Activation of secondary metabolite gene clusters in Chaetomium olivaceum via the deletion of a histone deacetylase.

Histone acetylation modifications in filamentous fungi play a crucial role in epigenetic gene regulation and are closely linked to the transcription of secondary metabolite (SM) biosynthetic gene clusters (BGCs). Histone deacetylases (HDACs) play a pivotal role in determining the extent of histone acetylation modifications and act as triggers for the expression activity of target BGCs. The genus Chaetomium is widely recognized as a rich source of novel and bioactive SMs. Deletion of a class I HDAC gene of Chaetomium olivaceum SD-80A, g7489, induces a substantial pleiotropic effect on the expression of SM BGCs. The C. olivaceum SD-80A ∆g7489 strain exhibited significant changes in morphology, sporulation ability, and secondary metabolic profile, resulting in the emergence of new compound peaks. Notably, three polyketides (A1-A3) and one asterriquinone (A4) were isolated from this mutant strain. Furthermore, our study explored the BGCs of A1-A4, confirming the function of two polyketide synthases (PKSs). Collectively, our findings highlight the promising potential of molecular epigenetic approaches for the elucidation of novel active compounds and their biosynthetic elements in Chaetomium species. This finding holds great significance for the exploration and utilization of Chaetomium resources. KEY POINTS: • Deletion of a class I histone deacetylase activated secondary metabolite gene clusters. • Three polyketides and one asterriquinone were isolated from HDAC deleted strain. • Two different PKSs were reported in C. olivaceum SD-80A.

Antimicrobial sesterterpenoids with a unique 5/8/6/5 tetracyclic carbon-ring-system and diepoxide polyketides from a deep sea-sediment-sourced fungus Chaetomium globosum SD-347.

Two new sesterterpenoids, sesterchaetins A and B (1 and 2), and two new diepoxide polyketides, chaetoketoics A and B (3 and 4), were characterized from the culture extract of Chaetomium globosum SD-347, a fungal strain derived from deep sea-sediment. Their structures and absolute configurations were unambiguously determined by detailed NMR, mass spectra, and X-ray crystallographic analysis. Compounds 1 and 2 contained a distinctive 5/8/6/5 tetracyclic carbon-ring-system, which represented a rarely occurring natural product framework. The new isolates 1-4 exhibited selective antimicrobial activities against human and aquatic pathogenic bacteria and plant-pathogenic fungi.

Reconstitution of the Early Stage of Chetomin Biosynthesis in Aspergillus fumigatus Leads to the Production of Epipolythiodioxopiperazines.

Using CRISPR-Cas9 technology and a microhomology-mediated end-joining repair system, we substituted genes of the gliotoxin pathway in Aspergillus fumigatus with genes responsible for chetomin biosynthesis from Chaetomium cochliodes, leading to the production of three new epipolythiodioxopiperazines (ETPs). This work represents the first successful endeavor to produce ETPs in a non-native host. Additionally, the simultaneous disruption of five genes in a single transformation marks the most extensive gene knockout event in filamentous fungi to date.

Chaetoxylariones A-G: undescribed chromone-derived polyketides from co-culture of Chaetomium virescens and Xylaria grammica enabled via the molecular networking strategy.

By co-culturing two endophytic fungi (Chaetomium virescens and Xylaria grammica) collected from the medicinal and edible plant Smilax glabra Roxb. and analyzing them with MolNetEnhancer module on GNPS platform, seven undescribed chromone-derived polyketides (chaetoxylariones A-G), including three pairs of enantiomer ones (2a/2b, 4a/4b and 6a/6b) and four optical pure ones (1, 3, 5 and 7), as well as five known structural analogues (8-12), were obtained. The structures of these new compounds were characterized by NMR spectroscopy, single-crystal X-ray diffraction, 13C NMR calculation and DP4+ probability analyses, as well as the comparison of the experimental electronic circular dichroism (ECD) data. Structurally, compound 1 featured an unprecedented chromone-derived sulfonamide tailored by two isoleucine-derived δ-hydroxy-3-methylpentenoic acids via the acylamide and NO bonds, respectively; compound 2 represented the first example of enantiomeric chromone derivative bearing a unique spiro-[3.3]alkane ring system; compound 3 featured a decane alkyl side chain that formed an undescribed five-membered lactone ring between C-7' and C-10'; compound 4 contained an unexpected highly oxidized five-membered carbocyclic system featuring rare adjacent keto groups; compound 7 featured a rare methylsulfonyl moiety. In addition, compound 10 showed a significant inhibition towards SW620/AD300 cells with an IC50 value of PTX significantly decreased from 4.09 µM to 120 nM, and a further study uncovered that compound 10 could obviously reverse the MDR of SW620/AD300 cells.

