Isolation and identification of three new 5-alkenyl-3,3(2H)-furanones from two streptomyces species using a genomic screening approach

MAR4 Streptomyces: A Unique Resource for Natural Product Discovery

Marine-derived Streptomyces have long been recognized as a source of novel, pharmaceutically relevant natural products. Among these bacteria, the MAR4 clade within the genus Streptomyces has been identified as metabolically rich, yielding over 93 different compounds to date. MAR4 strains are particularly noteworthy for the production of halogenated hybrid isoprenoid natural products, a relatively rare class of bacterial metabolites that possess a wide range of biological activities. MAR4 genomes are enriched in vanadium haloperoxidase and prenyltransferase genes, thus accounting for the production of these compounds. Functional characterization of the enzymes encoded in MAR4 genomes has advanced our understanding of halogenated, hybrid isoprenoid biosynthesis. Despite the exceptional biosynthetic capabilities of MAR4 bacteria, the large body of research they have stimulated has yet to be compiled. Here we review 35 years of natural product research on MAR4 strains and update the molecular diversity of this unique group of bacteria.

Streptomyces phytophilus sp. nov., an endophytic actinobacterium with biosynthesis potential as an antibiotic producer

An endophytic actinobacterium, strain PIP175^T, was isolated from the root sample of a native apricot tree (Pittosporum angustifolium) growing on the Bedford Park campus of Flinders University, Adelaide, South Australia. This strain is a Gram stain-positive, aerobic actinobacterium with well-developed substrate mycelia. Aerial mycelia rarely produce spores and the spore chain is spiral. Strain PIP175^T showed the highest 16S rRNA gene sequence similarity to Streptomyces aculeolatus DSM 41644^T (99.4 %). Other closely related phylogenetic representatives include Streptomyces synnematoformans DSM 41902^T (98.3 %), Streptomyces albospinus NBRC 13846^T (97.6 %), Streptomyces cacaoi subsp. cacaoi NRRL B-1220^T (97.5 %) and Streptomyces ruber NBRC 14600^T (97.4 %). The major cellular fatty acid of this strain was iso-C_16 : 0 and the major menaquinone was MK-9(H₆). The whole-cell sugar contained galactose, glucose and mannose. Chemotaxonomic data confirmed that strain PIP175^T belonged to the genus Streptomyces. Digital DNA-DNA hybridization, average nucleotide identity based on blast and OrthoANIu results between strain PIP175^T and S. aculeolatus DSM 41644^T were 60.0, 94.1 and 94.9 %, respectively. Genotypic and phenotypic data and genome analysis results allowed the differentiation of strain PIP175^T from its closest species with validly published names. Strain PIP175^T showed good activity against methicillin-resistant Staphylococcus aureus 03120385. Genome mining of strain PIP175^T revealed biosynthetic genes encoding proteins relating to antibiotic production, plant growth promotion and biodegradation enzymes. The name proposed for the new species is Streptomyces phytophilus sp. nov. The type strain is PIP175^T (=DSM 103379^T=TBRC 6026^T).

Untargeted Metabolomics of Streptomyces Species Isolated from Soils of Nepal

Actinomycetes are natural architects of numerous secondary metabolites including antibiotics. With increased multidrug-resistant (MDR) pathogens, antibiotics that can combat such pathogens are urgently required to improve the health care system globally. The characterization of actinomycetes available in Nepal is still very much untouched which is the reason why this paper showcases the characterization of actinomycetes from Nepal based on their morphology, 16S rRNA gene sequencing, and metabolic profiling. Additionally, antimicrobial assays and liquid chromatography-high resolution mass spectrometry (LC-HRMS) of ethyl acetate extracts were performed. In this study, we employed a computational-based dereplication strategy for annotating molecules which is also time-efficient. Molecular annotation was performed through the GNPS server, the SIRIUS platform, and the available databases to predict the secondary metabolites. The sequencing of the 16S rRNA gene revealed that the isolates BN6 and BN14 are closely related to Streptomyces species. BN14 showed broad-spectrum antibacterial activity with the zone of inhibition up to 30 mm against Staphylococcus aureus (MIC: 0.3051 µg/mL and MBC: 9.7656 µg/mL) and Shigella sonnei (MIC: 0.3051 µg/mL and MBC: 4.882 µg/mL). Likewise, BN14 also displayed significant inhibition to Acinetobacter baumannii, Klebsiella pneumoniae, and Salmonella typhi. GNPS approach suggested that the extracts of BN6 and BN14 consisted of diketopiperazines ((cyclo(D-Trp-L-Pro), cyclo(L-Leu-L-4-hydroxy-Pro), cyclo(L-Phe-D-Pro), cyclo(L-Trp-L-Pro), cyclo(L-Val-L-Pro)), and polypeptide antibiotics (actinomycin D and X2). Additional chemical scaffolds such as bacterial alkaloids (bohemamine, venezueline B, and G), anthramycin-type antibiotics (abbeymycin), lipase inhibitor (ebelactone B), cytocidal (oxopropaline D), antifungal and antitumor antibiotics (reductiomycin, streptimidone, deoxynybomycin), alaremycin, fumaramidmycin, anisomycin, and others were also annotated, which were further confirmed by using the SIRIUS platform, and literature survey. Thus, the bioprospecting of natural products from Streptomyces species from Nepal could be a potential source for the discovery of clinically significant and new antimicrobial agents in the future.

