The combination of high oxygen and nanocomposite packaging alleviated quality deterioration by promoting antioxidant capacity and phenylpropane metabolism in Volvariella volvacea

Volvariella volvacea is a highly perishable mushroom that severely affects its postharvest commercial value. This study aimed to investigate the impact of high oxygen (O2) levels combined with nanocomposite packaging on the shelf-life quality of V. volvacea. Results showed that treatment with high concentrations of O2 (80% and 100% O2) and nanocomposite packaging effectively delayed the quality deterioration of V. volvacea, resulting in better postharvest appearance, higher firmness, lower weight loss, malondialdehyde (MDA) content, and leakage of membrane electrolytes. Further analysis revealed the combination treatments ameliorated oxidative stress by inducing antioxidant enzymes and the glutathione-ascorbate (GSH-AsA) cycle at both enzymatic and transcriptional levels, thereby activating the antioxidant system. Additionally, the treatments enhanced activities of key enzymes in phenylpropane metabolism, leading to a reduction in the decrease of total phenolics and flavonoids. This work provides new insights into the development of postharvest technologies to prolong the storage life of V. volvacea.

Overexpression of cat2 restores antioxidant properties and production traits in degenerated strains of Volvariella volvacea

Strain degeneration is an important factor hindering the development of the edible fungus industry. Strain degeneration is associated with the excessive accumulation of reactive oxygen species (ROS) in vivo. Catalase (CAT), an important antioxidant enzyme, can promote the clearance of ROS. In this study, the cat2 gene of Volvariella volvacea was first cloned into an overexpression plasmid via homologous recombination. Finally, through Agrobacterium-mediated transformation, this plasmid was inserted into degenerated strains of V. volvacea T19. The physiological properties, antioxidant properties, ROS content, matrix degradation activity, and cultivation properties of the transformants were tested. The results showed that the cloned cat2 gene was 99.94% similar to the reference sequence. Screening revealed that six positive transformants were successfully obtained. After the overexpression of cat2, the growth rate and biomass of the mycelium increased significantly in the transformant strains (versus the V. volvacea T19 degenerated strains). Moreover, the accumulation of superoxide radical (O2•-) and hydrogen peroxide (H2O2) was significantly reduced, and the activity of the enzymes CAT, superoxide dismutase (SOD), glutathione reductase (GR), and glutathione peroxidase (GPX) was significantly increased. Meanwhile, the expression of cat2, Mnsod1, Mnsod2, gpx, and gr was significantly upregulated, and the activity of eight matrix degradation-related enzymes was increased to varying degrees. More importantly, the overexpression of the cat2 gene promoted the regrowth of fruiting bodies in degenerated strains of V. volvacea T19. This study provides a new biotechnological strategy to control the degeneration of V. volvacea and other edible fungi.

A Comparative Transcriptome Analysis of Volvariella volvacea Identified the Candidate Genes Involved in Fast Growth at the Mycelial Growth Stage

The edible straw mushroom, Volvariella volvacea, is one of the most important cultivated mushrooms in tropical and sub-tropical regions. Strain improvement for V. volvacea is difficult because of the unknown mechanisms involved in its growth regulation and substrate utilization. A comparative physiological and transcriptomic study was conducted between two commercially available straw mushroom strains (v9 and v26) to explore their fast-growth regulation mechanism(s). The physiological study showed that V. volvacea v9 had a shorter growth cycle and higher biological efficiency (4% higher) than that in v26. At least 14,556 unigenes were obtained from the four cDNA libraries (two replicates per strain). Among them, the expression of 1597 unigenes was up-regulated while 1352 were down-regulated. Four heat-shock proteins were highly expressed in v9, showing that v9 has the better ability to handle stresses and/or environmental changes. Moreover, up to 14 putative transporter genes were expressed at a higher level in v9 than those in v26, implying that v9 has a better ability to transport nutrients or export xenobiotics efficiently. Our report allows to identify the candidate genes involved in the fast growth requirement of V. volvacea, which represents a valuable resource for strain improvement in this commercially important edible mushroom.

