Antibacterial diphenyl ether production induced by co-culture of Aspergillus nidulans and Aspergillus fumigatus

Bioinformatics assisted construction of the link between biosynthetic gene clusters and secondary metabolites in fungi

Fungal secondary metabolites are considered as important resources for drug discovery. Despite various methods being employed to facilitate the discovery of new fungal secondary metabolites, the trend of identifying novel secondary metabolites from fungi is inevitably slowing down. Under laboratory conditions, the majority of biosynthetic gene clusters, which store information for secondary metabolites, remain inactive. Therefore, establishing the link between biosynthetic gene clusters and secondary metabolites would contribute to understanding the genetic logic underlying secondary metabolite biosynthesis and alleviating the current challenges in discovering novel natural products. Bioinformatics methods have garnered significant attention due to their powerful capabilities in data mining and analysis, playing a crucial role in various aspects. Thus, we have summarized successful cases since 2016 in which bioinformatics methods were utilized to establish the link between fungal biosynthetic gene clusters and secondary metabolites, focusing on their biosynthetic gene clusters and associated secondary metabolites, with the goal of aiding the field of natural product discovery.

New natural products from Aspergillus candidus NRRL 5214 and their glycosylation by Streptomyces chromofuscus ATCC 49982

Fungi represent a rich source of bioactive natural products. In this study, we present the isolation and identification of two new diphenyl ethers, named aspergilluscandidus A (1) and aspergilluscandidus B (2), along with a known compound terphenyllin (3), from the fungal strain Aspergillus candidus NRRL 5214. The chemical structures of compounds 1-3 were characterized through extensive 1D and 2D NMR analysis. Compounds 1 and 3 were subsequently biotransformed into two new glycosides, namely aspergilluscandidus C (4) and terphenyllin-4″-O-β-d-glucuronide (5) by the actinomycete strain Streptomyces chromofuscus ATCC 49982. The cytotoxicity assay revealed that the glycosylated products 4 and 5 exhibited significantly improved activity against the glioblastoma 33 cell line compared to their respective substrates, decreasing the IC50 from 8.15 ± 1.09 μM (1) to 5.41 ± 0.30 μM (4) and from 88.29 ± 10.54 μM (3) to 31.25 ± 4.20 μM (5), respectively. Our study emphasizes A. candidus NRRL 5214 as a promising source of new natural products and presents an effective strategy for modifying both diphenyl ether and p-terphenyl compounds using S. chromofuscus ATCC 49982 to enhance their cytotoxicity activity.

Rediscovery of viomellein as an antibacterial compound and identification of its biosynthetic gene cluster in dermatophytes

Fungi produce a wide variety of compounds, especially those that exhibit biological activity. Such compounds may aid the survival of fungi in the environment or may contribute to host infection for pathogenic species. Regarding dermatophytes, which affect a large number of patients worldwide, studies on metabolites that exhibit biological activity are scarce. In this study, to gain insight into the interaction with skin microbiota at the site of infection, we searched for compounds that exhibit antibacterial activity among the metabolites of Trichophyton rubrum. We rediscovered viomellein, a red pigment, as a potent antibacterial compound and identified its biosynthetic gene (vio) cluster by RNA-sequencing and gene deletion analyses. Sequential reconstruction of the vio cluster genes in Aspergillus oryzae revealed the biosynthetic pathway for viomellein via nor-toralactone, semivioxanthin, and vioxanthin production. The vio gene cluster is widely conserved among dermatophytes and is also present in some Aspergillus and Penicillium species. Consistent with the results, viomellein and its structural analogs, xanthomegnin, and vioxanthin, were shown to be produced by most dermatophyte species. These results suggest that dermatophytes can produce diverse naphthopyranone compounds, some of which have strong growth inhibitory effects against bacteria. This study provides a previously unknown molecular entity for antibiotic production by dermatophytes and provides insight into the interaction between commensal bacteria and dermatophytes.IMPORTANCEDermatophytes are widespread human pathogens in the world, but the mechanisms of infection have been little studied. Although bacterial density at the site of infection is abundant, interaction between dermatophytes and the bacterial community has not yet been studied. Here, to understand the infection ecology of dermatophytes, we searched for antimicrobial substances that would be effective against the dermal bacterial community. We discovered viomellein, which exhibits strong antibacterial activity against gram-positive bacteria such as Staphylococcus aureus, and its biosynthetic genes are shared not only by dermatophytes but also by other fungi. Since many dermatophytes showed the ability to produce viomellein, it is likely that this is the initial infection strategy of dermatophytes, which has been a mystery for long.