Isolation and characterization of polyketide drug molecule from Streptomyces species with antimicrobial activity against clinical pathogens

BACKGROUND

Natural products derived from marine microbes have more potential toward to treatment of various diseases. Among the microbes, the secondary metabolites recovered from the marine actinomycetes were more added values.

OBJECTIVE

A promising antimicrobial metabolite producing filamentous actinomycete SCA-7 recovered from Alkhobar marine region was investigated for its potential to inhibit Gram positive Enterococcus sp. In addition to the chemical characterization, the polyketide gene cluster of the actinomycete SCA-7 was sequenced.

RESULTS

Among the 8 actinomycetes isolated from the marine sample, the isolate SCA-7 produced significant antimicrobial activity against Enterococcus sp. The biochemical, physiological and morphological characteristics and fermentation assimilation pattern confirmed that the isolate belonged to the genus Streptomyces. The 16S rRNA gene amplification and sequencing results showed 99% sequence similarity to Streptomyces felleus. The antimicrobial activity of the crude ethyl acetate extract was performed by disc diffusion method. The spectral characterization was done by ¹³C NMR and ¹H NMR. The compound was polyketide in nature. The Minimum Inhibitory Concentration (MIC) of the polyketide compound against Enterococcus sp. was 25μg/mL. Among the agro-industrial waste materials, wheat bran showed increased secondary metabolite production. Antibacterial activity was found to be high when the isolate SCA-7 was grown in wheat bran substrate and maximum zone of inhibition (22mm) was recorded in it. Among the carbon and nitrogen sources, lactose enhanced the production of secondary metabolites and the zone of inhibition against Enterococcus sp. was 25mm. The amplification and sequencing of the ketoacyl synthase gene clearly indicated that it was type I polyketide synthase (PKS) gene of Streptomyces species.

CONCLUSION

Overall, the therapeutic drug molecule isolated from the marine Streptomyces species might be used for the treatment of disease causing microbial clinical pathogen.

Native roles of Baeyer–Villiger monooxygenases in the microbial metabolism of natural compounds

Baeyer–Villiger monooxygenases function in the primary metabolism of atypical carbon sources, as well as the synthesis of complex microbial metabolites.

Actinofuranones D-I from a Lichen-Associated Actinomycetes, Streptomyces gramineus, and Their Anti-Inflammatory Effects

Six new metabolites, actinofuranones D-I (compounds 1–6), were isolated together with three known compounds—JBIR-108 (7), E-975 (8), and E-492 (9)—from a fermentation broth of Streptomyces gramineus derived from the lichen Leptogium trichophorum. The structures of the new compounds 1–6 were established using comprehensive NMR spectroscopic data analysis, as well as UV, IR, and MS data. The anti-inflammatory activity of these isolated compounds were evaluated by examining their ability to inhibit nitric oxide (NO) production in LPS-stimulated RAW 264.7 macrophage cells. Compounds 4, 5, 8, and 9 attenuated the production of NO due to the suppression of the expression of nitric oxide synthase (iNOS) in LPS-induced RAW 264.7 cells. Moreover, 4, 5, 8, and 9 also inhibited LPS-induced release of proinflammatory cytokines interleukin-6 (IL-6) and tumor necrosis factor α (TNF-α).