The NADPH oxidase in Volvariella volvacea and its differential expression in response to mycelial ageing and mechanical injury

NADPH oxidases are enzymes that have been reported to generate reactive oxygen species (ROS) in animals, plants and many multicellular fungi in response to environmental stresses. Six genes of the NADPH oxidase complex components, including vvnoxa, vvnoxb, vvnoxr, vvbema, vvrac1 and vvcdc24, were identified based on the complete genomic sequence of the edible fungus Volvariella volvacea. The number of vvnoxa, vvrac1, vvbema and vvcdc24 transcripts fluctuated with ageing, and the gene expression patterns of vvnoxa, vvrac1 and vvbema were significantly positively correlated. However, the expression of vvnoxb and vvnoxr showed no significant difference during ageing. In hyphae subjected to mechanical injury stress, both O₂^- and H₂O₂ concentrations were increased. The expression of vvnoxa, vvrac1, vvbema and vvcdc24 was substantially upregulated, but vvnoxb and vvnoxr showed no response to mechanical injury stress at the transcriptional level. Additionally, the transcription of vvnoxa, vvrac1, vvbema and vvcdc24 could be repressed when the intracellular ROS were eliminated by diphenyleneiodonium (DPI) chloride and reduced glutathione (GSH) treatments. These results indicated a positive feedback loop involving NADPH oxidase and intracellular ROS, which might be the reason for the oxidative burst during injury stress.

Selection and Evaluation of Appropriate Reference Genes for RT-qPCR Normalization of Volvariella volvacea Gene Expression under Different Conditions

Volvariella volvacea (V. volvacea), commonly referred to as Chinese (paddy straw) mushroom, is a basidiomycete with a protein-rich volva and pileus. Selecting appropriate reference genes is a crucial step in the normalization of quantitative real-time PCR data. Therefore, 12 candidate reference genes were selected from the V. volvacea transcriptome based on previous studies and then BestKeeper, geNorm, and NormFinder were used to identify reference genes stably expressed during different developmental stages and conditions. Of the 12 candidate reference genes, SPRY domain protein (SPRYp), alpha-tubulin (TUBα), cyclophilin (CYP), L-asparaginase (L-asp), and MSF1-domain-containing protein (MSF1) were the most stably expressed under different experimental conditions, while 18S ribosomal RNA (18S), 28S ribosomal RNA (28S), and beta-actin (ACTB) were the least stably expressed. This investigation not only revealed potential factors influencing the suitability of reference genes, but also identified optimal reference genes from a pool of candidate genes under a wide range of conditions.

Small GTPases and Stress Responses of vvran1 in the Straw Mushroom Volvariella volvacea

Small GTPases play important roles in the growth, development and environmental responses of eukaryotes. Based on the genomic sequence of the straw mushroom Volvariella volvacea, 44 small GTPases were identified. A clustering analysis using human small GTPases as the references revealed that V. volvacea small GTPases can be grouped into five families: nine are in the Ras family, 10 are in the Rho family, 15 are in the Rab family, one is in the Ran family and nine are in the Arf family. The transcription of vvran1 was up-regulated upon hydrogen peroxide (H₂O₂) stress, and could be repressed by diphenyleneiodonium chloride (DPI), a NADPH oxidase-specific inhibitor. The number of vvran1 transcripts also increased upon cold stress. Diphenyleneiodonium chloride, but not the superoxide dismutase (SOD) inhibitor diethy dithiocarbamate (DDC), could suppress the up-regulation of vvran1 gene expression to cold stress. These results combined with the high correlations between gene expression and superoxide anion (O₂⁻) generation indicated that vvran1 could be one of the candidate genes in the downstream of O₂⁻ mediated pathways that are generated by NADPH oxidase under low temperature and oxidative stresses.

The Sequence Characteristics and Expression Models Reveal Superoxide Dismutase Involved in Cold Response and Fruiting Body Development in Volvariella volvacea

As the first defence for cells to counteract the toxicity of active oxygen, superoxide dismutase (SOD) plays an important role in the response of living organisms to stress and cell differentiation. One extracellular Cu-ZnSOD (ecCu-ZnSOD), and two MnSODs, were identified based on the Volvariella volvacea genome sequence. All three genes have complicated alternative splicing modes during transcription; only when the fourth intron is retained can the Vv_Cu-Znsod1 gene be translated into a protein sequence with SOD functional domains. The expression levels of the three sod genes in the pilei are higher than in the stipe. The Vv_Cu-Znsod1 and the Vv_Mnsod2 are co-expressed in different developmental stages of the fruiting body, with the highest level of expression in the pilei of the egg stage, and they show a significant, positive correlation with the efficiency of karyogamy, indicating the potential role of these two genes during karyogamy. The expression of the ecCu-Znsod and two Vv_Mnsod genes showed a significant up-regulated when treated by cold stress for one hour; however, the lack of the intracellular Cu-ZnSOD encoding gene (icCu-Znsod) and the special locus of the ecCu-Znsod gene initiation codon suggested a possible reason for the autolysis phenomenon of V. volvacea in cold conditions.

