An intracellular phosphorus-starvation signal activates the PhoB/PhoR two-component system in Salmonella enterica
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ABSTRACT:
PROVIDER: PRJNA946702 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23919100.fastq.gz | Fastqsanger.gz | |||
| SRR23919101.fastq.gz | Fastqsanger.gz | |||
| SRR23919102.fastq.gz | Fastqsanger.gz | |||
| SRR23919103.fastq.gz | Fastqsanger.gz | |||
| SRR23919104.fastq.gz | Fastqsanger.gz |
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Project description:Bacteria acquire P primarily as inorganic orthophosphate (Pi, PO43-). Once internalized, Pi is rapidly assimilated into biomass during the synthesis of ATP. Because Pi is essential, but excessive ATP is toxic, the acquisition of environmental Pi is tightly regulated. In the bacterium Salmonella enterica (Salmonella), growth in Pi-limiting environments activates the membrane sensor histidine kinase PhoR, leading to the phosphorylation of its cognate transcriptional regulator PhoB and subsequent transcription of genes involved in adaptations to low Pi. Pi limitation is thought to promote PhoR kinase activity by altering the conformation of a membrane signaling complex comprised by PhoR, the multicomponent Pi transporter system PstSACB and the regulatory protein PhoU. The identity of the low Pi signal and how it controls PhoR activity remain unknown. Here we characterize the PhoB-dependent and independent transcriptional changes elicited by Salmonella in response to P starvation, and identify PhoB-independent genes that are required for the utilization of several organic-P sources. We use this knowledge to identify the cellular compartment where the PhoR signaling complex senses the low Pi signal. We demonstrate that the PhoB and PhoR signal transduction proteins can be maintained in an inactive state even when Salmonella is grown in media lacking Pi. Our results establish that PhoR activity is controlled by by an intracellular signal resulting from P insufficiency.
2023-08-07 | GSE227715 | GEO
Project description:Bacteria acquire P primarily as inorganic orthophosphate (Pi, PO43-). Once internalized, Pi is rapidly assimilated into biomass during the synthesis of ATP. Because Pi is essential, but excessive ATP is toxic, the acquisition of environmental Pi is tightly regulated. In the bacterium Salmonella enterica (Salmonella), growth in Pi-limiting environments activates the membrane sensor histidine kinase PhoR, leading to the phosphorylation of its cognate transcriptional regulator PhoB and subsequent transcription of genes involved in adaptations to low Pi. Pi limitation is thought to promote PhoR kinase activity by altering the conformation of a membrane signaling complex comprised by PhoR, the multicomponent Pi transporter system PstSACB and the regulatory protein PhoU. However, the identity of the low Pi signal and how it controls PhoR activity remain unknown. Here we characterize the PhoB-dependent and independent transcriptional changes elicited by Salmonella in response to P starvation, and identify PhoB-independent genes that are required for the utilization of several organic-P sources. We use this knowledge to identify the cellular compartment where the PhoR signaling complex senses the Pi-limiting signal. We demonstrate that the PhoB and PhoR signal transduction proteins can be maintained in an inactive state even when Salmonella is grown in media lacking Pi. Our results establish that PhoR activity is controlled by an intracellular signal resulting from P insufficiency.
| S-EPMC10055408 | biostudies-literature
Project description:An ability to sense and respond to changes in extracellular phosphate is critical to the survival of most bacteria. For Caulobacter crescentus, which typically lives in phosphate-limited environments, this process is especially crucial. Like many bacteria, Caulobacter responds to phosphate limitation through a conserved two-component signaling pathway called PhoR-PhoB, but the direct regulon of PhoB in this organism is unknown. Here, we use ChIP-Seq to map the global binding patterns of the phosphate-responsive transcriptional regulator PhoB in both phosphate-limited and -replete conditions. Combined with genome-wide expression profiling, our work demonstrates that PhoB is induced to regulate nearly 50 genes in phosphate-starved conditions. The PhoB regulon is comprised primarily of genes known or predicted to help Caulobacter scavenge for and import inorganic phosphate, including 15 different membrane transporters. We also investigated the regulatory role of PhoU, a widely conserved protein proposed to coordinate phosphate import with expression of the PhoB regulon by directly modulating the histidine kinase PhoR. However, our studies show that it likely does not play such a role in Caulobacter as depleting PhoU has no significant effect on PhoB-dependent gene expression. Instead, cells lacking PhoU exhibit a striking accumulation of large polyphosphate granules suggesting that PhoU participates in controlling intracellular phosphate metabolism.
