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Nitrate and ammonium affect the overall maize response to nitrogen availability by triggering specific and common transcriptional signatures in root

ABSTRACT: Nitrate and ammonium affect the overall maize response to nitrogen availability by triggering specific and common transcriptional signatures in root

PROVIDER: PRJNA594965 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10669772.fastq.gz	Fastqsanger.gz
	SRR10669773.fastq.gz	Fastqsanger.gz
	SRR10669774.fastq.gz	Fastqsanger.gz
	SRR10669775.fastq.gz	Fastqsanger.gz
	SRR10669776.fastq.gz	Fastqsanger.gz

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Similar Datasets

Nitrate and ammonium affect the overall maize response to nitrogen availability by triggering specific and common transcriptional signatures in root

Project description:Nitrogen (N) is an essential macronutrient for crops. Plants developed several responses to N fluctuations, thus optimizing the root architecture in response to N availability. Nitrate and ammonium are the main N inorganic forms taken up by plants and act as both nutrients and signals, affecting gene expression and plant development. In this study, RNA-sequencing was applied to gain comprehensive information on the pathways underlying the response of maize root, pre-treated in an N-deprived solution, to the provision of nitrate or ammonium. To assess the physiological response to these nutrients the shoot and root growth, the leaf pigment content and the amino acid amount in root and shoot were assessed. The analysis of the transcriptome shows that nitrate and ammonium regulate overlapping and distinct pathways, thus leading to different responses. NH4+ activates the response to stress, while NO3- acts as a negative regulator of transmembrane transport. Both the N-source repress genes related to the cytoskeleton and reactive oxygen species detoxification. Moreover, the presence of ammonium induces the accumulation of anthocyanins, while reduces biomass and chlorophyll and flavonoids accumulation. The profiles observed for hydrolysed and free amino acids highlighted common and distinct features in response to the two nitrogen forms.

2020-02-27 | GSE141860 | GEO

Nitrate and Ammonium Affect the Overall Maize Response to Nitrogen Availability by Triggering Specific and Common Transcriptional Signatures in Roots.

Project description:Nitrogen (N) is an essential macronutrient for crops. Plants have developed several responses to N fluctuations, thus optimizing the root architecture in response to N availability. Nitrate and ammonium are the main inorganic N forms taken up by plants, and act as both nutrients and signals, affecting gene expression and plant development. In this study, RNA-sequencing was applied to gain comprehensive information on the pathways underlying the response of maize root, pre-treated in an N-deprived solution, to the provision of nitrate or ammonium. The analysis of the transcriptome shows that nitrate and ammonium regulate overlapping and distinct pathways, thus leading to different responses. Ammonium activates the response to stress, while nitrate acts as a negative regulator of transmembrane transport. Both the N-source repress genes related to the cytoskeleton and reactive oxygen species detoxification. Moreover, the presence of ammonium induces the accumulation of anthocyanins, while also reducing biomass and chlorophyll and flavonoids accumulation. Furthermore, the later physiological effects of these nutrients were evaluated through the assessment of shoot and root growth, leaf pigment content and the amino acid concentrations in root and shoot, confirming the existence of common and distinct features in response to the two nitrogen forms.

| S-EPMC7013554 | biostudies-literature

The signal transduction protein PII controls ammonium, nitrate and urea uptake in cyanobacteria

Project description:PII signal transduction proteins are widely spread among all domains of life where they regulate a multitude of carbon and nitrogen metabolism related processes. Non-diazotrophic cyanobacteria can utilize a high variety of organic and inorganic nitrogen sources. In recent years, several physiological studies indicated an involvement of the cyanobacterial PII protein in regulation of ammonium, nitrate/nitrite and cyanate uptake. However, direct interaction of PII has not been demonstrated so far. In this study, we used biochemical, molecular genetic and physiological approaches to demonstrate that PII regulates all relevant nitrogen uptake systems in Synechocystis sp. strain PCC 6803: PII controls ammonium uptake by interacting with the Amt1 ammonium permease, probably similar to the known regulation of E. coli ammonium permease AmtB by the PII homologue GlnK. We could further clarify that PII mediates the ammonium- and dark-induced inhibition of nitrate uptake by interacting with the NrtC and NrtD subunits of the nitrate/nitrite transporter NrtABCD. We further identified the ABC-type urea transporter UrtABCDE as novel PII target. PII interacts with the UrtE subunit without involving the standard interaction surface of PII interactions. The deregulation of urea uptake in a PII deletion mutant causes ammonium excretion when urea is provided as nitrogen source. Furthermore, the urea hydrolyzing urease enzyme complex appears to be coupled to urea uptake. Overall, this study underlines the great importance of the PII signal transduction protein in the regulation of nitrogen utilization in cyanobacteria.

2019-07-10 | PXD013411 | Pride

Early transcriptional responses of Arabidopsis thaliana to ammonium and nitrate deprivation

2016-05-31 | GSE73903 | GEO

Nitrate fertilizer alleviates ammonium toxicity by enhancing ACLA-3 in Panax notoginseng roots

Project description:Nitrogen is one of the essential elements for plant growth. NH4+ and NO3- are two major forms of absorbing element N for higher plants. In this study we found that the growth of Panax notoginseng is inhibited when only adding ammonium nitrogen fertilizer, and adding nitrate fertilizer can alleviate the toxicity caused by ammonium. We use RNA-seq to identify genes that are related to the alleviated phenotypes after introducing NO3- to Panax notoginseng roots under NH4+ stresses. Twelve RNA-seq profiles in four sample groups, i.e., control, samples treated with NH4+, samples treated with NO3- only, and treated with both NH4+ and NO3- were obtained and analyzed to identify deregulated genes in samples with different treatments. ACLA-3 gene is downregulated in NH4+ treated samples, but is upregulated in samples treated with NO3- and with both NH4+ and NO3-, which is further validated in another set of samples using qRT-PCR. Our results suggest that unbalanced metabolism of nitrogen and nitrogen is the main cause of ammonium poisoning in roots of Panax notoginseng, and NO3- may significantly upregulate the activity of ACLA-3 which subsequently enhances the citrate cycle and many other metabolic pathways in Panax notoginseng root. These potentially increase the integrity of the Panax notoginseng roots. Our results suggest that introducing NO3- fertilizer is an effective means to prevent the occurrence of toxic ammonium in Panax notoginseng root.

2019-12-31 | GSE112437 | GEO

Early transcriptional responses of Arabidopsis thaliana to ammonium and nitrate deprivation

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

HCL Overall Analysis

Project description:HCL Overall Analysis

| PRJNA671384 | ENA

Measuring transcriptional differences between Caulobacter crescentus cultured in nitrate versus ammonium as the sole nitrogen source

Project description:This study is measuring the steady-state levels of mRNA in wild-type Caulobacter crescentus grown in M2 defined medium containing either ammonium or nitrate as the sole nitrogen source.

2010-06-21 | GSE21203 | GEO

Nitrate-dependent anaerobic propane and butane oxidation coupled to anaerobic ammonium oxidation

Project description:Nitrate-dependent anaerobic propane and butane oxidation coupled to anaerobic ammonium oxidation

2024-05-24 | PXD039266 | Pride

Comparative transcriptomics for growth of engineered Pseudomonas putida strains when grown using ammonium or nitrate nitrogen sources

Project description:We report the transcriptomic profiles of 2 different Pseudomonas putida derivatives when they are grown in MME medium supplemented with either ammonium or nitrate as the sole nitrogen source. Expression of both heterologous and native genes are examined.

2021-01-12 | GSE147420 | GEO

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