[Sequence characterization and differential expression of a glutathione S-transferase gene vv-gto1 from Volvariella volvacea]

OBJECTIVE

Based on the analysis of omics data of Volvariella volvacea, a gene encoding glutathione S- transferase (GSTs) named vv-gtol was obtained. To reveal the role of GSTs in the growth and development in edible fungi, the structure, the sequence characters and the expression profile of a GST gene vv-gto1 of Volvariella volvacea were analyzed.

METHODS

ZOOM software was used to map sequencing read (reads) from genome and transcriptome against the splicing sequence of genome, to confirm the complete length and the accuracy of the gene sequence, and to visualize gene structure. The MEGA 5.1 was used to do the multiple sequence alignment and phylogenetic tree analysis. Real time fluorescent quantitative PCR was used to determine the expression levels of vv-gtol at different growth periods of Volvariella volvacea.

RESULTS

The full sequence of vv-gtol covered 2083 bp, containing 11 exons and 10 introns, and encoded a protein with 356 amino acids. 5'UTR was 305 bp which contains one intron region, and 3'UTR was 86bp. Two intron retentions could be recognized during RNA processing, and the transcripts formed by the intron retention could not translate the correct conservative functional domains. The full-length of vv-gtol had more than 50 accurate positioning genome sequencing reads, suggesting that genome sequencing and assembly results are accurate and reliable. The phylogenetic tree showed that GTO1 of Volvariella volvacea belonged to the subclass I of the Omega class of glutathione S-transferase superfamily, and had the closest relationship with GTO1 and GTO2 in Phanerochaete chrysosporium. The analysis of digital gene expression profiling, fluorescence quantitative PCR and proteomics showed that vv-gtol had the highest expression level in the heterokaryotic hyphae.

CONCLUSIONS

This is the first time to obtain a gene encoding glutathione S-transferase from Volvariella volvacea which belongs to Omega class. Our study showed that the gene may play an important role during the special biological functions of heterokaryotic hyphae. This study also suggested that Volvariella volvacea heterokaryotic hyphae in H1521 had stronger resistance ability than other samples. In addition, vv-gto1 could form different alternative splicesome to regulate gene transcription and translation, and ultimately affect the function of the protein.

[Phylogenomic analysis reveals the significant expansion of gene families of Volvariella volvacea ]

[OBJECTIVE] Cryogenic autolysis of Volvariella volvacea is an unusual phenomenon of abnormal metabolism. The aim of this study was to describe this molecular feature of abnormal metabolism at the genome-level. [METHODS] We used 21 fungal species for the phylogenomic analysis and then selected 9 representative species in basidiomycetes for the comparative genomic analysis. [ RESULTS] The phylogenomic analysis shows that V. volvacea was located at the bottom of the cluster consisting of grass-degrading fungi. Phylogenetic tree shows that basidiomycetes and ascomycetes fungi have independent evolutionary trajectories. Therefore, nine representative species in basidiomycetes were chosen for the comparative genomic analysis. The result shows that compared to other grass-degrading fungi, V. volvacea has the tendency of contraction. The comparison of the number of gene families on a different scale shows that there was a significant expansion of 3 large size ( > 200) gene families (faml, fam4 and fam6) in V. volvacea with their total number significantly more than other species, representing that the molecular feature of V. volvacea is correlated with its abnormal metabolism. [ CONCLUSION] The significant expansion of 3 gene families ( > 200) in V. volvacea indicates the enhancement of their function in specific gene families, which is most likely associated with cryogenic autolysis of V. volvacea.

