The PHR2-DGP1 Signaling Integrates Carbon and Nitrogen Assimilatory Metabolisms under Phosphorus Deficiency Stress in Rice Plants [ChIP-Seq]
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ABSTRACT:
PROVIDER: PRJNA1067655 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27683871_1.fastq.gz | Fastqsanger.gz | |||
| SRR27683871_2.fastq.gz | Fastqsanger.gz | |||
| SRR27683872_1.fastq.gz | Fastqsanger.gz | |||
| SRR27683872_2.fastq.gz | Fastqsanger.gz | |||
| SRR27683873_1.fastq.gz | Fastqsanger.gz |
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Project description:Carbon (C), nitrogen (N) and phosphorus (Pi) are crucial macronutrients for plants. While substantial knowledge exists on C/N balance signaling physiological and molecular perspectives, the core regulatory mechanism governing C/N and Pi balance remains largely unexplored. This study reveals that C/N assimilatory metabolisms matching the Pi-deficiency stress is integrated by a DEEP GREEN PANICLE1 (DGP1)-mediated regulatory network in rice (Oryza sativa). We found that low-Pi stress triggers DGP1 expression in a dose-responsive manner, facilitated by the PHOSPHATE STARVATION RESPONSE REGULATOR (PHR2). Intriguingly, DGP1 interacts with transcription factors (GLK1 and GLK2) and mitochondrial factors (GDCH and QCR9), modulating their roles in photosynthetic gene expression, the glycine cleavage system and the mitochondrial electron transport chain (mETC), respectively. Additionally, DGP1 influences aminoacyl-tRNA synthetases and ribosomal subunits, impacting protein biosynthesis, and intervenes in various metabolic pathways, including glycolysis and the citrate cycle. Phenotypically, we observed that under short-term Pi-deficiency, wild-type plants exhibit compromised photosynthesis, photorespiration and mETC-driven ATP synthesis, whereas dgp1 and phr2 mutants display reduced sensitivity to these conditions. Conversely, DGP1 overexpressors show decreased yield under normal conditions due to altered cell metabolomes and protein biosynthesis inadequacy, despite unaffected 15NO3– uptake and transport. In conclusion, the PHR2-DGP1 module orchestrates a comprehensive signaling network, harmonizing C and N metabolic fluxes under Pi limitation through coordinated interactions among cytoplast, chloroplast and mitochondria.
2025-01-27 | GSE253911 | GEO
Project description:Carbon (C), nitrogen (N) and phosphorus (Pi) are crucial macronutrients for plants. While substantial knowledge exists on C/N balance signaling physiological and molecular perspectives, the core regulatory mechanism governing C/N and Pi balance remains largely unexplored. This study reveals that C/N assimilatory metabolisms matching the Pi-deficiency stress is integrated by a DEEP GREEN PANICLE1 (DGP1)-mediated regulatory network in rice (Oryza sativa). We found that low-Pi stress triggers DGP1 expression in a dose-responsive manner, facilitated by the PHOSPHATE STARVATION RESPONSE REGULATOR (PHR2). Intriguingly, DGP1 interacts with transcription factors (GLK1 and GLK2) and mitochondrial factors (GDCH and QCR9), modulating their roles in photosynthetic gene expression, the glycine cleavage system and the mitochondrial electron transport chain (mETC), respectively. Additionally, DGP1 influences aminoacyl-tRNA synthetases and ribosomal subunits, impacting protein biosynthesis, and intervenes in various metabolic pathways, including glycolysis and the citrate cycle. Phenotypically, we observed that under short-term Pi-deficiency, wild-type plants exhibit compromised photosynthesis, photorespiration and mETC-driven ATP synthesis, whereas dgp1 and phr2 mutants display reduced sensitivity to these conditions. Conversely, DGP1 overexpressors show decreased yield under normal conditions due to altered cell metabolomes and protein biosynthesis inadequacy, despite unaffected 15NO3– uptake and transport. In conclusion, the PHR2-DGP1 module orchestrates a comprehensive signaling network, harmonizing C and N metabolic fluxes under Pi limitation through coordinated interactions among cytoplast, chloroplast and mitochondria.
