Label-Free Proteomics Reveals the Molecular Mechanism of Subculture Induced Strain Degeneration and Discovery of Indicative Index for Degeneration in <i>Pleurotus ostreatus</i>
<i>Pleurotus ostreatus</i> is one of the widely cultivated edible fungi across the world. Mycelial subculture is an indispensable part in the process of cultivation and production for all kinds of edible fungi. However, successive subcultures usually lead to strain degeneration. The dege...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2020-10-01
|
| Series: | Molecules |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1420-3049/25/21/4920 |
| _version_ | 1797549977396838400 |
|---|---|
| author | Weiwei Zhu Jinbo Hu Jingliang Chi Yang Li Bing Yang Wenli Hu Fei Chen Chong Xu Linshan Chai Yongming Bao |
| author_facet | Weiwei Zhu Jinbo Hu Jingliang Chi Yang Li Bing Yang Wenli Hu Fei Chen Chong Xu Linshan Chai Yongming Bao |
| author_sort | Weiwei Zhu |
| collection | DOAJ |
| description | <i>Pleurotus ostreatus</i> is one of the widely cultivated edible fungi across the world. Mycelial subculture is an indispensable part in the process of cultivation and production for all kinds of edible fungi. However, successive subcultures usually lead to strain degeneration. The degenerated strains usually have a decrease in stress resistance, yield, and an alteration in fruiting time, which will subsequently result in tremendous economic loss. Through proteomic analysis, we identified the differentially expressed proteins (DEPs) in the mycelium of <i>Pleurotus ostreatus</i> from different subcultured generations. We found that the DNA damage repair system, especially the double-strand breaks (DSBs), repairs via homologous recombination, was impaired in the subcultured mycelium, and gradual accumulation of the DSBs would lead to the strain degeneration after successive subculture. The TUNEL assay further confirmed our finding about the DNA breaks in the subcultured mycelium. Interestingly, the enzyme activity of laccase, carboxylic ester hydrolase, α-galactosidase, and catalase directly related to passage number could be used as the characteristic index for strain degeneration determination. Our results not only reveal for the first time at the molecular level that genomic instability is the cause of degeneration, but also provide an applicable approach for monitoring strain degeneration in process of edible fungi cultivation and production. |
| first_indexed | 2024-03-10T15:22:44Z |
| format | Article |
| id | doaj.art-7c6ebb69bae449beaf79ab3e3cd5dee8 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-10T15:22:44Z |
| publishDate | 2020-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-7c6ebb69bae449beaf79ab3e3cd5dee82023-11-20T18:22:35ZengMDPI AGMolecules1420-30492020-10-012521492010.3390/molecules25214920Label-Free Proteomics Reveals the Molecular Mechanism of Subculture Induced Strain Degeneration and Discovery of Indicative Index for Degeneration in <i>Pleurotus ostreatus</i>Weiwei Zhu0Jinbo Hu1Jingliang Chi2Yang Li3Bing Yang4Wenli Hu5Fei Chen6Chong Xu7Linshan Chai8Yongming Bao9School of Bioengineering, Dalian University of Technology, Dalian 116024, ChinaLaboratory of Photosynthesis and Environment, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, ChinaMicrobial Research Institute of Liaoning Province, Chaoyang 122000, ChinaMicrobial Research Institute of Liaoning Province, Chaoyang 122000, ChinaLaboratory of Photosynthesis and Environment, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, ChinaCore Facility Center, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, ChinaMicrobial Research Institute of Liaoning Province, Chaoyang 122000, ChinaMicrobial Research Institute of Liaoning Province, Chaoyang 122000, ChinaMicrobial Research Institute of Liaoning Province, Chaoyang 122000, ChinaSchool of Bioengineering, Dalian University of Technology, Dalian 116024, China<i>Pleurotus ostreatus</i> is one of the widely cultivated edible fungi across the world. Mycelial subculture is an indispensable part in the process of cultivation and production for all kinds of edible fungi. However, successive subcultures usually lead to strain degeneration. The degenerated strains usually have a decrease in stress resistance, yield, and an alteration in fruiting time, which will subsequently result in tremendous economic loss. Through proteomic analysis, we identified the differentially expressed proteins (DEPs) in the mycelium