Clostridium beijerinckii NCIMB 8052
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA279317 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The impacts of ferulic acid, a phenolic compound commonly found in lignin hydrolysates, on the growth, solvent production and transcriptional responses of C. beijerinckii NCIMB 8052 were determined. Addition of ferulic acid to growing cultures resulted in a decrease in the growth and solvent production by 30 and 25%, respectively, when compared to the control cultures. To better understand the toxicity of this compound, microarray analyses were performed using samples taken from these cultures at three different growth states. Several gene ontology terms and KEGG pathways were identified showing significant change at each status, including ABC transporters, two component system and oxidoreductase activity. Moreover, genes related with efflux systems and heat shock proteins were also strongly up- regulated. Among these, expression of the groESL operon was induced by more than 4-fold and was consequently selected for overexpression to improve C. beijerinckii tolerance to ferulic acid. Overall design: Clostridium beijerinckii NCIMB 8052 was anaerobically pre-cultured in P2 media at 37°C for 9 hours to reach an optical density (OD) at 600nm of 2.0. Then, the culture was transferred to fresh media with or without 0.5 g/L of ferulic acid and cultured for 84 hours. During culturing, the samples were taken from the culture at OD 0.3, 1.4 and 5, which were used to prepare total RNA. For microarray experiment, 100 ng of RNA were finally converted to fluorescent cRNA, which was followed by hybridization, feature scanning and data analysis. Three replicates were tested for OD 0.3 and 1.4 whereas two replicates were used for OD 5.
2015-03-25 | GSE67244 | GEO
Project description:Phenolic compounds generated in hydrolysis of lignocellulosic materials are major limiting factors for biological production of solvents by Clostridia, but it lacks the attention on the study of adaptation or resistance mechanisms in response to phenolic compounds.Gene Cbei_3304, encoding a hypothetical membrane transport protein, was analyzed by bioinformatic method. After insertional inactivation of the functionally uncertain gene Cbei_3304 in Clostridium beijerinckii NCIMB 8052, resulted in enhanced phenolic compounds tolerance. Compared to the parent strain C. beijerinckii NCIMB 8052, evaluation of toxicity showed the recombination stain C. beijerinckii 3304::int had a higher level of tolerance to four model phenolic compounds of lignocellulose-derived microbial inhibitory compounds. A comparative transcriptome analysis showed that the genes were involved in membrane transport proteins (ABC and MFS family) and were up-regulated expression after disrupting gene Cbei_3304. Additionally, the adaptation of C. beijerinckii NCIMB 8052 in response to non-detoxified hemicellulosic hydrolysate was improved by disrupting gene Cbei_3304.Toxicity evaluation of lignocellulose-derived phenolic compounds shows that Cbei_3304 plays a significant role in regulating toxicities tolerance for ABE fermentation by C. beijerinckii, and the adaptation of non-detoxified hemicellulosic hydrolysate is significantly improved after inactivation of Cbei_3304 in wild-type strain C. beijerinckii NCIMB 8052. It provided a potential strategy for generating high inhibitor tolerance strains for using lignocellulosic materials to produce solvents by clostridia in this study.
1000-01-01 | S-EPMC5834869 | BioStudies
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. Overall design: 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 | GSE12358 | 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. 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 | ArrayExpress
Project description:BACKGROUND: Clostridium beijerinckii is a valuable bacteria species which has the ability of ABE (acetone, butanol and ethanol) production. It has been shown that Phosphotransferase (PTS) is an important and common system for both carbohydrate uptake and phosphorylation in bacteria, but detailed study of the system, especially its fructose/mannose/sorbose family is scant. RESULTS: In the genome of Clostridium beijerinckii NCIMB 8052, a model strain recently sequenced, there are large number of PTS genes, among them 9 complete sets belong to the fructose/mannose/sorbose family of its enzyme II complex. Our study, based on evidences provided by phylogenetic relationship, analyses of gene contents and clusters, as well as synteny examination, indicates that it is possible to further classify this PTS family into three sub-groups, which are corresponding to the three sugar substrates. Furthermore, we proposed a model how these PTS systems are evolved in bacteria. CONCLUSION: This work may explain the experimental result that Clostridium beijerinckii NCIMB 8052 can better utilize fructose as substrate, thus could lead to a better understanding of the ABE-producing mechanism in Clostridium beijerinckii and other microbial species. It may help to illustrate a higher butanol-productivity future.
