Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DNA microarray analysis of ClosTron-mediated knock-out mutants of C. acetobutylicum ATCC 824 growing in a pH-controlled phosphate-limited chemostat system

ABSTRACT: DNA microarray analysis of C.acetobutylicum mutants with defects in several fermentative branch points

ORGANISM(S): Clostridium acetobutylicum

SUBMITTER: Daniel Hoenicke

PROVIDER: E-MTAB-2058 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Functions and adaptive responses to oxidative stress of the thioredoxin and glutathione pathways in Clostridium acetobutylicum

Project description:Oxidative stress is harmful for organism and occurs when the cells exposed to superoxid, hydrogen peroxide and alkylhydroperoxides. In microorganism, the glutathione- and thioredoxin-dependent reduction systems are universal and play an important role in response to defending oxidative stress. The _-glutamylcysteine synthetase (_-GCS) is an essential enzyme to biosynthesize the tripeptide glutathione (GSH) in organism. Similarly, thioredoxin reductase is an important enzyme in thioredoxin-dependent reduction system. In Clostridium acetobutylicum, the _-glutamylcysteine synthetase (encoded by CAC1539, gcs) and thioredoxin reductase (encoded by CAC1548, trxB) were inactivated using ClosTron technology. The gcs mutant grew insufficiently and consumed less glucose in the phosphate-limited continuous culture and exhibited more sensitive to oxidative stress. The trxB mutant just exhibited lower growth rate and less glucose uptake in the solventogenic phase, compared to wild type. The DNA microarrays were performed to investigate the transcripome difference between wild type and the mutants. In gcs mutant, the genes related to chemotaxis and flagella biosynthesis proteins were induced significantly and in the trxB mutant, the sporulation genes were induced largely. Based on the phenotypes and transcriptome comparison results, the relationship between GSH- and Trx-dependent induction systems was discussed in Clostridium acetobutylicum.

2015-04-13 | E-MTAB-2747 | biostudies-arrayexpress

DNA microarray analysis of a ClosTron-mediated knock-out mutant of C. acetobutylicum ATCC 824 with a defect in the pyruvate formate lyase

Project description:C. acetobutylicum pflB::int(1335) and its parental wild-type strain were cultivated in a batch culture to identify, via DNA microarray analyses, changes in the gene expression.

2014-04-01 | E-MTAB-2059 | biostudies-arrayexpress

The sulfur metabolism during Acetogenesis and Solventogenesis of Clostridium acetobutylicum

Project description:The batch fermentation of Clostridium acetobutylicum is characterized by an acetogenic growth phase during exponential growth when mainly acetate and butyrate are fermentation products. Then, at the end of exponential growth and during stationary phase, the organism switches to solventogenic growth and large amounts of acetone, ethanol and butanol are produced. These growth phases can be studied independent from each other in a phosphate-limited continuous culture. In transcription analysis of continuous cultures using DNA microarrays it became evident that, among others, operons involved in sulfur assimilation are strongly up-regulated during solventogenesis. Using the ClosTron technique we constructed two knock-out mutants in the genes CAC0105 and CAC0930 annotated as involved in sulfate reduction and cysteine biosynthesis. Complementation experiments were carried out with sulfite and cysteine to prove the predicted function. The fermentation experiments of wild type and mutants using phosphate-limited and sulfur-limited continuous culture demonstrated that less sulfur source was consumed in solventogenic phase and the efficiency of cysteine uptake became lower. DNA microarrays were performed to study the difference of transcriptional expression when the wild type was challenged with insufficient sulfur source and the mccB (CAC0930) mutant was inactivated in the continuous culture. The result provided insights into understanding the sulfur metabolism regulatory.

2015-04-15 | E-MTAB-2745 | biostudies-arrayexpress

Confirmation of glucose transporters through targeted mutagenesis and transcriptional analysis in Clostridium acetobutylicum

Project description:Glucose uptake in Escherichia coli had been studied extensively, but the lack of basic information of glucose uptake systems in C. acetobutylicum has limited the understanding of glucose assimilation in this strain. There is a main glucose transporter which is very efficient for glucose uptake and the maltose, mannose and galactose transport systems are also able to transport glucose into cytoplasm of E.coli. Therefore, it is very interesting to investigate whether a similar glucose transport mechanism exists in C. acetobutylicum.

