Editorial

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2 pages, 176 KiB

Open AccessEditorial

Biotechnology of Edible Fungi

by

Gen Zou

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Jing Zhu

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Mingwen Zhao

J. Fungi 2023, 9(10), 1025; https://doi.org/10.3390/jof9101025 - 19 Oct 2023

Viewed by 656

Abstract

Edible fungi are generally defined as macrofungi with large fruiting bodies that may be consumed by humans and are commonly referred to as mushrooms [...] Full article

(This article belongs to the Special Issue Biotechnology of Edible Fungi)

Research

Jump to: Editorial

16 pages, 2634 KiB

Open AccessArticle

Spermidine Synthase and Saccharopine Reductase Have Co-Expression Patterns Both in Basidiomycetes with Fusion Form and Ascomycetes with Separate Form

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J. Fungi 2023, 9(3), 352; https://doi.org/10.3390/jof9030352 - 14 Mar 2023

Cited by 1 | Viewed by 1060

Abstract

Gene fusion is a process through which two or more distinct genes are fused into a single chimeric gene. Unlike most harmful fusion genes in cancer cells, in this study, we first found that spermidine synthetase- (SPDS, catalyst of spermidine biosynthesis) and saccharopine [...] Read more.

Gene fusion is a process through which two or more distinct genes are fused into a single chimeric gene. Unlike most harmful fusion genes in cancer cells, in this study, we first found that spermidine synthetase- (SPDS, catalyst of spermidine biosynthesis) and saccharopine reductase- (SR, catalyst of the penultimate step of lysine biosynthesis) encoding genes form a natural chimeric gene, FfSpdsSr, in Flammulina filiformis. Through the cloning of full-length ORFs in different strains and the analysis of alternative splicing in developmental stages, FfSpdsSr has only one copy and unique transcript encoding chimeric SPDS-SR in F. filiformis. By an orthologous gene search of SpdsSr in more than 80 fungi, we found that the chimeric SpdsSr exists in basidiomycetes, while the two separate Spds and Sr independently exist in ascomycetes, chytridiomycetes, and oomycetes. Further, the transcript level of FfSpdsSr was investigated in different developmental stages and under some common environmental factors and stresses by RT-qPCR. The results showed that FfSpdsSr mainly up-regulated in the elongation stage and pileus development of F. filiformis, as well as under blue light, high temperature, H₂O₂, and MeJA treatments. Moreover, a total of 15 sets of RNA-Seq data, including 218 samples of Neurospora crassa, were downloaded from the GEO database and used to analyze the expression correlation of NcSpds and NcSr. The results showed that the separate NcSpds and NcSr shared highly similar co-expression patterns in the samples with different strains and different nutritional and environmental condition treatments. The chimeric SpdsSr in basidiomycetes and the co-expression pattern of the Spds and Sr in N. crassa indicate the special link of spermidine and lysine in fungi, which may play an important role in the growth and development of fruiting body and in response to the multiple environmental factors and abiotic stresses. Full article

(This article belongs to the Special Issue Biotechnology of Edible Fungi)

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16 pages, 2507 KiB

Open AccessArticle

Two Strains of Lentinula edodes Differ in Their Transcriptional and Metabolic Patterns and Respond Differently to Thermostress

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J. Fungi 2023, 9(2), 179; https://doi.org/10.3390/jof9020179 - 29 Jan 2023

Cited by 1 | Viewed by 1234

Abstract

Temperature type is one of the key traits determining the cultivation regime of Lentinula edodes. However, the molecular and metabolic basis underling temperature type remain unclear. Here, we investigated the phenotypic, transcriptomic, and metabolic features of L. edodes with different temperature types [...] Read more.

