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ABSTRACT:
PROVIDER: PRJNA428209 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The goal was to study the dfactionation of different lignocelullose (glucose, wheat bran, wheat straw) by Streptomyces coelicolor A3(2) and the corresponding production of secondary metabolites. This was performed by multi-omic experiment such as transcriptomic/metabolomic and leads to the production of new metabolites. For that, the strain Streptomyces coelicolor A3(2) was subjected to two carbon sources in triplicate (wheat bran and glucose as control). Enzymatic activities were studied at different times and the expression of CAZYmes was studied by transcriptomic in order to detect which enzymes are needed for each carbon source
2020-10-01 | E-MTAB-8971 | biostudies-arrayexpress
Project description:Digital gene expression profiling (DGE) was used to compare the responses of Penicillium decumbens strains to different carbon sources including glucose, cellulose and cellulose-wheat bran. In both wild-type strain 114-2 and cellulase hyperproducing mutant JU-A10-T, transcription of lignocellulolytic enzymes were significantly up-regulated in the presense of cellulose. Relative to 114-2, coordinated up-regulation of lignocellulolytic enzymes and down-regulation of amylases and proteases were observed in JU-A10-T, especially in the cellulose-wheat bran medium. The expression of the principal β-glucosidase BGLI gene was not elevated in JU-A10-T, like the cellulases and hemicellulases, suggesting a different regulatory mechanism for this enzyme. Functional analysis of genes up-regulated in JU-A10-T relative to 114-2 also showed enrichment of proteins involved in amino acid synthesis, protein synthesis, and post-translational modification, compatible with the higher level of production of secreted proteins in JU-A10-T.
2013-01-18 | GSE34288 | GEO
Project description:Plant biomass is the most abundant and renewable carbon source for many fungal species. The composition of biomass consists of about 40-45% cellulose, 20-30% hemicellulose, and 15-25% lignin and varies among plant species. In the bio-based industry, Aspergillus species and other fungi are used for the production of lignocellulolytic enzymes to pretreat agricultural waste biomass (e.g. wheat bran). In this study, we aimed to evaluate if it would be possible to create an Aspergillus strain that releases but does not metabolize hexoses from plant biomass. For this purpose, metabolic mutants were generated that were (partially) impaired in glycolysis, by deleting the hexokinase (hxkA) and glucokinase (glkA) genes. To prevent repression of enzyme production due to the accumulation of hexoses, strains were generated in which these mutations were combined with a mutation in creA, encoding the repressor involved in carbon catabolism. Phenotypic analysis revealed that growth of the ΔhxkAΔglkA mutant was reduced on wheat bran. However, hexoses did not accumulate during growth of the mutants on wheat bran, suggesting that glucose metabolism is re-routed towards alternative carbon catabolic pathways. Deletion of creA combined with blocking glycolysis resulted in an increased expression of pentose catabolic and phosphate pathway genes. This indicates that the reduced ability to use hexoses as carbon sources has resulted in a shift towards the pentose fraction of wheat bran as a major carbon source to support growth.
2018-02-26 | GSE94775 | GEO
Project description:Here comparative transcriptomic analyses of Penicillium oxalicum grown on wheat bran (WB), WB plus rice straw (WR) and WB plus Avicel (WA) as the sole carbon source under solid-state fermentation (SSF) revealed that most of differentially expressed genes (DEGs) were involved in metabolism specifically carbohydrate metabolism.
2019-10-15 | GSE131173 | GEO
Project description:Fungi produce a wide range of enzymes that allow them to grow on diverse plant biomass. Wheat bran is a low-cost substrate with high potential for biotechnological applications. It mainly contains cellulose and (arabino)xylan, with starch, proteins, lipids and lignin as minor components. In this study, we dissected the regulatory network governing wheat bran degradation in Aspergillus niger. Deletion of genes encoding transcription factors involved in (hemi-)cellulose utilization (XlnR, AraR, ClrA and ClrB) individually and in combination significantly reduced production of polysaccharide-degrading enzymes, but retained substantial growth on wheat bran. Proteomic analysis suggested the ability of A. niger to grow on minor carbon components, such as starch, which was confirmed by the additional deletion of the amylolytic regulator AmyR. Growth was further reduced but not impaired, indicating that other minor components provide sufficient energy for residual growth, displaying the flexibility of A. niger, and likely other fungi, in carbon utilization.