1000-01-01 | S-EPMC3024867 | BioStudies
Project description:BACKGROUND: Clostridium beijerinckii is an important solvent producing microorganism. The genome of C. beijerinckii NCIMB 8052 has recently been sequenced. Although transcriptome structure is important in order to reveal the functional and regulatory architecture of the genome, the physical structure of transcriptome for this strain, such as the operon linkages and transcript boundaries are not well understood. RESULTS: In this study, we conducted a single-nucleotide resolution analysis of the C. beijerinckii NCIMB 8052 transcriptome using high-throughput RNA-Seq technology. We identified the transcription start sites and operon structure throughout the genome. We confirmed the structure of important gene operons involved in metabolic pathways for acid and solvent production in C. beijerinckii 8052, including pta-ack, ptb-buk, hbd-etfA-etfB-crt (bcs) and ald-ctfA-ctfB-adc (sol) operons; we also defined important operons related to chemotaxis/motility, transcriptional regulation, stress response and fatty acids biosynthesis along with others. We discovered 20 previously non-annotated regions with significant transcriptional activities and 15 genes whose translation start codons were likely mis-annotated. As a consequence, the accuracy of existing genome annotation was significantly enhanced. Furthermore, we identified 78 putative silent genes and 177 putative housekeeping genes based on normalized transcription measurement with the sequence data. We also observed that more than 30% of pseudogenes had significant transcriptional activities during the fermentation process. Strong correlations exist between the expression values derived from RNA-Seq analysis and microarray data or qRT-PCR results. CONCLUSIONS: Transcriptome structural profiling in this research provided important supplemental information on the accuracy of genome annotation, and revealed additional gene functions and regulation in C. beijerinckii.
2011-01-01 | S-EPMC3271303 | BioStudies
Project description:BACKGROUND:Plant-based cellulose presents the best source of renewable sugars for biofuel production. However, the lignin associated with plant cellulose presents a hurdle as hydrolysis of this component leads to the production of inhibitory compounds, such as ferulic acid. RESULTS:The impacts of ferulic acid, a phenolic compound commonly found in lignin hydrolysates, on the growth, solvent production, and transcriptional responses of Clostridium beijerinckii NCIMB 8052 were determined. Addition of ferulic acid to growing cultures resulted in a decrease in the growth and solvent production by 30% and 25%, respectively, when compared to the control cultures. To better understand the toxicity of this compound, microarray analyses were performed using samples taken from these cultures at three different growth states. Several gene ontology terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified showing significant change at each status, including ATP-binding cassette (ABC) transporters, two component system, and oxidoreductase activity. Moreover, genes related with efflux systems and heat shock proteins were also strongly up-regulated. Among these, expression of the groESL operon was induced by more than fourfold and was consequently selected to improve C. beijerinckii tolerance to ferulic acid. Real-time quantitative PCR (RT-qPCR) analysis confirmed that C. beijerinckii harboring the plasmid, pSAAT-ptb_Gro, had a two- to fivefold increased groESL operon expression during growth of these cultures. Moreover, this strain was more tolerant to ferulic acid as the growth of this recombinant strain and its bioconversion of glucose into solvents were both improved. CONCLUSIONS:Using transcriptomics, we identified numerous genes that are differentially expressed when C. beijerinckii cultures were exposed to ferulic acid for varying amounts of time. The operon expressing groESL was consistently up-regulated, suggesting that this gene cluster may contribute to strain tolerance. This was confirmed as recombinant cultures showed both an enhanced growth and solvent yield in the presence of 0.5 g/L ferulic acid.