Anti-inflammatory Polyketides from an Endophytic Fungus Chaetomium sp. UJN-EF006 of Vaccinium bracteatum.

Seven new polyketides including three chromone derivatives (1-3) and four linear ones incorporating a tetrahydrofuran ring (4-7), along with three known compounds (8-10), were obtained from the fermentation of an endophytic fungus (Chaetomium sp. UJN-EF006) isolated from the leaves of Vaccinium bracteatum. The structures of these fungal metabolites have been elucidated by spectroscopic means including MS, NMR and electronic circular dichroism. A preliminary anti-inflammatory screening with the lipopolysaccharide (LPS) induced RAW264.7 cell model revealed moderate NO production inhibitory activity for compounds 1 and 4. In addition, the expression of three LPS-induced inflammatory factors IL-6, iNOS and COX-2 was also blocked by 1 and 4.

Chae-type cytochalasans from coculture of Aspergillus flavipes and Chaetomium globosum.

Cocultivation of the high cytochalasan-producing fungi Aspergillus flavipes and Chaetomium globosum resulted in the isolation of 11 undescribed Chae-type cytochalasans. Their structures were determined by spectroscopic data and NMR data calculations. Asperchaetoglobin A (1) was the first Chae-type cytochalasan possessing an unprecedented nitrogen bridge between C-17 and C-20 to generate a surprising 5/6/12/5 multiple ring system; asperchaetoglobins B and C (2 and 3) displayed higher oxidation with an additional epoxide at the thirteen-member ring; asperchaetoglobin D (4) was the second Chae-type cytochalasin featuring a 5/6/12 tricyclic ring system. The cytotoxic activities against five human cancer cell lines and antibacterial activities against Staphylococcus aureus and Colon bacillus of selected compounds were evaluated in vitro.

Phytochemical Analysis and Antioxidant Activity of Endophytic Fungi Isolated from Dillenia indica Linn.

Endophytic fungi live symbiotically inside plants and are hidden source of natural bioactive molecules. The present study was carried out to investigate the phytochemical analysis and antioxidant activity of endophytic fungi isolated from the ethnomedicinal plant Dillenia indica L. The ethyl acetate crude extracts of the endophytic fungal strains were preliminarily evaluated for their phytochemical analysis, and the results showed the presence of alkaloids, flavonoids, phenolics, terpene, and saponins. The crude extracts of more than 60% of the isolates showed 50-90% antioxidant activity by DPPH and H2O2 assay. The inhibition percentage of ethyl acetate extracts ranges from 34.05 to 91.5%, whereas IC50 values vary from 72.2 to 691.14%. Among all the strains, Fomitopsis meliae crude extract showed a maximum inhibition percentage, i.e., 91.5%, with an IC50 value of 88.27 µg/mL. Chaetomium globosum showed significant activity having an inhibition percentage of 89.88% and an IC50 value of 74.44 µg/mL. The total phenolic and flavonoid content in the crude extract of Chaetomium globosum was 37.4 mg gallic acid equivalent (GAE)/g DW and 31.0 mg quercetin equivalent (GAE)/g DW. GC-MS analysis of crude extract of C. globosum revealed different compounds, such as squalene; butanoic acid, 2-methyl-; hexadecanoic acid; 2-propanone, 1-phenyl-; 5-oxo-pyrrolidine-2-carboxylic acid methyl ester; 9,12-octadecadienoic acid (z)- etc. Many of these belong to phenolics, which are natural antioxidant compounds. The findings suggested that endophytic fungi associated with Dillenia indica L. can be a potential source of novel antioxidant compounds.

Facile fabrication and antibacterial properties of chitosan/acrylamide/gold nanocomposite hydrogel incorporated with Chaetomium globosium extracts from Gingko biloba leaves.

