中获得的知识为转录组学和代谢组学的综合分析提供了蓝图，并为鉴定未知基因提供了应用。
Sulfur is an essential macronutrient for plant growth and development. Reaching a thorough understanding of the molecular basis for changes in plant metabolism depending on the sulfur-nutritional status at the systems level will advance our basic knowledge and help target future crop improvement. Although the transcriptional responses induced by sulfate starvation have been studied in the past, knowledge of the regulation of sulfur metabolism is still fragmentary. This work focuses on the discovery of candidates for regulatory genes such as transcription factors (TFs) using ‘omics technologies. For this purpose a short term sulfate-starvation/re-supply approach was used. ATH1 microarray studies and metabolite determinations yielded 21 TFs which responded more than 2-fold at the transcriptional level to sulfate starvation. Categorization by response behaviors under sulfate-starvation/re-supply and other nutrient starvations such as nitrate and phosphate allowed determination of whether the TF genes are specific for or common between distinct mineral nutrient depletions. Extending this co-behavior analysis to the whole transcriptome data set enabled prediction of putative downstream genes. Additionally, combinations of transcriptome and metabolome data allowed identification of relationships between TFs and downstream responses, namely, expression changes in biosynthetic genes and subsequent metabolic responses. Effect chains on glucosinolate and polyamine biosynthesis are discussed in detail. The knowledge gained from this study provides a blueprint for an integrated analysis of transcriptomics and metabolomics and application for the identification of uncharacterized genes.
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