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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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A tri-species Aspergillus array

ABSTRACT: This SuperSeries is composed of the following subset Series: GSE9275: A tri-species Aspergillus array (nidulans arrays) GSE9276: A tri-species Aspergillus array (niger arrays) GSE9277: A tri-species Aspergillus array (oryzae arrays) Keywords: SuperSeries Refer to individual Series

ORGANISM(S): Aspergillus oryzae

SUBMITTER: Mikael Andersen

PROVIDER: E-GEOD-9298 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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A trispecies Aspergillus microarray: comparative transcriptomics of three Aspergillus species.

Andersen Mikael R MR Vongsangnak Wanwipa W Panagiotou Gianni G Salazar Margarita P MP Lehmann Linda L Nielsen Jens J

Proceedings of the National Academy of Sciences of the United States of America 20080310 11

The full-genome sequencing of the filamentous fungi Aspergillus nidulans, Aspergillus niger, and Aspergillus oryzae has opened possibilities for studying the cellular physiology of these fungi on a systemic level. As a tool to explore this, we are making available 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 was used to validat ...[more]

PMID: 18332432

Similar Datasets

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

Attachment of Bacillus subtilis to the hyphae of Aspergillus niger results in altered metabolism and defense mechanisms in both partner

Project description:Interaction of microbes affects the growth, metabolism and differentiation of members of the community. While direct and indirect competitions, like spite and nutrient consumption have negative effect on each other, microbes also evolved in nature not only to fight, but in some cases to adapt or support each other while increasing the fitness of the community. Presence of bacteria and fungi in the soil results in interactions and various examples were described, including mutualism. Bacilli attach to the plant root and form complex communities in the rhizosphere. Bacillus subtilis, when grown in the presence of Aspergillus niger interacts with the fungal partner, attaches and grows on the hyphae. Using dual transcriptome experiment, we show that both fungi and bacteria alter their metabolisms during the interaction. Interestingly, the transcription of genes related to the antifungal and antibacterial defense mechanism of B. subtilis and A. niger, respectively, are decreased upon attachment of bacteria to the mycelia. Our microarray experiments provide a novel insight into the mutual interaction of a bacterium and a fungus. Aspergillus niger were grown with and without Bacillus subtilis. Biological triplicates were made for both conditions, Affymetrix microarray experiments were performed on these samples.

2014-10-07 | E-GEOD-46187 | 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

The galactose regulator GalX regulates the D-galactose oxido-reductive pathway in Aspergillus niger.

Project description:Galactose catabolism in Aspergillus nidulans is regulated by at least two regulators, GalR and GalX. In Aspergillus niger only GalX is present, and its role in D-galactose catabolism in this fungus was investigated. Phenotypic and gene expression analysis of a wild type and a galX disruptant revealed that GalX does not substitute for the absence of GalR in A. niger, it regulates the D-galactose oxido-reductive pathway, but not the Leloir pathway. Four genes, including the recently characterized ladB (galactitol dehydrogenase) were found to have differencial expressions that are highly relevant to GalX , indicating a novel oxido-reductive pathway in A.niger . We aim to discover differentially expressed genes in A.niger wild type strain N402 and M-NM-^TgalX mutant while growing on galactose as carbon source. Biological duplicates were made for both strains. The strains were grown O/N in complete medium with 2% frunctose and mycelium was then washed and transferred to minimal medium with 25 mM D-galactose and incubated for 2 hours. Affymetrix microarray experiments were performed RNA isolated from these samples.

2012-09-20 | E-GEOD-40219 | biostudies-arrayexpress

Protein production by Aspergillus oryzae

Project description:The filamentous fungus Aspergillus oryzae is an important microbial cell factory for industrial production of useful enzymes, such as α-amylase. In order to optimize the industrial enzyme production process, there is a need to understand fundamental processes underlying protein production, here under how protein production links to metabolism through global regulatory structures. In this study, two α-amylase-producing strains of A. oryzae, a wild type strain and a transformant strain containing additional copies of the α-amylase gene, were characterized at a systematic level. Based on integrated analysis of ome-data together with genome-scale metabolic network and flux calculation, we identified key genes, key enzymes, key proteins, and key metabolites involved in the processes of protein synthesis and secretion, nucleotide metabolism, and amino acid metabolism that can be the potential targets for improving industrial protein production. Keywords: Two Aspergillus oryzae strains and two different carbon sources Two carbon sources (glucose, maltose) with three biological replicates for A. oryzae strain A1560 and strain CF1.1

2012-02-12 | E-GEOD-22566 | biostudies-arrayexpress

Aspergillus niger RhaR, a regulator involved in L-rhamnose release and catabolism

Project description:The genome of the filamentous fungus Aspergillus niger is rich in genes encoding pectinases, a broad class of enzymes that have been extensively studied due to their use in industrial applications. The sequencing of the A. niger genome provided more knowledge concerning the individual pectinolytic genes, but relatively little is still known about the regulatory genes involved in pectin degradation. Understanding regulation of the pectinolytic genes provides a tool to optimize the production of pectinases in this industrially important fungus. This study describes the identification and characterization of one of the activators of pectinase-encoding genes, RhaR. Inactivation of the gene encoding this regulator resulted in down-regulation of genes involved in the release and catabolism of L-rhamnose from the pectinolytic substructure rhamnogalacturonan I. We aim to discover differencial expressed genes in A.niger wild type strain N402 and M-NM-^TrhaR mutant while growing on rhamnose as carbon source. Biological duplicates were made for both strain at the growth of 2 hours, Affymetrix microarray experiments were performed on these samples.

2014-03-13 | E-GEOD-51023 | biostudies-arrayexpress

Recovery of phenotypes obtained by adaptive evolution through inverse metabolic engineering

Project description:Reconstructed mutants of yeast by inverse metabolic engineering were characterized by fermentation physiology and tools from systems biology. Six reconstructed mutants of yeast were grown on aerobic batch with galactose as carbon source

2012-02-29 | E-GEOD-36118 | biostudies-arrayexpress

Comparative transcriptome analysis of yeast expressing the fungal desaturases

Project description:To study how the presence of PUFAs influences central cellular processes, and in order to perform lipidome, transcriptome and molecular studies we decided to use yeast as a model organism. We therefore co-expressed Δ12-desaturase and Δ6- desaturase genes from Mucor rouxii in S. cerevisiae with the objective to obtain a yeast strain that contains PUFAs, especially linoleic acid (LA, C18:2Δ9,12) and γ-linolenic acid (GLA, C18:3Δ6,9,12), in its membranes. The resulting yeast strain was analyzed in details in order to quantify the fluxes through the fatty acid biosynthetic pathways and the genome-wide transcriptional response to production of LA and GLA. Three recombinant yeasts were constructed and grown in glucose-limited condition. Steady-state cultures were harvested for RNA extraction and hybridization on Affymetrix microarrays. Comparative transcriptome analysis between S. cerevisiae recombinants expressing M. rouxii D12-desaturase (D12) and co-expressing D12-desaturase and D6-desaturase genes (D126) and the reference strain (REF) was implemented.

2010-12-27 | E-GEOD-20155 | biostudies-arrayexpress

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