Comprehensive Transcriptomic Analysis of Cordyceps militaris Cultivated on Germinated Soybeans

The ascomycete fungus Cordyceps militaris infects lepidopteran larvae and pupae and forms characteristic fruiting bodies. Owing to its immune-enhancing effects, the fungus has been used as a medicine. For industrial application, this fungus can be grown on geminated soybeans as an alternative protein source. In our study, we performed a comprehensive transcriptomic analysis to identify core gene sets during C. militaris cultivation on germinated soybeans. RNA-Seq technology was applied to the fungal cultures at seven-time points (2, 4, and 7-day and 2, 3, 5, 7-week old cultures) to investigate the global transcriptomic change. We conducted a time-series analysis using a two-step regression strategy and chose 1460 significant genes and assigned them into five clusters. Characterization of each cluster based on Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases revealed that transcription profiles changed after two weeks of incubation. Gene mapping of cordycepin biosynthesis and isoflavone modification pathways also confirmed that gene expression in the early stage of GSC cultivation is important for these metabolic pathways. Our transcriptomic analysis and selected genes provided a comprehensive molecular basis for the cultivation of C. militaris on germinated soybeans.

Draft Genome Sequence of the White-Rot Fungus Schizophyllum commune IUM1114-SS01

The monokaryotic strain, Schizophyllum commune strain IUM1114-SS01, was generated from a basidiospore of dikaryotic parental strain IUM1114. It even showed the decolorizing activities for several textile dyes much better than its parental strain. Based on the results of a single-molecule real-time sequencing technology, we present the draft genome of S. commune IUM1114-SS01, comprising 41.1 Mb with GC contents of the genome were 57.44%.Among 13,380 protein-coding genes, 534 genes are carbon hydrate-active enzyme coding genes.

The Antifungal Test: An Efficient Screening Tool for the Discovery of Microbial Metabolites with Respiratory Inhibitory Activity

Valuable natural compounds produced by a variety of microorganisms can be used as lead molecules for development of new agrochemicals. Furthermore, high-throughput in vitro screening systems with specific modes of action can increase the probability of discovery of new fungicides. In the current study, a rapid assay tested with various microbes was developed to determine the degree of respiratory inhibition of Saccharomyces cerevisiae in two different liquid media, YG (containing a fermentable carbon source) and NFYG (containing a non-fermentable carbon source). Based on this system, we screened 100 fungal isolates that were classified into basidiomycetes, to find microbial secondary metabolites that act as respiratory inhibitors. Consequently, of the 100 fungal species tested, the culture broth of an IUM04881 isolate inhibited growth of S. cerevisiae in NFYG medium, but not in YG medium. The result is comparable to that from treatment with kresoxim-methyl used as a control, suggesting that the culture broth of IUM04881 isolate might contain active compounds showing the inhibition activity for respiratory chain. Based on the assay developed in this study and spectroscopic analysis, we isolated and identified an antifungal compound (-)-oudemansin A from culture broth of IUM04881 that is identified as Oudemansiella venosolamellata. This is the first report that (-)-oudemansin A is identified from O. venosolamellata in Korea. Taken together, the development of this assay will accelerate efforts to find and identify natural respiratory inhibitors from various microbes.

Antioxidant, Anti-Melanogenic and Anti-Wrinkle Effects of Phellinus vaninii

In this study, the antioxidant, anti-xanthine oxidase, anti-melanogenic and anti-wrinkle effects of methanol (ME) and hot water (HE) extracts from the fruiting bodies of Phellinus vaninii were investigated. The 1,1-diphenyl-2-picryl-hydrazyl free radical scavenging activity of 2.0 mg/mL HE (95.38%) was comparable to that of butylated hydroxytoluene (96.97%), the reference standard. The hydroxyl radical scavenging activities of ME (98.19%) and HE (97.55%) were higher than that of butylated hydroxytoluene (92.66%) at 2.0 mg/mL. Neither ME nor HE was cytotoxic to murine melanoma B16-F10 cells at 25–750 µg/mL. Although the xanthine oxidase (XO) inhibitory effects of ME and HE were significantly lower than that of allopurinol, the values were higher than 84 percent. The in vitro tyrosinase inhibitory activities of ME and HE were comparable to kojic acid at 2.0 mg/mL. The cellular tyrosinase and melanin synthetic activities of ME and HE on B16-F10 melanoma cells at 500 µg/mL were higher than arbutin, indicating that the inhibitory effects of arbutin on the tyrosinase and melanin synthesis were higher than those of ME and HE. The collagenase inhibitory activity of HE was comparable to EGCG at 2.0 mg/mL, however, the elastase inhibitory activity of ME and HE was lower than EGCG at the concentration tested. The study results demonstrated that the fruiting bodies of Ph. vaninii possessed good antioxidant, anti-xanthine oxidase, cell-free anti-tyrosinase, cellular anti-tyrosinase, anti-collagenase, and moderate anti-elastase activities, which might be used for the development of novel anti-gout, skin-whitening, and skin anti-wrinkle agents.