2016-08-06 | GSE71857 | GEO
Project description:An ability to sense and respond to changes in extracellular phosphate is critical to the survival of most bacteria. For Caulobacter crescentus, which typically lives in phosphate-limited environments, this process is especially crucial. Like many bacteria, Caulobacter responds to phosphate limitation through a conserved two-component signaling pathway called PhoR-PhoB, but the direct regulon of PhoB in this organism is unknown. Here, we use ChIP-Seq to map the global binding patterns of the phosphate-responsive transcriptional regulator PhoB in both phosphate-limited and -replete conditions. Combined with genome-wide expression profiling, our work demonstrates that PhoB is induced to regulate nearly 50 genes in phosphate-starved conditions. The PhoB regulon is comprised primarily of genes known or predicted to help Caulobacter scavenge for and import inorganic phosphate, including 15 different membrane transporters. We also investigated the regulatory role of PhoU, a widely conserved protein proposed to coordinate phosphate import with expression of the PhoB regulon by directly modulating the histidine kinase PhoR. However, our studies show that it likely does not play such a role in Caulobacter as depleting PhoU has no significant effect on PhoB-dependent gene expression. Instead, cells lacking PhoU exhibit a striking accumulation of large polyphosphate granules suggesting that PhoU participates in controlling intracellular phosphate metabolism.
2016-08-06 | GSE71860 | GEO
Project description:An ability to sense and respond to changes in extracellular phosphate is critical to the survival of most bacteria. For Caulobacter crescentus, which typically lives in phosphate-limited environments, this process is especially crucial. Like many bacteria, Caulobacter responds to phosphate limitation through a conserved two-component signaling pathway called PhoR-PhoB, but the direct regulon of PhoB in this organism is unknown. Here, we use ChIP-Seq to map the global binding patterns of the phosphate-responsive transcriptional regulator PhoB in both phosphate-limited and -replete conditions. Combined with genome-wide expression profiling, our work demonstrates that PhoB is induced to regulate nearly 50 genes in phosphate-starved conditions. The PhoB regulon is comprised primarily of genes known or predicted to help Caulobacter scavenge for and import inorganic phosphate, including 15 different membrane transporters. We also investigated the regulatory role of PhoU, a widely conserved protein proposed to coordinate phosphate import with expression of the PhoB regulon by directly modulating the histidine kinase PhoR. However, our studies show that it likely does not play such a role in Caulobacter as depleting PhoU has no significant effect on PhoB-dependent gene expression. Instead, cells lacking PhoU exhibit a striking accumulation of large polyphosphate granules suggesting that PhoU participates in controlling intracellular phosphate metabolism. An allele of phoB bearing a C-terminal 3x-flag tag was integrated at its native locus, and ChIP followed by deep sequencing on Illumina MiSeq was performed on samples grown in rich medium, phosphate-limited medium, and in a pstS::Tn5 mutant background in rich medium.
2016-08-06 | E-GEOD-71860 | biostudies-arrayexpress
Project description:An ability to sense and respond to changes in extracellular phosphate is critical to the survival of most bacteria. For Caulobacter crescentus, which typically lives in phosphate-limited environments, this process is especially crucial. Like many bacteria, Caulobacter responds to phosphate limitation through a conserved two-component signaling pathway called PhoR-PhoB, but the direct regulon of PhoB in this organism is unknown. Here, we use ChIP-Seq to map the global binding patterns of the phosphate-responsive transcriptional regulator PhoB in both phosphate-limited and -replete conditions. Combined with genome-wide expression profiling, our work demonstrates that PhoB is induced to regulate nearly 50 genes in phosphate-starved conditions. The PhoB regulon is comprised primarily of genes known or predicted to help Caulobacter scavenge for and import inorganic phosphate, including 15 different membrane transporters. We also investigated the regulatory role of PhoU, a widely conserved protein proposed to coordinate phosphate import with expression of the PhoB regulon by directly modulating the histidine kinase PhoR. However, our studies show that it likely does not play such a role in Caulobacter as depleting PhoU has no significant effect on PhoB-dependent gene expression. Instead, cells lacking PhoU exhibit a striking accumulation of large polyphosphate granules suggesting that PhoU participates in controlling intracellular phosphate metabolism. RNA was collected from cultures grown to mid-exponential phase in rich medium (PYE) at 30 degrees C. The strain grown in the presence of 50 mM vanillate was compared to the same strain grown in the absence of vanillate.
