Supplementary code - Peiro et al., 2019.

Content

This repository contains supporting information of the following publication:

Chemical and metabolic controls on dihydroxyacetone metabolism lead to a suboptimal growth of E. coli

Peiro et al., Appl Environ Microbiol, 2019, doi: 10.1128/AEM.00768-19

We provide:

• the data used to calculate extracellular (uptake and production) fluxes and growth rate of the wild type and deletion mutant strains, and the calculation results. These data are provided in folder 'extracellular_flux_calculations'.

• the R script used to perform genome-scale flux balance analysis and flux variability analysis of Escherichia coli K-12 during aerobic growth on DHA. These data are provided in folder 'genome-scale_modeling'. All calculations are performed using the E. coli genome scale metabolic model iJO1366 (Orth et al., 2011, DOI: 10.1038/msb.2011.65). The model can be found in Biomodels database (http://www.ebi.ac.uk/biomodels/ ; ID MODEL1108160000) and BiGG database (http://bigg.ucsd.edu ; ID iJO1366). It is also provided in folder 'iJO1366' in three different formats (SBML, TSV, and modelorg object provided in an RData file). Details on the calculations can be found in the code (DHA.R).

Dependencies for genome-scale modeling

Some R packages (lattice, glpkAPI, Matrix, sybil) are required. They can be installed with the following command in an R console:

$ install.packages(c("lattice", "glpkAPI", "Matrix", "sybil"))

Usage

To run flux calculations as detailed in the publication:

• go to the code directory, e.g.:

$ cd /home/usr/data/Peiro_2019/genome-scale_modeling/

• open an R session:

$ R

• run calculations:

$ source("DHA.R")

The code is open-source, and available under GPLv3 license.

Authors

Pierre Millard, St�phanie Heux

Contact

📧 Pierre Millard, [email protected] 📧 St�phanie Heux, [email protected]