Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA302108 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2922630.fastq.gz | Fastqsanger.gz | |||
| SRR2922625.fastq.gz | Fastqsanger.gz | |||
| SRR2922626.fastq.gz | Fastqsanger.gz | |||
| SRR2922627.fastq.gz | Fastqsanger.gz | |||
| SRR2922628.fastq.gz | Fastqsanger.gz |
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Project description:We first compared the transcriptomes of the roots of WT seedlings grown under P+ and P- conditions. Using a 2-fold change and a FDR (false discovery rate) of <0.05 as the cut-off for selecting the differentially expressed transcripts, we found that the expression of 581 genes was induced and that the expression of 120 genes was repressed by Pi starvation. We then compared the expression levels of these 581 PSI genes in the WT and phl2. The results showed that the average expression level of these genes was 51% lower in phl2 relative to the WT. If we arbitrarily defined a 30% reduction in the expression level of PSI genes as “a significant reduction”, the expression of 87.6% of PSI genes was significantly reduced in P- phl2 relative to P- WT seedlings. Thus, we conclude that PHL2 is a key component of the central regulatory system controlling transcriptional responses to Pi starvation.
2016-01-03 | GSE74972 | GEO
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.
2010-12-09 | GSE16722 | GEO
Project description:We first compared the transcriptomes of the roots of WT seedlings grown under P+ and P- conditions. Using a 2-fold change and a FDR (false discovery rate) of <0.05 as the cut-off for selecting the differentially expressed transcripts, we found that the expression of 581 genes was induced and that the expression of 120 genes was repressed by Pi starvation. We then compared the expression levels of these 581 PSI genes in the WT and phl2. The results showed that the average expression level of these genes was 51% lower in phl2 relative to the WT. If we arbitrarily defined a 30% reduction in the expression level of PSI genes as â??a significant reductionâ??, the expression of 87.6% of PSI genes was significantly reduced in P- phl2 relative to P- WT seedlings. Thus, we conclude that PHL2 is a key component of the central regulatory system controlling transcriptional responses to Pi starvation. We performed a RNA-seq analysis on WT and phl2 plants. Total RNAs were extracted from the roots of P+ and P- WT seedlings (i.e., seedling grown on P-sufficient and P-deficient media) and of P- phl2 seedlings. The extracted RNAs were subjected to RNA deep sequencing. Our RNA-seq analyses showed that among the 581 PSI genes, the expression of 87% is significantly reduced in phl2, demonstrating that PHL2 positively regulates the transcription of a large number of PSI genes at the genomic level
2016-07-05 | E-GEOD-74972 | biostudies-arrayexpress
Project description:<Background> The pstSCAB operon of Corynebacterium glutamicum, which encodes an ABC transport system for uptake of phosphate (Pi), is induced during the P i starvation response. The two-component regulatory system PhoRS is involved in this response, but partial Pi starvation induction of pstSCAB in a ∆phoRS mutant indicated the involvement of additional regulator(s). Regulation of pstSCAB also involves the global transcriptional regulator GlxR. <Results> DNA affinity chromatography identified the regulator of acetate metabolism RamB as a protein binding to pstS promoter DNA in vitro. Gel mobility shift assays and mutational analysis of the pstS promoter region revealed that RamB binds to two sites localized at positions -74 to -88 and -9 to +2 with respect to the transcriptional start site of pstSCAB. Reporter gene studies supported the in vivo relevance of both binding sites for activation of pstSCAB by RamB. DNA microarray analysis revealed that expression of many Pi starvation inducible genes reached higher levels during the Pi starvation response on minimal medium with glucose as sole carbon source than in Pi starved acetate-grown C. glutamicum cells. <Conclusions> In C. glutamicum, RamB is involved in expression control of pstSCAB operon. Thus, transcriptional regulation of pstSCAB is complex involving activation by the phosphate-responsive two-component regulatory system PhoSR and the regulators of carbon metabolism GlxR and RamB.
2015-03-19 | GSE67012 | GEO
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
Project description:Cells must appropriately sense and integrate multiple metabolic resources to commit to proliferation. Here, we report that cells regulate nitrogen (amino acid) and carbon metabolic homeostasis through tRNA U34-thiolation. Despite amino acid sufficiency, tRNA-thiolation deficient cells appear amino acid starved. In these cells, carbon flux towards nucleotide synthesis decreases, and trehalose synthesis increases, resulting in metabolic a starvation-signature. Thiolation mutants have only minor translation defects. However, these cells exhibit strongly decreased expression of phosphate homeostasis genes, mimicking a phosphate-limited state. Reduced phosphate enforces a metabolic switch, where glucose-6-phosphate is routed towards storage carbohydrates. Notably, trehalose synthesis, which releases phosphate and thereby restores phosphate availability, is central to this metabolic rewiring. Thus, cells use thiolated tRNAs to perceive amino acid sufficiency, and balance amino acid and carbon metabolic flux to maintain metabolic homeostasis, by controlling phosphate availability. These results further biochemical explain how phosphate availability determines a switch to a ‘starvation-state’.
