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Nitrate regulates maize root transcriptome through nitric oxide dependent and independent mechanisms

ABSTRACT: Nitrate regulates maize root transcriptome through nitric oxide dependent and independent mechanisms

PROVIDER: PRJNA723826 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14300954.fastq.gz	Fastqsanger.gz
	SRR14300955.fastq.gz	Fastqsanger.gz
	SRR14300956.fastq.gz	Fastqsanger.gz
	SRR14300957.fastq.gz	Fastqsanger.gz
	SRR14300958.fastq.gz	Fastqsanger.gz

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Nitrate regulates maize root transcriptome through nitric oxide dependent and independent mechanisms

Project description:Maize root responds to nitrate by modulating its development thorough the coordinated action of many players, interacting one each other. Among them, nitric oxide is produced in primary root of previously deprived seedlings early after the nitrate provision, thus inducing root elongation. In this study, a molecular untargeted approach was applied to discriminate the signaling and physiological pathways regulated by nitrate through nitric oxide from those regulated by nitrate itself of by further downstream factors. To this aim an RNA-sequencing approach was applied to discover the main molecular signatures distinguishing the response of maize root to nitrate according to their dependency, or independency on nitric oxide. A set of subsequent detailed functional annotation tools (Gene Ontology enrichment, MapMan, KEGG reconstruction pathway, transcription factors detection) were used to try to gain further information on the importance of this molecule in the regulation of the maize transcriptional response to nitrate. Besides, the lateral root density was measured both in the presence of nitrate and in the presence of nitrate plus cPTIO, a specific NO scavenger, and compared to that observed for N-depleted roots. Our results led to identify six clusters of transcripts according to their responsiveness to nitric oxide and to their regulation by nitrate provision. In general, common and specific features for the six clusters were identified allowing to discompose the overall root response to nitrate according to its dependency on nitric oxide.

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Project description:DNA microarray analysis was employed to investigate the transcriptome response to nitric oxide in Pseudomonas aeruginosa. We focused on the role played by the nitric oxide-response regulators DNR and FhpR and an oxygen-response regulator ANR in the response. The transcriptome profiles of the P. aeruginosa strains before and after exposure to nitric oxide under the microaerobic conditions were analyzed. Wild type, its anr, dnr, and fhpR mutants, and the anr mutant that express dnr were used for the analyses. Pseudomonas aeruginosa wild type (PAO1ut), anr mutant (RManr), dnr mutant (RMdnr), anr mutant that constitutively expresses DNR (RManrEXdnr), and fhpR mutant (PDM2665) were cultivated microaerobically in LB in 1-liter jar fermenter. When optical density at 600 nm reached 0.3, nitric oxide-saturated water was added to the medium (final nitric oxide concentration was 20 micro-M). RNA was isolated from a 10 ml aliquot of the culture prior to the addition of nitric oxide and at 5 min after the addition. The experiment was performed in duplicate independent cultures.

2014-12-08 | E-GEOD-58862 | biostudies-arrayexpress

Nitrate Regulates Maize Root Transcriptome through Nitric Oxide Dependent and Independent Mechanisms.

Project description:Maize root responds to nitrate by modulating its development through the coordinated action of many interacting players. Nitric oxide is produced in primary root early after the nitrate provision, thus inducing root elongation. In this study, RNA sequencing was applied to discover the main molecular signatures distinguishing the response of maize root to nitrate according to their dependency on, or independency of, nitric oxide, thus discriminating the signaling pathways regulated by nitrate through nitric oxide from those regulated by nitrate itself of by further downstream factors. A set of subsequent detailed functional annotation tools (Gene Ontology enrichment, MapMan, KEGG reconstruction pathway, transcription factors detection) were used to gain further information and the lateral root density was measured both in the presence of nitrate and in the presence of nitrate plus cPTIO, a specific NO scavenger, and compared to that observed for N-depleted roots. Our results led us to identify six clusters of transcripts according to their responsiveness to nitric oxide and to their regulation by nitrate provision. In general, shared and specific features for the six clusters were identified, allowing us to determine the overall root response to nitrate according to its dependency on nitric oxide.

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