Aspergillus niger WT: Control vs. steam-exploded sugarcane induction
Ontology highlight
ABSTRACT:
ORGANISM(S): Aspergillus niger
PROVIDER: GSE24798 | GEO | 2010/10/20
SECONDARY ACCESSION(S): PRJNA132289
REPOSITORIES: GEO
Similar Datasets
Project description:Transcriptional profiling of A. niger comparing WT strain vs. ÎXlnR strain treated with steam-exploded sugarcane bagasse (SESB) for 6, 12 and 24 h. The main objective was to identifiy genes related to cellulases and hemicellulases, comparing the differences between WT strain and the strain with the disrupted xylanolytic transcriptional activator gene, XlnR, after treatment with steam-exploded sugarcane. The experiment was further validated by real-time PCR, mass spectrometry of secreted proteins and enzymatic assays. Three-condition experiment : WT-SESB or ÎXlnR-SESB for 6, 12 and 24 h at 30 oC in batch culture. Firstly, WT and ÎXlnR strains were grown in minimal medium with fructose as carbon source (control), and then transferred to SESB as carbon source.
2010-10-20 | E-GEOD-24798 | biostudies-arrayexpress
Project description:Transcriptional profiling of A. niger comparing mutant strains with the disrupted xylanolytic transcriptional activator gene, XlnR, the arabinolytic transcriptional activator gene, AraR, and the double mutant (ΔXlnR, ΔaraR and ΔaraRΔXlnR, repsectively) treated with steam-exploded sugarcane bagasse (SEB) for 12 and 24 h. The main objective was to identify genes related to cellulases and hemicellulases in mutant strains grown on SEB, with indirect comparisons with the WT strain grown on SEB [the (WT/SEB) data deposited in GSE24798]. The experiment was further validated by real-time PCR and enzymatic assay.
2012-05-07 | GSE37758 | GEO
Project description:Transcriptional profiling of A. niger comparing mutant strains with the disrupted xylanolytic transcriptional activator gene, XlnR, the arabinolytic transcriptional activator gene, AraR, and the double mutant (M-NM-^TXlnR, M-NM-^TaraR and M-NM-^TaraRM-NM-^TXlnR, repsectively) treated with steam-exploded sugarcane bagasse (SEB) for 12 and 24 h. The main objective was to identify genes related to cellulases and hemicellulases in mutant strains grown on SEB, with indirect comparisons with the WT strain grown on SEB [the (WT/SEB) data deposited in GSE24798]. The experiment was further validated by real-time PCR and enzymatic assay. Two-condition experiment : A. niger mutant strains on SEB for 12 and 24 h at 30 oC in batch culture. Firstly, the strains were pre-grown in minimal medium with fructose as carbon source (control), and then transferred to SEB as carbon source.
2012-05-06 | E-GEOD-37758 | biostudies-arrayexpress
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.
2020-05-22 | GSE151004 | GEO
Project description:Transcriptional profiling of A. niger comparing different strains (WT, ΔXlnR, ΔaraR and ΔaraRΔXlnR) treated with 25mM xylose + 25mM arabinose for 2 and 8h. The main objective was to identifiy genes related to primary metabolism and carbohydrate metabolism in general, for instance, cellulases and hemicellulases. The study will compare the differences between WT strain and the strains with the disrupted xylanolytic transcriptional activator gene, XlnR, the arabinolytic transcriptional activator gene, AraR, and the double mutant,after treatment with xylose+arabinose (XA treatment). The experiment was further validated by real-time PCR and enzymatic assays.
2012-05-07 | GSE37760 | GEO
Project description:Transcriptional profiling of A. niger comparing different strains (WT, M-NM-^TXlnR, M-NM-^TaraR and M-NM-^TaraRM-NM-^TXlnR) treated with 25mM xylose + 25mM arabinose for 2 and 8h. The main objective was to identifiy genes related to primary metabolism and carbohydrate metabolism in general, for instance, cellulases and hemicellulases. The study will compare the differences between WT strain and the strains with the disrupted xylanolytic transcriptional activator gene, XlnR, the arabinolytic transcriptional activator gene, AraR, and the double mutant,after treatment with xylose+arabinose (XA treatment). The experiment was further validated by real-time PCR and enzymatic assays. Two-condition experiment : A. niger mutant strains on XA for 2 and 8 h at 30 oC in batch culture. Firstly, the strains were pre-grown in minimal medium with fructose as carbon source (control), and then transferred to xylose+arabinose (25 mM each) as carbon source.
