Environment-driven changes of mRNA and protein levels in Pseudomonas aeruginosa
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PROVIDER: PRJNA478032 | ENA |
REPOSITORIES: ENA
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Project description:Systems biology approaches address the challenge of translating sequence information into function. In this study, we described the Pseudomonas aeruginosa PA14 proteomic landscape and quantified environment-driven changes in protein levels by the use of LC-MS techniques. Previously recorded mRNA data allowed a comparison of RNA to protein ratios for each individual gene and, thus, to explore the relationship between an mRNA being differentially expressed between environmental conditions and the mRNA-protein correlation for that gene. We developed a Random Forest-based predictor for protein levels and found that the mRNA to protein correlation was higher for genes/proteins that undergo dynamic changes. One example of a discrepancy between protein and predicted protein levels was observed for a phage-related gene cluster, which was translated into low protein levels under standard growth conditions. However, under SOS-inducing conditions more protein was produced and the prediction of protein levels based on mRNA abundancy became more accurate. In conclusion, our systems biology approach sheds light on complex mRNA to protein level relationships and uncovered condition-dependent post-transcriptional regulatory events.
2020-06-25 | GSE116308 | GEO
Project description:LFQ proteome datasets of Pseudomonas aeruginosa type strain PA14 cultured at different enviromental conditions: Exponential-, transition- and stationary(12 h and 24 h)growth phases. Biofilm (24 h and 48 h), low osmolarity conditions (control = exponential phase), iron starvation and respective control, Sub-MIC ciproflox treatment and respective control.
2018-11-20 | PXD010200 | Pride
Project description:Pseudomonas aeruginosa strain:bcsir_p4_s20 | isolate:Environment Genome sequencing
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Project description:C-di-GMP signaling can directly influence bacterial behavior by affecting the functionality of c-di-GMP-binding proteins. In addition, c-di-GMP can exert an indirect and more global effect on gene transcription or translation, e.g. via riboswitches or by binding to transcription factors. In this study, we investigated the effects of changes in intracellular c-di-GMP levels on gene expression and protein production in the opportunistic pathogen Pseudomonas aeruginosa. We induced c-di-GMP production via an ectopically introduced diguanylate cyclase and recorded the transcriptional, translational as well as proteomic profile of the cells. We demonstrate that rising levels of c-di-GMP in P. aeruginosa under growth conditions otherwise characterized by low c-di-GMP levels immediately cause a switch to a non-motile, auto-aggregative phenotype. This switch became apparent before any c-di-GMP-dependent role on transcription, translation, or protein abundance could be observed. Our results indicate that sudden rises in global c-di-GMP pools affect the P. aeruginosa phenotype via an alteration of protein functionality, rather than an impact on global gene transcription or translation.
2024-09-03 | GSE183394 | GEO
Project description:Anthropogenic pollution has increased the levels of heavy metals in the environment. Bacterial populations continue to thrive in highly polluted environments and bacteria must have mechanisms to counter heavy metal stress. We chose to examine the response of the environmentally-relevant organism Pseudomonas aeruginosa to two different copper treatments. A short, 45 min exposure to copper was done in the Cu shock treatment to examine the immediate transcriptional profile to Cu stress. The Cu adapted treatment was designed to view the transcriptional profile of cells that were actively growing in the presence of Cu. Experiment Overall Design: We analyzed 2 biological replicates of Pseudomonas aeruginosa exposed to a 45 min Cu shock as compared to a control that was exposed to HCl to bring the pH to similar levels. We analyzed 2 biological replicates of Pseudomonas aeruginosa that were grown in the presence of Cu for approx. 6h (Cu adapted) as compared to an untreated control.
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Project description:Pseudomonas aeruginosa is a common bacterium in the terminal plumbing system of buildings and it is from this niche that a substantial fraction of infections are acquired. To better understand P. aeruginosa biology in this environment, we examined the transcriptomes in tap water and pond water.
2017-10-24 | GSE104819 | GEO
Project description:To analyze the impact of elevated c-di-GMP concentrations in P. aeruginosa, we expressed pleD* on an inducible vector (pHERD20T) in the PAO1 wild-type strain. PleD is a DGC from Caulobacter cresentusand the pleD* construct variant encodes for a constitutively active enzyme due to four amino acid exchanges (T120N, T214A, P234H, N357Y).We aimed to analyze the cellular consequences of increased c-di-GMP levels in the opportunistic pathogen P. aeruginosa on a global scale. We therefore grew the pleD* harboring PAO1 as well as the empty vector control PAO1 in LB medium, added arabinose (0.2%) to the medium to induce pleD* expression and harvested the cells in exponential growth phase, when the cells exhibited elevated c-di-GMP levels of about two-fold (see manuscript). We are discribing the characteristics of elevated c-di-GMP with a Multi-Omics-Dataset.
2022-07-25 | PXD027098 | Pride
Project description:Alternative splicing events driven by altered levels of Gemin5 undergo translation
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Project description:Anthropogenic pollution has increased the levels of heavy metals in the environment. Bacterial populations continue to thrive in highly polluted environments and bacteria must have mechanisms to counter heavy metal stress. We chose to examine the response of the environmentally-relevant organism Pseudomonas aeruginosa to two different copper treatments. A short, 45 min exposure to copper was done in the Cu shock treatment to examine the immediate transcriptional profile to Cu stress. The Cu adapted treatment was designed to view the transcriptional profile of cells that were actively growing in the presence of Cu. Keywords: stress response
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