Label-Free Proteomics Reveals the Molecular Mechanism of Subculture Induced Strain Degeneration and Discovery of Indicative Index for Degeneration in Pleurotus ostreatus
Abstract
:1. Introduction
2. Results
2.1. High-Throughput Proteomics Identification and Quantitative Analysis of the Hyphae from P1 and P10 in P. ostreatus
2.2. GO and KEGG Annotation of DEPs in P. ostreatus
2.3. GO Enrichment Analysis Revealed an Asynchronous Repair System in P10 in Response to DNA Damages
2.3.1. Base Excision Repair System Was Activated in the Subcultured Mycelium
2.3.2. Double-Strand Break (DSB) Repair System Impaired in the Subcultured Mycelium
2.4. KEGG Enrichment Analysis Revealed the Cell Cycle Was Stalled in P10
2.5. Enzymatic Activity Assays Showed Consistent Results with the Quantitative Expression of the DEPs
2.6. TUNEL Assay Further Confirmed the Accumulation of DNA Damages from the 1st Generation to the 15th Generation
2.7. Application of the Enzymatic Activity Assay for Strain Degenerative Determination in the Process of P. ostreatus Production
3. Discussion
3.1. Where Are the DNA Damages in the Cells of Hyphae Coming From?
3.2. Multiple Level and Coordinated Regulation of the Cellular Processes in Response to DNA Damage through Cell Cycle Regulation, MAPK Signaling, Chromatin Remodeling, and Epigenetic Modification
3.3. Effective Ways of Preventing the Strain Degeneration During Mushroom Production
4. Materials and Methods
4.1. Mycelium Subculture and Fruiting Body Culture Conditions
4.2. Protein Extraction, Digestion, and Quantification
4.3. LC-MS/MS Analysis
4.4. Data Processing and Analysis
4.5. Bioinformatic Analysis
4.6. Enzymatic Activity Assay
4.7. TUNEL Assay
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Accession | Description | P10/P1 | p Value |
---|---|---|---|
A0A067NEP6 | Laccase OS = Pleurotus ostreatus PC15 OX = 1137138 GN = LACC10 PE = 3 SV = 1 | 40.59462 | 1.83 × 10−6 |
A0A067NLM3 | Laccase OS = Pleurotus ostreatus PC15 OX = 1137138 GN = LACC2 PE = 3 SV = 1 | 19.24952 | 1.69 × 10−6 |
A0A067NMI4 | Small subunit of laccase POXA3a OS = Pleurotus ostreatus PC15 OX = 1137138 GN = PLEOSDRAFT_1067572 PE = 4 SV = 1 | 13.86408 | 0.001334 |
A0A067NQH1 | Laccase OS = Pleurotus ostreatus PC15 OX = 1137138 GN = LACC6 PE = 3 SV = 1 | 2.9906 | 2.97 × 10−5 |
A0A067NW26 | Alpha-galactosidase (Fragment) OS = Pleurotus ostreatus PC15 OX = 1137138 GN = PLEOSDRAFT_1035175 PE = 3 SV = 1 | 6.665047 | 0.000484 |
A0A067NTX6 | Alpha-galactosidase OS = Pleurotus ostreatus PC15 OX = 1137138 GN = PLEOSDRAFT_51341 PE = 3 SV = 1 | 5.675188 | 0.000174 |
A0A067NVN8 | Alpha-galactosidase OS = Pleurotus ostreatus PC15 OX = 1137138 GN = PLEOSDRAFT_1111105 PE = 3 SV = 1 | 1.706567 | 0.025545 |
A0A067NN26 | Carboxylic ester hydrolase OS = Pleurotus ostreatus PC15 OX = 1137138 GN = PLEOSDRAFT_170071 PE = 3 SV = 1 | 13.35758 | 6.89 × 10−5 |
A0A067NDF5 | Carboxylic ester hydrolase OS = Pleurotus ostreatus PC15 OX = 1137138 GN = PLEOSDRAFT_1047336 PE = 3 SV = 1 | 1.457164 | 0.032554 |
A0A067NDV5 | Carboxylic ester hydrolase OS = Pleurotus ostreatus PC15 OX = 1137138 GN = PLEOSDRAFT_46151 PE = 3 SV = 1 | 1.775427 | 0.014483 |
A0A067NFA3 | Carboxylic ester hydrolase OS = Pleurotus ostreatus PC15 OX = 1137138 GN = PLEOSDRAFT_1051283 PE = 3 SV = 1 | 1.893255 | 0.039742 |
A0A067NL60 | Carboxylic ester hydrolase OS = Pleurotus ostreatus PC15 OX = 1137138 GN = PLEOSDRAFT_1078816 PE = 3 SV = 1 | 3.875206 | 0.002788 |
A0A067NLN4 | Carboxylic ester hydrolase OS = Pleurotus ostreatus PC15 OX = 1137138 GN = PLEOSDRAFT_1047807 PE = 3 SV = 1 | 1.67987 | 0.000325 |
A0A067NQW6 | Carboxylic ester hydrolase OS = Pleurotus ostreatus PC15 OX = 1137138 GN = PLEOSDRAFT_160636 PE = 3 SV = 1 | 2.516542 | 0.005202 |
A0A067NZ51 | Carboxylic ester hydrolase OS = Pleurotus ostreatus PC15 OX = 1137138 GN = PLEOSDRAFT_1040351 PE = 3 SV = 1 | 2.404623 | 5.04 × 10−7 |
A0A067P113 | Carboxylic ester hydrolase OS = Pleurotus ostreatus PC15 OX = 1137138 GN = PLEOSDRAFT_1091241 PE = 3 SV = 1 | 2.192162 | 0.000768 |
A0A067NHY5 | Catalase OS = Pleurotus ostreatus PC15 OX = 1137138 GN = PLEOSDRAFT_1090819 PE = 3 SV = 1 | 0.337985 | 1.12 × 10−5 |
Sample Availability: Samples of the P1 and P10 mycelium are available from the authors. |
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Zhu, W.; Hu, J.; Chi, J.; Li, Y.; Yang, B.; Hu, W.; Chen, F.; Xu, C.; Chai, L.; Bao, Y. Label-Free Proteomics Reveals the Molecular Mechanism of Subculture Induced Strain Degeneration and Discovery of Indicative Index for Degeneration in Pleurotus ostreatus. Molecules 2020, 25, 4920. https://doi.org/10.3390/molecules25214920
Zhu W, Hu J, Chi J, Li Y, Yang B, Hu W, Chen F, Xu C, Chai L, Bao Y. Label-Free Proteomics Reveals the Molecular Mechanism of Subculture Induced Strain Degeneration and Discovery of Indicative Index for Degeneration in Pleurotus ostreatus. Molecules. 2020; 25(21):4920. https://doi.org/10.3390/molecules25214920
Chicago/Turabian StyleZhu, Weiwei, Jinbo Hu, Jingliang Chi, Yang Li, Bing Yang, Wenli Hu, Fei Chen, Chong Xu, Linshan Chai, and Yongming Bao. 2020. "Label-Free Proteomics Reveals the Molecular Mechanism of Subculture Induced Strain Degeneration and Discovery of Indicative Index for Degeneration in Pleurotus ostreatus" Molecules 25, no. 21: 4920. https://doi.org/10.3390/molecules25214920