Reconstruction and validation of a genome-scale metabolic model for Rhizophagus irregularis

Description

This repository contains all code and result files that were generated to analyse the R. irregularis genome-scale metabolic model iRi1574.

Requirements

• IBM CPLEX solver 12.9
• Gurobi solver 9.1.1 (only myristate uptake analysis)
• MATLAB (tested with MATLAB 2017b and 2020b)
• COBRA toolbox for MATLAB (v3.0) https://github.com/opencobra/cobratoolbox
• R (3.6.3) with additional packages: wesanderson, plotrix, scales, pheatmap, ape
• Python (3.6)
• all simulations were run under both a Fedora operating system and Windows 10

Usage

• make sure software requirements are met
• add all MATLAB code files to the MATLAB search path
• change into top-level directory (RhiirGEM/) or update topDir variable in the analysis scripts

Repository structure

• RhiirGEM/code/analysis
  • MATLAB code files that were used for the analysis of the iRi1574 model
• RhiirGEM/code/kcats
  • get-kcats.sh calls three python scripts that were used to retrieve information on enzyme turnover numbers and full organism lineages
• RhiirGEM/code/plotting
  • contains one R script per figure/subfigure
• RhiirGEM/data
  • corrected-EC-numbers.csv is a two-column file containing updates from old to new EC standard
  • uniprot.tab contains information on all enzymes of R. irregularis that are present in UniProt
• RhiirGEM/data/kcats
  • kcat-reference-data.tsv contains all turnover numbers retrieved from BRENDA and SABIO-RK
  • kcats_model.txt contains a list of turnover numbers per (irreversible) reaction in the iRi1574 model
• RhiirGEM/data/transcriptomic-data
  • contains averaged expression data of three replicates from the three developmental stages (ERM, IRM, ARB)
  • the data were published by Zeng et al. (2018) https://doi.org/10.1111/tpj.13908
• RhiirGEM/memote-report
  • contains the html-formatted file that was obtained by running the memote test suite on the iRi1574 model
• RhiirGEM/model
  • contains the iRi1574 model as sbml, xlsx, and mat file
• RhiirGEM/results/carbon-sources
  • results from growth predictions and flux sampling of the iRi1574 model with different media conditions
• RhiirGEM/results/developmental-stages
  • results from growth predictions and flux sampling of the iRi1574 model at three simulated developmental stages
• RhiirGEM/results/figures
  • contains all figures shown in the manuscript
• RhiirGEM/results/fungal-models
  • fungal model files that were used for comparisons (references given in Suppl. Table 2)
• RhiirGEM/results/stats
  • model statistics for summarizing the iRi1574 model

To reproduce the results:

Run the following MATLAB scripts to reproduce the results of our study (RhiirGEM/code/analysis/)

• Create files for plotting model statistics:
  • generate_model_stat_files.m (several minutes)
• Comparison to published fungal models:
  • compare_subsystems_fungal_models.m (about 30 minutes)
• Growth simulations on single carbon sources:
  • growth_on_single_carbon_sources.m (about a minute)
• Growth prediction on myristate:
  • growth_on_myristate_fba.m (seconds)
  • growth_on_myristate_emoment.m (several minutes)
• Simulation of growth on different media:
  • analysis_carbon_source_concentration.m (1-2 hours)
• Growth prediction at developmental stages:
  • analysis_fungal_structures.m (about 1 hour)

Output files of these scripts are stored in the respective subdirectories of RhiirGEM/results/.

All figures were generated using R scripts (RhiirGEM/code/plotting/), which are named according to their output figure, which is stored at RhiirGEM/results/figures/.

Reference

Wendering and Nikoloski (2022) mSystems 7(1): e01216-21. doi:10.1128/msystems.01216-21