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Analysis of the nitrate-responsive transcriptome of the Arabidopsis root

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE44062 | GEO | 2013/07/01

SECONDARY ACCESSION(S): PRJNA188503

REPOSITORIES: GEO

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Analysis of the nitrate-responsive transcriptome of the Arabidopsis root

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

Root nitrate response of Col-0 plants and tga1/tga4 mutant plants

2013-03-31 | GSE43011 | GEO

Root nitrate response of Col-0 plants and tga1/tga4 mutant plants

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

NLP7 transcription factor is a plant nitrate sensor

Project description:NLP1-9 are plant unique transcrition facotrs. To identify NLP1-9 target genes, we transiently expressed NLP1-9 in Arabidopsis mesophyll protoplasts and performed RNA-seq analysis. NLP1-9 individually induced specific gene expression and co-activated nitrate responsive genes expression. To study genome-wide transcriptional landscape modulated by NLP, we performed transcriptome analysis at 20 min after nitrate induction in wild type and nlp2,4,5,6,7,8,9. All nitrate responsive genes were significant reduced in nlp2,4,5,6,7,8,9 indicated that NLP transcription factors are central regulators in PNR.

2022-11-17 | GSE198475 | GEO

Phosphoproteomics of WT and nrt1.1 under high nitrate and low nitrate

Project description:We performed a comparative phosphoproteomic analysis of Arabidopsis root membrane proteins of WT and nrt1.1-1 under low nitrate (LN) and high nitrate (HN) availability in order to identify the downstream components that may be involved in NRT1.1-dependent LR growth and signal transduction.

2024-02-22 | PXD048853 | Pride

CHL1 functions as a nitrate sensor and also is one of major nitrate transporters responsible for nitrate responses and uptake.

Project description:CHL1 functions as a nitrate sensor and also is one of major nitrate transporters responsible for nitrate responses and uptake. ANI is a protein phosphatase particiates in temporal nitrate response, its influence was analyzed in a global transcriptome study using Affymetrix ATH1 array. Two biological replicates of 10-day-old Arabidopsis root tissue from wild-type and ani1 plants were performed to explore differences in gene expression between the wild-type and ani1 mutants exposed to 200 μM nitrate for 0h (T0), 0.5h (T0.5), or 16h (T16) using Affymetrix ATH1 microarray.

2014-10-26 | E-GEOD-33242 | biostudies-arrayexpress

Root nitrate response of Ws plants and afb3-1 mutant plants

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.

2012-05-01 | GSE35544 | GEO

Expression data from low nitrate culture in root in maize

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

CPK signaling orchestrates the plant nitrate regulatory network

Project description:Nitrate is the limiting nitrogen nutrient enabling photosynthetic plants to support the conversion of inorganic elements to organic biomass, which sustains all lives. Plants evolved multifaceted nitrate responses to modulate global gene expression, metabolism and developmental programs. However, primary nitrate signaling mechanisms remained elusive. Using an ultrasensitive Ca2+ biosensor, unique nitrate-induced Ca2+ signaling was illuminated in Arabidopsis cells and plants. Integrative functional genomic screens, chemical genetics, genome-wide transcript sequencing, and analyses of nitrate-associated traits uncovered the surprising roles of Ca2+ sensor protein kinases (CPKs) in orchestrating diverse primary and long-term nitrate responses. Nitrate specifies CPK signaling to reprogram transcriptome and govern N-assimilation, metabolism, transport, hormones, shoot growth, and root system architecture. CPKs may be targeted to enhance nitrogen-use-efficiency, reduce fertilizer demands, and alleviate ecosystem pollution.

2017-05-19 | GSE73437 | GEO

Characterization of temporal and spatial patterns of gene expression in response to nitrate in Arabidopsis roots

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

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