Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

106 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA sequencing for Comparisons of Vibrio Cholerae Wild Type and VchM Knock Out

ABSTRACT: DNA methylation is a key epigenetic regulator in all domains of life, yet the effects of most bacterial DNA methyltransferases on cellular processes are largely undefined. Here, we used diverse techniques, including bisulfite sequencing, transcriptomics, and transposon insertion site sequencing to extensively characterize a 5-methylcytosine (5mC) methyltransferase, VchM, in the cholera pathogen, Vibrio cholerae. We have comprehensively defined VchM's DNA targets, its genetic interactions and the gene networks that it regulates. Although VchM is a relatively new component of the V. cholerae genome, it is required for optimal V. cholerae growth in vitro and during infection. Unexpectedly, the usually essential ÏE cell envelope stress pathway is dispensable in ÎvchM V. cholerae, likely due to its lower activation in this mutant and the capacity for VchM methylation to limit expression of some cell envelope modifying genes. Our work illuminates how an acquired DNA methyltransferase can become integrated within complex cell circuits to control critical housekeeping processes. Duplicates were used for all samples. For each strain background (C6706 and O395), there were control (Wildtype) samples and experimental samples (VchM knockout)

ORGANISM(S): Vibrio cholerae

SUBMITTER: Shijia Zhu

PROVIDER: E-GEOD-73975 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Bisulfite Sequencing for Studying 5mC DNA Methylation Distribution in Vibrio Cholerae

Project description:DNA methylation is a key epigenetic regulator in all domains of life, yet the effects of most bacterial DNA methyltransferases on cellular processes are largely undefined. Here, we used diverse techniques, including bisulfite sequencing, transcriptomics, and transposon insertion site sequencing to extensively characterize a 5-methylcytosine (5mC) methyltransferase, VchM, in the cholera pathogen, Vibrio cholerae. We have comprehensively defined VchM's DNA targets, its genetic interactions and the gene networks that it regulates. Although VchM is a relatively new component of the V. cholerae genome, it is required for optimal V. cholerae growth in vitro and during infection. Unexpectedly, the usually essential ÏE cell envelope stress pathway is dispensable in ÎvchM V. cholerae, likely due to its lower activation in this mutant and the capacity for VchM methylation to limit expression of some cell envelope modifying genes. Our work illuminates how an acquired DNA methyltransferase can become integrated within complex cell circuits to control critical housekeeping processes. Duplicates samples were analyzed for wildtype cells grown under 3 conditions: exponential phase, stationary phase and rabbit intestinal infection

2015-10-26 | E-GEOD-73974 | biostudies-arrayexpress

Chemoproteomic profiling of host and pathogen enzymes active in cholera

Project description:Activity-based protein profiling (ABPP) is a chemoproteomic tool for detecting active enzymes in complex biological systems. We used ABPP to identify secreted bacterial and host serine hydrolases that are active in animals infected with the cholera pathogen Vibrio cholerae. Four V. cholerae proteases were consistently active in infected rabbits, and one, VC0157 (renamed IvaP), was also active in human cholera stool. Inactivation of IvaP influenced the activity of other secreted V. cholerae and rabbit enzymes in vivo, while genetic disruption of all four proteases increased the abundance and binding of an intestinal lectin—intelectin—to V. cholerae in infected rabbits. Intelectin also bound to other enteric bacterial pathogens, suggesting it may constitute a previously unrecognized mechanism of bacterial surveillance in the intestine that is inhibited by pathogen-secreted proteases. Our work demonstrates the power of activity-based proteomics to reveal host-pathogen enzymatic dialogue in an animal model of infection.

