GEO DataSets

(Submitter supplied) In bacteria, the availability of environmental inorganic phosphate is typically sensed by the conserved PhoRB two-component signaling pathway, which uses the flux through the Pst phosphate trans­porter as a readout of the extracellular phosphate level to control a variety of phosphate-responsive genes. While the sensing of environmental phosphate is well-established, the regulatory effects of cyto­plas­mic phos­phate are still unclear. more...

Organism:

Caulobacter vibrioides NA1000

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26188

12 Samples

Download data: TXT

(Submitter supplied) We sought to define the transcriptional regulon of the ChvI response regulator in Caulobacter crescentus. This study compares gene expression between ∆chvI cells and cells overexpressing the constitutively-active chvI(D52E) mutant. Our work provides a global view of the genes directly and indirectly regulated by the ChvGI two-component system in C. crescentus.

Organism:

Caulobacter vibrioides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24555

12 Samples

Download data: TXT

(Submitter supplied) Intracellular zinc concentration needs to be maintained within strict limits due to its toxicity at high levels, and this is achieved by a finely regulated balance between uptake and efflux. Many bacteria use the Zinc Uptake Regulator Zur to orchestrate zinc homeostasis, but little is known regarding the transport of this metal across the bacterial outer membrane. In this work we determined the C. crescentus Zur regulon by global transcriptional and in silico analyses. more...

Organism:

Caulobacter vibrioides CB15; Caulobacter vibrioides NA1000

Type:

Expression profiling by array

Platform:

GPL10469

3 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Bifidobacterium breve UCC2003

Type:

Expression profiling by array

Platform:

GPL8878

12 Samples

Download data: TXT

(Submitter supplied) Potassium (K+) is an essential physiological element determining membrane potential, intracellular pH, osmotic/turgor pressure, and protein synthesis in cells. Nevertheless, K+ homeostasis remains poorly studied in bacteria. Here we describe the regulation of potassium uptake systems in the oligotrophic -proteobacterium Caulobacter crescentus known as a model for asymmetric cell division. We show that C. more...

Organism:

Caulobacter vibrioides

Type:

Other

Platform:

GPL24555

4 Samples

Download data: XLSX

(Submitter supplied) Potassium (K+) is an essential physiological element determining membrane potential, intracellular pH, osmotic/turgor pressure, and protein synthesis in cells. Nevertheless, K+ homeostasis remains poorly studied in bacteria. Here we describe the regulation of potassium uptake systems in the oligotrophic -proteobacterium Caulobacter crescentus known as a model for asymmetric cell division. We show that C. more...

Organism:

Caulobacter vibrioides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32153

6 Samples

Download data: XLSX

(Submitter supplied) Potassium (K+) is an essential physiological element determining membrane potential, intracellular pH, osmotic/turgor pressure, and protein synthesis in cells. Here we describe the regulation of potassium uptake systems in the oligotrophic alpha-proteobacterium Caulobacter crescentus known as a model for asymmetric cell division. We show that C. crescentus can grow in concentrations from the micromolar to the millimolar range by mainly using two K+ transporters to maintain potassium homeostasis, the low affinity Kup and the high affinity Kdp uptake systems. more...

Organism:

Caulobacter vibrioides

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL32154

6 Samples

Download data: XLSX

(Submitter supplied) The alpha-proteobacterium Caulobacter crescentus thrives in oligotrophic environments and is able to optimally exploit minimal resources by entertaining an intricate network of gene expression control mechanisms. Numerous transcriptional activators and repressors have been reported to contribute to these processes, but only few studies have focused on regulation at the post-transcriptional level in C. more...

Organism:

Caulobacter vibrioides

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24555

2 Samples

Download data: XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Caulobacter vibrioides

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21016 GPL28356

10 Samples

Download data

(Submitter supplied) In this study we determined the target spectrum of C. crescentus sRNA R0199 via pulse-expression followed by RNA-sequencing.

Organism:

Caulobacter vibrioides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28356

6 Samples

Download data: XLSX

(Submitter supplied) In this study we used RNA co-immunoprecipitation followed by RNA-sequencing to identify Hfq-binding RNAs in C. crescentus.

Organism:

Caulobacter vibrioides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21016

4 Samples

Download data: XLSX

(Submitter supplied) In the alpha subclass of proteobacteria iron homeostasis is controlled by diverse iron responsive regulators. Caulobacter crescentus, an important freshwater α-proteobacterium, uses the ferric uptake repressor (Fur) for such purpose. However, the impact of the iron availability on the C. crescentus transcriptome and an overall perspective of the regulatory networks involved remain unknown. In this work we report the identification of iron-responsive and Fur-regulated genes in C. more...

Organism:

Caulobacter vibrioides NA1000; Caulobacter vibrioides CB15

Type:

Expression profiling by array

Platform:

GPL10469

4 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Escherichia coli; Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL10416 GPL3154

7 Samples

Download data: CEL, PAIR

(Submitter supplied) 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. more...

Organism:

Escherichia coli; Escherichia coli str. K-12 substr. MG1655

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10416

3 Samples

Download data: PAIR

(Submitter supplied) 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. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

4 Samples

Download data: CEL

(Submitter supplied) We report gene expression responses of Caulobacter crescentus to osmotic upshock (150 mM sucrose). The goal of this study is compare the transcriptional responses of wild type, sigT deletion, and gsrN overexpression (gsrN++) strains. The data provide a high resolution view of how two major regulators of the general stress response (sigT and gsrN) shape transcription upon shift to a hyperosmotic environment.

Organism:

Caulobacter vibrioides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21015

31 Samples

Download data: TXT

(Submitter supplied) phyR encodes a general stress regulator protein that is conserved among several alpha-proteobacteria. This experiment is quantifying transcription in two Caulobacter strains: one strain is overexpressing phyR (gene CC3477); the other carries a phyR in-frame deletion. Both strains were cultured in M2 defined medium with xylose as the sole carbon source. The first strain (FC626) carries a plasmid integrated into the xylX locus; phyR is fused to the xylX promoter in this plasmid, generating a xylose-inducible phyR overexpression strain. more...

Organism:

Caulobacter vibrioides

Type:

Expression profiling by array

Platform:

GPL10149

4 Samples

Download data: CEL

(Submitter supplied) This experiment is testing the effects of coordinate overexpression of the lovK-lovR two-component system on gene expression in Caulobacter crescentus relative to an empty vector control strain.

Organism:

Caulobacter vibrioides

Type:

Expression profiling by array

Platform:

GPL10149

4 Samples

Download data: CEL

(Submitter supplied) The purpose of this experiment was to examine the differential transcriptional profiles of Caulobacter CB15N grown in M2-Glucose versus M2-Inositol.

Organism:

Caulobacter vibrioides

Type:

Expression profiling by array

Platform:

GPL2749

2 Samples

Download data

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Caulobacter vibrioides; Caulobacter vibrioides NA1000

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL22063 GPL22472

7 Samples

Download data: WIG