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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of Vibrio cholerae isolated from clinical samples, grown in minimal media with maltose and rich media in order to validate predicted metabolic pathways

ABSTRACT: Growth to mid exponential phase in M9 minimal media supplemented with 0.5% maltose versus growth in rich LB media

ORGANISM(S): Vibrio cholerae

SUBMITTER: Janos Demeter

PROVIDER: E-SMDB-3688 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Evidence supporting predicted metabolic pathways for Vibrio cholerae: gene expression data and clinical tests.

Shi Jing J Romero Pedro R PR Schoolnik Gary K GK Spormann Alfred M AM Karp Peter D PD

Nucleic acids research 20060508 8

Vibrio cholerae, the etiological agent of the diarrheal illness cholera, can kill an infected adult in 24 h. V.cholerae lives as an autochthonous microbe in estuaries, rivers and coastal waters. A better understanding of its metabolic pathways will assist the development of more effective treatments and will provide a deeper understanding of how this bacterium persists in natural aquatic habitats. Using the completed V.cholerae genome sequence and PathoLogic software, we created VchoCyc, a pathw ...[more]

PMID: 16682451

Similar Datasets

Growth in minimal media with maltose

Project description:Growth to mid exponential phase in M9 minimal media supplemented with 0.5% maltose versus growth in rich LB media Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Media: M9 minimal media with 0.5% maltose Keywords: Logical Set

2006-05-20 | GSE4876 | GEO

Growth in minimal media with maltose

2006-05-20 | E-GEOD-4876 | biostudies-arrayexpress

Transcription profiling of Vibrio cholerae, isolated from clinical samples, grown in minimal media with lactate or rich media to validate predicted metabolic pathways

Project description:Growth to mid exponential phase in M9 minimal media supplemented with 0.5% lactate versus growth in rich LB media

2006-06-06 | E-SMDB-3687 | biostudies-arrayexpress

Transcription profiling of Vibrio cholerae isolated from clinical samples, grown in minimal and rich media in order to validate predicted metabolic pathways

Project description:Vibrio cholerae, the etiological agent of the diarrheal illness cholera, can kill an infected adult in 24 h. V.cholerae lives as an autochthonous microbe in estuaries, rivers and coastal waters. A better understanding of its metabolic pathways will assist the development of more effective treatments and will provide a deeper understanding of how this bacterium persists in natural aquatic habitats. Using the completed V.cholerae genome sequence and PathoLogic software, we created VchoCyc, a pathway-genome database that predicted 171 likely metabolic pathways in the bacterium. We report here experimental evidence supporting the computationally predicted pathways. The evidence comes from microarray gene expression studies of V.cholerae in the stools of three cholera patients [D. S. Merrell, S. M. Butler, F. Qadri, N. A. Dolganov, A. Alam, M. B. Cohen, S. B. Calderwood, G. K. Schoolnik and A. Camilli (2002) Nature, 417, 642-645.], from gene expression studies in minimal growth conditions and LB rich medium, and from clinical tests that identify V.cholerae. Expression data provide evidence supporting 92 (53%) of the 171 pathways. The clinical tests provide evidence supporting seven pathways, with six pathways supported by both methods. VchoCyc provides biologists with a useful tool for analyzing this organism's metabolic and genomic information, which could lead to potential insights into new anti-bacterial agents. VchoCyc is available in the BioCyc database collection (http://BioCyc.org).

2013-01-30 | E-SMDB-3690 | biostudies-arrayexpress

Vibrio cholerae

Project description:Growth in minimal media with maltose

| PRJNA104489 | ENA

Evidence supporting predicted metabolic pathways for Vibrio cholerae: gene expression data and clinical tests

