CHL1 functions as a nitrate sensor and also is one of major nitrate transporters responsible for nitrate responses and uptake.
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Cheng-Hsun Ho
PROVIDER: E-GEOD-33242 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:CHL1 is one of major nitrate transporters responsible for nitrate uptake and some studies suggest that it may be also play a role in regulating the nitrate response, its influence was analyzed in a global transcriptome study using Affymetrix ATH1 array. Experiment Overall Design: Three biological replicates of 10-day-old Arabidopsis root tissue from wild-type and chl1-5 plants were performed to explore differences in gene expression between the wild-type and chl1-5 mutants exposed to 25 mM nitrate for 0h (T0) or 0.5h (T0.5) using Affymetrix ATH1 microarray.
2008-06-16 | E-GEOD-9148 | biostudies-arrayexpress
Project description:As multicellular organisms, plants must integrate responses to environmental cues across different cell types and also over time. Nitrate is the major source of available Nitrogen for plants, and a limiting factor for plant growth and productivity. Plant root s are highly impacted by nitrate availability, modifying their architecture to optimize nitrate uptake from soils. In order to understand how this functional response is dynamically orchestrated across different cell types of the root, space and time must be addressed within the same experimental setup. We performed a transcriptomic analysis in five major root cell types of Arabidopsis plants in response to nitrate treatments considering short and long time exposure to this macronutrient. We found nitrate treatment triggers a dynamic reprogramming of root cell gene expression that follows a spatial pattern over time consistent with an early regulation of nitrate transport and assimilation in external layers of the root and a later regulation of hormonal and developmental processes in more internal layers of the root.
2022-01-01 | E-MTAB-9519 | biostudies-arrayexpress
Project description:Nitrate regulates plant growth and development and acts as a potent signal to control gene expression in Arabidopsis. Using an integrative bioinformatics approach we identified TGA1 and TGA4 as putative regulatory factors that mediate nitrate responses in Arabidopsis thaliana roots. We showed that both TGA1 and TGA4 mRNAs accumulate strongly and quickly after nitrate treatments in root organs in a tissue-specific manner. Phenotypic analysis of tga1/tga4 double mutant plants indicated that TGA1 and TGA4 are necessary for nitrate modulation of both primary and lateral root growth. Global gene expression analysis revealed that 97% of the genes with altered expression in tga1/tga4 double mutant plants are regulated by nitrate treatments indicating these transcription factors have a specific role in nitrate responses in Arabidopsis root organs. Among the nitrate-responsive genes that depend on TGA1/TGA4 for normal regulation of gene expression, we found nitrate transporters NRT2.1, NRT2.2 and nitrite reductase (NIR) genes. Specific binding of TGA1 to its cognate DNA sequence on the target gene promoters was confirmed by chromatin immunoprecipitation assays. These results identify TGA1 and TGA4 as important regulatory factors of the nitrate response in Arabidopsis roots. Arabidopsis seedlings of the Col-0 and tga1/tga4 genotypes were grown on hydroponic medium containing 1X MS salts without Nitrogen, supplemented with 0.5 mM ammonium succinate as Nitrogen source and 3 mM sucrose on a Percival chamber under a photoperiod of 16 hours of light (100 ?E/m2/sec) and 8 hours of dark at 22°C for 14 days. The plants were treated at the onset of the light cycle with 5 mM KNO3 or 5 mM KCl as control for 2 hours. Whole roots were cut from seedlings and frozen on liquid Nitrogen. Total RNA was extracted using the TriZol reagent. 3 independent biological replicates were performed.
