Aspergillus niger
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ABSTRACT:
PROVIDER: PRJNA243615 | ENA |
REPOSITORIES: ENA
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Project description:Transcriptomics signatures of Aspergillus niger were used to predict regulator proteins mediating the survival responses against these stressors and the phenotypes of selected null mutant strains were studied. This integrated approach allowed us to reconstruct a model for the cell wall salvage gene network of A. niger that ensures survival of the fungus upon cell surface stress. The model predicts that (i) caspofungin and aureobasidin A induce the cell wall integrity pathway as main compensatory response including RhoB, RhoD, MkkA and RlmA as regulator proteins. (ii) RlmA is the main transcription factor required for the protection against calcofluor white but cooperates with MsnA and CrzA to ensure survival of A. niger when challenged with caspofungin or aureobasidin A. All three transcription factors are important for these compensatory responses and involve induction of glucan and chitin synthesising genes amongst others. (iii) Membrane stress provoked by aureobasidin A via disturbance of sphingolipid synthesis induces cell wall stress in A. niger, but membrane stress provoked by fenpropimorph via disturbance of ergosterol synthesis does not. The present work uncovered different defence strategies of A. niger to protect itself against cell wall stress conditions. At least three transcription factors - RlmA, MsnA and CrzA – are employed in a well-balanced manner. The data also predicts a fourth transfactor, SrbA, which seems to be specifically important during fenpropimorph-induced cell membrane stress. Future studies will disclose how these regulators are interlocked in different signalling pathways to secure survival of A. niger under different cell wall stress conditions.
2014-12-31 | GSE56471 | GEO
Project description:Expression data from batch cultivations of Aspergillus niger wild type strain ATCC 1015 and adrA, facB and creA deletion mutants constructed on ATCC 1015 background strain with glucose or glycerol as carbon sources. Genome-wide transcriptome analysis was used to identify genes either affected directly or indirectly by each transcription factor investigated during growth on a repressing or a derepressing carbon source. For this purpose, batch cultivations under well-controlled conditions were performed with Aspergillus niger wild type strain ATCC 1015 and the three deletion mutants of the corresponding transcription factors AdrA, FacB and CreA. Samples for RNA extraction were collected and further processed for hybridization in custom-designed Affymetrix microarrays containing probes for three Aspergillus species, including A. niger.
2011-01-31 | GSE19952 | GEO
Project description:Expression data from batch cultivations of Aspergillus niger wild type strain ATCC 1015 and adrA, facB and creA deletion mutants constructed on ATCC 1015 background strain with glucose or glycerol as carbon sources. Genome-wide transcriptome analysis was used to identify genes either affected directly or indirectly by each transcription factor investigated during growth on a repressing or a derepressing carbon source. For this purpose, batch cultivations under well-controlled conditions were performed with Aspergillus niger wild type strain ATCC 1015 and the three deletion mutants of the corresponding transcription factors AdrA, FacB and CreA. Samples for RNA extraction were collected and further processed for hybridization in custom-designed Affymetrix microarrays containing probes for three Aspergillus species, including A. niger. Triplicate batch fermentations of each of the four Aspergillus niger strains used, the wild type A. niger strain ATCC 1015 and three gene deletion mutants, were carried out using glucose or glycerol as carbon source, and transcriptome analysis was performed. Biomass from each batch cultivation was harvested in the exponential phase of growth and further processed for RNA extraction and hybridization on Affymetrix microarrays.
