Exploiting acetate for glucose-based bioproduction in Escherichia coli

Overview

This R code perform all analyses detailed in the following publication:

Acetate as a metabolic booster for glucose-based bioproduction in Escherichia coli.

T. Gosselin-Monplaisir, D. Jallet, E. Harscoet, S. Uttenweiler-Joseph, S. Heux, P. Millard. bioRxiv preprint, 2025, doi: 10.1101/2025.06.17.659982

The models are available in COPASI format in the ./model/ directory, and in SBML format from the Biomodels database (http://www.ebi.ac.uk/biomodels/) under identifiers MODEL2506160001 (acetyl-CoA-insensitive pathway) and MODEL2506160002 (acetyl-CoA-sensitive pathway). Additional details on model construction and calibration can be found in Millard et al. 2021 (eLife, doi: 10.7554/eLife.63661) and in Gosselin-Monplaisir et al. 2025 (bioRxiv preprint, doi: 10.1101/2025.06.17.659982). Figures are saved in the ./results/ directory.

Details on the calculations can be found in the original publication and in the Rmd notebook.

We distribute an HTML file showing the notebook’s output after execution

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

Dependencies

If not yet done, download and install Rstudio.

Some R packages are also required.

RColorBrewer, gplots, pso, colorspace and optimx can be installed by running the following command in the Rstudio console:

install.packages(c("RColorBrewer", "gplots", "pso", "optimx", "colorspace"))

CoRC can be installed using the following commands:

install.packages("remotes")
library(remotes)
remotes::install_github("jpahle/CoRC")
library(CoRC)
CoRC::getCopasi()

Additional information on CoRC installation and usage are available from the CoRC repository (https://github.com/jpahle/CoRC) and the associated publication (Föster et al., Bioinformatics, 2021, doi: 10.1093/bioinformatics/btab033).

Usage

To run all analyses detailed in the publication and reproduce Figures 2 and 4:

• download the GitHub repository tarball and unpack it somewhere on your disk

• start Rstudio

• open the file ./notebook.Rmd

The notebook will open in Rstudio, in each cell you can read/modify/execute the code as well as read accompanying comments.

Questions

If you have any question, please open a new issue to our GitHub issue tracker so we could discuss together.

How to cite

Gosselin-Monplaisir T., Jallet D., Harscoet E., Uttenweiler-Joseph S., Heux S., Millard P. Acetate as a metabolic booster for glucose-based bioproduction in Escherichia coli. bioRxiv preprint, 2025, doi: 10.1101/2025.06.17.659982

Authors

Pierre Millard

Contact

📧 Pierre Millard, pierre.millard@insa-toulouse.fr