Ontology highlight
ABSTRACT:
PROVIDER: PRJNA184028 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Quorum sensing (QS) is a cell density regulated communication system that bacteria use to coordinate activities, including biofilm formation, involved in colonization and pathogenesis. We have previously shown that inactivation of the QS master regulator LitR attenuates the Vibrio (Allivibrio) salmonicida strain LFI1238 in a fish model. In this work we show that LFI1238 as well as a panel of naturally occurring V. salmonicidia strains are poor biofilm producers. Inactivation of litR strongly enhances medium and temperature dependent adhesion, rugose colony morphology and biofilm formation. Chemical treatment and scanning electron microscopy of the biofilm identified an extracellular matrix consisting mainly of protein filaments and polysaccharides. Further, microarray analysis of planktonic and biofilm cells identified a number of genes regulated by LitR, and among these were homologues of the Vibrio fischeri symbiosis polysaccharide (syp) genes. Disruption of syp alleviated the different phenotypes regulated by LitR in V. salmonicida. Hence, LitR is a repressor of syp expression that is necessary for rugose colony morphology, adhesion and biofilm formation, three phenotypes of the DlitR mutant that are expressed at temperatures below 12M-BM-:C. The DlitR mutant mimics low cell density behavior suggesting that these phenotypes are important during the initial steps of colonization. Although the syp operon in V. salmonicida shows identical gene synteny to the one in the squid symbiont V. fischeri, its regulation is probably more related to vibrio polysaccharide (vps) expression in the human pathogenic Vibrio cholera which is controlled by the LitR homologue HapR. V. salmonicida wild type strain LFI1238 (control) and the isogenic DlitR mutant were grown as statical biofilm in SWT medium, at 4M-BM-0C and harvested after 72 hours. Biological replicates for each sample: 4 wild type, 4 DlitR mutant (including one dye swap), independently grown and harvested. One replicate per array.
2012-12-19 | E-GEOD-42995 | biostudies-arrayexpress
Project description:Quorum sensing (QS) is a cell density regulated communication system that bacteria use to coordinate activities, including biofilm formation, involved in colonization and pathogenesis. We have previously shown that inactivation of the QS master regulator LitR attenuates the Vibrio (Allivibrio) salmonicida strain LFI1238 in a fish model. In this work we show that LFI1238 as well as a panel of naturally occurring V. salmonicidia strains are poor biofilm producers. Inactivation of litR strongly enhances medium and temperature dependent adhesion, rugose colony morphology and biofilm formation. Chemical treatment and scanning electron microscopy of the biofilm identified an extracellular matrix consisting mainly of protein filaments and polysaccharides. Further, microarray analysis of planktonic and biofilm cells identified a number of genes regulated by LitR, and among these were homologues of the Vibrio fischeri symbiosis polysaccharide (syp) genes. Disruption of syp alleviated the different phenotypes regulated by LitR in V. salmonicida. Hence, LitR is a repressor of syp expression that is necessary for rugose colony morphology, adhesion and biofilm formation, three phenotypes of the DlitR mutant that are expressed at temperatures below 12M-BM-:C. The DlitR mutant mimics low cell density behavior suggesting that these phenotypes are important during the initial steps of colonization. Although the syp operon in V. salmonicida shows identical gene synteny to the one in the squid symbiont V. fischeri, its regulation is probably more related to vibrio polysaccharide (vps) expression in the human pathogenic Vibrio cholera which is controlled by the LitR homologue HapR. V. salmonicida wild type strain LFI1238 (control) and the isogenic DlitR deletion mutant were grown in suspension in SWT medium at 8M-BM-0C with 200 rpm and harvested at OD=0.8. Biological replicates for each sample: 4 wild type, 4 DlitR mutant (including one dye swap), independently grown and harvested. One replicate per array.