of <i>Pleurotus ostreatus</i> from different subcultured generations. We found that the DNA damage repair system, especially the double-strand breaks (DSBs), repairs via homologous recombination, was impaired in the subcultured mycelium, and gradual accumulation of the DSBs would lead to the strain degeneration after successive subculture. The TUNEL assay further confirmed our finding about the DNA breaks in the subcultured mycelium. Interestingly, the enzyme activity of laccase, carboxylic ester hydrolase, α-galactosidase, and catalase directly related to passage number could be used as the characteristic index for strain degeneration determination. Our results not only reveal for the first time at the molecular level that genomic instability is the cause of degeneration, but also provide an applicable approach for monitoring strain degeneration in process of edible fungi cultivation and production.https://www.mdpi.com/1420-3049/25/21/4920<i>pleurotus ostreatus</i>proteomicssubculturestrain degenerationDNA damage repairhomologous recombination |
| spellingShingle | Weiwei Zhu Jinbo Hu Jingliang Chi Yang Li Bing Yang Wenli Hu Fei Chen Chong Xu Linshan Chai Yongming Bao Label-Free Proteomics Reveals the Molecular Mechanism of Subculture Induced Strain Degeneration and Discovery of Indicative Index for Degeneration in <i>Pleurotus ostreatus</i> Molecules <i>pleurotus ostreatus</i> proteomics subculture strain degeneration DNA damage repair homologous recombination |
| title | Label-Free Proteomics Reveals the Molecular Mechanism of Subculture Induced Strain Degeneration and Discovery of Indicative Index for Degeneration in <i>Pleurotus ostreatus</i> |
| title_full | Label-Free Proteomics Reveals the Molecular Mechanism of Subculture Induced Strain Degeneration and Discovery of Indicative Index for Degeneration in <i>Pleurotus ostreatus</i> |
| title_fullStr | Label-Free Proteomics Reveals the Molecular Mechanism of Subculture Induced Strain Degeneration and Discovery of Indicative Index for Degeneration in <i>Pleurotus ostreatus</i> |
| title_full_unstemmed | Label-Free Proteomics Reveals the Molecular Mechanism of Subculture Induced Strain Degeneration and Discovery of Indicative Index for Degeneration in <i>Pleurotus ostreatus</i> |
| title_short | Label-Free Proteomics Reveals the Molecular Mechanism of Subculture Induced Strain Degeneration and Discovery of Indicative Index for Degeneration in <i>Pleurotus ostreatus</i> |
| title_sort | label free proteomics reveals the molecular mechanism of subculture induced strain degeneration and discovery of indicative index for degeneration in i pleurotus ostreatus i |
| topic | <i>pleurotus ostreatus</i> proteomics subculture strain degeneration DNA damage repair homologous recombination |
| url | https://www.mdpi.com/1420-3049/25/21/4920 |
| work_keys_str_mv | AT weiweizhu labelfreeproteomicsrevealsthemolecularmechanismofsubcultureinducedstraindegenerationanddiscoveryofindicativeindexfordegenerationinipleurotusostreatusi AT jinbohu labelfreeproteomicsrevealsthemolecularmechanismofsubcultureinducedstraindegenerationanddiscoveryofindicativeindexfordegenerationinipleurotusostreatusi AT jingliangchi labelfreeproteomicsrevealsthemolecularmechanismofsubcultureinducedstraindegenerationanddiscoveryofindicativeindexfordegenerationinipleurotusostreatusi AT yangli labelfreeproteomicsrevealsthemolecularmechanismofsubcultureinducedstraindegenerationanddiscoveryofindicativeindexfordegenerationinipleurotusostreatusi AT bingyang labelfreeproteomicsrevealsthemolecularmechanismofsubcultureinducedstraindegenerationanddiscoveryofindicativeindexfordegenerationinipleurotusostreatusi AT wenlihu labelfreeproteomicsrevealsthemolecularmechanismofsubcultureinducedstraindegenerationanddiscoveryofindicativeindexfordegenerationinipleurotusostreatusi AT feichen labelfreeproteomicsrevealsthemolecularmechanismofsubcultureinducedstraindegenerationanddiscoveryofindicativeindexfordegenerationinipleurotusostreatusi AT chongxu labelfreeproteomicsrevealsthemolecularmechanismofsubcultureinducedstraindegenerationanddiscoveryofindicativeindexfordegenerationinipleurotusostreatusi AT linshanchai labelfreeproteomicsrevealsthemolecularmechanismofsubcultureinducedstraindegenerationanddiscoveryofindicativeindexfordegenerationinipleurotusostreatusi AT yongmingbao labelfreeproteomicsrevealsthemolecularmechanismofsubcultureinducedstraindegenerationanddiscoveryofindicativeindexfordegenerationinipleurotusostreatusi |