Secondary Metabolites from the Endophytic FungusXylaria cubensis

Diverse Metabolites and Pharmacological Effects from the Basidiomycetes Inonotus hispidus

Inonotus hispidus mushroom is a popular edible and medicinal mushroom with a long history of use. It is well known as a medicinal fungus with various health benefits for its significant anticancer and immunomodulatory activities. Over the last 60 years, secondary metabolites derived from I. hispidus and their biological activities have been discovered and investigated. Structurally, these compounds are mainly polyphenols and triterpenoids, which have anticancer, anti-inflammatory, antioxidant, antimicrobial, and enzyme inhibitor activities. Here, the secondary metabolites derived from I. hispidus and their activities were systematically and comprehensively classified and summarized, and the biosynthetic pathway of stylylpyrones was deduced and analyzed further. This review contributes to our understanding of I. hispidus and will help with research into natural product chemistry, pharmacology, and the biosynthesis of I. hispidus metabolites. According to this review, I. hispidus could be a promising source of bioactive compounds for health promotion and the development of functional foods.

Four New Pale-Spored Species of Xylaria (Xylariaceae, Xylariales) with a Key to Worldwide Species on Fallen Fruits and Seeds

Xylaria, a large and cosmopolitan genus of Ascomycota, plays an important ecological role in forest ecology as wood-decomposers, and serve as a source of bioactive secondary metabolites. The present work concerns a survey of Xylaria from Southwest China. Four new species of Xylaria with pale-colored ascospores associated with fallen fruits and seeds are described and illustrated based on morphological and phylogenetic evidences. The phylogeny inferred from a combined dataset of ITS-RPB2-β-tubulin sequences supports these four species as distinct species. The four new taxa, namely Xylariarogersii, X. schimicola, X. theaceicola, and X. wallichii, are compared and contrasted against morphologically similar species. A dichotomous identification key to all the accepted species of Xylaria associated with fallen fruits and seeds is given.

DU8ML: Machine Learning-Augmented Density Functional Theory Nuclear Magnetic Resonance Computations for High-Throughput In Silico Solution Structure Validation and Revision of Complex Alkaloids

Machine learning (ML) profoundly improves the accuracy of the fast DU8+ hybrid density functional theory/parametric computations of nuclear magnetic resonance spectra, allowing for high throughput in silico validation and revision of complex alkaloids and other natural products. Of nearly 170 alkaloids surveyed, 35 structures are revised with the next-generation ML-augmented DU8 method, termed DU8ML.

Xylaria necrophora, sp. nov., is an emerging root-associated pathogen responsible for taproot decline of soybean in the southern United States

Taproot decline (TRD) is a disease of soybean that has been reported recently from the southern United States (U.S.). Symptoms of TRD include foliar interveinal chlorosis followed by necrosis. Darkened, charcoal-colored areas of thin stromatic tissue are evident on the taproot and lateral roots along with areas of necrosis within the root and white mycelia within the pith. Upright stromata typical of Xylaria can be observed on crop debris and emerging from infested roots in fields where taproot decline is present, but these have not been determined to contain fertile perithecia. Symptomatic plant material was collected across the known range of the disease in the southern U.S., and the causal agent was isolated from roots. Four loci, ⍺-actin (ACT), β-tubulin (TUB2), the nuclear rDNA internal transcribed spacers (nrITS), and the RNA polymerase subunit II (RPB2), were sequenced from representative isolates. Both maximum likelihood and Bayesian phylogenetic analyses showed consistent clustering of representative TRD isolates in a highly supported clade within the Xylaria arbuscula species complex in the "HY" clade of the family Xylariaceae, distinct from any previously described taxa. In order to understand the origin of this pathogen, we sequenced herbarium specimens previously determined to be "Xylaria arbuscula" based on morphology and xylariaceous endophytes collected in the southern U.S. Some historical specimens from U.S. herbaria collected in the southern region as saprophytes as well as a single specimen from Martinique clustered within the "TRD" clade in phylogenetic analyses, suggesting a possible shift in lifestyle. The remaining specimens that clustered within the family Xylariaceae, but outside of the "TRD" clade, are reported. Both morphological evidence and molecular evidence indicate that the TRD pathogen is a novel species, which is described as Xylaria necrophora.

Phenolic and Steroidal Metabolites from the Cultivated Edible Inonotus hispidus Mushroom and Their Bioactivities

A chemical study on the fruiting bodies of cultivated edible mushroom Inonotus hispidus resulted in 14 metabolites including three new hispolon congeners, named inonophenols A-B and one new lanostane triterpenoid, named inonoterpene A. These structures were identified by NMR, high-resolution electrospray ionization mass spectrometry (HRESIMS), and electronic circular dichroism (ECD) data analysis. All metabolites were assessed for neurotrophic, anti-inflammatory, and antioxidative activities. Among them, inonophenols B and C were the most active in promoting PC-12 cell neurite outgrowth at a concentration of 10 μM. The phenolic derivatives reduced NO generation by lipopolysaccharide (LPS)-induced BV-2 microglial cells by suppressing the expression of toll-like receptor-4 (TLR-4) and the nuclear factor-kappa-B (NF-κB) signaling pathway as well as the inflammatory mediators including inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2). Moreover, the phenolics showed antioxidant effects in DPPH scavenging assay with the IC₅₀ values of 9.82-21.43 μM. These findings showed that I. hispidus may be a new source of neurotrophic and protective agents against neurodegenerative disorders.