2016-02-22 | PXD003000 | Pride

RNA sequencing for Comparisons of Vibrio Cholerae Wild Type and VchM Knock Out

Project description:DNA methylation is a key epigenetic regulator in all domains of life, yet the effects of most bacterial DNA methyltransferases on cellular processes are largely undefined. Here, we used diverse techniques, including bisulfite sequencing, transcriptomics, and transposon insertion site sequencing to extensively characterize a 5-methylcytosine (5mC) methyltransferase, VchM, in the cholera pathogen, Vibrio cholerae. We have comprehensively defined VchM's DNA targets, its genetic interactions and the gene networks that it regulates. Although VchM is a relatively new component of the V. cholerae genome, it is required for optimal V. cholerae growth in vitro and during infection. Unexpectedly, the usually essential σE cell envelope stress pathway is dispensable in ΔvchM V. cholerae, likely due to its lower activation in this mutant and the capacity for VchM methylation to limit expression of some cell envelope modifying genes. Our work illuminates how an acquired DNA methyltransferase can become integrated within complex cell circuits to control critical housekeeping processes.

2015-10-26 | GSE73975 | GEO

Bisulfite Sequencing for Studying 5mC DNA Methylation Distribution in Vibrio Cholerae

Project description:DNA methylation is a key epigenetic regulator in all domains of life, yet the effects of most bacterial DNA methyltransferases on cellular processes are largely undefined. Here, we used diverse techniques, including bisulfite sequencing, transcriptomics, and transposon insertion site sequencing to extensively characterize a 5-methylcytosine (5mC) methyltransferase, VchM, in the cholera pathogen, Vibrio cholerae. We have comprehensively defined VchM's DNA targets, its genetic interactions and the gene networks that it regulates. Although VchM is a relatively new component of the V. cholerae genome, it is required for optimal V. cholerae growth in vitro and during infection. Unexpectedly, the usually essential σE cell envelope stress pathway is dispensable in ΔvchM V. cholerae, likely due to its lower activation in this mutant and the capacity for VchM methylation to limit expression of some cell envelope modifying genes. Our work illuminates how an acquired DNA methyltransferase can become integrated within complex cell circuits to control critical housekeeping processes.

2015-10-26 | GSE73974 | GEO

A dual RNA regulator balancing carbon uptake and 1 central metabolism in Vibrio cholerae

Project description:Bacterial small RNAs (sRNAs) are well-known to modulate gene expression by base-pairing with trans-coded transcripts and are typically considered to be non-coding. However, several sRNAs have been reported to also contain an open reading frame and thus are considered dual regulators. In this study, we discovered a dual regulator from Vibrio cholerae, called VcdRP, harboring a 29 amino acid protein (VcdP), as well as a base-pairing sequence. Using a forward genetic screen, we identified VcdRP as a repressor of cholera toxin production and we link this phenotype to inhibition of carbon transport by the base-pairing segment of the regulator. By contrast, we demonstrate that VcdP acts downstream of carbon transport by binding to citrate synthase (GltA), the first enzyme of the citric cycle. Interaction of VcdP with GltA results in increased enzyme activity and together VcdR and VcdP reroute carbon metabolism. We further show that transcription of vcdRP is repressed by CRP allowing us to provide a model in which VcdRP employs two different molecular mechanisms to synchronize sugar uptake and metabolism in V. cholerae.

2021-07-22 | PXD025275 | Pride

Microarray analysis of V. cholerae genes differentially expressed in rabbit ileal loop fluid and mucus

Project description:This SuperSeries is composed of the following subset Series: GSE6217: Microarray analysis of V. cholerae genes differentially expressed in 12 h rabbit ileal loop fluid GSE24405: Microarray analysis of V. cholerae genes differentially expressed in 8 h rabbit ileal loop mucus GSE24406: Microarray analysis of V. cholerae genes differentially expressed in 12 h rabbit ileal loop mucus GSE24407: Microarray analysis of V. cholerae genes differentially expressed in 8h rabbit ileal loop fluid Refer to individual Series

2010-09-28 | E-GEOD-24408 | biostudies-arrayexpress

Proteomic analysis of the pathogen surface in cholera identifies host proteins involved in defense and microbiota recognition

