Phylogenetic Assignment of the Fungicolous Hypoxylon invadens (Ascomycota, Xylariales) and Investigation of its Secondary Metabolites

Multi-Locus Phylogeny and Morphology Reveal Two New Species of Hypoxylon (Hypoxylaceae, Xylariales) from Motuo, China

Hypoxylaceous fungi are abundant in China, but their discovery and report are uneven in various provinces, with more fungi in Yunnan and Hainan and fewer fungi in Tibet. During the investigation of macro-fungi in Motuo county, Tibet Autonomous Region, we collected a number of xylarialean specimens. Six hypoxylaceous specimens growing on dead angiosperm were collected from the forests of Motuo county, and they were described and illustrated as two new species in Hypoxylon based on a combination of morphological characters and molecular evidence. Hypoxylon diperithecium was characterized by its bistratal perithecia, purple-brown stromatal granules, citrine to rust KOH-extractable pigments, and light brown to brown ascospores ellipsoid-inequilateral with conspicuous coil-like ornamentation. Hypoxylon tibeticum was distinct from other species by having pulvinate and applanate stromata, surface vinaceous, with orange granules, orange KOH-extractable pigments, and brown ascospores with inconspicuous ornamentation. The multi-gene phylogenetic analyses (ITS-LSU-RPB2-TUB) supported the two new taxa as separate lineages in the genus Hypoxylon. A key to all known Hypoxylon taxa from China is provided.

Profiling Expression Strategies for a Type III Polyketide Synthase in a Lysate-Based, Cell-free System

Some of the most metabolically diverse species of bacteria (e.g., Actinobacteria) have higher GC content in their DNA, differ substantially in codon usage, and have distinct protein folding environments compared to tractable expression hosts like Escherichia coli. Consequentially, expressing biosynthetic gene clusters (BGCs) from these bacteria in E. coli frequently results in a myriad of unpredictable issues with protein expression and folding, delaying the biochemical characterization of new natural products. Current strategies to achieve soluble, active expression of these enzymes in tractable hosts, such as BGC refactoring, can be a lengthy trial-and-error process. Cell-free expression (CFE) has emerged as 1) a valuable expression platform for enzymes that are challenging to synthesize in vivo, and as 2) a testbed for rapid prototyping that can improve cellular expression. Here, we use a type III polyketide synthase from Streptomyces griseus, RppA, which catalyzes the formation of the red pigment flaviolin, as a reporter to investigate BGC refactoring techniques. We synergistically tune promoter and codon usage to improve flaviolin production from cell-free expressed RppA. We then assess the utility of cell-free systems for prototyping these refactoring tactics prior to their implementation in cells. Overall, codon harmonization improves natural product synthesis more than traditional codon optimization across cell-free and cellular environments. Refactoring promoters and/or coding sequences via CFE can be a valuable strategy to rapidly screen for catalytically functional production of enzymes from BCGs. By showing the coordinators between CFE versus in vivo expression, this work advances CFE as a tool for natural product research.

Segregation of the genus Parahypoxylon (Hypoxylaceae, Xylariales) from Hypoxylon by a polyphasic taxonomic approach

During a mycological survey of the Democratic Republic of the Congo, a fungal specimen that morphologically resembled the American species Hypoxylon papillatum was encountered. A polyphasic approach including morphological and chemotaxonomic together with a multigene phylogenetic study (ITS, LSU, tub2, and rpb2) of Hypoxylon spp. and representatives of related genera revealed that this strain represents a new species of the Hypoxylaceae. However, the multi-locus phylogenetic inference indicated that the new fungus clustered with H. papillatum in a separate clade from the other species of Hypoxylon. Studies by ultrahigh performance liquid chromatography coupled to diode array detection and ion mobility tandem mass spectrometry (UHPLC-DAD-IM-MS/MS) were carried out on the stromatal extracts. In particular, the MS/MS spectra of the major stromatal metabolites of these species indicated the production of hitherto unreported azaphilone pigments with a similar core scaffold to the cohaerin-type metabolites, which are exclusively found in the Hypoxylaceae. Based on these results, the new genus Parahypoxylon is introduced herein. Aside from P. papillatum, the genus also includes P. ruwenzoriensesp. nov., which clustered together with the type species within a basal clade of the Hypoxylaceae together with its sister genus Durotheca.

