Label-Free Proteomics Reveals the Molecular Mechanism of Subculture Induced Strain Degeneration and Discovery of Indicative Index for Degeneration in Pleurotus ostreatus

Abstract

Pleurotus ostreatus 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 Pleurotus ostreatus 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.

Insights into the Global Transcriptome Response of Lentinula edodes Mycelia during Aging

“…Besides gene expression regulation, gene mutation also might be involved in strain degeneration by inducing aging. The generation of ROS has been implicated in mtDNA mutation and aging; meanwhile, organisms have many repair systems that respond to DNA damage, such as mutations caused by ROS [ 40 , 41 ]. Here, we found base excision repair genes, e.g., AP endonuclease 1 (gene- Led05208-sp3 ) and endonuclease 3 (gene- Led021048-sp3 ), and nucleotide excision repair genes, e.g., transcription initiation factor (gene- Led05557-sp3 ), and DNA excision repair protein (gene- Led00888-sp3 ) presented in blue-module DEGS.…”

Application progress of CRISPR/Cas9 genome-editing technology in edible fungi

“…With the rapid expansion of the edible fungi market, the need for high-quality and high-yield strains has been rapidly increasing. At present, there are various defects in the existing edible fungi production, such as strain degeneration (Zhu et al, 2020 ; Pérez et al, 2021 ; Chen et al, 2022b ), unstable quality, poor resistance to diseases and insects, and easily becoming soft and brown during storage (Zhang et al, 2021 ). However, the traditional breeding method is inefficient, time-consuming, and labor-intensive (Boontawon et al, 2021b ), and the breeding direction is uncertain, which limited molecular breeding for the improvement of cultivars.…”

Prediction of global potential suitable habitats of Nicotiana alata Link et Otto based on MaxEnt model

“…With the development of GIS (Geographic Information System) and the application of new statistical techniques, a variety of ecological niche models have been established internationally for the prediction of species suitable habitats 17 , such as the generalized additive model (GARP), domain model (DOMAIN), bioclimatic model (BIOCLIM), niche factor analysis model (ENFA), maximum entropy model (MaxEnt), etc 18 . Among these models, MaxEnt is the most widely used ecological niche model because of its easy operation, fast running speed 19 , and accurate prediction of the potential suitable habitats of species based on the longitude and latitude of known presence points and climate factors or even small sample data. MaxEnt has been widely used in invasion management of biological species [20][21][22] , protection of endangered plants and animals [23][24][25][26] , control of pests and diseases 19 , and environmental risk assessment of species habitats 27 .…”

“…Among these models, MaxEnt is the most widely used ecological niche model because of its easy operation, fast running speed 19 , and accurate prediction of the potential suitable habitats of species based on the longitude and latitude of known presence points and climate factors or even small sample data. MaxEnt has been widely used in invasion management of biological species [20][21][22] , protection of endangered plants and animals [23][24][25][26] , control of pests and diseases 19 , and environmental risk assessment of species habitats 27 .…”