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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression data from Col-0 and sp1,spx2 under phosphate starvation stress and recovery after resupplying phosphate

ABSTRACT: We performed a transcriptomic analysis of Pi-starvation and recovery after resupplying Pi in Arabidopsis thaliana (Columbia-0) wild type plants and double mutant spx1,spx2. Results show that SPX1 is a Pi-dependent inhibitor of the transcription factor PHR1, a central regulatory protein in the control of transcriptional responses to Pi starvation. The analysis was performed in wild-type and double spx1,spx2 double mutant plants grown for seven days in complete (+Pi) and Pi-lacking (-Pi) Johnson solid media. Then, plants were transferred to complete medium for 4 hours to analyze the effect of resupplying plants with Pi.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Enrique Rojo

PROVIDER: E-GEOD-52046 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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SPX1 is a phosphate-dependent inhibitor of Phosphate Starvation Response 1 in Arabidopsis.

Puga María Isabel MI Mateos Isabel I Charukesi Rajulu R Wang Zhiye Z Franco-Zorrilla José M JM de Lorenzo Laura L Irigoyen María L ML Masiero Simona S Bustos Regla R Rodríguez José J Leyva Antonio A Rubio Vicente V Sommer Hans H Paz-Ares Javier J

Proceedings of the National Academy of Sciences of the United States of America 20140930 41

To cope with growth in low-phosphate (Pi) soils, plants have evolved adaptive responses that involve both developmental and metabolic changes. Phosphate Starvation Response 1 (PHR1) and related transcription factors play a central role in the control of Pi starvation responses (PSRs). How Pi levels control PHR1 activity, and thus PSRs, remains to be elucidated. Here, we identify a direct Pi-dependent inhibitor of PHR1 in Arabidopsis, SPX1, a nuclear protein that shares the SPX domain with yeast ...[more]

PMID: 25271326

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Expression data from Arabidopsis thaliana PHR1 primary targets genes under phosphate starvation stress

Project description:We performed a transcriptomic analysis of Pi starvation responses in Arabidopsis thaliana (Columbia-0) phr1 mutant plants expressing PHR1 in presence of cicloheximide, that inhibit protein translation, thus preventing any effect of PHR1 on the expression of indirect targets. Results show the primary target genes of PHR1 in the responses to Pi starvation. The analysis was performed in phr1 plants and phr1 plants overexpressing a fusion GR:PHR1 (OXGR:PHR1) whose activity is postranslationally controlled by dexamethasone (DEX), that allows studying gene expression upon PHR1 activation and the concomitant inhibition of translation with cycloheximide (CHX), thus preventing any effect of PHR1 on the expression of indirect targets. To perform this study, phr1 and OXGR:PHR1 phr1 plants were grown for seven days in complete Johnson liquid media (+Pi), 2 days in Pi-lacking media (-Pi) and then supplemented with 5 µM DEX and 10 µM CHX for 6 hours before harvesting. Three independent biological samples of total RNA from shoot and root were hybridized separately.

2010-12-09 | E-GEOD-20955 | biostudies-arrayexpress

Expression data from Col-0 and sp1,spx2 under phosphate starvation stress and recovery after resupplying phosphate

Project description:We performed a transcriptomic analysis of Pi-starvation and recovery after resupplying Pi in Arabidopsis thaliana (Columbia-0) wild type plants and double mutant spx1,spx2. Results show that SPX1 is a Pi-dependent inhibitor of the transcription factor PHR1, a central regulatory protein in the control of transcriptional responses to Pi starvation.

2014-09-30 | GSE52046 | GEO

Expression data from Arabidopsis thaliana under phosphate starvation stress

Project description:We performed a transcriptomic analysis of Pi starvation responses in Arabidopsis thaliana (Columbia-0) wild type plants under phosphate starvation stress and in plants with altered PHR1(-like) activity, comparing mutants of phr1 and phr1-phl1 grown in phosphate-lacking medium. Results show the central role of PHR1 and functionally redundant members of its family in the control of transcriptional responses to Pi starvation. The analysis was performed in wild-type plants grown for seven days in complete (+Pi) and Pi-lacking (-Pi) Johnson solid media and the single phr1 and double phr1-phl1 mutants grown for 7 days in –Pi medium. Three independent biological samples of total RNA from shoot and root were hybridized separately.