Temperature type is one of the key traits determining the cultivation regime of Lentinula edodes. However, the molecular and metabolic basis underling temperature type remain unclear. Here, we investigated the phenotypic, transcriptomic, and metabolic features of L. edodes with different temperature types under both control (25 °C) and high (37 °C) temperature conditions. We found that under the control condition, the high- and low-temperature types of L. edodes harbored distinct transcriptional and metabolic profiles. The high-temperature (H-)-type strain had a higher expression level of genes involved in the toxin processes and carbohydrate binding, while the low-temperature (L-)-type strain had a high expression level of oxidoreductase activity. Heat stress significantly inhibited the growth of both H- and L-type strains, while the latter had a higher growth inhibition rate. Upon exposure to heat, the H-type strain significantly up-regulated genes associated with the components of the cellular membrane, whereas the L-type strain markedly up-regulated genes involved in the extracellular region and carbohydrate binding. Metabolome data showed that thermostress altered purine and pyrimidine metabolism in the H-type strain, whereas it altered cysteine, methionine, and glycerophospholipid metabolism in the L-type strain. Transcriptome and metabolome integrative analysis was able to identify three independent thermotolerance-related gene–metabolite regulatory networks. Our results deepen the current understanding of the molecular and metabolic basis underlying temperature type and suggest, for the first time, that thermotolerance mechanisms can be temperature-type-dependent for L. edodes. Full article

(This article belongs to the Special Issue Biotechnology of Edible Fungi)

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18 pages, 4950 KiB

Open AccessArticle

Transcriptome Profiling Reveals Candidate Genes Related to Stipe Gradient Elongation of Flammulina filiformis

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J. Fungi 2023, 9(1), 64; https://doi.org/10.3390/jof9010064 - 31 Dec 2022

Cited by 4 | Viewed by 1151

Abstract

Stipe gradient elongation is an important and remarkable feature in the development of most mushroom fruiting bodies. However, its molecular mechanism has rarely been described. Here, the decreasing trend of stipe elongation and increasing trend of cell length in a gradient from the [...] Read more.

Stipe gradient elongation is an important and remarkable feature in the development of most mushroom fruiting bodies. However, its molecular mechanism has rarely been described. Here, the decreasing trend of stipe elongation and increasing trend of cell length in a gradient from the top to the base of the stipe were determined in a model basidiomycete mushroom: Flammulina filiformis. According to RNA-seq results, 1409 differentially expressed genes (DEGs) were identified among elongation region (ER), transition region (TR), and stable region (SR) samples, including 26 transcription factors (TFs). Based on Short Time-series Expression Miner (STEM) clustering of DEGs, clusters 1 and 3, with obvious expression trends that were consistent with or in contrast to the elongation rate, were screened. The cluster 1 DEGs were mainly involved in the GO cellular component category and KEGG genetic information processing class; however, the cluster 3 DEGs were mainly involved in metabolic processes. Furthermore, qRT-PCR confirmed that key genes of the long-chain fatty acid synthesis pathway were involved in stipe gradient elongation and regulated by NADPH oxidase-derived ROS signaling molecules. These findings provide an essential basis for understanding the molecular mechanism of stipe gradient elongation. Full article

(This article belongs to the Special Issue Biotechnology of Edible Fungi)

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12 pages, 3211 KiB

Open AccessArticle

Phylogenesis of the Functional 1-Aminocyclopropane-1-Carboxylate Oxidase of Fungi and Plants

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J. Fungi 2023, 9(1), 55; https://doi.org/10.3390/jof9010055 - 29 Dec 2022

Cited by 3 | Viewed by 1578

Abstract

The 1-aminocyclopropane-1-carboxylic acid (ACC) pathway that synthesizes ethylene is shared in seed plants, fungi and probably other organisms. However, the evolutionary relationship of the key enzyme ACC oxidase (ACO) in the pathway among organisms remains unknown. Herein, we cloned, expressed and characterized five [...] Read more.

