Abstract
BackgroundYarrowia lipolytica is an oleaginous ascomycete yeast that stores lipids in response to limitation of nitrogen. While the enzymatic pathways responsible for neutral lipid accumulation in Y. lipolytica are well characterized, regulation of these pathways has received little attention. We therefore sought to characterize the response to nitrogen limitation at system-wide levels, including the proteome, phosphoproteome and metabolome, to better understand how this organism regulates and controls lipid metabolism and to identify targets that may be manipulated to improve lipid yield.ResultsWe found that ribosome structural genes are down-regulated under nitrogen limitation, during which nitrogen containing compounds (alanine, putrescine, spermidine and urea) are depleted and sugar alcohols and TCA cycle intermediates accumulate (citrate, fumarate and malate). We identified 1219 novel phosphorylation sites in Y. lipolytica, 133 of which change in their abundance during nitrogen limitation. Regulatory proteins, including kinases and DNA binding proteins, are particularly enriched for phosphorylation. Within lipid synthesis pathways, we found that ATP-citrate lyase, acetyl-CoA carboxylase and lecithin cholesterol acyl transferase are phosphorylated during nitrogen limitation while many of the proteins involved in β-oxidation are down-regulated, suggesting that storage lipid accumulation may be regulated by phosphorylation of key enzymes. Further, we identified short DNA elements that associate specific transcription factor families with up- and down-regulated genes.ConclusionsIntegration of metabolome, proteome and phosphoproteome data identifies lipid accumulation in response to nitrogen limitation as a two-fold result of increased production of acetyl-CoA from excess citrate and decreased capacity for β-oxidation.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2471-2) contains supplementary material, which is available to authorized users.
Highlights
Yarrowia lipolytica is an oleaginous ascomycete yeast that stores lipids in response to limitation of nitrogen
When high quality nitrogen sources are available, the GATA type transcription factors Gln3p and Gat1p become phosphorylated and remain bound to Ure2p in the cytosol, whereas they localize to the nucleus and activate nitrogen utilization genes in poor nitrogen conditions
Comparison of the transcriptional regulators found that regulation of β-oxidation and peroxisome biogenesis by FarA and amino acid biosynthesis by Gcn4 are likely to be conserved between Y. lipolytica and filamentous fungi [22]
Summary
Yarrowia lipolytica is an oleaginous ascomycete yeast that stores lipids in response to limitation of nitrogen. When high quality nitrogen sources are available, the GATA type transcription factors Gln3p and Gat1p become phosphorylated and remain bound to Ure2p in the cytosol, whereas they localize to the nucleus and activate nitrogen utilization genes in poor nitrogen conditions. A second set of GATA type transcription factors, Gzf3p and Dal80p, act as repressors that compete for binding sites with and are regulated by Gln3p and Gat1p [19, 20]. It is unknown whether the pathways above operate in Y. lipolytica. Comparison of the transcriptional regulators found that regulation of β-oxidation and peroxisome biogenesis by FarA and amino acid biosynthesis by Gcn are likely to be conserved between Y. lipolytica and filamentous fungi [22]
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