2011-01-31 | E-GEOD-19952 | biostudies-arrayexpress
Project description:The full genome sequencing of the filamentous fungi Aspergillus nidulans, Aspergillus niger and Aspergillus oryzae has opened the possibilities for studying the cellular physiology of these fungi on a systemic level. As a tool to explore this, we are presenting an Affymetrix GeneChip developed for transcriptome analysis of any of the three above-mentioned aspergilli. Transcriptome analysis of triplicate batch cultivations of all three aspergilli on glucose-and xylose media has been performed, and used to validate the performance of the micro array. By doing gene comparisons of all three species, and cross-analysing this with the expression data, 23 genes, including the xylose transcriptional activator XlnR, have been identified to be a conserved response across the Aspergillus sp. Promoter analysis of the upregulated genes in all three species suggest the XlnR-binding site to be 5’-GGNTAAA-3’. We are thus presenting a validated tool for transcription analysis of three Aspergillus species and a methodology for comparative transcriptomics. Keywords: Physiological response
2008-02-15 | GSE9276 | GEO
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:Conserved transcriptional regulation of glycerol metabolism was investigated in three Aspergillus species, A. nidulans, A. oryzae and A. niger. For this purpose, batch cultivations under well controlled conditions were performed with the three Aspergilli. Samples for RNA extraction were collected and further processed for hybridization in custom designed Affymetrix microarrays containing probes for the three Aspergillus species. Protein comparisons and cross analysis with gene expression data of all three species resulted in the identification of 88 genes having a conserved response across the three Aspergillus species. A promoter analysis of the up-regulated genes led to the identification of a conserved binding site for a putative regulator.
2009-10-21 | GSE15702 | GEO
Project description:Genomic and proteomic characterization of the Aspergillus niger isolate, JSC-093350089, collected from U.S. segment surfaces of the International Space Station (ISS) is reported, along with a comparison to the experimentally established strain ATCC 1015. Whole-genome sequencing of JSC-093350089 revealed enhanced genetic variance when compared to publicly available sequences of A. niger strains. Analysis of the isolate’s proteome revealed significant differences in the molecular phenotype of JSC-093350089, including increased abundance of proteins involved in the A. niger starvation response, oxidative stress resistance, cell wall integrity and modulation, and nutrient acquisition. Together, these data reveal the existence of a distinct strain of A. niger onboard the ISS and provide insight into the molecular phenotype that is selected for by melanized fungal species inhabiting spacecraft environments.
2018-08-21 | PXD008588 | Pride
Project description:We have studied the physiological response of the fungus Aspergillus niger when exposed to wheat straw as a model lignocellulosic substrate. Using RNA-sequencing we showed that, 24 hours after exposure to straw, gene expression of known plant cell wall degrading enzymes represents a huge investment for the cells (about 20 % of the total mRNA). Our results also uncovered new esterases and surface interacting proteins that might form part of the fungal degradative arsenal. We also show that antisense transcripts are abundant and that their expression can be regulated by conditions. Triplicate samples of A. niger N402 taken at each of three timepoints: After 48 h growth in minimal media with Glucose as sole carbon source, After transfer to Wheat Straw media for 24 h and 5 h after after the exogenous addition of glucose to the wheat starw media.
2012-08-27 | E-GEOD-33852 | biostudies-arrayexpress
Project description:The aim of this study was to investigate the regulatory role of Aspergillus niger AmyR and InuR during growth on inulin and sucrose
2023-05-03 | GSE204768 | GEO
Project description:The full genome sequencing of the filamentous fungi Aspergillus nidulans, Aspergillus niger and Aspergillus oryzae has opened the possibilities for studying the cellular physiology of these fungi on a systemic level. As a tool to explore this, we are presenting an Affymetrix GeneChip developed for transcriptome analysis of any of the three above-mentioned aspergilli. Transcriptome analysis of triplicate batch cultivations of all three aspergilli on glucose-and xylose media has been performed, and used to validate the performance of the micro array. By doing gene comparisons of all three species, and cross-analysing this with the expression data, 23 genes, including the xylose transcriptional activator XlnR, have been identified to be a conserved response across the Aspergillus sp. Promoter analysis of the upregulated genes in all three species suggest the XlnR-binding site to be 5’-GGNTAAA-3’. We are thus presenting a validated tool for transcription analysis of three Aspergillus species and a methodology for comparative transcriptomics. Keywords: Physiological response Two conditions (glucose and xylose) and three biological replicates
2008-02-15 | E-GEOD-9276 | biostudies-arrayexpress