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Streptomycetes are bacteria known for their extraordinary biosynthetic capabilities. Herein, we describe the genome and metabolome of a particularly talented strain, Streptomyces ID71268. Its 8.4-Mbp genome harbors 32 bioinformatically predicted biosynthetic gene clusters (BGCs), out of which 10 are expressed under a single experimental condition. In addition to five families of known metabolites with previously assigned BGCs (nigericin, azalomycin F, ectoine, SF2766, and piericidin), we were able to predict BGCs for three additional metabolites: streptochlorin, serpetene, and marinomycin. The strain also produced two families of presumably novel metabolites, one of which was associated with growth inhibitory activity against the human opportunistic pathogen Acinetobacter baumannii in an iron-dependent manner. Bioassay-guided fractionation, followed by extensive liquid chromatography-mass spectrometry (LC-MS) and NMR analyses, established that the molecule responsible for the observed antibacterial activity is an unusual tridecapeptide siderophore with a ring-and-tail structure: the heptapeptide ring is formed through a C-C bond between a 2,3-dihydroxybenzoate (DHB) cap on Gly1 and the imidazole moiety of His7, while the hexapeptide tail is sufficient for binding iron. This molecule, named megalochelin, is the largest known siderophore. The megalochelin BGC encodes a 13-module nonribosomal peptide synthetase for the synthesis of the tridecapeptide, and a copper-dependent oxidase, likely responsible for the DHB-imidazole cross-link, whereas the genes for synthesis of the DHB starter unit are apparently specified in trans by a different BGC. Our results suggest that prolific producers of specialized metabolites may conceal hidden treasures within a background of known compounds.

In the search for structurally novel metabolites with antibacterial activity, innovative approaches must be implemented to increase the probability of discovering novel chemistry from microbial sources. Here we report on the application of metabolomic tools to the genus Actinoallomurus, a poorly explored member of the Actinobacteria. From examining extracts derived from 88 isolates belonging to this genus, we identified a family of cyclodepsipeptides acylated with a C20 polyketide chain, which we named allopeptimicins. These molecules possess unusual structural features, including several double bonds in the amino-polyketide chain and four non-proteinogenic amino acids in the octapeptide. Remarkably, allopeptimicins are produced as a complex of active and inactive congeners, the latter carrying a sulfate group on the polyketide amine. This modification is also a mechanism of self-protection in the producer strain. The structural uniqueness of allopeptimicins is reflected in a biosynthetic gene cluster showing a mosaic structure, with dedicated gene cassettes devoted to formation of specialized precursors and modular assembly lines related to those from different pathways.

The increasing incidence of infections caused by drug-resistant pathogens requires new efforts for the discovery of novel antibiotics. By screening microbial extracts in an assay aimed at identifying compounds interfering with cell wall biosynthesis, based on differential activity against a Staphylococcus aureus strain and its isogenic l-form, the potent enduracyclinones (1, 2), containing the uncommon amino acid enduracididine linked to a six-ring aromatic skeleton, were discovered from different Nonomuraea strains. The structures of 1 and 2 were established through a combination of derivatizations, oxidative cleavages, and NMR analyses of natural and 13C–15N-labeled compounds. Analysis of the biosynthetic cluster provides the combination of genes for the synthesis of enduracididine and type II polyketide synthases. Enduracyclinones are active against Gram-positive pathogens (especially Staphylococcus spp.), including multi-drug-resistant strains, with minimal inhibitory concentrations in the range of 0....

