On the origin of bird's nest fungi: Phylogenomic analyses of fungi in the Nidulariaceae (Agaricales, Basidiomycota).

Nidulariaceae, also known as bird's nest fungi, is an understudied group of mushroom-forming fungi. The common name is derived from their nest-like morphology. Bird's nest fungi are ubiquitous wood decomposers or saprobes on dung. Recent studies showed that species in the Nidulariaceae form a monophyletic group with five sub-clades. However, phylogenetic relationships among genera and placement of Nidulariaceae are still unclear. We present phylogenomic analyses of bird's nest fungi and related Agaricales fungi to gain insight into the evolution of Nidulariaceae. A species tree with 17 newly generated genomes of bird's nest fungi and representatives from all major clades of Agaricales was constructed using 1044 single-copy genes to explore the intergeneric relationships and pinpoint the placement of Nidulariaceae within Agaricales. We corroborated the hypothesis that bird's nest fungi are sister to Squamanitaceae, which includes mushroom-shaped fungi with a stipe and pileus that are saprobes and mycoparasites. Lastly, stochastic character mapping of discrete traits on phylogenies (SIMMAP) suggests that the ancestor of bird's nest fungi likely possessed an evanescent, globose peridium without strings attaching to the spore packets (funiculi). This analysis suggests that the funiculus was gained twice and that the persistent, cupulate peridium form was gained at least four times and lost once. However, alternative coding schemes and datasets with a wider array of Agaricales produced conflicting results during ancestral state reconstruction, indicating that there is some uncertainty in the number of peridium transitions and that taxon sampling may significantly alter ancestral state reconstructions. Overall, our results suggest that several key morphological characters of Nidulariaceae have been subject to homoplasy.

Striatal Isolated from Cyathus striatus Extracts Induces Apoptosis in Human Pancreatic Cancer Cells.

The aim of the present study was to identify the structure of active compounds in Cyathus stratus that previously demonstrated anti-pancreatic cancer activity. The active compounds were purified from a crude extract by a series of RP-18 preparative chromatography using homemade octadecyl silica gel column. HPLC injection of the crude extract revealed a chromatogram with three main peaks with retention times (RT) 15.6, 18.2, and 22.5 min. Each fraction that exhibited promising activity in vitro was further separated using various available chromatographic techniques. The purified compound with the ultimate anti-cancer activity appeared at RT of 15.8 in the HPLC chromatogram with more than 90% purity. The main peak at the mass spectra appeared at m/z = 446.2304 with the calculated molecular formula of C25H34O7. One- and two-dimensional NMR analyses indicated that the structure of the active molecule (peak 15.8 min in HPLC) was identified as striatal C. Exposure of human pancreatic cancer cells to purified striatal C resulted in induction of apoptosis. Further studies are needed in order to develop a method for the synthesis of striatal in order to use it in clinical studies for treatment of cancer.

Sesquiterpenes with diverse skeletons from histone deacetylase inhibitor modified cultures of the basidiomycete Cyathus stercoreus (Schwein.) De Toni HFG134.

Epigenetic modifiers are proved to be effective specialized products-mining tools by rationally regulating the gene expression of fungal biosynthetic pathways. Chemical investigation on the histone deacetylase inhibitor (HDI) vorinostat (also known as SAHA)-modified cultures of the basidiomycete Cyathus stercoreus (Schwein.) De Toni (Nidulariaceae) led to the isolation of nine previously undescribed sesquiterpenes, and four previously described ones. The structures of the nine undescribed compounds were determined by extensive NMR spectroscopic analysis, HRESIMS analysis, as well as ECD and NMR calculations. Notably, the isolated sesquiterpenes are exclusive or overproduced from the epigenetic modified cultures compared to the negative control cultures. Additionally, the skeleton types of the isolated sesquiterpenes include protoilludalane, illudalane, 1,11-seco-protoilludalane, 10,11-seco-illudalane, and 14(11→10)abeo-illudalane. It is noteworthy that the 14(11→10)abeo-illudalane skeleton is reported for the first time. Cystercorodiol A, 4-O-acetylcybrodol, cystercorotone, and cybrodol showed weak inhibitory activity against the bacterium Escherichia coli ATCC25922 with the inhibitory rates 34.7%, 33.0%, 32.3%, and 29.6% at the concentration 200 µM, respectively. This study suggested that epigenetic modifiers are also an effective tool for specialized metabolite-mining in basidiomycetes.