Fungal Endophytes as Efficient Sources of Plant-Derived Bioactive Compounds and Their Prospective Applications in Natural Product Drug Discovery: Insights, Avenues, and Challenges

Fungal endophytes are well-established sources of biologically active natural compounds with many producing pharmacologically valuable specific plant-derived products. This review details typical plant-derived medicinal compounds of several classes, including alkaloids, coumarins, flavonoids, glycosides, lignans, phenylpropanoids, quinones, saponins, terpenoids, and xanthones that are produced by endophytic fungi. This review covers the studies carried out since the first report of taxol biosynthesis by endophytic Taxomyces andreanae in 1993 up to mid-2020. The article also highlights the prospects of endophyte-dependent biosynthesis of such plant-derived pharmacologically active compounds and the bottlenecks in the commercialization of this novel approach in the area of drug discovery. After recent updates in the field of 'omics' and 'one strain many compounds' (OSMAC) approach, fungal endophytes have emerged as strong unconventional source of such prized products.

Phylogenetic and Chemotaxonomic Studies Confirm the Affinities of Stromatoneurospora phoenix to the Coprophilous Xylariaceae

The genus Stromatoneurospora was erected in 1973 by Jong and Davis to accommodate the pyrophilic pyrenomycete Sphaeria phoenix and has traditionally been placed in the family Xylariaceae based on morphological features. However, no living culture of this genus has so far been available in the public domain. Molecular data were restricted to an internal transcribed spacer (ITS) sequence that only confirmed the familial position, and was generated from a strain that is not deposited in a public culture collection. We have recently collected fresh material and were able to culture this fungus from Thailand. The secondary metabolites of this strains were analysed after fermentation in multiple media. The the prominent components of these fermentation were purified, using preparative chromatography. Aside from two new eremophilane sesquiterpenoids named phoenixilanes A–B (1–2), four other components that are known from species of the xylariaceous genera Xylaria and Poronia were identified by spectral methods (nuclear magnetic resonance spectroscopy and high resolution mass spectrometry). Notably, (−)-(R)-6-hydroxy-3-methyl-4-dihydroisocoumarin-5-carboxylic acid (6) has not been reported as a natural product before. Moreover, DNA sequences of Stromatoneurospora phoenix clustered with members of the genera Poronia and Podosordaria in a multi-locus molecular phylogeny. These results confirmed that the genus belongs to the same evolutionary lineage as the coprophilic Xylariaceae. The results also suggest that this lineage has evolved independently from the plant-inhabiting saprotrophs and endophytes that are closely related to the genus Xylaria. These findings are discussed in relation to some theories about the endophytic vs. the pyrophilic/coprophilic fungal life style.

Naturally Occurring Isocoumarins Derivatives from Endophytic Fungi: Sources, Isolation, Structural Characterization, Biosynthesis, and Biological Activities

Recently, the metabolites separated from endophytes have attracted significant attention, as many of them have a unique structure and appealing pharmacological and biological potentials. Isocoumarins represent one of the most interesting classes of metabolites, which are coumarins isomers with a reversed lactone moiety. They are produced by plants, microbes, marine organisms, bacteria, insects, liverworts, and fungi and possessed a wide array of bioactivities. This review gives an overview of isocoumarins derivatives from endophytic fungi and their source, isolation, structural characterization, biosynthesis, and bioactivities, concentrating on the period from 2000 to 2019. Overall, 307 metabolites and more than 120 references are conferred. This is the first review on these multi-facetted metabolites from endophytic fungi.

Anti-inflammatory and cytotoxic agents from Xylaria sp. SWUF09-62 fungus

The ongoing search for anti-cancer agents from microorganisms led to the isolation of four new compounds including 6-ethyl-8-hydroxy-4H-chromen-4-one (1), 6-ethyl-7,8-dihydroxy-4H-chromen-4-one (2), (3S)-3,4-dihydro-8-hydroxy-7-methoxy-3-methylisocoumarin (3) and (3S)-3,4-dihydro-5,7,8-trihydroxy-3-methylisocoumarin (4), together with eleven known compounds (5-15) from Xylaria sp. SWUF09-62 fungus. The chemical structures were deduced from IR, 1D and 2D NMR, and MS data. The absolute configurations of 3 and 4 were determined by ECD experiment. Compounds 2 and 4 indicated possible chemo-prevention and chemo-therapeutic properties, exhibited anti-inflammatory properties by reducing nitric oxide production in LPS-stimulated RAW264.7 cells (IC₅₀ = 1.57 ± 0.25 and 3.02 ± 0.27 μg/mL) and cytotoxicity against HT29 cells (IC₅₀ = 16.46 ± 0.48 and 97.78 ± 7.14 μg/mL).