Linfuranones B and C, Furanone-Containing Polyketides from a Plant-Associated Sphaerimonospora mesophila

Two new furanone-containing polyketides, linfuranones B and C, were isolated from a plant-associated actinomycete of the genus Sphaerimonospora. Their structures were determined by NMR and MS spectroscopic analyses, and the absolute configurations were established by anisotropic methods and chemical degradation approaches. In silico analysis of biosynthetic genes suggested that linfuranone B is generated from linfuranone C by oxidative cleavage of the polyketide chain. Linfuranones B and C induced preadipocyte differentiation into matured adipocytes at 20-40 μM without showing cytotoxicity.

Natural products chemistry: The emerging trends and prospective goals

The role and contributions of natural products chemistry in advancements of the physical and biological sciences, its interdisciplinary domains, and emerging of new avenues by providing novel applications, constructive inputs, thrust, comprehensive understanding, broad perspective, and a new vision for future is outlined. The developmental prospects in bio-medical, health, nutrition, and other interrelated sciences along with some of the emerging trends in the subject area are also discussed as part of the current review of the basic and core developments, innovation in techniques, advances in methodology, and possible applications with their effects on the sciences in general and natural products chemistry in particular. The overview of the progress and ongoing developments in broader areas of the natural products chemistry discipline, its role and concurrent economic and scientific implications, contemporary objectives, future prospects as well as impending goals are also outlined. A look at the natural products chemistry in providing scientific progress in various disciplines is deliberated upon.

Epoxynemanione A, nemanifuranones A-F, and nemanilactones A-C, from Nemania serpens, an endophytic fungus isolated from Riesling grapevines

Ten polyketide specialized metabolites, epoxynemanione A, nemanifuranones A-F, and nemanilactones A-C, were isolated from the culture filtrate of Nemania serpens (Pers.) Grey (1821), an endophytic fungus from a Riesling grapevine (Vitis vinifera) found in Canada's Niagara region. Additionally, four known metabolites 2-(hydroxymethyl)-3-methoxy-benzoic acid, phyllostine, 5-methylmellein and a nordammarane triterpenoid were isolated. A related known metabolite 2,3-dihydro-2-hydroxy-2,4-dimethyl-5-trans-propenylfuran-3-one has also been included for structural and biological comparison to the nemanifuranones. The latter was isolated from the culture filtrates of Mollisia nigrescens, an endophytic fungus from the leaves and stems of lowbush blueberry (Vaccinium angustifolium) found in the Acadian forest of Nova Scotia, Canada. Their structures were elucidated based on 1D and 2D NMR, HRESIMS measurements, X-ray crystallographic analysis of nemanifuranone A, the nordammarane triterpenoid and 2,3-dihydro-2-hydroxy-2,4-dimethyl-5-trans-propenylfuran-3-one compounds, and comparison of NOE and vicinal ¹H-¹H coupling constants to literature data for relative stereochemical assignments. Nemanifuranone A possesses a rare C2 hemiacetal and was active against both Gram-negative and Gram-positive bacteria.

Streptomyces sp. AT37 isolated from a Saharan soil produces a furanone derivative active against multidrug-resistant Staphylococcus aureus

A novel actinobacterium strain, named AT37, showed a strong activity against some multidrug-resistant Staphylococcus aureus, including methicillin-resistant S. aureus MRSA ATCC 43300, other clinical isolates of MRSA and vancomycin resistant S. aureus VRSA S1. The strain AT37 was isolated from a Saharan soil by a dilution agar plating method using chitin-vitamin agar medium supplemented with rifampicin. The morphological and chemical studies indicated that this strain belonged to the genus Streptomyces. Its 16S rRNA gene sequence was determined and a database search indicated that it was closely associated with the type strain of Streptomyces novaecaesareae NBRC 13368^T with 99.6% of similarity. However, the comparison of the morphological and the physiological characteristics of the strain with those of the nearest species showed significant differences. The strain AT37 secreted the antibiotic optimally during mid-stationary phase of growth. One active compound (AT37-1) was extracted from the culture broth with dichloromethane, separated on silica gel plates and purified by HPLC. Based on spectroscopic analysis of UV-Visible, infrared, and ¹H and ¹³C NMR spectra and spectrometric analysis, the chemical structure of the compound AT37-1 was identified as 5-[(5E,7E,11E)-2,10-dihydroxy-9,11-dimethyl-5,7,11-tridecatrien-1-yl]-2-hydroxy-2-(1-hydroxyethyl)-4-methyl-3(2H)-furanone. Minimum inhibitory concentrations and minimum biofilm inhibitory concentration (MBIC₅₀) of this compound showed significant activity against multidrug-resistant S. aureus with 15-30 and 10-15 μg/mL, respectively.

