Activation of dormant secondary metabolite production by introducing neomycin resistance into the deep-sea fungus, Aspergillus versicolor ZBY-3

Research on the Action and Mechanism of Pharmacological Components of Omphalia lapidescens

Omphalia lapidescens is a macrofungus that is used in traditional Chinese medicine for its insecticidal and stagnation-relieving properties. The active ingredients of this fungus including proteins, polysaccharides and sterols have been demonstrated to exhibit antiparasitic, anti-inflammatory, and antitumor effects. Omphalia has been used in clinical cancer treatment. Many studies on Omphalia have concentrated on its cytotoxicity and anticancer effects. However, the investigation of its natural metabolites remains a significant area for further research. This review presents a comprehensive analysis of the research progress concerning the pharmacological components of Omphalia. The aim of this discussion is to provide a reference for further in-depth study of Omphalia, with the objective of exploring its potential value. Therefore, the focus of this review was on the classification of metabolites in Omphalia and their mechanisms of action.

The role of food preservatives in shaping metabolic profile and chemical sensitivity of fungi - an extensive study on crucial mycological food contaminants from the genus Neosartorya (Aspergillus spp.)

Food preservatives are crucial in fruit production, but fungal resistance is a challenge. The main objective was to compare the sensitivity of Neosartorya spp. isolates to preservatives used in food security applications and to assess the role of metabolic properties in shaping Neosartorya spp. resistance. Sodium metabisulfite, potassium sorbate, sodium bisulfite and sorbic acid showed inhibitory effects, with sodium metabisulfite the most effective. Tested metabolic profiles included fungal growth intensity and utilization of amines and amides, amino acids, polymers, carbohydrates and carboxylic acids. Significant decreases in the utilization of all tested organic compound guilds were observed after fungal exposure to food preservatives compared to the control. Although the current investigation was limited in the number of predominately carbohydrate substrates and the breadth of metabolic responses, extensive sensitivity panels are logical step in establishing a course of action against spoilage agents in food production being important approach for innovative food chemistry.

Secondary metabolites isolated from Trichoderma hamatum b-3 and their fungicidal activity

An undescribed trichodenone derivative (1), two new diketopiperazines (3 and 4) along with a bisabolane analog (2) were isolated from Trichoderma hamatum b-3. The structures of the new findings were established through comprehensive analyses of spectral evidences in HRESIMS, 1D and 2D NMR, Marfey's analysis as well as comparisons of ECD. The absolute configuration of 2 was unambiguously confirmed by NMR, ECD calculation and Mo2(AcO)4 induced circular dichroism. Compounds 1-4 were tested for their fungicidal effects against eight crop pathogenic fungi, among which 1 showed 51% inhibition against Sclerotinia sclerotiorum at a concentration of 50 μg/mL.

Cytotoxic Compounds from Marine Fungi: Sources, Structures, and Bioactivity

Marine fungi, such as species from the Penicillium and Aspergillus genera, are prolific producers of a diversity of natural products with cytotoxic properties. These fungi have been successfully isolated and identified from various marine sources, including sponges, coral, algae, mangroves, sediment, and seawater. The cytotoxic compounds derived from marine fungi can be categorized into five distinct classes: polyketides, peptides, terpenoids and sterols, hybrids, and other miscellaneous compounds. Notably, the pre-eminent group among these compounds comprises polyketides, accounting for 307 out of 642 identified compounds. Particularly, within this collection, 23 out of the 642 compounds exhibit remarkable cytotoxic potency, with IC50 values measured at the nanomolar (nM) or nanogram per milliliter (ng/mL) levels. This review elucidates the originating fungal strains, the sources of isolation, chemical structures, and the noteworthy antitumor activity of the 642 novel natural products isolated from marine fungi. The scope of this review encompasses the period from 1991 to 2023.