A new amino amidine derivative from the wood-decaying fungus Xylaria cf. cubensis SWUF08-86

The secondary metabolites of Xylaria cf. cubensis SWUF08-86 fungus were investigated, and the chromatographic separation of the crude extracts yielded seventeen compounds. The structure elucidation by spectroscopic analysis including 1D and 2D NMR and the comparison of these data with literature, along with HREIMS spectrometry, revealed one new amino amidine derivative (1), together with five known simple cyclic dipeptide analogs, diketopiperazines (2-6) and eleven other known compounds, including one hemi-cycline (10), three aromatic derivatives (11-13), one sesquiterpene (14) and three sterols (15-17). The isolated compounds were screened for anticancer and anti-pathogenic bacterial and fungal activities. Based on this work, Xylaria cf. cubensis SWUF08-86 has proven to be a diverse secondary metabolites producer.

Muscarine, imidazole, oxazole and thiazole alkaloids

Covering: July 2012 to June 2015. Previous review: Nat. Prod. Rep., 2013, 30, 869-915The structurally diverse imidazole-, oxazole-, and thiazole-containing secondary metabolites are widely distributed in terrestrial and marine environments, and exhibit extensive pharmacological activities. In this review the latest progress involving the isolation, biological activities, and chemical and biogenetic synthesis studies on these natural products has been summarized.

Secondary metabolites of endophytic Xylaria species with potential applications in medicine and agriculture

Fungal endophytes are important sources of bioactive secondary metabolites. The genus Xylaria Hill (ex Schrank, 1789, Xylariaceae) comprises various endophytic species associated to both vascular and non vascular plants. The secondary metabolites produced by Xylaria species include a variety of volatile and non-volatile compounds. Examples of the former are sesquiterpenoids, esters, and alcohols, among others; and of the latter we find terpenoids, cytochalasins, mellein, alkaloids, polyketides, and aromatic compounds. Some of these metabolites have shown potential activity as herbicides, fungicides, and insecticides; others possess antibacterial, antimalarial, and antifungal activities, or α-glucosidase inhibitory activity. Thus metabolites from Xylaria are promising compounds for applications in agriculture for plague control as biopesticides, and biocontrol agents; and in medicine, for example as drugs for the treatment of infectious and non-infectious diseases. This review seeks to show the great value of the secondary metabolites of Xylaria, particularly in the agriculture and medicine fields.

Contributions of North American endophytes to the phylogeny, ecology, and taxonomy of Xylariaceae (Sordariomycetes, Ascomycota)

The Xylariaceae (Sordariomycetes) comprise one of the largest and most diverse families of Ascomycota, with at least 85 accepted genera and ca. 1343 accepted species. In addition to their frequent occurrence as saprotrophs, members of the family often are found as endophytes in living tissues of phylogenetically diverse plants and lichens. Many of these endophytes remain sterile in culture, precluding identification based on morphological characters. Previous studies indicate that endophytes are highly diverse and represent many xylariaceous genera; however, phylogenetic analyses at the family level generally have not included endophytes, such that their contributions to understanding phylogenetic relationships of Xylariaceae are not well known. Here we use a multi-locus, cumulative supermatrix approach to integrate 92 putative species of fungi isolated from plants and lichens into a phylogenetic framework for Xylariaceae. Our collection spans 1933 isolates from living and senescent tissues in five biomes across the continental United States, and here is analyzed in the context of previously published sequence data from described species and additional taxon sampling of type specimens from culture collections. We found that the majority of strains obtained in our surveys can be classified in the hypoxyloid and xylaroid subfamilies, although many also were found outside of these lineages (as currently circumscribed). Many endophytes were placed in lineages previously not known for endophytism. Most endophytes appear to represent novel species, but inferences are limited by potential gaps in public databases. By linking our data, publicly available sequence data, and records of ascomata, we identify many geographically widespread, host-generalist clades capable of symbiotic associations with diverse photosynthetic partners. Concomitant with such cosmopolitan host use and distributions, many xylariaceous endophytes appear to inhabit both living and non-living plant tissues, with potentially important roles as saprotrophs. Overall, our study reveals major gaps in the availability of multi-locus datasets and metadata for this iconic family, and provides new hypotheses regarding the ecology and evolution of endophytism and other trophic modes across the family Xylariaceae.

Diterpenoids of terrestrial origin

This review covers the isolation and chemistry of diterpenoids from terrestrial as opposed to marine sources and includes, labdanes, clerodanes, pimaranes, abietanes, kauranes, gibberellins, cembranes and their cyclization products. The literature from January to December, 2014 is reviewed.