The Uncommon Enzymology of Cis-Acyltransferase Assembly Lines

The enzymology of 135 assembly lines containing primarily cis-acyltransferase modules is comprehensively analyzed, with greater attention paid to less common phenomena. Diverse online transformations, in which the substrate and/or product of the reaction is an acyl chain bound to an acyl carrier protein, are classified so that unusual reactions can be compared and underlying assembly-line logic can emerge. As a complement to the chemistry surrounding the loading, extension, and offloading of assembly lines that construct primarily polyketide products, structural aspects of the assembly-line machinery itself are considered. This review of assembly-line phenomena, covering the literature up to 2017, should thus be informative to the modular polyketide synthase novice and expert alike.

Zincophorin - biosynthesis in Streptomyces griseus and antibiotic properties

Zincophorin is a polyketide antibiotic that possesses potent activity against Gram-positive bacteria, including human pathogens. While a number of total syntheses of this highly functionalized natural product were reported since its initial discovery, the genetic basis for the biosynthesis of zincophorin has remained unclear. In this study, the co-linearity inherent to polyketide pathways was used to identify the zincophorin biosynthesis gene cluster in the genome of the natural producer Streptomyces griseus HKI 0741. Interestingly, the same locus is fully conserved in the streptomycin-producing actinomycete S. griseus IFO 13350, suggesting that the latter bacterium is also capable of zincophorin biosynthesis. Biological profiling of zincophorin revealed a dose-dependent inhibition of the Gram-positive bacterium Streptococcus pneumoniae. The antibacterial effect, however, is accompanied by cytotoxicity. Antibiotic and cytotoxic activities were completely abolished upon esterification of the carboxylic acid group in zincophorin.

Characterization of saltern based Streptomyces sp. and statistical media optimization for its improved antibacterial activity

A moderately halotolerant Streptomyces strain, designated JAJ13 was characterized and a culture medium was statistically optimized to improve its antibacterial activity. Based on the phenotypic and molecular characteristics, strain JAJ13 was identified as a moderately halotolerant Streptomyces sp. JAJ13. Novelty of the strain JAJ13 in production of antibacterial compound was assessed by sequence analysis of KSα gene and LC-MS analysis of the active compound. Optimization of the culture medium for antibacterial compound production by the strain JAJ13 was performed with statistical methodology based on experimental designs. Initially, a starch based basal production medium was selected out of eight different production media screened for antibacterial compound production by Streptomyces sp. JAJ13. Plackett-Burman design was employed to screen the influential media components affecting the antibacterial compound production. Subsequently, statistical optimization of selected medium components was performed by employing the response surface methodology (RSM) with Box-Behnken design. The optimum initial level of CuSO₄.5H₂O, (NH₄)₂SO₄ and K₂HPO₄ for the highest antibacterial activity was determined to be at 4.45 mg, 1.96 g, and 1.15 g in 1 L of distilled H₂O, respectively. PBD and RSM guided design of experiments resulted in a maximum antibacterial activity of 23.37 ± 2.08 mm, which is a 78.8% increase in comparison with that obtained in the unoptimized medium. This study points the success of statistical model in developing an optimized production media for enhanced antibacterial compound production by Streptomyces sp. JAJ13.

3(2H)-Furanone as a promising scaffold for the synthesis of novel fluorescent organic dyes: an experimental and theoretical investigation

Novel 3(2H)-furanone compounds have been synthesised and characterized. Experimental and theoretical studies indicated that these compounds exhibit interesting solvatochromic effects.

Hyafurones, hyapyrrolines, and hyapyrones: polyketides from Hyalangium minutum

Seven new polyketides, for which the trivial names hyafurones A1-B (1-3), hyapyrrolines A (4) and B (5), and hyapyrones A (6) and B (7) are proposed, were isolated from the fermentation broth of the myxobacteria Hyalangium minutum, strains NOCB-2(T) and Hym-3. Their structures were elucidated from NMR and HRESIMS data, and their geometric configuration was assigned based on NOE and vicinal (1)H coupling data. Both hyafurone B (3) and hyapyrone B (7) inhibited growth of the Gram-positive bacterium Nocardia flava, while 7 showed antifungal activity against Mucor hiemalis.

