Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete genome sequence of Vibrio parahaemolyticus CHN25 and transcriptomic analysis of cold shock proteins of VpaCspA and VpaCspD in the adaptation of low temperature growth

ABSTRACT: To investigate low-temperature tolerance of the bacterium, three in-frame gene deletion mutants of VpacspA and VpacspD were constructed using homologous recombination method. When compared to the wild type strain, the growth of ΔVpacspA mutant was strongly repressed at 10 0C, whereas the deletion of VpacspD gene greatly activated the bacterium growth at the low temperature. Transcriptome data revealed that 12.4% of the expressed genes in V. parahaemolyticus CHN25 was significantly changed in ΔVpacspA mutant grown at 10 0C, including those involved in amino acid degradation, ATP-binding cassette (ABC) transporters, secretion systems, sulfur and glycerophospholipid metabolisms, whereas the low temperature elicited 10.0% of the genes from ΔVpacspD mutant, such as phosphotransferase system, nitrogen and amino acid metabolisms. Moreover, the major changed metabolic pathways in dual-gene deletion mutant (ΔVpacspAD) differed radically from those in single-gene mutants. Comparison of transcriptome profiles further revealed a number of differentially expressed genes shared among the three mutants, as well as regulators specifically, coordinately and or antagonistically regulating in the adaptation of V. parahaemolyticus CHN25 to the low-temperature growth. mRNA profiles of mid-log phase WT(G), ΔVpacspA, ΔVpacspD and ΔVpacspAD at 10 °C were generated by deep sequencing using Illumina HiSeq 2500

ORGANISM(S): Vibrio parahaemolyticus

SUBMITTER: Lanming Chen

PROVIDER: E-GEOD-65998 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Complete genome sequence of Vibrio parahaemolyticus CHN25 and transcriptomic analysis of cold shock proteins of VpaCspA and VpaCspD in the adaptation of low temperature growth

Project description:To investigate low-temperature tolerance of the bacterium, three in-frame gene deletion mutants of VpacspA and VpacspD were constructed using homologous recombination method. When compared to the wild type strain, the growth of ΔVpacspA mutant was strongly repressed at 10 0C, whereas the deletion of VpacspD gene greatly activated the bacterium growth at the low temperature. Transcriptome data revealed that 12.4% of the expressed genes in V. parahaemolyticus CHN25 was significantly changed in ΔVpacspA mutant grown at 10 0C, including those involved in amino acid degradation, ATP-binding cassette (ABC) transporters, secretion systems, sulfur and glycerophospholipid metabolisms, whereas the low temperature elicited 10.0% of the genes from ΔVpacspD mutant, such as phosphotransferase system, nitrogen and amino acid metabolisms. Moreover, the major changed metabolic pathways in dual-gene deletion mutant (ΔVpacspAD) differed radically from those in single-gene mutants. Comparison of transcriptome profiles further revealed a number of differentially expressed genes shared among the three mutants, as well as regulators specifically, coordinately and or antagonistically regulating in the adaptation of V. parahaemolyticus CHN25 to the low-temperature growth.

2015-02-18 | GSE65998 | GEO

Differential expression analysis of a Vibrio parahaemolyticus ∆luxO mutant compared to wild-type in mouse intestinal mucus

Project description:Vibrio parahaemolyticus is the leading bacterial cause for seafood-related gastroenteritis worldwide. As an intestinal pathogen, V. parahaemolyticus competes with other commensal bacteria for the same pool of nutrients. The major source of nutrition for intestinal bacteria is intestinal mucus. We wanted to determine the expression profile of wild-type V. parahaemolyticus in mouse intestinal mucus and then perform a differential expression analysis in a ∆luxO deletion mutant, in which the high cell density quorum sensing regulator OpaR is constitutively expressed and low cell density regulator AphA is repressed.

2017-01-13 | GSE93547 | GEO

RIMD 2210633 wild type versus vtrA or vtrB mutants

Project description:Vibrio parahaemolyticus is a Gram-negative marine bacterium. A limited population of the organisms causes acute gastroenteritis in humans. Vibrio parahaemolyticus wild type strain RIMD 2210633 compared with the mutants of VtrA and VtrB have a winged helix-turn-helix DNA binding motif that genes encoded on pathogenicity island loci, at OD600=1.0 in Luria-Bertani containing medium 0.5 % NaCl at 37˚C. Our goal is to determine the VtrA or VtrB regulon. Cohybridized wild type versus vtrA or vtrB mutants on a single array. Biological replicates: three of wild type, three of vtrA mutants and three of vtrB mutants were independently grown and harvested.

2010-07-16 | E-GEOD-17242 | biostudies-arrayexpress

RIMD 2210633 wild type versus vtrA or vtrB mutants

2010-07-16 | GSE17242 | GEO

Changes in global gene expression of Vibrio parahaemolyticus induced by cold- and heat-stress

Project description:Vibrio (V.) parahaemolyticus is the leading cause of seafood borne gastro-intestinal infections in humans worldwide. It is widely found in marine environments and is isolated frequently from seawater, estuarine waters, sediments and raw or insufficiently cooked seafood. Within the food chain, V. parahaemolyticus encounters different temperature conditions that might alter the metabolism and pathogenicity of the bacterium. In this study, we performed gene expression profiling of V. parahaemolyticus RIMD 2210633 after exposure to 4°C, 15°C, 20°C, 37°C and 42°C to describe the cold and heat shock response. Analysis of transcriptomics data resulted in differential expression of 19 genes at 20°C, 193 genes at 4°C, 625 genes at 42°C and 639 genes at 15°C. Thus the highest portion of significantly expressed genes was observed at 15°C and 42°C with 13.3% and 13%, respectively. Genes of many functional categories were highly regulated even at lower temperatures. Our results showed that virulence associated genes (tdh1, tdh2, toxR, toxS, vopC, T6SS1, T6SS2) remained largely unaffected by heat or cold stresses. Along with folding and temperature shock depending systems, an overall temperature depended regulation of expression could be shown. Particularly the energy metabolism was affected most by changed temperatures. Whole-genome gene expression studies of food related pathogens such as V. parahaemolyticus reveal how these pathogens react to stress impacts for prediction of its behaviour under conditions like storage and transport.