2022-12-28 | E-MTAB-12054 | biostudies-arrayexpress

Transcription profiling of continuous cultures of Clostridium acetobutylicum during the metabolic switch from acidogenesis to solventogenesis

Project description:effect of pH on continuous cultures of Clostridium acetobutylicum

2010-09-30 | E-MEXP-2314 | biostudies-arrayexpress

Transcription profiling by array of Clostridium acetobutylicum on glucose and xylose substrates under exponential, continuous and diauxie growth.

Project description:Clostridium acetobutylicum was grown in a batch-culture with minimal medium containing glucose and xylose as substrate. Diauxie growth was observed after glucose was consumed. Following the organism grows on xylose. Transcriptional analysis was done to pursue the cellular processes during the switch from growth on glucose to growth on xylose. We compared DNA-Microarray data from cells grown during the exponential phase on glucose (A), with cells growing during the start of diauxie growth lag (B), during the end of diauxie growth lag (C) and during exponential growth on xylose (D). We used cells grown in a continuous culture with glucose as substrate as common reference for the samples A-D.

2010-09-30 | E-MEXP-2613 | biostudies-arrayexpress

Fur in Clostridium acetobutylicum

Project description:Clostridium acetobutylicum is a Gram-positive, endospore-forming bacterium that is considered as a strict anaerobe. It ferments sugars to the organic acids acetate and butyrate or shifts to formation of the solvents - ethanol, butanol and acetone. In most bacteria the major regulator of iron homeostasis is Fur (ferric uptake regulator). Analysis of the genome of Clostridium acetobutylicum has revealed three genes encoding Fur-like proteins. The amino acid sequece of one of them showed 70% similarity to the Fur protein of the closely related Bacillus subtilis.<br>Thus, to gain insight into the role of Fur and the mechanisms for maintenance of iron homeostasis in this strict anaerobic organism, we determined its transcriptional profile in response to iron limitation and inactivation of fur.

2012-03-30 | E-MEXP-3401 | biostudies-arrayexpress

A transcriptional study of acidogenic chemostat cells of Clostridium acetobutylicum - cellular behavior in adaptation to n-butanol

Project description:Clostridium acetobutylicum is well-known for its butanol production. Butanol toxicity is a major drawback for the generation of high-butanol producing strains. Here, the transcriptional response a steady state, acidogenic (pH 6), phosphate-limited Clostridium acetobutylicum chemostat culture to different levels of n-butanol (0.25-1%) was investigated. For the butanol challenge experiments butanol (1-butanol) was added (a) to the supplying medium and (b) to the culture vessel to guarantee an immediate change in the butanol concentration. Addition of butanol to the culture was timed to match the supply of the new medium through the feedlines. The butanol concentration was increased stepwise in intervals of 66.6 h (5 volume changes) to moderate butanol concentrations of 0.25%, 0.5%, 0.75% and 1% (v/v).

2012-01-30 | E-MEXP-3571 | biostudies-arrayexpress

Lactococcus lactis subsp. cremoris GE2-14 (GE2-14) vs Lactococcus lactis subsp. cremoris GE2-14 ?aguR (GE2-14 ?aguR)

Project description:Trancriptional profiling of GE2-14 ?aguR mutant strain in which the aguR gene of the agmatine deiminase cluster has been deleted. We compared the expression profiling of GE2-14 cells with the expression profiling of GE2-14 ?aguR mutant cells. The goal was to determine the effect of the aguR deletion on the transcriptional profiling of GE2-14 Two strains GE2-14 (reference) vs. GE2-14 ?aguR (test) cells in same conditions. Three biological replicates, two technical replicates and one dye swap.

2015-07-08 | E-GEOD-59514 | biostudies-arrayexpress

Transcription profiling by array of Ralstonia eutropha H16 grown with organic sulfur compounds TDP and DTDP

Project description:Catabolism of the organic sulfur compounds TDP and DTDP in Ralstonia eutropha and the accumulation of the copolymer poly(3HB-co-3MP)

2011-05-31 | E-MEXP-2744 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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