Computational Methods for Identification of Novel Secondary Metabolite Biosynthetic Pathways by Genome Analysis

Secondary metabolites belonging to polyketide and nonribosomal peptide families constitute a major class of natural products with diverse biological functions and a variety of pharmaceutically important properties. Experimental studies have shown that the biosynthetic machinery for polyketide and nonribosomal peptides involves multi-functional megasynthases like Polyketide Synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) which utilize a thiotemplate mechanism similar to that for fatty acid biosynthesis. Availability of complete genome sequences for an increasing number of microbial organisms has provided opportunities for using in silico genome mining to decipher the secondary metabolite natural product repertoire encoded by these organisms. Therefore, in recent years there have been major advances in development of computational methods which can analyze genome sequences to identify genes involved in secondary metabolite biosynthesis and help in deciphering the putative chemical structures of their biosynthetic products based on analysis of the sequence and structural features of the proteins encoded by these genes. These computational methods for deciphering the secondary metabolite biosynthetic code essentially involve identification of various catalytic domains present in this PKS/NRPS family of enzymes; a prediction of various reactions in these enzymatic domains and their substrate specificities and also precise identification of the order in which these domains would catalyze various biosynthetic steps. Structural bioinformatics analysis of known secondary metabolite biosynthetic clusters has helped in formulation of predictive rules for deciphering domain organization, substrate specificity, and order of substrate channeling. In this chapter, the progress in development of various computational methods is discussed by different research groups, and specifically, the utility in identification of novel metabolites by genome mining and rational design of natural product analogs by biosynthetic engineering studies.

Antibacterial and antifungal activities of polyketide metabolite from marine Streptomyces sp. AP-123 and its cytotoxic effect

A Gram positive, filamentous, spore forming antagonistic Streptomyces sp. AP-123 derived from marine region of Andra Pradesh, India, was studied for its medical importance. Among the 210 Streptomyces strains screened at 64.3% exhibited activity against Gram positive bacteria, 48.5% showed activity towards Gram negative bacteria, 38.8% exhibited both Gram positive and negative bacteria and 80.85% strains revealed significant antifungal activity. However, primary screening revealed that Streptomyces sp. AP-123 exhibited significant antimicrobial activity against all the tested bacteria compared to other Streptomyces strains. The presence of l-diaminopimelic acid and glycine in the cell wall hydrolysates and streptomycin resistance indicated the strain belonged to Streptomyces genus. The 16S rDNA gene based phylogenetic affiliation was determined by using bioinformatic tools and it was identified as Streptomyces sp. AP-123 with 99% sequence similarity to Streptomyces flavogriseus. The antimicrobial substances were extracted by hexane and ethyl acetate from spent medium in which Streptomyces sp. AP-123 was cultivated at 30 °C for 5 d. The antimicrobial activity was assessed using broth micro-dilution technique. A compound was obtained by eluting the crude extract using varying concentrations of solvents followed by the chromatographic purification. Based on the IR, (13)C NMR and (1)H NMR spectral data, the compound was identified as polyketide related antibiotic. It exhibited significant antibacterial activity against Gram positive and Gram negative bacteria and also showed a potent cytotoxic activity against cell lines viz. Vero (Green monkey kidney) and HEP2 (laryngeal carcinoma cells) in vitro. The lowest Minimum Inhibitory Concentration (MIC) of the compound against Bacillus subtilis and Staphylococcus aureus were 25 and 37.5 μg mL(-1), respectively. Against Escherichia coli and Pseudomonas aeruginosa it exhibited MIC of 50 and 37.58 μg mL(-1), respectively. However, against Candida albicans and filamentous fungus, Aspergillus niger the MIC values were 12.5 and 25 μg mL(-1), respectively. Cloning and sequence analysis of ketoacyl synthase (KS) gene revealed similarity to the type II polyketide synthase (PKS) gene of Streptomyces species.

