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