Hyperlipidemic Inhibitory Effects of Phellinus pini in Rats Fed with a High Fat and Cholesterol Diet

This study evaluated the in vitro and in vivo hypolipidemic effects of the medicinal mushroom Phellinus pini. The methanol extract (ME) of the fruiting body of Ph. pini was active against pancreatic lipase and cholesterol esterase with 99.14% and 67.23% inhibited activity at 1.0 mg/mL, respectively. It also inhibited 81.81% and 55.33% of α-glucosidase and α-amylase activities, respectively, at 2.0 mg/mL. Hyperlipidemia as induced by feeding rats with a high fat and cholesterol diet (HFC). HFC supplemented with a 5% fruiting body powder of Ph. pini (HFC + PhP) significantly reduced plasma total cholesterol, low-density lipoprotein cholesterol, and triglycerides in rats compared with HFC. The reduced levels were comparable to rats fed the normal control diet (NC). The atherogenic index of HFC + PhP rats was significantly lower than that of the HFC rats. The excretion of fecal total lipid and cholesterol in the HFC + PhP rats was significantly higher than those in the NC and HFC rats. Histopathological examinations demonstrated scant deposition of lipids in the liver of rats fed HFC + PhP. The dietary supplementation with the fruiting body powder provided natural plasma lipid and glucose lowering effects in experimental rats without adverse effects on the plasma biochemical parameters and liver function related enzyme activities. Therefore, the hypolipidemic effects of Ph. pini may be due to the inhibitory effects on pancreatic lipase, cholesterol esterase, α-glucosidase, and α-amylase, and excretion of excess lipids and cholesterol in the feces.

Evaluation of Antioxidant, Anti-cholinesterase, and Anti-inflammatory Effects of Culinary Mushroom Pleurotus pulmonarius

Culinary mushroom Pleurotus pulmonarius has been popular in Asian countries. In this study, the anti-oxidant, cholinesterase, and inflammation inhibitory activities of methanol extract (ME) of fruiting bodies of P. pulmonarius were evaluted. The 1,1-diphenyl-2-picryl-hydrazy free radical scavenging activity of ME at 2.0 mg/mL was comparable to that of butylated hydroxytoluene, the standard reference. The ME exhibited significantly higher hydroxyl radical scavenging activity than butylated hydroxytoluene. ME showed slightly lower but moderate inhibitory activity against acetylcholinesterase (AChE) and butyrylcholinesterase than galantamine, a standard AChE inhibitor. It also exhibited protective effect against cytotoxicity to PC-12 cells induced by glutamate (10~100 µg/mL), inhibitory effect on nitric oxide (NO) production and inducible nitric oxide synthase protein expression in lipopolysaccharide-stimulated RAW 264.7 macrophages, and carrageenan-induced paw edema in a rat model. High-performance liquid chromatography analysis revealed the ME of P. pulmonarius contained at least 10 phenolic compounds and some of them were identified by the comparison with known standard phenolics. Taken together, our results demonstrate that fruiting bodies of P. pulmonarius possess antioxidant, anti-cholinesterase, and inflammation inhibitory activities.

Ethanol Production from Various Sugars and Cellulosic Biomass by White Rot Fungus Lenzites betulinus

Lenzites betulinus, known as gilled polypore belongs to Basidiomycota was isolated from fruiting body on broadleaf dead trees. It was found that the mycelia of white rot fungus Lenzites betulinus IUM 5468 produced ethanol from various sugars, including glucose, mannose, galactose, and cellobiose with a yield of 0.38, 0.26, 0.07, and 0.26 g of ethanol per gram of sugar consumed, respectively. This fungus relatively exhibited a good ethanol production from xylose at 0.26 g of ethanol per gram of sugar consumed. However, the ethanol conversion rate of arabinose was relatively low (at 0.07 g of ethanol per gram sugar). L. betulinus was capable of producing ethanol directly from rice straw and corn stalks at 0.22 g and 0.16 g of ethanol per gram of substrates, respectively, when this fungus was cultured in a basal medium containing 20 g/L rice straw or corn stalks. These results indicate that L. betulinus can produce ethanol efficiently from glucose, mannose, and cellobiose and produce ethanol very poorly from galactose and arabinose. Therefore, it is suggested that this fungus can ferment ethanol from various sugars and hydrolyze cellulosic materials to sugars and convert them to ethanol simultaneously.

Eukaryotic DNAJ/K Database: A Comprehensive Phylogenomic Analysis Platform for the DNAJ/K Family

Proteins in DNAJ/K families are ubiquitous, from prokaryotes to eukaryotes, and function as molecular chaperones. For systematic phylogenomics of the DNAJ/K families, we developed the Eukaryotic DNAJ/K Database (EDD). A total of 12,908 DNAJs and 4,886 DNAKs were identified from 339 eukaryotic genomes in the EDD. Kingdom-wide comparison of DNAJ/K families provides new insights on the evolutionary relationship within these families. Empowered by 'class', 'cluster', and 'taxonomy' browsers and the 'favorite' function, the EDD provides a versatile platform for comparative genomic analyses of DNAJ/K families.

The cAMP/Protein Kinase A Pathway and Virulence in Cryptococcus neoformans

The basidiomycete fungus Cryptococcus neoformans is an important pathogen of immunocompromised people. The ability of the fungus to sense its environment is critical for proliferation and the generation of infectious propagules, as well as for adaptation to the mammalian host during infection. The conserved cAMP/protein kinase A pathway makes an important contribution to sensing, as demonstrated by the phenotypes of mutants with pathway defects. These phenotypes include loss of the ability to mate and to elaborate the key virulence factors capsule and melanin. This review summarizes recent work that reveals new targets of the pathway, new phenotypic consequences of signaling defects, and a more detailed understanding of connections with other aspects of cryptococcal biology including iron regulation, pH sensing, and stress.

Functional genomics in the rice blast fungus to unravel the fungal pathogenicity / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

A rapidly growing number of successful genome sequencing projects in plant pathogenic fungi greatly increase the demands for tools and methodologies to study fungal pathogenicity at genomic scale. Magnaporthe oryzae is an economically important plant pathogenic fungus whose genome is fully sequenced. Recently we have reported the development and application of functional genomics platform technologies in M. oryzae. This model approach would have many practical ramifications in design and implementation of upcoming functional genomics studies of filamentous fungi aimed at understanding fungal pathogenicity.