The genome of the Tiger Milk mushroom,Lignosus rhinocerotis,provides insights into the genetic basis of its medicinal properties

Background

The sclerotium of Lignosus rhinocerotis (Cooke) Ryvarden or Tiger milk mushroom (Polyporales, Basidiomycota) is a valuable folk medicine for indigenous peoples in Southeast Asia. Despite the increasing interest in this ethnobotanical mushroom, very little is known about the molecular and genetic basis of its medicinal and nutraceutical properties.

Results

The de novo assembled 34.3 Mb L. rhinocerotis genome encodes 10,742 putative genes with 84.30% of them having detectable sequence similarities to others available in public databases. Phylogenetic analysis revealed a close evolutionary relationship of L. rhinocerotis to Ganoderma lucidum, Dichomitus squalens, and Trametes versicolor in the core polyporoid clade. The L. rhinocerotis genome encodes a repertoire of enzymes engaged in carbohydrate and glycoconjugate metabolism, along with cytochrome P450s, putative bioactive proteins (lectins and fungal immunomodulatory proteins) and laccases. Other genes annotated include those encoding key enzymes for secondary metabolite biosynthesis, including those from polyketide, nonribosomal peptide, and triterpenoid pathways. Among them, the L. rhinocerotis genome is particularly enriched with sesquiterpenoid biosynthesis genes.

Conclusions

The genome content of L. rhinocerotis provides insights into the genetic basis of its reported medicinal properties as well as serving as a platform to further characterize putative bioactive proteins and secondary metabolite pathway enzymes and as a reference for comparative genomics of polyporoid fungi.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-635) contains supplementary material, which is available to authorized users.     

Chemical characterization of the lipophilic extract of Hydrilla verticillata: a widely spread aquatic weed

The composition of the lipophilic extract from Hydrilla verticillata, the common aquatic weed collected from Sasthamkotta Lake, the largest freshwater lake in Kerala, south of the west coast of India, was investigated. The lake is a designated wetland of international importance under the Ramsar Convention since 2002. GC-MS study of the unsaponifiable lipophilic extract of H. verticillata confirmed the presence of 3,5,11,15-tetramethyl 1- hexadecen-3-ol (C₂₀H₄₀O) and phytol (C₂₀H₄₀O) as major components, and their structures were elucidated. Phytol and 3,5,11,15-tetramethyl 1- hexadecen3-ol are the two isomers of the diterpeneol (C₂₀H₄₀O) found in the unsaponifible lipophilic extract of H. verticillata and are formed by the hydrolysis of the alcohol moiety of chlorophyll. On quantification, an appreciable concentration of phytol (6.39 g?Kg^?1) was estimated. The feasibility to utilize H. verticillata to produce phytol is to be addressed by further studies since H. verticillata is considered as one of the world’s fast widely spread aquatic weeds on account of its numerous mechanisms of vegetative reproductions.     

The Potential of Mycelium and Culture Broth of Lignosus rhinocerotis as Substitutes for the Naturally Occurring Sclerotium with Regard to Antioxidant Capacity,Cytotoxic Effect,and Low-Molecular-Weight Chemical Constituents

Previous studies on the nutritional and nutraceutical properties of Lignosus rhinocerotis focused mainly on the sclerotium; however, the supply of wild sclerotium is limited. In this investigation, the antioxidant capacity and cytotoxic effect of L. rhinocerotis cultured under different conditions of liquid fermentation (shaken and static) were compared to the sclerotium produced by solid-substrate fermentation. Aqueous methanol extracts of the mycelium (LR-MH, LR-MT) and culture broth (LR-BH, LR-BT) demonstrated either higher or comparable antioxidant capacities to the sclerotium extract (LR-SC) based on their radical scavenging abilities, reducing properties, metal chelating activities, and inhibitory effects on lipid peroxidation. All extracts exerted low cytotoxicity (IC₅₀>200 µg/ml, 72 h) against selected mammalian cell lines. Several low-molecular-weight compounds, including sugars, fatty acids, methyl esters, sterols, amides, amino acids, phenolics, and triterpenoids, were identified using GC-MS and UHPLC-ESI-MS/MS. The presence of proteins (<40 kDa) in the extracts was confirmed by SDS-PAGE and SELDI-TOF-MS. Principal component analysis revealed that the chemical profiles of the mycelial extracts under shaken and static conditions were distinct from those of the sclerotium. Results from bioactivity evaluation and chemical profiling showed that L. rhinocerotis from liquid fermentation merits consideration as an alternative source of functional ingredients and potential substitute for the sclerotium.     

