GEO DataSets

(Submitter supplied) Using transcriptomics, we studied the transcriptional response of Vibrio cholerae to 10 min of exogenously supplied peptidoglycan at 300 µg/mL.

Organism:

Vibrio cholerae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30059

6 Samples

Download data: XLSX

(Submitter supplied) Vibrio cholerae harbours a primary chromosome derived from the monochromosomal ancestor of the Vibrionales (ChrI) and a secondary chromosome derived from a megaplasmid (ChrII). Both carry a single origin of replication with replication terminating in a diametrically opposite zone, TerI and TerII, respectively. The choreography of TerI and TerII segregation determines when and where cell division occurs. more...

Organism:

Vibrio cholerae

Type:

Other

Platforms:

GPL34020 GPL25005

23 Samples

Download data: FA, TXT

(Submitter supplied) Vibrio cholerae harbours a primary chromosome derived from the monochromosomal ancestor of the Vibrionales (ChrI) and a secondary chromosome derived from a megaplasmid (ChrII). Both carry a single origin of replication with replication terminating in a diametrically opposite zone, TerI and TerII, respectively. The choreography of TerI and TerII segregation determines when and where cell division occurs. more...

Organism:

Vibrio cholerae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL31913

14 Samples

Download data: FA, TXT

(Submitter supplied) Vibrio cholerae harbours a primary chromosome derived from the monochromosomal ancestor of the Vibrionales (ChrI) and a secondary chromosome derived from a megaplasmid (ChrII). Both carry a single origin of replication with replication terminating in a diametrically opposite zone, TerI and TerII, respectively. The choreography of TerI and TerII segregation determines when and where cell division occurs. more...

Organism:

Vibrio cholerae

Type:

Other

Platform:

GPL19265

2 Samples

Download data: FA, MATRIX

(Submitter supplied) Gene regulation at the post-transcriptional level is prevalent in all domains of life. In bacteria, ProQ-like proteins have emerged as important RNA chaperones facilitating RNA stability and RNA duplex formation. In the major human pathogen V. cholerae, post-transcriptional gene regulation is key for virulence, biofilm formation, and antibiotic resistance, yet the role of ProQ has not been studied. Here, we show that ProQ interacts with hundreds of transcripts in V. cholerae, including the highly abundant FlaX small RNA (sRNA). Global analyses of RNA duplex formation using RIL-Seq (RNA interaction by ligation and sequencing) revealed a vast network of ProQ-assisted interactions and identified a role for FlaX in motility regulation. Specifically, FlaX base-pairs with multiple sites on the flaB flagellin mRNA, preventing 30S ribosome binding and translation initiation. V. cholerae cells lacking flaX display impaired motility gene expression, altered flagella composition, and reduced swimming in liquid environments. Our results provide a global view on ProQ-mediated RNA duplex formation and pinpoint the mechanistic and phenotypic consequences associated with ProQ-associated sRNAs in V. cholerae.

Organism:

Vibrio cholerae

Type:

Other

Platform:

GPL33935

4 Samples

Download data: XLSX

(Submitter supplied) Gene regulation at the post-transcriptional level is prevalent in all domains of life. In bacteria, ProQ-like proteins have emerged as important RNA chaperones facilitating RNA stability and RNA duplex formation. In the major human pathogen V. cholerae, post-transcriptional gene regulation is key for virulence, biofilm formation, and antibiotic resistance, yet the role of ProQ has not been studied. Here, we show that ProQ interacts with hundreds of transcripts in V. cholerae, including the highly abundant FlaX small RNA (sRNA). Global analyses of RNA duplex formation using RIL-Seq (RNA interaction by ligation and sequencing) revealed a vast network of ProQ-assisted interactions and identified a role for FlaX in motility regulation. Specifically, FlaX base-pairs with multiple sites on the flaB flagellin mRNA, preventing 30S ribosome binding and translation initiation. V. cholerae cells lacking flaX display impaired motility gene expression, altered flagella composition, and reduced swimming in liquid environments. Our results provide a global view on ProQ-mediated RNA duplex formation and pinpoint the mechanistic and phenotypic consequences associated with ProQ-associated sRNAs in V. cholerae.