2015-01-01 | S-EPMC4406174 | BioStudies
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. Overall design: Clostridium beijerinckii NCIMB8052 degenerated strain cells in P2 medium vs. Clostridium beijerinckii NCIMB8052 degenerated strain cells in P2 medium with 4g/L CaCO3 Two-fermentation time points (12h and 24h) experiments (degenerated strain cells in P2 vs.degenerated strain cells in P2 with CaCO3);Biological replicates: 3 replicates of degenerated strain cells in P2 at 12h; 3 replicates of degenerated strain cells in P2 at 24h;3 replicates of degenerated cells in P2 with CaCO3 at 12h;3 replicates of degenerated cells with CaCO3 at 24h.
2017-01-02 | GSE81808 | GEO
Project description:BACKGROUND:Furfural is the prevalent microbial inhibitor generated during pretreatment and hydrolysis of lignocellulose biomass to monomeric sugars, but the response of acetone butanol ethanol (ABE) producing Clostridium beijerinckii NCIMB 8052 to this compound at the molecular level is unknown. To discern the effect of furfural on C. beijerinckii and to gain insight into molecular mechanisms of action and detoxification, physiological changes of furfural-stressed cultures during acetone butanol ethanol (ABE) fermentation were studied, and differentially expressed genes were profiled by genome-wide transcriptional analysis. RESULTS:A total of 5,003 C. beijerinckii NCIMB 8052 genes capturing about 99.7% of the genome were examined. About 111 genes were differentially expressed (up- or down-regulated) by C. beijerinckii when it was challenged with furfural at acidogenic growth phase compared with 721 genes that were differentially expressed (up- or down-regulated) when C. beijerinckii was challenged with furfural at solventogenic growth phase. The differentially expressed genes include genes related to redox and cofactors, membrane transporters, carbohydrate, amino sugar and nucleotide sugar metabolisms, heat shock proteins, DNA repair, and two-component signal transduction system. While C. beijerinckii exposed to furfural stress during the acidogenic growth phase produced 13% more ABE than the unstressed control, ABE production by C. beijerinckii ceased following exposure to furfural stress during the solventogenic growth phase. CONCLUSION:Genome-wide transcriptional response of C. beijerinckii to furfural stress was investigated for the first time using microarray analysis. Stresses emanating from ABE accumulation in the fermentation medium; redox balance perturbations; and repression of genes that code for the phosphotransferase system, cell motility and flagellar proteins (and combinations thereof) may have caused the premature termination of C. beijerinckii 8052 growth and ABE production following furfural challenge at the solventogenic phase.This study provides insights into basis for metabolic engineering of C. beijerinckii NCIMB 8052 for enhanced tolerance of lignocellulose-derived microbial inhibitory compounds, thereby improving bioconversion of lignocellulose biomass hydrolysates to biofuels and chemicals. Indeed, two enzymes encoded by Cbei_3974 and Cbei_3904 belonging to aldo/keto reductase (AKR) and short-chain dehydrogenase/reductase (SDR) families have been identified to be involved in furfural detoxification and tolerance.
2013-01-01 | S-EPMC3681630 | BioStudies
Project description:Clostridium beijerinckii is an anaerobic bacterium used for the fermentative production of acetone and butanol. The recent availability of genomic sequence information for C. beijerinckii NCIMB 8052 has allowed for an examination of gene expression during the shift from acidogenesis to solventogenesis over the time course of a batch fermentation using a ca. 500-gene set DNA microarray. The microarray was constructed using a collection of genes which are orthologs of members of gene families previously found to be important to the physiology of C. acetobutylicum ATCC 824. Similar to the onset of solventogenesis in C. acetobutylicum 824, the onset of solventogenesis in C. beijerinckii 8052 was concurrent with the initiation of sporulation. However, forespores and endospores developed more rapidly in C. beijerinckii 8052 than in C. acetobutylicum 824, consistent with the accelerated expression of the sigE- and sigG-regulated genes in C. beijerinckii 8052. The comparison of gene expression patterns and morphological changes in C. beijerinckii 8052 and the hyper-butanol-producing C. beijerinckii strain BA101 indicated that BA101 was less efficient in sporulation and phosphotransferase system-mediated sugar transport than 8052 but that it exhibited elevated expression of several primary metabolic genes and chemotaxis/motility genes.
2008-01-01 | S-EPMC2607153 | BioStudies