2021-06-28 | PXD023338 | Pride
Project description:Functional redundancy in bacterial communities is expected to allow microbial assemblages to survive perturbation by allowing continuity in function despite compositional changes in communities. Recent evidence suggests, however, that microbial communities change both composition and function as a result of disturbance. We present evidence for a third response: resistance. We examined microbial community response to perturbation caused by nutrient enrichment in salt marsh sediments using deep pyrosequencing of 16S rRNA and functional gene microarrays targeting the nirS gene. Composition of the microbial community, as demonstrated by both genes, was unaffected by significant variations in external nutrient supply, despite demonstrable and diverse nutrient–induced changes in many aspects of marsh ecology. The lack of response to external forcing demonstrates a remarkable uncoupling between microbial composition and ecosystem-level biogeochemical processes and suggests that sediment microbial communities are able to resist some forms of perturbation.
2010-11-13 | GSE25227 | GEO
Project description:We aimed to elucidate biological function of A Disintegrin and Metalloprotease (Adm) A and AdmB in Aspergillus oryzae. To observe influences of admA and admB deletions, each gene deletion strain was analyzed by RNA-Seq. mRNA of Deletion-control, ∆admA∆admB, ∆admA and ∆admB cultivated in wheat bran solid culture were sequenced, in quintuplicate, using Illumina GAIIx.
2019-06-07 | GSE83207 | GEO
Project description:To investigate the effect of soy peptides on gut microial composition during juvenile social isolation, group-house (GH) and social isolation (SI) mice were fed a diet consisting of soy peptides or a control diet for 4 weeks post-weaning. We then performed microbial community analysis using data obtained from bacterial 16S rRNA gene sequencing in the fecal samples of 4 mice groups (control diet-fed GH, soy peptide-diet fed GH, control diet-fed SI, and soy peptide-diet fed SI mice).
2024-05-29 | GSE231557 | GEO
Project description:Functional redundancy in bacterial communities is expected to allow microbial assemblages to survive perturbation by allowing continuity in function despite compositional changes in communities. Recent evidence suggests, however, that microbial communities change both composition and function as a result of disturbance. We present evidence for a third response: resistance. We examined microbial community response to perturbation caused by nutrient enrichment in salt marsh sediments using deep pyrosequencing of 16S rRNA and functional gene microarrays targeting the nirS gene. Composition of the microbial community, as demonstrated by both genes, was unaffected by significant variations in external nutrient supply, despite demonstrable and diverse nutrient–induced changes in many aspects of marsh ecology. The lack of response to external forcing demonstrates a remarkable uncoupling between microbial composition and ecosystem-level biogeochemical processes and suggests that sediment microbial communities are able to resist some forms of perturbation. nirS gene diversity from two salt marsh experiments, GSM (4 treatments, 8 samples, duplicate arrays, four replicate blocks per array, 8 arrays per slide) and PIE (2 treatments, 16 samples, duplicate arrays four replicate blocks per array, 8 arrays per slide)
2010-11-13 | E-GEOD-25227 | biostudies-arrayexpress
Project description:A. niger and A. oryzae are two filamentous fungi widely used in industry to produce various enzymes (e.g. pectinases, amylases) and metabolites (e.g. citric acid). Using proteomics, the co-cultivation of these two fungi in wheat bran showed an equal distribution of the two strains forming mixed colonies with a broad range of carbohydrate active enzymes produced. This stable mixed microbial system seems suitable for subsequent commercial processes such as enzyme production. XlnR knock-out strains for both aspergilli were used to study the influence of plant cell wall degrading enzyme production on the fitness of the mixed culture.
2017-02-27 | PXD005532 | Pride