Plant metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA531340 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10364100_1.fastq.gz | Fastqsanger.gz | |||
| SRR10364100_2.fastq.gz | Fastqsanger.gz | |||
| SRR10364200_1.fastq.gz | Fastqsanger.gz | |||
| SRR10364200_2.fastq.gz | Fastqsanger.gz | |||
| SRR10364300_1.fastq.gz | Fastqsanger.gz |
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Project description:The effects of soil phosphorous content on microbiota are driven by the plant phosphate starvation response
| PRJNA531167 | ENA
Project description:Although phosphorus is one of the most important essential elements for plant growth and development, the epigenetic regulation of inorganic phosphate (Pi) signaling is poorly understood. In this study, we identified the high-mobility-group protein OsHMGB1 as a key regulator of phosphate homeostasis and plant growth in rice (Oryza sativa). OsHMGB1 expression is induced by Pi starvation and encodes a nucleus-localized protein. Relative to wild-type plants, Oshmgb1 mutant plants had lower Pi content in their leaves, whereas plants overexpressing OsHMGB1 had higher Pi content, indicating that OsHMGB1 positively regulates Pi accumulation. Transcriptome deep sequencing and chromatin immunoprecipitation followed by sequencing showed that OsHMGB1 regulated the expression of a series of phosphate starvation responsive (PSR) genes by binding to their promoters. Furthermore, Assay for Transposase-Accessible Chromatin followed by sequencing revealed that OsHMGB1 was involved in maintaining chromatin accessibility. Indeed, OsHMGB1 occupancy positively correlated with genome-wide chromatin accessibility and gene expression levels. Notably, we determined that OsHMGB1 interacted with RNA polymerase II to help regulate transcription, especially under low Pi conditions. Taken together, our results suggest that OsHMGB1 functions as a transcriptional facilitator, revealing a key epigenetic mechanism to regulate Pi homeostasis and fine-tune plant acclimation responses to Pi-limited environments.
2025-12-09 | GSE227769 | GEO
Project description:Although phosphorus is one of the most important essential elements for plant growth and development, the epigenetic regulation of inorganic phosphate (Pi) signaling is poorly understood. In this study, we identified the high-mobility-group protein OsHMGB1 as a key regulator of phosphate homeostasis and plant growth in rice (Oryza sativa). OsHMGB1 expression is induced by Pi starvation and encodes a nucleus-localized protein. Relative to wild-type plants, Oshmgb1 mutant plants had lower Pi content in their leaves, whereas plants overexpressing OsHMGB1 had higher Pi content, indicating that OsHMGB1 positively regulates Pi accumulation. Transcriptome deep sequencing and chromatin immunoprecipitation followed by sequencing showed that OsHMGB1 regulated the expression of a series of phosphate starvation responsive (PSR) genes by binding to their promoters. Furthermore, Assay for Transposase-Accessible Chromatin followed by sequencing revealed that OsHMGB1 was involved in maintaining chromatin accessibility. Indeed, OsHMGB1 occupancy positively correlated with genome-wide chromatin accessibility and gene expression levels. Notably, we determined that OsHMGB1 interacted with RNA polymerase II to help regulate transcription, especially under low Pi conditions. Taken together, our results suggest that OsHMGB1 functions as a transcriptional facilitator, revealing a key epigenetic mechanism to regulate Pi homeostasis and fine-tune plant acclimation responses to Pi-limited environments.
