GEO DataSets

(Submitter supplied) The aniline-degrading strain T1 can efficiently degrade aniline, however, it is not clear which key genes are associated with aniline degradation, and we have adopted a genome-wide and transcriptomic approach to fully understand the microbial degradation mechanism of aniline.

Organism:

Pseudomonas veronii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34605

6 Samples

Download data: TXT

(Submitter supplied) Identify genes involved in catabolism of the compound Methyl 3-(4-hydroxyphenyl)propionate

Organism:

Pseudomonas fluorescens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33279

8 Samples

Download data: CSV

(Submitter supplied) transcriptomics was used to explore the regulation mechanism of QS in dual-species spoilage at mRNA molecular level.

Organism:

Hafnia alvei; Pseudomonas fluorescens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33855

6 Samples

Download data: TXT

(Submitter supplied) The survival of a population during environmental shifts depends on whether the rate of phenotypic adaptation keeps up with the rate of changing conditions. A common way to achieve this is via change to gene regulatory network (GRN) connections – known as rewiring – that facilitate novel interactions and innovation of transcription factors. To understand the success of rapidly adapting organisms, we therefore need to determine the rules that create and constrain opportunities for GRN rewiring. more...

Organism:

Pseudomonas fluorescens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29078

15 Samples

Download data: CSV, TXT

(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) Members of the bacterial genus Pseudomonas form associations with diverse hosts. Comparative transcriptomics revealed that the ColR regulon has diverged between P. aeruginosa and P. fluorescens and deleting components of the ColR regulon revealed strain-specific, but not host-specific, requirements for ColR-dependent genes.

Organism:

Pseudomonas aeruginosa; Pseudomonas fluorescens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21297 GPL31044

24 Samples

Download data: TXT

(Submitter supplied) Purpose: Generalist protozoan predators change the pace of evolution in microbial communities, but investigations into the molecular consequences of predation for the genomic evolution of defence or coadaptation are scarce. We have previously performed a 90-day co-evolution experiment to address these effects using the bacterium Pseudomonas fluorescens SBW25 on solid media in the presence and absence of a wild Acanthamoeba sp. more...

Organism:

Acanthamoeba sp.; Pseudomonas fluorescens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL32161 GPL28120

24 Samples

Download data: TXT

(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

(Submitter supplied) Purpose: Protozoan predators affect the structure of bacterial communities, but investigations into how predation influences bacterial evolution and antagonistic behaviours are scarce. We performed a 20-day predator-prey evolution experiment on solid media to investigate the adaptive traits that arise in bacterial prey under continuous protozoan predation. Methods: Pseudomonas fluorescens SBW25 and a wild Acanthamoeba sp. more...

Organism:

Acanthamoeba sp.; Pseudomonas fluorescens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL32161 GPL28120

24 Samples

Download data: TXT

(Submitter supplied) InvF, an AraC-type transcriptional activator, regulated the expression of genes that encoded the secreted effector molecules SipABCD, SigD, SptP, and SopE in Salmonella typhimurium. However, it seems that almost all effector homologs were lost in P. fluorescens 2P24. To identify the InvF regulon in strain 2P24, the invF deficient mutant 2P24ΔinvF was constructed, and we implemented transcriptome sequencing (RNA-seq). more...

Organism:

Pseudomonas fluorescens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30468

12 Samples

Download data: TXT

(Submitter supplied) Aim: to identify the transcriptional responses to acquisition of conjugative megaplasmids by Pseudomonas fluorescens, and how these effects are impacted by known compensatory mutations. Full abstract TBC.

Organism:

Pseudomonas [fluorescens] SBW25

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28611

30 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) 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) We identified binding sites genome-wide for carbon metabolism transcriptional response regulators in Pseudomonas stutzeri RCH2, Pseudomonas putida KT2240, Pseudomonas fluorescens FW300-N2E2 and FW300-N2C3 by DNA-affinity-purified (DAP) sequencing.

Organism:

Pseudomonas fluorescens; Pseudomonas putida; Stutzerimonas stutzeri

Type:

Other

Platforms:

GPL29080 GPL29079 GPL29078

96 Samples

Download data: WIG

(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) 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) We report RNA-seq data for four Pseudomonas fluorescens SBW25 types: SBW25 (wild type) and dervied types 6A4, 6B4-Cap- and 6B4-Cap+. The aim of the study is to see the effect of a mutation in rpoD (carried by 6B4) on the transcriptome.

Organism:

Pseudomonas [fluorescens] SBW25

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25322

12 Samples

Download data: TXT

(Submitter supplied) To determine whether PT modifications are involved in the epigenetic control of specific genes, RNA-seq analysis was conducted to define global transcriptional changes in early log-phase cultures of wild-type pf0-1 and the PT modifacation related genes(dndBCDE) deletion mutant TT-5. Compared with wild-type pf0-1, a total of ten genes in TT-5 exhibited differential expression of greater than 2-fold (log2-ratio>1 or <-1, p-value<0.05, FDR≤0.001), including 6 up-regulated genes and 4 down-regulated genes (Table 1). more...

Organism:

Pseudomonas fluorescens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24598

2 Samples

Download data: XLS

(Submitter supplied) An incompatibility P-7 plasmid pCAR1 can be efficiently transferred among artificial microcosms in the presence of divalent cations Ca2+ and Mg2+. One on one mating assays between Pseudomonas strains with different plasmids showed that the promotion of transfer efficiency by divalent cations was also found in other plasmids including pB10 and NAH7, whereas the impacts were larger in IncP-7 plasmids. more...

Organism:

Pseudomonas; Pseudomonas fluorescens Pf0-1; Pseudomonas putida KT2440

Type:

Expression profiling by genome tiling array

Platforms:

GPL8298 GPL8296 GPL6591

24 Samples

Download data: BAR, CEL

(Submitter supplied) We study the transcriptional reactions of bacteria interesting for biodegradation under laboratory conditions that mimic water stress. We compared the transcriptomes of cultures growing exponential phase under optimal conditions versus their responses to an osmotic shock of 30 min in exponential phase. The osmotic shock consisted in a reduction of water potential induced by salt (NaCl, solute stress) or by polyethylene glycol (PEG8000, matric stress). more...

Organism:

Pseudomonas veronii 1YdBTEX2

Type:

Expression profiling by array

Platform:

GPL20216

12 Samples

Download data: TXT