Ontology highlight
ABSTRACT:
PROVIDER: PRJEB39199 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR4315047_1.fastq.gz | Fastqsanger.gz | |||
| ERR4315047_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 2 of 2 |
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE12358: Clostridium beijerinckii NCIMB 8052 wild-type fermentation time course GSE12359: Clostridium beijerinckii BA101 mutant fermentation time course Refer to individual Series
2009-06-02 | E-GEOD-12365 | biostudies-arrayexpress
Project description:The Clostridium beijerinckii NCIMB 8052 wild-type culture was monitored from exponential growth to stationary phase. During this period the culture underwent a shift from acidogenesis to solventogenesis. Acetone and butanol production was initiated with the onset of the solventogenic phase. Using DNA microarray changes in gene expression were examined during the transitional period. RNA samples were taken from Clostridium beijerinckii NCIMB 8052 wild-type fermentation culture at individual time points during the acidogenic phase and the solventogenic phase. The samples were used for microarray hybridization.
2009-06-02 | E-GEOD-12358 | biostudies-arrayexpress
Project description:Solventogenic Clostridium species ferment carbohydrates to acetone, butanol and ethanol which are well-known next-generation biofuels. However, repeated subculture of or continuous fermentation by Clostridium often decreases and eventually terminates the solvent production and spore formation, which is a process called strain degeneration. Supplementation of CaCO3 to fermentation medium could partially recover metabolism of degenerated strain by more than 50% increase of cell growth and solvent production. The transcriptome profile of Clostridium beijerinckii NCIMB 8052 (DG-8052) and its response to CaCO3 treatment were analysed by microarray. Since fermentation by C. beijerinckii NCIMB 8052 is a biphasic process, gene expressions of two fermentations were compared at each stage, i.e. 12h and 24h fermentation time representing acidogenic phase and solventogenic phase, respectively. This study examined expression of 5168 genes capturing 98.6% of the C. beijerinckii NCIMB 8052 genome. With the addition of CaCO3, DG-8052 had 565 and 916 genes significantly up-regulated at acidogenic phase and solventogenic phase, respectively. According to the enrichment analysis of pathway and Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, these genes were significantly overrepresented in cellular functions such as Amino acid transport and metabolism, organic acid biosynthetic process, bacteria chemotaxis and defense mechanisms. On the other hand, there were 704 and 1044 genes significantly down-regulated at acidogenic phase and solventogenic phase, respectively. These repressed genes were mainly enriched in functions such as ion transmembrane transport, ATP synthesis, oxidative phosphorylation.
2017-01-02 | GSE81808 | GEO
Project description:The Clostridium beijerinckii NCIMB 8052 wild-type culture was monitored from exponential growth to stationary phase. During this period the culture underwent a shift from acidogenesis to solventogenesis. Acetone and butanol production was initiated with the onset of the solventogenic phase. Using DNA microarray changes in gene expression were examined during the transitional period.
2009-06-02 | GSE12358 | GEO
Project description:Furfural is the prevalent microbial inhibitor generated during pretreatment and hydrolysis of lignocellulosic biomass to monomeric sugars, but the molecular response of Clostridium beijerinckii NCIMB 8052 to this compound is unknown. To discern the effect of furfural on C. beijerinckii and to gain insights into the molecular mechanisms of action and detoxification, we studied the physiological changes of furfural-stressed cultures during acetone-butanol-ethanol (ABE) fermentation, and profiled differentially expressed genes by genome-wide transcriptional analysis. C. beijerinckii exposed to furfural stress during the acidogenic growth phase produced 13% more ABE than the unstressed control. The growth and ABE by C. beijerinckii ceased following exposure to furfural stress during the solventogenic growth phase. By comparing gene expression of furfural-stressed cultures to that of the unstressed control, at both the acidogenic and solventogenic phases, we ascertained that furfural induces expression of several genes including those that code for heat shock proteins, redox enzymes and cofactor associated proteins, and ATP-binding cassette transporters, and represses genes belonging to the phosphotransferase system, two-component system, chemotaxis and cell motility. Based on these results, we discuss the underpinning for furfural-mediated change in ABE fermentation by the solventogenic Clostridium species. C. beijerinckii 8052 pre-culture was incubated anaerobically to attain acidogenic or solventogenic growth phase. The culture was then subdivided into two bottles. One bottle was challenged with furfural and the other bottle was left unchallenged. After 3 h growth, C. beijerinckii 8052 samples were collected, during which the original concentration of furfural in the growth medium was reduced to more than half. Total RNA was isolated, purified, converted to enriched mRNA, and dye-coupled (Alexa Fluor 555) complementary cRNA. This was followed by hybridization and microarray data analysis.
