Metabolic and co-expression network-based analyses associated with nitrate response in rice.
Metabolic and co-expression network-based analyses associated with nitrate response in rice.
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DOI：
10.1186/1471-2164-15-1056
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发表时间：
2014-12-03
期刊：
影响因子：
4.4
通讯作者：
Rothstein SJ
中科院分区：
文献类型：
--
作者：
Coneva V;Simopoulos C;Casaretto JA;El-Kereamy A;Guevara DR;Cohn J;Zhu T;Guo L;Alexander DC;Bi YM;McNicholas PD;Rothstein SJ
了解作物植物中响应于限制氮（N）条件而发生的基因表达和代谢重编程对于开发具有改善的氮利用效率（NUE）的品种的持续进展至关重要。要解开新的细节的分子和代谢的反应，氮的可用性在主要粮食作物，我们进行了分析加权基因共表达网络和代谢谱数据从适应足够的和有限的氮，以及转移后，他们限制（减少）和足够的（诱导）N条件下的水稻植株的叶和根。一个基因共表达网络，代表了在四种氮素条件和两种组织类型的水稻基因簇具有相似的表达模式。分析所得的18个聚类以富集显著的基因本体（GO）术语。四个聚类与限制和减少硝酸盐处理呈显著相关。在鉴定的富集的GO术语中，富集了与核苷/核苷酸、嘌呤和ATP结合、防御反应、糖/碳水化合物结合、蛋白激酶活性、细胞死亡和细胞壁酶活性相关的那些。虽然一个子集的功能类别更广泛地与水稻器官的反应，限制氮和氮减少，我们的分析表明，氮减少elaborate区别于适应限制氮的反应，特别是在叶片。这一观察结果进一步得到了代谢谱的支持，代谢谱显示，叶片中的几种化合物与硝酸盐水平成比例地变化（即，充足N比限制N更高），并且当硝酸盐水平降低时，以甚至更高的水平响应。值得注意的是，这些化合物直接参与N同化，运输和储存（谷氨酰胺，天冬酰胺，谷氨酸和尿囊素），并延伸到大多数氨基酸。基于这些数据，我们假设，植物响应迅速动员存储液泡硝酸盐时，氮赤字被认为是，该响应可能涉及磷酸化信号级联和转录调控。在水稻中进行的共表达网络分析和代谢谱分析指出了信号转导组件和N动员的调节在响应限制N条件下的相关性，并加深了我们对作物中N响应和N利用的理解。本文的在线版本（doi：10.1186/1471-2164-15-1056）包含补充材料，可供授权用户使用。
Understanding gene expression and metabolic re-programming that occur in response to limiting nitrogen (N) conditions in crop plants is crucial for the ongoing progress towards the development of varieties with improved nitrogen use efficiency (NUE). To unravel new details on the molecular and metabolic responses to N availability in a major food crop, we conducted analyses on a weighted gene co-expression network and metabolic profile data obtained from leaves and roots of rice plants adapted to sufficient and limiting N as well as after shifting them to limiting (reduction) and sufficient (induction) N conditions. A gene co-expression network representing clusters of rice genes with similar expression patterns across four nitrogen conditions and two tissue types was generated. The resulting 18 clusters were analyzed for enrichment of significant gene ontology (GO) terms. Four clusters exhibited significant correlation with limiting and reducing nitrate treatments. Among the identified enriched GO terms, those related to nucleoside/nucleotide, purine and ATP binding, defense response, sugar/carbohydrate binding, protein kinase activities, cell-death and cell wall enzymatic activity are enriched. Although a subset of functional categories are more broadly associated with the response of rice organs to limiting N and N reduction, our analyses suggest that N reduction elicits a response distinguishable from that to adaptation to limiting N, particularly in leaves. This observation is further supported by metabolic profiling which shows that several compounds in leaves change proportionally to the nitrate level (i.e. higher in sufficient N vs. limiting N) and respond with even higher levels when the nitrate level is reduced. Notably, these compounds are directly involved in N assimilation, transport, and storage (glutamine, asparagine, glutamate and allantoin) and extend to most amino acids. Based on these data, we hypothesize that plants respond by rapidly mobilizing stored vacuolar nitrate when N deficit is perceived, and that the response likely involves phosphorylation signal cascades and transcriptional regulation. The co-expression network analysis and metabolic profiling performed in rice pinpoint the relevance of signal transduction components and regulation of N mobilization in response to limiting N conditions and deepen our understanding of N responses and N use in crops. The online version of this article (doi:10.1186/1471-2164-15-1056) contains supplementary material, which is available to authorized users.
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影响因子：
3.7
作者：
Guevara DR;El-Kereamy A;Yaish MW;Mei-Bi Y;Rothstein SJ
通讯作者：
Rothstein SJ
DOI：
10.1186/1478-811x-8-15
发表时间：
2010-06-25
期刊：
Cell communication and signaling : CCS
影响因子：
--
作者：
Gehring C
通讯作者：
Gehring C
影响因子：
2.9
作者：
Cai, Hongmei;Lu, Yongen;Lian, Xingming
通讯作者：
Lian, Xingming
影响因子：
7.3
作者：
Alamillo, Josefa M.;Luis Diaz-Leal, Juan;Pineda, Manuel
通讯作者：
Pineda, Manuel
影响因子：
5.7
作者：
do Amarante, L.;Lima, J. D.;Sodek, L.
通讯作者：
Sodek, L.