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After the successful discoveries of numerous antibiotics from microorganisms, frequent reisolation of known compounds becomes an obstacle in further development of new drugs from natural products. Exploration of biological sources that can provide novel scaffolds is thus an urgent matter in drug lead screening. As an alternative source to the conventionally used soil microorganisms, we selected endophytic actinomycetes, marine actinomycetes, and actinomycetes in tropical areas for investigation and found an array of new bioactive compounds. Furthermore, based on the analysis of the distribution pattern of biosynthetic gene clusters in bacteria together with available genomic data, we speculated that biosynthetic gene clusters for secondary metabolites are specific to each genus. Based on this assumption, we investigated actinomycetal and marine bacterial genera from which no compounds have been reported, which led to the discovery of a variety of skeletally novel bioactive compounds. These findings suggest that consideration of environmental factor and taxonomic position is critically effective in the selection of potential strains producing structurally unique compounds.

A new pluramycin-class polyketide, rausuquinone (1), and its known congener hydramycin (2) were isolated from the culture extract of the deep-sea water-derived Rhodococcus sp. RD015140. Compound 1 possesses a γ-pyrone-fused anthraquinone core with a 3-butene-1,2-diol side chain. Structures of 1 was determined by extensive analysis of 1D and 2D NMR spectroscopic data. Compound 1 showed antimicrobial activity against Gram-positive bacteria. This is the first discovery of aromatic polyketides from the genus Rhodococcus.

A new catecholate-containing siderophore, labrenzbactin (1), was isolated from the fermentation broth of a coral-associated bacterium Labrenzia sp. The structure and absolute configuration of 1 was determined by spectroscopic methods and Marfey’s analysis. Overall, 1 showed antimicrobial activity against Ralstonia solanacearum SUPP1541 and Micrococcus luteus ATCC9341 with MIC values of 25 and 50 µg ml−1, respectively, and cytotoxicity against P388 murine leukemia cells with an IC50 of 13 µM.

Two new naphthohydroquinone derivatives designated iseoic acids A (1) and B (2) and a new symmetrical glycerol bisester of naphthoquinonepropanoic acid designated bisiseoate (3) were isolated from the culture extract of a marine-derived actinomycete Streptomyces sp. DC4-5. The structures of 1–3 were determined by analyzing one- and two-dimensional NMR data and MS analytical data. The absolute configurations were determined by NOESY analysis and the phenylglycine methyl ester (PGME) method for 1 and by considering the structural similarity and biosynthesis for 2 and 3. Compound 3 exhibited modest cytotoxicity against P388 murine leukemia cells with an IC50 value of 19 μM.

Iseolides A–C (1–3), three new glycosylated macrolides, were identified from the culture extract of Streptomyces sp. DC4-5 isolated from a stony coral Dendrophyllia. Extensive analysis of one- and two-dimensional NMR data, coupled with MS/MS analytical data, revealed that iseolides are new congeners of 36-membered macrolides, PM100117 and PM100118, previously reported from a marine-derived Streptomyces. Iseolides showed potent antifungal activity against a plant pathogen Glomerella cingulata and human pathogens Candida albicans and Trichophyton rubrum with MIC in the range of 0.19–6.25 μg/mL.

Botryorhodines K (1) and L (2), two new depsidone derivatives, along with one known metabolite, 4-O-demethylbarbatic acid (3), were isolated from the culture extract of a fungus of the genus Arcopilus. The structures of 1‒3 were determined by the analysis of NMR and MS spectral data and the absolute configuration of 1 was established by single-crystal X-ray diffraction analysis. Compounds 1 and 2 showed antimicrobial activity against Gram-positive bacteria and cytotoxicity against murine leukemia P388 cells.

Trehangelin E (1), a new bisacyl trehalose, was isolated from the culture extract of an actinomycete Polymorphospora sp. RD064483, along with three known congeners, trehangelins A, B, and D. Compound 1 is a new trehalose derivative acylated with (Z)-2-methyl-2-butenoic acid (angelic acid) at 3- and 6ʹ-positions, as determined by NMR and MS analyses. Compound 1 promoted root elongation of germinated lettuce seeds by 30% at 1 μM and 90% at 10 μM compared to the nontreated seeds. Similar promoting activity of root elongation was also observed with trehangelins A and B at the same level.

Streptomyces sp. CHI39, isolated from a rock soil sample, is a producer of abyssomicin I. The taxonomic status was clarified by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain was closely related to Streptomyces fragilis, with similarity of 99.9%. Strain CHI39 comprised LL-diaminopimelic acid, glutamic acid, glycine, and alanine in its peptidoglycan. The predominant menaquinones were MK-9(H6), and major fatty acids were anteiso-C15:0, anteiso-C17:0, and iso-C16:0. The chemotaxonomic features matched those described for the genus Streptomyces. Genome sequencing was conducted for strain CHI39 and S. fragilis NBRC 12862T. The results of digital DNA–DNA hybridization along with differences in phenotypic characteristics between the strains suggested strain CHI39 to be a novel species, for which Streptomyces abyssomicinicus sp. nov. is proposed; the type strain is CHI39T (=NBRC 110469T). Next, we surveyed polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) gene clusters in genomes of S. abyssomicinicus CHI39T and S. fragilis NBRC 12862T. These strains encoded 9 and 12 clusters, respectively, among which only four clusters were shared between them while the others are specific in each strain. This suggests that strains classified to distinct species each harbor many specific secondary metabolite-biosynthetic pathways even if the strains are taxonomically close.

A rare actinomycetal strain of the genus Actinomycetospora was found to produce a new tryptophan derivative, designated mycetoindole (1). The structure of 1 was determined to be N-3-methylcrotonoyl (Z)-dehydrotryptophan by NMR and MS analytical methods. Compound 1 reduced the root growth of lettuce Lactuca sativa seedlings at concentrations above 0.1 μM and almost completely inhibited seed germination at 10 μM.