GEO DataSets

(Submitter supplied) In this study we compare logarithmically grown Pseudomonas aeruginosa wildtype to a transposon mutant that is disrupted in gshA, which is involved in glutathione biosynthesis using RNASeq to identify novel pathways where glutathione may be involved.

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24583

6 Samples

Download data: TXT, XLSX

(Submitter supplied) The role of the intracellular signaling molecule diadenosine tetraphosphate (Ap4A) has not so far been investigated in Pseudomonas aeruginosa. To fill this gap, we performed RNA sequencing (RNA-seq) analysis to compare the transcriptome of the reference strain P. aeruginosa PAO1 and an isogenic deletion mutant (ΔapaH) which is deficient in the Ap4A hydrolysing enzyme ApaH and accumulates high intracellular levels of Ap4A.

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26913

6 Samples

Download data: TXT

(Submitter supplied) Detecting chemical signals is important for identifying food sources and avoiding harmful agents. Like many animals, C. elegans use olfaction to chemotax towards their main food source, bacteria. However, little is known about the bacterial compounds governing C. elegans attraction to bacteria and the physiological importance of these compounds to bacteria. Here, we address these questions by investigating the function of a small RNA, P11, in the pathogen, Pseudomonas aeruginosa, that was previously shown to mediate learned pathogen avoidance. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33271

9 Samples

Download data: XLSX

(Submitter supplied) We aimed to illuminate the effects on the transcriptome upon translation knockdown (KD) of core genes and other characterised genes or early expressed genes in PHIKZ through anti-sense-based technology. We identified phage transcripts that are affected in level upon KD and clustering allowed to group these together that likely are expressed at a similar stage and dependency in the phage replication cycle. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34599

126 Samples

Download data: CSV, FASTA, GFF3, WIG

(Submitter supplied) ChmA forms the phage nucleus in PhiKZ-infected PAO1 cells, we aimed to illuminate the effects on the transcriptome upon knockdown (KD) of ChmA translation through anti-sense-based technology. We identified phage transcripts that are affected in level upon KD of ChmA and clustering allowed to group these together that likely are expressed at a similar stage and dependency in the phage replication cycle.

Organism:

Pseudomonas aeruginosa; Pseudomonas phage phiKZ

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34574

20 Samples

Download data: CSV, FA, GFF3, WIG

(Submitter supplied) Clinical case studies have reported that the combined use of specific lytic phage(s) and antibiotics reduces the severity of difficult-to-treat Pseudomonas aeruginosa infections in many patients. In vitro methods that attempt to reproduce specific pathophysiological conditions can provide a reliable assessment of the antibacterial effects of phages. Here, we measured bacterial killing kinetics and individual phage replication in different growth phases, including biofilms, elucidating factors influencing the efficacy of two phages against the laboratory strain P. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34679

12 Samples

Download data: XLSX

(Submitter supplied) Pyruvate dehydrogenase (PDH) catalyses the irreversible decarboxylation of pyruvate to acetyl-CoA, which feeds the tricarboxylic acids cycle. We analysed how the lack of PDH affects Pseudomonas putida metabolism. Inactivating PDH generated a strain that can no longer use compounds whose assimilation converges into pyruvate, including sugars and several amino acids. Compounds generating acetyl-CoA supported growth. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18287

6 Samples

Download data: TXT

(Submitter supplied) It is becoming increasingly apparent that commensal skin bacteria have an important role in wound healing and infection progression. However, the precise mechanisms underpinning many of these probiotic interactions remain to be fully uncovered. In this work, we demonstrate that the common skin commensal Cutibacterium acnes can limit the pathogenicity of the prevalent wound pathogen Pseudomonas aeruginosa in vivo. more...

Organism:

Pseudomonas aeruginosa PA14

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33546

6 Samples

Download data: TSV

(Submitter supplied) Although RNA structures play important roles in regulating gene expression, the mechanism and function of mRNA folding in plant bacterial pathogens remain elusive. Therefore, we perform dimethyl sulfate sequencing (DMS-seq) on the Pseudomonas syringae under nutrition-rich and deficient conditions, revealing that the mRNA structure changes substantially in the minimal medium (MM) that tunes global translation efficiency (TE), thereby inducing virulence. more...

Organism:

Pseudomonas savastanoi pv. phaseolicola 1448A

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24018

28 Samples

Download data: BED, TXT

(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) The model Gram-negative plant pathogen Pseudomonas syringae utilizes hundreds of transcription factors (TFs) to manipulate its functional processes, including virulence and metabolic pathways to control its infection to host plants. Although the molecular mechanisms of regulators have been studied for decades, the comprehensive understanding throughout the genome-wide TFs in P. syringae remains uncertain. more...