How to Completely Squeeze a Fungus-Advanced Genome Mining Tools for Novel Bioactive Substances

Fungal species have the capability of producing an overwhelming diversity of bioactive substances that can have beneficial but also detrimental effects on human health. These so-called secondary metabolites naturally serve as antimicrobial "weapon systems", signaling molecules or developmental effectors for fungi and hence are produced only under very specific environmental conditions or stages in their life cycle. However, as these complex conditions are difficult or even impossible to mimic in laboratory settings, only a small fraction of the true chemical diversity of fungi is known so far. This also implies that a large space for potentially new pharmaceuticals remains unexplored. We here present an overview on current developments in advanced methods that can be used to explore this chemical space. We focus on genetic and genomic methods, how to detect genes that harbor the blueprints for the production of these compounds (i.e., biosynthetic gene clusters, BGCs), and ways to activate these silent chromosomal regions. We provide an in-depth view of the chromatin-level regulation of BGCs and of the potential to use the CRISPR/Cas technology as an activation tool.

Chemical mutagenesis and high throughput media optimization in Tolypocladium inflatum MTCC-3538 leads to enhanced production of cyclosporine A

Diethyl sulphate-based mutagenesis was performed on fungal strain Tolypocladium inflatum MTCC-3538. Two mutant morphotypes MT1-3538 and MT2-3538 were selected for further chemo-profiling studies. LCMS/MS profiling of fungal crude extract confirmed that the wild-type and mutant strains (MT1-3538, MT2-3538) were competent to produce cyclosporine A. MT2-3538 produced 2.1 fold higher cyclosporine A in comparison to the wild type. Further, LCMS-based high throughput media optimization was performed for MT2-3538 in 20 different media combinations to increase cyclosporine A yield. On the basis of ion-intensity profiling, media combination consisting of Glucose 0.1 g/L; Peptone 0.005 g/L and Valine 0.005 g/L was selected and used for up-scaling purpose. Mutant MT2-3538 with optimized media combination increased cyclosporine yield 16 fold and could potentially be exploited for commercial outcomes.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03219-x.

Cleaning the Cellular Factory-Deletion of McrA in Aspergillus oryzae NSAR1 and the Generation of a Novel Kojic Acid Deficient Strain for Cleaner Heterologous Production of Secondary Metabolites

The use of filamentous fungi as cellular factories, where natural product pathways can be refactored and expressed in a host strain, continues to aid the field of natural product discovery. Much work has been done to develop host strains which are genetically tractable, and for which there are multiple selectable markers and controllable expression systems. To fully exploit these strains, it is beneficial to understand their natural metabolic capabilities, as such knowledge can rule out host metabolites from analysis of transgenic lines and highlight any potential interplay between endogenous and exogenous pathways. Additionally, once identified, the deletion of secondary metabolite pathways from host strains can simplify the detection and purification of heterologous compounds. To this end, secondary metabolite production in Aspergillus oryzae strain NSAR1 has been investigated via the deletion of the newly discovered negative regulator of secondary metabolism, mcrA (multicluster regulator A). In all ascomycetes previously studied mcrA deletion led to an increase in secondary metabolite production. Surprisingly, the only detectable phenotypic change in NSAR1 was a doubling in the yields of kojic acid, with no novel secondary metabolites produced. This supports the previous claim that secondary metabolite production has been repressed in A. oryzae and demonstrates that such repression is not McrA-mediated. Strain NSAR1 was then modified by employing CRISPR-Cas9 technology to disrupt the production of kojic acid, generating the novel strain NSARΔK, which combines the various beneficial traits of NSAR1 with a uniquely clean secondary metabolite background.

Identification of antibiotics for use in selection of the chytrid fungi Batrachochytrium dendrobatidis and Batrachochytrium salamandrivorans

Global amphibian populations are being decimated by chytridiomycosis, a deadly skin infection caused by the fungal pathogens Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal). Although ongoing efforts are attempting to limit the spread of these infections, targeted treatments are necessary to manage the disease. Currently, no tools for genetic manipulation are available to identify and test specific drug targets in these fungi. To facilitate the development of genetic tools in Bd and Bsal, we have tested five commonly used antibiotics with available resistance genes: Hygromycin, Blasticidin, Puromycin, Zeocin, and Neomycin. We have identified effective concentrations of each for selection in both liquid culture and on solid media. These concentrations are within the range of concentrations used for selecting genetically modified cells from a variety of other eukaryotic species.

