Jiangsu Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
Int J Mol Sci. 2020 Feb 20;21(4):1445. doi: 10.3390/ijms21041445.
Plants have evolved complex mechanisms to respond to the fluctuation of available nitrogen (N) in soil, but the genetic mechanisms underlying the N response in crops are not well-documented. In this study, we generated a time series of NO-mediated transcriptional profiles in roots of maize and sorghum, respectively. Using weighted gene co-expression network analysis, we identified modules of co-expressed genes that related to NO treatments. A cross-species comparison revealed 22 conserved modules, of which four were related to hormone signaling, suggesting that hormones participate in the early nitrate response. Three other modules are composed of genes that are mainly upregulated by NO and involved in nitrogen and carbohydrate metabolism, including , , , , and . Two G2-like transcription factors ( and ), induced by NO stimulation, were identified as hub transcription factors (TFs) in the modules. Transient assays demonstrated that ZmNIGT1 and SbNIGT1 are transcriptional repressors. We identified the target genes of ZmNIGT1 by DNA affinity-purification sequencing (DAP-Seq) and found that they were significantly enriched in catalytic activity, including carbon, nitrogen, and other nutrient metabolism. A set of ZmNIGT1 targets encode transcription factors (ERF, ARF, and AGL) that are involved in hormone signaling and root development. We propose that ZmNIGT1 and SbNIGT1 are negative regulators of nitrate responses that play an important role in optimizing nutrition metabolism and root morphogenesis. Together with conserved N responsive modules, our study indicated that, to encounter N variation in soil, maize and sorghum have evolved an NO-regulatory network containing a set of conserved modules and transcription factors.
植物已经进化出复杂的机制来应对土壤中可利用氮 (N) 的波动，但作物中 N 响应的遗传机制尚未得到很好的记录。在这项研究中，我们分别生成了玉米和高粱根中 NO 介导的转录谱的时间序列。使用加权基因共表达网络分析，我们鉴定了与 NO 处理相关的共表达基因模块。种间比较揭示了 22 个保守模块，其中 4 个与激素信号有关，表明激素参与早期硝酸盐响应。另外三个模块由主要受 NO 上调且与氮和碳水化合物代谢相关的基因组成，包括、、、和。两个受 NO 刺激诱导的 G2 样转录因子（和）被鉴定为模块中的枢纽转录因子（TFs）。瞬时测定表明，ZmNIGT1 和 SbNIGT1 是转录抑制剂。我们通过 DNA 亲和纯化测序 (DAP-Seq) 鉴定了 ZmNIGT1 的靶基因，并发现它们在催化活性中显著富集，包括碳、氮和其他营养代谢。一组 ZmNIGT1 靶基因编码参与激素信号和根发育的转录因子（ERF、ARF 和 AGL）。我们提出，ZmNIGT1 和 SbNIGT1 是硝酸盐响应的负调节剂，在优化营养代谢和根形态发生中起着重要作用。与保守的 N 响应模块一起，我们的研究表明，为了应对土壤中 N 的变化，玉米和高粱已经进化出一个包含一组保守模块和转录因子的 NO 调节网络。