Thirteen cyathane diterpenoids with acetylcholinesterase inhibitory effects from the fungus Cyathus africanus.

Eight undescribed cyathane diterpenoids, representative specialised metabolites of the genus Cyathus, named cyathins Q-X, along with five known congeners, were isolated from the liquid fermentation of Cyathus africanus. Their structures and absolute configurations were elucidated by integrating NMR spectroscopic analyses, electronic circular dichroism (ECD) calculations, and X-ray diffraction. Reasonable correction to the C-12 configuration of cyathin I was corroborated by the crystal data. The structural identification in this research expanded the number of candidates to allow for more bioactivity-screening options. Among them, (12S)-11α,14α-epoxy-13α,14ß,15-trihydroxycyath-3-ene displayed significant acetylcholinesterase (AChE) inhibitory effect with an IC50 value of 4.60 ± 0.85 µM. Molecular docking studies were also performed to unravel the underlying modes of interactions with the active sites of AChE for active compounds.

Molecular systematics and taxonomic overview of the bird's nest fungi (Nidulariaceae).

Fungi in the Nidulariaceae, otherwise known as 'bird's nest fungi', are among the least studied groups of Agaricomycetes (Basidiomycota). Bird's nest fungi are globally distributed and typically grow on woody debris or animal dung as saprotrophs. This group of fungi is morphologically diverse with ca. 200 described species. Phylogenetic relationships of bird's nest fungi were investigated with four commonly used loci (ITS, LSU, tef, and rpb2). The family was resolved as a monophyletic group with Squamanitaceae as a potential sister taxon. Cyathus and Crucibulum each formed its own independent and well-supported clade. Nidula and Nidularia formed a clade together, but each genus is polyphyletic. Two Mycocalia species included in our analyses were on their own separate branches, indicating that this genus is also polyphyletic. Misidentifications were detected in most genera, suggesting that species concepts need to be revisited and refined throughout Nidulariaceae. Several bird's nest fungi species have global geographical distributions whereas others may have more limited ranges. Basic morphological characters of bird's nest fungi have likely been lost or gained multiple times. The phylogenetic placement of Crucibulum is unclear and the sister lineage of bird's nest fungi is not conclusive. Further studies with data from rare species and additional informative genes are needed to fully resolve the topology of Nidulariaceae and identify its sister group with more certainty.

An insight into transcriptome of Cyathus bulleri for lignocellulase expression on wheat bran.

To identify enzymes that can be effectively used for hydrolysis of lignocellulosic biomass, an attractive carbon source in biorefineries, transcriptome analysis was carried out of wheat bran grown fungus, Cyathus bulleri. A comprehensive set of transcripts, encoding carbohydrate active enzymes, were identified. These belonged to 55, 32, 12, 11 and 7 different families of the enzyme classes of Glycoside Hydrolases (GHs), Glycosyl Transferases (GTs), Auxiliary Activities (AAs), Carbohydrate Esterases (CEs) and Polysaccharide Lyases (PLs) respectively. Higher levels of transcripts were obtained for proteins encoding cellulose and hemicellulose degrading activities (of the GH class) with the highest diversity found in the transcripts encoding the hemicellulases. Several transcripts encoding pectin degrading activity were also identified indicating close association of the pectin with the cellulose/hemicellulose in the cell wall of this fungus. Transcripts encoding ligninases were categorized into Cu radical oxidase, Glucose-Methanol-Choline oxidoreductase (with 37 different transcripts in the AA3 sub-family), Laccase and Manganese peroxidases. Temporal gene expression profile for laccase isoforms was studied to understand their role in lignin degradation. To our knowledge, this is the first analysis of the transcriptome of a member belonging to the family Nidulariaceae.

