- Brief Repository Description
This repository contains a genome-scale metabolic model iNR1329 for Cordyceps militaris.
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Abstract: Cordyceps militaris is an entomopathogenic fungus which is often used in Asia as a traditional medicine developed from age-old wisdom. Presently, cordycepin from C. militaris is a great interest in medicinal applications. However, cellular growth of C. militaris and the association with cordycepin production remain poorly understood. To explore the metabolism of C. militaris as potential cell factories in medical and biotechnology applications, this study developed a high-quality genome-scale metabolic model of C. militaris, iNR1329, based on its genomic content and physiological data. The model included a total of 1,329 genes, 1,821 biochemical reactions, and 1,171 metabolites among 4 different cellular compartments. Its in silico growth simulation results agreed well with experimental data on different carbon sources. iNR1329 was further used for optimizing the growth and cordycepin overproduction using a novel approach, POPCORN, for rational design of synthetic media. In addition to the high-quality GEM iNR1329, the presented POPCORN approach was successfully used to rationally design an optimal synthetic medium with C:N ratio of 8:1 for enhancing 3.5-fold increase in cordycepin production. This study thus provides a novel insight into C. militaris physiology and highlights a potential GEM-driven method for synthetic media design and metabolic engineering application. The iNR1329 and the POPCORN approach are available at the GitHub repository: https://github.com/sysbiomics/Cordyceps_militaris-GEM.
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Model KeyWords: Cordycepin, Cordyceps militaris, Genome-scale modeling, Synthetic media design, Systems biology GEM Category: Species; Utilisation: Predictive simulation; Field: Genome-scale modeling; Metabolic engineering; Type of Model: Reconstruction and refinement; Taxonomy: Cordyceps_militaris ; Metabolic System: General Metabolism; Condition: Synthetic media;
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Reference: Raethong N, Wang H, Nielsen J, Vongsangnak W. 2019. Optimizing cultivation of Cordyceps militaris for fast growth and cordycepin overproduction using rational design of synthetic media. Computational and Structural Biotechnology Journal doi:https://doi.org/10.1016/j.csbj.2019.11.003.
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Pubmed ID: 31890138
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PMC ID: PMC6926140
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Last update: 2020-04-19
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The model contains:
| Taxonomy | Model Name | Reactions | Metabolites | Genes |
|---|---|---|---|---|
| Cordyceps militaris | iNR1329 | 1,821 | 1,171 | 1,329 |
This repository is administered by Nachon Raethong (@sysbiomics), Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand
- A functional Matlab installation (MATLAB 7.3 or higher).
- RAVEN Toolbox 2.0 for MATLAB (required for contributing to development).
- libSBML MATLAB API (version 5.16.0 is recommended).
- Gurobi Optimizer for MATLAB.
- For contributing to development: a git wrapper added to the search path.
- Clone the master branch from sysbiomics GitHub.
- Nachon Raethong (https://www.researchgate.net/profile/Nachon_Raethong) (@nachonase), Faculty of Science, Kasetsart University, Bangkok, Thailand
- Hao Wang (https://www.chalmers.se/en/staff/Pages/hao-wang.aspx) (@Hao-Chalmers), Chalmers University of Technology, Göteborg, Sweden