Engineering microbial metabolic homeostasis for chemicals production

Microbial-based bio-refining promotes the development of a biotechnology revolution to encounter and tackle the enormous challenges in petroleum-based chemical production by biomanufacturing, biocomputing, and biosensing. Nevertheless, microbial metabolic homeostasis is often incompatible with the efficient synthesis of bioproducts mainly due to: inefficient metabolic flow, robust central metabolism, sophisticated metabolic network, and inevitable environmental perturbation. Therefore, this review systematically summarizes how to optimize microbial metabolic homeostasis by strengthening metabolic flux for improving biotransformation turnover, redirecting metabolic direction for rewiring bypass pathway, and reprogramming metabolic network for boosting substrate utilization. Future directions are also proposed for providing constructive guidance on the development of industrial biotechnology.

Aspergillus-Penicillium co-culture: An investigation of bioagents for controlling Fusarium proliferatum-induced basal rot in onion

Fungal co-culture is a method that allows the detection of interactions between fungi, enabling the examination of bioactive novel metabolites induction that may not be produced in monocultures. Worldwide, Fusarium basal rot is a primary limitation to onion yield, being caused by different Fusarium species. Current research directions encourage biological control of plant diseases as a replacement for routine chemical treatments. The current study aimed to investigate the co-culturing technique for mining new sources of bioagents that could be used as fungicides. Aspergillus ochraceus AUMC15539 was co-cultured with Penicillium chrysogenum AUMC15504, and their ethyl acetate extract was tested in vitro and in a greenhouse against Fusarium proliferatum AUMC15541. The results showed that Aspergillus-Penicillium (AP) co-culture extract significantly inhibited the growth of F. proliferatum with an MIC value of 0.78 mg/mL and showed antioxidant efficiency with an IC50 value of 1.31 mg/mL. The brine shrimp toxicity testing showed a LC50 value of 2.77 mg/mL. In addition, the co-culture extract showed the highest phenolic content at 114.71 GAE mg/g, with a 27.82 QE mg/g flavonoid content. Profiling of AP co-culture and its monoculture extracts by HPLC revealed a change in the metabolites profile in AP co-culture. Principal component analysis verified a positive correlation between the obtained HPLC data of A. ochraceus (A), P. chrysogenum (P), and AP extracts. Greenhouse experiments demonstrated that treating infected onion plants with the AP co-culture extract significantly enhanced all growth parameters. Additionally, the co-culture extract treatment resulted in the highest levels of total pigments (3.46 mg/g), carbohydrates (52.10 mg/g dry weight), proteins (131.44 mg/g), phenolics (41.66 GAE mg/g), and flavonoids (9.43 QE mg/g) compared with other treatments. This indicates a promising potential for fungal co-cultures in discovering new bioagents with antifungal properties and growth-promoting capabilities.

Interspecific cross-talk: The catalyst driving microbial biosynthesis of secondary metabolites

Microorganisms co-exist and co-evolve in nature, forming intricate ecological communities. The interspecies cross-talk within these communities creates and sustains their great biosynthetic potential, making them an important source of natural medicines and high-value-added chemicals. However, conventional investigations into microbial metabolites are typically carried out in pure cultures, resulting in the absence of specific activating factors and consequently causing a substantial number of biosynthetic gene clusters to remain silent. This, in turn, hampers the in-depth exploration of microbial biosynthetic potential and frequently presents researchers with the challenge of rediscovering compounds. In response to this challenge, the coculture strategy has emerged to explore microbial biosynthetic capabilities and has shed light on the study of cross-talk mechanisms. These elucidated mechanisms will contribute to a better understanding of complex biosynthetic regulations and offer valuable insights to guide the mining of secondary metabolites. This review summarizes the research advances in microbial cross-talk mechanisms, with a particular focus on the mechanisms that activate the biosynthesis of secondary metabolites. Additionally, the instructive value of these mechanisms for developing strategies to activate biosynthetic pathways is discussed. Moreover, challenges and recommendations for conducting in-depth studies on the cross-talk mechanisms are presented.