Fermentation for tailoring the technological and health related functionality of food products

Fermented foods are experiencing a resurgence due to the consumers' growing interest in foods that are natural and health promoting. Microbial fermentation is a biotechnological process which transforms food raw materials into palatable, nutritious and healthy food products. Fermentation imparts unique aroma, flavor and texture to food, improves digestibility, degrades anti-nutritional factors, toxins and allergens, converts phytochemicals such as polyphenols into more bioactive and bioavailable forms, and enriches the nutritional quality of food. Fermentation also modifies the physical functional properties of food materials, rendering them differentiated ingredients for use in formulated foods. The science of fermentation and the technological and health functionality of fermented foods is reviewed considering the growing interest worldwide in fermented foods and beverages and the huge potential of the technology for reducing food loss and improving nutritional food security.

The Application of Ribosome Engineering to Natural Product Discovery and Yield Improvement in Streptomyces

Microbial natural product drug discovery and development has entered a new era, driven by microbial genomics and synthetic biology. Genome sequencing has revealed the vast potential to produce valuable secondary metabolites in bacteria and fungi. However, many of the biosynthetic gene clusters are silent under standard fermentation conditions. By rational screening for mutations in bacterial ribosomal proteins or RNA polymerases, ribosome engineering is a versatile approach to obtain mutants with improved titers for microbial product formation or new natural products through activating silent biosynthetic gene clusters. In this review, we discuss the mechanism of ribosome engineering and its application to natural product discovery and yield improvement in Streptomyces. Our analysis suggests that ribosome engineering is a rapid and cost-effective approach and could be adapted to speed up the discovery and development of natural product drug leads in the post-genomic era.

From genomics to metabolomics, moving toward an integrated strategy for the discovery of fungal secondary metabolites

Fungal secondary metabolites are defined by bioactive properties that ensure adaptation of the fungus to its environment. Although some of these natural products are promising sources of new lead compounds especially for the pharmaceutical industry, others pose risks to human and animal health. The identification of secondary metabolites is critical to assessing both the utility and risks of these compounds. Since fungi present biological specificities different from other microorganisms, this review covers the different strategies specifically used in fungal studies to perform this critical identification. Strategies focused on the direct detection of the secondary metabolites are firstly reported. Particularly, advances in high-throughput untargeted metabolomics have led to the generation of large datasets whose exploitation and interpretation generally require bioinformatics tools. Then, the genome-based methods used to study the entire fungal metabolic potential are reported. Transcriptomic and proteomic tools used in the discovery of fungal secondary metabolites are presented as links between genomic methods and metabolomic experiments. Finally, the influence of the culture environment on the synthesis of secondary metabolites by fungi is highlighted as a major factor to consider in research on fungal secondary metabolites. Through this review, we seek to emphasize that the discovery of natural products should integrate all of these valuable tools. Attention is also drawn to emerging technologies that will certainly revolutionize fungal research and to the use of computational tools that are necessary but whose results should be interpreted carefully.

Marine Fungi: Biotechnological Perspectives from Deep-Hypersaline Anoxic Basins

Deep-sea hypersaline anoxic basins (DHABs) are one of the most hostile environments on Earth. Even though DHABs have hypersaline conditions, anoxia and high hydrostatic pressure, they host incredible microbial biodiversity. Among eukaryotes inhabiting these systems, recent studies demonstrated that fungi are a quantitatively relevant component. Here, fungi can benefit from the accumulation of large amounts of organic material. Marine fungi are also known to produce bioactive molecules. In particular, halophilic and halotolerant fungi are a reservoir of enzymes and secondary metabolites with valuable applications in industrial, pharmaceutical, and environmental biotechnology. Here we report that among the fungal taxa identified from the Mediterranean and Red Sea DHABs, halotolerant halophilic species belonging to the genera Aspergillus and Penicillium can be used or screened for enzymes and bioactive molecules. Fungi living in DHABs can extend our knowledge about the limits of life, and the discovery of new species and molecules from these environments can have high biotechnological potential.