Planobispora rosea is the natural producer of the potent thiopeptide antibiotic GE2270A. Here, we present the results of a metabolomics and transcriptomics analysis of P. rosea during production of GE2270A. The data generated provides useful insights into the biology of this genetically intractable bacterium. We characterize the details of the shutdown of protein biosynthesis and the respiratory chain associated with the end of the exponential growth phase. We also provide the first description of the phosphate regulon in P. rosea. Based on the transcriptomics data, we show that both phosphate and iron are limiting P. rosea growth in our experimental conditions. Additionally, we identified and validated a new biosynthetic gene cluster associated with the production of the siderophores benarthin and dibenarthin in P. rosea. Together, the metabolomics and transcriptomics data are used to inform and refine the very first genome-scale metabolic model for P. rosea, which will be a valuable framework for the interpretation of future studies of the biology of this interesting but poorly characterized species. IMPORTANCE Planobispora rosea is a genetically intractable bacterium used for the production of GE2270A on an industrial scale. GE2270A is a potent thiopeptide antibiotic currently used as a precursor for the synthesis of two compounds under clinical studies for the treatment of Clostridium difficile infection and acne. Here, we present the very first systematic multi-omics investigation of this important bacterium, which provides a much-needed detailed picture of the dynamics of metabolism of P. rosea while producing GE2270A. Author Video: An author video summary of this article is available.

International audience; Genomics and metabolomics are widely used to explore specialized metabolite diversity. The Paired Omics Data Platform is a community initiative to systematically document links between metabolome and (meta)genome data, aiding identification of natural product biosynthetic origins and metabolite structures.

Natural products have provided many molecules to treat and prevent illnesses in humans, animals and plants. While only a small fraction of the existing microbial diversity has been explored for bioactive metabolites, tens of thousands of molecules have been reported in the literature over the past 80 years. Thus, the main challenge in microbial metabolite screening is to avoid the re-discovery of known metabolites in a cost-effective manner. In this perspective, we report and discuss different approaches used in our laboratory over the past few years, ranging from bioactivity-based screening to looking for metabolic rarity in different datasets to deeply investigating a single Streptomyces strain. Our results show that it is possible to find novel chemistry through a limited screening effort, provided that appropriate selection criteria are in place.

We report a metabolomic analysis of Streptomyces sp. ID38640, a soil isolate that produces the bacterial RNA polymerase inhibitor pseudouridimycin. The analysis was performed on the wild type, on three newly constructed and seven previously reported mutant strains disabled in different genes required for pseudouridimycin biosynthesis. The results indicate that Streptomyces sp. ID38640 is able to produce, in addition to lydicamycins and deferroxiamines, as previously reported, also the lassopeptide ulleungdin, the non-ribosomal peptide antipain and the osmoprotectant ectoine. The corresponding biosynthetic gene clusters were readily identified in the strain genome. We also detected the known compound pyridindolol, for which we propose a previously unreported biosynthetic gene cluster, as well as three families of unknown metabolites. Remarkably, the levels of most metabolites varied strongly in the different mutant strains, an observation that enabled detection of metabolites unnoticed in the wild type. Systematic investigation of the accumulated metabolites in the ten different pum mutants identified shed further light on pseudouridimycin biosynthesis. We also show that several Streptomyces strains, able to produce pseudouridimycin, have distinct genetic relationship and metabolic profile with ID38640.

We report a metabolomic analysis of Streptomyces sp. ID38640, a soil isolate that produces the bacterial RNA polymerase inhibitor pseudouridimycin. The analysis was performed on the wild type and on ten different pum mutants blocked at different steps in pseudouridimycin biosynthesis. The results indicate that Streptomyces sp. ID38640 is able to produce, in addition to pseudouridimcyin, lydicamycins and deferroxiamines, as previously reported, also the lassopeptide ulleungdin, the non-ribosomal peptide antipain and the osmoprotectant ectoine. The corresponding biosynthetic gene clusters were readily identified in the strain genome. We also detected the known compound pyridindolol, for which we propose a previously unreported biosynthetic gene cluster, as well as three families of unknown metabolites. Remarkably, the levels of the different metabolites varied strongly in the different mutant strains, allowing detection of metabolites not normally seen in the wild type. Three newly constructed pum mutants, along with systematic investigation of the accumulated metabolites, shed further lights on pseudouridimycin biosynthesis. We also show that several Streptomyces strains, harboring the pum biosynthetic gene cluster and unrelated to ID38640, readily produce pseudouridimycin.