[Codon usage bias in the straw mushroom Volvariella volvacea]

We analyzed the whole genome coding sequence of Volvariella volvacea to study the pattern utilization of codons by Codon W 1.4.2. As results, 24 optimal codons were identified. Moreover, the frequency of codons usage was calculated by CUSP program. We compared the frequency of codons usage of V. volvacea with other organisms including 6 modal value species (Homo sapiens, Saccharomys cerevisiae, Arabidopsis thalian, Mus musculus, Danio rerio and Drosophila melanogaster) and 4 edible fungi (Coprinopsis cinerea, Agaricus bisporus, Lentinula edodes and Pleurotus ostreatus). We found that there were less differences in 3 edible fungi (excluding Pleurotus ostreatus) than 6 modal value species, comparing with the frequency of codons usage of V. volvacea. With software SPSS16.0, cluster analysis which showed differences in the size of codon bias, reflects the evolutionary relationships between species, which can be used as a reference of evolutionary relationships of species. This was the first time for analysis the codon preference among the whole coding sequences of edible fungi, serving as theoretical basis to apply genetic engineering of V. volvacea.

Microsatellites in the genome of the edible mushroom, Volvariella volvacea

Using bioinformatics software and database, we have characterized the microsatellite pattern in the V. volvacea genome and compared it with microsatellite patterns found in the genomes of four other edible fungi: Coprinopsis cinerea, Schizophyllum commune, Agaricus bisporus, and Pleurotus ostreatus. A total of 1346 microsatellites have been identified, with mono-nucleotides being the most frequent motif. The relative abundance of microsatellites was lower in coding regions with 21 No./Mb. However, the microsatellites in the V. volvacea gene models showed a greater tendency to be located in the CDS regions. There was also a higher preponderance of trinucleotide repeats, especially in the kinase genes, which implied a possible role in phenotypic variation. Among the five fungal genomes, microsatellite abundance appeared to be unrelated to genome size. Furthermore, the short motifs (mono- to tri-nucleotides) outnumbered other categories although these differed in proportion. Data analysis indicated a possible relationship between the most frequent microsatellite types and the genetic distance between the five fungal genomes.

Sequencing and comparative analysis of the straw mushroom (Volvariella volvacea) genome

Volvariella volvacea, the edible straw mushroom, is a highly nutritious food source that is widely cultivated on a commercial scale in many parts of Asia using agricultural wastes (rice straw, cotton wastes) as growth substrates. However, developments in V. volvacea cultivation have been limited due to a low biological efficiency (i.e. conversion of growth substrate to mushroom fruit bodies), sensitivity to low temperatures, and an unclear sexuality pattern that has restricted the breeding of improved strains. We have now sequenced the genome of V. volvacea and assembled it into 62 scaffolds with a total genome size of 35.7 megabases (Mb), containing 11,084 predicted gene models. Comparative analyses were performed with the model species in basidiomycete on mating type system, carbohydrate active enzymes, and fungal oxidative lignin enzymes. We also studied transcriptional regulation of the response to low temperature (4°C). We found that the genome of V. volvacea has many genes that code for enzymes, which are involved in the degradation of cellulose, hemicellulose, and pectin. The molecular genetics of the mating type system in V. volvacea was also found to be similar to the bipolar system in basidiomycetes, suggesting that it is secondary homothallism. Sensitivity to low temperatures could be due to the lack of the initiation of the biosynthesis of unsaturated fatty acids, trehalose and glycogen biosyntheses in this mushroom. Genome sequencing of V. volvacea has improved our understanding of the biological characteristics related to the degradation of the cultivating compost consisting of agricultural waste, the sexual reproduction mechanism, and the sensitivity to low temperatures at the molecular level which in turn will enable us to increase the industrial production of this mushroom.

A combined approach for improving alkaline acetyl xylan esterase production in Pichia pastoris, and effects of glycosylation on enzyme secretion, activity and stability

High level expression of axe1, a gene previously cloned from Volvariella volvacea that encodes an acetyl xylan esterase with two potential N-linked glycosylation sites, has been achieved in Pichia pastoris using a codon-optimized axe1 synthesized by the primer extension PCR procedure. The GC content of the codon-optimized axe1 was 48.62% compared with 55.49% in the native gene. Using the codon-optimized construct, AXE1 expression in P. pastoris was increased from an undetectable level to 136.45 U/ml six days after induction of yeast cultures grown in BMMY medium. A further increase (to 463 U/ml) was achieved when conditions for yeast culture were optimized as follows: 2.8% methanol, 0.63% casamino acids, and pH 8.0. This latter value represented a 3.4-fold and 246-fold increase in the enzyme levels recorded in non-optimized P. pastoris cultures and in rice straw-grown cultures of V. volvacea, respectively. N-linked glycosylation played an essential role in AXE1 secretion but had only a slight effect on the catalytic activity and stability of the recombinant enzyme.