The 1-aminocyclopropane-1-carboxylic acid (ACC) pathway that synthesizes ethylene is shared in seed plants, fungi and probably other organisms. However, the evolutionary relationship of the key enzyme ACC oxidase (ACO) in the pathway among organisms remains unknown. Herein, we cloned, expressed and characterized five ACOs from the straw mushroom (Volvariella volvacea) and the oyster mushroom (Pleurotus ostreatus): VvACO1-4 and PoACO. The five mushroom ACOs and the previously identified AbACO of the button mushroom contained all three conserved residues that bound to Fe(II) in plant ACOs. They also had variable residues that were conserved and bound to ascorbate and bicarbonate in plant ACOs and harbored only 1–2 of the five conserved ACO motifs in plant ACOs. Particularly, VvACO2 and AbACO had only one ACO motif 2. Additionally, VvACO4 shared 44.23% sequence identity with the cyanobacterium Hapalosiphon putative functional ACO. Phylogenetic analysis showed that the functional ACOs of monocotyledonous and dicotyledonous plants co-occurred in Type I, Type II and Type III, while putative functional gymnosperm ACOs also appeared in Type III. The putative functional bacterial ACO, functional fungi and slime mold ACOs were clustered in ancestral Type IV. These results indicate that ACO motif 2, ACC and Fe(II) are essential for ACO activity. The ACOs of the other organisms may come from the horizontal transfer of fungal ACOs, which were found ordinarily in basidiomycetes. It is mostly the first case for the horizontal gene transfers from fungi to seed plants. The horizontal transfer of ACOs from fungi to plants probably facilitates the fungal-plant symbioses, plant–land colonization and further evolution to form seeds. Full article

(This article belongs to the Special Issue Biotechnology of Edible Fungi)

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14 pages, 3994 KiB

Open AccessArticle

Characteristics of the Genome, Transcriptome and Ganoderic Acid of the Medicinal Fungus Ganoderma lingzhi

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J. Fungi 2022, 8(12), 1257; https://doi.org/10.3390/jof8121257 - 28 Nov 2022

Cited by 2 | Viewed by 1079

Abstract

Ganoderma (Ganodermaceae) is a genus of edible and medicinal mushrooms that create a diverse set of bioactive compounds. Ganoderma lingzhi has been famous in China for more than 2000 years for its medicinal properties. However, the genome information of G. lingzhi has not been [...] Read more.

Ganoderma (Ganodermaceae) is a genus of edible and medicinal mushrooms that create a diverse set of bioactive compounds. Ganoderma lingzhi has been famous in China for more than 2000 years for its medicinal properties. However, the genome information of G. lingzhi has not been characterized. Here, we characterized its 49.15-Mb genome, encoding 13,125 predicted genes which were sequenced by the Illumina and PacBio platform. A wide spectrum of carbohydrate-active enzymes, with a total number of 519 CAZymes were identified in G. lingzhi. Then, the genes involved in sexual recognition and ganoderic acid (GA, key bioactive metabolite) biosynthesis were characterized. In addition, we identified and deduced the possible structures of 20 main GA constituents by UPLC-ESI-MS/MS, including a new special ganochlearic acid A. Furthermore, 3996 novel transcripts were discovered, and 9276 genes were predicted to have the possibility of alternative splicing from RNA-Seq data. The alternative splicing genes were enriched for functional categories involved in protein processing, endocytosis, and metabolic activities by KEGG. These genomic, transcriptomic, and GA constituents’ resources would enrich the toolbox for biological, genetic, and secondary metabolic pathways studies in G. lingzhi. Full article

(This article belongs to the Special Issue Biotechnology of Edible Fungi)

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12 pages, 2782 KiB

Open AccessArticle

The Effect of Mitochondria on Ganoderma lucidum Growth and Bioactive Components Based on Transcriptomics

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J. Fungi 2022, 8(11), 1182; https://doi.org/10.3390/jof8111182 - 09 Nov 2022

Cited by 3 | Viewed by 1197

Abstract

Mitochondria are the power source of living cells and implicated in the oxidative metabolism. However, the effect of mitochondria on breeding is usually ignored in conventional research. In this study, the effect of mitochondria on Ganoderma lucidum morphology, yield, and main primary bioactive [...] Read more.