2025-01-27 | GSE253909 | GEO
Project description:The PHR2-DGP1 Signaling Integrates Carbon and Nitrogen Assimilatory Metabolisms under Phosphorus Deficiency Stress in Rice Plants [RNA-seq]
| PRJNA1067651 | ENA
Project description:Members of the plant family Leguminosae (Fabaceae) are unique in that they have evolved a symbiotic relationship with rhizobia (a group of soil bacteria that can fix atmospheric nitrogen). Rhizobia infect and form root nodules on their specific host plants before differentiating into bacteroids, the symbiotic form of rhizobia. This complex relationship involves the supply of C4-dicarboxylate and phosphate by the host plants to the microsymbionts that utilize them in the energy-intensive process of fixing atmospheric nitrogen into ammonium, which is in turn made available to the host plants as a source of nitrogen, a macronutrient for growth. Although nitrogen-fixing bacteroids are no longer growing, they are metabolically active. The symbiotic process is complex and tightly regulated by both the host plants and the bacteroids. The metabolic pathways of carbon, nitrogen, and phosphate are heavily regulated in the host plants, as they need to strike a fine balance between satisfying their own needs as well as those of the microsymbionts. A network of transporters for the various metabolites are responsible for the trafficking of these essential molecules between the two partners through the symbiosome membrane (plant-derived membrane surrounding the bacteroid), and these are in turn regulated by various transcription factors that control their expressions under different environmental conditions. Understanding this complex process of symbiotic nitrogen fixation is vital in promoting sustainable agriculture and enhancing soil fertility.
| S-EPMC6305480 | biostudies-literature
Project description:Nitrogen (N) and phosphorus (P) are pivotal element for proper plant growth and development. We performed microarray analysis of rice shoot and root after nitrogen deficiency (-N) treatment under phosphorus deficiency (-P) condition to obtain a global view of gene regulations associated with plant response to -N under -P condition.
2019-10-06 | GSE73775 | GEO
Project description:Forming symbiotic associations with beneficial microbes are important strategies for sessile plants to acquire nitrogen and phosphorus nutrients from the soil. Root exudates play key roles on set-up of the rhizosphere microbiome. According to the needs for nitrogen or phosphorus, plants can adjust the root exudates composition to attract proper microbes. Flavonoids are a group of secondary metabolites that are well studied in shaping the root microbiome, especially the root nodule symbiosis in legumes. Here, we show the medicago truncatula phosphate sensors SPX1 and SPX3 regulate flavonoids biosynthesis to recruit nitrogen-fixing microbes for nitrogen acquisition. Nitrogen-fixing microbes were less recruited in spx1spx3 double mutant root rhizosphere. This was caused by lower flavonoids biosynthesis related genes expression, which resulted in lower flavonoids levels in the root exudates compared to wild type plant R108. Further analysis indicates the regulation of flavonoids biosynthesis is through the SPX1 and SPX3 interaction transcription factor PHR2. We propose the SPX-PHR phosphate homeostasis regulation network also control microbe-dependent nitrogen acquisition according to phosphate levels. Thus, SPX1 and SPX3 play important roles to keep a microbe-dependent nitrogen and phosphorus absorption balance for optimal growth.
2025-02-28 | GSE289310 | GEO
Project description:BackgroundIn China, nitrogen (N)-deficiency often occurs in Citrus orchards, which is one of the main causes of yield loss and fruit quality decline. Little information is known about the adaptive responses of Citrus carbon (C) and N metabolisms to N-deficiency. Seedlings of 'Xuegan' (Citrus sinensis (L.) Osbeck) were supplied with nutrient solution at an N concentration of 0 (N-deficiency), 5, 10, 15 or 20 mM for 10 weeks. Thereafter, we examined the effects of N supply on the levels of C and N in roots, stems and leaves, and the levels of organic acids, nonstructural carbohydrates, NH4+-N, NO3--N, total soluble proteins, free amino acids (FAAs) and derivatives (FAADs), and the activities of key enzymes related to N assimilation and organic acid metabolism in roots and leaves.ResultsN-deficiency elevated sucrose export from leaves to roots, C and N distributions in roots and C/N ratio in roots, stems and leaves, thus enhancing root dry weight/shoot dry weight ratio and N use efficiency. N-deficient leaves displayed decreased accumulation of starch and total nonstructural carbohydrates (TNC) and increased sucrose/starch ratio as well as a partitioning trend of assimilated C toward to sucrose, but N-deficient roots displayed elevated accumulation of starch and TNC and reduced sucrose/starch ratio as well as a partitioning trend of assimilated C toward to starch. N-deficiency reduced the concentrations of most FAADs and the ratios of total FAADs (TFAADs)/N in leaves and roots. N-deficiency reduced the demand for C skeleton precursors for amino acid biosynthesis, thus lowering TFAADs/C ratio in leaves and roots. N-deficiency increased (decreased) the relative amounts of C-rich (N-rich) FAADs, thus increasing the molar ratio of C/N in TFAADs in leaves and roots.ConclusionsOur findings corroborated our hypothesis that C and N metabolisms displayed adaptive responses to N-deficiency in C. sinensis seedlings, and that some differences existed between roots and leaves in N-deficiency-induced alterations of and C and N metabolisms.
| S-EPMC9316421 | biostudies-literature
Project description:In Aspergillus nidulans, nitrogen and carbon metabolism are under the control of wide-domain regulatory systems, including nitrogen metabolite repression, carbon catabolite repression. Transcriptomic analysis of the wild type strain grown under different combinations of carbon and nitrogen regimes was performed, to identify differentially regulated genes. Carbon metabolism predominates as the most important regulatory signal but for many genes, both carbon and nitrogen metabolisms coordinate regulation.