Four metabolites, designated paramagnetoquinone A, B, C, and D (1-4), were isolated from three strains belonging to the actinomycete genus Actinoallomurus. Compounds 1 and 2 showed potent antibacterial activity with MIC values lower than 0.015 μg/mL against Gram-positive pathogens, including antibiotic-resistant strains. Since compounds 1 and 2 were NMR-silent due to the presence of an oxygen radical, structure elucidation was achieved through a combination of derivatizations, oxidations, and analysis of 13C-labeled compounds. The paramagnetoquinones share the same carbon scaffold as tetracenomycin but carry two quinones and a five-membered lactone fused to the aromatic system. Compounds 2 and 1 are identical except for an unprecedented replacement of a methoxy in 2 by a methylamino group in 1. Related compounds devoid of methyl group(s) and of antibacterial activity were isolated from a different Actinoallomurus strain. The likely pmq biosynthetic gene cluster was identified from strain ID145113. While the cluster encodes many of the expected enzymes involved in the formation of aromatic polyketides, it also encodes a dedicated ketoacid dehydrogenase complex and an unusual acyl carrier protein transacylase, suggesting that an unusual starter unit might prime the polyketide synthase.

There is an increased need for new drug leads to treat diseases in humans, animals and plants. A dramatic example is represented by the need for novel and more effective antibiotics to combat multidrug-resistant microbial pathogens. Natural products represent a major source of approved drugs and still play an important role in supplying chemical diversity, despite a decreased interest by large pharmaceutical companies. Novel approaches must be implemented to decrease the chances of rediscovering the tens of thousands of known natural products. In this review, we present an overview of natural product screening, focusing particularly on microbial products. Different approaches can be implemented to increase the probability of finding new bioactive molecules. We thus present the rationale and selected examples of the use of hypersensitive assays; of accessing unexplored microorganisms, including the metagenome; and of genome mining. We then focus our attention on the technology platform that we are currently using, consisting of approximately 70 000 microbial strains, mostly actinomycetes and filamentous fungi, and discuss about high-quality screening in the search for bioactive molecules. Finally, two case studies are discussed, including the spark that arose interest in the compound: in the case of orthoformimycin, the novel mechanism of action predicted a novel structural class; in the case of NAI-112, structural similarity pointed out to a possible in vivo activity. Both predictions were then experimentally confirmed.

NAI-107, a lantibiotic produced by Microbispora sp. 107891, shows potent activity against multi-drug-resistant bacterial pathogens. It is produced as a complex of related molecules, which is unusual for ribosomally synthesized peptides. Here we describe the identification, characterization, and antibacterial activity of the congeners produced by Microbispora sp. 107891 and by the related Microbispora corallina NRRL 30420. These molecules differ by the presence of two, one, or zero hydroxyl groups at Pro-14, by the presence of a chlorine at Trp-4, and/or by the presence of a sulfoxide on the thioether of the first lanthionine.

Pseudouridimycin (PUM) is a selective nucleoside-analog inhibitor of bacterial RNA polymerase with activity against Gram-positive and Gram-negative bacteria. PUM, produced by Streptomyces sp. ID38640, consists of a formamidinylated, N-hydroxylated Gly-Gln dipeptide conjugated to 5′-aminopseudouridine. We report the characterization of the PUM gene cluster. Bioinformatic analysis and mutational knockouts of pum genes with analysis of accumulated intermediates, define the PUM biosynthetic pathway. The work provides the first biosynthetic pathway of a C-nucleoside antibiotic and reveals three unexpected features: production of free pseudouridine by the dedicated pseudouridine synthase, PumJ; nucleoside activation by specialized oxidoreductases and aminotransferases; and peptide-bond formation by amide ligases. A central role in the PUM biosynthetic pathway is played by the PumJ, which represents a divergent branch within the TruD family of pseudouridine synthases. PumJ-like sequences are associated with diverse gene clusters likely to govern the biosynthesis of different classes of C-nucleoside antibiotics. Sosio et al. describe the biosynthetic pathway for the C-nucleoside antibiotic pseudouridimycin. Biosynthesis proceeds through formation of pseudouridine by the pseudouridine synthase PumJ, with specialized oxidoreductase, aminotransferase, and amide ligases leading to the final compound. Microbial genomes harbor diverse gene clusters encoding PumJ-related sequences.

