Combined Omics Analysis Of The Response Mechanism Of Rhodotorula Glutinis YM25079 To Glucose Starvation Stress

Rhodotorula glutinis YM25079 is a cold-tolerant oleaginous red yeast isolated from Lugu Lake,Lijiang,Yunnan.It has excellent properties and can be used for producing valuable compounds,such as oil,carotenoids,extracellular polysaccharides.Nutrient starvation is one of the major stresses on microorganisms in nature.At present,most studies on the adaption mechanisms of yeasts to nutrient starvation stress focus on phenotypic characterization,gene transcription,protein expression or metabolic changes.However,the comprehensive analysis of the relationships among fermentation performance,gene expression differences and metabolite changes are still limited,making it difficult to reveal the mechanisms of yeast stress adaptation.Therefore,this study took YM25079 strain as the object to investigate the effects of glucose starvation stress on the synthesis of carotenoids.Furthermore,the response mechanisms of YM25079 strain to glucose starvation stress and the molecular mechanisms by which Carotenoid synthesis is regulated under basal glucose stress were studied via transcriptomics and metabolomics.The study aiming to lay the foundation for further theoretical and applied research.The YM25079 strain was cultured in YPD liquid medium containing 20 g/L glucose for 120 h.After 72 h,the glucose was depleted in the medium,leading to the glucose starvation stress on the strain.During 72-120 h,the intracellular reactive oxygen species(ROS)level and carotenoid content continued to increase,but the accumulation level of lipid gradually decreased.These results indicated that the ROS levels in the YM25079 strain was increased under glucose starvation stress,which further led to oxidative stress.In this case,the strain may degrade fatty acids to produce acetyl-Co A,thereby promoting carotenoid synthesis to enhance the strain stress adaptability.The transcriptome sequencing results obtained a total of 1432 downregulated genes and 1437 upregulated genes(P ≤ 0.05,|FC| ≥ 2.0).Through KEGG enrichment analysis,53 pathways were identified,with oxidative phosphorylation and metabolic pathways containing the highest number of differentially expressed genes(DEGs).The metabolic pathways included terpenoid and polyketonoid metabolism,steroid biosynthesis,fatty acid biosynthesis,unsaturated fat biosynthesis,fatty acid degradation,amino acid metabolism,glucose metabolism.These pathways were closely related to the changes of ROS,carotenoids,lipids content during fermentation process,indicating that the metabolism of these substances may be related to the stress adaptability of the strain.Further metabolomic analysis identified a total of 418 metabolites,among which149 differentially regulated metabolites(DRMs)were screened(VIP > 1,P < 0.05).54 DRMs were significantly up-regulated,while 95 DRMs were significantly down-regulated.These DRMs were enriched in 60 pathways by KEGG,including amino acid metabolism,oxidative phosphorylation,glucose metabolism,fatty acid biosynthesis,unsaturated fatty acid biosynthesis,terpenoid biosynthesis.The metabolomic analysis showed that the starvation stress may have different effects on the synthesis or decomposition of these substances.Additionally,the combined analysis of transcriptomics and metabolomics showed a high correlation between DEGs and DRMs.A total of 32 metabolic pathways were found to involve both DEGs and DRMs,including oxidative phosphorylation,glucose metabolism,amino acid metabolism.These results suggested that these pathways may be related to the adaptation of the YM25079 to glucose starvation stress environment.Research on the molecular mechanism of synthetic regulation of carotenoid:transcriptomics showed that sesquiterpenoid and triterpenoid biosynthesis,terpenoid backbone biosynthesis are related to the synthetic regulation of carotenoid,and glucose starvation activates the pyruvate dehydrogenase bypass pathway,causing more acetyl-Co A to flow to the carotenoid.Metabolomic results showed that ubiquinone and other terpenoid-quinone biosynthesis was related to the regulation of carotenoid biosynthesis.Transcriptomics showed that the biosynthesis of sesquiterpenes and terpenes,and the biosynthesis of terpenes,were related to the regulation of carotenoid biosynthesis,and glucose starvation activates the pyruvate dehydrogenase bypass pathway,leading to more acetyl-Co A synthesis toward the carotenoid;Biosynthesis of ubiquinones and other terpenoid quinones was regulated by the synthesis of carotenoid.Overall,this study comprehensively analyzed the response mechanisms of the YM25079 strain to glucose starvation stress by integrating the phenomenon of fermentation culture,differential gene expression,and metabolite changes.The findings demonstrated the relationship between metabolism regulation of carotenoid and the adaptability of the YM25079 to starvation stress.This study lays a foundation for further investigation into the response mechanisms of the YM25079 strain to glucose starvation stress and the application of these mechanisms in the development of bioactive compounds.