Exploring Proteomes of RobustYarrowia lipolyticaIsolates Cultivated in Biomass Hydrolysate Reveal Key Processes Impacting Mixed Sugar Utilization, Lipid Accumulation, and Degradation

Abstract

Yarrowia lipolytica is an oleaginous yeast exhibiting robust phenotypes beneficial for industrial biotechnology. The phenotypic diversity found within the undomesticated Y. lipolytica clade from various origins illuminates desirable phenotypic traits not found in the conventional laboratory strain CBS7504, which include xylose utilization, lipid accumulation, and growth on undetoxified biomass hydrolysates. Currently, the related phenotypes of lipid accumulation and degradation when metabolizing non-preferred sugars (e.g., xylose) associated with biomass hydrolysates are poorly understood, making it difficult to control and engineer in Y. lipolytica To fill this knowledge gap, we analyzed the genetic diversity of five undomesticated Y. lipolytica strains and identified singleton genes and genes exclusively shared by strains exhibiting desirable phenotypes. Strain characterizations from controlled bioreactor cultures revealed that the undomesticated strain YB420 used xylose to support cell growth and maintained high lipid levels while the conventional strain CBS7504 degraded cell biomass and lipids when xylose was the sole remaining carbon source. From proteomic analysis, we identified carbohydrate transporters, xylose metabolic enzymes and pentose phosphate pathway proteins stimulated during the xylose uptake stage for both strains. Furthermore, we distinguished proteins in lipid metabolism (e.g., lipase, NADPH generation, lipid regulators, β-oxidation) activated by YB420 (lipid maintenance phenotype) or CBS7504 (lipid degradation phenotype) when xylose was the sole remaining carbon source. Overall, the results relate genetic diversity of undomesticated Y. lipolytica strains to complex phenotypes of superior growth, sugar utilization, lipid accumulation and degradation in biomass hydrolysates.

Insights into the glycerol transport of Yarrowia lipolytica

“…Yl Stl4p, which was selected due to its interesting expression profile, was not verified as a glycerol transporter and may have another, not yet determined function. A recent proteome study emphasizes a role of Yl Stl4p in the transport of xylose (Walker et al, 2021). Surprisingly, Yl Stl8p did not enable the growth of YldSF on glycerol although it restored growth of S. cerevisiae stl1Δ in the preceding complementation assay (Figure 2).…”

“…The expression of the putative glycerol transporters of Y. lipolytica has already been analyzed in several transcriptome and proteome studies. In particular, one orthologous protein to Sc Fps1p, that is, YALI0F00462p, was shown to be strongly induced by glycerol (Lubuta et al, 2019), whereas some of the Sc Stl1p‐like proteins were found to be upregulated on xylose (Ryu et al, 2016; Walker et al, 2021) or at low nitrogen concentrations (Hapeta et al, 2020). Although several expression studies are available, only one experimental study with one of the nine proteins has been conducted so far to support the expected glycerol transport function.…”