GEO DataSets

(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) RNA-based regulation of gene expression is substantially contributing to the ability of bacteria to rapidly adapt to changing environmental conditions. This study employs RNAseq to define the transcriptome of Caulobacter in response to treatment with the DNA-crosslinking agent mitomycin C. We identify a small, regulatory RNA ChvR synthesized under the control of the conserved ChvIG two-component system which represses production of a TonB-dependent receptor, ChvT, in Caulobacter crescentus. more...

Organism:

Caulobacter vibrioides NA1000

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21317

6 Samples

Download data: WIG

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

Organism:

Caulobacter vibrioides NA1000

Type:

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

Platform:

GPL33463

16 Samples

Download data

(Submitter supplied) Caulobacter species are dimorphic Gram-negative bacteria that inhabit diverse terrestrial and aquatic ecosystems. A suite of molecular sensory systems enables these microbes to control growth, development, and reproduction in response to levels of essential elements, including carbon, nitrogen, and phosphorus. Although the enhancer binding protein NtrC and its cognate sensor histidine kinase NtrB are well-established regulators of bacterial nitrogen assimilation, their precise functions in Caulobacter metabolism and cell development remained largely undefined. more...

Organism:

Caulobacter vibrioides NA1000

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL33463

2 Samples

Download data: BIGWIG

(Submitter supplied) Caulobacter species are dimorphic Gram-negative bacteria that inhabit diverse terrestrial and aquatic ecosystems. A suite of molecular sensory systems enables these microbes to control growth, development, and reproduction in response to levels of essential elements, including carbon, nitrogen, and phosphorus. Although the enhancer binding protein NtrC and its cognate sensor histidine kinase NtrB are well-established regulators of bacterial nitrogen assimilation, their precise functions in Caulobacter metabolism and cell development remained largely undefined. more...

Organism:

Caulobacter vibrioides NA1000

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33463

14 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) To investigate the R. sphaeroides NtrYX two component system on RNA transcript levels, we used global RNA sequencing (RNA-seq) to compare transcript abundance in parent and DntrYX strains grown under aerobic conditions. Our previous studies were performed in strains deficient at synthesizing the polyhydroxybutyrate, so we used strains D0382 and DNtrYXD0382, herein referred to as parent and DntrYX, respectively. more...

Organism:

Cereibacter sphaeroides 2.4.1

Type:

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

Platforms:

GPL18842 GPL28141

11 Samples

Download data: WIG, XLSX

(Submitter supplied) Cell fate determination in the asymmetric bacterium Caulobacter crescentus (Caulobacter) is triggered by the localization of the developmental regulator SpmX to the old (stalked) cell pole during the G1-S transition. While SpmX is required to localize and activate the cell fate-determining kinase DivJ at the stalked pole in Caulobacter, it is also required for organelle (stalk) positioning in the cousin Asticaccaulis. more...

Organism:

Caulobacter vibrioides NA1000

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21317

5 Samples

Download data: XLSX

(Submitter supplied) Performed RNASeq analysis comparing A. tumefaciens C58 (fabrum) harboring a plasmid driving ectopic expression of mirA regulator gene (ATU_RS08050) from Plac promoter with the isogenic strain haboring the same plasmid with no mirA (Vector control)

Organism:

Agrobacterium fabrum str. C58

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30075

6 Samples

Download data: TXT

(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) The extracytoplasmic function sigma factor σT is the master regulator of general stress response in Caulobacter crescentus, and controls the expression of its paralogue σU. This work showed that PhyR and NepR act as positive and negative regulators, respectively, of σT expression and function. Biochemical data also indicated that NepR directly binds σT and the phosphorylated form of PhyR. We also demonstrated the essential role of the histidine kinase gene CC3474, here denominated phyK, for expression of σT-dependent genes and for resistance to stress conditions. more...

Organism:

Caulobacter vibrioides NA1000; Caulobacter vibrioides CB15

Type:

Expression profiling by array

Platform:

GPL10469

15 Samples

Download data: TXT

(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) 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) 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