2016-08-06 | E-GEOD-71857 | biostudies-arrayexpress
Project description:Iron (Fe) and phosphorus (P) are essential nutrients with close geochemical association. They exist at low concentrations in surface waters and may be co-limiting resources for phytoplankton growth. However, the adaptive strategies of photosynthetic organisms to Fe/P co-limitation remain largely unknown. Here, we show that phosphorus deficiency increases the growth of Fe-limited cyanobacteria through a PhoB-mediated regulatory network. In addition to its well-recognized role in controlling phosphate homeostasis, PhoB regulates key metabolic processes crucial for Fe-limited cyanobacteria, including ROS detoxification and Fe uptake. Transcript abundances of PhoB-targeted genes are enriched in samples from the P-deplete ocean, and a conserved PhoB binding site is widely present in the promoters of the targets, suggesting that the strategy we discovered may be highly conserved. Our findings provide important molecular insights into the response of cyanobacteria to simultaneous Fe/P nutrient limitation and help in understanding how nutrient availability affects primary productivity in aquatic environments.
2024-03-06 | GSE260812 | GEO
Project description:The purpose of the present study is to determine the effect of Phosphorus deficiency on gene expression level using microarray analysis to identify genes responsible for root hair development. Phosphorus deficiency induced the formation of root hairs to explore a greater soil volume but molecular mechanisms were unknown. Therefore, microarray experiments were performed using root tips of Brassica carinata cultivars Bale and Bacho, respectively differing in root hair length during Phosphorus deficiency. Experimental design was carried out in nutrient solution in a climate chamber with controlled environmental conditions (20°C, 16h day/8h night cycle, 70% relative humidity) in a randomized design. 25 root tips from 10 day old seedlings grown without Phosphorus of 1cm length were harvested and immediately frozen in liquid nitrogen. Gene expression analyses were performed
2010-07-29 | GSE22677 | GEO
Project description:The purpose of the present study is to determine the effect of Phosphorus deficiency on gene expression level using microarray analysis to identify genes responsible for root hair development. Phosphorus deficiency induced the formation of root hairs to explore a greater soil volume but molecular mechanisms were unknown. Therefore, microarray experiments were performed using root tips of Brassica carinata cultivars Bale and Bacho, respectively differing in root hair length during Phosphorus deficiency. Experimental design was carried out in nutrient solution in a climate chamber with controlled environmental conditions (20°C, 16h day/8h night cycle, 70% relative humidity) in a randomized design. 25 root tips from 10 day old seedlings grown without Phosphorus of 1cm length were harvested and immediately frozen in liquid nitrogen. Gene expression analyses were performed Results from xy microarrays are summarized in this study. The samples originate from roots of cultivars Bale and Bacho grown in Phosphorus deficient conditions. Microarrays were hybridized with Cy3 and Cy5 labeled cDNA from Bale and Bacho both during Phosphorus deficiency using a dye swap approach
2010-07-29 | E-GEOD-22677 | biostudies-arrayexpress
Project description:Chromatin immunoprecipitation was combined with high-density tiling array (ChIP-chip) and gene expression microarray to reveal the adaptive responses of Escherichia coli to phosphate starvation. The first sketch of the genome-wide distribution of PhoB binding profile was unveiled and 43 regions were identified as the PhoB binding regions. The presence of a significant common motif in these binding regions allowed us to reconstruct the PhoB binding pattern. By comparing the ChIP-chip and microarray datasets, we were also able to identify genes directly or indirectly affected through PhoB regulation. Nineteen out of the 287 differentially expressed genes in the presence and absence of PhoB activity were considered as the genes directly regulated by PhoB. The adaptive responses affected through PhoB regulation are discussed and these responses involve in several important biological functions including transcriptional regulation, transportation, membrane component arrangement, sigma factor modulation and DNA replication inhibition.
2012-10-21 | GSE21856 | GEO