A community-driven reconstruction of the Aspergillus niger metabolic network

• DOI: 10.1186/s40694-018-0060-7
• Publication Date: 2018-09-26T11:27:04Z
• Authors: Julian Brandl; Maria Victoria Ag...; Paul Schäpe; Anders Noerregaard; Mikko Arvas; Arthur F. J. Ram; Vera Meyer; Adrian Tsang; Ronald P. de Vries; Mikael R. Andersen
• Keywords: SBML; Aspergillus niger; Flux Balance Analysis; Metabolic network; Experimental data; Metabolic Engineering

Aspergillus niger is an important fungus used in industrial applications for enzyme and acid production. To enable rational metabolic engineering of the species, available information can be collected integrated a genome-scale model to devise strategies improving its performance as host organism. In this paper, we update existing A. metabolism include from 876 publications, thereby expanding coverage by 940 reactions, 777 metabolites 454 genes. presented consensus iJB1325 , experimental data publications patents, well our own experiments, into consistent network. This has been included standardized way, allowing automated testing continuous improvements future. repository allowed definition 471 individual test cases, which complies with 373 them. We further re-analyzed transcriptomics quantitative physiology gain new insights on metabolism. Additionally, contains 3482 checks structure, representing best validated developed until now. Strain-specific versions strains ATCC 1015 CBS 513.88 have created containing all building, users adopt models check updated version against data. The resulting compliant SBML standard therefore enables easily simulate it using their preferred software solution. Experimental most organisms are scattered across hundreds several repositories.To allow systems level understanding metabolism, must knowledge here integrates highly curated facilitate simulation flux distributions, interpretation other providing context.