Investigating the Influence of Glycerol on the Utilization of Glucose in Yarrowia lipolytica Using RNA-Seq-Based Transcriptomics

Abstract

Glycerol is considered as a promising substrate for biotechnological applications and the non-conventional yeast Yarrowia lipolytica has been used extensively for the valorization of this compound. Contrary to S. cerevisiae, Y. lipolytica seems to prefer glycerol over glucose and it has been reported previously that the presence of glycerol can suppress the consumption of glucose in co-substrate fermentations. Based on these observations, we hypothesized glycerol repression-like effects in Y. lipolytica, which are converse to well described carbon repression mechanisms ensuring the prioritized use of glucose (e.g., in S. cerevisiae). We therefore aimed to investigate this effect on the level of transcription. Strains varying in the degree of glucose suppression were chosen and characterized in high-resolution growth screenings, resulting in the detection of different growth phenotypes under glycerol-glucose mixed conditions. Two strains, IBT and W29, were selected and cultivated in chemostats using glucose, glycerol and glucose/glycerol as carbon sources, followed by an RNA-Seq-based transcriptome analysis. We could show that several transporters were significantly higher expressed in W29, which is potentially related to the observed physiological differences. However, most of the expression variation between the strains were regardless of the carbon source applied, and cross-comparisons revealed that the strain-specific carbon source responses underwent in the opposite direction. A deeper analysis of the substrate specific carbon source response led to the identification of several differentially expressed genes with orthologous functions related to signal transduction and transcriptional regulation. This study provides an initial investigation on potentially novel carbon source regulation mechanisms in yeasts.

Biovalorisation of crude glycerol and xylose into xylitol by oleaginous yeast Yarrowia lipolytica

“…The preference of Y. lipolytica for glycerol is also well documented in literature. The yeast prefers glycerol over glucose and presence of glycerol but not that of glucose represses the uptake of other carbon sources including glucose in co-fermentations [18,19]. Workman et al, (2013) [16] found that glycerol assimilation was accompanied with higher oxygen uptake rates in comparison to glucose and maximum growth rate of Y. lipolytica on glycerol (0.30 h -1 ) was 25% higher than on glucose (0.24 h -1 ).…”

“…The hypothesis for glycerol preference/repression like effects by Y. lipolytica is that its genome contain only one hexose transporter but three genes linked with glycerol transport [37]. Lubuta et al, (2019) [18] performed RNA-Seq-based transcriptome analysis in Y. lipolytica and argued that the higher expression of several transporters could be potentially related to the phenotypic observation of glycerol preference. A similar kind of phenomenon can be envisaged in the present strain as well.…”

“…The ability of S. cerevisiae to utilize glycerol is limited and therefore, the yeast is not an attractive cell factory to use glycerol, a major industrial byproduct. Contrary to S. cerevisiae, Y. lipolytica prefer glycerol over glucose and exhibits higher growth rates on glycerol than glucose [16,18,19]. Hallborn et al designed the recombinant strain of S. cerevisiae by overexpressing xylose reductase to enable xylitol production in the yeast whereas Y. lipolytica used in the current work cannot grow on xylose but has the natural ability to transform of xylose to xylitol [19].…”

“…The unique features of Y. lipolytica make it a promising cell factory for the production of value-added chemicals. Glycerol is the most preferred carbon source for Y. lipolytica and can metabolize it with great e ciency [16][17][18]. According to the literature, the majority of the Yarrowia strain cannot grow on xylose as they possess strong xylose reductase activity but have low xylitol dehydrogenase activity, however, some can biotransform xylose into xylitol [19,20].…”

Nitrogen as the major factor influencing gene expression in Yarrowia lipolytica

“…Moreover, when grown in a medium containing glycerol and glucose, glycerol is consumed first or co-consumed with glucose (Rywińska et al ., 2010), suggesting an as yet unknown regulatory mechanism(s) controlling this behaviour. An attempt to elucidate the background of this phenomenon using whole transcriptome sequencing under carbon limiting conditions has recently been taken (Lubuta et al ., 2019). In the current work, we expand on this by considering the interplay between carbon sources and carbon to nitrogen ratios.…”