Yarrowia_lipolytica_W29-GEM

• Brief Model Description

This repository contains the current genome-scale metabolic model of Yarrowia lipolytica W29, named iYali. Various different updated versions can be downloaded as releases.

• Abstract

Yarrowia lipolytica is a promising microbial cell factory for the production of lipids to be used as fuels and chemicals, but there are few studies on regulation of its metabolism. Here we performed the first integrated data analysis of Y. lipolytica grown in carbon and nitrogen limited chemostat cultures. We first reconstructed a genome-scale metabolic model and used this for integrative analysis of multilevel omics data. Metabolite profiling and lipidomics was used to quantify the cellular physiology, while regulatory changes were measured using RNAseq. Analysis of the data showed that lipid accumulation in Y. lipolytica does not involve transcriptional regulation of lipid metabolism but is associated with regulation of amino-acid biosynthesis, resulting in redirection of carbon flux during nitrogen limitation from amino acids to lipids. Lipid accumulation in Y. lipolytica at nitrogen limitation is similar to the overflow metabolism observed in many other microorganisms, e.g. ethanol production by Sacchromyces cerevisiae at nitrogen limitation.

• Model KeyWords

GEM Category: Species; Utilisation: experimental data reconstruction; Field: metabolic-network reconstruction; Type of Model: curated; Model Source: yeast-GEM; Omic Source: Transcriptomics, Proteomics, Metabolomics; Taxonomy: Yarrowia lipolytica W29; Metabolic System: General Metabolism; Bioreactor; Strain: W29; Condition: Minimal medium;

• Reference:

Kerkhoven EJ, Pomraning KR, Baker SE, Nielsen J (2016) "Regulation of amino-acid metabolism controls flux to lipid accumulation in Yarrowia lipolytica." npj Systems Biology and Applications 2:16005. doi:10.1038/npjsba.2016.5

• Pubmed ID: 28725468

• Last update: 2018-05-18

• The model:

Taxonomy	Template Model	Reactions	Metabolites	Genes
Yarrowia lipolytica W29	yeast-GEM	1924	1671	847

This repository is administered by @edkerk, Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology

Installation

Recommended Software:

• A functional Matlab installation (MATLAB 7.3 or higher).
• RAVEN Toolbox 2 for MATLAB (required for contributing to development).
• libSBML MATLAB API (version 5.16.0 is recommended).
• Gurobi Optimizer for MATLAB.
• For contributing to development: a git wrapper added to the search path.

Installation Instructions

• Clone the master branch from SysBioChalmers GitHub.
• Add the directory to your Matlab path, instructions here.

Contribute To Development

1. Fork the repository to your own Github account
2. Create a new branch from devel.
3. Make changes to the model
   • RAVEN Toolbox 2 for MATLAB is highly recommended for making changes
   • Before each commit, run in Matlab the newCommit(model) function from the ComplementaryScripts folder, this exports the necessary txt, yml and xml files that can be used to track changes between different model versions
   • Make a Pull Request to the devel folder, including changed txt, yml and xml files

Contributors

• Eduard J. Kerkhoven (@edkerk), Chalmers University of Technology, Göteborg, Sweden