2012-05-06 | E-GEOD-37760 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE37758: Aspergillus niger : Control (fructose) vs. steam-exploded sugarcane induction (SEB) GSE37760: Aspergillus niger : Control (fructose) vs. xylose + arabinose (XA) Refer to individual Series
2012-05-06 | E-GEOD-37795 | biostudies-arrayexpress
Project description:Hemicellulose, the second most abundant plant biomass fraction after cellulose, is widely viewed as a potential feedstock for the production of liquid fuels and other value-added materials. Degradation of hemicellulose by filamentous fungi requires production of many different enzymes, which are induced by biopolymers or its derivatives and regulated mainly at the transcriptional level through transcription factors (TFs). Neurospora crassa has been shown to express and secrete plant cell wall associated enzymes. To better understand genes specifically associated with degradation of hemicellulose, we identified 353 genes by transcriptome analysis of N. crassa wild type strain grown on beechwood xylan. Exposure to xylan induces 9 of the 19 predicted hemicellulase genes. The xylanolytic phenotype of strains with deletions in genes identified from the secretome and transcriptome analysis of wild type showed that none were essential for growth on beechwood xylan. The transcription factor XlnR/Xyr1 in Aspergillus and Trichoderma species is considered to be the major transcriptional regulator of genes encoding both cellulases and hemicellulases. We identified a xlnR/xyr1 homolog in N. crassa, NCU06971, termed xlr-1 (xylanase regulator 1). Deletion of xlr-1 in N. crassa abolishes the growth on xylan and xylose, but growth on cellulose was indistinguishable from wild type. To determine regulatory mechanisms associated with hemicellulose degradation, we explored the transcriptional regulon of XLR-1 under xylose and xylanolytic versus cellulolytic conditions. XLR-1 regulated only some predicted hemicellulase genes in N. crassa and was required for a full induction of several cellulase genes. Hemicellulase gene expression was induced by a combination of release from carbon catabolite repression (CCR) and induction. However, in N. crassa, xlr-1 is subject to non-CRE-1 mediated CCR. This systematic analysis provides the similarities and differences of hemicellulose degradation and regulation mechanisms used by N. crassa in comparison to other filamentous fungi. Four-condition experiments (minimal medium, xylan medium,xylose and Avicel medium) of mutant strain(xlr-1) compared to wild type strain; Cy3 and Cy5 dye swap
2012-03-26 | E-GEOD-34098 | biostudies-arrayexpress
Project description:Hemicellulose, the second most abundant plant biomass fraction after cellulose, is widely viewed as a potential feedstock for the production of liquid fuels and other value-added materials. Degradation of hemicellulose by filamentous fungi requires production of many different enzymes, which are induced by biopolymers or its derivatives and regulated mainly at the transcriptional level through transcription factors (TFs). Neurospora crassa has been shown to express and secrete plant cell wall associated enzymes. To better understand genes specifically associated with degradation of hemicellulose, we identified 353 genes by transcriptome analysis of N. crassa wild type strain grown on beechwood xylan. Exposure to xylan induces 9 of the 19 predicted hemicellulase genes. The xylanolytic phenotype of strains with deletions in genes identified from the secretome and transcriptome analysis of wild type showed that none were essential for growth on beechwood xylan. The transcription factor XlnR/Xyr1 in Aspergillus and Trichoderma species is considered to be the major transcriptional regulator of genes encoding both cellulases and hemicellulases. We identified a xlnR/xyr1 homolog in N. crassa, NCU06971, termed xlr-1 (xylanase regulator 1). Deletion of xlr-1 in N. crassa abolishes the growth on xylan and xylose, but growth on cellulose was indistinguishable from wild type. To determine regulatory mechanisms associated with hemicellulose degradation, we explored the transcriptional regulon of XLR-1 under xylose and xylanolytic versus cellulolytic conditions. XLR-1 regulated only some predicted hemicellulase genes in N. crassa and was required for a full induction of several cellulase genes. Hemicellulase gene expression was induced by a combination of release from carbon catabolite repression (CCR) and induction. However, in N. crassa, xlr-1 is subject to non-CRE-1 mediated CCR. This systematic analysis provides the similarities and differences of hemicellulose degradation and regulation mechanisms used by N. crassa in comparison to other filamentous fungi.
2012-03-26 | GSE34098 | GEO
Project description:Aspergillus niger WT: Control vs. steam-exploded sugarcane induction
| PRJNA132289 | ENA