2012-12-06 | E-GEOD-42597 | biostudies-arrayexpress
Project description:Furfural is the prevalent microbial inhibitor generated during pretreatment and hydrolysis of lignocellulosic biomass to monomeric sugars, but the molecular response of Clostridium beijerinckii NCIMB 8052 to this compound is unknown. To discern the effect of furfural on C. beijerinckii and to gain insights into the molecular mechanisms of action and detoxification, we studied the physiological changes of furfural-stressed cultures during acetone-butanol-ethanol (ABE) fermentation, and profiled differentially expressed genes by genome-wide transcriptional analysis. C. beijerinckii exposed to furfural stress during the acidogenic growth phase produced 13% more ABE than the unstressed control. The growth and ABE by C. beijerinckii ceased following exposure to furfural stress during the solventogenic growth phase. By comparing gene expression of furfural-stressed cultures to that of the unstressed control, at both the acidogenic and solventogenic phases, we ascertained that furfural induces expression of several genes including those that code for heat shock proteins, redox enzymes and cofactor associated proteins, and ATP-binding cassette transporters, and represses genes belonging to the phosphotransferase system, two-component system, chemotaxis and cell motility. Based on these results, we discuss the underpinning for furfural-mediated change in ABE fermentation by the solventogenic Clostridium species.
2012-12-06 | GSE42597 | GEO
Project description:Clostridium beijerinckii NCIMB 8052 Transcriptome or Gene expression
| PRJNA288788 | ENA
Project description:Milne2011 - Genome-scale metabolic network of
Clostridium beijerinckii (iCB925)
This model is described in the article:
Metabolic network
reconstruction and genome-scale model of butanol-producing
strain Clostridium beijerinckii NCIMB 8052.
Milne CB, Eddy JA, Raju R, Ardekani
S, Kim PJ, Senger RS, Jin YS, Blaschek HP, Price ND.
BMC Syst Biol 2011; 5: 130
Abstract:
BACKGROUND: Solventogenic clostridia offer a sustainable
alternative to petroleum-based production of butanol--an
important chemical feedstock and potential fuel additive or
replacement. C. beijerinckii is an attractive microorganism for
strain design to improve butanol production because it (i)
naturally produces the highest recorded butanol concentrations
as a byproduct of fermentation; and (ii) can co-ferment pentose
and hexose sugars (the primary products from lignocellulosic
hydrolysis). Interrogating C. beijerinckii metabolism from a
systems viewpoint using constraint-based modeling allows for
simulation of the global effect of genetic modifications.
RESULTS: We present the first genome-scale metabolic model
(iCM925) for C. beijerinckii, containing 925 genes, 938
reactions, and 881 metabolites. To build the model we employed
a semi-automated procedure that integrated genome annotation
information from KEGG, BioCyc, and The SEED, and utilized
computational algorithms with manual curation to improve model
completeness. Interestingly, we found only a 34% overlap in
reactions collected from the three databases--highlighting the
importance of evaluating the predictive accuracy of the
resulting genome-scale model. To validate iCM925, we conducted
fermentation experiments using the NCIMB 8052 strain, and
evaluated the ability of the model to simulate measured
substrate uptake and product production rates. Experimentally
observed fermentation profiles were found to lie within the
solution space of the model; however, under an optimal growth
objective, additional constraints were needed to reproduce the
observed profiles--suggesting the existence of selective
pressures other than optimal growth. Notably, a significantly
enriched fraction of actively utilized reactions in
simulations--constrained to reflect experimental
rates--originated from the set of reactions that overlapped
between all three databases (P = 3.52 × 10-9, Fisher's
exact test). Inhibition of the hydrogenase reaction was found
to have a strong effect on butanol formation--as experimentally
observed. CONCLUSIONS: Microbial production of butanol by C.
beijerinckii offers a promising, sustainable, method for
generation of this important chemical and potential biofuel.
iCM925 is a predictive model that can accurately reproduce
physiological behavior and provide insight into the underlying
mechanisms of microbial butanol production. As such, the model
will be instrumental in efforts to better understand, and
metabolically engineer, this microorganism for improved butanol
production.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180034.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2015-07-30 | MODEL1507180034 | BioModels