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PMID: 18364712 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger.

Molecular systems biology ·Vol. 4 ·2008-00-00 ·Pages 178

Andersen MR, Nielsen ML, Nielsen J

Abstract

The release of the genome sequences of two strains of Aspergillus niger has allowed systems-level investigations of this important microbial cell factory. To this end, tools for doing data integration of multi-ome data are necessary, and especially interesting in the context of metabolism. On the basis of an A. niger bibliome survey, we present the largest model reconstruction of a metabolic network reported for a fungal species. The reconstructed gapless metabolic network is based on the reportings of 371 articles and comprises 1190 biochemically unique reactions and 871 ORFs. Inclusion of isoenzymes increases the total number of reactions to 2240. A graphical map of the metabolic network is presented. All levels of the reconstruction process were based on manual curation. From the reconstructed metabolic network, a mathematical model was constructed and validated with data on yields, fluxes and transcription. The presented metabolic network and map are useful tools for examining systemwide data in a metabolic context. Results from the validated model show a great potential for expanding the use of A. niger as a high-yield production platform.

MeSH Terms
Aspergillus niger/genetics,growth & development,metabolism Biomass Energy Metabolism Gene Expression Regulation, Fungal Genes, Fungal Genome, Fungal Metabolic Networks and Pathways Models, Biological Open Reading Frames/genetics Oxygen/metabolism Reproducibility of Results
Chemicals
Oxygen
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Andersen Mikael Rørdam
Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
Nielsen Michael Lynge
Nielsen Jens
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Article Info
Journal
Molecular systems biology
Abbr.
Mol Syst Biol
ISSN
1744-4292
DOI
10.1038/msb.2008.12
Published
2008-00-00
Epub
2008-00-25
Pages
178
Language
English
Region
England
NLM ID
101235389
PMCID
PMC2290933
Subset
IM
External Links
PubMed source DOI: 10.1038/msb.2008.12 PMC Full Text View journal details
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