A comparative study was performed on the sorption capacity of the phenoxy acid herbicide cyhalofop on polymerin (from olive oil mill effluents), ferrihydrite, and a ferrihydrite-polymerin complex, by using a batch equilibrium method. The most efficient sorbent showed to be ferrihydrite followed by the ferrihydrite-polymerin complex and polymerin. Cyhalofop acid bound to ferrihydrite by a combination of ionic and ion-dipole bonding, whereas the same herbicide bound to the ferrihydrite-polymerin complex by ionic bonding and to polymerin by hydrogen bonding. Simulated wastewaters contaminated with cyhalofop acid were completely purified by two sorption cycles on ferrihydrite and five cycles on the ferrihydrite-polymerin complex, whereas the same wastewaters maintained a constant residue even after five sorption cycles on polymerin. For the first time, the possible use of a mineral (ferrihydrite) and an organo-mineral complex (ferrihydrite-polymerin) as a filter for the control of the herbicide contamination in point sources is proposed and briefly discussed.

This study investigated the sorption of paraquat and 2,4-D on polymerin, the humic acid-like fraction of olive mill wastewater. Effects of pH, contact time, initial concentration and sorbent dosage on the sorption of both herbicides were studied. The sorption mechanism of paraquat on polymerin was consistent with the ion exchange of this herbicide with Ca, Mg and K natively occurring in the sorbent; in contrast, 2,4-D was bound to polymerin by hydrogen bonding. Simulated wastewaters contaminated with paraquat were purified after three sorption cycles on polymerin renewed at each cycle, at a solid/liquid ratio of 0.5, whereas those containing 2,4-D showed a maximal residue removal of 44% after two sorption cycles at the same ratio. The possible application of this model to other water-soluble herbicides, as well as the possible exploitation of polymerin as a bio-filter for the decontamination of pollution point sources is briefly discussed.

We identified an Actinoallomurus strain producing NAI-107, a chlorinated lantibiotic effective against multidrug-resistant Gram-positive pathogens and previously reported from the distantly related genus Microbispora. Inclusion of KBr in the production medium of either the Actinoallomurus or the Microbispora producer readily afforded brominated variants of NAI-107, which were designated as NAI-108. The other post-translational modifications naturally occurring in this lantibiotic family (i.e., hydroxylation of Pro-14 and C-terminal decarboxylation) were unaffected by the presence of a brominated tryptophan. In addition to being the first example of a bromine-containing lantibiotic, NAI-108 displayed a small but consistent improvement in antibacterial activity against all tested strains. The brominated lantibiotic maintained the same rapid bactericidal activity as NAI-107 but at reduced concentrations, consistent with its increased potency and with the role played by the hydrophobicity of the first lanthionine ring. NAI-108 thus represents an interesting addition to a promising family of potent and effective lantibiotics.

Olive mill waste water (OMWW) contains high concentrations of phenols that are responsible for the high toxicity of the effluent. A one step precipitation process of OMWW by cold methanol yielded a polymeric organic precipitate (polymerin) and a supernatant (OMWW-S) rich in phenols, which were further concentrated in an ethyl acetate extract (OMWW-E). This extract was comparatively adsorbed on: i) a layered double hydroxide of magnesium and aluminium (LDH); ii) the LDH after calcination at 450 °C (LDH-450); iii) a hydroxyaluminium–iron-co-precipitate (HyAlFe); and iv) a hydroxy-aluminium–iron–montmorillonite complex (HyAlFe-Mt). Adsorption behaviour and kinetics of phenols with these materials were investigated. The Langmuir model better described adsorption (R 2 > 0.97) in comparison to the Freundlich model (R 2 > 0.89). Phenols were sorbed according to the following order: LDH-450 > LDH > HyAlFe > HyAlFe-Mt. Phenol adsorption on LDH matrices was strong, since desorption with simulated soil solution under dynamic conditions never exceeded 20%. Cyclic adsorption conducted with LDH-450 removed most phenols, ~ 94% from OMWW-E, consequently reducing its phytotoxicity. The study evidenced that calcined LDH represented an effective remediation process for OMWW.

