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PROVIDER: PRJNA401311 | ENA |
REPOSITORIES: ENA
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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: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: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: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:The thermophilic fungus Malbranchea cinnamomea belongs to the order of Onygenales and is a promising source of thermostable, industrially relevant biocatalysts, as it can grow at temperatures of more than 50°C and is able to utilise many different types of plant biomass. Enzymes from M. cinnamomea that have been characterised so far include an α-amylase, an α-glucosidase, xylanases and an alkaline β-1,3-1,4-glucanase (lichenase), all of which have been reported to have temperature optima between 50°C and 80°C. With this study, we complement the knowledge of the enzymatic repertoire of M. cinnamomea with a transcriptomic analysis of strain FCH 10.5 to provide a more comprehensive view of its lignocellulolytic enzyme system. Genes differentially expressed during growth on two different polymeric substrates, beechwood xylan and wheat bran, point to differences in the fungal response to the deconstruction of a hardwood hemicellulose (beechwood xylan) and a cereal hemicellulose (wheat bran). The data presented here will form the basis for a systematic exploration of the full potential of this fungus as a source of thermostable enzymes. We sequenced the genome of M. cinnamomea FCH 10.5, which was isolated from the compost of a waste treatment plant in Hanoi, Vietnam (PMC5604768, https://www.ncbi.nlm.nih.gov/nuccore/FQSS02000000). For RNAseq, the fungus was grown on three different carbon sources (glucose, wheat bran, beechwood xylan) at 50°C. Mycelium was harvested after 4h and 48h and RNA was extracted. For RNAseq analysis, the RNA of 4h and 48h samples was mixed 1:1, to get information about both early- and late-response genes during growth on the different carbon sources. Two independent duplicate experiments were done for each substrate. Total RNA was extracted using TRIzol (Invitrogen) and chloroform, and further purified with the RNeasy Plant RNA Kit with on-column DNAse digestion (QIAGEN). The quality of the purified RNA was verified by agarose gel electrophoresis, Nanodrop (Thermo Scientific) and Qubit (Life Technologies). The NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs) was used to process the samples according to the manufacturer’s instructions. Briefly, mRNA was isolated from total RNA using oligo-dT magnetic beads and used to synthesise cDNA. The cDNA was ligated with sequencing adapters and PCR amplified. The quality and yield after sample preparation were determined with the Fragment Analyzer (Advanced Analytical). The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp). Standard Illumina primers for Illumina cBot and HiSeq 2500, and the HiSeq control software HCS v2.2.58 were used according to manufacturer’s protocols for clustering and DNA sequencing with a concentration of 16.0 pM. The Illumina data analysis pipelines RTA v1.18.64 and Bcl2fastq v2.17 were used for image analysis, base calling, and quality check. Sequencing was performed on an Illumina HiSeq 2500 sequencer. The assembled genome from the DNA sequencing was used as a reference to map the reads using the packages Tophat (v2.0.14. Linux_x86_64) and Bowtie (v2-2.1.0) with a default mismatch rate of 2%. The frequency with which a read was mapped on a transcript was determined based on the mapped locations from the alignment. To normalise for transcript length, fpkm (fragments per kilobase of transcript per million mapped reads) were calculated. For differential expression analysis, the read counts were loaded into the DESeq package v 1.10.1. Genes were considered differentially expressed if they showed a log2 fold change ≥ 1 and the adjusted p-value was < 0.05.
2017-10-27 | E-MTAB-6157 | biostudies-arrayexpress
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:To better undersand the effects of drought stress on wheat developing seeds, the transcription profile of early developing wheat seeds under control and drought stress conditions were comparatively analyzed by using the Affymetrix wheat geneChip. Drought stress is a major yield-limiting factor for wheat. Wheat yields are particularly sensitive to drought stress during reproductive development. Early seed development stage is an important determinant of seed size, one of the yield components. We specifically examined the impact of drought stress imposed during postzygotic early seed development in wheat. We imposed a short-term drought stress on plants with day-old seeds and observed that even a short-duration drought stress significantly reduced the size of developing seeds as well as mature seeds. Drought stress delayed the developmental transition from syncytial to cellularized stage of endosperm. Coincident with reduced seed size and delayed endosperm development, a subset of genes associated with cytoskeleton organization was misregulated in developing seeds under drought-stressed. Several genes linked to hormone pathways were also differentially regulated in response to drought stress in early seeds. Notably, drought stress strongly repressed the expression of wheat storage protein genes such as gliadins, glutenins and avenins as early as 3 days after pollination. Our results provide new insights on how some of the early seed developmental events are impacted by water stress, and the underlying molecular pathways that can possibly impact both grain size and quality in wheat.
2015-09-15 | GSE70443 | GEO