Project description:The microbial cell surface is a critical site of microbe-host interactions that often control infection outcomes. Defining the set of host proteins present at this interface has been challenging. Here, we used a surface biotinylation approach coupled to quantitative mass spectrometry to identify and quantify both bacterial and host proteins present on the surface of diarrheal fluid-derived V. cholerae in an infant rabbit model of cholera. Our data showed that V. cholerae surfaces were coated with numerous host proteins, whose abundance were driven by the presence of cholera toxin, including the C type lectin SP-D. Mice lacking SP-D had enhanced V. cholerae intestinal colonization. Additional host proteins (AnxA1, LPO and ZAG) capable of binding V. cholerae were also found to recognize distinct taxa of the murine intestinal microbiota, suggesting that these host factors may play roles in intestinal homeostasis in addition to host defense. Proteomic analysis of microbial surfaces is valuable for identifying host interactions that regulate infection and homeostasis with both pathogens and endogenous microbiota alike.

2021-10-02 | PXD027076 | Pride

Exploiting Dynamics of Genomic Islands to Edit the Genome of Vibrio cholerae and Identify Novel Interactions Between Core and Acquired Genome

Project description:Horizontally acquired genetic elements (HGEs) plays a major for determination of virulence, antimicrobial resistance, adaptation and evolution in pathogenic bacteria. Conserved integrative mobile genetic elements (MGEs) of Vibrio cholerae contribute in the disease development, antimicrobial resistance and metabolic functions. To understand the dynamics of integrative MGEs and cross talk between MGEs and core genome, engineered genome of V. cholerae was monitored in the presence and absence of horizontally acquired genetic elements. Deletion of more than 250 revealed that CTX contributes to the essentiality of SOS response master regulator LexA in V. cholerae. Also, he core genome encoded RecA helps CTX to bypass the host immunity and replicate in the host cell in the presence of similar prophage in the host chromosome. Finally, our multiomics data reveal importance of MGEs in modulating the level of cellular proteome and metabolome in V. cholerae. This study for the first time engineered the genome of V. cholerae strains to eliminate all the GIs, ICE and prophages from their genome and revealed new interactions between core and acquired genomes. The engineered strain could be a potential candidate for understanding evolution of cholera pathogen and development of therapeutics.

2020-09-28 | PXD017801 | Pride

S-Nitrosylation of the Virulence Regulator AphB Promotes Vibrio cholerae Pathogenesis

Project description:S-Nitrosylation of the Virulence Regulator AphB Promotes Vibrio cholerae Pathogenesis

2022-05-31 | PXD031615 | Pride

Differential RNA-seq analysis of Vibrio cholerae identifies the VqmR sRNA as a regulator of collective behaviors

Project description:Quorum sensing (QS) is a process of cell-cell communication that enables bacteria to transition between individual and collective lifestyles. QS controls virulence in Vibrio cholerae, the causative agent of the disease cholera. Differential RNA-sequencing (dRNA-seq) analyses of wild-type V. cholerae and a locked low cell density QS-mutant strain identified a total of 7641 transcriptional start sites (TSS) with ~40% initiated in the antisense direction. Genome-wide TSS mapping combined with phylogenetic comparisons enabled re-annotation of 129 genes from the NCBI database. 107 of the transcripts we identified do not appear to encode proteins suggesting they could specify non-coding RNAs. We focused on one such transcript that we name VqmR. vqmR is located upstream of the vqmA gene that encodes a DNA-binding transcription factor. Mutagenesis and microarray analyses demonstrate that VqmA activates vqmR transcription; that vqmR encodes a regulatory RNA, and VqmR directly controls at least eight mRNA targets including the rtxBA toxin genes and the vpsT transcriptional regulator of biofilm production. We show that VqmR inhibits biofilm formation through repression of vpsT. Together, these data provide the first global annotation of the V. cholerae transcription landscape and they highlight the importance of post-transcriptional regulation for collective behaviors in this human pathogen. Global mapping TSS in V. cholerae

2014-12-08 | E-GEOD-62084 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data