Four pairs of proline-containing cyclic dipeptides from Nocardiopsis sp. HT88, an endophytic bacterium of Mallotus nudiflorus L

Strain HT88 was isolated from the fresh stems of Mallotus nudiflorus L, and it was identified as Nocardiopsis sp. by analyzing its morphology and the 16S rRNA sequence. The extracts of fermented HT88 showed potent antimicrobial activities. Bioassay guided separation of extracts led to eight proline (or hydroxyproline, Hyp)-containing cyclic dipeptides. Their structures were determined by 1D and 2D NMR spectroscopy and ESI mass spectrometry and further comparison with existing ¹H and ¹³C NMR, melting points and specific rotation data. The eight 2,5-diketopiperazines (DKPs) were identified as cyclo(L-Pro-L-Leu) (1), cyclo(Pro-Leu) (2), cyclo(L-trans-Hyp-L-Leu) (3), cyclo(D-trans-Hyp-D-Leu) (4), and cyclo(D-Pro-L-Phe) (5), cyclo(L-Pro-L-Phe) (6), and cyclo(D-cis-Hyp-L-Phe) (7), cyclo(L-trans-Hyp-L-Phe) (8), respectively. Up to date, this is the first isolation of four pairs of proline based DKPs from Nocardiopsis sp.

Four new antitumor metabolites isolated from a mutant 3-f-31 strain derived from Penicillium purpurogenum G59

Penicimutanolones A (1) and B (2), penicimutanolone A methyl ether (3), and penicimumide (4), four new antitumor metabolites, were isolated from a neomycin-resistant mutant of the marine-derived fungus Penicillium purpurogenum G59. The structures of the compounds were elucidated by spectroscopic methods, and the absolute configurations were determined by X-ray crystallography and calculated ECD. In MTT and SRB assays, compounds 1-3 showed strong inhibitory effects on 14 human cancer cell lines. Compounds 1 and 2 maybe induce apoptosis of cancer cells mainly due to the inhibition of the expression of survivin, a client protein of HSP90. In addition, in vivo antitumor activity was observed for compound 1 in murine sarcoma HCT116 tumor-bearing Kunming mice, using docetaxel as a positive control.

Marine Fungi: A Source of Potential Anticancer Compounds

Metabolites from marine fungi have hogged the limelight in drug discovery because of their promise as therapeutic agents. A number of metabolites related to marine fungi have been discovered from various sources which are known to possess a range of activities as antibacterial, antiviral and anticancer agents. Although, over a thousand marine fungi based metabolites have already been reported, none of them have reached the market yet which could partly be related to non-comprehensive screening approaches and lack of sustained lead optimization. The origin of these marine fungal metabolites is varied as their habitats have been reported from various sources such as sponge, algae, mangrove derived fungi, and fungi from bottom sediments. The importance of these natural compounds is based on their cytotoxicity and related activities that emanate from the diversity in their chemical structures and functional groups present on them. This review covers the majority of anticancer compounds isolated from marine fungi during 2012-2016 against specific cancer cell lines.

Strategies to diversify natural products for drug discovery

Natural product libraries contain specialized metabolites derived from plants, animals, and microorganisms that play a pivotal role in drug discovery due to their immense structural diversity and wide variety of biological activities. The strategies to greatly extend natural product scaffolds through available biological and chemical approaches offer unique opportunities to access a new series of natural product analogues, enabling the construction of diverse natural product-like libraries. The affordability of these structurally diverse molecules has been a crucial step in accelerating drug discovery. This review provides an overview of various approaches to exploit the diversity of compounds for natural product-based drug development, drawing upon a series of examples to illustrate each strategy.

