Integration of Untargeted Metabolomics with Transcriptomics Provides Insights into Beauvericin Biosynthesis in Cordyceps chanhua under H2O2-Induced Oxidative Stress
Abstract
:1. Introduction
2. Materials and Methods
2.1. Fungal Culture and Sample Preparation
2.2. LC–MS Data Acquisition
2.3. Data Processing and Metabolites Identification
2.4. Total RNA Extraction, Library Establishment, and Transcriptome Sequencing
2.5. Transcriptome Assembly and Bioinformatics Analysis
2.6. GO Function Classification and KEGG Pathway Enrichment Analysis of DEGs
2.7. Quantitative Real-Time PCR (qRT-PCR) Validation
2.8. BEA Production Assay
3. Results
3.1. Effect of H2O2 on Metabolites of C. chanhua
3.2. Transcriptomics Analysis of C. chanhua under Oxidative Stress
3.3. Differentially Expressed Genes (DGEs) in C. chanhua
3.4. GO Analysis and KEGG Pathway Enrichment of DEGs
3.5. BEA Synthesis Pathway
3.6. qRT-PCR Validation
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Pathway ID | Pathway Name | Level 1 | Level 2 | DEGs | All Genes | Rich Ratio | p-Value |
---|---|---|---|---|---|---|---|
ko04011 | MAPK signaling pathway—yeast | Environmental Information Processing | Signal transduction | 296 | 2250 | 13.16% | 0.0000151 |
ko00520 | Amino sugar and nucleotide sugar metabolism | Metabolism | Carbohydrate metabolism | 258 | 1934 | 13.34% | 0.0000244 |
ko00920 | Sulfur metabolism | Metabolism | Energy metabolism | 20 | 78 | 25.64% | 0.00014653 |
ko00600 | Sphingolipid metabolism | Metabolism | Lipid metabolism | 20 | 87 | 22.99% | 0.000691245 |
ko00460 | Cyanoamino acid metabolism | Metabolism | Metabolism of other amino acids | 32 | 180 | 17.78% | 0.002592972 |
ko00590 | Arachidonic acid metabolism | Metabolism | Lipid metabolism | 6 | 15 | 40% | 0.003140305 |
ko01130 | Biosynthesis of antibiotics | Metabolism | Global and overview maps | 109 | 800 | 13.63% | 0.0038334 |
ko00073 | Cutin, suberine, and wax biosynthesis | Metabolism | Lipid metabolism | 2 | 2 | 100% | 0.01141278 |
ko00380 | Tryptophan metabolism | Metabolism | Amino acid metabolism | 28 | 169 | 16.57% | 0.01216486 |
ko00620 | Pyruvate metabolism | Metabolism | Carbohydrate metabolism | 30 | 188 | 15.96% | 0.0160634 |
ko00480 | Glutathione metabolism | Metabolism | Metabolism of other amino acids | 15 | 80 | 18.75% | 0.02103369 |
ko01200 | Carbon metabolism | Metabolism | Global and overview maps | 51 | 360 | 14.17% | 0.02131817 |
ko01230 | Biosynthesis of amino acids | Metabolism | Global and overview maps | 49 | 342 | 14.33% | 0.01963021 |
ko00670 | One carbon pool by folate | Metabolism | Metabolism of cofactors and vitamins | 8 | 35 | 22.86% | 0.0283667 |
ko00071 | Fatty acid degradation | Metabolism | Lipid metabolism | 22 | 140 | 15.71% | 0.04119299 |
Enzymes | EC Number | Gene ID | Transcriptional Level Treat/Control, Log2 Fold Change(Treat/Control) |
---|---|---|---|
Fructose-bisphosphate aldolase, class II | 4.1.2.13 | CL2518.Contig2 | 32.6/18.1, 0.90 |
2,3-Bisphosphoglycerate-independent phosphoglycerate mutase | 5.4.2.12 | CL863.Contig2 | 76.8/40.2, 0.96 |
Pyruvate kinase | 2.7.1.40 | Unigene4061 | 447.2/271.9, 0.76 |
D-Lactate dehydrogenase | 1.1.2.4 | CL800.Contig2 | 50.2/27.1, 0.93 |
Alanine transaminase | 2.6.1.2 | CL1908.Contig3 | 24.6/18.1, 0.49 |
L-Serine/L-threonine ammonia-lyase | 4.3.1.17 | Unigene1709 | 61.1/20.4, 1.58 |
Malate dehydrogenase | 1.1.1.40 | CL1818.Contig5 | 51.0/18.7, 1.47 |
Dihydroxy-acid dehydratase | 4.2.1.9 | Unigene5252 | 7.6/4.0, 0.99 |
CL146.Contig5 | 2.3/1.1, 1.12 | ||
Branched-chain amino acid aminotransferase | 2.6.1.42 | CL4308.Contig1 | 40.4/54.5, −0.38 |
3-Deoxy-7-phosphoheptulonate synthase | 2.5.1.54 | CL2696.Contig4 | 93.2/45.8, 1.05 |
CL2696.Contig3 | 169.6/45.7, 1.76 | ||
Pentafunctional AROM polypeptide | 4.2.3.4 | Unigene3610 | 38.2/20.0, 0.99 |
4.2.1.10 | |||
1.1.1.25 | |||
2.7.1.71 | |||
2.5.1.19 | |||
Chorismate synthase | 4.2.3.5 | Unigene4335 | 10.7/6.7, 0.72 |
Chorismate mutase | 5.4.99.5 | CL2040.Contig1 | 3.4/1.8, 0.90 |
Ketoisovalerate reductase | 1.1.1.169 | Unigene1653 | 42.9/1.6, 3.97 |
BEAS beauvericin nonribosomal cyclodepsipeptide synthetase | Fpbeas | Unigene6975 | 0.24/2.1, 2.47 |
Fpbeas | Unigene3578 | 0.18/3.97, 2.54 | |
Fpbeas | Unigene2977 | 0.33/5.85, 3.33 |
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Zhao, C.; Bu, H.; Zhu, J.; Wang, Y.; Oliver, K.M.; Hu, F.; Huang, B.; Li, Z.; Peng, F. Integration of Untargeted Metabolomics with Transcriptomics Provides Insights into Beauvericin Biosynthesis in Cordyceps chanhua under H2O2-Induced Oxidative Stress. J. Fungi 2022, 8, 484. https://doi.org/10.3390/jof8050484
Zhao C, Bu H, Zhu J, Wang Y, Oliver KM, Hu F, Huang B, Li Z, Peng F. Integration of Untargeted Metabolomics with Transcriptomics Provides Insights into Beauvericin Biosynthesis in Cordyceps chanhua under H2O2-Induced Oxidative Stress. Journal of Fungi. 2022; 8(5):484. https://doi.org/10.3390/jof8050484
Chicago/Turabian StyleZhao, Cheng, Haifen Bu, Jiahua Zhu, Yulong Wang, Kerry M. Oliver, Fenglin Hu, Bo Huang, Zengzhi Li, and Fan Peng. 2022. "Integration of Untargeted Metabolomics with Transcriptomics Provides Insights into Beauvericin Biosynthesis in Cordyceps chanhua under H2O2-Induced Oxidative Stress" Journal of Fungi 8, no. 5: 484. https://doi.org/10.3390/jof8050484