Microorganisms are a unique part of our ecosystem because they affect the survival of living organisms. Although pathogenic microorganisms could be detrimental to the plants, animals, and humans, beneficial microbes have provided significant improvement in the growth and development of living organisms. In this study, the fungus Chaetomium globosium was isolated from the medicinal tree Gingko biloba, and then incorporated into a polymerization system to fabricate chitosan/acrylamide/gold (CS/Am/Au) nanocomposite hydrogels. The as-prepared hydrogel displayed increased mechanical strength due to the reinforcement of Au (gold) nanocomposites within the hydrogel matrix. Also, the equilibrium pH responsive swelling rates of the hydrogels gradually increased as the pH increases due to partial acid and basic hydrolysis occurring in the hydrogel as well as formation of hydrogen bond. In addition, the hydrogel demonstrated promising antibacterial activities against selected gram-positive (Staphylococcus epidermidis and Staphylococcus aureus) and gram-negative (Pseudomonas aeruginosa) bacterial strains with an average MIC90 of 0.125 mg/mL at a dosage of 1.0 mg/L. The obtained results are quite promising towards resolving several health challenges and advancing the pharmaceutical industries.

Atg15 is a vacuolar phospholipase that disintegrates organelle membranes.

Atg15 (autophagy-related 15) is a vacuolar phospholipase essential for the degradation of cytoplasm-to-vacuole targeting (Cvt) bodies and autophagic bodies, hereinafter referred to as intravacuolar/intralysosomal autophagic compartments (IACs), but it remains unknown if Atg15 directly disrupts IAC membranes. Here, we show that the recombinant Chaetomium thermophilum Atg15 lipase domain (CtAtg15(73-475)) possesses phospholipase activity. The activity of CtAtg15(73-475) was markedly elevated by limited digestion. We inserted the human rhinovirus 3C protease recognition sequence and found that cleavage between S159 and V160 was important to activate CtAtg15(73-475). Our molecular dynamics simulation suggested that the cleavage facilitated conformational change around the active center of CtAtg15, resulting in an exposed state. We confirmed that CtAtg15 could disintegrate S. cerevisiae IAC in vivo. Further, both mitochondria and IAC of S. cerevisiae were disintegrated by CtAtg15. This study suggests Atg15 plays a role in disrupting any organelle membranes delivered to vacuoles by autophagy.

Antimicrobial Potential of Different Isolates of Chaetomium globosum Combined with Liquid Chromatography Tandem Mass Spectrometry Chemical Profiling.

The antimicrobial resistance of pathogenic microorganisms against commercial drugs has become a major problem worldwide. This study is the first of its kind to be carried out in Egypt to produce antimicrobial pharmaceuticals from isolated native taxa of the fungal Chaetomium, followed by a chemical investigation of the existing bioactive metabolites. Here, of the 155 clinical specimens in total, 100 pathogenic microbial isolates were found to be multi-drug resistant (MDR) bacteria. The Chaetomium isolates were recovered from different soil samples, and wild host plants collected from Egypt showed strong inhibitory activity against MDR isolates. Chaetomium isolates displayed broad-spectrum antimicrobial activity against C. albicans, Gram-positive, and Gram-negative bacteria, with inhibition zones of 11.3 to 25.6 mm, 10.4 to 26.0 mm, and 10.5 to 26.5 mm, respectively. As a consecutive result, the minimum inhibitory concentration (MIC) values of Chaetomium isolates ranged from 3.9 to 62.5 µg/mL. Liquid chromatography combined with tandem mass spectrometry (LC-MS/MS) analysis was performed for selected Chaetomium isolates with the most promising antimicrobial potential against MDR bacteria. The LC-MS/MS analysis of Chaetomium species isolated from cultivated soil at Assuit Governate, Upper Egypt (3), and the host plant Zygophyllum album grown in Wadi El-Arbaein, Saint Katherine, South Sinai (5), revealed the presence of alkaloids as the predominant bioactive metabolites. Most detected bioactive metabolites previously displayed antimicrobial activity, confirming the antibacterial potential of selected isolates. Therefore, the Chaetomium isolates recovered from harsh habitats in Egypt are rich sources of antimicrobial metabolites, which will be a possible solution to the multi-drug resistant bacteria tragedy.

