Huanglongmycin A-C, Cytotoxic Polyketides Biosynthesized by a Putative Type II Polyketide Synthase From Streptomyces sp. CB09001

Herbidomicins, two pairs of polyketide tautomers produced by an actinomycete of the genus Herbidospora

Herbidospora is one of the underexplored actinomycete genera from which only a limited number of secondary metabolites are reported. In our continuing investigation on less explored actinomycetes, a liquid culture of Herbidospora sp. RD 11066 was found to contain unknown metabolites that had no match in our in-house UV database. Chromatographic separation and following structural analysis using NMR and MS identified these metabolites to be chromanone and chromene derivatives, which were respectively composed of an inseparable mixture of two isomeric forms. The former polyketides, designated to be herbidomicins A1 (1) and A2 (2), are positional isomers in terms of a methyl substituent on an aromatic ring that mutually interconvert by acetal exchange by two phenolic hydroxy groups. The latter pair, herbidomicins B1 (3) and B2 (4), is Z/E-isomers regarding an enol ether double bond. Herbidomicins 1-4 were weakly antifungal against a dermatophytic fungus Trichophyton rubrum and were moderately cytotoxic against murine leukemia P388 cells.

Bioactive Naphthoquinone and Phenazine Analogs from the Endophytic Streptomyces sp. PH9030 as α-Glucosidase Inhibitors

A talented endophytic Streptomyces sp. PH9030 is derived from the medicinal plant Kadsura coccinea (Lem.) A.C. Smith. The undescribed naphthoquinone naphthgeranine G (5) and seven previously identified compounds, 6-12, were obtained from Streptomyces sp. PH9030. The structure of 5 was identified by comprehensive examination of its HRESIMS, 1D NMR, 2D NMR and ECD data. The inhibitory activities of all the compounds toward α-glucosidase and their antibacterial properties were investigated. The α-glucosidase inhibitory activities of 5, 6, 7 and 9 were reported for the first time, with IC50 values ranging from 66.4 ± 6.7 to 185.9 ± 0.2 μM, as compared with acarbose (IC50 = 671.5 ± 0.2 μM). The molecular docking and molecular dynamics analysis of 5 with α-glucosidase further indicated that it may have a good binding ability with α-glucosidase. Both 9 and 12 exhibited moderate antibacterial activity against methicillin-resistant Staphylococcus aureus, with minimum inhibitory concentration (MIC) values of 16 μg/mL. These results indicate that 5, together with the naphthoquinone scaffold, has the potential to be further developed as a possible inhibitor of α-glucosidase.

The geomicrobiology of limestone, sulfuric acid speleogenetic, and volcanic caves: basic concepts and future perspectives

Caves are ubiquitous subterranean voids, accounting for a still largely unexplored surface of the Earth underground. Due to the absence of sunlight and physical segregation, caves are naturally colonized by microorganisms that have developed distinctive capabilities to thrive under extreme conditions of darkness and oligotrophy. Here, the microbiomes colonizing three frequently studied cave types, i.e., limestone, sulfuric acid speleogenetic (SAS), and lava tubes among volcanic caves, have comparatively been reviewed. Geological configurations, nutrient availability, and energy flows in caves are key ecological drivers shaping cave microbiomes through photic, twilight, transient, and deep cave zones. Chemoheterotrophic microbial communities, whose sustenance depends on nutrients supplied from outside, are prevalent in limestone and volcanic caves, while elevated inorganic chemical energy is available in SAS caves, enabling primary production through chemolithoautotrophy. The 16S rRNA-based metataxonomic profiles of cave microbiomes were retrieved from previous studies employing the Illumina platform for sequencing the prokaryotic V3-V4 hypervariable region to compare the microbial community structures from different cave systems and environmental samples. Limestone caves and lava tubes are colonized by largely overlapping bacterial phyla, with the prevalence of Pseudomonadota and Actinomycetota, whereas the co-dominance of Pseudomonadota and Campylobacterota members characterizes SAS caves. Most of the metataxonomic profiling data have so far been collected from the twilight and transient zones, while deep cave zones remain elusive, deserving further exploration. Integrative approaches for future geomicrobiology studies are suggested to gain comprehensive insights into the different cave types and zones. This review also poses novel research questions for unveiling the metabolic and genomic capabilities of cave microorganisms, paving the way for their potential biotechnological applications.