Chemical constituents from Elytropappus rhinocerotis (L.f.) Less.

Phytochemical investigation of the ethyl acetate extract of the aerial parts of Elytropappus rhinocerotis (L.f.) Less. led to the isolation of a coumarin (1), four flavonoids (2–5), and four labdane diterpenes (6–9). The structural characterization of the isolated compounds was based on spectroscopic data. All compounds are reported for the first time from this species and from the genus Elytropappus Cass. The isolation of labdane diterpenes and methoxylated flavones is of taxonomical significance.     

Comparative Study on the Suitability of Two Techniques for Measuring the Transfer of Lipophilic Drug Models from Lipid Nanoparticles to Lipophilic Acceptors

Due to their particle size in the submicrometer range, lipid nanoparticles are suitable for parenteral administration. In order to obtain information on their potential in vivo performance, a simple and effective in vitro assay to evaluate the drug release behavior of such particles is required. This study compares the use of different experimental setups for this purpose. Lipid nanoparticles from trimyristin which were loaded with fluorescent lipophilic drug models (a temoporfin and Nile red) were used as donor particles. The transfer of the two drug models to multilamellar vesicles (MLV) and emulsion droplets as lipophilic acceptor compartments was examined. The determination of the transferred substance was performed either after separation by centrifugation or by an in situ flow cytometric technique. The transfer of temoporfin was slow to the acceptor MLV and very rapid to the acceptor emulsion. With both acceptors, the transfer of temoporfin stopped at a concentration much lower than the theoretical equilibrium values. The transfer of the less lipophilic drug Nile red was very rapid to both acceptors with equilibrium concentrations close to the expected values. The transfer results of temoporfin especially to the acceptor MLV obtained with the two detection techniques were comparable while the centrifugation technique indicated an apparently higher Nile red transfer rate than the flow cytometric technique. Both techniques are equally suitable to study the transfer of temoporfin, while the flow cytometric technique is advantageous to measure the very rapid transfer of Nile red.Key words: drug transfer, flow cytometry, lipid nanoparticles, liposomes, ultracentrifugation     

Synthesis and anti-OXPHOS,antitumor activities of DLC modified spinosyn derivatives

A series of DLC (delocalized lipophilic cation) modified spinosyn derivatives were synthesized and evaluated for antitumor efficacies both in vitro and in vivo. Cancer cell based antiproliferative assays indicated that the more lipophilic derivatives had stronger inhibitory effects on the tested cancer cell lines. Compound 7b and 8b exhibited strong anti-OXPHOS and apoptosis inducing ability. Notable antitumor efficacies of 7b (5 mg/kg) and 8b (2.5 mg/kg) were observed in the in vivo tumor xenograft experiments, however, lethal toxicities were observed on higher dosages. Our findings indicated that DLC modification is a viable strategy to enhance the anti-OXPHOS and antitumor efficacies of spinosyn derivatives.     

Chemical Composition and Content of Lipophilic Seed Extractives of Some Abies and Picea Species

The chemical content and composition of the lipophilic extracts from seeds of some fir species: Abies alba, A. cephalonica, A. concolor, and A. koreana, as well as of a few spruce species: Picea abies, P. orientalis, and P. pungens, were examined. The amount of lipophilic extractives is diverse among the tree species and it varies from 9.8% to 41% of seeds. The chemical characterization showed significant differences, not only in the content, but also in the composition of extractives. However, most of the identified compounds like resin alcohols, ‐aldehydes, and ‐acids, as well as fatty acids, were detected in the seed extracts of all the examined tree species. The dominating identified compound group was esterified fatty acids (2.5 – 55.4% w/w of dry extract), occurring mainly as tri‐ and diglycerides, as well as free acids. The main representatives of this group were linoleic and oleic acids. The resin acids, among which the main were abietic, neoabietic, dehydroabietic, and palustric acids, were also detected at high levels, from 1.8% to 16.9% of the dry seed extracts. Phytosterols, tocopherols, resin hydrocarbons, and resin esters, as well as fatty alcohols were also identified. The coniferous tree seeds, as a renewable natural material, could represent a prospective raw material for producing valuable chemicals.     