Isolation and initial characterization of a novel type of Baeyer-Villiger monooxygenase activity from a marine microorganism

A novel type of Baeyer–Villiger monooxygenase (BVMO) has been found in a marine strain of Stenotrophomonas maltophila strain PML168 that was isolated from a temperate intertidal zone. The enzyme is able to use NADH as the source of reducing power necessary to accept the atom of diatomic oxygen not incorporated into the oxyfunctionalized substrate. Growth studies have establish that the enzyme is inducible, appears to serve a catabolic role, and is specifically induced by one or more unidentified components of seawater as well as various anthropogenic xenobiotic compounds. A blast search of the primary sequence of the enzyme, recovered from the genomic sequence of the isolate, has placed this atypical BVMO in the context of the several hundred known members of the flavoprotein monooxygenase superfamily. A particular feature of this BVMO lies in its truncated C‐terminal domain, which results in a relatively small protein (357 amino acids; 38.4 kDa). In addition, metagenomic screening has been conducted on DNA recovered from an extensive range of marine environmental samples to gauge the relative abundance and distribution of similar enzymes within the global marine microbial community. Although low, abundance was detected in samples from many marine provinces, confirming the potential for biodiscovery in marine microorganisms.

Phylogenetic-affiliation, antimicrobial potential and PKS gene sequence analysis of moderately halophilic Streptomyces sp. inhabiting an Indian saltpan

A Gram-positive, moderately halophilic Streptomyces strain, designated JAJ06, was isolated from saltpan soil collected at Tuticorin, India, and subjected to a polyphasic characterization with an insight into their biotechnological importance. Growth characteristics and antimicrobial com-pound producing capabilities of Streptomyces sp. JAJ06 were observed on various International Streptomyces Project (ISP) media and production media. Optimum growth was observed on modified ISP 4 medium supplemented with 4% NaCl (w/v) at 29 °C incubated for 7 days. Maximum antibacterial compound production with good mycelial growth was observed on starch-yeast extract-peptone medium prepared with seawater (90%, v/v). The 16S rRNA gene based phylogenetic affiliation was determined by using various bioinformatics tools and the strain was identified as Streptomyces sp. JAJ06 with 99% sequence similarity to Streptomyces radiopugnans(T) . An antimicrobial assay of antimicrobial compound derived from Streptomyces sp. JAJ06 against a set of bacteria and a yeast strain revealed antimicrobial activity with significant minimal inhibitory concentrations. The potential antimicrobial compound produced by Streptomyces sp. JAJ06 was found to be polyketide in nature. Cloning and sequence analysis of 613-bp fragment of ketosynthase gene from the type-II polyketide operon revealed that Streptomyces sp. JAJ06 has the KSα gene with 91% sequence similarity to the type II polyketide synthase gene of Streptomyces peucetius.

Genomics-inspired discovery of natural products

The massive surge in genome sequencing projects has opened our eyes to the overlooked biosynthetic potential and metabolic diversity of microorganisms. While traditional approaches have been successful at identifying many useful therapeutic agents from these organisms, new tactics are needed in order to exploit their true biosynthetic potential. Several genomics-inspired strategies have been successful in unveiling new metabolites that were overlooked under standard fermentation and detection conditions. In addition, genome sequences have given us valuable insight for genetically engineering biosynthesis gene clusters that remain silent or are poorly expressed in the absence of a specific trigger. As more genome sequences are becoming available, we are noticing the emergence of underexplored or neglected organisms as alternative resources for new therapeutic agents.

Sequence-based analysis of secondary-metabolite biosynthesis in marine actinobacteria

A diverse collection of 60 marine-sediment-derived Actinobacteria representing 52 operational taxonomic units was screened by PCR for genes associated with secondary-metabolite biosynthesis. Three primer sets were employed to specifically target adenylation domains associated with nonribosomal peptide synthetases (NRPSs) and ketosynthase (KS) domains associated with type I modular, iterative, hybrid, and enediyne polyketide synthases (PKSs). In total, two-thirds of the strains yielded a sequence-verified PCR product for at least one of these biosynthetic types. Genes associated with enediyne biosynthesis were detected in only two genera, while 88% of the ketosynthase sequences shared greatest homology with modular PKSs. Positive strains included representatives of families not traditionally associated with secondary-metabolite production, including the Corynebacteriaceae, Gordoniaceae, Intrasporangiaceae, and Micrococcaceae. In four of five cases where phylogenetic analyses of KS sequences revealed close evolutionary relationships to genes associated with experimentally characterized biosynthetic pathways, secondary-metabolite production was accurately predicted. Sequence clustering patterns were used to provide an estimate of PKS pathway diversity and to assess the biosynthetic richness of individual strains. The detection of highly similar KS sequences in distantly related strains provided evidence of horizontal gene transfer, while control experiments designed to amplify KS sequences from Salinispora arenicola strain CNS-205, for which a genome sequence is available, led to the detection of 70% of the targeted PKS pathways. The results provide a bioinformatic assessment of secondary-metabolite biosynthetic potential that can be applied in the absence of fully assembled pathways or genome sequences. The rapid identification of strains that possess the greatest potential to produce new secondary metabolites along with those that produce known compounds can be used to improve the process of natural-product discovery by providing a method to prioritize strains for fermentation studies and chemical analysis.