Secondary metabolites from endophytic fungus Chaetomium sp. induce colon cancer cell apoptotic death

A rare depsipeptide, chaetomiamide A (1), together with two known diketopiperazines (2, 3) were isolated from the cultures of endophytic fungus Chaetomium sp., which was isolated from the root of Cymbidium goeringii. Compound 1 represents a rare skeleton with a 13-membered ring system. It structure was established on the basis of spectroscopic data interpretation. The configuration of 1 was determined by NOESY and Marfey's analysis. These isolates were evaluated for anticancer activity and 3 displayed more potent cytotoxicity than the positive control cisplatin associated with G2/M cell cycle arrest. In addition, 3 induced apoptosis via caspase-3 induction and PARP cleavage, concomitantly with the increase of Bax and decrease of Bcl-2.

Diketopiperazines as Cross-Communication Quorum-Sensing Signals between Cronobacter sakazakii and Bacillus cereus

Herein, we reveal a second quorum-sensing system produced by Cronobacter sakazakii. A cyclo(l-Pro-l-Leu) diketopiperazine, detected in pure and mixed cultures of C. sakazakii and Bacillus cereus explains the coexistence of both in the same industrial environments. The molecule was identified by gas chromatography-mass spectrometry (GC-MS), ¹H, and ¹³C NMR, including 2D NMR (correlation spectroscopy, heteronuclear multiple bond correlation, and heteronuclear single quantum correlation), and the absolute configuration was compared with that of four synthetic standards produced by solid phase peptide synthesis using a chiral column on a GC-flame ionization detection. This article provides a new method to determine the absolute configuration of cyclo(Pro-Leu) diketopiperazine replacing the joint use of ¹H NMR and Marfey's method.

Penicimutamides D–E: two new prenylated indole alkaloids from a mutant of the marine-derived Penicillium purpurogenum G59

Two new prenylated indole alkaloids, penicimutamides D–E (1–2), were discovered via activating silent pathways in a marine-derived fungus.

Marine natural products

This review covers the literature published in 2014 for marine natural products (MNPs), with 1116 citations (753 for the period January to December 2014) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1378 in 456 papers for 2014), together with the relevant biological activities, source organisms and country of origin. Reviews, biosynthetic studies, first syntheses, and syntheses that lead to the revision of structures or stereochemistries, have been included.

A novel oxaphenalenone, penicimutalidine: activated production of oxaphenalenones by the diethyl sulphate mutagenesis of marine-derived fungus Penicillium purpurogenum G59

One new (1) and three known oxaphenalenones (2–4) were obtained by activating silent pathways in a marine-derived fungus.

Chromosulfine, a novel cyclopentachromone sulfide produced by a marine-derived fungus after introduction of neomycin resistance

The discovery of chromosulfine, a novel cyclopentachromone sulfide generated by activating silent fungal pathways in a marine-derived fungus, was reported.

Penicimutamides A–C: rare carbamate-containing alkaloids from a mutant of the marine-derived Penicillium purpurogenum G59

Three new and rare carbamate-containing penicimutamides A–C (1–3) were discovered via activating silent pathways in a marine-derived fungus.

Rare Chromones from a Fungal Mutant of the Marine-Derived Penicillium purpurogenum G59

Three new and rare chromones, named epiremisporine B (2), epiremisporine B1 (3) and isoconiochaetone C (4), along with three known remisporine B (1), coniochaetone A (5) and methyl 8-hydroxy-6-methyl-9-oxo-9H-xanthene-1-carboxylate (6) were isolated from a mutant from the diethyl sulfate (DES) mutagenesis of a marine-derived Penicillium purpurogenum G59. The structures of 2–4 including the absolute configurations were determined by spectroscopic methods, especially by NMR analysis and electronic circular dichroism (ECD) experiments in conjunction with calculations. The absolute configuration of the known remisporine B (1) was determined for the first time. Compounds 2 and 3 have a rare feature that has only been reported in one example so far. The compounds 1–6 were evaluated for their cytotoxicity against several human cancer cell lines. The present work explored the great potential of our previous DES mutagenesis strategy for activating silent fungal pathways, which has accelerated the discovery of new bioactive compounds.

