Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression data from Aspergillus oryzae grown under hypoxic condition.

ABSTRACT: Hypoxia imposes stress on filamentous fungi that require oxygen to proliferate. Global transcription analysis of Aspergillus oryzae grown under hypoxic conditions found that the expression of about 50% of 4,244 affected genes was either induced or repressed more than 2-fold. A comparison of these genes with the hypoxically-regulated genes of A. nidulans (Masuo et al., Mol. Gen. Genet. 2010, 284:415-424) based on their predicted amino acid sequences classified them as bi-directional best hit (BBH), one-way best hit (extra homolog: EH) and no-hit (non-syntenic genes: NSG) genes. Clustering analysis of the BBH genes indicated that A. oryzae and A. nidulans down-regulated global translation and transcription under hypoxic conditions, respectively. Under hypoxic conditions, both fungi up-regulated genes for alcohol fermentation and the γ-aminobutyrate shunt of the tricarboxylate cycle, whereas A. oryzae up-regulated the glyoxylate pathway, indicating that both fungi eliminate NADH accumulation under hypoxic conditions. The A. oryzae NS genes included specific genes for secondary and nitric oxide metabolism under hypoxic conditions. This comparative transcriptomic analysis discovered common and strain-specific responses to hypoxia in hypoxic Aspergillus species.

ORGANISM(S): Aspergillus oryzae RIB40

PROVIDER: GSE31046 | GEO | 2011/07/31

SECONDARY ACCESSION(S): PRJNA144865

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Expression data from Aspergillus oryzae grown under hypoxic condition.

Project description:Hypoxia imposes stress on filamentous fungi that require oxygen to proliferate. Global transcription analysis of Aspergillus oryzae grown under hypoxic conditions found that the expression of about 50% of 4,244 affected genes was either induced or repressed more than 2-fold. A comparison of these genes with the hypoxically-regulated genes of A. nidulans (Masuo et al., Mol. Gen. Genet. 2010, 284:415-424) based on their predicted amino acid sequences classified them as bi-directional best hit (BBH), one-way best hit (extra homolog: EH) and no-hit (non-syntenic genes: NSG) genes. Clustering analysis of the BBH genes indicated that A. oryzae and A. nidulans down-regulated global translation and transcription under hypoxic conditions, respectively. Under hypoxic conditions, both fungi up-regulated genes for alcohol fermentation and the γ-aminobutyrate shunt of the tricarboxylate cycle, whereas A. oryzae up-regulated the glyoxylate pathway, indicating that both fungi eliminate NADH accumulation under hypoxic conditions. The A. oryzae NS genes included specific genes for secondary and nitric oxide metabolism under hypoxic conditions. This comparative transcriptomic analysis discovered common and strain-specific responses to hypoxia in hypoxic Aspergillus species. We transferred A. oryzae cells from normoxic to hypoxic conditions for 6 h, and then back to normoxic conditions to examine the effect of hypoxia on gene expression. Total RNA was prepared for DNA microarray analysis from the cells after 1, 3, and 6 h of exposure to hypoxia, followed by 1, 3, and 6 h of reoxygenation.

2011-07-30 | E-GEOD-31046 | biostudies-arrayexpress

Expression data from Aspergillus nidulans grown under hypoxic condition.

Project description:Hypoxia imposes a challenge upon most of the filamentous fungi that require oxygen for proliferation. Here, we used whole genome DNA microarrays to investigate global transcriptional changes in Aspergillus nidulans gene expression after exposure to hypoxia followed by normoxia. Aeration affected the expression of 2,864 genes (27% of the total number of genes in the fungus), of which 50% were either induced or repressed under hypoxic conditions. Up-regulated genes included those for glycolysis, ethanol production, the tricarboxylic acid (TCA) cycle, and for the γ-aminobutyrate (GABA) shunt that bypasses two steps of the TCA cycle. Ethanol and lactate production under hypoxic conditions indicated that glucose was fermented to these compounds via the glycolytic pathway. Since the GABA shunt bypasses the NADH-generating reaction of the TCA cycle catalyzed by oxoglutarate dehydrogenase, hypoxic A. nidulans cells eliminated excess NADH. Hypoxia down-regulated some genes involved in transcription initiation by RNA polymerase II, and lowered the cellular mRNA content. These functions were resumed by reoxygenation, indicating that A. nidulans controls global transcription to adapt to a hypoxic environment. This study is the first to show that hypoxia elicits systematic transcriptional responses in A. nidulans.

2010-08-14 | GSE23605 | GEO

Expression data from Aspergillus nidulans grown under hypoxic condition.

2010-08-14 | E-GEOD-23605 | biostudies-arrayexpress

Genome-wide analysis of maltose utilization and regulation in aspergilla

Project description:Comparative genomics and transcriptomics of the filamentous fungi Aspergillus oryzae and Aspergillus niger have opened possibilities for investigating the cellular metabolism and regulation of these fungi on a systemic level. The aim of this work was to understand how metabolism is regulated and to identify common regulatory responses between A. oryzae and A. niger. We therefore conducted batch fermentations with A. oryzae and A. niger grown on three different carbon sources (glucose, maltose, and xylose) in order to investigate their genome-wide transcription response Keywords: Two Aspergillus species and different carbon sources Three conditions (glucose, maltose and xylose) with three biological replicates for A. oryzae and A. niger

2009-10-21 | E-GEOD-13868 | biostudies-arrayexpress

Expression data from batch cultivations with A. niger, A. oryzae and A. nidulans grown on glucose and glycerol

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

A tri-species Aspergillus array (oryzae arrays)

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-9277 | biostudies-arrayexpress

A tri-species Aspergillus array (niger arrays)

2008-02-15 | E-GEOD-9276 | biostudies-arrayexpress

A tri-species Aspergillus array (nidulans arrays)

Project description:The full genome sequencing of the ?lamentous 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 A?ymetrix 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 identi?ed 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 of each.

2008-02-15 | E-GEOD-9275 | biostudies-arrayexpress

Genome-wide analysis of maltose utilization and regulation in aspergilla

2009-10-22 | GSE13868 | GEO

Project description:The transcriptional activator XlnR (Xlr1/Xyr1) is a major regulator in fungal xylan and cellulose degradation as well as in the utilization of d-xylose via the pentose catabolic pathway. XlnR homologs are commonly found in filamentous ascomycetes and often assumed to have the same function in different fungi. However, a comparison of the saprobe Aspergillus niger and the plant pathogen Magnaporthe oryzae showed different phenotypes for deletion strains of XlnR. In this study wild type and xlnR/xlr1/xyr1 mutants of five fungi were compared: Fusarium graminearum, M. oryzae, Trichoderma reesei, A. niger and Aspergillus nidulans. Growth profiling on relevant substrates and a detailed analysis of the secretome as well as extracellular enzyme activities demonstrated a common role of this regulator in activating genes encoding the main xylanolytic enzymes. However, large differences were found in the set of genes that is controlled by XlnR in the different species, resulting in the production of different extracellular enzyme spectra by these fungi. This comparison emphasizes the functional diversity of a fine-tuned (hemi-)cellulolytic regulatory system in filamentous fungi, which might be related to the adaptation of fungi to their specific biotopes.

2014-08-01 | PXD001190 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data