Genomic basis for natural product biosynthetic diversity in the actinomycetes

The phylum Actinobacteria hosts diverse high G + C, Gram-positive bacteria that have evolved a complex chemical language of natural product chemistry to help navigate their fascinatingly varied lifestyles. To date, 71 Actinobacteria genomes have been completed and annotated, with the vast majority representing the Actinomycetales, which are the source of numerous antibiotics and other drugs from genera such as Streptomyces, Saccharopolyspora and Salinispora . These genomic analyses have illuminated the secondary metabolic proficiency of these microbes – underappreciated for years based on conventional isolation programs – and have helped set the foundation for a new natural product discovery paradigm based on genome mining. Trends in the secondary metabolomes of natural product-rich actinomycetes are highlighted in this review article, which contains 199 references.

TLN-05220, TLN-05223, new Echinosporamicin-type antibiotics, and proposed revision of the structure of bravomicins(*)

The deposited strain of the hazimicin producer, Micromonospora echinospora ssp. challisensis NRRL 12255 has considerable biosynthetic capabilities as revealed by genome scanning. Among these is a locus containing both type I and type II PKS genes. The presumed products of this locus, TLN-05220 (1) and TLN-05223 (2), bear a core backbone composed of six fused rings starting with a 2-pyridone moiety. The structures were confirmed by conventional spectral analyses including MS, and 1D and 2D NMR experiments. Comparison of both the 1H and 13C NMR data of the newly isolated compound with those of echinosporamicin and bravomicin A led us to propose a revision of the structure of the latter to include a 2-pyridone instead of the pyran originally postulated. Both compounds (1 and 2) possessed strong antibacterial activity against a series of gram-positive pathogens including several strains of methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococci (VRE), and cytotoxic activities against several human tumor cell lines. The TLN compounds are the first of this group with reported anticancer activity.

Advances in the understanding and use of the genomic base of microbial secondary metabolite biosynthesis for the discovery of new natural products

Over the past decade major changes have occurred in the access to genome sequences that encode the enzymes responsible for the biosynthesis of secondary metabolites, knowledge of how those sequences translate into the final structure of the metabolite, and the ability to alter the sequence to obtain predicted products via both homologous and heterologous expression. Novel genera have been discovered leading to new chemotypes, but more surprisingly several instances have been uncovered where the apparently general rules of modular translation have not applied. Several new biosynthetic pathways have been unearthed, and our general knowledge grows rapidly. This review aims to highlight some of the more striking discoveries and advances of the decade.

Triggering cryptic natural product biosynthesis in microorganisms

Natural products from microorganisms are a crucial source for novel therapeutics. Even so, it seems that many valuable compounds are overlooked when culturing microbes under standardized laboratory conditions. Many biosynthesis genes remain silent and such "cryptic" or "orphan" pathways are only activated under specific conditions. This report gives an overview on the strategies to trigger biosynthetic pathways to yield "cryptic natural products" through external cues, co-cultivation and genomic approaches such as genome-mining, epigenetic remodeling, and engineered pathway activation.

Novel approaches to discovery of antibacterial agents

Antimicrobial resistance is a rapidly increasing problem impacting the successful treatment of bacterial infectious disease. To combat resistance, the development of new treatment options is required. Recent advances in technology have aided in the discovery of novel antibacterial agents, specifically through genome mining for novel natural product biosynthetic gene clusters and improved small molecule high-throughput screening methods. Novel targets such as lipopolysaccharide and fatty acid biosyntheses have been identified by essential gene studies, representing a shift from traditional antibiotic targets. Finally, inhibiting non-essential genes with small molecules is being explored as a method for rescuing the activity of ‘old’ antibiotics, providing a novel synergistic approach to antimicrobial discovery.