2013-03-31 | E-GEOD-43011 | biostudies-arrayexpress
Project description:Plants take up nitrate in soils and utilize it both for nitrogen assimilation and as a signaling molecule. Thus, an essential role of nitrate in plants is triggering changes in gene expression patterns, including immediate induction of the expression of genes involved in nitrate transport and assimilation as well as several transcription factor genes and genes related with carbon metabolism and cytokinin biosynthesis and response. Recently we identified NIN-like proteins (NLPs) as transcription factors governing nitrate-inducible gene expression in Arabidopsis. Because of their similar DNA-binding property, nine NLP proteins may play redundant roles in controlling nitrate-regulated gene expression in Arabidopsis. The physiological roles of NLPs were therefore assessed by generating transgenic Arabidopsis plants expressing NLP6 fused to the transcriptional repression domain of SUPERMAN (SUPRD), which has an ability to convert transcriptional activators into transcriptional repressors. Our transcriptome analysis revealed that levels of nitrate-inducible expression of nitrate transporter genes (NRT1.1 and NRT2.1), nitrate reduction enzyme genes (NIA1, NIA2 and NIR1), the genes associated with ammonium assimilation (GLT1 for glutamine-2-oxoglutarate aminotransferase and ASN2 for asparagine synthetase), LBD37-39 transcription factor genes and genes encoding homologs of rice nitrate-inducible NIGT1 transcriptional repressor, were reduced in the NLP6-SUPRD lines. Furthermore, levels of nitrate-inducible expression of the genes associated with the oxidative pentose phosphate pathway (G6PD2 and G6PD3 for glucose-6-phosphate dehydrogenases, and 6-phosphogluconate dehydrogenase genes), cytokinin biosynthesis (IPT3) and signal transduction (A-type ARR genes), a gene encoding a Ser/Thr protein kinase associated with a calcineurin BM-bM-^@M-^Slike calcium sensor (CIPK3) were also found to be largely decreased by reductions in NLP activity. Because induction folds by nitrate and reduction folds by decreases in the NLP activity were well proportional, the NLP activity appeared to be responsible for most of nitrate responsiveness of the genes whose expression occurs immediately after nitrate treatment. Overall design: Gene expression in 3.5-day-old seedlings treated with or without 10 mM potassium nitrate was compared between the transgenic lines expressing a chimeric repressor form of NLP6 (NLP6-SUPRD) and the parental control line.
2014-01-07 | E-GEOD-53852 | biostudies-arrayexpress
Project description:Identification of the earliest transcriptional responses of adult Arabidopsis plant roots towards N-deprivation. Hydroponically grown Plants (35 days old) were 5 days adapted to nitrate or ammonium,respectively, as sole N-source to detect N-form specific transcripts. 24 Samples: 2 Pre-Treatments (5 Day adaptation to 3mM Ammonium/Nitrate) x 3 sampling time-points (0min, 15 min, 180 min) x 3 independent replications per time-point + 6 additional controls (2 x 15min, 1x 180min per Pre-Treatment)
2016-05-31 | E-GEOD-73903 | biostudies-arrayexpress
Project description:Nitrate and other nitrogen metabolites can act as signals that regulate global gene expression in plants. Adaptive changes in plant morphology and physiology triggered by changes in nitrate availability are partly explained by these changes in gene expression. Despite several genome-wide efforts to identify nitrate-regulated genes, no comprehensive study of the Arabidopsis root transcriptome under contrasting nitrate conditions has been carried out. In this work, we employed the Illumina high throughput sequencing technology to perform an integrated analysis of the poly-A+ enriched and the small RNA fractions of the Arabidopsis thaliana root transcriptome in response to nitrate treatments. Our sequencing strategy identified new nitrate-regulated genes including 40 genes not represented in the ATH1 Affymetrix GeneChip, a novel nitrate-responsive antisense transcript and a new nitrate responsive miRNA/TARGET module consisting of a novel microRNA, miR5640 and its target, AtPPC3. This nitrate-responsive miRNA/target module might be involved in controlling carbon flux to assimilate nitrate into amino acids, suggesting that microRNAs can have both developmental and metabolic functions in the nitrate response of Arabidopsis roots. Arabidopsis thaliana wild-type Col-0 plants were grown in hydroponic nitrate-free medium with 0.5 mM ammonium succinate as the only N-source for two weeks and were treated with 5 mM KNO3, or 5 mM KCl as control, for 2 hours. Total RNA from two independent sets of plants (biological replicates) was extracted from roots, and poly-A+ enriched and sRNA fractions were used to construct libraries for Illumina sequencing.
