Pseudomonas aeruginosa PAO1 strain:PA01
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA401973 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6012510_1.fastq.gz | Fastqsanger.gz | |||
| SRR6012510_2.fastq.gz | Fastqsanger.gz | |||
| SRR6012507_1.fastq.gz | Fastqsanger.gz | |||
| SRR6012507_2.fastq.gz | Fastqsanger.gz | |||
| SRR6012508_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Reducing intracellular c-di-GMP content increases quorum sensing-regulated virulence in Pseudomonas aeruginosa
| PRJNA381683 | ENA
Project description:Pseudomonas aeruginosa is a Gram-negative bacterium able to survive and adapt in a multitude of niches as well as thriving within many different hosts. This versatility lies within a large genome of ca 6Mbp and a tight control in the expression of thousands of genes. Among the regulatory mechanisms widely spread in bacteria, cyclic-di-GMP signaling is one which influences all levels of control. It is made by diguanylate cyclases and broken by phosphodiesterases while the intracellular level of this molecule drives phenotypic responses. The signaling involve modification of enzymes or proteins function upon c-di-GMP binding, including modifying the activity of regulators which in turn will impact the transcriptome. In P. aeruginosa, there are ca 40 genes encoding putative DGC or PDE. The combined activity of those enzymes should reflect the c-di-GMP concentration while specific phenotypic output could be correlated to a given set of dgc/pde. This notion of specificity has been addressed in several studies and different strains of P. aeruginosa. Here, we engineered a mutant library for the 41 individual dgc/pde genes in P. aeruginosa PAO1. In most cases, we observed a significant to slight variation in the global c-di-GMP pool, with essentially an impact on biofilm phenotypes including initial attachment and maturation, while very little is observed on motility which differs from previous studies. We observe that minor changes in c-di-GMP level have a drastic phenotypic impact thus supporting the idea of local vs global c-di-GMP pool. Our RNA-seq analysis indicates that all PAO1 dgc/pde genes are expressed in both planktonic and biofilm growth conditions and our work suggests that c-di-GMP networks owe to be reconstructed in one single strain and cannot be built by cross-comparison with studies in other strains.
2022-05-23 | GSE203348 | GEO
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:Pseudomonas aeruginosa is a significant opportunistic pathogen responsible for numerous human infections. Its high pathogenicity resides in a diverse array of virulence factors and an ability to adapt to hostile environments. We report that these factors are tied to the activity of condensins, SMC and MksBEF, which primarily function in structural chromosome maintenance. This study revealed that both proteins are required for P. aeruginosa virulence during corneal infection. The reduction in virulence was traced to broad changes in gene expression. Transcriptional signatures of smc and mksB mutants were largely dissimilar and non-additive, with the double mutant displaying a distinct gene expression profile. Affected regulons included those responsible for lifestyle control, primary metabolism, surface adhesion and biofilm growth, iron and sulfur assimilation, and numerous virulence factors, including type 3 and type 6 secretion systems. The in vitro phenotypes of condensin mutants mirrored their transcriptional profiles and included impaired production and secretion of multiple virulence factors, growth deficiencies under nutrient limiting conditions, and altered c-di-GMP signaling. Notably, c-di-GMP mediated some but not all transcriptional responses of the mutants. Thus, condensins are integrated into the control of multiple genetic programs related to epigenetic and virulent behavior of P. aeruginosa.
2022-01-05 | GSE161971 | GEO
Project description:In the Pseudomonas aeruginosa type strain PA14, 40 genes are known to encode for diguanylate cyclases (DGCs) and/or phosphodiesterases (PDEs), which modulate the intracellular pool of the nucleotide second messenger c-di-GMP. While in general, high levels of c-di-GMP drive the switch from highly motile phenotypes towards a sessile lifestyle, the different c-di-GMP modulating enzymes are responsible for smaller and in parts non-overlapping phenotypes. In this study, we sought to utilize previously recorded P. aeruginosa gene expression datasets on 414 clinical isolates to uncover transcriptional changes as a result of a high expression of genes encoding diguanylate cyclases. We demonstrate that the selection of sub-groups of clinical isolates with high versus low expression of regulatory genes served the identification of their downstream regulons. Thus, analyzing transcriptional profiles of clinical isolates with variant expression of diguanylate cyclase genes might provide a unique opportunity to bypass the problem that for many c-di-GMP modulating enzymes it is not known under which conditions their expression is activated. However, because the high c-di-GMP associated phenotypes were rapidly lost in the clinical isolates, we were unable to confirm diguanylate specific gene regulation. It is possible that the elevated c-di-GMP concentrations observed in the clinical P. aeruginosa isolates were due to a memory response, in which the bacteria maintain a certain level of c-di-GMP even after being removed from the conditions that induced the production of c-di-GMP. Further studies would be needed to determine the specific mechanisms underlying this memory response in P. aeruginosa.