Mitochondria are the power source of living cells and implicated in the oxidative metabolism. However, the effect of mitochondria on breeding is usually ignored in conventional research. In this study, the effect of mitochondria on Ganoderma lucidum morphology, yield, and main primary bioactive components was analyzed via structuring and comparing isonuclear alloplasmic strains. The crucial biological pathways were then explored based on the transcriptome. The results showed that isonuclear alloplasmic exhibited difference in mycelial growth rate in potato dextrose agar medium (PDA), basidiospore yield, and polysaccharide and triterpenoid content. Otherwise, mitochondria did not change colony and fruit body morphology, mushroom yield, or mycelial growth rate in solid-state fermentation cultivation material. The transcriptome data of two significant isonuclear alloplasmic strains S1 and S5 revealed that the involvement of differentially expressed genes (DEGs) was mainly in pentose and glucuronate interconversions, starch and sucrose metabolism, and steroid biosynthesis. The result was further confirmed by the other isonuclear alloplasmic strains. The above results further proved that mitochondria could affect the active components of G. lucidum. Our results provide information which will contribute to understanding of mitochondria and will be helpful for breeding improved varieties. Full article

(This article belongs to the Special Issue Biotechnology of Edible Fungi)

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18 pages, 2266 KiB

Open AccessArticle

Whole-Genome Sequencing and Transcriptome Analysis of Ganoderma lucidum Strain Yw-1-5 Provides New Insights into the Enhanced Effect of Tween80 on Exopolysaccharide Production

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J. Fungi 2022, 8(10), 1081; https://doi.org/10.3390/jof8101081 - 14 Oct 2022

Cited by 4 | Viewed by 1528

Abstract

Ganoderma lucidum is an important medicinal mushroom widely cultured in Asian countries. Exopolysaccharides are bioactive compounds of G. lucidum with health benefits. Limited exopolysaccharide content hinders its extraction from G. lucidum. The addition of Tween80 had an enhanced effect on G. lucidum [...] Read more.

Ganoderma lucidum is an important medicinal mushroom widely cultured in Asian countries. Exopolysaccharides are bioactive compounds of G. lucidum with health benefits. Limited exopolysaccharide content hinders its extraction from G. lucidum. The addition of Tween80 had an enhanced effect on G. lucidum exopolysaccharide production in submerged fermentation. However, the mechanism of this effect remains unclear. In this study, we report on a high-quality assembly of G. lucidum strain yw-1-5 to lay the foundation for further transcriptome analysis. The genome sequence was 58.16 Mb and consisted of 58 scaffolds with an N50 of 4.78 Mb. A total of 13,957 protein-coding genes were annotated and Hi-C data mapped to 12 pseudo-chromosomes. Genes encoding glycosyltransferases and glycoside hydrolases were also obtained. Furthermore, RNA-seq was performed in a Tween80-treated group and control group for revealing the enhanced effect of Tween80 on exopolysaccharide production. In total, 655 genes were identified as differentially expressed, including 341 up-regulated and 314 down-regulated. Further analysis of differentially expressed genes showed that groups of MAPK, amino sugar and nucleotide sugar metabolism, autophagy, ubiquitin-mediated proteolysis, peroxisome, starch and sucrose metabolism, TCA cycle, glycolysis/gluconeogenesis KEGG pathway, glycosyltransferases and glycoside hydrolases played important roles in the enhanced effect of Tween80 on exopolysaccharide production. This work provides a valuable resource for facilitating our understanding of the synthesis of polysaccharides and accelerating the breeding of new strains with a high content of exopolysaccharides. Full article

(This article belongs to the Special Issue Biotechnology of Edible Fungi)

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11 pages, 3156 KiB

Open AccessArticle

A Simple and Efficient CRISPR/Cas9 System Using a Ribonucleoprotein Method for Flammulina filiformis

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J. Fungi 2022, 8(10), 1000; https://doi.org/10.3390/jof8101000 - 23 Sep 2022

Cited by 3 | Viewed by 1591

Abstract

CRISPR/Cas9 systems were established in some edible fungi based on in vivo expressed Cas9 and guide RNA. Compared with those systems, the in vitro assembled Cas9 and sgRNA ribonucleoprotein complexes (RNPs) have more advantages, but only a few examples were reported, and the [...] Read more.