Project description:Abstract: Vibrio cholerae, the etiological agent of the diarrheal illness cholera, can kill an infected adult in 24 h. V.cholerae lives as an autochthonous microbe in estuaries, rivers and coastal waters. A better understanding of its metabolic pathways will assist the development of more effective treatments and will provide a deeper understanding of how this bacterium persists in natural aquatic habitats. Using the completed V.cholerae genome sequence and PathoLogic software, we created VchoCyc, a pathway-genome database that predicted 171 likely metabolic pathways in the bacterium. We report here experimental evidence supporting the computationally predicted pathways. The evidence comes from microarray gene expression studies of V.cholerae in the stools of three cholera patients [D. S. Merrell, S. M. Butler, F. Qadri, N. A. Dolganov, A. Alam, M. B. Cohen, S. B. Calderwood, G. K. Schoolnik and A. Camilli (2002) Nature, 417, 642-645.], from gene expression studies in minimal growth conditions and LB rich medium, and from clinical tests that identify V.cholerae. Expression data provide evidence supporting 92 (53%) of the 171 pathways. The clinical tests provide evidence supporting seven pathways, with six pathways supported by both methods. VchoCyc provides biologists with a useful tool for analyzing this organism's metabolic and genomic information, which could lead to potential insights into new anti-bacterial agents. VchoCyc is available in the BioCyc database collection (http://BioCyc.org). This SuperSeries is composed of the following subset Series: GSE3104: Hyperinfectivity study GSE4875: Growth in minimal media with lactate GSE4876: Growth in minimal media with maltose Refer to individual Series

2006-05-20 | E-GEOD-4877 | biostudies-arrayexpress

Thermotoga maritima wild type minimal media expression analysis

Project description:An eight chip study using total RNA recovered from separate wild-type cultures of Thermotoga maritima at mid-log with 3 different minimal sugar media. A eight-chip study using total RNA recovered from separate wild-type cultures of Thermotoga maritima at mid-log with 3 different minimal sugar media. 4 biological replicates maltose, 2 biological replicates L-arabinose, 2 biological replicates cellobiose.

2012-07-02 | E-GEOD-28822 | biostudies-arrayexpress

V. cholerae transcriptome in MH, supplemented or not with glucose 0.4% or maltose 0.4%

Project description:We study gene expression levels of V. cholerae N16961 WT and crp mutant strains/V. cholerae N16961 hapR+ corrected strain, ravAviA mutant and ravAviA overexpressing strains in exponential phase in MH, MH+maltose 0.4% and MH+glucose 0.4%

2022-02-16 | GSE196651 | GEO

Growth in minimal media with lactate

Project description:Growth to mid exponential phase in M9 minimal media supplemented with 0.5% lactate versus growth in rich LB media Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Media: M9 minimal media with 0.5% lactate Keywords: Logical Set

2006-05-20 | GSE4875 | GEO

Prolonged Maltose-Limited Cultivation of Saccharomyces cerevisiae

Project description:Prolonged cultivation (>25 generations) of Saccharomyces cerevisiae in aerobic, maltose-limited chemostat cultures led to profound physiological changes. Maltose hypersensitivity was observed when cells from prolonged cultivations were suddenly exposed to excess maltose. This substrate hypersensitivity was evident from massive cell lysis and loss of viability. During prolonged cultivation at a fixed specific growth rate, the affinity for the growth-limiting nutrient (i.e., maltose) increased, as evident from a decreasing residual maltose concentration. Furthermore, the capacity of maltose-dependent proton uptake increased up to 2.5-fold during prolonged cultivation. Genome-wide transcriptome analysis showed that the increased maltose transport capacity was not primarily due to increased transcript levels of maltose-permease genes upon prolonged cultivation. We propose that selection for improved substrate affinity (ratio of maximum substrate consumption rate and substrate saturation constant) in maltose-limited cultures leads to selection for cells with an increased capacity for maltose uptake. At the same time, the accumulative nature of maltose-proton symport in S. cerevisiae leads to unrestricted uptake when maltose-adapted cells are exposed to a substrate excess. These changes were retained after isolation of individual cell lines from the chemostat cultures and nonselective cultivation, indicating that mutations were involved. The observed trade-off between substrate affinity and substrate tolerance may be relevant for metabolic engineering and strain selection for utilization of substrates that are taken up by proton symport. Keywords: Evolution

2007-08-31 | GSE8897 | GEO

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