2012-12-19 | E-GEOD-42994 | biostudies-arrayexpress
Project description:Quorum sensing (QS) is a cell density regulated communication system that bacteria use to coordinate activities, including biofilm formation, involved in colonization and pathogenesis. We have previously shown that inactivation of the QS master regulator LitR attenuates the Vibrio (Allivibrio) salmonicida strain LFI1238 in a fish model. In this work we show that LFI1238 as well as a panel of naturally occurring V. salmonicidia strains are poor biofilm producers. Inactivation of litR strongly enhances medium and temperature dependent adhesion, rugose colony morphology and biofilm formation. Chemical treatment and scanning electron microscopy of the biofilm identified an extracellular matrix consisting mainly of protein filaments and polysaccharides. Further, microarray analysis of planktonic and biofilm cells identified a number of genes regulated by LitR, and among these were homologues of the Vibrio fischeri symbiosis polysaccharide (syp) genes. Disruption of syp alleviated the different phenotypes regulated by LitR in V. salmonicida. Hence, LitR is a repressor of syp expression that is necessary for rugose colony morphology, adhesion and biofilm formation, three phenotypes of the DlitR mutant that are expressed at temperatures below 12ºC. The DlitR mutant mimics low cell density behavior suggesting that these phenotypes are important during the initial steps of colonization. Although the syp operon in V. salmonicida shows identical gene synteny to the one in the squid symbiont V. fischeri, its regulation is probably more related to vibrio polysaccharide (vps) expression in the human pathogenic Vibrio cholera which is controlled by the LitR homologue HapR.
2012-12-19 | GSE42994 | GEO
Project description:Quorum sensing (QS) is a cell density regulated communication system that bacteria use to coordinate activities, including biofilm formation, involved in colonization and pathogenesis. We have previously shown that inactivation of the QS master regulator LitR attenuates the Vibrio (Allivibrio) salmonicida strain LFI1238 in a fish model. In this work we show that LFI1238 as well as a panel of naturally occurring V. salmonicidia strains are poor biofilm producers. Inactivation of litR strongly enhances medium and temperature dependent adhesion, rugose colony morphology and biofilm formation. Chemical treatment and scanning electron microscopy of the biofilm identified an extracellular matrix consisting mainly of protein filaments and polysaccharides. Further, microarray analysis of planktonic and biofilm cells identified a number of genes regulated by LitR, and among these were homologues of the Vibrio fischeri symbiosis polysaccharide (syp) genes. Disruption of syp alleviated the different phenotypes regulated by LitR in V. salmonicida. Hence, LitR is a repressor of syp expression that is necessary for rugose colony morphology, adhesion and biofilm formation, three phenotypes of the DlitR mutant that are expressed at temperatures below 12ºC. The DlitR mutant mimics low cell density behavior suggesting that these phenotypes are important during the initial steps of colonization. Although the syp operon in V. salmonicida shows identical gene synteny to the one in the squid symbiont V. fischeri, its regulation is probably more related to vibrio polysaccharide (vps) expression in the human pathogenic Vibrio cholera which is controlled by the LitR homologue HapR.
2012-12-19 | GSE42995 | GEO
Project description:Bacteria can link gene expression to population density to promote group behaviors using quorum sensing. Quorum sensing controls a multitude of bacterial processes such as virulence, motility, and biofilm formation. In Vibrio fischeri, the quorum sensing-dependent transcription factor LitR inhibits biofilm formation. A previous study showed that LitR modestly inhibits transcription of the bcs locus, which comprises the genes responsible for producing the cellulose polysaccharide. However, beyond that, the mechanism of LitR’s inhibitory effect on biofilm formation was unknown. Here, we find that LitR transcriptionally activates pdeV, which encodes a c-di-GMP phosphodiesterase that indirectly promotes cleavage of the large adhesive protein LapV from the surface of V. fischeri, leading to biofilm dispersal. LitR also induces transcription of the sensor kinase VF_A1016, which we determined to be important for biofilm inhibition. Like loss of LitR, loss of VF_A1016 modestly increased bcs transcription. Through chromatin immunoprecipitation sequencing (ChIP-seq), we found that LitR directly binds to the VF_A1016 and pdeV regulatory regions. In total, we identified 147 LitR binding sites in the genome and confirmed LitR’s transcriptional control over a subset of these putative regulatory targets. Of note, we determined that LitR induces transcription of the genes encoding the diguanylate cyclase VF_1200 and the glyoxylate shunt protein AceB and inhibits expression of the putative transcription factor TfoY. LitR also differentially regulates the response regulator ArcA in static and shaking conditions. These data define the mechanism of LitR regulation of genes involved in biofilm formation and the physiology of V. fischeri.
