Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

56 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of Clostridium acetobutylicum during acidogenesis and solventogenesis

ABSTRACT: Clostridium acetobutylicum is characterized by its acetone-butanol (AB) fermentation which
can be reproducibly established under continuous grow conditions in a chemostat.
At pH 5.7 cells show typical acidogenic metabolism and mainly produce the acids
acetate and butyrate. After lowering and further control the external pH at 4.5
the exponentially growing cells switch towards stable solvent production with the
dominating fermentation products acetone and butanol.
Here we present a comprehensive comparison of proteome and transcriptome
data of continuously growing cells of C. acetobutylicum in a chemostat culture
under phosphate limitation at pH 5.7 (acidogenesis) and pH 4.5 (solventogenesis).

ORGANISM(S): Clostridium acetobutylicum

SUBMITTER: Holger Janssen

PROVIDER: E-MEXP-2503 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

A transcriptional study of acidogenic chemostat cells of Clostridium acetobutylicum following a single n-butanol pulse

Project description:In this study the transcriptional behavior of the natural solvent producing bacterium Clostridium acetobutylicum was investigated following n-butanol stress using DNA microarray analysis. Therefore, a phosphate-limited chemostat culture was established and n-butanol stress (0.9%) was added to acidogenic cells at pH 5.7.

2012-04-30 | E-MEXP-3264 | biostudies-arrayexpress

A transcriptional study of acidogenic chemostat cells of Clostridium acetobutylicum following a single n-butanol pulse_Exp2

Project description:In this study the transcriptional behavior of the natural solvent producing bacterium Clostridium acetobutylicum was investigated following n butanol stress using DNA microarray analysis. Therefore, a phosphate-limited chemostat culture was established and n-butanol stress (0.9%) was added to acidogenic cells at pH 5.7.

2012-04-30 | E-MEXP-3265 | biostudies-arrayexpress

Global transcriptional changes of Clostridium acetobutylicum cultures with increased butanol-acetone ratios

Project description:Artificial electron carriers have been widely used to shift the solvent ratio towards butanol in acetone-butanol-ethanol (ABE) fermentation of solventogenic clostridia according to decreased hydrogen production. In this study, first insights on the molecular level were gained to explore the effect of methyl viologen addition to cultures of Clostridium acetobutylicum. Employing batch fermentation in mineral salts medium, the butanol:acetone ratio was successively increased from 2.3 to 12.4 on a 100 ml scale in serum bottles and from 1.4 to 16.5 on a 1,300 ml scale in bioreactors, respectively. The latter cultures were used for DNA microarray analyses to provide new information on the transcriptional changes referring to methyl viologen exposure and thus, exhibing gene expression patterns according to the manipulation of the cellular redox balance.

2012-03-31 | E-MEXP-3417 | 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. 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

An impaired respiratory electron chain triggers down-regulation of the energy metabolism and de-ubiquitination of solute carrier amino acid transporters

Project description:We integrated metabolome and proteome profiles of the parental cell line 143B.TK- versus ρ0, including PTM analyses such as phosphorylation and ubiquitination to characterize the impact of the absence of mtDNA for the entire cell. For quantitative proteome profiling, we used a shotgun LC-MS/MS approach including the classical SILAC labeling. For comprehensive metabolome profiling, we applied a targeted LC-MS approach, based on multiple reaction monitoring (MRM).Our study revealed that mtDNA depletion leads to a non-uniform down-regulation of the mitochondrial energy metabolism in ρ0 cells on the proteome level. Metabolites of the TCA cycle were highly dysregulated which in turn had an impact on the amino acid levels, which were up regulated. Perturbation of the mitochondrial energy metabolism could lead to an activation of the retrograde response, indicated by sets of up-regulated signaling pathways in ρ0 cells, further supported by altered phosphorylation in signaling pathways and the cytoskeleton as well as de-ubiquitination of SLC transporters.

