Comparative Proteomic Analysis within the Developmental Stages of the Mushroom White Hypsizygus marmoreus

Abstract

(1) Background: The white Hypsizygus marmoreus is a popular edible mushroom in East Asia markets. Research on the systematic investigation of the protein expression changes in the cultivation process of this mushroom are few. (2) Methods: Label-free LC-MS/MS quantitative proteomics analysis technique was adopted to obtain the protein expression profiles of six groups of samples collected in different growth stages. A total of 3468 proteins were identified. The UpSetR plot analysis, Pearson correlation coefficient (PCC) analysis, and principal component (PC) analysis were performed to reveal the correlation among the six groups of samples. The differentially expressed proteins (DEPs) were organised by One-way ANOVA test and divided into four clusters. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed to divide the DEPs into different metabolic processes and pathways in each cluster. (3) Results: The DEPs in cluster 1 are of the highest abundance in the mycelium and are mainly involved in protein biosynthesis, biosynthesis of cofactors, lipid metabolism, spliceosome, cell cycle regulation, and MAPK signaling pathway. The DEPs in cluster 2 are enriched in the stem and are mainly associated with protein biosynthesis, biosynthesis of cofactors, carbon, and energy metabolism. The DEPs in cluster 3 are highly expressed in the primordia and unmatured fruiting bodies and are related to amino acids metabolism, carbon and carbohydrate metabolism, protein biosynthesis and processing, biosynthesis of cofactors, cell cycle regulation, MAPK signaling pathway, ubiquitin-mediated proteolysis, and proteasome. The DEPs in cluster 4 are of the highest abundance in the cap and are mainly associated with spliceosome, endocytosis, nucleocytoplasmic transport, protein processing, oxidative phosphorylation, biosynthesis of cofactors, amino acids metabolism, and lipid metabolism. (4) Conclusions: This research reports the proteome analysis of different developmental stages during the cultivation of the commercially relevant edible fungi the white H. marmoreus. In the mycelium stage, most of the DEPs are associated with cell proliferation, signal response, and mycelium growth. In the primordia and unmatured fruiting bodies stage, the DEPs are mainly involved in biomass increase, cell proliferation, signal response, and differentiation. In the mature fruiting body stage, the DEPs in the stem are largely associated with cell elongation and increase in biomass, and most of the DEPs in the cap are mainly related to pileus expansion. Several carbohydrate-active enzymes, transcription factors, heat shock proteins, and some DEPs involved in MAPK and cAMP signaling pathways were determined. These proteins might play vital roles in metabolic processes and activities. This research can add value to the understanding of mechanisms concerning mushroom development during commercial production.

Comparative Proteomic Analyses within Three Developmental Stages of the Mushroom White Hypsizygus marmoreus

“…The protein concentration was determined using the Bradford Protein Assay Kit (Thermo Fisher, Waltham, MA, USA). The proteins were reduced by adding 15 mg DTT and incubated at 37 °C for 1 h [ 23 , 24 ].…”

“…Samples for proteomic analyses were taken from the thirteenth day after scratching in our previous study. However, the development and protein changes in the transition stage are unclear [ 1 , 23 ]. In this research, proteomic analysis of three stages of H. marmoreus from scratching to primordium were carried out, which supplemented data of the developmental stages to our previous research.…”

Responses of the Mushroom Pleurotus ostreatus under Different CO2 Concentration by Comparative Proteomic Analyses

“…Protein concentration was determined using the Micro BCA Protein Assay Kit (Thermo Fisher, Waltham, MA, USA). After adding 15 mg dithiothreitol (DTT), the sample was incubated at 37 °C for 1 h [ 24 ].…”

“…The Orbitrap Fusion was operated in positive ion mode with spray voltage set at 2.2 KV and source temperature at 275 • C. The MS instrument was operated in data-dependent acquisition mode (DDA), with full MS scans over a mass range of m/z 350-1500 with detection in the Orbitrap (120 K resolution) and with auto gain control (AGC) set to 100,000 or a maximum ion injection time of 50 ms. For the survey scan, ten of the most abundance precursor ions with a charge state of 2+ to 6+ were selected for higher-energy collisional-dissociation (HCD) fragment analysis. The dynamic exclusion parameter was set at 60 s. For each group, four biological repeats were performed [24].…”

Transcriptional Responses for Biosynthesis of Triterpenoids in Exogenous Inducers Treated Inonotus Hispidus Using RNA-Seq

“…An increasing number of studies have focused on the transcriptome and genome levels with an understanding of plant secondary metabolic pathways including Cordyceps [ 14 ], Ophiocordyceps sinensis [ 15 ] and white Hypsizygus marmoreus [ 16 ], among others. However, there has still not been a genome-wide expression study of I. hispidus .…”