Protein production by Aspergillus oryzae
Ontology highlight
ABSTRACT:
ORGANISM(S): Aspergillus niger Aspergillus nidulans Aspergillus oryzae
PROVIDER: GSE22566 | GEO | 2012/02/12
SECONDARY ACCESSION(S): PRJNA128431
REPOSITORIES: GEO
Similar Datasets
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
Project description:Fungal endo-β-mannanases (β-mannanases) are widely used as industrial enzymes; however, no transcriptional regulator of β-mannanases has been identified in fungi or other eukaryotic cells to date. To identify a transcriptional regulator of β-mannanases in Aspergillus oryzae, a gene-disruptant library of transcriptional regulators was screened for mutants exhibiting reduced β-mannanase activity by using konjac glucomannan as the substrate, and ManR, a Zn(II)2Cys6 type DNA binding protein was identified. Moreover, a manR-overexpressing strain showed significantly increased β-mannanase activity. DNA microarray analysis of the manR-disruptant strain and the manR-overexpressing strain further indicated that when konjac glucomannan is used as the carbon source, ManR positively regulates the gene expression of not only β-mannanase, but also the enzymes involved in the degradation of galactomannans and glucomannans such as α-galactosidase, β-mannosidase, acetylmannan esterase, and β-glucosidase. Therefore, we conclude that ManR is a positive regulator of the β-mannan utilization system in A. oryzae.
2012-11-08 | GSE40590 | GEO
Project description:Vongsangnak2008 - Genome-scale metabolic
network of Aspergillus oryzae (iWV1314)
This model is described in the article:
Improved annotation through
genome-scale metabolic modeling of Aspergillus oryzae.
Vongsangnak W, Olsen P, Hansen K,
Krogsgaard S, Nielsen J.
BMC Genomics 2008; 9: 245
Abstract:
BACKGROUND: Since ancient times the filamentous fungus
Aspergillus oryzae has been used in the fermentation industry
for the production of fermented sauces and the production of
industrial enzymes. Recently, the genome sequence of A. oryzae
with 12,074 annotated genes was released but the number of
hypothetical proteins accounted for more than 50% of the
annotated genes. Considering the industrial importance of this
fungus, it is therefore valuable to improve the annotation and
further integrate genomic information with biochemical and
physiological information available for this microorganism and
other related fungi. Here we proposed the gene prediction by
construction of an A. oryzae Expressed Sequence Tag (EST)
library, sequencing and assembly. We enhanced the function
assignment by our developed annotation strategy. The resulting
better annotation was used to reconstruct the metabolic network
leading to a genome scale metabolic model of A. oryzae.
RESULTS: Our assembled EST sequences we identified 1,046 newly
predicted genes in the A. oryzae genome. Furthermore, it was
possible to assign putative protein functions to 398 of the
newly predicted genes. Noteworthy, our annotation strategy
resulted in assignment of new putative functions to 1,469
hypothetical proteins already present in the A. oryzae genome
database. Using the substantially improved annotated genome we
reconstructed the metabolic network of A. oryzae. This network
contains 729 enzymes, 1,314 enzyme-encoding genes, 1,073
metabolites and 1,846 (1,053 unique) biochemical reactions. The
metabolic reactions are compartmentalized into the cytosol, the
mitochondria, the peroxisome and the extracellular space.
Transport steps between the compartments and the extracellular
space represent 281 reactions, of which 161 are unique. The
metabolic model was validated and shown to correctly describe
the phenotypic behavior of A. oryzae grown on different carbon
sources. CONCLUSION: A much enhanced annotation of the A.
oryzae genome was performed and a genome-scale metabolic model
of A. oryzae was reconstructed. The model accurately predicted
the growth and biomass yield on different carbon sources. The
model serves as an important resource for gaining further
insight into our understanding of A. oryzae physiology.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180056.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
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2015-07-30 | MODEL1507180056 | BioModels
Project description:Sirtuin is considered to play a significant role in the growth phase-dependent gene expression. In this study, we characterized sirtuin in the white koji fungus, Aspergillus kawachii, to examine their role on regulation of amylolytic enzymes and citric acid productions during the solid-state culture (koji). Characterization of rice-koji made using five putative sirtuin gene disruptants indicated that they are involved in amylolytic activity and acidity of rice koji; especially the sirD disruptant showed lower levels of α-amylase activity and citric acid production per mycelial weight in the koji compared the control strain. In addition, the sirD disruptant also showed a change in mycelial pigmentation, higher sensitivity to cell wall biogenesis inhibitor such as calcofluor white and Congo red, and reduced conidia formation, indicating that SirD is required for secondary metabolism, cell wall integrity, and conidial development. The cap analysis gene expression (CAGE) indicated that the transcriptional changes related to the characteristic phenotype of the sirD disruptant (e.g., a reduced transcript level of acid-stable α-amylase gene and a citric acid exporter) in rice koji. These results indicated that SirD has a significant role on the global transcriptional regulation including productions of α-amylase and citric acid in A. kawachii during the solid-state fermentation process.