Among the growing family of ribosomally synthesized, post-translationally modified peptides, particularly intriguing are class III lanthipeptides containing the triamino acid labionin. In the course of a screening program aimed at finding bacterial cell wall inhibitors, we discovered a new lanthipeptide produced by an Actinoplanes sp. The molecule, designated NAI-112, consists of 22 amino acids and contains an N-terminal labionin and a C-terminal methyl-labionin. Unique among lanthipeptides, it carries a 6-deoxyhexose moiety N-linked to a tryptophan residue. Consistently, the corresponding gene cluster encodes, in addition to the LanKC enzyme characteristic of this lanthipeptide class, a glycosyl transferase. Despite possessing weak antibacterial activity, NAI-112 is effective in experimental models of nociceptive pain, reducing pain symptoms in mice in both the formalin and the chronic constriction injury tests. Thus, NAI-112 represents, after the labyrinthopeptins, the second example of a lanthipeptide effective against nociceptive pain. © 2013 American Chemical Society.

Two different strategies for the removal of trivalent chromium (Cr(3+)) from contaminated water are reported. The first one is based on the sorption process on an organo-mineral complex, named LDH-HP, obtained in turn by sorption of polymerin, the humic acid-like fraction occurring in olive oil mill wastewater, on a layered double hydroxide (LDH) of magnesium and aluminium with carbonate in the interlayer. This sorption process is preliminary developed on simulated wastewater (SW) as theoretical model and successively applied on tannery process wastewaters (TPWs) natively containing Cr(3+). The removal of Cr(3+) from TPW is lower than that observed for SW, because of the large compositional variability of TPW. The second one is based on the direct production of a LDH of magnesium and chromium (Cr(3+)), using as starting material TPW, naming LDH-TPW the complex produced. This process allows the complete removal of Cr(3+) from TPW and also the abatement of chemical oxygen demand, indicating to be a very promising purification process for an industrial application.

Examination of the metabolites produced by an Actinospica strain led to the identification of 6-hydroxychrolactomycin (compound 1), which is produced along with minor amounts of chrolactomycin (compound 2). The structure of 1 was established on the basis of extensive spectroscopic analysis, including one- and two-dimensional NMR. Compound 1 showed antimicrobial activity against Gram-positive bacteria, although it was generally less active than 2.

Here we report onthe isolation, structure elucidation and properties of madurastatin C1(1), the antimicrobial compound produced by this actinomycete.A 10-ml seed culture of Actinomadura sp. DSMZ 13491, preparedby inoculating a frozen cell stock into 30ml of AFT medium (2%glucose, 0.2% yeast extract, 0.8% soybean meal, 0.5% tryptone, 0.1%NaCl, 0.4% CaCO

Disposal of olive mill waste waters (OMWW) represents a serious problem due to its elevated toxicity and pollution risk for environmental and aquatic bodies, which is mainly related to its polyphenol content. The use of layered double hydroxides (LDHs) or anionic clays for OMWW detoxification may represent an effective remediation process. In the current study, OMWW was treated with cold methanol to obtain a dark humic acid-like precipitate made of high molecular weight organic compounds named polymerin and a supernatant made of low molecular weight organics named OMWW-S. After precipitation with methanol, phenol content decreased from 2.14 g L−1 to 0.80 and 1.20 g L−1, in polymerin and OMWW-S, respectively. The chemical oxygen demand of OMWW-S decreased by about 30% with respect to raw OMWW, from 62.2 to 40.2 g L−1. A phenolic concentrate, named OMWW-E was also obtained by ethyl acetate extraction of OMWW-S at pH 2.0. LDHs of zinc and aluminium (LDH) were obtained at room temperature and after calcination at 450 °C (LDH-450). An organo-mineral complex of LDH with polymerin (LDH-Pol) was also synthesised. Phenols from OMWW-E were sorbed preferentially on three matrices according to the following order: LDH-450 > LDH > LDH-Pol, with percent sorption of up to 73% for LDH-450. Repeated cycles of sorption of OMWW-S onto LDH-450 decreased phenol concentration by about 90%. Use of remediated water in a phytotoxicity bioassay revealed scant inhibition of germination and coleoptile elongation rate in tomato seeds and seedlings. Thus, OMWW-S after sorption onto LDH-450 could represent a low cost source of irrigation water for arid soil of the Mediterranean region.