Identification and characterization of sugar-regulated promoters in Chaetomium thermophilum.

The thermophilic fungus Chaetomium thermophilum has been used extensively for biochemical and high-resolution structural studies of protein complexes. However, subsequent functional analyses of these assemblies have been hindered owing to the lack of genetic tools compatible with this thermophile, which are typically suited to other mesophilic eukaryotic model organisms, in particular the yeast Saccharomyces cerevisiae. Hence, we aimed to find genes from C. thermophilum that are expressed under the control of different sugars and examine their associated 5' untranslated regions as promoters responsible for sugar-regulated gene expression. To identify sugar-regulated promoters in C. thermophilum, we performed comparative xylose- versus glucose-dependent gene expression studies, which uncovered a number of enzymes with induced expression in the presence of xylose but repressed expression in glucose-supplemented media. Subsequently, we cloned the promoters of the two most stringently regulated genes, the xylosidase-like gene (XYL) and xylitol dehydrogenase (XDH), obtained from this genome-wide analysis in front of a thermostable yellow fluorescent protein (YFP) reporter. With this, we demonstrated xylose-dependent YFP expression by both Western blotting and live-cell imaging fluorescence microscopy. Prompted by these results, we expressed the C. thermophilum orthologue of a well-characterized dominant-negative ribosome assembly factor mutant, under the control of the XDH promoter, which allowed us to induce a nuclear export defect on the pre-60S subunit when C. thermophilum cells were grown in xylose- but not glucose-containing medium. Altogether, our study identified xylose-regulatable promoters in C. thermophilum, which might facilitate functional studies of genes of interest in this thermophilic eukaryotic model organism.

Hexasome-INO80 complex reveals structural basis of noncanonical nucleosome remodeling.

Loss of H2A-H2B histone dimers is a hallmark of actively transcribed genes, but how the cellular machinery functions in the context of noncanonical nucleosomal particles remains largely elusive. In this work, we report the structural mechanism for adenosine 5'-triphosphate-dependent chromatin remodeling of hexasomes by the INO80 complex. We show how INO80 recognizes noncanonical DNA and histone features of hexasomes that emerge from the loss of H2A-H2B. A large structural rearrangement switches the catalytic core of INO80 into a distinct, spin-rotated mode of remodeling while its nuclear actin module remains tethered to long stretches of unwrapped linker DNA. Direct sensing of an exposed H3-H4 histone interface activates INO80, independently of the H2A-H2B acidic patch. Our findings reveal how the loss of H2A-H2B grants remodelers access to a different, yet unexplored layer of energy-driven chromatin regulation.

Caryophyllene Sesquiterpenes from a Chaetomium globosum Endophyte of the Canadian Medicinal Plant Empetrum nigrum.

Punctaporonins T (1) and U (2), new caryophyllene sesquiterpenes, were isolated with three known punctaporonins, A (3), B (4), and C (5), from the endophytic fungus Chaetomium globosum (TC2-041). The structures and relative configurations of punctaporonins T and U were elucidated based on a combination of HRESIMS, 1D/2D NMR spectroscopic analysis, and X-ray diffraction analysis, while their absolute configuration is presumed to be consistent with the co-isolated 3-5 on biogenetic arguments. Compound 1 showed weak inhibitory activity against both Mycobacterium tuberculosis and Staphylococcus aureus.

Conformational dynamics of the RNA binding channel regulates loading and translocation of the DEAH-box helicase Prp43.

The DEAH-box helicase Prp43 has essential functions in pre-mRNA splicing and ribosome biogenesis, remodeling structured RNAs. To initiate unwinding, Prp43 must first accommodate a single-stranded RNA segment into its RNA binding channel. This allows translocation of the helicase on the RNA. G-patch (gp) factors activate Prp43 in its cellular context enhancing the intrinsically low ATPase and RNA unwinding activity. It is unclear how the RNA loading process is accomplished by Prp43 and how it is regulated by its substrates, ATP and RNA, and the G-patch partners. We developed single-molecule (sm) FRET reporters on Prp43 from Chaetomium thermophilum to monitor the conformational dynamics of the RNA binding channel in Prp43 in real-time. We show that the channel can alternate between open and closed conformations. Binding of Pfa1(gp) and ATP shifts the distribution of states towards channel opening, facilitating the accommodation of RNA. After completion of the loading process, the channel remains firmly closed during successive cycles of ATP hydrolysis, ensuring stable interaction with the RNA and processive translocation. Without Pfa1(gp), it remains predominantly closed preventing efficient RNA loading. Our data reveal how the ligands of Prp43 regulate the structural dynamics of the RNA binding channel controlling the initial binding of RNA.