2019-06-15 | GSE132729 | GEO
Project description:In this study, we focused on chemically defined inducers or substrates to drive expression of cellulases, hemicellulases and accessory enzymes in the model filamentous fungus Aspergillus oryzae. Cellohexaose (O-CHE), mannohexaose (O-MHE), xylopentaose (O-XPE), arabinoheptaose (O-AHP), 1,3:1,4-β-glucohexaose (O-BGHEXA), 63-α-D-glucosyl-maltotriosyl-maltotriose (O-GMH), 61-α-D-galactosyl-mannotriose (O-GM3), xyloglucan (X3Glc4-borohydride reduced; O-X3G4R), turanose (TYR) and sophorose (SOP) were used to induce the plant polysaccharide degradation machinery of A. oryzae.
2013-07-15 | GSE48864 | GEO
Project description:Honey promotes health and is an effective non-pharmacological home remedy against common respiratory infections. However, industrial processing and manipulation of raw honey can have a detrimental effect on its biological activities, including antibacterial ones, and hence its health-benefiting qualities. Therefore, this study aimed to compare the honey’s antibacterial activity, its total protein content, and the abundance of the most dominant bee-derived proteins in honey between raw (n=92) and supermarket (n=17) samples. We showed that raw honey samples were much more effective in inhibiting the growth of Staphylococcus aureus with a median minimal inhibitory concentration (MIC) value of 4.5% compared to supermarket honey samples ceasing bacterial growth with a median MIC value of 36%. Moreover, raw honey samples contained significantly higher amounts of total protein as well as the content of particular bee-derived proteins (major royal jelly protein 1 (MRJP1), glucose oxidase (GOX), and α-glucosidase) in contrast to supermarket honey samples. These data hint that some marketed honey samples could be deliberately manipulated with syrup, especially those that exhibited low protein content. In addition, the supermarket honey sample with the lowest protein content contained α-amylase (diastase) from Aspergillus oryzae. Strikingly, the content of this foreign enzyme in honey was roughly 60 times higher than the naturally occurring bee α-amylase. Our findings highlight the burning need to refine and monitor the specific quality parameters, ensuring the authenticity of honey and maintaining its reputation as a functional food.
2023-08-12 | PXD040190 | Pride
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
2009-10-22 | GSE13868 | GEO
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
Project description:Fungal endo-M-NM-2-mannanases (M-NM-2-mannanases) are widely used as industrial enzymes; however, no transcriptional regulator of M-NM-2-mannanases has been identified in fungi or other eukaryotic cells to date. To identify a transcriptional regulator of M-NM-2-mannanases in Aspergillus oryzae, a gene-disruptant library of transcriptional regulators was screened for mutants exhibiting reduced M-NM-2-mannanase activity by using konjac glucomannan as the substrate, and ManR, a Zn(II)2Cys6 type DNA binding protein was identified. Moreover, a manR-overexpressing strain showed significantly increased M-NM-2-mannanase activity. DNA microarray analysis of the manR-disruptant strain and the manR-overexpressing strain further indicated that when konjac glucomannan is used as the carbon source, ManR positively regulates the gene expression of not only M-NM-2-mannanase, but also the enzymes involved in the degradation of galactomannans and glucomannans such as M-NM-1-galactosidase, M-NM-2-mannosidase, acetylmannan esterase, and M-NM-2-glucosidase. Therefore, we conclude that ManR is a positive regulator of the M-NM-2-mannan utilization system in A. oryzae. manR disruptant, manR-overexpressing strain and A. oryzae RkuptrP2-1M-bM-^HM-^FAF/P (derivative of A. oryzae RIB40) were cultivated in minimal medium containing 1% konjac glucomannan as the sole carbon source. After 6 h cultivation, total RNAs from the mycelia were extracted, and DNA microarray analysis was carried out. The analysis of manR disruptant was conducted with 4 biological replications, the analysis of manR overexpressing strain was conducted with 3 biological replications.
2012-11-08 | E-GEOD-40590 | biostudies-arrayexpress