Note that in 2020 Sco4 has been merged with other Streptomyces coelicolor models to construct the consensus model Sco-GEM.

Streptomyces_coelicolor-GEM

• Brief Repository Description

This repository contains a genome-scale metabolic model Sco4 for the antibiotic producer Streptomyces coelicolor A3(2), a representative species of Actinomycetales.

• Abstract:

Streptomyces coelicolor is a representative species of soil-dwelling, filamentous and gram-positive actinobacterium harbouring enriched secondary metabolite biosynthesis gene clusters. As a well-known pharmaceutical and bioactive compound producer, S. coelicolor has been exploited for antibiotic and secondary metabolite production. Here, we present the updated model Sco4, which refers to the fourth major release of S. coelicolor GEM and with increased coverage of both primary and secondary metabolism through using the RAVEN Toolbox ver 2.0. The Sco4 model was expanded with 398 new metabolic reactions and 314 newly associated enzyme-coding genes, which encoded a variety of biosynthetic pathways for known secondary metabolites (e.g. 2-methylisoborneol, albaflavenone, desferrioxamine, geosmin, hopanoid and flaviolin dimer). The Sco4 model can be used as an upgraded platform for future systems biology research on S. coelicolor and related species.

• Model KeyWords:

GEM Category: Species; Utilisation: Predictive simulation; Field: Metabolic-network reconstruction; Type of Model: Reconstruction and refinement; Model Source: iMK1208; Omic Source: Genomics; Taxonomy: Streptomyces coelicolor; Metabolic System: General Metabolism; Strain: A3(2); Condition: Complex medium;

• Reference:

Wang H et al. (2018) "RAVEN 2.0: a versatile platform for metabolic network reconstruction and a case study on Streptomyces coelicolor" bioRxiv doi:10.1101/321067

• Pubmed ID: TBA

• Last update: 2018-05-14

• The model contains:

Taxonomy	Template Model	Reactions	Metabolites	Genes
Streptomyces coelicolor A3(2)	iMK1208	2322	1906	1506

This repository is administered by Hao Wang (@SysBioChalmers), Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology

Installation

Recommended Software:

• A functional Matlab installation (MATLAB 7.3 or higher).
• RAVEN Toolbox 2 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.

Installation Instructions

• Clone the master branch from SysBioChalmers GitHub.
• Add the directory to your Matlab path, instructions here.

Contribute To Development

1. Fork the repository to your own Github account
2. Create a new branch from devel.
3. Make changes to the model
   • RAVEN Toolbox 2 for MATLAB is highly recommended for making changes
   • Before each commit, run in Matlab the newCommit(model) function from the ComplementaryScripts folder
   • Make a Pull Request to the devel folder, including changed txt, yml and xml files

Contributors

• Hao Wang (@Hao-Chalmers), Chalmers University of Technology, Göteborg, Sweden
• Eduard J. Kerkhoven (@edkerk), Chalmers University of Technology, Göteborg, Sweden