N-(ϱ-coumaryl)-tryptamine and N-ferulyl tryptamine in kernels of Zea mays

N-(?-coumaryl)tryptamine and N-ferulyltryptamine were isolated from aqueous acetone extracts of ground kernels of Zea mays by successive column chromatography on partially sulfonated styrenedivinylbenzene copolymer resin, lipophilic Sephadex and preparative TLC. Identification of these compounds was made by GCMS of their trimethylsilyl derivatives and the trimethylsilyl derivatives of their acid hydrolysis products.     

A critical assessment of the use of lipophilic cations as membrane potential probes

A critical review has been made of the literature on the use of lipophilic cations, such as triphenylmethyl phosphonium (TPMP⁺) as membrane potential probes in prokaryotes, uekaryote organelles in vitro, and eukaryote cells. An ideal lipophilic cation should be capable of penetrating through a biological membrane and obey the Nernst equation between a membrane bound phase and its environment. Many different forms of the Nernst equation are presented, useful in the calculation equilibrium potentials of lipophilic cations across membranes. Lipophilic cations appear to behave as valid membrane potential probes in prokaryotes and eukaryote organelles in vitro and even in vivo although some technical difficulties may be involved. On the other hand in valid forms of the Nernst equation have often been used to calculate the equilibrium potential of lipophilic cations across the plasma membranes of eukaryotic cells. In particular, the problem of intracellular compartmentation of lipophilic cations has often not been appreciated. Lipophilic cations do not appear to behave as reliable plasma membrane potential probes in eukaryotic cells. Some other avenues are discussed which might be useful in the determination of the plasma membrane potentials of small eukaryotic cells, e.g. the use of lipophilic anions as membrane potential probes.     

Dammarane triterpenes from the resin of Boswellia freerana

The resin of Boswellia freerana afforded in addition to the known 3β,20(S)-dihydroxydammar-24-ene, its 3-acetyl derivative and (20S)-protopanaxadiol, a new triterpene that was characterized as 3β-acetoxy-16(S),20(R)-dihydroxydammar-24-ene on the basis of chemical and physico-chemical evidence.     

Enhanced Human Tissue Microdialysis Using Hydroxypropyl-?-Cyclodextrin as Molecular Carrier

Microdialysis sampling of lipophilic molecules in human tissues is challenging because protein binding and adhesion to the membrane limit recovery. Hydroxypropyl-ß-cyclodextrin (HP-ß-CD) forms complexes with hydrophobic molecules thereby improving microdialysis recovery of lipophilic molecules in vitro and in rodents. We tested the approach in human subjects. First, we determined HP-ß-CD influences on metabolite stability, delivery, and recovery in vitro. Then, we evaluated HP-ß-CD as microdialysis perfusion fluid supplement in 20 healthy volunteers. We placed 20 kDa microdialysis catheters in subcutaneous abdominal adipose tissue and in the vastus lateralis muscle. We perfused catheters with lactate free Ringer solution with or without 10% HP-ß-CD at flow rates of 0.3–2.0 µl/min. We assessed tissue metabolites, ultrafiltration effects, and blood flow. In both tissues, metabolite concentrations with Ringer+HP-ß-CD perfusate were equal or higher compared to Ringer alone. Addition of HP-ß-CD increased dialysate volume by 10%. Adverse local or systemic reactions to HP-ß-CD did not occur and analytical methods were not disturbed. HP-ß-CD addition allowed to measure interstitial anandamide concentrations, a highly lipophilic endogenous molecule. Our findings suggest that HP-ß-CD is a suitable supplement in clinical microdialysis to enhance recovery of lipophilic molecules from human interstitial fluid.     

Identification of serotonin 5-HT1A receptor partial agonists in ginger

Animal studies suggest that ginger (Zingiber officinale Roscoe) reduces anxiety. In this study, bioactivity-guided fractionation of a ginger extract identified nine compounds that interact with the human serotonin 5-HT_1A receptor with significant to moderate binding affinities (K_i = 3–20 μΜ). [³⁵S]-GTPγS assays indicated that 10-shogaol, 1-dehydro-6-gingerdione, and particularly the whole lipophilic ginger extract (K_i = 11.6 μg/ml) partially activate the 5-HT_1A receptor (20–60% of maximal activation). In addition, the intestinal absorption of gingerols and shogaols was simulated and their interactions with P-glycoprotein were measured, suggesting a favourable pharmacokinetic profile for the 5-HT_1A active compounds.     

