Dataset Information

Genomics and lipidomics analysis of the biotechnologically important oleaginous red yeast Rhodotorula glutinis ZHK provides new insights into its lipid and carotenoid metabolism.

ABSTRACT:

Background

Rhodotorula glutinis is recognized as a biotechnologically important oleaginous red yeast, which synthesizes numerous meritorious compounds with wide industrial usages. One of the most notable properties of R. glutinis is the formation of intracellular lipid droplets full of carotenoids. However, the basic genomic features that underlie the biosynthesis of these valuable compounds in R. glutinis have not been fully documented. To reveal the biotechnological potential of R. glutinis, the genomics and lipidomics analysis was performed through the Next-Generation Sequencing and HPLC-MS-based metabolomics technologies.

Results

Here, we firstly assemble the genome of R. glutinis ZHK into 21.8 Mb, containing 30 scaffolds and 6774 predicted genes with a N50 length of 14, 66,672 bp and GC content of 67.8%. Genome completeness assessment (BUSCO alignment: 95.3%) indicated the genome assembly with a high-quality features. According to the functional annotation of the genome, we predicted several key genes involved in lipids and carotenoids metabolism as well as certain industrial enzymes biosynthesis. Comparative genomics results suggested that most of orthologous genes have underwent the strong purifying selection within the five Rhodotorula species, especially genes responsible for carotenoids biosynthesis. Furthermore, a total of 982 lipids were identified using the lipidomics approaches, mainly including triacylglycerols, diacylglyceryltrimethylhomo-ser and phosphatidylethanolamine.

Conclusion

Using whole genome shotgun sequencing, we comprehensively analyzed the genome of R. glutinis and predicted several key genes involved in lipids and carotenoids metabolism. By performing comparative genomic analysis, we show that most of the ortholog genes have undergone strong purifying selection within the five Rhodotorula species. Furthermore, we identified 982 lipid species using lipidomic approaches. These results provided valuable resources to further advance biotechnological applications of R .glutinis.

SUBMITTER: Li CJ

PROVIDER: S-EPMC7690147 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Background and objectivesCarotenoid pigments are among the most important pigments and have many applications in various food, cosmetics, hygiene industries and biotechnology. These pigments are produced by plants and microorganisms including Rhodotorula spp. This research intended to study the antimicrobial and antibiofilm effects of the carotenoid pigment from Rhodotorula glutinis on food spoilage bacteria (Staphylococcus aureus and Salmonella Typhimurium).Materials and methodsThe R. glutinis was isolated from milk samples of cows with mastitis and ITS sequence-based typing was performed on them. After extracting the pigment from R. glutinis, its purity was examined using thin-layer chromatography. Following that, the broth microdilution method was used to evaluate antimicrobial effects of the pigment and MtP assay and subsequently scanning electron microscopy were used to assess the antibiofilm effects. In addition, the sub-MIC effects of the pigment on expression of quorum-sensing (QS) genes in S. Typhimurium isolates (sdiA and luxS) and S. aureus isolates (hld) were studied. Finally, the degree of toxicity of the pigment was analyzed using the MTT assay.ResultsITS sequence analysis of R. glutinis revealed that the recently separated isolates exhibited strong differences with the strains recorded in NCBI database in genetic structure. The pigment produced by R. glutinis had strong antimicrobial effects and its mean MIC against S. Typhimurium isolates (17.0 μl.ml-1) was higher than the mean MIC against the S. aureus isolates (4.1 μl.ml-1). Electron microscope images and real-time observations indicated that the sub-MIC values of the pigment suppressed biofilm formation by suppressing expression of QS genes. In addition, the mentioned pigment at high MIC concentrations did not have toxic effects on Vero cells.ConclusionThis research suggests that R. glutinis pigment is effective in destroying the planktonic form of food spoilage bacteria and degrading food spoilage biofilm-forming bacteria. Moreover, considering the low toxicity level of R. glutinis pigment for eukaryotic cells, we can suggest its use as a natural antibacterial preservative in various food materials.