Heavy tools for genome mining

In this issue of Chemistry & Biology, Gross et al. report development of a novel genome mining method for isolating products of orphan biosynthetic gene clusters, and the application of this method to the isolation of orfamide A, a novel cyclic lipopeptide.

From genetic diversity to metabolic unity: studies on the biosynthesis of aurafurones and aurafuron-like structures in myxobacteria and streptomycetes

The myxobacterial polyketide secondary metabolites aurafuron A and B were identified by genome mining in the myxobacterial strain Stigmatella aurantiaca DW4/3-1. The compounds contain an unusual furanone moiety and resemble metabolites isolated from soil-dwelling and marine actinobacteria, a fungus and mollusks. We describe here the cloning and functional analysis of the aurafuron biosynthetic gene cluster, including site-directed mutagenesis and feeding studies using labeled precursors. The polyketide core of the aurafurones is assembled by a modular polyketide synthase (PKS). As with many such systems described from myxobacteria, the aurafuron PKS exhibits a number of unusual features, including the apparent iterative use of a module, redundant modules and domains, a trans acting dehydratase and the absence of a terminal thioesterase domain. Four oxidoreductases are encoded within the gene locus, some of which likely participate in formation of the furanone moiety via a Baeyer-Villiger type oxidation. Indeed, inactivation of a gene encoding a cytochrome P(450) monooxygenase completely abolished production of both compounds. We also compare the complete gene locus to biosynthetic gene clusters from two Streptomyces sp., which produce close structural analogues of the aurafurones. A portion of the post-PKS biosynthetic machinery is strikingly similar in all three cases, in contrast to the PKS genes, which are highly divergent. Phylogenetic analysis of the ketosynthase domains further indicates that the PKSs have developed independently (polyphyletically) during evolution. These findings point to a currently unknown but important biological function of aurafuron-like compounds for the producing organisms.

New aspects of natural products in drug discovery

During the past 15 years, most large pharmaceutical companies have decreased the screening of natural products for drug discovery in favor of synthetic compound libraries. Main reasons for this include the incompatibility of natural product libraries with high-throughput screening and the marginal improvement in core technologies for natural product screening in the late 1980s and early 1990 s. Recently, the development of new technologies has revolutionized the screening of natural products. Applying these technologies compensates for the inherent limitations of natural products and offers a unique opportunity to re-establish natural products as a major source for drug discovery. Examples of these new advances and technologies are described in this review.

The value of natural products to future pharmaceutical discovery

Natural products have provided considerable value to the pharmaceutical industry over the past half century. In particular, the therapeutic areas of infectious diseases and oncology have benefited from numerous drug classes derived from natural product sources. Unfortunately, pharmaceutical companies have significantly decreased activities in natural product discovery during the past several years. Biotechnology companies working in the fields of combinatorial biosynthesis, genetic engineering and metagenomic approaches to identify novel natural product lead molecules have had limited success. Despite what appears to be a slow death of natural product discovery research, many new and interesting molecules with biological activity have been published in the past few years. If natural product materials continue to be tested for desirable therapeutic activities, we believe that significant progress in identifying new antibiotics, oncology therapeutics and other useful medicines will be made.

Molecular basis for chloronium-mediated meroterpene cyclization: cloning, sequencing, and heterologous expression of the napyradiomycin biosynthetic gene cluster

Structural inspection of the bacterial meroterpenoid antibiotics belonging to the napyradiomycin family of chlorinated dihydroquinones suggests that the biosynthetic cyclization of their terpenoid subunits is initiated via a chloronium ion. The vanadium-dependent haloperoxidases that catalyze such reactions are distributed in fungi and marine algae and have yet to be characterized from bacteria. The cloning and sequence analysis of the 43-kb napyradiomycin biosynthetic cluster (nap) from Streptomyces aculeolatus NRRL 18422 and from the undescribed marine sediment-derived Streptomyces sp. CNQ-525 revealed 33 open reading frames, three of which putatively encode vanadium-dependent chloroperoxidases. Heterologous expression of the CNQ-525-based nap biosynthetic cluster in Streptomyces albus produced at least seven napyradiomycins, including the new analog 2-deschloro-2-hydroxy-A80915C. These data not only revealed the molecular basis behind the biosynthesis of these novel meroterpenoid natural products but also resulted in the first in vivo verification of vanadium-dependent haloperoxidases.