Fermentation metagenome isolate:CR | breed:Prokaryotic | cultivar:Batch reactor
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA383576 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5469563.fastq.gz | Fastqsanger.gz |
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Project description:Batch fermentation reactor Metagenome
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Project description:The present work aimed to compare the transcriptome of three major ethanol-producer Saccharomyces cerevisiae strains in Brazil when fermenting sugarcane juice for fuel ethanol production. This was motivated by the reports presenting physiological and genomics differences among them, and by the attempt to identify genes that could be related to their fermentation capacity and adaptation for different industrial processes.
2012-11-27 | GSE42433 | GEO
Project description:The phytopathogenic fungus Chrysoporthe cubensis is a relevant source of lignocellulolytic enzymes. This work aimed to compare the profile of lignocellulose- degrading proteins secreted by C. cubensis grown under semi-solid state fermentation using wheat bran and sugarcane bagasse. The proteins from the fungus extract grown in wheat bran (WBE) and sugarcane bagasse (SBE) were qualitative and quantitatively analyzed by liquid chromatography-electrospray ionization tandem mass spectrometry (LC–ESI–MS/MS). Label-free proteomic analysis of WBE and SBE showed that the fungus produced a spectrum of carbohydrate-active enzymes (CAZymes) with exclusive characteristics from each extract. While SBE resulted in an enzymatic profile directed towards the depolymerization of cellulose, the enzymes in WBE were more adaptable to the degradation of biomass rich in hemicellulose and other non-lignocellulosic polymers. Saccharification of alkaline pre-treated sugarcane bagasse with SBE promoted glucose release higher than commercial cocktails (8.11 g L -1 ), while WBE promoted the higher release of xylose (5.71 g L -1 ). Our results allowed an in-depth knowledge of the complex set of enzymes secreted by C. cubensis responsible for its high lignocellulolytic activity and still provided the identification of promising target proteins for biotechnological applications in the context of biorefinery.
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Project description:Previously, we performed DNA array-based transcriptomic analysis of Clostridium acetobutylicum biofilm adsorbed onto fibrous matrix in batch fermentation. Here, to further shed light on the transcriptomic modulation of maturing Clostridium acetobutylicum biofilm, we performed the DNA array-based transcriptomic analysis in repeated-batch fermentation. Significant time course changes in expression levels were observed for the genes involved in amino acid metabolism, oligopeptide ABC transporter, nitrogen fixation, and various other processes.
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Project description:The present work aimed to compare the transcriptome of three major ethanol-producer Saccharomyces cerevisiae strains in Brazil when fermenting sugarcane juice for fuel ethanol production. This was motivated by the reports presenting physiological and genomics differences among them, and by the attempt to identify genes that could be related to their fermentation capacity and adaptation for different industrial processes. Two-condition experiment, T0h vs. T6h fermetations assay. Biological replicates: 3 T0h replicates, 5 T6h replicates.
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Project description:Background: Wood-decay basidiomycetes are effective for the degradation of highly lignified and recalcitrant substrates. Brown-rot strain produces carbohydrate-active enzymes involved in the degradation of lignocellulosic materials, along with a non-enzymatic mechanism, via Fenton reaction. Differences in the lignocellulose metabolism occurring even among closely related brown-rots are not completely understood, bringing attention to a multi-omics study of brown-rot L. sulphureus. Results: To evidence the oxidative-hydrolytic mechanism, the Laetiporus sulphureus ATCC 52600 genome was sequenced and the response to lignocellulosic substrates was analyzed by transcriptomics and proteomics. The transcriptomic profile in response to a short cultivation period on in natura sugarcane bagasse revealed 128 out of 12,802 upregulated transcripts. The high upregulated transcripts included a set of redox enzymes along with hemicellulases. The exoproteome in response to extended-time cultivation with Avicel, and steam-exploded sugarcane bagasse, sugarcane straw, and Eucalyptus grandis revealed 121 proteins. Contrasting to the mainly oxidative profile observed in the transcriptome, the secretomes showed a diverse hydrolytic repertoire including constitutive cellulases and hemicellulases, in addition to 19 proteins upregulated relative to glucose. The secretome produced on sugarcane bagasse was evaluated in the saccharification of pretreated sugarcane straw by supplementing a commercial cocktail. Additionally, growth analysis revealed that L. sulphureus ATCC 52600 has higher efficiency to assimilate glucose than other mono and disaccharides. Conclusion: This study shows the singularity of L. sulphureus ATCC 52600 relative to other Polyporales brown-rots, regarding the presence of cellobiohydrolase and peroxidase class II. The multi-omic analysis reinforces the oxidative-hydrolytic metabolism involved in lignocellulose deconstruction, providing insights into the overall mechanisms as well as specific proteins of each step.
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Project description:Four C. thermocellum DSM-1313 derived strains were assessed using metabolite and DNA microarray tools in order to better understand carbon and electron flow within this organism. C. thermocellum is able to ferment cellulose into its fermentation end products L-lactate, acetate, formate, hydrogen gas, and ethanol, with the latter being the desired end product to be used as biorenewable fuel. In addition to the parent strain (genotype: hpt spo0A), strains with either or both of the genes encoding lactate dehydrogenase (ldh) and phosphate acetyltransferase (pta) deleted were studied. The strains used are a parent strain (M1726: genotype: hpt spo0A), and strains with either the gene encoding lactate dehydrogenase (M1629: hpt spo0A ldh) or phosphate acetyltransferase (M1630: hpt spo0A pta) deleted, or with both genes deleted (M1725: hpt spo0A ldh pta). Controlled batch fermentations using cellobiose as sole carbon source were grown for each strain, and samples in mid-exponential phase and at the time of carbon depletion were examined by DNA microarray. Four strains were grown each as three independent biological replicates (fresh batch of media was made before each run). Per fermentation, two samples were taken for DNA microarray analysis as was determined by the optical density: mid-exponential was defined as O.D. 0.4 (measured by Dasgip probe); point of carbon depletion was defined by both the maximum O.D. reached and observation that no base was added to the fermentation to control pH. In total, 4 strains x 3 fermentation x 2 time points per fermentor = 24 arrays. Parent strain was used as reference strain.
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