2025-12-09 | GSE227767 | GEO
Project description:Although phosphorus is one of the most important essential elements for plant growth and development, the epigenetic regulation of inorganic phosphate (Pi) signaling is poorly understood. In this study, we identified the high-mobility-group protein OsHMGB1 as a key regulator of phosphate homeostasis and plant growth in rice (Oryza sativa). OsHMGB1 expression is induced by Pi starvation and encodes a nucleus-localized protein. Relative to wild-type plants, Oshmgb1 mutant plants had lower Pi content in their leaves, whereas plants overexpressing OsHMGB1 had higher Pi content, indicating that OsHMGB1 positively regulates Pi accumulation. Transcriptome deep sequencing and chromatin immunoprecipitation followed by sequencing showed that OsHMGB1 regulated the expression of a series of phosphate starvation responsive (PSR) genes by binding to their promoters. Furthermore, Assay for Transposase-Accessible Chromatin followed by sequencing revealed that OsHMGB1 was involved in maintaining chromatin accessibility. Indeed, OsHMGB1 occupancy positively correlated with genome-wide chromatin accessibility and gene expression levels. Notably, we determined that OsHMGB1 interacted with RNA polymerase II to help regulate transcription, especially under low Pi conditions. Taken together, our results suggest that OsHMGB1 functions as a transcriptional facilitator, revealing a key epigenetic mechanism to regulate Pi homeostasis and fine-tune plant acclimation responses to Pi-limited environments.
2025-12-09 | GSE227768 | GEO
Project description:Although phosphorus is one of the most important essential elements for plant growth and development, the epigenetic regulation of inorganic phosphate (Pi) signaling is poorly understood. In this study, we identified the high-mobility-group protein OsHMGB1 as a key regulator of phosphate homeostasis and plant growth in rice (Oryza sativa). OsHMGB1 expression is induced by Pi starvation and encodes a nucleus-localized protein. Relative to wild-type plants, Oshmgb1 mutant plants had lower Pi content in their leaves, whereas plants overexpressing OsHMGB1 had higher Pi content, indicating that OsHMGB1 positively regulates Pi accumulation. Transcriptome deep sequencing and chromatin immunoprecipitation followed by sequencing showed that OsHMGB1 regulated the expression of a series of phosphate starvation responsive (PSR) genes by binding to their promoters. Furthermore, Assay for Transposase-Accessible Chromatin followed by sequencing revealed that OsHMGB1 was involved in maintaining chromatin accessibility. Indeed, OsHMGB1 occupancy positively correlated with genome-wide chromatin accessibility and gene expression levels. Notably, we determined that OsHMGB1 interacted with RNA polymerase II to help regulate transcription, especially under low Pi conditions. Taken together, our results suggest that OsHMGB1 functions as a transcriptional facilitator, revealing a key epigenetic mechanism to regulate Pi homeostasis and fine-tune plant acclimation responses to Pi-limited environments. Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for HMG-GFP transgenic plants
2025-12-09 | GSE227770 | GEO
Project description:Plants establish mutualistic association with beneficial microbes while deploy the immune system to defend against pathogens. Little is known about the interplay between mutualism and immunity and about the mediator molecules. Here we show that plants respond differently to a bacterial volatile compound through integral modulation of the immune system and the phosphate starvation response (PSR) system, resulting in either mutualism or immunity. We found that the same exposure of a recognized plant growth-promoting rhizobacterium unexpectedly causes either beneficial or deleterious effects to plants. The beneficial-to-deleterious transition is dependent on plant nutrition of phosphorus (P) and is mediated by diacetyl (DA), a bacterial volatile compound. In P-sufficient plants, DA partially suppresses plant production of reactive oxygen species (ROS) and enhances symbiont colonization without compromising disease resistance. In P-deficient plants, DA elevates phytohormone-mediated immunity and consequently causes plant hypersensitivity to P deficiency. Therefore, DA affects the types of relation between plants and certain rhizobacteria in a way that depends on plant PSR system and phytohormone-mediated immunity.