2010-12-09 | E-GEOD-16722 | biostudies-arrayexpress

Expression data from Arabidopsis thaliana under phosphate starvation stress

2010-12-09 | GSE16722 | GEO

Expression data from Arabidopsis thaliana PHR1 primary targets genes under phosphate starvation stress

2010-12-09 | GSE20955 | GEO

Inositol pyrophosphate InsP8 acts as intracellular phosphate signal in Arabidopsis

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SHORT-ROOT Stabilizes PHOSPHATE1 to Regulate Phosphate Allocation in Arabidopsis

Project description:Coordinated distribution of Pi between roots and shoots is an important process that plants use to maintain Pi homeostasis. SHR (SHORT-ROOT) is well-characterized for its function in root radial patterning1-3. Here, we demonstrate a new role of SHR in controlling phosphate (Pi) allocation from roots to shoots by regulating PHOSPHATE1 (PHO1) in the root differentiation zone. We recovered a weak mutant allele of SHR in Arabidopsis which accumulates much less Pi in the shoot and shows constitutive Pi starvation response (PSR) under Pi-sufficient condition. Besides, Pi starvation suppresses SHR protein accumulation and releases its inhibition on the HD-ZIP Ⅲ transcription factor PHB. PHB accumulates and directly binds the promoter of PHO2 to upregulate its transcription, resulting in PHO1 degradation in the xylem-pole pericycle cells. Our findings reveal a previously unrecognized mechanism of how plants repress Pi translocation from roots to shoots in response to Pi starvation.

2022-06-24 | GSE199834 | GEO

Deubiquitinating Enzyme OTU5 Contributes to DNA Methylation Patterns and Is Critical for Phosphate Nutrition Signals

Project description:Phosphate (Pi) starvation induces a suite of adaptive responses aimed at recalibrating cellular Pi homeostasis. Plants harboring a mutation in OVARIAN TUMOR DOMAIN-CONTAINING DEUBIQUITINATING ENZYME5 (OTU5) showed altered DNA methylation of root hair-related genes and altered Pi-responsive root traits. Unlike the wild type, homozygous otu5 mutants did not respond to Pi starvation by increased lateral root formation and increased root hair length but formed very short root hairs when grown on low-Pi media. Under Pi-replete conditions, otu5 plants developed more root hairs than the wild type due to attenuated primary root growth, a phenotype that resembled that of Pi-deficient plants. Growth of plants on low-Pi media altered both H3K4 and H3K27 trimethylation levels at the transcriptional start site of a subset of genes encoding key players in Pi homeostasis, which was correlated with mRNA abundance changes of these genes. Pi starvation had a minor impact on DNA methylation. Differentially methylated regions were enriched in transposable elements, suggesting that DNA methylation associated with low Pi supply is required for maintaining genome integrity. It is concluded that DNA methylation and histone methylation constitute critical, interdependent regulatory components that orchestrate the activity of a subset of Pi-responsive genes.

2017-11-02 | GSE81407 | GEO

Whole Genome Bisulfite sequencing of Arabidopsis thaliana High and Low phosphate methylomes

Project description:Pi availability is a significant limiting factor for plant growth in both natural and agricultural systems. To cope with such limiting conditions, plants have adapted developmental and biochemical strategies to enhance Pi acquisition and to avoid starvation. A myriad of genes that are involved in the regulation and display of these strategies have been identified. However, the possible epigenetic components regulating the phosphate starvation responses have not been thoroughly investigated. DNA methylation is a major epigenetic mark involved in diverse biological processes and it may play a critical role in Pi starvation stress adaptation, also changes in DNA methylation can lead to a unique gene expression pattern in response to specific developmental and environmental conditions. Here in we demonstrate that non-CpG DNA methylation is required for proper expression of a number of Pi-limitation responsive genes in Arabidopsis thaliana and results in altered morphologic and physiologic phosphate starvation responses.Our data suggest that DNA methylation is involved in the modulation of Pi starvation responses via the transcriptional regulation of a set of phosphate-starvation responsive genes.

2015-12-31 | GSE72770 | GEO

A specific protective mechanism against chloroplast photo-reactive oxygen species in phosphate-starved rice plants [ChIP-seq]

Project description:Phosphorus (Pi) starvation prevents a good match between light energy absorption and photosynthetic carbon metabolism. Photosynthetic electron-transport chain switches to use molecular oxygen as an electron carrier, generating photo-reactive oxygen species (photo-ROS) in chloroplast. In rice (Oryza sativa), DEEP GREEN PANICLE1 (DGP1) is robustly up-regulated in response to Pi-deficiency stress. DGP1 decreases the DNA-binding activities of the photosynthetic activators GLK1/2 on the genes involved in chlorophyll biosynthesis, light harvesting and electron transport. This Pi-starvation-induced mechanism dampens electron transport rates (ETRI and ETRII) and alleviates the electron-excessive stress in mesophyll cells. Meanwhile, DGP1 hijacks glycolytic enzymes GAPC1/2/3, redirecting glucose metabolism toward pentose phosphate pathway with superfluous NADPH production. Phenotypically, light irradiation induces O2– accumulation in Pi-starved WT leaves, but was observably accelerated in dgp1 mutant and impaired in GAPCsRNAi line and glk1glk2 double mutant. Interestingly, overexpression of DGP1 in rice caused hyposensitivity to the ROS-inducers (catechin and methyl viologen) and dgp1 mutant shows a similar inhibitory growth with the WT plants. We conclude that DGP1 gene serves as a specific antagonizer against Pi-starvation-induced photo-ROS, which integrates light-absorbing and anti-oxidative systems by orchestrating transcriptional and metabolic regulations, respectively.

2023-04-15 | GSE225476 | GEO

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