2018-12-28 | GSE124428 | GEO
Project description:In E. coli the phosphate homeostasis is regulated by the Pst system and the two-component system PhoB/R. Pathogens like E. coli O157:H7 are responsible for many outbreaks and can be found and survive in poor inorganic phosphate (Pi) environments. To understand global EHEC O157:H7 EDL933 strain responses to Pi-starvation, we compared the transcriptomes of EDL933 the WT strain grown in MOPS Pi rich medium and that grown in MOPS Pi poor medium, using the Affymetrix GeneChip® E. coli Genome 2.0 Array. Also we investigated the EDL933 global response to the absence of PhoB by comparing the transcriptomes of the WT strain the ΔphoB mutant both grown in Low Pi
2014-03-15 | GSE50529 | GEO
Project description:This work reports on the identification and molecular characterization of a two-component regulatory system (2CRS), encoded by phoRP in Bifidobacterium breve UCC2003, which controls the response to phosphate (Pi) starvation. The response regulator PhoP was shown to bind to the promoter region of pstSCAB, specifying a predicted Pi transporter system, as well as that of phoU, which specifies a putative Pi-responsive regulatory protein. This interaction is assumed to cause transcriptional activation under conditions of Pi limitation. The phoRP genes appear to be subject to positive auto-regulation, and with pstSCAB and phoU, represent the complete regulon controlled by the phoRP-encoded 2CRS in B. breve UCC2003. Determination of the minimal PhoP binding region combined with bioinformatic analysis revealed the probable recognition sequence of PhoP, designated here as the PHO box, which together with phoRP is conserved among many high GC-content Gram+ bacteria. The importance of the phoRP 2CRS in the response of B. breve to Pi starvation conditions was confirmed by generating a B. breve::phoP insertion mutant which exhibited decreased growth under phosphate-limiting conditions as compared to its parent strain UCC2003. In order to investigate differences in global gene expression upon growth of B. breve UCC2003 under low phosphate conditions compared to normal growing cells, DNA microarray experiments were performed in CDM. Total RNA was isolated from B. breve UCC2003 cultures under normal conditions and cultures grown under low phosphate conditions. Starvation experiments with wildtype and overexpression strains were performed in triplicate, while knockout array experiments where performed as single experiments and targets were confirmed with QRT-PCR.
2012-09-06 | E-GEOD-34983 | biostudies-arrayexpress
Project description:The Chlamydomonas reinhardtii transcription factor PSR1 is required for the control of activities involved in scavenging phosphate from the environment during periods of phosphorus limitation. Increased scavenging activity reflects the development of high-affinity phosphate transport and the expression of extracellular phosphatases that can cleave phosphate from organic compounds in the environment. A comparison of gene expression patterns using microarray analyses and quantitative PCRs with wild-type and psr1 mutant cells deprived of phosphorus has revealed that PSR1 also controls genes encoding proteins with potential "electron valve" functions--these proteins can serve as alternative electron acceptors that help prevent photodamage caused by overexcitation of the photosynthetic electron transport system. In accordance with this finding, phosphorus-starved psr1 mutants die when subjected to elevated light intensities; at these intensities, the wild-type cells still exhibit rapid growth. Acclimation to phosphorus deprivation also involves a reduction in the levels of transcripts encoding proteins involved in photosynthesis and both cytoplasmic and chloroplast translation as well as an increase in the levels of transcripts encoding stress-associated chaperones and proteases. Surprisingly, phosphorus-deficient psr1 cells (but not wild-type cells) also display expression patterns associated with specific responses to sulfur deprivation, suggesting a hitherto unsuspected link between the signal transduction pathways involved in controlling phosphorus and sulfur starvation responses. Together, these results demonstrate that PSR1 is critical for the survival of cells under conditions of suboptimal phosphorus availability and that it plays a key role in controlling both scavenging responses and the ability of the cell to manage excess absorbed excitation energy. Set of arrays that are part of repeated experiments Biological Replicate Computed
2006-08-18 | E-GEOD-4568 | biostudies-arrayexpress
Project description:Depletion of essential nutrients triggers regulatory programs that prolong cell growth and survival. Starvation-induced processes increase nutrient transport, mobilize nutrient storage, and recycle nutrients between cellular components. This leads to an effective increase in intracellular nutrients, which may act as a negative feedback that down-regulates the starvation program. To examine how cells overcome this potential instability, we followed the transcription response of budding yeast transferred to medium lacking phosphate. Genes were induced in two temporal waves. The first wave was stably maintained and persisted even upon phosphate replenishment, indicating a positive feedback loop. This commitment was abolished after two hours with the induction of the second expression wave, coinciding with the reduction in cell growth rate. We identify genes that mediate this loss of commitment, and show that the overall temporal stability of the expression response depends on the sequential pattern of gene induction. Our results emphasize the key role of gene expression dynamics in optimizing cellular adaptation. pho90_OX cells were grown at high Phosphate medium, washed and transferred to no phosphate medium. Sample were taken every 15 minuets for 6 hours 25 samples were taken during the time course. Expression data was normalized to the first time point (cells grown at high phosphate medium)
2014-09-24 | E-GEOD-61665 | biostudies-arrayexpress