2013-07-01 | E-GEOD-44062 | biostudies-arrayexpress
Project description:Auxin is a key phytohormone regulating central processes in plants that include embryo development, lateral root growth and flower maturation among others. Auxin is sensed by a set of F-Box proteins of the TIR1/AFB3 family triggering auxin dependent responses by a pathway that involves an interplay between the Aux/IAA transcription repressors and the ARF transcription factors. We have previously shown that the AFB3 auxin receptor has a specific role in coordinating primary and lateral root growth to external and internal nitrate availability (Vidal et al., 2010). In this work, we used an integrated genomics, bioinformatics and molecular genetics approach to dissect regulatory networks acting downstream AFB3 that are activated by a transient nitrate treatment in Arabidopsis roots. Our systems approach unraveled key components of the AFB3 regulatory network leading to changes in lateral root growth in response to nitrate. Arabidopsis seedlings of the Ws and afb3-1 genotypes were grown on hydroponic medium containing 1X MS salts without Nitrogen, supplemented with 0.5 mM ammonium succinate as Nitrogen source and 3 mM sucrose on a Percival chamber under a photoperiod of 16 hours of light (100 μE/m2/sec) and 8 hours of dark at 22°C for 14 days. The plants were treated at the onset of the light cycle with 5 mM KNO3 or 5 mM KCl as control for 2 hours. Whole roots were cut from seedlings and frozen on liquid Nitrogen. Total RNA was extracted using the TriZol reagent. 3 independent biological replicates were performed.
2012-04-30 | E-GEOD-35544 | biostudies-arrayexpress
Project description:Nitrate is the major source of nitrogen available for many crop plants and is often the limiting factor for plant growth and agricultural productivity especially for maize. Many studies have been done identifying the transcriptome changes under low nitrate conditions. However, the microRNAs (miRNAs) varied under nitrate limiting conditions in maize has not been reported. MiRNAs play important roles in abiotic stress responses and nutrient deprivation. Root is the organ that plants transport nitrate. we used the microarray systems to perform a genome-wide search to detect miRNAs responding to the chronic and transient nitrate limiting conditions in maize. MicroRNAs (miRNAs) are small, endogenous RNAs that are regulators of gene expression in plants and animals. And, miRNAs have been known for years to be important for phosphate, sulphate and copper deprivation responses in plants. In Arabidopsis, small RNA deep sequencing associated with nitrate response had been analyzed. However, information about the way by which miRNA are regulated by abiotic stresses in general and by low nitrate in particular is unavailable for maize. In this study, we used GeneChip® microarray systems to perform a genome-wide search to detect miRNAs responding to the chronic and transient nitrate limiting conditions in roots in maize.
2011-08-31 | E-GEOD-31231 | biostudies-arrayexpress
Project description:The conversion of nitrate to ammonium, known as nitrate reduction, consumes large amounts of reductants in plants. Previous studies have observed that mitochondrial alternative oxidase (AOX) is upregulated under conditions of limited nitrate reduction, such as low or no nitrate availability, or when ammonium serves as the sole nitrogen (N) source. Electron transfer from ubiquinone to AOX bypasses the proton-pumping complexes III and IV, thereby consuming reductants efficiently. Therefore, the upregulation of AOX under conditions of limited nitrate reduction may help dissipate excessive reductants and mitigate oxidative stress. However, firm evidence supporting this hypothesis is lacking due to the absence of experimental systems capable of directly analyzing the relationship between nitrate reduction and AOX. To address this gap, we developed a novel culturing system that allows for the manipulation of nitrate reduction and AOX activities separately, without inducing N starvation, ammonium toxicity, or disrupting the nitrate signal. Using this system, we investigated genome-wide gene expression with RNA-seq to gain insight into the relationship between AOX and nitrate reduction.
2024-04-23 | E-MTAB-14027 | biostudies-arrayexpress
Project description:Transcriptional profile of leaves from poplar plants transformed with a pine GS1a gene under two different nitrate nutrition level (50mM and 10mM). Two conditions: nitrate nutrition (50mM and 10 mM) and genotype (GS1a transgenic poplar vs WT poplar)
2015-04-02 | E-GEOD-62449 | biostudies-arrayexpress