GEO DataSets

(Submitter supplied) HutC in Pseudomonas is a representative member of the HutC/GntR family of transcriptional regulators, which possess a N-terminal winged helix-turn-helix (wHTH) DNA-binding domain and a C-terminal substrate binding domain. HutC is generally known to represses expression of histidine utilization (hut) genes through binding to the PhutU promoter with urocanate (the first intermediate of the histidine degradation pathway) as the direct inducer. more...

Organism:

Pseudomonas fluorescens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28231

2 Samples

Download data: CSV

(Submitter supplied) Histidine is a good source of nutrient for many bacteria, but its utilization poses a significant challenge as it delivers excess nitrogen over carbon. The rate of histidine catabolism (hut) must thus be tightly regulated. Here, in Pseudomonas fluorescens SBW25, we show that the CbrAB two-component system directly activates the transcription of hut genes, while mediating succinate-induced carbon catabolite repression of hut at the translational level via the CbrAB-CrcYZ-Hfq/Crc regulatory cascade. more...

Organism:

Pseudomonas fluorescens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28231

2 Samples

Download data: CSV

(Submitter supplied) Pseudomonas species are ubiquitous in plant-associated environments and produce an array of volatiles, enzymes and antimicrobials. The biosynthesis of many metabolites is regulated by the GacS/GacA two-component regulatory system. Transcriptome analysis of Pseudomonas fluorescens SBW25 revealed that 702 genes were differentially regulated (fold change>4, P<0.0001) in a gacS::Tn5 mutant, with 300 and 402 genes up- and down-regulated, respectively. more...

Organism:

Pseudomonas [fluorescens] SBW25

Type:

Expression profiling by array

Platform:

GPL16495

8 Samples

Download data: TXT

(Submitter supplied) In this study wild-type, fur mutant, and complemented fur mutant strains of the human pathogen Neisseria gonorrhoeae F62 were grown under high (100 uM iron) or low (100 uM desferal) iron conditions to identify genes whose expression was regulated by iron and/or Fur

Organism:

Neisseria gonorrhoeae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20721

10 Samples

Download data: TXT

(Submitter supplied) The goal of this study was to evaluate the molecular mechanisms by which Brachypodium distachyon grown with and without Pseudomonas fluorescens (P. fluorescens) strain SBW25 respond to Fe deprivation. Fe deprivation induced Brachypodium secretion of phytosiderophores and reduced biomass production while inoculation with P. fluorescens resulted in alterations of extracellular metabolite abundances. Results provide insight into the role of iron in interactions between a host plant and root associated bacteria.

Organism:

Pseudomonas fluorescens; Brachypodium distachyon

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL29168 GPL29167

30 Samples

Download data: TXT

(Submitter supplied) Members of the genus Bifidobacterium are Gram-positive bacteria which are commonly found in the gastrointestinal tract (GIT) of mammals, including humans. Growth of bifidobacteria has been shown to be selectively stimulated by various carbohydrates found in the human diet. To extend our understanding of the regulation of bifidobacterial carbohydrate utilization systems, we investigated the regulation of two carbohydrate utilisation clusters dedicated to the metabolism of raffinose type sugars and melezitose. more...

Organism:

Bifidobacterium breve UCC2003

Type:

Expression profiling by array

Platform:

GPL8878

6 Samples

Download data: TXT

(Submitter supplied) Mature tRNA pools were measured using an adaptation of Y-shaped Adapter-ligated MAture tRNA sequencing (YAMAT-seq) (Shigematsu et al., 2017) in nine strains derived from the model bacterium, Pseudomonas fluorescens SBW25. The aim of the experiment was to determine the effect on the mature tRNA pool of (i) removing the single-copy serCGA gene by genetic engineering, and (ii) duplicating the serTGA gene during a subsequent, compensatory evolution experiment. more...

Organism:

Pseudomonas fluorescens

Type:

Other

Platform:

GPL28120

27 Samples

Download data: XLSX

(Submitter supplied) These transcriptomic data are used in two distinct but subsequent and complementary studies:(i) the role of the mfsR gene on the expression of the mfsABC operon as well as on its own promoter, (ii) the role of the mfsR operon on the activation of the core genes of ICEclc.

Organism:

Pseudomonas putida UWC1; Pseudomonas knackmussii

Type:

Expression profiling by array

Platform:

GPL10091

12 Samples

Download data: TXT

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

Organism:

Pseudomonas aeruginosa PAO1

Type:

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

Platform:

GPL23999

40 Samples

Download data

(Submitter supplied) Determination of the binding sites of 7 transcription factors (PA0535, PA1359, PA1884, PA2312, PA4499 (PsdR), PA4987 and PA5301 (PauR)) in Pseudomonas aeruginosa PAO1.

Organism:

Pseudomonas aeruginosa PAO1

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23999

24 Samples

Download data: XLSX

(Submitter supplied) Determination of the impact of the individual deletion of 7 transcription factors (PA0535, PA1359, PA1884, PA2312, PA4499 (PsdR), PA4987 and PA5301 (PauR)) in Pseudomonas aeruginosa PAO1.

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23999

16 Samples

Download data: XLSX

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

Organism:

Brevundimonas subvibrioides

Type:

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

Platforms:

GPL27605 GPL27606

15 Samples

Download data: BW

(Submitter supplied) Transcriptional rewiring is the regulation of different targets genes by orthologous regulators in different organisms. While this phenomenon has been observed, it has not been extensively studied, particularly in core regulatory systems. Several global cell cycle regulators are conserved in the Alphaproteobacteria, providing an excellent model to study this phenomenon. First characterized in Caulobacter crescentus, GcrA and CcrM compose a DNA methylation-based regulatory system that helps coordinate the complex life cycle of this organism. more...

Organism:

Brevundimonas subvibrioides

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27606

6 Samples

Download data: BED, BW, TXT

(Submitter supplied) Transcriptional rewiring is the regulation of different targets genes by orthologous regulators in different organisms. While this phenomenon has been observed, it has not been extensively studied, particularly in core regulatory systems. Several global cell cycle regulators are conserved in the Alphaproteobacteria, providing an excellent model to study this phenomenon. First characterized in Caulobacter crescentus, GcrA and CcrM compose a DNA methylation-based regulatory system that helps coordinate the complex life cycle of this organism. more...

Organism:

Brevundimonas subvibrioides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27605

9 Samples

Download data: TXT, XLSX

(Submitter supplied) Mature tRNA pools were measured using an adaptation of YAMAT-seq (Shigematsu et al., 2017; doi:10.1093/nar/gkx005 ) and further described in (Ayan et al., 2020; doi:10.7554/eLife.57947) in eight strains dervied from the model bacterium, Pseudomonas fluorescens SBW25. The aim of the experiment was to determine the effect on the mature tRNA pool of (i) removing multi-copy tRNA genes by genetic engineering, and (ii) duplicating tRNA genes during a subsequent, compensatory evolution experiment. more...

Organism:

Pseudomonas fluorescens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL28120

24 Samples

Download data: XLSX

(Submitter supplied) Accelerating the design of synthetic biological circuits for biosensing requires expanding the currently available genetic toolkit. Although whole-cell biosensors have been successfully engineered and deployed, particularly in applications such as environmental and medical diagnostics, novel sensing applications necessitate the discovery and optimization of novel biosensors. Here we develop a data-driven approach that combines dynamic mode decomposition and observability analysis to extract salient, endogenous genetic sensors for analytes of interest from dynamic gene expression profiles. more...

Organism:

Pseudomonas fluorescens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31044

40 Samples

Download data: JSON, TSV