Organism:

Vibrio cholerae C6706

Type:

Other

Platform:

GPL34845

12 Samples

Download data: XLSX

(Submitter supplied) The signaling molecule cyclic di-GMP (cdG) controls the switch between bacterial motility and biofilm production, and fluctuations in cellular levels of cdG have been implicated in Vibrio cholerae pathogenesis. Intracellular concentrations of cdG are controlled by the interplay of diguanylate cyclase (DGC) enzymes, which synthesize cdG to promote biofilms, and phosphodiesterase (PDE) enzymes, which hydrolyse cdG to drive motility. more...

Organism:

Vibrio cholerae C6706

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34804

45 Samples

Download data: BEDGRAPH, TSV

(Submitter supplied) The signaling molecule cyclic di-GMP (cdG) controls the switch between bacterial motility and biofilm production, and fluctuations in cellular levels of cdG have been implicated in Vibrio cholerae pathogenesis. Intracellular concentrations of cdG are controlled by the interplay of diguanylate cyclase (DGC) enzymes, which synthesize cdG to promote biofilms, and phosphodiesterase (PDE) enzymes, which hydrolyse cdG to drive motility. more...

Organism:

Vibrio cholerae C6706

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL34804

91 Samples

Download data: BEDGRAPH, BW

(Submitter supplied) Gene regulation at the post-transcriptional level is prevalent in all domains of life. In bacteria, ProQ-like proteins have emerged as important RNA chaperones facilitating RNA stability and RNA duplex formation. In the major human pathogen V. cholerae, post-transcriptional gene regulation is key for virulence, biofilm formation, and antibiotic resistance, yet the role of ProQ has not been studied. Here, we show that ProQ interacts with hundreds of transcripts in V. cholerae, including the highly abundant FlaX small RNA (sRNA). Global analyses of RNA duplex formation using RIL-Seq (RNA interaction by ligation and sequencing) revealed a vast network of ProQ-assisted interactions and identified a role for FlaX in motility regulation. Specifically, FlaX base-pairs with multiple sites on the flaB flagellin mRNA, preventing 30S ribosome binding and translation initiation. V. cholerae cells lacking flaX display impaired motility gene expression, altered flagella composition, and reduced swimming in liquid environments. Our results provide a global view on ProQ-mediated RNA duplex formation and pinpoint the mechanistic and phenotypic consequences associated with ProQ-associated sRNAs in V. cholerae.

Organism:

Vibrio cholerae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33935

18 Samples

Download data: XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Vibrio cholerae

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL34020 GPL31913 GPL28681

76 Samples

Download data: BEDGRAPH, H5, TSV

(Submitter supplied) Vibrio cholerae, the causative agent of the diarrheal disease cholera, poses an ongoing health threat due to its wide repertoire of horizontally acquired elements (HAEs) and virulence factors. New clinical isolates of the bacterium with improved fitness abilities, often associated with HAEs, frequently emerge. The appropriate control and expression of such genetic elements is critical for the bacteria to thrive in different environments. more...

Organism:

Vibrio cholerae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34020

19 Samples

Download data: H5, R, TSV

(Submitter supplied) Vibrio cholerae, the causative agent of the diarrheal disease cholera, poses an ongoing health threat due to its wide repertoire of horizontally acquired elements (HAEs) and virulence factors. New clinical isolates of the bacterium with improved fitness abilities, often associated with HAEs, frequently emerge. The appropriate control and expression of such genetic elements is critical for the bacteria to thrive in different environments. more...

