Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1027243 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26397449_1.fastq.gz | Fastqsanger.gz | |||
| SRR26397449_2.fastq.gz | Fastqsanger.gz | |||
| SRR26397450_1.fastq.gz | Fastqsanger.gz | |||
| SRR26397450_2.fastq.gz | Fastqsanger.gz | |||
| SRR26397451_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
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: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:The dimerization and binding of DNA by BldD is affected by its interaction with cyclic di-GMP. The D116A mutant of BldD is partially impaired in its biding of cyclic di-GMP. ChIP-Seq was carried out to determine the difference in the degree of DNA binding by the wild type and D116A mutated BldD in Streptomyces venezuelae.
2017-11-01 | E-MTAB-5328 | biostudies-arrayexpress
Project description:Cyclic di-GMP (c-di-GMP) is a ubiquitous second messenger that regulates many biological processes in bacteria. The genome in Mycobacterium tuberculosis encodes a single copy of the diguanylate cyclase gene (dgc) responsible for c-di-GMP synthesis. To determine the role of c-di-GMP signaling in M. tuberculosis, the mutant strain of Δdgc was generated in the virulent H37Rv strain. We used whole genome microarray expression profiling as a discovery platform to identify the genes controlled by c-di-GMP in M. tuberculosis, providing molecular proof for the phenotypes modulated by the signaling.
2013-10-09 | GSE37973 | GEO
Project description:The innate immune system responds to unique molecular signatures that are widely conserved among microbes but that are not normally present in host cells. Compounds that stimulate innate immune pathways may be valuable in the design of novel adjuvants, vaccines, and other immunotherapeutics.The cyclic dinucleotide cyclic-di-guanosine monophosphate (c-di-GMP) is a recently appreciated second messenger that plays critical regulatory roles in many species of bacteria but is not produced by eukaryotic cells. In vivo and in vitro studies have previously suggested that c-di-GMP is a potent immunostimulatory compound recognized by mouse and human cells. Here we provide evidence that c-di-GMP is sensed in the cytosol of mammalian cells via a novel immunosurveillance pathway. The potency of cytosolic signaling induced by cyclic-di- GMP is comparable to that induced by cytosolic delivery of DNA, and both nucleic acids induce a similar transcriptional profile, including triggering of type I interferons and coregulated genes via induction of TBK1, IRF3, NF-!B and MAP kinases. However, the cytosolic pathway that senses c-di-GMP appears to be distinct from all known nucleic acid-sensing pathways.Our results suggest a novel mechanism by which host cells can induce an inflammatory response to a widely produced bacterial ligand. Three-condition experiment: macrophages transfected with mono-GMP (negative control), double-stranded DNA (positive control), or cyclic-di-GMP (experimental condition). Biological replicates: two, independently treated, harvested, and hybridized to arrays. One replicate per array, except two technical replicates were performed for one of the positive control samples.
2009-07-21 | E-GEOD-16943 | biostudies-arrayexpress
Project description:Bacterial lifestyles are dictated by the conditions encountered during colonization of a specific ecological niche or host. A wide range of environmental stimuli triggers sensory modules, that modify activity of proteins, or/and initiate a transfer of information in complex regulatory networks, which modulate gene expression, and therefore adaptation. The transition between planktonic and biofilm growth is dependent on the homeostasis of the intracellular second messenger c-di-GMP. High c-di-GMP levels driven by diguanylate cyclase (DGC) activity favor biofilm while low levels maintained by phosphodiesterase (PDE) enzymes encourage planktonic style or biofilm dispersal. In Pseudomonas aeruginosa over 40 PDE/DGC are involved in c-di-GMP homeostasis, including 16 dual enzymes possessing both canonical DGC and PDE motifs, i.e. GGDEF and EAL, respectively. It has been previously reported that the deletion of the PDE/DGC dual enzyme PA0285, one of 5 c-di-GMP-related enzymes conserved across all Pseudomonas species, impacts biofilms and causes elevated c-di-GMP levels in P. aeruginosa. Here we confirm that this role is conserved in various P. aeruginosa (PAO1, PA14 and PAK) and Pseudomonas putida strains. Deletion of PA0285 has the highest impact during the early stage of surface colonization, and RNA-seq analysis in biofilm context indicates that it may be associated with upregulation of cupA fimbrial genes. We demonstrate that the C-terminal portion of PA0285 encompassing the GGDEF and EAL domains binds the respective GTP (GGDEF) and c-di-GMP (EAL) substrates but only exhibits PDE activity in vitro. Both GGDEF and EAL domains are important for PA0285 PDE activity in vivo as suggested by site-directed mutants in each of the key motifs. Complementation of the PA0285 mutant strain with the C-terminal GGDEF/EAL portion in trans is not as effective as with the full-length gene suggesting that the transmembrane region and PAS domains contained in PA0285’s N-terminal portion influence its PDE activity in vivo. We speculate that the transmembrane portion or/and PAS domains of PA0285 impede its PDE activity in vivo through modulating the conformation of the enzyme, as shown for P. aeruginosa RbdA, in response to an unknown stimulus.
2023-07-01 | GSE223663 | GEO
Project description:Cyclic di-GMP (c-di-GMP) is a ubiquitous second messenger that regulates many biological processes in bacteria. The genome in Mycobacterium tuberculosis encodes a single copy of the diguanylate cyclase gene (dgc) responsible for c-di-GMP synthesis. To determine the role of c-di-GMP signaling in M. tuberculosis, the mutant strain of Δdgc was generated in the virulent H37Rv strain. We used whole genome microarray expression profiling as a discovery platform to identify the genes controlled by c-di-GMP in M. tuberculosis, providing molecular proof for the phenotypes modulated by the signaling. Wild-type H37Rv and Δdgc cultures were analyzed under aerobic conditions or in an in vitro dormancy model. Bacteria were collected at OD600 =1.3 for the aerobic cultures and upon the beginning of anaerobiosis for the cultures in the dormancy model. One culture for each experiment was assayed except for Δdgc under anaerobiosis (2 independent cultures).
2013-10-09 | E-GEOD-37973 | biostudies-arrayexpress
Project description:Bacterial biofilms of V. cholerae, V. fischeri, and P. aeruginosa grown on agar we analyzed by MALDI mass spectrometry imaging in negative mode for the detection of cyclic dimeric guanosine monophosphate (c-di-GMP). P. aeruginosa samples were also analyzed in positive mode for the detection of additional metabolites. The presence of c-di-GMP was confirmed by MALDI MSMS of a V. cholerae extract. All raw data files are provided, .imzml datafiles provided as supplementary files.
| MSV000092966 | MassIVE