Treatment of Arabidopsis with low concentration of nitrate

The genomic response to low levels of nitrate was studied in Arabidopsis using the Affymetrix ATH1 chip containing more than 22,500 probe sets. Arabidopsis plants were grown hydroponically in sterile liquid culture on ammonium as the sole source of nitrogen for 10 d, then treated with 250 um nitrate for 20 min. The response to nitrate was much stronger in roots (1,176 genes showing increased or decreased mRNA levels) than in shoots (183 responding genes). In addition to known nitrate-responsive genes (e.g. those encoding nitrate transporters, nitrate reductase, nitrite reductase, ferredoxin reductase, and enzymes in the pentose phosphate pathway), genes encoding novel metabolic and potential regulatory proteins were found. These genes encode enzymes in glycolysis (glucose-6-phosphate isomerase and phosphoglycerate mutase), in trehalose-6-P metabolism (trehalose-6-P synthase and trehalose-6-P phosphatase), in iron transport/metabolism (nicotianamine synthase), and in sulfate uptake/reduction. In many cases, only a few select genes out of several in small gene families were induced by nitrate. These results show that the effect of nitrate on gene expression is substantial (affecting almost 10% of the genes with detectable mRNA levels) yet selective and affects many genes involved in carbon and nutrient metabolism. Keywords: Expression profilling by array 8 samples were used in this experiment

本研究以拟南芥（Arabidopsis）为实验材料，利用搭载超过22500个探针组的Affymetrix ATH1基因芯片，探究了其对低浓度硝酸盐的基因组响应。将拟南芥植株以无菌水培液体培养体系种植，以铵态氮作为唯一氮源培养10天，随后用250 μM硝酸盐处理20分钟。结果显示，拟南芥根系对硝酸盐的响应强度远高于地上组织：根系共有1176个基因的mRNA水平出现上调或下调，而地上组织仅183个基因存在响应。除已报道的硝酸盐响应基因（如编码硝酸盐转运蛋白、硝酸还原酶、亚硝酸还原酶、铁氧还蛋白还原酶及磷酸戊糖途径相关酶的基因）外，本研究还鉴定出一批编码新型代谢蛋白与潜在调控蛋白的基因。这些基因分别参与糖酵解途径（葡萄糖-6-磷酸异构酶、磷酸甘油酸变位酶）、海藻糖-6-磷酸代谢途径（海藻糖-6-磷酸合酶、海藻糖-6-磷酸磷酸酶）、铁转运/代谢（烟酰胺合酶）以及硫酸盐摄取/还原过程。值得注意的是，在诸多小型基因家族中，往往仅少数经筛选的基因会被硝酸盐诱导表达。本研究结果表明，硝酸盐对基因表达的调控作用十分显著——影响了近10%可检测到mRNA水平的基因，且具有高度选择性，同时涉及众多参与碳代谢与营养代谢的相关基因。关键词：基于芯片的基因表达谱分析 本实验共使用8个样本