Organism:

Pseudomonas syringae pv. actinidiae str. Shaanxi_M228; Pseudomonas syringae pv. syringae B728a; Pseudomonas syringae pv. tomato str. DC3000; Pseudomonas savastanoi pv. phaseolicola 1448A

Type:

Genome binding/occupancy profiling by high throughput sequencing

4 related Platforms

396 Samples

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(Submitter supplied) RNA helicases—central enzymes in RNA metabolism— often feature intrinsically disordered regions (IDRs) that enable phase separation and complex interactions with other proteins and/or RNA molecules. IDRs are varied and fast evolving, which makes their function hard to predict. In the bacterial pathogen Pseudomonas aeruginosa, two non-redundant RNA helicases, RhlE1 and RhlE2, share a conserved REC catalytic core but have different C-terminal extensions (CTEs) composed of IDRs of diverse length and amino acid composition. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26913

36 Samples

Download data: XLSX

(Submitter supplied) Pseudomonas aeruginosa (PA) is an opportunistic pathogen frequently isolated from cutaneous chronic wounds. How PA, in the presence of oxidative stress (OS), colonizes chronic wounds and forms a biofilm is still unknown. The purpose of this study is to investigate the changes in gene expression seen when PA is challenged with the high levels of OS present in chronic wounds. We used a biofilm-forming PA strain isolated from the chronic wounds of our murine model (RPA) and performed a qPCR to obtain gene expression patterns as RPA developed a biofilm in vitro in the presence of high levels of OS, and then compared the findings in vivo, in our mouse model of chronic wounds. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33271

18 Samples

Download data: TXT

(Submitter supplied) Purpose: The purpose of this study was to investigate the effect of quorum sensing on phage infection. Methods: We constructed the lasR gene knockout strain of Pseudomonas aeruginosa PAO1 and performed transcriptome sequencing.

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18644

6 Samples

Download data: TSV, TXT

(Submitter supplied) Pseudomonas syringae pv. syringae 9644 (Pss9644) is a causal agent of bacterial cherry canker causing necrotic symptoms on leaves, fruits, gummosis and canker in woody tissues of sweet cherry (Prunus avium). To understand which virulent factor genes were expressed in vitro, Pss9644 was grown in rich media (King's B Broth) and minimum media (hrp-inducing minimum media). The latter mimics the in planta environment.

Organism:

Pseudomonas syringae pv. syringae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34164

6 Samples

Download data: TXT

(Submitter supplied) Methylrhodomelol (1) is a bromophenol from the red alga Vertebrata lanosa (L.) T.A.Christensen that has been associated with antimicrobial properties. Aim of the current study was therefore, to assess the antimicrobial potential of this compound in more detail against the gram-negative pathogen Pseudomonas aeruginosa. 1 exerted weak bacteriostatic activity against different strains when grown in minimal medium, whereas other phenolics were inactive. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33271

6 Samples

Download data: TXT

(Submitter supplied) RNA modifications have a substantial impact on tRNA function. While modifications in the anticodon loop play an important role in translational fidelity, modifications in the tRNA core influence tRNA structural stability. In bacteria, tRNA modifications play important roles in the stress response and expression of virulence factors. While tRNA modifications are well characterized in a few model organisms, our knowledge of tRNA modifications in human pathogens, such as Pseudomonas aeruginosa is lacking. more...

Organism:

Pseudomonas aeruginosa PA14; Escherichia coli BW25113

Type:

Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL25344 GPL33546 GPL30881

27 Samples

Download data: CSV, FA, 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) Efflux pumps of the resistance-nodulation-division (RND) superfamily, particularly the AcrAB-TolC and MexAB-OprM, besides mediating intrinsic and acquired resistance, also intervene in bacterial pathogenicity. Inhibitors of such pumps could restore activities of antibiotics and curb bacterial virulence. Here, we identify pyrrole-based compounds that boost antibiotic activity in Escherichia coli and Pseudomonas aeruginosa by inhibiting their archetype RND transporters. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26913

6 Samples

Download data: XLSX

(Submitter supplied) The opportunistic pathogen Pseudomonas aeruginosa has complex quorum sensing (QS) circuitry, which involves two acylhomoserine lactone (AHL) systems, the LasI AHL synthase and LasR AHL-dependent transcriptional activator system and the RhlI AHL synthase-RhlR AHL-responsive transcriptional activator. There is also a quinoline signaling system (the Pseudomonas quinolone signal, PQS, system). Although there is a core set of genes regulated by the AHL circuits, there is substantial strain-to-strain variation in the non-core QS regulated genes. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24583

16 Samples

Download data: CSV, TXT