Highly hydrophilic 1,3-oxazol-5-yl benzenesulfonamide inhibitors of carbonic anhydrase II for reduction of glaucoma-related intraocular pressure

Four inhibitors of human carbonic anhydrase II (hCA II) were designed based on the previously reported subnanomolar 1,3-oxazole-based sulfonamide inhibitors of the enzyme to incorporate primary and secondary amine functionality in the carboxamide side chain. The new hydrophilic compounds were found to inhibit the target isoform in sub-nanomolar to low nanomolar range with a good degree of selectivity to several other hCA isoforms. The hydrophilic character of these compounds is advantageous for intraocular residence time but not for corneal permeability which generally requires that a drug be sufficiently lipophilic. Two of the four compounds investigated, however, were found to exert comparable efficacy as 1% eye drops in PBS to that of the clinically used 2% dorzolamide (Trusopt®) eye drops. This indicated that the absorption of the compounds may occur via alternative route across conjunctiva and sclera.     

Metabolomics Reveals the Origins of Antimicrobial Plant Resins Collected by Honey Bees

The deposition of antimicrobial plant resins in honey bee, Apis mellifera, nests has important physiological benefits. Resin foraging is difficult to approach experimentally because resin composition is highly variable among and between plant families, the environmental and plant-genotypic effects on resins are unknown, and resin foragers are relatively rare and often forage in unobservable tree canopies. Subsequently, little is known about the botanical origins of resins in many regions or the benefits of specific resins to bees. We used metabolomic methods as a type of environmental forensics to track individual resin forager behavior through comparisons of global resin metabolite patterns. The resin from the corbiculae of a single bee was sufficient to identify that resin''s botanical source without prior knowledge of resin composition. Bees from our apiary discriminately foraged for resin from eastern cottonwood (Populus deltoides), and balsam poplar (P. balsamifera) among many available, even closely related, resinous plants. Cottonwood and balsam poplar resin composition did not show significant seasonal or regional changes in composition. Metabolomic analysis of resin from 6 North American Populus spp. and 5 hybrids revealed peaks characteristic to taxonomic nodes within Populus, while antimicrobial analysis revealed that resin from different species varied in inhibition of the bee bacterial pathogen, Paenibacillus larvae. We conclude that honey bees make discrete choices among many resinous plant species, even among closely related species. Bees also maintained fidelity to a single source during a foraging trip. Furthermore, the differential inhibition of P. larvae by Populus spp., thought to be preferential for resin collection in temperate regions, suggests that resins from closely related plant species many have different benefits to bees.     

Short-term resin tapping activities had a minor influence on physiological responses recorded in the tree-ring isotopes of Chinese pine (Pinus tabuliformis)

Resin tapping might affect tree-ring growth, but details on the physiological responses of trees to resin tapping are still lacking, particularly for long-term responses. This study aimed to explore the physiological processes underlying resin-tapping of Chinese pine (Pinus tabuliformis) by using tree-ring stable isotopes. We compared tree-ring earlywood and latewood stable carbon (δ¹³C) and oxygen (δ¹⁸O) isotopes in the pre-resin tapping and post-resin tapping period for tapped trees and compared their values between tapped and untapped trees and their responses to climate variables in a forest stand from 1984 to 2017. Furthermore, we used a dual isotope model to distinguish between the effects of the photosynthetic assimilation rate and stomatal conductance. Results indicated that tapped and untapped trees showed similar inter-annual variation for two isotopes, while the absolute values of tapped trees were slightly (P > 0.05) lower than tapped trees in the two years following resin tapping. Climate response analysis indicated that resin tapping had no significant effect on climatic sensitivity for either stable isotope. Earlywood stable isotopes were mainly influenced by temperature, relative humidity, and Palmer Drought Severity Index (PDSI) from May to July, while latewood isotopes were mainly influence by relative humidity form July to August and PDSI from July to September. The conceptual model results indicated that resin tapping lead to a slight, but not significant, decrease in the intrinsic water-use efficiency caused by increased stomatal conductance for the first two to three years following resin tapping. We conclude that tree-ring physiological responses could be less affected by short-term resin tapping activities.     