Chaetomium globosum KPC3: An Antagonistic Fungus Against the Potato Cyst Nematode, Globodera rostochiensis.

The potato cyst nematode (Globodera rostochiensis) is one of the most economically important pests of potato (Solanum tuberosum L.), causing significant economic losses worldwide. The identification of biocontrol agents for the sustainable management of G. rostochiensis is crucial. In this study, a potential biocontrol agent, Chaetomium globosum KPC3, was identified based on sequence analysis of the DNA internal transcribed spacer (ITS) region, the translation elongation factor 1-alpha (TEF1-α) gene, and the second largest subunit of the RNA polymerase II (RPB2) gene. The pathogenicity test of C. globosum KPC3 against cysts and second-stage juveniles (J2s) revealed that fungus mycelium fully parasitized the cyst after 72 h of incubation. The fungus was also capable of parasitizing the eggs inside the cysts. The culture filtrate of C. globosum KPC3 caused 98.75% mortality in J2s of G. rostochiensis after 72 h of incubation. The pot experiments showed that the combined application of C. globosum KPC3 as a tuber treatment at a rate of 1 lit kg-1 of tubers and a soil application at a rate of 500 ml kg-1 of farm yard manure (FYM) resulted in significantly lesser reproduction of G. rostochiensis compared to the rest of the treatments. Altogether, C. globosum KPC3 has the potential to be used as a biocontrol agent against G. rostochiensis and can be successfully implemented in integrated pest management programs.

Chemical diversity and biological activities of specialized metabolites from the genus Chaetomium: 2013-2022.

Chaetomium (Chaetomiaceae), a large fungal genus consisting of at least 400 species, has been acknowledged as a promising resource for the exploration of novel compounds with potential bioactivities. Over the past decades, emerging chemical and biological investigations have suggested the structural diversity and extensive potent bioactivity of the specialized metabolites in the Chaetomium species. To date, over 500 compounds with diverse chemical types have been isolated and identified from this genus, including azaphilones, cytochalasans, pyrones, alkaloids, diketopiperazines, anthraquinones, polyketides, and steroids. Biological research has indicated that these compounds possess a broad range of bioactivities, including antitumor, anti-inflammatory, antimicrobial, antioxidant, enzyme inhibitory, phytotoxic, and plant growth inhibitory activities. This paper summarizes current knowledge referring to the chemical structure, biological activity, and pharmacologic potency of the specialized metabolites in the Chaetomium species from 2013 to 2022, which might provide insights for the exploration and utilization of bioactive compounds in this genus both in the scientific field and pharmaceutical industry.

Tricrilactones A-H, Potent Antiosteoporosis Macrolides with Distinctive Ring Skeletons from Trichocladium crispatum, an Alpine Moss-Associated Fungus.

Tricrilactones A-H (1-8), a new family of oligomeric 10-membered macrolides featuring collectively five unique ring skeletons, were isolated from a hitherto unexplored fungus, Trichocladium crispatum. Compounds 1 and 7 contain two unconventional bridged (aza)tricyclic core skeletons, 2, 3, 5, and 6 share an undescribed tetracyclic 9/5/6/6 ring system, 4 bears an uncommon 9/5/6/10/3-fused pentacyclic architecture, and 8 is a dimer bridged by an unexpected C-C linkage. Their structures, including absolute configurations, were elucidated by spectroscopic analysis, quantum chemical calculations, and X-ray diffraction analysis. Importantly, the absolute configuration of the highly flexible side chain of 1 was resolved by the asymmetric synthesis of its four stereoisomers. The intermediate-trapping and isotope labeling experiments facilitated the proposal of the biosynthetic pathway for these macrolides. In addition, their antiosteoporosis effects were evaluated in vivo (zebrafish).

