Comparative Analysis of the Characteristics of Triterpenoid Transcriptome from Different Strains of Wolfiporia cocos

Chromosome-Scale Genome and Transcriptomic Analyses Reveal Differential Regulation of Terpenoid Secondary Metabolites in Hericium coralloides

Construction of the genome of Hericium coralloides, a species of edible mushroom, and identification of the genes involved in terpenoid biosynthesis can determine the biology and genetics of terpenoids. The present study describes the assembly of a high-quality chromosome-scale genome of H. coralloides using Pacbio HiFi sequencing and Hi-C technology. This genome consisted of 13 chromosomes, a total size of 43.6 Mb, contigs of N50 3.6 Mb, GC content at 54%, and BUSCOs integrity of 96.9%. Genes associated with terpenoid biosynthesis were predicted by KEGG enrichment analysis and homologous alignment. The Her011461 and Her008335 genes, encoding proteins in the terpenoid backbone synthesis pathway, were found to encode geranylgeranyl pyrophosphate and farnesyl diphosphate synthases, key enzymes in the biosynthesis of geranylgeranyl diphosphate, a precursor of several diterpenoids. Her011463 was found to be involved in regulating diterpene cyclase. The Her005433, Her006724, Her010605, and Her010608 genes were found to encode sesquiterpene synthesis. Most of these genes were more highly expressed in dikaryotic mycelia than in the primordium and fruiting bodies, indicating that terpenoids may be more abundant in dikaryotic mycelia. To our knowledge, this study is the first to assemble the H. coralloides genome at the chromosome scale and to identify the genes involved in terpenoid biosynthesis.

Transcriptomic and metabolomic correlation analysis: effect of initial SO2 addition on higher alcohol synthesis in Saccharomyces cerevisiae and identification of key regulatory genes

Introduction

Higher alcohols are volatile compounds produced during alcoholic fermentation that affect the quality and safety of the final product. This study used a correlation analysis of transcriptomics and metabolomics to study the impact of the initial addition of SO2 (30, 60, and 90 mg/L) on the synthesis of higher alcohols in Saccharomyces cerevisiae EC1118a and to identify key genes and metabolic pathways involved in their metabolism.

Methods

Transcriptomics and metabolomics correlation analyses were performed and differentially expressed genes (DEGs) and differential metabolites were identified. Single-gene knockouts for targeting genes of important pathways were generated to study the roles of key genes involved in the regulation of higher alcohol production.

Results

We found that, as the SO2 concentration increased, the production of total higher alcohols showed an overall trend of first increasing and then decreasing. Multi-omics correlation analysis revealed that the addition of SO2 affected carbon metabolism (ko01200), pyruvate metabolism (ko00620), glycolysis/gluconeogenesis (ko00010), the pentose phosphate pathway (ko00030), and other metabolic pathways, thereby changing the precursor substances. The availability of SO2 indirectly affects the formation of higher alcohols. In addition, excessive SO2 affected the growth of the strain, leading to the emergence of a lag phase. We screened the ten most likely genes and constructed recombinant strains to evaluate the impact of each gene on the formation of higher alcohols. The results showed that ADH4, SER33, and GDH2 are important genes of alcohol metabolism in S. cerevisiae. The isoamyl alcohol content of the EC1118a-ADH4 strain decreased by 21.003%; The isobutanol content of the EC1118a-SER33 strain was reduced by 71.346%; and the 2-phenylethanol content of EC1118a-GDH2 strain was reduced by 25.198%.

Conclusion

This study lays a theoretical foundation for investigating the mechanism of initial addition of SO2 in the synthesis of higher alcohols in S. cerevisiae, uncovering DEGs and key metabolic pathways related to the synthesis of higher alcohols, and provides guidance for regulating these mechanisms.

Identification of squalene epoxidase in triterpenes biosynthesis in Poria cocos by molecular docking and CRISPR-Cas9 gene editing

BACKGROUND

Squalene epoxidase is one of the rate-limiting enzymes in the biosynthetic pathway of membrane sterols and triterpenoids. The enzyme catalyzes the formation of oxidized squalene, which is a common precursor of sterols and triterpenoids.

RESULT

In this study, the squalene epoxidase gene (PcSE) was evaluated in Poria cocos. Molecular docking between PcSE and squalene was performed and the active amino acids were identified. The sgRNA were designed based on the active site residues. The effect on triterpene synthesis in P. cocos was consistent with the results from ultra-high-performance liquid chromatography-quadruplex time-of-flight-double mass spectrometry (UHPLC-QTOF-MS/MS) analysis. The results showed that deletion of PcSE inhibited triterpene synthesis. In vivo verification of PcSE function was performed using a PEG-mediated protoplast transformation approach.

