Integrated Transcriptomics and Metabolomics Analysis Reveal the Regulatory Mechanisms Underlying Sodium Butyrate-Induced Carotenoid Biosynthesis in Rhodotorula glutinis

Abstract

Sodium butyrate (SB) is a histone deacetylase inhibitor that can induce changes in gene expression and secondary metabolite titers by inhibiting histone deacetylation. Our preliminary analysis also indicated that SB significantly enhanced the biosynthesis of carotenoids in the Rhodotorula glutinis strain YM25079, although the underlying regulatory mechanisms remained unclear. Based on an integrated analysis of transcriptomics and metabolomics, this study revealed changes in cell membrane stability, DNA and protein methylation levels, amino acid metabolism, and oxidative stress in the strain YM25079 under SB exposure. Among them, the upregulation of oxidative stress may be a contributing factor for the increase in carotenoid biosynthesis, subsequently enhancing the strain resistance to oxidative stress and maintaining the membrane fluidity and function for normal cell growth. To summarize, our results showed that SB promoted carotenoid synthesis in the Rhodotorula glutinis strain YM25079 and increased the levels of the key metabolites and regulators involved in the stress response of yeast cells. Additionally, epigenetic modifiers were applied to produce fungal carotenoid, providing a novel and promising strategy for the biosynthesis of yeast-based carotenoids.

Keywords: Rhodotorula glutinis; carotenoids; metabolome; sodium butyrate; transcriptome.

Figure 1

Effects of treatment with SB on the total biomass, carotenoid content, and carotenoid production by YM25079. (a) Total biomass, (b) carotenoid content, (c) carotenoid production. The data are presented as the mean ± standard deviation of triplicates.

Figure 2

Effects of 10 mM SB on the growth curve, biomass, carotenoid content, carotenoid production of YM25079. (a) Growth curve, (b) total biomass, (c) carotenoid content, and (d) carotenoid production. The data are presented as the mean ± standard deviation of triplicates.

Figure 3

(a) Effects of 10 mM SB on ROS at 96 h. (b) The lipid content after the addition of SB at 120 h. The data are presented as the mean ± standard deviation of triplicates.

Figure 4

Comparative transcriptome analysis of YM25079 after treatment with 10 mM SB. (a) Correlation heatmap analysis. (b) DEGs scatter plot. (c) Top 20 KEGG pathways enriched by DEGs. Note: Y79 is the abbreviation of YM25079, 96 represents the culture time, and SB represents bu-tyrate treatment.

Figure 5

General overview of differentially accumulated metabolites (DAMs) in YM25079 after treatment with 10 mM SB. (a) PCA score scatter plots. (b) OPLS−DA scatter diagram. (c) Volcano plots of the DAMs. (d) The top 20 KEGG enrichment terms for RG120 and RG120SB.

Figure 6

Integrated analysis of the top 20 KEGG pathways enriched in DEGs and DAMs. The X-axis indicates the enrichment score of the DEGs and DAMs. The p-value is indicated using a color scale; the size of the dots and triangles indicate the number of DEGs and DAMs mapped in each pathway, respectively.

Figure 7

Overview of selected antioxidant-related metabolic pathways in response to treatment with SB. The colors of ellipses and rectangles indicate significance, which is presented on a color scale. Arrows of different colors represent different metabolic pathways (Blue—glutathione metabolism, yellow—methionine and cysteine metabolism, pink—arginine and proline metabolism, green—vitamin B6 metabolism, gray—other related pathways). Dashed arrows indicate the simplified pathways.

Figure 8

Overview of a part of the fructose and mannose metabolism in response to treatment with SB. The colors of ellipses and rectangles indicate significances, which are presented as a color scale. Arrows of different colors represent different metabolic pathways (Blue—glycerolipid metabolism, yellow—fructose and man-nose metabolism, pink—glycolysis/gluconeogenesis, purple—glycerophospholipid metabolism, gray—other related pathways). Dashed arrows indicate the simplified pathways.

Figure 9

Overview of selected acetyl-CoA-related metabolic pathways in response to treatment with SB. The colors of ellipses and rectangles indicate significances, which are presented as a color scale. Arrows of different colors represent different metabolic pathways (Blue—TCA cycle, purple—fatty acid metabolism, pink—pyruvate metabolism, green—alanine, aspartate, and glutamate metabolism, gray—other related pathways). Dashed arrows indicate the simplified pathways.