Organism:

Vibrio cholerae

Type:

Other

Platforms:

GPL28681 GPL31913 GPL34020

57 Samples

Download data: BEDGRAPH, NARROWPEAK

(Submitter supplied) Many, if not all, bacteria use quorum sensing (QS) to control gene expression and collective behaviours, and more recently QS has also been discovered in bacteriophages (phages). Phages can produce communication molecules of their own, or “listen in” on the host’s communication processes, in order to switch between lytic and lysogenic modes of infection. In this project, we studied the interaction of Vibrio cholerae, the causative agent of cholera disease, with the lysogenic vibriophage VP882. more...

Organism:

Vibrio cholerae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25005

18 Samples

Download data: XLSX

(Submitter supplied) Many, if not all, bacteria use quorum sensing (QS) to control gene expression and collective behaviours, and more recently QS has also been discovered in bacteriophages (phages). Phages can produce communication molecules of their own, or “listen in” on the host’s communication processes, in order to switch between lytic and lysogenic modes of infection. In this project, we studied the interaction of Vibrio cholerae, the causative agent of cholera disease, with the lysogenic vibriophage VP882. more...

Organism:

Vibrio cholerae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33935

18 Samples

Download data: XLSX

(Submitter supplied) Many, if not all, bacteria use quorum sensing (QS) to control gene expression and collective behaviours, and more recently QS has also been discovered in bacteriophages (phages). Phages can produce communication molecules of their own, or “listen in” on the host’s communication processes, in order to switch between lytic and lysogenic modes of infection. In this project, we studied the interaction of Vibrio cholerae, the causative agent of cholera disease, with the lysogenic vibriophage VP882. more...

Organism:

Vibrio cholerae

Type:

Other

Platform:

GPL33935

12 Samples

Download data: XLSX

(Submitter supplied) Many, if not all, bacteria use quorum sensing (QS) to control gene expression and collective behaviours, and more recently QS has also been discovered in bacteriophages (phages). Phages can produce communication molecules of their own, or “listen in” on the host’s communication processes, in order to switch between lytic and lysogenic modes of infection. In this project, we studied the interaction of Vibrio cholerae, the causative agent of cholera disease, with the lysogenic vibriophage VP882. more...

Organism:

Vibrio cholerae

Type:

Other

Platform:

GPL33935

12 Samples

Download data: XLSX

(Submitter supplied) Integrons are genetic elements that enable bacterial adaptation by collecting new genes encoded in integron cassettes (ICs) to create a reservoir of adaptive functions. These cassettes typically lack their own promoters and rely on the integron platform for their expression. Integrons, well-known for spreading antibiotic resistance genes in clinically relevant Gram-negative species, include Mobile Integrons (MIs), that transport over 170 resistance genes. more...

Organism:

Vibrio cholerae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28681

12 Samples

Download data: TSV

(Submitter supplied) Artemisinin (ARS) displayed bactericidal activity against Vibrio cholerae. To assess the mechanistic details of its antibacterial action, we have isolated V. cholerae mutants with enhanced ARS resistance and identified a gene (VCA0767), whose loss-of-function resulted in the ARS resistance phenotypes. This gene (atrR) encodes a TetR family transcriptional regulator, and its deletion mutant displayed the reduction in ARS-induced ROS formation and DNA damage. more...

Organism:

Vibrio cholerae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21023

8 Samples

Download data: TXT

(Submitter supplied) Mutation in flagellar transcriptional regulatory gene (flrA) result in increased V. cholerae growth and intracellular survival in the amoeba host Acanthamoeba castellanii. To identify molecular mechanisms behind the increased survival and growth of the flrA mutant transcriptomics assay was done.

Organism:

Vibrio cholerae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21023

5 Samples

Download data: TSV

(Submitter supplied) RNA-sequencing of Vibrio cholerae A1552 wild-type and ∆VCA0257 (∆rvvA) strains grown under virulence-inducing conditions (AKI).

Organism:

Vibrio cholerae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21023

6 Samples

Download data: CSV