Metabolomic and Transcriptomic Analyses Revealed Lipid Differentiation Mechanisms in Agaricus bisporus at Ambient Conditions

Abstract

Agaricus bisporus is one of the most popular mushroom species in the world; however, mushrooms are highly susceptible to browning due to the absence of a protective cuticle layer and high respiration rate. The molecular mechanism underlying the process of mushroom browning needs to be explored. Here, we analyzed the transcriptomic and metabolomic data from A. bisporus at ambient temperature. Specifically, a total of 263 significantly changed metabolites and 4492 differentially expressed genes were identified. Lipid metabolites associated with cell membrane degradation were predominantly up-regulated during ambient storage. Transcriptomic data further revealed the alterations of the expression of membrane lipid metabolism-related enzymes. Additionally, energy metabolic processes and products such as glycolysis and linoleic acid changed significantly during ambient storage, indicating their potential roles in the quality deterioration of A. bisporus. These findings provide new insights into the underlying lipid metabolic mechanisms of A. bisporus during postharvest ambient storage and will provide values for mushroom preservation techniques.

Keywords: Agaricus bisporus; metabolomics; postharvest storage; transcriptomics.

Figure 1

Button mushroom changes in appearance (A), browning index (B), firmness (C), and weight loss (D) during postharvest storage at 23 °C. Vertical bars represent standard deviation (n = 3). Different lower-case letters represent significant differences between samples under different storage points.

Figure 2

Changes in the cellular ultrastructure of A. bisporus before storage at room temperature (A1–A3) and after 24 h of storage (B1–B3). CW, cell wall; CM, cell membrane; ER, endoplasmic reticulum; M, mitochondria; Magnification power: (A1,B1). ×2500; (A2,B2). ×5000; (A3,B3). ×10,000. Images are representative of three replicates.

Figure 3

Metabonomic analysis of the button mushrooms under different storage times at 23 °C. (A) PCA and (B) Pearson’s correlation coefficients of different storage times. (C) Pie chart of the types and quantities of metabolites identified. (D) The blue and purple bars indicate the numbers of up- and down-regulated DAMs between each comparison group.

Figure 4

Lipidomic analysis of button mushroom flesh under different storage times at 23 °C. (A) The contents of different lipid families and species. Heatmap of contents of phospholipids (B), fatty acids (C), and sphingolipids (D) differentially accumulated in the comparison of CK, RT_6, and RT_24. The red, yellow, and green denote low, middle, and high content. PC, phosphatidylcholine; LPC, lysophosphatidylcholine; LPE, lysophosphatidylethanolamine.

Figure 5

Transcriptomic analysis of button mushroom flesh under different storage times at 23 °C. (A) The blue and purple bars indicate the numbers of up- and down-regulated DEGs between each comparison group, respectively. (B) Venn diagram of up- and down-regulated differentially expressed genes, respectively. (C) KEGG annotation and classification of differentially expressed genes for RT_6 vs. CK, RT_6 vs. RT_24, and CK vs. RT_24. 3.5. Alterations of lipid metabolism pathway genes in the flesh under different storage times.

Figure 6

Modulation of lipid metabolism pathway genes during storage at 23 °C. Solid arrows indicate biosynthetic steps and dashed arrows indicate catabolic steps. The expression patterns are presented by heatmap on the basis of log2 FPKM. The color gradient from green to red corresponds to transcript levels from low to high. Abbreviations used are as follows: MCMT, malonyl-CoA: acyl carrier protein malonyltransferase; LACS, long-chain acyl-CoA synthetase; GPAT, glycerol-3-phosphate acyltransferase; LPA, lysophosphatidic acid; LPAT, lysophosphatidic acid acyltransferase; PLA, phospholipase A; PA, phosphatidic acid; PAP, PA phosphatase; CDS, CDP-diacylglycerol synthase; PSS, base-exchange-type phosphatidylserine synthase; PLD, phospholipase D; PI3K, PI 3-kinase; KSR, ketosphinganine reductase; SK, sphingosine kinase; SPL, sphingosine 1-phosphate lyase; LOH, lag1 longevity assurance homolog; SBH, sphingosine base hydroxylase; CDase, ceramidase; ∆8SLD, delta8 sphingolipid long-chain base desaturase; FAH, fatty acid alpha-hydroxylase; IPUT, inositol phosphoryl ceramide glucuronosyltransferase.

Figure 7

Differentially expressed transcription factors (TFs) in button mushrooms. (A) The ratios of differentially expressed transcription factors from different classes. (B) Expression profiles of differentially expressed C₂H₂ and Zn(II)₂Cys₆ family members. Up-regulated (red) and down-regulated (green) genes are indicated.

Figure 8

Transcriptome (gene) and metabolome (meta)-combined KEGG enrichment analysis. Joint KEGG enrichment of histograms for RT_6 vs. CK (A), RT_24 vs. RT_6 (B), and RT_24 vs. CK (C).