Deciphering the Molecular Adapting Mechanism of Lactic Acid-Tolerant Saccharomyces cerevisiae Through Genomic and Transcriptomic Analysis
Abstract
:1. Introduction
2. Materials and Methods
2.1. Materials and Culture
2.2. Measurement of Growth, Reducing Sugar Content, and Ethanol Content of S. cerevisiae Under Lactic Acid Stress
2.3. Measurement of Reactive Oxygen Species (ROS) Content of S. cerevisiae Under Lactic Acid Stress
2.4. Measurement of Antioxidant Enzyme Activity of S. cerevisiae Under Lactic Acid Stress
2.5. Re-Sequencing of Whole Genome
2.5.1. Genomic DNA Library Preparation and Sequencing
2.5.2. Variant Discovery
2.6. Transcriptomic
2.6.1. RNA Extraction
2.6.2. Library Preparation and Sequencing
2.6.3. Differential Expression Analysis and Functional Enrichment
2.6.4. Validation of the Key Genes by RT-qPCR
2.7. Statistical Analysis
3. Results
3.1. Growth Curve, Reducing Sugar Content, and Ethanol Content of S. Cerevisiae Under Lactic Acid Stress
3.2. ROS Content of S. cerevisiae Under Lactic Acid Stress
3.3. Antioxidant Enzyme Activity of S. cerevisiae Under Lactic Acid Stress
3.4. Genomic Results
3.5. Transcriptomic Results
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
Abbreviations
ARTP | Atmospheric and Room Temperature Plasma |
MMC | Microbial Microdroplet Culture |
NCBI | National Center for Biotechnology Information |
YPD | Yeast extract peptone dextrose |
ROS | Reactive oxygen species |
SOD | Superoxide dismutase |
CAT | Catalase |
GPx | Glutathione peroxidase |
PBS | Phosphate-buffered saline |
DEGs | Differentially expressed genes |
SNP | Single-nucleotide polymorphisms |
InDels | Insertions/deletions |
FC | Fold change |
GO | Gene Ontology |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
RT-qPCR | Quantitative real-time polymerase chain reaction |
MAPK | Mitogen-activated protein kinase |
GSH | Glutathione |
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Groups | Time (h) | ||||||
---|---|---|---|---|---|---|---|
8 | 16 | 24 | 32 | 40 | 48 | ||
SOD (U/g) | NCUF309.5 | 26.67 ± 0.32 | 27.25 ± 0.33 | 26.38 ± 0.67 | 24.97 ± 0.97 | 24.28 ± 0.60 | 23.14 ± 0.53 |
NCUF309.5-44 | 19.57 ± 0.61 ** | 18.71 ± 0.37 ** | 17.56 ± 0.62 ** | 16.21 ± 0.35 ** | 14.38 ± 0.36 ** | 14.20 ± 0.62 ** | |
CAT (U/g) | NCUF309.5 | 16.63 ± 0.42 | 17.23 ± 0.38 | 16.72 ± 0.74 | 16.16 ± 0.31 | 15.78 ± 0.59 | 15.21 ± 0.22 |
NCUF309.5-44 | 9.60 ± 0.39 ** | 9.86 ± 0.57 ** | 9.26 ± 0.44 ** | 9.06 ± 0.21 ** | 8.71 ± 0.08 ** | 8.32 ± 0.14 ** | |
GPx (U/g) | NCUF309.5 | 0.64 ± 0.02 | 0.59 ± 0.04 | 0.45 ± 0.06 | 0.41 ± 0.03 | 0.37 ± 0.01 | 0.32 ± 0.07 |
NCUF309.5-44 | 0.94 ± 0.02 ** | 1.05 ± 0.10 ** | 0.89 ± 0.15 ** | 0.80 ± 0.09 ** | 0.70 ± 0.04 ** | 0.66 ± 0.03 ** |
Position | Gene | Type | Reference | Allele | Protein Change | Description |
---|---|---|---|---|---|---|
45019 | ACS1 | SNPs | A | G | Ser2Pro | Acetyl-CoA synthetase |
175314 | TIR1 | SNPs | C | G | Gln23Glu | GPI-anchored mannoprotein |
167729 | CYB2 | SNPs | A | G | Ile18Thr | L-lactate dehydrogenase |
712385 | ERG8 | SNPs | A | C | Thr24Pro | Ergosterol synthesis |
483359 | PMA2 | SNPs | G | T | Val173Phe | H+-ATPase |
207682 | FLO1 | InDels | C | CAACTATCAATACTG | Ile1428fs | Cell wall protein |
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Fan, H.; Wan, Y.; Cai, W.; Li, F.; Fan, J.; Du, J.; Yi, M.; Yuan, J.; Fu, G. Deciphering the Molecular Adapting Mechanism of Lactic Acid-Tolerant Saccharomyces cerevisiae Through Genomic and Transcriptomic Analysis. Foods 2025, 14, 2027. https://doi.org/10.3390/foods14122027
Fan H, Wan Y, Cai W, Li F, Fan J, Du J, Yi M, Yuan J, Fu G. Deciphering the Molecular Adapting Mechanism of Lactic Acid-Tolerant Saccharomyces cerevisiae Through Genomic and Transcriptomic Analysis. Foods. 2025; 14(12):2027. https://doi.org/10.3390/foods14122027
Chicago/Turabian StyleFan, Haowei, Yin Wan, Wenqin Cai, Feng Li, Jiahui Fan, Juan Du, Mingjing Yi, Jiayi Yuan, and Guiming Fu. 2025. "Deciphering the Molecular Adapting Mechanism of Lactic Acid-Tolerant Saccharomyces cerevisiae Through Genomic and Transcriptomic Analysis" Foods 14, no. 12: 2027. https://doi.org/10.3390/foods14122027
APA StyleFan, H., Wan, Y., Cai, W., Li, F., Fan, J., Du, J., Yi, M., Yuan, J., & Fu, G. (2025). Deciphering the Molecular Adapting Mechanism of Lactic Acid-Tolerant Saccharomyces cerevisiae Through Genomic and Transcriptomic Analysis. Foods, 14(12), 2027. https://doi.org/10.3390/foods14122027