A Brief Review of Bioactive Metabolites Derived from Deep-Sea Fungi

Deep-sea fungi, the fungi that inhabit the sea and the sediment at depths of over 1000 m below the surface, have become an important source of industrial, agricultural, and nutraceutical compounds based on their diversities in both structure and function. Since the first study of deep-sea fungi in the Atlantic Ocean at a depth of 4450 m was conducted approximately 50 years ago, hundreds of isolates of deep-sea fungi have been reported based on culture-dependent methods. To date more than 180 bioactive secondary metabolites derived from deep-sea fungi have been documented in the literature. These include compounds with anticancer, antimicrobial, antifungal, antiprotozoal, and antiviral activities. In this review, we summarize the structures and bioactivities of these metabolites to provide help for novel drug development.

Activation of the silent secondary metabolite production by introducing neomycin-resistance in a marine-derived Penicillium purpurogenum G59

Introduction of neomycin-resistance into a marine-derived, wild-type Penicillium purpurogenum G59 resulted in activation of silent biosynthetic pathways for the secondary metabolite production. Upon treatment of G59 spores with neomycin and dimethyl sulfoxide (DMSO), a total of 56 mutants were obtained by single colony isolation. The acquired resistance of mutants to neomycin was testified by the resistance test. In contrast to the G59 strain, the EtOAc extracts of 28 mutants inhibited the human cancer K562 cells, indicating that the 28 mutants have acquired the capability to produce bioactive metabolites. HPLC-photodiode array detector (PDAD)-UV and HPLC-electron spray ionization (ESI)-MS analyses further indicated that diverse secondary metabolites have been newly produced in the bioactive mutant extracts. Followed isolation and characterization demonstrated that five bioactive secondary metabolites, curvularin (1), citrinin (2), penicitrinone A (3), erythro-23-O-methylneocyclocitrinol (4) and 22E-7α-methoxy-5α,6α-epoxyergosta-8(14),22-dien-3β-ol (5), were newly produced by a mutant, 4-30, compared to the G59 strain. All 1–5 were also not yet found in the secondary metabolites of other wild type P. purpurogenum strains. Compounds 1–5 inhibited human cancer K562, HL-60, HeLa and BGC-823 cells to varying extents. Both present bioassays and chemical investigations demonstrated that the introduction of neomycin-resistance into the marine-derived fungal G59 strain could activate silent secondary metabolite production. The present work not only extended the previous DMSO-mediated method for introducing drug-resistance in fungi both in DMSO concentrations and antibiotics, but also additionally exemplified effectiveness of this method for activating silent fungal secondary metabolites. This method could be applied to other fungal isolates to elicit their metabolic potentials to investigate secondary metabolites from silent biosynthetic pathways.

The synthesis and antitumor activity of twelve galloyl glucosides

Twelve galloyl glucosides 1-12, showing diverse substitution patterns with two or three galloyl groups, were synthesized using commercially available, low-cost D-glucose and gallic acid as starting materials. Among them, three compounds, methyl 3,6-di-O-galloyl-α-D-glucopyranoside (9), ethyl 2,3-di-O-galloyl-α-D-glucopyranoside (11) and ethyl 2,3-di-O-galloyl-β-D-glucopyranoside (12), are new compounds and other six, 1,6-di-O-galloyl-β-D-glucopyranose (1), 1,4,6-tri-O-galloyl-β-D-glucopyranose (2), 1,2-di-O-galloyl-β-D-glucopyranose (3), 1,3-di-O-galloyl-β-D-glucopyranose (4), 1,2,3-tri-O-galloyl-α-D-glucopyranose (6) and methyl 3,4,6-tri-O-galloyl-α-D-glucopyranoside (10), were synthesized for the first time in the present study. In in vitro MTT assay, 1-12 inhibited human cancer K562, HL-60 and HeLa cells with inhibition rates ranging from 64.2% to 92.9% at 100 μg/mL, and their IC50 values were determined to be varied in 17.2-124.7 μM on the tested three human cancer cell lines. In addition, compounds 1-12 inhibited murine sarcoma S180 cells with inhibition rates ranging from 38.7% to 52.8% at 100 μg/mL in the in vitro MTT assay, and in vivo antitumor activity of 1 and 2 was also detected in murine sarcoma S180 tumor-bearing Kunming mice using taxol as positive control.