Integrated transcriptomics and metabolomics analysis reveal the regulatory mechanisms underlying the combined effects of heat and glucose starvation on carotenoid biosynthesis in Rhodotorula glutinis YM25079

Abstract

Rhodotorula glutinis is an important oleaginous yeast that can synthesize various valuable compounds, including carotenoids, lipids, and exopolysaccharides. The effect of combined heat stress and glucose starvation on carotenoid biosynthesis in R. glutinis was investigated in this study. Carotenoid production in R. glutinis was promoted by heat stress, and this effect was further enhanced when glucose starvation was applied to the strain. The results of multiomics analysis revealed that the effects of heat stress and glucose starvation on promoting carotenoid biosynthesis appeared to be additive, with the combined stress leading to a further increase in reactive oxygen species (ROS) levels and a reduction in enzymatic antioxidant capacity, while carotenoid biosynthesis was prioritized simultaneously. The key responses of R. glutinis to combined stress include the regulation of the cell cycle and energy metabolism, maintenance of membrane integrity, an increase in ROS scavenging capacity, and non-enzymatic antioxidant activity. Additionally, several candidate genes and metabolites associated with the combined stress response were identified. To summarize, we provided new insights into optimizing fermentation processes for increased carotenoid production in Rhodotorula glutinis and established a molecular basis for further genetic engineering to increase carotenoid yield.

Keywords: Rhodotorula glutinis; Carotenoids; Combined stress between heat and glucose starvation; Transcriptome and metabolome.

Fig. 1

Effects of heat stress on the total biomass, carotenoid content, and residual sugars of YM25079; a total biomass, b carotenoid content, and c residual sugars. The data are presented as the mean ± standard deviation of triplicate samples

Fig. 2

Comparative transcriptome analysis of YM25079 after heat stress and glucose starvation stress. a Venn diagram; b Violin plot; c PCA; d DEG scatter plot. Note: Y79 represents YM25079, 36 and 96 represent the culture time, and HT represents heat stress

Fig. 3

Enrichment analysis of the KEGG functional pathways. a Top 20 functional pathways associated with glucose starvation stress. b Top 20 functional pathways associated with combined stress. The color of the bubble indicates the enrichment degree of the pathway

Fig. 4

General overview of DAMs in YM25079 after heat stress and glucose starvation stress. a Correlation heatmap analysis. b PCA score scatter plots. c Bar chart of the DAMs. d The top 20 enriched KEGG terms related to glucose starvation stress. e The top 20 KEGG enrichment terms for combined stress. Note: Y79 represents YM25079, 36 and 120 represent the culture time, and HT represents heat stress

Fig. 5

a The top 20 KEGG pathways enriched in DEGs and DAMs associated with glucose starvation stress. b The top 20 KEGG pathways enriched in DEGs and DAMs associated with combined stress. The X-axis indicates the enrichment score of the DEGs and DAMs. The p-value is indicated via a color scale; the size of the dots and triangles indicates the number of DEGs and DAMs mapped in each pathway, respectively

Fig. 6

Changes in the main metabolic pathways in YM25079 after heat stress and glucose starvation stress. Based on the data generated by the KEGG database and with some modifications, a path was established. Dashed arrows indicate the simplified pathways. The colors of rectangles indicate significances, which are presented as a color scale

Fig. 7

Analysis of the weighted gene and metabolite coexpression network. a Analysis of weighted genes. (i) Trend analysis of DEGs under heat stress and starvation stress. (ii) Top 20 hub genes for Trend 5. (iii) The top 20 hub genes for Trend 2. b Coexpression network of genes and metabolites. Genes and metabolites are represented by dots of different colors