Transcription profiling of Aspergillus niger wild type and inuR deletion strains grown in sucrose and/or xylose to identify genes that are involved in inulin and sucrose metabolism
Ontology highlight
ABSTRACT:
ORGANISM(S): Aspergillus niger
SUBMITTER: Xiaolian Yuan
PROVIDER: E-TABM-319 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Microarray experiments were performed for identifying genes that are involved in starch metabolism by analyzing the transcriptomes of wild type strain N402 and amyR deletion strain grown in maltose, as well as by analyzing the transcriptomes of wild type strain N402 grown in maltose and xylose.
2008-06-01 | E-TABM-324 | biostudies-arrayexpress
Project description:The effect of sucrose feeding on gene expression in Arabidopsis thaliana leaves was investigated using affymetrix ATH1 microarrays. For this, petioles of detached leaves were put in a solution containing either sucrose or sorbitol (control). Sugars were taken up into the leaf via the respiration stream for 13 hours. After that, leaves were frozen in liquid nitrogen and RNA was extracted for analysis. Experiment Overall Design: The effect of sucrose feeding on gene expression was investigated using affymetrix ATH1 microarrays. For this, petioles of detached leaves were put in a solution containing either sucrose or sorbitol (control). Sugars were taken up into the leaf via the respiration stream for 13 hours. After that, leaves were frozen in liquid nitrogen and RNA was extracted for analysis.
2008-06-12 | E-GEOD-4022 | biostudies-arrayexpress
Project description:Transcriptional profiling of the A. niger WT (N402) strain treated with xylan (1%, w/v) for 6, 12 and 24 h. The main objective was to identify genes related to cellulases and hemicellulases after treatment with the polysaccharide xylan. The experiment was further validated by enzymatic assays. Three-condition experiment: WT-Xylan for 6, 12 and 24 h at 30oC in batch culture. Firstly, the WT (N402) strain was grown in minimal medium with fructose as carbon source (control), and then transferred to 1% (w/v) xylan as carbon source. 2 biological replicates per time point.
2010-10-21 | E-GEOD-24848 | biostudies-arrayexpress
Project description:Seedlings are grown on a mesh covering MS media without carbon source, and subsequently transferred at 9 DAS to control media without sucrose or medium supplemented with 15 mM sucrose. 3 hours and 24 hours after transfer, seedlings were harvested and the third leaf micro-dissected for RNA extraction.
2017-12-14 | E-MTAB-4262 | biostudies-arrayexpress
Project description:Sucrose is a major carbon source for industrial bioethanol production by Saccharomyces cerevisiae. In yeasts, two modes of sucrose metabolism occur: (i) extracellular hydrolysis by invertase, followed by uptake and metabolism of glucose and fructose, and (ii) uptake via sucrose-H+ symport followed by intracellular hydrolysis and metabolism. Although alternative start codons in the SUC2 gene enable synthesis of extracellular and intracellular invertase isoforms, sucrose hydrolysis in S. cerevisiae predominantly occurs extracellularly. In anaerobic cultures, intracellular hydrolysis theoretically enables a 9 % higher ethanol yield than extracellular hydrolysis, due to energy costs of sucrose-proton symport. This prediction was tested by engineering the promoter and 5’ coding sequences of SUC2, resulting in relocation of invertase to the cytosol. In anaerobic sucrose-limited chemostats, this iSUC2-strain showed an only 4% increased ethanol yield and high residual sucrose concentrations indicated suboptimal sucrose-transport kinetics. To improve sucrose-uptake affinity, it was subjected to 95 generations of anaerobic, sucrose-limited chemostat cultivation, resulting in a 20-fold decrease of residual sucrose concentrations and a 10-fold increase of the sucrose-transport capacity. A single-cell isolate showed an 11 % higher ethanol yield on sucrose in chemostat and batch cultures than an isogenic SUC2 reference strain, while transcriptome analysis revealed elevated expression of AGT1, encoding a disaccharide-proton symporter, and other maltose-related genes. Deletion of AGT1, which had been duplicated during laboratory evolution, restored the growth characteristics of the unevolved iSUC2 strain. This study demonstrates that engineering the topology of sucrose metabolism is an attractive strategy to improve ethanol yields in industrial processes. The goal of the present study was to investigate whether a relocation of sucrose hydrolysis to the cytosol can be used to improve ethanol yields on sucrose and which additional steps may be required to improve sucrose utilization by strains that only express intracellular invertase. To this end, the SUC2 gene was modified to cause an exclusive intracellular localization. Growth and product formation by the engineered strain were compared with that of the parental strain in anaerobic sucrose-limited chemostat cultures. Subsequently, evolutionary engineering was used to improve sucrose uptake kinetics and an evolved strain was characterized for growth and product formation in chemostat cultures. Transcriptome analysis and gene deletion studies were used to identify genetic changes in the evolved strain that contribute to its improved sucrose-uptake kinetics.
2011-09-05 | E-GEOD-30535 | biostudies-arrayexpress
Project description:We used quantitative proteomics (8-plex iTRAQ labeling) to investigate pathways and enzymes potentially important for sucrose metabolism in the halophilic archaeon Halohasta litchfieldiae. The data provided insights into the dynamics of the Hht. litchfieldiae proteome in response to sucrose, advancing the understanding of sucrose and fructose metabolism in haloarchaea.
