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Open Access Highly Accessed Open Badges Research article

A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica

Nicolas Loira14, Thierry Dulermo23, Jean-Marc Nicaud23 and David James Sherman1*

Author Affiliations

1 Inria / Université Bordeaux / CNRS joint project-team MAGNOME, Talence, F-33405, France

2 INRA, UMR1319 Micalis, Jouy-en-Josas, F-78352, France

3 CNRS, Micalis, Jouy-en-Josas, F-78352, France

4 Center for Genome Regulation, Universidad de Chile, Av. Blanco Encalada 2085, 3er piso, Santiago, Chile

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BMC Systems Biology 2012, 6:35  doi:10.1186/1752-0509-6-35

Published: 4 May 2012



Yarrowia lipolytica is an oleaginous yeast which has emerged as an important microorganism for several biotechnological processes, such as the production of organic acids, lipases and proteases. It is also considered a good candidate for single-cell oil production. Although some of its metabolic pathways are well studied, its metabolic engineering is hindered by the lack of a genome-scale model that integrates the current knowledge about its metabolism.


Combining in silico tools and expert manual curation, we have produced an accurate genome-scale metabolic model for Y. lipolytica. Using a scaffold derived from a functional metabolic model of the well-studied but phylogenetically distant yeast S. cerevisiae, we mapped conserved reactions, rewrote gene associations, added species-specific reactions and inserted specialized copies of scaffold reactions to account for species-specific expansion of protein families. We used physiological measures obtained under lab conditions to validate our predictions.


Y. lipolytica iNL895 represents the first well-annotated metabolic model of an oleaginous yeast, providing a base for future metabolic improvement, and a starting point for the metabolic reconstruction of other species in the Yarrowia clade and other oleaginous yeasts.