- Brief Repository Description
This repository contains a genome-scale metabolic model iPs1474 for Cordyceps militaris.
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Abstract:The genome-scale metabolic model (GSMM) of Cordyceps militaris has provided a com-prehensive basis of carbon assimilation for cell growth and metabolite production. However, the model with a simple mass balance concept shows limited capability to probe the metabolic re-sponses of C. militaris under light exposure. This study, therefore, employed the transcrip-tome-integrated GSMM approach to extend the investigation of C. militaris‘s metabolism under light conditions. Through the gene inactivity moderated by metabolism and expression (GIMME) framework, the iPS1474-tiGSMM model was furnished with the transcriptome data, then giving simulation that reasonably well described metabolic response underlying the phenotypic ob-servation of C. militaris in the particular light conditions. The iPS1474-tiGSMM obviously showed an improved prediction of metabolic fluxes in correlation with expressed genes involved in cordycepin and carotenoid biosynthetic pathways under the sucrose culturing condition. Further analysis of reporter metabolites suggested that central carbon metabolism, purine and fatty acids metabolisms towards carotenoid biosynthesis were predominant metabolic processes responsible to light conditions. The finding highlights the key responsive processes enabling acclimatization of C. militaris metabolism in varying light conditions. This study provides a valuable perspective in manipulating the metabolic genes and fluxes towards the target metabolite production.
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Model Keywords:Cordyceps militaris, Light, Metabolism, Transcriptome-integrated GSMM (tiGSMM), Systems bi-ology
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: (under review)
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Pubmed ID:
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PMC ID:
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Last update: 2024-02-01
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The model contains:
| Taxonomy | Model Name | Reactions | Metabolites | Genes |
|---|---|---|---|---|
| Cordyceps militaris | iPS1474 | 1,916 | 1,699 | 1,474 |
- 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.