2016-02-08 | PXD002425 | Pride

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

Transcription profiling of Baseline gene expression in circulating peripheral blood mononuclear cells isolated from 18 apparently healthy volunteers (10 females and 8 males)

Project description:Baseline gene expression in circulating peripheral blood mononuclear cells isolated from 18 apparently healthy volunteers (10 females and 8 males). The volunteers fasted overnight for 10 hours prior to collection of blood samples (but they were allowed water). 5 blood samples were collected from each volunteer at consecutive 8-day intervals. Volunteers were included in this study provided they met the following selection criteria, that they should be ?Aged between 20 and 45 years of age; ?A non-smoker (or an ex-smoker); ?Not pregnant or been pregnant in the last 12 months ?Not diagnosed with any long-term medical condition; ?Or have not (in the previous 4 months) donated blood, received any inoculations and are not taking regular prescribed medicine (including HRT and oral contraception) Prior to inclusion in this study volunteers were screened for general health and had a blood sample taken for routine screening of Hb content etc. Only those volunteers who were in good general health were allowed to participate in the study. The age of all volunteers has been reported here as being 20-45 years in order to preserve the anonymity of the data, and so that the individuals involved may not be able to track down their own specific data. Please contact us if the details of volunteers' ages are required.

2013-01-30 | E-TABM-7 | biostudies-arrayexpress

Transcriptomics of drougth stress in L. japonicus under normal air conditions

Project description:L. japonicus (Regel) Larsen cv, Gifu were initially obtained from Prof. Jens Stougaard (University Aarhus, Denmark) and then self-propagated at the University of Seville. Seeds were scarified and surface-sterilized, germinated in 1% agar Petri dishes, and transferred to pots using a 1:1 (v/v) mixture of vermiculite and sand as solid support. Five seedlings were planted in each pot and grown during 35 days in a growth chamber under 16/8 hours day/night, 20/18M-oM-?M-=C, with a photosynthetic photon flux density of 250 M-oM-?M-=mol/m2M-oM-?M-=s and a constant humidity of 70%. Plants were watered with Hornum nutrient solution. Drought was applied withholding irrigation for the reported period of time and sample plants or leaves were harvested for further analysis.

2012-10-06 | E-MEXP-3710 | biostudies-arrayexpress

Antibody microarray profiling of pancreatic cancer using 12 urine samples

Project description:Antibody microarray based profiling of twelve urine samples. 3 healthy female 3 heatlhy male 3 female with pancreatic cancer 3 male with pancreatic cancer

2012-05-03 | E-MEXP-3006 | biostudies-arrayexpress

Transcription profiling by array of Lotus japonicus leaves from wild type and Ljgln2-2 mutant plants exposed to drought.

Project description:L. japonicus (Regel) Larsen cv, Gifu were initially obtained from Prof. Jens Stougaard (University Aarhus, Denmark) and then self-propagated at the University of Seville. Ljgln2-2 mutant was isolated from photorespiratory mutant screening as described previously (Orea et al., 2002; Mï¿½rquez et al., 2005; Betti et al., 2006). The mutant progeny of two consecutive back-crosses with WT was used for the present work. WT and mutant seeds were scarified and surface-sterilized, germinated in 1% agar Petri dishes, and transferred to pots using a 1:1 (v/v) mixture of vermiculite and sand as solid support. Five seedlings were planted in each pot and grown during 35 days in a growth chamber under 16/8 hours day/night, 20/18ï¿½C, with a photosynthetic photon flux density of 250 ï¿½mol/m2ï¿½s and a constant humidity of 70%. CO2 was automatically injected to a final concentration of 0.7% (v/v), to allow for normal growth of Ljgln2-2 mutant in a photorespiration suppressed atmosphere. Plants were watered with Hornum nutrient solution (Handberg & Stougaard, 1992). Drought was applied withholding irrigation for the reported period of time and sample plants or leaves were harvested for further analysis.

2011-04-29 | E-MEXP-2690 | 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