Terpenoids with neurotrophic and anti-neuroinflammatory activities from the cultures of the fungus Cyathus stercoreus.

Three new cyathane diterpenoids named stercorins A-C (1-3), including one with unusual 4,9-seco-carbon skeleton, together with two new drimane sesquiterpenoids named stercorins D (4) and E (5) were isolated from the liquid cultures of the basidiomycete Cyathus stercoreus. Their structures were established by 1D and 2D NMR data in conjunction with HR-ESI-MS. All three cyathane diterpenoids showed neurotrophic activity in PC-12 cells at concentrations of 10 µM. Compounds 1-3 significantly suppressed LPS-induced NO production in culture medium in BV2 cells with the IC50 values of 1.64 µM, 9.25 µM and 8.71 µM, respectively. Notably, Compound 1, possessing an uncommon medium-sized 9/7 ring system showed the most promising role in the prevention of two activities-associated neurodegenerative diseases.

Laccase isoform diversity on basal medium in Cyathus bulleri and role in decolorization/detoxification of textile dyes and effluent.

Laccases (EC 1.10.3.2) are multi-copper oxidases that can degrade several xenobiotics, including textile dyes. Present study investigated the nature of laccase isoforms induced by 2,6-dimethylaniline in Cyathus bulleri cultivated on basal salt medium. Two isoforms, LacI and LacII were identified and purified by a combination of ultrafiltration and ion-exchange chromatography. The MS spectrum of the two proteins displayed a number of non-identical and identical molecular peaks (m/z), and, the latter were mapped to protein originating from the previously reported Laccase (Lcc) 1 gene. The LacI isoform exhibited higher catalytic efficiency (Kcat/Km) towards 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid), 2,6-dimethoxyphenol, guaiacol and pyrogallol and was tolerant to high levels of chloride ions and resistant to EDTA. Higher decolorization of several dyes such as Direct Scarlet B (67%), Reactive Brilliant blue-R (96%), Direct Orange 34 (50%) and Reactive Red198 (95%) by the LacI isoform makes it a good candidate for degradation of synthetic dyes. The decolorization of Direct Orange 34 by laccases is being reported for the first time. Many of the properties exhibited by this isoform make it a good candidate for large scale production and applications for use in the dyeing industry.

Investigation of the role of central metal ion of Cyathus bulleri laccase 1 using guanidinium chloride-induced denaturation.

The structure and folding/unfolding kinetics of Cyathus bulleri laccase 1 (Lcc1), expressed in Pichia pastoris, were analyzed by spectroscopic methods to understand the role of central metal ion. Far UV CD structure analysis revealed major ß-sheet and minor α helical segments present in the Lcc1. A significant change in the spectrum of Lcc1, indicative of unfolding of secondary structures, was observed with increasing concentrations of guanidinium chloride (GdnHCl) during Trp fluorescence, absorption and CD measurements. A similar trend was also noticed for enzyme activity with respect to GdnHCl concentrations. To establish the role of copper ion in the catalytic activity of laccase, a complete removal of copper was carried out and addition of copper was found to restore the structure and activity during the refolding process. The apo form was also reconstituted by addition of zinc ion which restored nearly 84% of enzyme activity, indicating non-essential role of copper in maintaining conformation and activity. Structural studies and inductively coupled plasma mass spectrometry data supported these observations.

New cyathane diterpenoids with neurotrophic and anti-neuroinflammatory activity from the bird's nest fungus Cyathus africanus.