Characterization of chaetoglobosin producing Chaetomium globosum for the management of Fusarium-Meloidogyne wilt complex in tomato.

AIM: Simultaneous management of FOL and RKN causing wilt complex in tomato by chaetoglobosin-producing Chaetomium globosum. METHODS AND RESULTS: Random survey was carried out to isolate Fusarium and Chaetomium. Twelve Fusarium isolates were characterized, and FOL4 (virulent) was molecularly identified. Wilt complex by FOL, RKN was assessed individually and in combination under greenhouse. RKN (1000 juveniles ml-1) inoculation followed by FOL4 (5 × 105 spores ml-1) accounted for 90% incidence. The chaetoglobosin-producing Chaetomium was isolated, characterized morphologically and molecularly. Among 55 isolates, nine showed >50% inhibition against FOL, and crude culture filtrate showed a significant reduction in RKN egg hatching (15.66%) and juvenile mortality (100%). Chaetomium Cg 40 was confirmed as C. globosum using SCAR marker (OK032373). Among 40 volatile compounds, hexadecanoic acid and 1,2-epoxy-5,9-cyclododecadiene exhibited antifungal and nematicidal properties in GC-MS. High-performance liquid chromatography revealed chaetoglobosin A (0.767 µg µl-1), and the presence of bioactive molecules chaetoglobosin (528.25 m/z), chaetomin (710 m/z), chaetocin (692.8 m/z), chaetoviridin (432.85 m/z), and chaetomugilin (390 m/z) was confirmed by LC/MS/MS. Cg 40 and Cg 6 were able to synthesize the pks1a, b gene responsible for chaetoglobosin, sporulation, and melanin biosynthesis was confirmed by PCR. The application of an aqueous formulation as seed treatment, seedling dip, and soil drenching (application) recorded lowest wilt incidence (11.11%) and gall index (1) with the maximum growth parameter (plant height 51.9 cm), fruit yield (287.5 g), and lycopene content (11.46 mg/100 g). CONCLUSIONS: Cg 40 and Cg 6, containing polyketides, secondary metabolites, antibiotics, chaetoglobosin, and plant growth-promoting ability, showed antifungal and nematicidal properties against the FOL-RKN wilt complex in tomato in vitro and pot culture experiments.

Key insights into secondary metabolites from various Chaetomium species.

Endophytic fungi have proved to be a major source of secondary metabolites, wherein the genus Chaetomium has emerged as a source of multifarious bioactive natural compounds belonging to diverse classes such as chaetoglobosins, epipolythiodioxopiperazines, azaphilones, xanthones, anthraquinone, chromones, depsidones, terpenoids, and steroids. The objective of this review is to encapsulate recent findings on various Chaetomium strains, such as C. globosum, C. cupreum, C. elatum, C. subspirale, C. olivaceum, C. indicum, and C. nigricolor known for production of beneficial secondary metabolites, with an insight into their origin and function. A thorough literature survey was conducted for obtaining Chaetomium-derived secondary metabolites, with a scope of future application into drug development efforts. More than 100 secondary metabolites, with various beneficial properties such as antitumor, cytotoxic, antimalarial, and enzyme inhibitory activities, were enlisted. We believe this review will enhance the understanding of beneficial effects conferred by various Chaetomium-derived secondary metabolites and emphasize their potential in serving novel drug development efforts. KEY POINTS: • Identified Chaetomium-derived metabolites with potential for drug development. • More than 100 beneficial metabolites are enlisted. • Benefits include anti-cancerous, antimalarial, and anti-enzymatic properties.

Infective endocarditis caused by Chaetomium globosum.

Chaetomium globosum is a dematiaceous, filamentous fungus belonging to the large genus saprobic ascomycetes and is rarely involved in human infection. We present the case of a 25-year-old man undergoing tricuspid valve replacement due to recurrent prosthetic ring endocarditis. Initially, it was considered culture-negative endocarditis; however, the diagnosis of Chaetomium globosum could only be provided by DNA isolation of the mold isolate grown in culture and the valve tissue samples taken from the patient. This report describes the first documented tricuspid endocarditis caused by Chaetomium species and discusses the importance of molecular tools to enhance the diagnostic process in culture-negative endocarditis, especially for fastidious and nonculturable microorganisms.