CRISPR/Cas9 systems were established in some edible fungi based on in vivo expressed Cas9 and guide RNA. Compared with those systems, the in vitro assembled Cas9 and sgRNA ribonucleoprotein complexes (RNPs) have more advantages, but only a few examples were reported, and the editing efficiency is relatively low. In this study, we developed and optimized a CRISPR/Cas9 genome-editing method based on in vitro assembled ribonucleoprotein complexes in the mushroom Flammulina filiformis. The surfactant Triton X-100 played a critical role in the optimal method, and the targeting efficiency of the genomic editing reached 100% on a selective medium containing 5-FOA. This study is the first to use an RNP complex delivery to establish a CRISPR/Cas9 genome-editing system in F. filiformis. Moreover, compared with other methods, this method avoids the use of any foreign DNA, thus saving time and labor when it comes to plasmid construction. Full article

(This article belongs to the Special Issue Biotechnology of Edible Fungi)

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16 pages, 4596 KiB

Open AccessArticle

The Influence of Different Pretreatment Methods of Highland Barley by Solid-State Fermentation with Agaricus sinodeliciosus var. Chaidam ZJU-TP-08 on Its Nutrient Content, Functional Properties and Physicochemical Characteristics

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J. Fungi 2022, 8(9), 940; https://doi.org/10.3390/jof8090940 - 07 Sep 2022

Cited by 3 | Viewed by 1321

Abstract

To enhance the nutritional value of highland barley (HB), this work investigated the effects of solid-state fermentation (SSF) by Agaricus sinodeliciosus var. Chaidam ZJU-TP-08 on nutrient content, phenolic components, antioxidant activities, and physicochemical characteristics of HB upon different pretreatments (germination, ultrasound and soaking). [...] Read more.

To enhance the nutritional value of highland barley (HB), this work investigated the effects of solid-state fermentation (SSF) by Agaricus sinodeliciosus var. Chaidam ZJU-TP-08 on nutrient content, phenolic components, antioxidant activities, and physicochemical characteristics of HB upon different pretreatments (germination, ultrasound and soaking). The results showed that germinated highland barley (GHB) exhibited higher levels of ergosterol (0.19 ± 0.01 mg/g) in all fermentation groups. The content of β-glucan was higher in the SSF-GHB, with an increase of 24.21% compared to the control. The content of total amino acids, dietary fiber, total phenols and flavonoids were higher in the fermentation HB pretreated by ultrasound, increasing respectively by 5.60%, 61.50%, 25.10% and 65.32% compared to the control group. In addition, the colonized HB exhibited excellent physicochemical characteristics, including increased water solubility index and decreased pasting characteristics. Herein, the nutritional value and the biological activities were enriched in the pretreated HB through SSF, indicating its potential application for nutrition-enriched functional foods. Full article

(This article belongs to the Special Issue Biotechnology of Edible Fungi)

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18 pages, 4471 KiB

Open AccessArticle

Multi-Omics Analysis of Low-Temperature Fruiting Highlights the Promising Cultivation Application of the Nutrients Accumulation in Hypsizygus marmoreus

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J. Fungi 2022, 8(7), 695; https://doi.org/10.3390/jof8070695 - 30 Jun 2022

Cited by 5 | Viewed by 1569

Abstract

Hypsizygus marmoreus is a representative edible mushroom with low-temperature fruiting after a long postripening (LFLP). Clarifying the mechanism of LFLP and applying a rigorous low-temperature-limited process will optimize the mushroom cultivation process. This study performed an integrative multi-omics analysis of the molecular mechanism [...] Read more.

Hypsizygus marmoreus is a representative edible mushroom with low-temperature fruiting after a long postripening (LFLP). Clarifying the mechanism of LFLP and applying a rigorous low-temperature-limited process will optimize the mushroom cultivation process. This study performed an integrative multi-omics analysis of the molecular mechanism of LFLP in combination with genetic, physiological, and cultivation confirmation. The results showed that the amino acid content was increased during LFLP, mainly arginine. pH analysis showed acidification in the postripening stage and alkalization in the substrates of the reproductive growth stage. An enzyme activity test confirmed the increased enzyme activity of arginase and citrate synthase in the postripening stage. Weighted gene coexpression network analysis of the transcriptome and metabolomics indicated that pH variation is correlated mainly with changes in citrate and arginine. Multi-omics reveals a straightforward way of providing enriched materials for amino acid biosynthesis, namely, synergistically elevating citric acid and arginine through enhanced activity of the arginine synthesis branch pathway in the citrate cycle. Our study confirmed that GCN2 mediated metabolic adaptation by enhancing protein translation, highlighting its regulatory role during LFLP. Exogenously added citric acid and arginine shortened the postripening period by 10 days and increased the fruiting body yield by 10.2~15.5%. This research sheds light on the molecular mechanism of LFLP in H. marmoreus and highlights the promising application of nutrient accumulation in high-efficiency cultivation. Full article