Eleven new cyathane diterpenoids, designated cyafricanins A-K (1-11), were isolated from the culture broth of the baisidiomycete Cyathus africanus (Nidulariaceae, Bird's nest fungi). Their structures were elucidated by comprehensive analysis of their NMR and HRESIMS data. Cyafricanins A (1) was found to possess an unusual 3,4-seco­carbon skeleton. All compounds were evaluated for their neurotrophic activity in PC-12 cells and anti-neuroinflammatory activity in BV2 microglia cells. All of the diterpenoids showed nerve growth factor induced neurite outgrowth-promoting activity at concentration of 20 µM. Among them, cyafricanin B (2) and cyafricanin G (7) exhibited promising neurotrophic activity, and cyafricanin A (1) showed strong inhibitory effects on both inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) expression. Furthermore, molecular docking studies revealed that cyafricanin A (1) showed strong interactions with the iNOs protein in the active cavity.

Cyathane diterpenoids and drimane sesquiterpenoids with neurotrophic activity from cultures of the fungus Cyathus africanus.

Five terpenoids, including two new cyathane diterpenoids neocyathin S (1) and neocyathin T (2), together with three drimane sesquiterpenoids, one known 3ß,6ß-dihydroxycinnamolide (3), two new ones 3ß,6α-dihydroxycinnamolide (4) and 2-keto-3ß,6ß-dihydroxycinnamolide (5), were isolated from the cultures of the basidiomycete Cyathus africanus. Their structures were established based on extensive spectroscopic methods including 2D NMR (HSQC, 1H‒1H-COSY, HMBC, ROESY) and HRESIMS experiments. The absolute configurations of two pairs of epimers, 1 and 2 as well as 3 and 4, were determined by ECD quantum chemical calculation. All the five compounds enhanced nerve growth factor (NGF)-mediated neurite outgrowth using rat pheochromocytoma (PC12) cells at concentration 10 µM.

[Allele-specific PCR to identification of Achyranthis Bidentatae Radix and Cyathulae Radix formula granules].

To establish a robust and accuracy molecular method to identify Achyranthis Bidentatae Radix and Cyathulae Radix formula granules. ITS sequences of Achyranthes bidentata and Cyathula officinalis were aligned, specific SNPs (single nucleotide polymorphisms) were excavated, specific primers were designed and allele-specific PCR method was established. The genomic DNA was successfully extracted from the herbal medicine and its formula granules by using an improved CTAB (cetyltrimethyl ammonium bromide) method and then performed PCR with the designed primers. The 187 bp specific band could be amplified only in the presentation of C. officinalis and its granules when use of C. officinalis specific primers, whereas the 162 bp band could be amplified only in the presentation of A. bidentata and its granules when use of A. bidentata specific primers. This method was also successfully applied in the identification of commercial formula granules.

Identification and evaluation of bioremediation potential of laccase isoforms produced by Cyathus bulleri on wheat bran.

Multiplicity in laccases among lignin degrading fungal species is of interest as it confers the ability to degrade several types of lignocellulosics. The combination of laccases produced on such substrates could be beneficial for treatment of complex aromatics, including dyes. In this study, we report on production of high units (679.6Ug-1 substrate) of laccase on solid wheat bran (WB) by Cyathus bulleri. Laccase, purified from the culture filtrates of WB grown fungus, was effective for oxidation of veratryl alcohol, Reactive blue 21 and textile effluent without assistance of externally added mediators. De novo sequencing of the 'purified' laccase lead to identification of several peptides that originated from different laccase genes. Transcriptome analysis of the fungus, cultivated on WB, confirmed presence of 8 isozymes, that were re-amplified and sequenced from the cDNA prepared from WB grown fungus. The 8 isozymes were grouped into 3 classes, based on their sequence relationship with other basidiomycete laccases. The isoforms produced on WB decolorized (by ∼57%) and degraded textile effluent far more effectively, compared to laccase obtained from Basal salt cultivated fungus. The decolorization and degradation was also accompanied by more than 95% reduction in phytotoxicity.

Molecular Diversity and Potential Anti-neuroinflammatory Activities of Cyathane Diterpenoids from the Basidiomycete Cyathus africanus.