Improving the biological activity of the antimicrobial peptide anoplin by membrane anchoring through a lipophilic amino acid derivative

The lipophilic amino acid, (S)-2-aminoundecanoic acid, was synthesized and incorporated at a number of specific positions within the peptide sequence of anoplin. These lipophilic anoplin analogs showed to be more active against Escherichia coli and Staphylococcus aureus compared to native anoplin, while the EC₅₀-value of hemolysis was at least one order of magnitude lower than the MIC values. This was in sharp contrast to the N-acylated anoplin derivative, where a gain in activity also led to a complete loss of selectivity. Thus, the incorporation of a lipophilic amino acid residue into anoplin enhanced the antimicrobial activity, while selectivity towards microbial membranes was retained.     

Discovery of a potent series of non-steroidal non α-trifluoromethyl carbinol glucocorticoid receptor agonists with reduced lipophilicity

A novel series of indazole non-steroidal glucocorticoid receptor agonist has been discovered. This series features a sulfonamide central core and meta amides which interact with the extended ligand binding domain. This series has produced some of the most potent and least lipophilic agonists of which we are aware such as 20a (NFκB pIC₅₀ 8.3 (100%), c log P 1.9). Certain analogues in this series also display evidence for modulated pharmacology.     

Functional effects of chemical modification of unstacked and stacked chloroplasts with glutaraldehyde.

Although glutaraldehyde alkylates protein NH₂ groups to the same extent in unstacked and stacked thylakoids, the photosynthetic electron transport of the stacked membranes is always more inhibited. Inhibition of photosystem II electron transport, measured in the presence of lipophilic Hill oxidants, is 20–30% in unstacked and 60–70% in stacked thylakoids. Photosystem I electron transport is nearly completely inhibited in both preparations, but in the case of stacked thylakoids maximal inhibition occurs at a lower glutaraldehyde level than in unstacked thylakoids. In contrast, the photooxidation of the reaction center chromophore of photosystem I (P700) is unaffected by the glutaraldehyde treatment of either stacked or unstacked chloroplasts. The results are discussed with regard to the accessibility of membrane sites to exogenous electron transport cofactors, in view of the observation that N-methylphenazonium methosulfate, a quencher of electronically excited chlorophyll a, partitions more easily into the pigment domains of the glutaraldehyde-fixed unstacked thylakoids.     

Isolation and characterization of a thermotolerant ene reductase from Geobacillus sp. 30 and its heterologous expression in Rhodococcus opacus

Rhodococcus opacus B-4 cells are adhesive to and even dispersible in water-immiscible hydrocarbons owing to their highly lipophilic nature. In this study, we focused on the high operational stability of thermophilic enzymes and applied them to a biocatalytic conversion in an organic reaction medium using R. opacus B-4 as a lipophilic capsule of enzymes to deliver them into the organic medium. A novel thermo- and organic-solvent-tolerant ene reductase, which can catalyze the enantioselective reduction of ketoisophorone to (6R)-levodione, was isolated from Geobacillus sp. 30, and the gene encoding the enzyme was heterologously expressed in R. opacus B-4. Another thermophilic enzyme which catalyzes NAD⁺-dependent dehydrogenation of cyclohexanol was identified from the gene-expression library of Thermus thermophilus and the gene was coexpressed in R. opacus B-4 for cofactor regeneration. While the recombinant cells were not viable in the mixture due to high reaction temperature, 634 mM of (6R)-levodione could be produced with an enantiopurity of 89.2 % ee by directly mixing the wet cells of the recombinant R. opacus with a mixture of ketoisophorone and cyclohexanol at 50 °C. The conversion rate observed with the heat-killed recombinant cells was considerably higher than that obtained with a cell-free enzyme solution, demonstrating that the accessibility between the substrates and enzymes could be improved by employing R. opacus cells as a lipophilic enzyme capsule. These results imply that a combination of thermophilic enzymes and lipophilic cells can be a promising approach for the biocatalytic production of water-insoluble chemicals.