Genus Streptomyces: Recent advances for biotechnological purposes

Actinomycetes are a distinct group of filamentous bacteria. The Streptomyces genus within this group has been extensively studied over the years, with substantial contributions to society and science. This genus is known for its antimicrobial production, as well as antitumor, biopesticide, and immunomodulatory properties. Therefore, the extraordinary plasticity of the Streptomyces genus has inspired new research techniques. The newest way of exploring Streptomyces has comprised the discovery of new natural metabolites and the application of emerging tools such as CRISPR technology in drug discovery. In this narrative review, we explore relevant published literature concerning the ongoing novelties of the Streptomyces genus.

Antifungal metabolites, their novel sources, and targets to combat drug resistance

Excessive antibiotic prescriptions as well as their misuse in agriculture are the main causes of antimicrobial resistance which poses a growing threat to public health. It necessitates the search for novel chemicals to combat drug resistance. Since ancient times, naturally occurring medicines have been employed and the enormous variety of bioactive chemicals found in nature has long served as an inspiration for researchers looking for possible therapeutics. Secondary metabolites from microorganisms, particularly those from actinomycetes, have made it incredibly easy to find new molecules. Different actinomycetes species account for more than 70% of naturally generated antibiotics currently used in medicine, and they also produce a variety of secondary metabolites, including pigments, enzymes, and anti-inflammatory compounds. They continue to be a crucial source of fresh chemical diversity and a crucial component of drug discovery. This review summarizes some uncommon sources of antifungal metabolites and highlights the importance of further research on these unusual habitats as a source of novel antimicrobial molecules.

Cave Microbes as a Potential Source of Drugs Development in the Modern Era

The world is constantly facing threats, including the emergence of new pathogens and antibiotic resistance among extant pathogens, which is a matter of concern. Therefore, the need for natural and effective sources of drugs is inevitable. The ancient and pristine ecosystems of caves contain a unique microbial world and could provide a possible source of antimicrobial metabolites. The association between humans and caves is as old as human history itself. Historically, cave environments have been used to treat patients with respiratory tract infections, which is referred to as speleotherapy. Today, the pristine environment of caves that comprise a poorly explored microbial world is a potential source of antimicrobial and anticancer drugs. Oligotrophic conditions in caves enhance the competition among microbial communities, and unique antimicrobial agents may be used in this competition. This review suggests that the world needs a novel and effective source of drug discovery. Therefore, being the emerging spot of modern human civilization, caves could play a crucial role in the current medical crisis, and cave microorganisms may have the potential to produce novel antimicrobial and anticancer drugs.

Microbial roles in cave biogeochemical cycling

Among fundamental research questions in subterranean biology, the role of subterranean microbiomes playing in key elements cycling is a top-priority one. Karst caves are widely distributed subsurface ecosystems, and cave microbes get more and more attention as they could drive cave evolution and biogeochemical cycling. Research have demonstrated the existence of diverse microbes and their participance in biogeochemical cycling of elements in cave environments. However, there are still gaps in how these microbes sustain in caves with limited nutrients and interact with cave environment. Cultivation of novel cave bacteria with certain functions is still a challenging assignment. This review summarized the role of microbes in cave evolution and mineral deposition, and intended to inspire further exploration of microbial performances on C/N/S biogeocycles.

Activation and Characterization of Lanthomicins A-C by Promoter Engineering in Streptomyces chattanoogensis L10

The emergence of drug resistance highlights the importance of new drug discovery. Microbial secondary metabolites encoded in biosynthetic gene clusters (BGCs) are a prolific source of drugs, whereas most of these BGCs are cryptic. Thus, taking strategies to activate these cryptic BGCs is of great importance for potential drug discovery. In this work, three novel pentangular polyphenols lanthomicin A-C were identified by activating a cryptic aromatic polyketide BGC through promoter engineering combined with optimization of fermentation conditions. We further confirmed the involvement of lanthomicin (ltm) BGC in biosynthesis by CRISPR-Cpf1-assisted gene editing. Based on functional analysis of homologous genes, a putative biosynthetic pathway was proposed for the three lanthomicins. Particularly, lanthomicin A showed antiproliferative activity with IC₅₀ 0.17 μM for lung cancer cell line A-549. The discovery of lanthomicins brings new members to the pentangular polyphenol subclade of aromatic polyketide and demonstrates the potential of Streptomyces as a source for drug discovery.