(This article belongs to the Special Issue Biotechnology of Edible Fungi)

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10 pages, 2456 KiB

Open AccessCommunication

Establishment of CRISPR/Cas9 Genome-Editing System Based on Dual sgRNAs in Flammulina filiformis

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J. Fungi 2022, 8(7), 693; https://doi.org/10.3390/jof8070693 - 30 Jun 2022

Cited by 11 | Viewed by 1956

Abstract

Flammulina filiformis, previously known as Asian Flammulina velutipes, is one of the most commercially important edible fungi, with nutritional value and medicinal properties worldwide. However, precision genome editing using CRISPR/Cas9, which is a revolutionary technology and provides a powerful tool for [...] Read more.

Flammulina filiformis, previously known as Asian Flammulina velutipes, is one of the most commercially important edible fungi, with nutritional value and medicinal properties worldwide. However, precision genome editing using CRISPR/Cas9, which is a revolutionary technology and provides a powerful tool for molecular breeding, has not been established in F. filiformis. Here, plasmids harboring expression cassettes of Basidiomycete codon-optimized Cas9 and dual sgRNAs targeting pyrG under the control of the gpd promoter and FfU6 promoter, respectively, were delivered into protoplasts of F. filiformis Dan3 strain through PEG-mediated transformation. The results showed that an efficient native U6 promoter of F. filiformis was identified, and ultimately several pyrG mutants exhibiting 5-fluorooric acid (5-FOA) resistance were obtained. Additionally, diagnostic PCR followed by Sanger sequencing revealed that fragment deletion between the two sgRNA target sites or small insertions and deletions (indels) were introduced in these pyrG mutants through the nonhomologous end joining (NHEJ) pathway, resulting in heritable changes in genomic information. Taken together, this is the first report in which a successful CRISPR/Cas9 genome-editing system based on dual sgRNAs was established in F. filiformis, which broadens the application of this advanced tool in Basidiomycetes. Full article

(This article belongs to the Special Issue Biotechnology of Edible Fungi)

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12 pages, 2869 KiB

Open AccessArticle

Effects of Oleic Acid Addition Methods on the Metabolic Flux Distribution of Ganoderic Acids R, S and T’s Biosynthesis

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J. Fungi 2022, 8(6), 615; https://doi.org/10.3390/jof8060615 - 09 Jun 2022

Cited by 2 | Viewed by 1331

Abstract

The effects of oleic acid addition methods on the metabolic flux distribution of ganoderic acids R, S and T’s biosynthesis from Ganoderma lucidum were investigated. The results showed that adding filter-sterilized oleic acid in the process of submerged fermentation and static culture is [...] Read more.

The effects of oleic acid addition methods on the metabolic flux distribution of ganoderic acids R, S and T’s biosynthesis from Ganoderma lucidum were investigated. The results showed that adding filter-sterilized oleic acid in the process of submerged fermentation and static culture is of benefit to the synthesis of ganoderic acids R, S and T. The metabolic fluxes were increased by 97.48%, 78.42% and 43.39%, respectively. The content of ganoderic acids R, S and T were 3.11 times, 5.19 times and 1.44 times higher, respectively, than they were in the control group, which was without additional oleic acid. Ganoderic acids R, S and T’s synthesis pathways (GAP), tricarboxylic acid cycles (TCA), pentose phosphate pathways (PP) and glycolysis pathways (EMP) were all enhanced in the process. Therefore, additional oleic acid can strengthen the overall metabolic flux distribution of G. lucidum in a submerged fermentation-static culture and it can reduce the accumulation of the by-product mycosterol. This study has laid an important foundation for improving the production of triterpenes in the submerged fermentation of G. lucidum. Full article

(This article belongs to the Special Issue Biotechnology of Edible Fungi)

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