2025-07-21 | GSE288643 | GEO
Project description:In Burkholderia cenocepacia H111, the large surface protein BapA plays a crucial role in the formation of highly structured communities, known as biofilms. We have recently demonstrated that Quorum sensing (QS) is necessary for the maximal expression of bapA. In this study we identify a protein from the IclR family of transcriptional regulators that, in conjunction with QS, controls biofilm formation by affecting the expression of bapA. We present evidence that, in addition to BapA, BapR influences the expression of extracellular protease, swimming motility and has a profound impact in the abundance of persister cells, making this regulator an interesting target for persister and biofilm eradication. Identification of a new regulator BapR controlling biofilm formation
2014-03-26 | E-GEOD-52769 | biostudies-arrayexpress
Project description:To address the question of how quorum sensing controls biofilm formation in Acidithiobacillus ferrooxidans ATCC23270, the transcriptome of this organism in conditions in which quorum sensing response is stimulated by a synthetic acyl homoserine lactone (AHL) analogue has been studied. Tetrazole 9c was used in DNA microarray experiments that allowed the identification of genes regulated by quorum sensing signalling, and more particularly those involved in early biofilm formation.
2017-03-15 | E-MTAB-4896 | biostudies-arrayexpress
Project description:In Burkholderia cenocepacia H111, the large surface protein BapA plays a crucial role in the formation of highly structured communities, known as biofilms. We have recently demonstrated that Quorum sensing (QS) is necessary for the maximal expression of bapA. In this study we identify a protein from the IclR family of transcriptional regulators that, in conjunction with QS, controls biofilm formation by affecting the expression of bapA. We present evidence that, in addition to BapA, BapR influences the expression of extracellular protease, swimming motility and has a profound impact in the abundance of persister cells, making this regulator an interesting target for persister and biofilm eradication.
2014-03-26 | GSE52769 | GEO
Project description:Acinetobacter baumannii A1S_1874 gene encodes as a LysR-type transcriptional regulator. LysR family regulators known to regulate biofilm formation, antibiotic resistance, and the expression of diverse genes in other Gram-negative bacteria. However, A1S-1874 has never been characterized in Acinetobacter baumannii, and the studies about the regulon of A1S-1874 are not discovered. In this study we revealed that A1S_1874 differentially regulates at least 302 genes including the csu pilus operon, N-acylhomoserine lactone synthese gene, A1S_0112-A1S_0118 operon, type 1v secretion system related genes that are involved in biofilm formation, surface motility, adherence, quorum sensing and virulence. Overall, our data suggests that A1S-1874 is a key regulator of Acinetobacter baumannii biofilm formation and gene expression.
2021-05-25 | GSE173626 | GEO
Project description:The animal symbiont Vibrio fischeri has served as a model organism for molecular processes underlying bacterial group behaviors, including quorum sensing and biofilm development. Here, using a genetic approach to identify negative regulators of biofilm formation in V. fischeri, we identified a membrane-bound RNA-binding protein, RtmR (VF_2432), that acts as an inhibitor of the symbiosis polysaccharide (SYP) biofilm. Membrane localization of the protein seems to be required for protein stability, as truncation of the transmembrane helices led to an inability to detect the protein. The conserved RNP1 and RNP2 motifs in RtmR’s cytoplasmic RNA recognition motif (RRM) domain are required for function, and we demonstrate binding to RNA substrates. Identification of RtmR RNA ligands was conducted with a CLIP-seq approach that revealed a large interactome. One transcript identified was that of the biofilm regulatory histidine kinase RscS. We found that RtmR biofilm inhibition depends on RscS activity and that RtmR negatively regulates levels of RscS. Overall, this work characterizes a novel type of bacterial RNA-binding protein.
2025-07-09 | GSE301959 | GEO