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Functional genomics for the oleaginous yeast Yarrowia lipolytica

ABSTRACT: Oleaginous yeasts are valuable systems for biosustainable production of hydrocarbon-based chemicals. Yarrowia lipolytica is one of the best characterized of these yeast with respect to genome annotation and flux analysis of metabolic processes. Nonetheless, progress is hampered by a dearth of genomewide tools enabling functional genomics. The Hermes DNA transposon was expressed to achieve saturation mutagenesis of the Y. lipolytica genome. Over 535 thousand independent insertions were identified by next-generation sequencing. Poisson analysis of insertion density classified ~22% of genes as essential. As expected, most essential genes not only have homologues in Saccharomyces cerevisiae and Schizosaccharomyces pombe, but the majority of those are also essential. As an obligate aerobe, Y. lipolytica has significantly more respiration - related genes that are classified as essential than do S. cerevisiae and S. pombe. The findings provide insights into biosynthetic pathways, compartmentalization of enzymes, and distinct functions of paralogs. Contributions of nonessential genes to fitness were determined in log growth cultures with glucose and glycerol carbon sources. Fluorescence-activated cell sorting identified mutants in which lipid accumulation is increased. Biological contributions of genes to growth were used to evaluate two recent genome-scale models Y. lipolytica metabolism. This study is the first functional genomic analysis of an oleaginous yeast and provides an important resource for modeling and bioengineering of Y. lipolytica.

ORGANISM(S): Yarrowia lipolytica

PROVIDER: GSE90993 | GEO | 2018/12/06

REPOSITORIES: GEO

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Project description:This model is from the article: A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica Nicolas Loira, Thierry Dulermo, Jean-Marc Nicaud and David J Sherman BMC Systems Biology 2012, 6:35 doi: 10.1186/1752-0509-6-35 , Abstract: Background 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. Results 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 inflected 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. Conclusions Y. lipolytica iNL895represents the first well-annotated metabolic model of an oleaginous yeast, providing a reference for future metabolic improvement, and a starting point for the metabolic reconstruction of other species in the Yarrowia clade and other oleaginous yeasts. Note: This SBML representation of the Yarrowia lipolytica metabolic network is made available under the Creative Commons Attribution-Share Alike 3.0 Unported Licence (see www.creativecommons.org). Nicolas Loira (loira@inria.fr, nloira@gmail.com); based on S.cerevisiae model yeast_4.36.xml (Herrgard, 2008)

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Functional genomics for the oleaginous yeast Yarrowia lipolytica

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