2014-08-27 | GSE60815 | GEO

Differential expression analysis of a Vibrio parahaemolyticus ∆rpoN mutant compared to wild-type in minimal media supplemented with glucose or mouse intestinal mucus

2020-02-14 | GSE95555 | GEO

Changes in global gene expression of Vibrio parahaemolyticus induced by cold- and heat-stress

Project description:Vibrio (V.) parahaemolyticus is the leading cause of seafood borne gastro-intestinal infections in humans worldwide. It is widely found in marine environments and is isolated frequently from seawater, estuarine waters, sediments and raw or insufficiently cooked seafood. Within the food chain, V. parahaemolyticus encounters different temperature conditions that might alter the metabolism and pathogenicity of the bacterium. In this study, we performed gene expression profiling of V. parahaemolyticus RIMD 2210633 after exposure to 4Â°C, 15Â°C, 20Â°C, 37Â°C and 42Â°C to describe the cold and heat shock response. Analysis of transcriptomics data resulted in differential expression of 19 genes at 20Â°C, 193 genes at 4Â°C, 625 genes at 42Â°C and 639 genes at 15Â°C. Thus the highest portion of significantly expressed genes was observed at 15Â°C and 42Â°C with 13.3% and 13%, respectively. Genes of many functional categories were highly regulated even at lower temperatures. Our results showed that virulence associated genes (tdh1, tdh2, toxR, toxS, vopC, T6SS1, T6SS2) remained largely unaffected by heat or cold stresses. Along with folding and temperature shock depending systems, an overall temperature depended regulation of expression could be shown. Particularly the energy metabolism was affected most by changed temperatures. Whole-genome gene expression studies of food related pathogens such as V. parahaemolyticus reveal how these pathogens react to stress impacts for prediction of its behaviour under conditions like storage and transport. Temperature induced gene expression was detected in total bacterial RNA of V. parahaemolyticus. Five different temperatures (4Â°C, 15Â°C, 20Â°C, 37Â°C, 42Â°C) were used in at least 3 biological replicates (4 replicates for 37Â°C). Gene expression at 37Â°C was used for normalization.

2014-08-27 | E-GEOD-60815 | biostudies-arrayexpress

Effect of high CO2 levels and low temperature storage on table grapes quality harvested at two maturity stages.

Project description:Table grapes cv. Cardinal are highly perishable and their quality deteriorates during postharvest storage at low temperature mainly because of sensitivity to fungal decay and senescence of rachis. The application of a 3-day CO2 treatment with 20 kPa CO2 at 0C reduced total decay and retained fruit quality in early and late-harvested table grapes during postharvest storage. In order to study the transcriptional responsiveness of table grapes to low temperature and high CO2 levels in the first stage of storage and how the maturity stage affect these changes, we have performed a comparative large-scale transcriptional analysis. In the first stage of storage, low temperature led to a significantly intense change in grape skin transcriptome irrespective of fruit maturity, although there were different changes within each stage. In the case of CO2 treated samples, in comparison to fruit at time zero, only slight differences were observed. Functional enrichment analysis revealed that major modifications in the transcriptome profile of early- and late-harvested grapes stored at 0C are linked to biotic and abiotic stress-responsive terms. However, in both cases there is a specific reprogramming of the transcriptome during the first stage of storage at 0C in order to withstand the cold stress. Thus, genes involved in gluconeogenesis, photosynthesis, mRNA translation and lipid transport were up-regulated in the case of early-harvested grapes, and genes related to protein folding stability and intracellular membrane trafficking in late-harvested grapes. The beneficial effect of high CO2 treatment maintaining table grape quality seems to be an active process requiring the induction of several transcription factors and kinases in early-harvested grapes, and the activation of processes associated to the maintenance of energy in late-harvested grapes.

2016-09-04 | GSE83275 | GEO

Ruegeria pomeroyi transporter mutant substrate drawdown

Project description:The goal of this project was to identify bacterial transporters responsible for uptake of environmentally relevant marine metabolites. We used the model marine heterotrophic bacterium Ruegeria pomeroyi DSS-3, for which an arrayed library of single gene knockout mutants has been generated by selecting isolated from a barcoded transposon mutant library (BasSeq). Knockout mutants of putative transporters were grown on minimal medium with a single substrate as sole carbon source. Mutant defect was assessed by comparing the substrate drawdown of isolated mutants to drawdown by a pooled mutant library (BarSeq), a proxy for wildtype fitness.

2022-11-16 | ST002381 | MetabolomicsWorkbench

Abscisic acid enhance cold tolerance in barley

Project description:ABA deficiency reduced low temperature responses via disturbing stability of chloro-plast ultrastructure, modifying the starch and sucrose metabolisms, and affecting an-tioxidant enzyme activities in barley.

2023-07-15 | PXD043642 | Pride

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