CONCLUSION

The findings from this study provide a foundation for further studies on heterologous biosynthesis of P. cocos secondary metabolites.

Metabolome analysis of key genes for synthesis and accumulation of triterpenoids in Wolfiporia cocos

Triterpenoid, the active ingredient in the dried sclerotia of Wolfiporia cocos, has a variety of pharmacological effects. The focus of this research was the cell engineered bacteria modified for triterpenoid biosynthesis, and we aimed to identify the key genes involved in triterpenoid biosynthesis and their roles. Two monospora strains, H and L, were selected from the sexually propagated progeny of W. coco strain 5.78, and their mycelia were cultured for 17, 34, and 51 days. Metabolite analysis showed that there were significantly more down-regulated metabolites of the two strains at three different culture periods than up-regulated metabolites. KEGG indicated that the differential metabolites were mainly concentrated in sterol biosynthesis and ABC transport. STEM analysis suggested that polysaccharide synthesis and accumulation might be greater in the L strain than the H strain. The correlation analysis of DEGs and differential metabolites between the two strain groups showed that erg11 and FDPS, which were closely positively correlated with differential metabolites associated with triterpenoids, were highly expressed in the L strain. This result suggested that the high expression of some genes in the L strain might shunt precursor substances of triterpenoids, which was the possible reason for the decrease in the synthesis and accumulation of triterpenoids.

Analysis of weighted gene co-expression network of triterpenoid-related transcriptome characteristics from different strains of Wolfiporia cocos

The fungus Wolfiporia cocos has wide-ranging and important medicinal value, and its dried sclerotia are used as a traditional Chinese medicine. Modern studies have shown that triterpenoid, the active ingredient of W. cocos, have a variety of pharmacological effects. The aim of our research was to determine the key genes related to triterpenoid biosynthesis, which may be useful for the genetic modification of cell-engineered bacteria for triterpenoid biosynthesis. In this study, two monospore strains, DZAC-WP-H-29 (high-yielding) and DZAC-WP-L-123 (low-yielding), were selected from the sexually propagated offspring of strain 5.78 of W. cocos, and the mycelia were cultured for 17, 34, and 51 days, respectively. Weighted gene co-expression network analysis (WGCNA) method was used to analyze transcriptional expressions. The results show that eight core genes (ACAT1-b, hgsA, mvd1, SQLE, erg6, TAT, erg26, and erg11) are associated with the triterpenoid synthesis pathway, and Pm20d2 and norA outside the pathway may be important genes that influence the biosynthesis and accumulation of W. cocos triterpenoid. The biosynthesis of W. cocos triterpenoid is closely related to the expression of sterol metabolic pathway genes. The role of these genes in triterpenoid synthesis complements our knowledge on the biosynthesis and accumulation of W. cocos triterpenoid, and also provides a reference for the target gene modification of engineered bacteria for the fermentation production of triterpenoid.

Enhancement of antroquinonol production via the overexpression of 4-hydroxybenzoate polyprenyltransferase biosynthesis-related genes in Antrodia cinnamomea

Antroquinonol (AQ) as one of the most potent bioactive components in Antrodia cinnamomea (Fomitopsidaceae) shows a broad spectrum of anticancer effects. The lower yield of AQ has hampered its possible clinical application. AQ production may potentially be improved by genetic engineering. In this study, the protoplast-polyethylene glycol method combined with hygromycin as a selection marker was used in the genetic engineering of A. cinnamomea S-29. The optimization of several crucial parameters revealed that the optimal condition for generating maximal viable protoplasts was digestion of 4-day-old germlings with a mixture of enzymes (lysing enzyme, snailase, and cellulase) and 1.0 M MgSO₄ for 4 h. The ubiA and CoQ2 genes, which are involved in the synthesis of 4-hydroxybenzoate polyprenyltransferase, were cloned and overexpressed in A. cinnamomea. The results showed that ubiA and CoQ2 overexpression significantly increased AQ production in submerged fermentation. The overexpressing strain produced maximum AQ concentrations of 14.75 ± 0.41 mg/L and 19.25 ± 0.29 mg/L in pCT74-gpd-ubiA and pCT74-gpd-CoQ2 transformants, respectively. These concentrations were 2.00 and 2.61 times greater than those produced by the control, respectively. This research exemplifies how the production of metabolites may be increased by genetic manipulation, and will be invaluable to guide the genetic engineering of other mushrooms that produce medically useful compounds.