Identification of Antibacterial Metabolites from Endophytic Fungus Aspergillus fumigatus, Isolated from Albizia lucidior Leaves (Fabaceae), Utilizing Metabolomic and Molecular Docking Techniques

The rapid spread of bacterial infection caused by Staphylococcus aureus has become a problem to public health despite the presence of past trials devoted to controlling the infection. Thus, the current study aimed to explore the chemical composition of the extract of endophytic fungus Aspergillus fumigatus, isolated from Albizia lucidior leaves, and investigate the antimicrobial activity of isolated metabolites and their probable mode of actions. The chemical investigation of the fungal extract via UPLC/MS/MS led to the identification of at least forty-two metabolites, as well as the isolation and complete characterization of eight reported metabolites. The antibacterial activities of isolated metabolites were assessed against S. aureus using agar disc diffusion and microplate dilution methods. Compounds ergosterol, helvolic acid and monomethyl sulochrin-4-sulphate showed minimal inhibitory concentration (MIC) values of 15.63, 1.95 and 3.90 µg/mL, respectively, compared to ciprofloxacin. We also report the inhibitory activity of the fungal extract on DNA gyrase and topoisomerase IV, which led us to perform molecular docking using the three most active compounds isolated from the extract against both enzymes. These active compounds had the required structural features for S. aureus DNA gyrase and topoisomerase IV inhibition, evidenced via molecular docking.

Discovery of a DNA Topoisomerase I Inhibitor Huanglongmycin N and Its Congeners from Streptomyces sp. CB09001

Huanglongmycin (HLM) congeners G-N (7-14) were isolated from Streptomyces sp. CB09001. Among them, 10-12 possesses a tricyclic scaffold with benzene-fused pyran/pyrone, confirmed by X-ray single crystal diffraction analysis of 12. The structure-activity relationship study of 1, 13, and 14 revealed not only the stronger cytotoxicity of 14 against tested cancer cells but also the critical role of the C-7 ethyl group of 14 in its binding to the DNA-topoisomerase I complex.

Antibacterial, Antifungal and Anticancer Activities of Compounds Produced by Newly Isolated Streptomyces Strains from the Szczelina Chochołowska Cave (Tatra Mountains, Poland)

Resistance of bacteria, fungi and cancer cells to antibiotics and other drugs is recognized as one of the major problems in current medicine. Therefore, a search for new biologically active compounds able to either kill pathogenic cells or inhibit their growth is mandatory. Hard-to-reach habitats appear to be unexplored sources of microorganisms producing previously unknown antibiotics and other molecules revealing potentially therapeutic properties. Caves belong to such habitats, and Actinobacteria are a predominant group of microorganisms occurring there. This group of bacteria are known for production of many antibiotics and other bioactive compounds. Interestingly, it was demonstrated previously that infection with bacteriophages might enhance production of antibiotics by them. Here, we describe a series of newly isolated strains of Actinobacteria that were found in caves from the Tatra Mountains (Poland). Phage induction tests indicated that some of them may bear active prophages able to produce virions upon treatment with mitomycin C or UV irradiation. Among all the examined bacteria, two newly isolated Streptomyces sp. strains were further characterized to demonstrate their ability to inhibit the growth of pathogenic bacteria (strains of Staphylococcus aureus, Salmonella enterica, Enterococcus sp., Escherichia coli, and Pseudomonas aeruginosa) and fungi (different species and strains from the genus Candida). Moreover, extracts from these Streptomyces strains reduced viability of the breast-cancer cell line T47D. Chemical analyses of these extracts indicated the presence of isomers of dichloranthrabenzoxocinone and 4,10- or 10,12-dichloro-3-O-methylanthrabenzoxocinone, which are putative antimicrobial compounds. Moreover, various previously unknown (unclassified) molecules were also detected using liquid chromatography-mass spectrometry, suggesting that tested Streptomyces strains may synthesize a battery of bioactive compounds with antibacterial, antifungal, and anticancer activities. These results indicate that further studies on the newly isolated Actinobacteria might be a promising approach to develop novel antibacterial, antifungal, and/or anticancer drugs.

