Cultivating Lentinula edodes on Substrate Containing Composted Sawdust Affects the Expression of Carbohydrate and Aromatic Amino Acid Metabolism-Related Genes

Abstract

In mushroom cultivation, composting the substrate can make the nutrients more easily absorbed by hyphae due to the degradation of lignin, cellulose, and other organic matter. However, the effects of cultivating Lentinula edodes on composted substrate and the related molecular mechanisms have not been studied systemically. We applied transcriptomics, qRT-PCR, and proteomics to study L. edodes cultivated on substrates with fresh (CK) and composted (ND) sawdust, focusing on the brown film formation stage. The time of brown film formation was shorter and the mycelium growth rate and crude polysaccharide content of the brown film were higher in ND than in CK. The faster growth rate in ND may have been due to the higher nitrogen content in ND than in CK. Among the 9,455 genes annotated using transcriptomics, 96 were upregulated and 139 downregulated in ND compared with CK. Among the 2,509 proteins identified using proteomics sequencing, 74 were upregulated and 113 downregulated. In the KEGG pathway analyses, both differentially expressed genes and proteins were detected in cyanoamino acid metabolism, inositol phosphate metabolism, pentose and glucuronate interconversions, phosphatidylinositol signaling system, RNA polymerase, starch and sucrose metabolism, and tyrosine metabolism pathways. A large number of differentially expressed genes (DEGs) related to aromatic amino acid metabolic and biosynthetic process were upregulated in ND. Most of the DEGs annotated to carbohydrate active enzymes were downregulated in L. edodes growing on composted sawdust containing substrate, possibly due to the lower hemicellulose and cellulose contents in the composted sawdust. The results suggested that using composted substrate may decrease the cultivation time and improve the quality of L. edodes and revealed the underlying molecular mechanisms. IMPORTANCE Composted substrates are not commonly used in the cultivation of Lentinula edodes, thus the effects of cultivating L. edodes on composted substrate and the related molecular mechanisms have not been studied systemically. We studied L. edodes cultivated on substrates with fresh (CK) and composted (ND) sawdust, focusing on the brown film formation stage, and determined the composting related differences in the substrate and in the growth and gene expression of L. edodes. Cultivation on composted substrate was beneficial and showed potential for decreasing the cultivation time and improving the quality of L. edodes. Analyzing the expression levels of genes and proteins in brown film revealed gene and metabolism pathway level changes that accompanied the cultivation on composted substrate.

Keywords: Lentinula edodes; brown film formation; composted sawdust; proteomics; transcriptomics.

FIG 1

(A) FPKM density distribution. (B) Differentially expressed genes (DEGs) in L. edodes brown film cultivated on substrate containing composted sawdust (ND) and fresh sawdust (CK). Genes were considered differentially expressed when FC ≥ 1.5 or ≤ 0.667 and P <0.05. (C) Twenty most significant GO terms in the GO enrichment analysis of DEGs.

FIG 2

Differentially expressed proteins in L. edodes brown film cultivated on substrate containing composted sawdust (ND) and fresh sawdust (CK). Proteins were considered differentially expressed when FC ≥ 1.2 or ≤ 0.833 and P < 0.05.

FIG 3

GO enrichment analysis at level 2 of differentially expressed proteins in L. edodes brown film cultivated on substrate containing composted sawdust and fresh sawdust.

FIG 4

Protein-protein interaction networks of differentially expressed proteins generated with STRING (v11). Nodes represent proteins and lines represent protein-protein interactions (PPIs). Only XP-007325271.1 is an acyl carrier protein/NADP ubiquinone oxidoreductase (ACP), the others are hypothetical proteins.

FIG 5

KEGG pathway analyses of differentially expressed genes (mRNA) and proteins in L. edodes brown film cultivated on substrate containing composted sawdust and fresh sawdust.

FIG 6

Pectin lyase, beta glucanase, cellulase, manganese peroxidase, laccase, and lignin peroxidase activities in L. edodes brown film cultivated on substrate containing composted sawdust (ND) and fresh sawdust (CK).