Novel fungal diphenyl ether biosynthetic gene clusters encode a promiscuous oxidase for elevated antibacterial activities

Diphenyl ethers (DPEs) are produced by filamentous fungi using polyketide synthases (PKSs) directly, or via Cu oxidase-catalyzed oxidative rearrangements of benzophenone intermediates. Here, we use heterologous expression to reveal a third route towards DPEs in Preussia isomera that relies on an oxidative multienzyme cascade to convert a PKS-generated, ester-linked didepside to depsidones and further to DPEs, and apply comparative genomics to identify conserved biosynthetic gene clusters for this pathway in multiple fungi. The distribution of DPE products is modulated by the expression chassis upon pathway reconstitution. Among the post-PKS enzymes, the DpeH tyrosinase shows considerable substrate promiscuity towards synthetic DPE analogues. By creating hybrid enzymes with a DpeH orthologue from Aspergillus nidulans, we identify the C-terminal region of DpeH to alter substrate recognition. Our work highlights an evolutionarily conserved way to produce DPEs, and provides enzymatic tools to generate DPE analogues with broad spectrum antibiotic activity against multidrug-resistant human pathogens.

Antarctic fungi produce pigment with antimicrobial and antiparasitic activities

Natural pigments have received special attention from the market and industry as they could overcome the harm to health and the environmental issues caused by synthetic pigments. These pigments are commonly extracted from a wide range of organisms, and when added to products they can alter/add new physical-chemical or biological properties to them. Fungi from extreme environments showed to be a promising source in the search for biomolecules with antimicrobial and antiparasitic potential. This study aimed to isolate fungi from Antarctic soils and screen them for pigment production with antimicrobial and antiparasitic potential, together with other previously isolated strains A total of 52 fungi were isolated from soils in front of the Collins Glacier (Southeast border). Also, 106 filamentous fungi previously isolated from the Collins Glacier (West border) were screened for extracellular pigment production. Five strains were able to produce extracellular pigments and were identified by ITS sequencing as Talaromyces cnidii, Pseudogymnoascus shaanxiensis and Pseudogymnoascus sp. All Pseudogymnoascus spp. (SC04.P3, SC3.P3, SC122.P3 and ACF093) extracts were able to inhibit S. aureus ATCC6538 and two (SC12.P3, SC32.P3) presented activity against Leishmania (L.) infantum, Leishmania amazonensis and Trypanossoma cruzii. Extracts compounds characterization by UPLC-ESI-QToF analysis confirmed the presence of molecules with biological activity such as: Asterric acid, Violaceol, Mollicellin, Psegynamide A, Diorcinol, Thailandolide A. In conclusion, this work showed the potential of Antartic fungal strains from Collins Glacier for bioactive molecules production with activity against Gram positive bacteria and parasitic protozoas.

Computation-aided studies related to the induction of specialized metabolite biosynthesis in microbial co-cultures: An introductory overview

Co-cultivation is an effective method of inducing the production of specialized metabolites (SMs) in microbial strains. By mimicking the ecological interactions that take place in natural environment, this approach enables to trigger the biosynthesis of molecules which are not formed under monoculture conditions. Importantly, microbial co-cultivation may lead to the discovery of novel chemical entities of pharmaceutical interest. The experimental efforts aimed at the induction of SMs are greatly facilitated by computational techniques. The aim of this overview is to highlight the relevance of computational methods for the investigation of SM induction via microbial co-cultivation. The concepts related to the induction of SMs in microbial co-cultures are briefly introduced by addressing four areas associated with the SM induction workflows, namely the detection of SMs formed exclusively under co-culture conditions, the annotation of induced SMs, the identification of SM producer strains, and the optimization of fermentation conditions. The computational infrastructure associated with these areas, including the tools of multivariate data analysis, molecular networking, genome mining and mathematical optimization, is discussed in relation to the experimental results described in recent literature. The perspective on the future developments in the field, mainly in relation to the microbiome-related research, is also provided.

Aspergillus co-cultures: A recent insight into their secondary metabolites and microbial interactions

There is an urgent need for novel antibiotics to combat emerging resistant microbial strains. One of the most pressing resources is Aspergillus microbial cocultures. The genome of Aspergillus species comprises a far larger number of novel gene clusters than previously expected, and novel strategies and approaches are essential to exploit this potential source of new drugs and pharmacological agents. This is the first review consulting recent developments and chemical diversity of Aspergillus cocultures and highlighting its untapped richness. The analyzed data revealed that cocultivation of several Aspergillus species with other microorganisms, including bacteria, plants, and fungi, is a source of novel bioactive natural products. Various vital chemical skeleton leads were newly produced or augmented in Aspergillus cocultures, among which were taxol, cytochalasans, notamides, pentapeptides, silibinin, and allianthrones. The possibility of mycotoxin production or complete elimination in cocultivations was detected, which pave the way for better decontamination strategies. Most cocultures revealed a remarkable improvement in their antimicrobial or cytotoxic behavior due to their produced chemical patterns; for instance, weldone and asperterrin whose antitumor and antibacterial activities, respectively, were superior. Microbial cocultivation elicited the upregulation or production of specific metabolites whose importance and significance are yet to be revealed. With more than 155 compounds isolated from Aspergillus cocultures in the last 10 years, showing overproduction, reduction, or complete suppression under the optimized coculture circumstances, this study filled a gap for medicinal chemists searching for new lead sources or bioactive molecules as anticancer agents or antimicrobials.

