Biofilm transcriptional pathways in the model symbiont Vibrio fischeri
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PROVIDER: PRJNA994146 | ENA |
REPOSITORIES: ENA
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Project description:Beneficial microbial symbionts are often horizontally acquired by their animal hosts from environmental sources, requiring the symbionts to complete a lifestyle transition from free-living in the environment to association with host tissues. In the model symbiosis between the Hawaiian bobtail squid and its microbial symbiont Vibrio fischeri, one mechanism used to make this transition during host colonization is the formation of biofilm-like aggregates on host mucosa. Extensive work has previously been conducted to isolate the critical factors controlling V. fischeri biofilm formation, yet much remains unknown regarding the full breadth of the biofilm-associated regulon. Here, we probed in vitro models of biofilm formation using transcriptomics, to identify novel regulatory pathways active within biofilms of the V. fischeri type strain ES114. Through comparing the gene-sets which became differentially regulated in multiple biofilm models, we discovered a shared set of 232 genes which demonstrated similar patterns in expression relative to uninduced controls. These genes contained representatives of multiple exopolysaccharide loci, genes involved in flagellar motility, and a diverse collection of other genes. Follow-up analysis suggested that these transcriptomic changes reflected true phenotypic effects, including changes in motility and cyclic-di-GMP production in biofilm-induced backgrounds. Beyond characterizing the shared biofilm response, we additionally profiled the regulatory activity of the sensor kinase RscS. This sensor kinase has previously been characterized to function as a phospho-donor within an established biofilm-inducing phospho-relay, yet our data suggests that RscS moonlights in at least one other phospho-relay that integrates downstream signaling from a homolog of the Vibrio cholerae response regulator VpsR, without a need for its established signaling partners. Overall, this study adds to our understanding of the genes involved in V. fischeri biofilm regulation, while revealing new regulatory pathways branching from previously characterized signaling networks.
2023-07-17 | GSE237189 | GEO
Project description:The marine bacterium Vibrio fischeri requires flagellar motility to undergo symbiotic initiation with its host, the Hawaiian bobtail squid Euprymna scolopes. We sought to identify the genes activated by the sigma54-dependent flagellar master regulator, FlrA, in V. fischeri, thereby determining the flagellar regulon in this model symbiont.
2013-04-05 | GSE45772 | GEO
Project description:The marine bacterium Vibrio fischeri requires flagellar motility to undergo symbiotic initiation with its host, the Hawaiian bobtail squid Euprymna scolopes. We sought to identify the genes activated by the sigma54-dependent flagellar master regulator, FlrA, in V. fischeri, thereby determining the flagellar regulon in this model symbiont. We performed microarray analysis on wild-type Vibrio fischeri ES114 and a flrA deletion mutant, DM159, grown to mid-log phase in seawater tryptone, a condition in which cells are highly motile (two biological replicates per condition).
2013-04-05 | E-GEOD-45772 | biostudies-arrayexpress
Project description:We used the bioluminescent squid symbiont, Vibrio fischeri, to identify essential regulatory factors that control expression and function of a strain-specific T6SS encoded within a genomic island. Random transposon mutagenesis revealed that three genes located on the T6SS2-encoding genomic island are necessary to activate expression of a T6SS reporter. We used a proteomics approach to identify proteins that were differentially abundant in mutant strains compared to the wild type when cells were grown in a high-viscosity media.
2021-08-24 | PXD017722 | Pride
Project description:Acyl-homoserine lactone (acyl-HSL) quorum sensing was first discovered in Vibrio fischeri where it serves as a key control element of the seven-gene luminescence (lux) operon. Since this initial discovery, other bacteria have been shown to control hundreds of genes by acyl-HSL quorum sensing. Until recently, it has been difficult to examine the global nature of quorum sensing in V. fischeri. However, the complete genome sequence of V. fischeri is now available and this has enabled us to use transcriptomics to identify quorum-sensing regulated genes and to study the quorum-controlled regulon of this bacterium. In this study, we used DNA microarray technology to identify over two-dozen V. fischeri genes regulated by the quorum sensing signal N-3-oxohexanoyl-L-homoserine lactone (3OC6-HSL). Keywords: Comparison of transcriptome profiles
2007-08-01 | GSE7485 | 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: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:The bioluminescent bacterium Vibrio fischeri initiates a specific, persistent symbiosis in the light organ of the squid Euprymna scolopes. During the early stages of colonization, V. fischeri is exposed to host-derived nitric oxide (NO). While NO can be both an antimicrobial component of innate immunity and a common signaling molecule of eukaryotes, its roles in beneficial host-microbe associations remain undescribed. V. fischeri encodes HnoX, a member of a family of bacterial NO-binding proteins of unknown function. We hypothesized that HnoX acts as a NO sensor that is involved in regulating symbiosis-related genes during initiation of symbiosis. With an aim to discover the genes whose regulations respond to NO signal, and in an HnoX-mediated fashion in particular, we carried out a whole-genome expression study on the wild-type and an insertional mutant of hnoX. The wild-type parent and an insertional mutant (hnoX-) of the hnoX gene were grown to early log phase in a minimal-salts medium. One half of each culture was treated with 80µM of the NO-generator, DEA-NONOate, and the other half was left untreated as a control. After 30 min, cells from all the cultures were fixed with RNAprotect Bacteria Reagent. Total RNA was isolated, labeled and hybridized to the Custom Vibrio fischeri GeneChip Array (Affymetrix). Three independent experiments were performed on separate days for statistical analysis.
2010-05-06 | E-GEOD-15522 | biostudies-arrayexpress
Project description:The bioluminescent bacterium Vibrio fischeri initiates a specific, persistent symbiosis in the light organ of the squid Euprymna scolopes. During the early stages of colonization, V. fischeri is exposed to host-derived nitric oxide (NO). While NO can be both an antimicrobial component of innate immunity and a common signaling molecule of eukaryotes, its roles in beneficial host-microbe associations remain undescribed. V. fischeri encodes HnoX, a member of a family of bacterial NO-binding proteins of unknown function. We hypothesized that HnoX acts as a NO sensor that is involved in regulating symbiosis-related genes during initiation of symbiosis. With an aim to discover the genes whose regulations respond to NO signal, and in an HnoX-mediated fashion in particular, we carried out a whole-genome expression study on the wild-type and an insertional mutant of hnoX.
2010-03-01 | GSE15522 | GEO
Project description:We report the full transcriptome (RNA-Seq) of Vibrio fischeri ES114 in rich medium, seawater, and after venting from the Hawaiian bobtail squid Euprymna scolopes. We also report the effects of ribodepletion on low-biomass samples, down to input amount of 1ng total RNA.
2016-04-26 | GSE80607 | GEO