Abstract
BackgroundYarrowia lipolytica is widely studied as a non-conventional model yeast owing to the high level of lipid accumulation. Therein, triacylglycerol (TAG) is a major component of liposome. In order to investigate the TAG biosynthesis mechanism at a systematic level, a novel genome-scale metabolic model of Y. lipolytica was reconstructed based on a previous model iYL619_PCP published by our lab and another model iYali4 published by Kerkhoven et al.ResultsThe novel model iYL_2.0 contains 645 genes, 1083 metabolites, and 1471 reactions, which was validated more effective on simulations of specific growth rate. The precision of 29 carbon sources utilities reached up to 96.6% when simulated by iYL_2.0. In minimal growth medium, 111 genes were identified as essential for cell growth, whereas 66 essential genes were identified in yeast extract medium, which were verified by database of essential genes, suggesting a better prediction ability of iYL_2.0 in comparison with other existing models. In addition, potential metabolic engineering targets of improving TAG production were predicted by three in silico methods developed in-house, and the effects of amino acids supplementation were investigated based on model iYL_2.0.ConclusionsThe reconstructed model iYL_2.0 is a powerful platform for efficiently optimizing the metabolism of TAG and systematically understanding the physiological mechanism of Y. lipolytica.
Highlights
Yarrowia lipolytica is widely studied as a non-conventional model yeast owing to the high level of lipid accumulation
The new model contains 645 genes, 1083 metabolites, and 1471 reactions across different compartments. This model was found superior to the two previous models when employed to simulate cell growth characteristics on glucose or other carbon sources
Gene essentiality analysis resulted in 111 essential genes for cells grown in minimal growth (MG) medium and 66 essential genes when cells cultivated in yeast extract (YE) medium
Summary
Yarrowia lipolytica is widely studied as a non-conventional model yeast owing to the high level of lipid accumulation. In order to investigate the TAG biosynthesis mechanism at a systematic level, a novel genome-scale metabolic model of Y. lipolytica was reconstructed based on a previous model iYL619_PCP published by our lab and another model iYali published by Kerkhoven et al. Yarrowia lipolytica is a non-conventional model oleaginous yeast, which is capable of accumulating substantial amounts of neutral lipids, even above than 50% of its dry cell weight (DCW) (Blazeck et al 2014; Papanikolaou et al 2002). Triacylglycerol (TAG) was discovered as the major constitute of liposome and predominant storage of metabolic energy in microorganism cells, which can be widely. Genes YALI0E32769g (DGA1) and YALI0E16797g (LRO1), encoding major triacylglycerol synthases, play important
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