2019-01-31 | PXD010137 | Pride
Project description:Arabidopsis thaliana ecotype Columbia glabra were grown for 4 days in the dark without added sucrose. Samples were subsequently kept for 6h either [1] under aerobic conditions, [2] under anoxia in absence of sucrose or [3] under anoxia in presence of sucrose.
2007-07-10 | E-GEOD-2133 | biostudies-arrayexpress
Project description:The ascomycete Trichoderma reesei is an industrial producer of cellulolytic and hemicellulolytic enzymes and also serves as a model for investigations on these enzymes and their genes. Most of them are obligatorily dependent on the Zn(II)Cys(VI) transcriptional activator XYR1. XYR1 is constitutively expressed at a low basal, but induced in the presence of cellulase- and hemicellulose inducers, and transported into the nucleus. The factors mediating its import and export across the nuclear pore complexes (karyopherins) are therefore expected to play a key role in its function. We identified 14 karyopherins in T. reesei, of which 8 were predicted to be involved nuclear protein import. Their systematic knock-out and testing for cellulase formation identified KAP8 (an orthologue of A. nidulans KapI, and Saccharomyces cerevisiae Kap121/Pse1p) to be essential for cellulase gene expression, and for the appearance of GFP-XYR1 in the nucleus. Transcriptomic analysis of Δkap8 and a retransformant under cellulase-inducing conditions revealed the downregulation of 64 Cazymes in the Δkap8 strain under inducing conditions, including all cellulases and hemicellulases known to be under XYR1 control, and of 12 transcription factors of which 2 were known to be associated with cellulase regulation (ACE3, CLR2). Together, these new observations underscore the role of nuclear transport of XYR1 in the regulation of cellulase and hemicellulose gene expression in T. reesei, and identify KAP8 as the major karyopherin involved in this process. Two strains were used: T. reesei ku70 (pyr4-), in which the kap8 (=kapI/Pse1/Kap121) reading frame has been replaced by the T. reesei pyr4 gene; and a kap8-retransformant of the same strain and two time points for each strain T0h and T3h. All samples are in tricplicate.
2015-03-03 | E-GEOD-59600 | biostudies-arrayexpress
Project description:Various saprotrophic microorganisms, especially filamentous fungi, can efficiently degrade lignocellulose that is one of the most abundant natural material on earth. It consists of complex carbohydrates and aromatic polymers found in plant cell wall and thus in plant debris. Aspergillus fumigatus Z5 was isolated from compost heaps and showed highly efficient plant biomass-degradation capability.Genome analysis revealed an impressive array of genes encoding cellulases, hemicellulases, and pectinases involved in lignocellulosic biomass degradation. We sequenced the transcriptomes of Aspergillus fumigatus Z5 induced by sucrose, xylan, cellulose and rice straw, respectively. There were 444, 1711 and 1386 significantly differently (q-value ⤠0.0001 and |log2 of the ratio of the RPM values| ⥠2) expressed genes in xylan, cellulose and rice straw,respectively, relative to sucrose control. After incubation at 45 â, 145rpm for 20 hours with sucrose as the carbon source, mycelia were induced for 16 hours using xylan, cellulose and rice straw, respectively. Transcriptome induced by sucrose was used as the control when comparing the differences between other three transcriptomes (induced by xylan, cellulose and rice straw, respectively).
2015-11-22 | E-GEOD-55086 | biostudies-arrayexpress
Project description:Sucrose is a major carbon source for industrial bioethanol production by Saccharomyces cerevisiae. In yeasts, two modes of sucrose metabolism occur: (i) extracellular hydrolysis by invertase, followed by uptake and metabolism of glucose and fructose, and (ii) uptake via sucrose-H+ symport followed by intracellular hydrolysis and metabolism. Although alternative start codons in the SUC2 gene enable synthesis of extracellular and intracellular invertase isoforms, sucrose hydrolysis in S. cerevisiae predominantly occurs extracellularly. In anaerobic cultures, intracellular hydrolysis theoretically enables a 9 % higher ethanol yield than extracellular hydrolysis, due to energy costs of sucrose-proton symport. This prediction was tested by engineering the promoter and 5’ coding sequences of SUC2, resulting in relocation of invertase to the cytosol. In anaerobic sucrose-limited chemostats, this iSUC2-strain showed an only 4% increased ethanol yield and high residual sucrose concentrations indicated suboptimal sucrose-transport kinetics. To improve sucrose-uptake affinity, it was subjected to 95 generations of anaerobic, sucrose-limited chemostat cultivation, resulting in a 20-fold decrease of residual sucrose concentrations and a 10-fold increase of the sucrose-transport capacity. A single-cell isolate showed an 11 % higher ethanol yield on sucrose in chemostat and batch cultures than an isogenic SUC2 reference strain, while transcriptome analysis revealed elevated expression of AGT1, encoding a disaccharide-proton symporter, and other maltose-related genes. Deletion of AGT1, which had been duplicated during laboratory evolution, restored the growth characteristics of the unevolved iSUC2 strain. This study demonstrates that engineering the topology of sucrose metabolism is an attractive strategy to improve ethanol yields in industrial processes.
2011-09-06 | GSE30535 | GEO