EG-bio-upcycling

Metabolic modelling for biological upcycling of ethylene glycol (EG)

Background

• Polyethylene terephthalate (PET) is a thermoplastic polyester of terephthalic acid (TPA) and ethylene glycol (EG) monomers (Kim and Lee, 2012).
• Sustainable hydrolysis of PET gives TPA and EG that can be used as a carbon source in yeast.
• Rhodotorula toruloides is a nonconventional, oleaginous yeast that can naturally accumulate high amounts of lipids and carotenoids, up to 76% as part of its dry biomass (Ageitos et al. 2011), and consume a wide variety of carbon substrates, including complex biomass mixtures (Bonturi et al. 2017).
• The repository contains the development of constraint-based metabolic models for EG utilisation as a carbon source in non-conventional yeast Rhodotorula toruloides.

Installation

1. Create a Conda environment: conda create -n jupyter-env python=3.11 conda activate jupyter-env
2. Clone the EG-bio-upcycling repository and avigate to the EG-bio-upcycling directory: git clone https://github.com/bioengtaltech/EG-bio-upcycling.git cd EG-bio-upcycling
3. For the operations, install Jupyter via conda: conda install -c conda-forge jupyterlab conda install -c conda-forge notebook (optional)
4. For Flux Balance Analysis optimizations, install Gurobi license (free for academic use): conda install -c gurobi gurobi (we used gurobi=11.0)
5. Launch Jupyter in your default browser at http://localhost:8888: jupyter notebook

References

Senatore VG, Reķēna A, Mapelli V, Lahtvee P-J, Branduardi P. Ethylene glycol metabolism in the oleaginous yeast Rhodotorula toruloides. Appl Microbiol Biotechnol. 2025

Last modified: 2025-04-03.