Tapping Into Actinobacterial Genomes for Natural Product Discovery

The presence of secondary metabolite biosynthetic gene clusters (BGCs) makes actinobacteria well-known producers of diverse metabolites. These ubiquitous microbes are extensively exploited for their ability to synthesize diverse secondary metabolites. The extent of their ability to synthesize various molecules is yet to be evaluated. Current advancements in genome sequencing, metabolomics, and bioinformatics have provided a plethora of information about the mechanism of synthesis of these bioactive molecules. Accessing the biosynthetic gene cluster responsible for the production of metabolites has always been a challenging assignment. The genomic approach developments have opened a new gateway for examining and manipulating novel antibiotic gene clusters. These advancements have now developed a better understanding of actinobacterial physiology and their genetic regulation for the prolific production of natural products. These new approaches provide a unique opportunity to discover novel bioactive compounds that might replenish antibiotics’ exhausted stock and counter the microbes’ resistance crisis.

Bioactive α-Pyrone Derivatives from the Endophytic Fungus Diaporthe sp. CB10100 as Inducible Nitric Oxide Synthase Inhibitors

Inducible nitric oxide synthase (iNOS) produces NO from l-arginine and plays critical roles in inflammation and immune activation. Selective and potent iNOS inhibitors may be potentially used in many indications, such as rheumatoid arthritis, pain, and neurodegeration. In the current study, five new compounds, including a dibenzo-α- pyrone derivative ellagic acid B (5) and four α-pyrones diaporpyrone A-D (9-12), together with three known compounds (6-8), were isolated from the endophytic fungus Diaporthe sp. CB10100. The structures of these new natural products were unambiguously elucidated using NMR, HRESIMS or electronic circular dichroism calculations. Ellagic acid B (5) features a tetracyclic 6/6/6/6 ring system with a fused 2H-chromene, which is different from ellagic acid (4) with a fused 2H-chromen-2-one. Both 2-hydroxy-alternariol (6) and alternariol (7) reduced the expression of iNOS at protein levels in a dose-dependent manner, using a lipopolysaccharide (LPS)-induced RAW264.7 cell models. Also, they decreased the protein expression levels of pro-inflammatory cytokines, such as tumor necrosis factor-α, interleukin-6 and monocyte chemotactic protein 1. Importantly, 6 and 7 significantly reduced the production of NO as low as 10 μM in LPS-induced RAW264.7 cells. Molecular docking of 6 and 7 to iNOS further suggests that both of them may interact with iNOS. Our study suggests that 6 and 7, as well as the alternariol scaffold may be further developed as potential iNOS inhibitors.

Chemical constituents from the Streptomyces morookaensis strain Sm4-1986

Three new compounds, including 6-methoxy-3,4,5,7-tetramethylisochromane-3,8-diol (1), 3,4,5,7-tetramethylisochromane-3,6,8-triol (2), streptimidone derivative (3), along with ten known compounds (4-13) were isolated from the Streptomyces morookaensis strain Sm4-1986. Their chemical structures were established based on the information from UV, IR, NMR (¹H NMR, ¹³C NMR, ¹H-¹H COSY, HSQC, HMBC, NOESY), and mass spectroscopic. Moreover, all the isolated new compounds were evaluated for antibacterial activities (S. aureus, B. cereus, S. epidermids and methicillin-resistant S. aureus) and their cytotoxicities against MCF-7, A549, Hela tumor cell lines and Marc-145 normal cell line.

Biosynthesis of aromatic polyketides in microorganisms using type II polyketide synthases

Aromatic polyketides have attractive biological activities and pharmacological properties. Different from other polyketides, aromatic polyketides are characterized by their polycyclic aromatic structure. The biosynthesis of aromatic polyketides is usually accomplished by the type II polyketide synthases (PKSs), which produce highly diverse polyketide chains by sequential condensation of the starter units with extender units, followed by reduction, cyclization, aromatization and tailoring reactions. Recently, significant progress has been made in characterization and engineering of type II PKSs to produce novel products and improve product titers. In this review, we briefly summarize the architectural organizations and genetic contributions of PKS genes to provide insight into the biosynthetic process. We then review the most recent progress in engineered biosynthesis of aromatic polyketides, with emphasis on generating novel molecular structures. We also discuss the current challenges and future perspectives in the rational engineering of type II PKSs for large scale production of aromatic polyketides.