2019-12-03 | GSE138478 | GEO
Project description:We analyzed the RNA expression profiles of the mutants of four memebrs of Arabidopsis PHR1 family to understand their roles in regulating plant responses to phosphate starvation
2022-11-06 | GSE217158 | GEO
Project description:Plant vacuoles serve as the primary intracellular compartments for inorganic phosphate (Pi) storage. Passage of Pi across vacuolar membranes plays a critical role in buffering the cytoplasmic Pi level against fluctuations of external Pi and metabolic activities. Here we demonstrate that the SPX-MFS proteins, designated as Phosphate Transporter 5 family (PHT5), also named Vacuolar Phosphate Transporter (VPT), function as vacuolar Pi transporters. Based on 31P-magnetic resonance spectroscopy analysis, Arabidopsis pht5;1 loss-of-function mutants accumulate less Pi and exhibit a lower vacuolar-to-cytoplasmic Pi ratio than controls. Conversely, overexpression of PHT5 leads to massive Pi sequestration into vacuoles and altered regulation of Pi starvation-responsive genes. Furthermore, we show that heterologous expression of OsSPX-MFS1, the rice PHT5 homolog, mediates Pi influx to yeast vacuoles. Our findings uncover a group of Pi transporters in vacuolar membranes that regulate the cytoplasmic Pi homeostasis required for the fitness of plant growth. 10-day seedlings grown on Pi-sufficient medium or followed by 1-day or 3-day Pi starvation, shoot RNA and root RNA were extracted separately
2016-03-28 | E-GEOD-74856 | biostudies-arrayexpress
Project description:Phosphorus (P) is an essential macronutrient for various biological processes in plant growth. Modern agricultural science has advanced the knowledge of regulatory mechanisms underlying phosphorus starvation responses (PSRs), aiming to develop phosphate-efficient crops with sustainable production under reduced Pi fertilizer application. However, information regarding coordinated shoot and root adaptation in response to combined nutrient stresses is limited. This study investigated the role of Phloem Phosphate Stress Repressed 1 (PPSR1) in modulating PSRs and other nutrient adaptation. The Arabidopsis functional homologue of Cucumis sativus PPSR1 (CsPPSR1), designated AtPPSR1, was identified. AtPPSR1 encodes a glycine-rich domain-containing protein, and its ectopic expression confers enhanced growth performance to plants. Transcriptomic analyses revealed AtPPSR1 as a regulatory mediator of PSRs, photosynthesis and root development. We revealed that AtPPSR1 interacted with PHOSPHATE STARVATION RESPONSE 1 (PHR1) to regulate PHR1-target genes for adaptive root development, in response to Pi-starvation stress. Additionally, AtPPSR1 was discovered as graft-transmissible, and the shoot-borne AtPPSR1 played a role in restoring the root phenotype of the ppsr1 mutant. Physiological analyses revealed that enhanced AtPPSR1 expression enabled resilience to nitrogen (N) and potassium (K)-starvation, as well as to Pi-deficiency. Furthermore, we identified homologues of CsPPSR1 and AtPPSR1 in Brassica napus (canola), which displayed similar expression patterns in response to Pi-starvation stress. Overexpression of PPSR1, identified from Arabidopsis, cucumber and canola, improved growth performance and seed yield in canola under N-, Pi- or K-deficient conditions. These findings provide novel insights into PPSR1-mediated molecular coordination to improve growth performance under mineral nutrient-stresses conditions.
2025-12-13 | GSE292879 | GEO
Project description:Plant vacuoles serve as the primary intracellular compartments for inorganic phosphate (Pi) storage. Passage of Pi across vacuolar membranes plays a critical role in buffering the cytoplasmic Pi level against fluctuations of external Pi and metabolic activities. Here we demonstrate that the SPX-MFS proteins, designated as Phosphate Transporter 5 family (PHT5), also named Vacuolar Phosphate Transporter (VPT), function as vacuolar Pi transporters. Based on 31P-magnetic resonance spectroscopy analysis, Arabidopsis pht5;1 loss-of-function mutants accumulate less Pi and exhibit a lower vacuolar-to-cytoplasmic Pi ratio than controls. Conversely, overexpression of PHT5 leads to massive Pi sequestration into vacuoles and altered regulation of Pi starvation-responsive genes. Furthermore, we show that heterologous expression of OsSPX-MFS1, the rice PHT5 homolog, mediates Pi influx to yeast vacuoles. Our findings uncover a group of Pi transporters in vacuolar membranes that regulate the cytoplasmic Pi homeostasis required for the fitness of plant growth.
2016-03-28 | GSE74856 | GEO