Mg-Al layered double hydroxides (LDHs) containing chloride (LDH-Cl) or carbonate (LDH-CO(3)) in the interlayer were obtained at room temperature and after calcitation at 450 degrees C (LDH-Cl-450 and LDH-CO(3)-450) and were characterized by X-ray diffraction and Fourier transform infrared analyses. Sorption isotherms of a humic acidlike fraction naturally occurring in olive oil mill waste waters, named polymerin, on these LDH minerals were carried out. Because LDH-CO(3) showed the highest capacity to sorb polymerin among the four LDH minerals synthesized, two organo-mineral complexes named LDH-CO(3)-LP (low polymerin) and LDH-CO(3)-HP (high polymerin) were prepared by coprecipitation (LDH-CO(3)-LP) and sorption onto a preformed LDH-CO(3) mineral (LDH-CO(3)-HP). These complexes were characterized chemically and physicochemically, and their stability to pH and after thermal treatment at 80 degrees C were evaluated. The diffuse reflectance infrared Fourier transform and X-ray analysis of the complexes indicated that polymerin was sorbed only on the external surfaces of LDH-CO(3) and no intercalation occurred. The LDH-polymerin complexes appeared to be more stable than LDH-CO(3) at pH 4.0 and showed that they were able to sorb both As(V) and Zn. Because the waste waters are usually contaminated with mixtures of pollutants in cationic and anionic forms, the LDH-polymerin complexes appear more suitable than the sorbents in a potential water remediation process.

Intent of this study was to explore the potential application of polymerin, the polymeric, dissolved organic matter fraction from olive oil wastewaters, in technologies aimed at remediating hydrophobic organic compounds (HOCs) point-source pollution. Phenanthrene binding with polymerin was investigated. Moreover, the effect of addition of micro and nanoscale aluminum oxides (Al2O3) was studied, as well as sorption of polymerin on the oxides. Phenanthrene binding capacity by polymerin was notably higher than the sorption capacities for both types of Al2O3 particles. Polymerin sorption on nanoparticles was nearly 100 times higher than microparticles. In a three-phase system, using microparticles, higher phenanthrene sorption was found by adding into water polymerin, oxides and phenanthrene simultaneously. In contrast, using nanoparticles, a considerable enhancement of phenanthrene sorption was shown by adding phenanthrene to a pre-formed and dried polymerin–oxide complex. These findings support the application of polymerin, especially associated with Al2O3 nanoparticles, in remediation of water contaminated with HOCs. This work highlights the significant role of nanoparticles.

A comparative study was performed on the sorption capacity of the phenoxy acid herbicide (4-chloro-2-methylphenoxyacetic acid), also known as MCPA, on a single-walled carbon nanotube (SWCNT), three multi-walled carbon nanotubes with average outer diameters of 15, 30 and 50 nm (MWCNT15, MWCNT30 and MWCNT50), and nanoscale metal oxides (Al2O3, TiO2 and ZnO). The most efficient sorbent was the SWCNT, followed by the three MWCNTs. The metal oxide nanoparticles showed a much lower sorption capacity. The herbicide bound to the tested carbon nanotubes, by a combination of electron donor–acceptor (π–π EDA) interactions and hydrogen bonds. On the contrary, MCPA bound to the considered metal oxide nanoparticles by electrostatic interactions occurring between the carboxylate anions of the same herbicide and OH2+ of the sorbent. Experiments of cyclic sorption showed the pesticides to be totally removed by only two sorption cycles on the SWCNT and MWCNT15, whereas the same waste water was purified after four cycles on nano Al2O3. Finally, desorption studies carried out in ethanol showed a potential re-use of the SWCNT.

Their biochemical versatility and biotechnological importance make actinomycete bacteria attractive targets for ambitious genetic engineering using the toolkit of synthetic biology. But their complex biology also poses unique challenges. This mini review discusses some of the recent advances in synthetic biology approaches from an actinomycete perspective and presents examples of their application to the rational improvement of industrially relevant strains., Recent advances in synthetic biology driven engineering of the actinomycetes for the production of valuable drug compounds.