Three New Species of Hypoxylon (Xylariales, Ascomycota) on a Multigene Phylogeny from Medog in Southwest China

During a survey of hypoxylaceous fungi in Medog county (Tibet Autonomous Region, China), three new species, including Hypoxylon damuense, Hypoxylon medogense, and Hypoxylon zangii, were described and illustrated based on morphological and multi-gene phylogenetic analyses. Hypoxylon damuense is characterized by its yellow-brown stromatal granules, light-brown to brown ascospores, and frequently indehiscent perispore. Hypoxylon medogense is morphologically and phylogenetically related to H. erythrostroma but differs in having larger ascospores with straight spore-length germ slit and conspicuously coil-like perispore ornamentation. Hypoxylon zangii shows morphological similarities to H. texense but differs in having Amber (47), Fulvous (43) and Sienna (8) KOH-extractable pigments and larger ascospores with straight spore-length germ slit. The multi-gene phylogenetic analyses inferred from the datasets of ITS-RPB2-LSU-TUB2 supported the three new taxa as separate lineages within Hypoxylon. A key to all known Hypoxylon species from China and related species worldwide is provided.

Multi-Gene Phylogeny and Taxonomy of Hypoxylon (Hypoxylaceae, Ascomycota) from China

The Hypoxylon species play an important ecological role in tropical rainforest as wood-decomposers, and some might have benefical effects on their hosts as endophytes. The present work concerns a survey of the genus Hypoxylon from Hainan Tropical Rainforest National Park of China. Four new species: H. wuzhishanense, H. hainanense, H.chrysalidosporum, and H.cyclobalanopsidis, were discovered based on a combination of morphological characteristics and molecular data. Hypoxylon wuzhishanense is characterized by Rust pulvinate stromata, amyloid apical apparatus and brown ascospores, with most of the perispore being indehiscent in 10% KOH. Hypoxylon hainanense has effused–pulvinate and Violet stromata, amyloid apical apparatus, light-brown to brown ascospores with straight germ slit and dehiscent perispore. Hypoxylonchrysalidosporum is distinguished by glomerate to pulvinate stromata, highly reduced or absent inamyloid apical apparatus, and light-brown to brown ascospores with very conspicuous coil-like ornamentation. Hypoxyloncyclobalanopsidis has Livid Purple pulvinate stromata, highly reduced amyloid apical apparatus, faint bluing, brown ascospores and dehiscent perispore, and it grows on dead branches of Cyclobalanopsis. Detailed descriptions, illustrations, and contrasts with morphologically similar species are provided. Phylogenetic analyses inferred from ITS, RPB2, LSU, and β-tubulin sequences confirmed that the four new species are distinct within the genus Hypoxylon.

Resolution of the Hypoxylon fuscum Complex (Hypoxylaceae, Xylariales) and Discovery and Biological Characterization of Two of Its Prominent Secondary Metabolites

Hypoxylon, a large, cosmopolitan genus of Ascomycota is in the focus of our current poly-thetic taxonomic studies, and served as an excellent source for bioactive secondary metabolites at the same time. The present work concerns a survey of the Hypoxylon fuscum species complex based on specimens from Iran and Europe by morphological studies and high performance liquid chromatography coupled to mass spectrometry and diode array detection (HPLC-MS-DAD). Apart from known chemotaxonomic markers like binaphthalene tetrol (BNT) and daldinin F, two unprece-dented molecules were detected and subsequently isolated to purity by semi preparative HPLC. Their structures were established by nuclear-magnetic resonance (NMR) spectroscopy as 3′-malonyl-daldinin F (6) and pseudofuscochalasin A (4). The new daldinin derivative 6 showed weak cytotoxicity towards mammalian cells but bactericidal activity. The new cytochalasin 4 was compared to cytochalasin C in an actin disruption assay using fluorescence microscopy of human osteo-sarcoma U2OS cells, revealing comparable activity towards F-actin but being irreversible compared to cytochalasin C. Concurrently, a multilocus molecular phylogeny based on ribosomal and proteinogenic nucleotide sequences of Hypoxylon species resulted in a well-supported clade for H. fuscum and its allies. From a comparison of morphological, chemotaxonomic and phylogenetic evidence, we introduce the new species H. eurasiaticum and H. pseudofuscum.

Recent progress in biodiversity research on the Xylariales and their secondary metabolism

The families Xylariaceae and Hypoxylaceae (Xylariales, Ascomycota) represent one of the most prolific lineages of secondary metabolite producers. Like many other fungal taxa, they exhibit their highest diversity in the tropics. The stromata as well as the mycelial cultures of these fungi (the latter of which are frequently being isolated as endophytes of seed plants) have given rise to the discovery of many unprecedented secondary metabolites. Some of those served as lead compounds for development of pharmaceuticals and agrochemicals. Recently, the endophytic Xylariales have also come in the focus of biological control, since some of their species show strong antagonistic effects against fungal and other pathogens. New compounds, including volatiles as well as nonvolatiles, are steadily being discovered from these ascomycetes, and polythetic taxonomy now allows for elucidation of the life cycle of the endophytes for the first time. Moreover, recently high-quality genome sequences of some strains have become available, which facilitates phylogenomic studies as well as the elucidation of the biosynthetic gene clusters (BGC) as a starting point for synthetic biotechnology approaches. In this review, we summarize recent findings, focusing on the publications of the past 3 years.