Ten new polyoxygenated cyathane diterpenoids, named neocyathins A-J (1-10), together with four known diterpenes (11-14), were isolated from the liquid culture of the medicinal basidiomycete fungus Cyathus africanus. The structures and configurations of these new compounds were elucidated through comprehensive spectroscopic analyses including 1D NMR, 2D NMR (HSQC, HMBC, NOESY) and HRESIMS, and electronic circular dichroism (ECD) data. Neuroinflammation is implicated in the pathogenesis of various neurodegenerative diseases, such as Alzheimers' disease (AD). All isolated compounds were evaluated for the potential anti-neuroinflammatory activities in BV2 microglia cells. Several compounds showed differential effects on the expression of inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) in lipopolysaccharide (LPS)-stimulated and Aß1-42-treated mouse microglia cell line BV-2. Molecular docking revealed that bioactive compounds (e.g., 11) could interact with iNOS protein other than COX-2 protein. Collectively, our results suggested that this class of cyathane diterpenoids might serve as important lead compounds for drug discovery against neuroinflammation in AD.

Decolorization of complex dyes and textile effluent by extracellular enzymes of Cyathus bulleri cultivated on agro-residues/domestic wastes and proposed pathway of degradation of Kiton blue A and reactive orange 16.

In this study, the white-rot fungus Cyathus bulleri was cultivated on low-cost agro-residues, namely wheat bran (WB), wheat straw (WS), and domestic waste orange peel (OP) for production of ligninolytic enzymes. Of the three substrates, WB and OP served as good materials for the production of laccase with no requirement of additional carbon or nitrogen source. Specific laccase activity of 94.4 U mg-1 extracellular protein and 21.01 U mg-1 protein was obtained on WB and OP, respectively. Maximum decolorization rate of 13.6 µmol h-1 U-1 laccase for reactive black 5 and 22.68 µmol h-1 U-1 laccase for reactive orange 16 (RO) was obtained with the WB culture filtrate, and 11.7 µmol h-1 U-1 laccase for reactive violet 5 was observed with OP culture filtrate. Importantly, Kiton blue A (KB), reported not to be amenable to enzymatic degradation, was degraded by culture filtrate borne activities. Products of degradation of KB and RO were identified by mass spectrometry, and a pathway of degradation proposed. WB-grown culture filtrate decolorized and detoxified real and simulated textile effluents by about 40%. The study highlights the use of inexpensive materials for the production of enzymes effective on dyes and effluents.

Pyristriatins A and B: Pyridino-Cyathane Antibiotics from the Basidiomycete Cyathus cf. striatus.

Two novel pyridino-cyathane diterpenoids, pyristriatins A and B (1 and 2), together with striatin C (3) were isolated from cultures of Cyathus cf. striatus, a basidiomycete that was found during a field trip in northern Thailand. The pyristriatins showed antimicrobial effects against Gram-positive bacteria and fungi. The isolation, structure elucidation, relative configuration, and biological and cytotoxic activity are described. Their structures were assigned by HRMS and NMR spectroscopy. We also describe the first 2D NMR assignment of striatin C. Pyristriatins A and B are the first cyathane natural products featuring a pyridine ring.

Three new cyathane diterpenoids from the medicinal fungus Cyathus africanus.

Three new cyathane diterpenoids, cyathin W (1), cyathin V (2), and cyathin T (3), were isolated from the solid culture of Cyathus africanus. The structures and configurations of these new compounds were elucidated on the basis of comprehensive spectroscopic analysis including 1D NMR, 2D NMR (HSQC, HMBC, NOESY), and HR-ESI-MS experiments. Compounds 1 and 3 showed moderate inhibition against nitric oxide production in lipopolysaccaride-activated macrophages with IC50 value of 80.07 and 88.87 µM, respectively. In cytotoxicity assay, compound 1 showed weak cytotoxicity against K562 cell line with IC50 value of 12.1 µM.

