ecRhtoGEM

Brief repository description:

• This repository contains the work on enzyme-constrained genome-scale model of oleaginous, non-conventional yeast Rhodotorula toruloides.

• Repository consists of code, data, model files and result files. Result visualisation is not provided.

Model files (xml, yml, mat, json)

• As a starting point for this work, a metabolic genome-scale model, named rhto-GEM, developed by Tiukova et al. 2019, was used.
• The initial model files used in this work are available here.

Scripts (m)

• The scripts were written in Matlab.
• Enzymatic constraints were applied and models were generated using the GECKO toolbox.
• The modelling was done with the RAVEN toolbox.

Visualisations (json)

• Metabolic network maps are available upon request. They were constructed for internal use using Escher software.

Instructions:

• Script edit_rhtoGEM.m introduces reactions for alternative xylose assimilation pathway.
• Script reconstruct_ecRhtoGEM.m generates condition-specific enzyme-constrained models with integrated absolute proteomics data. Models are reconstructed based on optimized parameters, including manually curated enzymatic kcat values, as provided in manualModifications.m. After downloading the GECKO folder, model reconstruction involves the following steps: 1) geckomat/enhanceGEM.m pipeline, which creates the first version of ec-model with an enzyme pool that is used for screening required kcat modifications; 2) geckomat/utilities/integrate_proteomics/generate_protModels.m pipeline, which sets constraints on high-quality measured individual enzymes from the provided proteomics dataset. Folder results/generate_protModels_pipeline provides the track of enzyme abundances which were automatically modified in order to reach the experimental conditions.
• Script analyze_ecRhtoGEM.m runs random sampling, calculates flux mean value and standard deviation, calculates enzyme usage, extracts ATP, NADPH, and NADH production balances from flux results, and converts fluxes to original, non-ecModel version.

Last update:

2022-09-15