2023-08-21 | GSE233207 | GEO
Project description:We analyzed a deletion mutant of the ECF M-OM-^C factor SigX and applied mRNA profiling to define the SigX dependent regulon in P. aeruginosa in response to low osmolarity medium conditions. Furthermore, the combination of transcriptional data with chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing led to the identification of the DNA binding motif of SigX. Genome-wide mapping of SigX-binding regions revealed enrichment of downstream genes involved in fatty acid biosynthesis, type III secretion, swarming and c-di-GMP signaling. In accordance, a sigX deletion mutant exhibited an altered fatty acid composition of the cell membrane, reduced cytotoxicity, impaired swarming activity, elevated c-di-GMP levels and increased biofilm formation. In conclusion, a combination of ChIP-seq with transcriptional profiling and bioinformatic approaches to define consensus DNA binding sequences proved to be effective for the elucidation of the regulon of the alternative M-OM-^C factor SigX revealing its role in complex virulence-associated phenotypes in P. aeruginosa. Transcriptome profiling of the SigX deletion mutant and overexpressing wildtype complemented by ChIP-seq
2013-11-11 | E-GEOD-50937 | biostudies-arrayexpress
Project description:We analyzed a deletion mutant of the ECF σ factor SigX and applied mRNA profiling to define the SigX dependent regulon in P. aeruginosa in response to low osmolarity medium conditions. Furthermore, the combination of transcriptional data with chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing led to the identification of the DNA binding motif of SigX. Genome-wide mapping of SigX-binding regions revealed enrichment of downstream genes involved in fatty acid biosynthesis, type III secretion, swarming and c-di-GMP signaling. In accordance, a sigX deletion mutant exhibited an altered fatty acid composition of the cell membrane, reduced cytotoxicity, impaired swarming activity, elevated c-di-GMP levels and increased biofilm formation. In conclusion, a combination of ChIP-seq with transcriptional profiling and bioinformatic approaches to define consensus DNA binding sequences proved to be effective for the elucidation of the regulon of the alternative σ factor SigX revealing its role in complex virulence-associated phenotypes in P. aeruginosa.
2013-11-11 | GSE50937 | GEO
Project description:In this study, we present a novel transcriptional regulator, PA1226, which modulates biofilm formation and virulence in P. aeruginosa. Mutation in this regulator abolished the ability of P. aeruginosa to produce biofilm in vitro, without any effect on the planktonic growth. This regulator is essential to the in vivo fitness and pathogenesis in both Drosophila melanogaster and BALB/c mouse lung infection models. Transcriptome analysis revealed that PA1226 regulates many essential virulence genes/pathways, including alginate, pili, and LPS biosynthesis.
2018-06-30 | GSE107640 | 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:We have previously reported that Mycobacterium tuberculosis Rv2837c (cnpB) encodes a phosphodiesterase that specifically cleaves cyclic di-AMP (c-di-AMP) into AMP. Deletion of cnpB results in significant virulence attenuation in a mouse pulmonary infection model, which is very likely due to the significantly elevated c-di-AMP levels as overexpression of Mtb diadenylate cyclase, disA, also leads to a similar outcome. An earlier study also demonstrated that CnpB functions similarly to E. coli oligoribonuclease (Orn) that hydrolyzes 2-5-mer nanoRNAs (short oligonucleotides of five residues or shorter in length) except that CnpB prefers 2-mer nanoRNA as a substrate. Additionally, a recent report showed that CnpB also degrades cyclic di-GMP (c-di-GMP), although we demonstrated that CnpB prefers c-di-AMP to c-di-GMP according to an in vitro enzymatic kinetics analysis In this study, we initially attempted to determine c-di-AMP-mediated gene regulation in Mtb by comparing the expression profiles between WT and ∆cnpB using RNA-Seq. We found that the CRISPR-Cas system of M. tuberculosis was highly upregulated by deletion of cnpB.
2018-02-27 | GSE102816 | GEO