Striatoids A-F, Cyathane Diterpenoids with Neurotrophic Activity from Cultures of the Fungus Cyathus striatus.

Six new highly oxygenated polycyclic cyathane-xylosides, named striatoids A-F (1-6), were isolated from the cultures of the basidiomycete Cyathus striatus. Their structures were established by comprehensive spectroscopic analysis including 2D NMR (HMBC, HSQC, ROESY, (1)H-(1)H-COSY) and HRESIMS experiments. Compounds 2 and 3 possess an unusual 15,4'-ether ring system. The isolated compounds dose-dependently enhanced nerve growth factor (NGF)-mediated neurite outgrowth in rat pheochromocytoma (PC-12) cells.

Development of an enzyme linked immunosorbent assay for detection of cyathane diterpenoids.

BACKGROUND: So-called cyathane type diterpenoids are produced as secondary metabolites by basidiomycetes. Based on their antibacterial, fungicidal, and cytotoxic properties, cyathane type terpenoids represent interesting target compounds in fungal biotechnology. RESULTS: An indirect competitive enzyme linked immunosorbent assay has been developed for detection of cyathane type diterpenoids. Rabbit polyclonal antibodies were raised against a mixture of striatal A and B conjugated to bovine serum albumin. The conditions for direct attachment of the hapten striatal B to a solid phase by passive adsorption were optimized. The cross reactivities of the striatals A, C and D, of the striatins A and B, and of the erinacines C and P to striatal B were determined. The validation study showed that the ELISA was precise and sensitive. The average IC50 of striatal B was 36.0 ng mL-1 with an inter-assay coefficient of variation (CV) of 13.2% (n = 5). Recoveries from striatal B spiked samples in the assay were in the range of 97.3 - 125.9%. A good correlation between the striatal B concentration measured by the ELISA and by HPLC-DAD (y = 1.1122× - 0.1585, R2 = 0.9942) was obtained from linear regression analysis. The suitability of the ELISA for detection of cyathane type diterpenoids in submerged cultures and fruiting bodies of H. erinaceus was studied. It showed cross reactivity with supernatants from submerged cultures and extracts thereof, but did not show cross reactivity with extracts from fruiting bodies. CONCLUSIONS: The developed method is appropriate for qualitative and quantitative detection of cyathane diterpenoids in complex mixtures. Due to its high sensitivity and specificity, it represents an ideal screening method for discovering new cyathane diterpenoids and new potential producers of them.

Structural insights into 2,2'-azino-Bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS)-mediated degradation of reactive blue 21 by engineered Cyathus bulleri Laccase and characterization of degradation products.

Advanced oxidation processes are currently used for the treatment of different reactive dyes which involve use of toxic catalysts. Peroxidases are reported to be effective on such dyes and require hydrogen peroxide and/or metal ions. Cyathus bulleri laccase, expressed in Pichia pastoris, catalyzes efficient degradation (78 to 85%) of reactive azo dyes (reactive black 5, reactive orange 16, and reactive red 198) in the presence of synthetic mediator ABTS [2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)]. This laccase was engineered to degrade effectively reactive blue 21 (RB21), a phthalocyanine dye reported to be decolorized only by peroxidases. The 816-bp segment (toward the C terminus) of the lcc gene was subjected to random mutagenesis and enzyme variants (Lcc35, Lcc61, and Lcc62) were selected based on increased ABTS oxidizing ability. Around 78 to 95% decolorization of RB21 was observed with the ABTS-supplemented Lcc variants in 30 min. Analysis of the degradation products by mass spectrometry indicated the formation of several low-molecular-weight compounds. Mapping the mutations on the modeled structure implicated residues both near and far from the T1 Cu site that affected the catalytic efficiency of the mutant enzymes on ABTS and, in turn, the rate of oxidation of RB21. Several inactive clones were also mapped. The importance of geometry as well as electronic changes on the reactivity of laccases was indicated.