In vitro rapid evolution of fungal immunomodulatory proteins by DNA family shuffling

Fungal immunomodulatory proteins (FIPs) found in a wide variety of mushrooms hold significant therapeutic potential. Despite much research, the structural determinants for their immunomodulatory functions remain unknown. In this study, a DNA shuffling technique was used to create two shuffled FIP protein libraries: an intrageneric group containing products of shuffling between FIP-glu (FIP gene isolated from Ganoderma lucidum) and FIP-gsi (FIP gene isolated from Ganoderma sinense) genes and an intergeneric group containing the products of shuffling between FIP-glu, FIP-fve (FIP gene isolated from Flammulina velutipes), and FIP-vvo (FIP gene isolated from Volvariella volvacea) genes. The gene shuffling generated 426 and 412 recombinant clones, respectively. Using colony blot analysis, we selected clones that expressed relatively high levels of shuffled gene products recognized by specific polyclonal antibodies. We analyzed the DNA sequences of the selected shuffled genes, and testing of their protein products revealed that they maintained functional abilities to agglutinate blood cells and induce cytokine production by splenocytes from Kunming mice in vitro. Meanwhile, the relationships between protein structure and the hemagglutination activity and between the changed nucleotide sites and expression levels were explored by bioinformatic analysis. These combined analyses identified the nucleotide changes involved in regulating the expression levels and hemagglutination activities of the FIPs. Therefore, we were able to generate recombinant FIPs with improved biological activities and expression levels by using DNA shuffling, a powerful tool for the generation of novel therapeutic proteins and for their structural and functional studies.

Improvement in fruiting body yield by introduction of the Ampullaria crossean multi-functional cellulase gene into Volvariella volvacea

The multi-functional cellulase gene, mfc, from Ampullaria crossean was transformed into Volvariella volvacea by PEG-mediated protoplast transformation to improve the biological efficiency and fruiting body yield. PCR and Southern blotting indicated that mfc was integrated into the genomes of four transformants. In laboratory and large scale cultivation experiments, the average biological efficiency of the transformants was 18.39+/-1.27% and 27.84+/-3.21%, respectively, considerably higher than the corresponding values for untransformed controls of 12.69+/-1.31% and 20.63+/-2.59%. This is the first report of an improvement in biological efficiency and fruiting body yield of V. volvacea through transgenesis.

[High-level production of neutral endoglucanase 1 in Pichia pastoris]

The gene (eg1) encoding for novel endoglucanase 1 was cloned previously from Chinese straw mushroom Volvariella volvacea. EG1 has high thermal stability and optimal pH at neutral and shows great potential in textile and paper industry applications. To improve the expression level of EG1 in Pichia pastoris, the increasing copy number of clone, and its high cell density fermentation in 3.2L fermenter for its high-level expression were investigated in this work. By electro-transformation of pPICZalphaB-egl into GS115EG11 integrated with single copy of eg1 gene, A resistant transformant with 3.8 times higher level expression than GS115EG11 was screened from YPDSZ plate containing 2000 microg/mL of Zeocin. The effect of initial cell density, pH and methanol on its expression and biomass accumulation was evaluated in shaking culture. Optimal EG1 production was observed when initial cell density OD600 was 5.0. EG1 production and biomass accumulation did not seem to vary when cells were induced at different pH values. Both of EG1 and cell density were found to increase with higher methanol concentrations, reaching 62.48 IU/mL and 31.7 (OD600) respectively after 120 h induction with 2.0% (V/V) methanol compared to 30.24 IU/mL and 17.79 (OD60) with 0.25% methanol induction. EG1 expression was further increased by 6.4 times higher than shaking culture after 95.5 hours induction with methanol in fed-batch fermentation, so totally 34 times higher than that for GS115EG11 was achieved by screening of high Zeocin resistant clone and high cell density fermentation. The production of EG1 with 543.36IU/mL CMC activity and 8.80mg/mL protein expression was obtained in Pichia pastoris.