2019-05-15 | GSE115021 | GEO
Project description:Abiotic stress causes disturbances in the cellular homeostasis. Re-adjustment of balance in carbon, nitrogen and phosphorus metabolism therefore plays a central role in stress adaptation. However, it is currently unknown which parts of the primary cell metabolism follow common patterns under different stress conditions and which represent specific responses. To address these questions, changes in transcriptome, metabolome and ionome were analyzed in maize source leaves from plants suffering low temperature, low nitrogen (N) and low phosphorus (P) stress. The selection of maize as study object provided data directly from an important crop species and the so far underexplored C4 metabolism. Growth retardation was comparable under all tested stress conditions. The only primary metabolic pathway responding similar to all stresses was nitrate assimilation, which was down-regulated. The largest group of commonly regulated transcripts followed the expression pattern: down under low temperature and low N, but up under low P. Several members of this transcript cluster could be connected to P metabolism and correlated negatively to different phosphate concentration in the leaf tissue. Accumulation of starch under low temperature and low N stress, but decrease in starch levels under low under low P conditions indicated that only low P treated leaves suffered carbon starvation. In conclusion, maize employs very different strategies for management of nitrogen and phosphorus metabolism under stress. While nitrate assimilation was regulated depending on demand by growth processes, phosphate concentrations changed depending on availability, thus building up reserves under excess conditions. Carbon and energy metabolism of the C4 maize leaves were particularly sensitive to P starvation.
2013-05-15 | GSE46704 | GEO
Project description:Abiotic stress causes disturbances in the cellular homeostasis. Re-adjustment of balance in carbon, nitrogen and phosphorus metabolism therefore plays a central role in stress adaptation. However, it is currently unknown which parts of the primary cell metabolism follow common patterns under different stress conditions and which represent specific responses. To address these questions, changes in transcriptome, metabolome and ionome were analyzed in maize source leaves from plants suffering low temperature, low nitrogen (N) and low phosphorus (P) stress. The selection of maize as study object provided data directly from an important crop species and the so far underexplored C4 metabolism. Growth retardation was comparable under all tested stress conditions. The only primary metabolic pathway responding similar to all stresses was nitrate assimilation, which was down-regulated. The largest group of commonly regulated transcripts followed the expression pattern: down under low temperature and low N, but up under low P. Several members of this transcript cluster could be connected to P metabolism and correlated negatively to different phosphate concentration in the leaf tissue. Accumulation of starch under low temperature and low N stress, but decrease in starch levels under low under low P conditions indicated that only low P treated leaves suffered carbon starvation. In conclusion, maize employs very different strategies for management of nitrogen and phosphorus metabolism under stress. While nitrate assimilation was regulated depending on demand by growth processes, phosphate concentrations changed depending on availability, thus building up reserves under excess conditions. Carbon and energy metabolism of the C4 maize leaves were particularly sensitive to P starvation. Responses of maize source leaves to low temperature, low nitrogen and low phosphorus conditions were tested in independent single-stress experiments. Seedlings were cultivated in pots containing nutrient-poor peat soil under the controlled conditions of a growth chamber. The plants were fertilized with modified Hoagland solutions, containing 15mM KNO3 and 0.5mM KH2PO4 for control conditions; for low N and low P treatment, the nutrient concentrations were reduced to 0.15mM KNO3 and 0.1mM KH2PO4, respectively. Low temperature treated plants were always supplied with control nutrient solution. Plants from the nitrogen and phosphorus experiment as well as the control temperature plants were exposed to 28°C during the day and 20°C during the night. Low temperature treatment was limited to the night period and was reduced to 4°C for the 10h dark period. Source leaf lamina were harvested at day 20 (low temperature experiment) or day 30 after start of germination (low nitrogen and low phosphorus experiment) for parallel analysis of transcriptome, metabolome and ion profiles. The molecular data is further supplemented by phenotypic characterization of the maize seedlings under investigation.
2013-05-15 | E-GEOD-46704 | biostudies-arrayexpress