Unlocking the magic in mycelium: Using synthetic biology to optimize filamentous fungi for biomanufacturing and sustainability

Filamentous fungi drive carbon and nutrient cycling across our global ecosystems, through its interactions with growing and decaying flora and their constituent microbiomes. The remarkable metabolic diversity, secretion ability, and fiber-like mycelial structure that have evolved in filamentous fungi have been increasingly exploited in commercial operations. The industrial potential of mycelial fermentation ranges from the discovery and bioproduction of enzymes and bioactive compounds, the decarbonization of food and material production, to environmental remediation and enhanced agricultural production. Despite its fundamental impact in ecology and biotechnology, molds and mushrooms have not, to-date, significantly intersected with synthetic biology in ways comparable to other industrial cell factories (e.g. Escherichia coli,Saccharomyces cerevisiae, and Komagataella phaffii). In this review, we summarize a suite of synthetic biology and computational tools for the mining, engineering and optimization of filamentous fungi as a bioproduction chassis. A combination of methods across genetic engineering, mutagenesis, experimental evolution, and computational modeling can be used to address strain development bottlenecks in established and emerging industries. These include slow mycelium growth rate, low production yields, non-optimal growth in alternative feedstocks, and difficulties in downstream purification. In the scope of biomanufacturing, we then detail previous efforts in improving key bottlenecks by targeting protein processing and secretion pathways, hyphae morphogenesis, and transcriptional control. Bringing synthetic biology practices into the hidden world of molds and mushrooms will serve to expand the limited panel of host organisms that allow for commercially-feasible and environmentally-sustainable bioproduction of enzymes, chemicals, therapeutics, foods, and materials of the future.

Aspergillus nidulans—Natural Metabolites Powerhouse: Structures, Biosynthesis, Bioactivities, and Biotechnological Potential

Nowadays, finding out new natural scaffolds of microbial origin increases at a higher rate than in the past decades and represents an auspicious route for reinvigorating the pool of compounds entering pharmaceutical industries. Fungi serve as a depository of fascinating, structurally unique metabolites with considerable therapeutic significance. Aspergillus genus represents one of the most prolific genera of filamentous fungi. Aspergillus nidulans Winter G. is a well-known and plentiful source of bioactive metabolites with abundant structural diversity, including terpenoids, benzophenones, sterols, alkaloids, xanthones, and polyketides, many of which display various bioactivities, such as cytotoxicity, antioxidant, anti-inflammatory, antiviral, and antimicrobial activities. The current work is targeted to survey the reported literature on A. nidulans, particularly its metabolites, biosynthesis, and bioactivities, in addition to recent reports on its biotechnological potential. From 1953 till November 2022, relying on the stated data, 206 metabolites were listed, with more than 100 references.

Enhancing chemical and biological diversity by co-cultivation

In natural product research, microbial metabolites have tremendous potential to provide new therapeutic agents since extremely diverse chemical structures can be found in the nearly infinite microbial population. Conventionally, these specialized metabolites are screened by single-strain cultures. However, owing to the lack of biotic and abiotic interactions in monocultures, the growth conditions are significantly different from those encountered in a natural environment and result in less diversity and the frequent re-isolation of known compounds. In the last decade, several methods have been developed to eventually understand the physiological conditions under which cryptic microbial genes are activated in an attempt to stimulate their biosynthesis and elicit the production of hitherto unexpressed chemical diversity. Among those, co-cultivation is one of the most efficient ways to induce silenced pathways, mimicking the competitive microbial environment for the production and holistic regulation of metabolites, and has become a golden methodology for metabolome expansion. It does not require previous knowledge of the signaling mechanism and genome nor any special equipment for cultivation and data interpretation. Several reviews have shown the potential of co-cultivation to produce new biologically active leads. However, only a few studies have detailed experimental, analytical, and microbiological strategies for efficiently inducing bioactive molecules by co-culture. Therefore, we reviewed studies applying co-culture to induce secondary metabolite pathways to provide insights into experimental variables compatible with high-throughput analytical procedures. Mixed-fermentation publications from 1978 to 2022 were assessed regarding types of co-culture set-ups, metabolic induction, and interaction effects.