An aberrant metabolic flow toward early shunt products in the granaticin biosynthetic machinery of Streptomyces vietnamensis GIMV4.0001

A systematic study of the secondary metabolites of the wild granaticin-producing strain Streptomyces vietnamensis GIMV4.0001 led to the isolation of six known early shunt products related to actinorhodin, SEK34 (3), SEK34b (4), mutactin (5), dehydromutactin (7), EM18 (8) and GTRI-02 (9). While the other shunt products were minor or trace products, the production ratio of SEK34 (3) and SEK34b (4) to granaticins was strikingly high. Nearly 64% of the intermediate with the first ring closed went to the SEK34/SEK34b aberrant pathway. The high level of the aberrant metabolic flow toward the early shunt products SEK34 and SEK34b indicated that the second ring closure of the granaticin (1) biosynthesis is a key limiting step in the granaticin biosynthetic machinery of S. vietnamensis GIMV4.0001.

Screening and Transcriptional Analysis of Polyketide Synthases and Non-ribosomal Peptide Synthetases in Bacterial Strains From Krubera-Voronja Cave

Identification of novel bioactive compounds represents an important field in modern biomedical research. Microorganisms of the underexplored environments, such as deserts, hot springs, oceans, and caves are highly promising candidates for screening such metabolites. Screening for biosynthetic genes is the most effective strategy to characterize bioactivity in a certain environment. However, knowledge is either scant or non-existent about the expression of the biosynthetic genes encoding for various bioactive compounds in the microorganisms from the caves. The aim of the current study was to screen for the genes of polyketide synthases and non-ribosomal peptide synthetases in Krubera–Voronja Cave (43.4184 N 40.3083 E, Western Caucasus) bacterial isolates as well as to evaluate the expression of these genes under laboratory conditions. In total, 91 bacterial strains isolated from the cave were screened for the presence of polyketide synthase and non-ribosomal peptide synthetase genes. Phenotypically inactive strains were the main focus (the test group) of our study, while the strains with the identified antibacterial activity served as the control group. Our PCR-based screening clearly showed that the majority of the strains harbored at least one biosynthetic gene. Prediction of the putative products allowed us to identify bioactive compounds with antibacterial, anticancer, antifungal, anti-inflammatory, antimycoplasmic, antiviral, insecticidal, and thrombolytic activity. For most polyketide synthases and non-ribosomal peptide synthetases, putative products could not be predicted; they are unknown. Qualitative transcriptional analysis did not show substantial differences between the test group and the control group of the strains. One to four biosynthetic genes were constitutively expressed in all the tested strains, irrespective of the group. Quantitative transcriptional analysis of the constitutively expressed biosynthetic genes demonstrated that the expression of a particular gene could be affected by both the amount of the nutrients in the culture medium and the growth phase.

Syn-2, 3-diols and anti-inflammatory indole derivatives from Streptomyces sp. CB09001

Two new natural diols, (2S, 3S, 4S)-4-methyl-1-phenylhexane-2,3-diol (1) and (2S, 3S)-4-methyl-1-phenylpentane-2,3-diol (2), together with five known compounds, xenocyloins B-D (3-5), lumichrome (6) and thymidine (7) were isolated from Streptomyces sp. CB09001. The absolute configurations of 1 and 2 were established by crystallographic structure analysis. The anti-inflammatory effects of 1-7 were also investigated in RAW246.7 murine macrophage cells stimulated by lipopolysaccharide. The indole derivative xenocyloin B (3) significantly inhibited inducible nitric oxide synthase expression in RAW264.7 cells and could be a potential anti-inflammatory drug lead.

Cave Actinobacteria as Producers of Bioactive Metabolites

Recently, there is an urgent need for new drugs due to the emergence of drug resistant pathogenic microorganisms and new infectious diseases. Members of phylum Actinobacteria are promising source of bioactive compounds notably antibiotics. The search for such new compounds has shifted to extreme or underexplored environments to increase the possibility of discovery. Cave ecosystems have attracted interest of the research community because of their unique characteristics and the microbiome residing inside including actinobacteria. At the time of writing, 47 species in 30 genera of actinobacteria were reported from cave and cave related habitats. Novel and promising bioactive compounds have been isolated and characterized. This mini-review focuses on the diversity of cultivable actinobacteria in cave and cave-related environments, and their bioactive metabolites from 1999 to 2018.