Biomedicinal Information Research Center

Kōtō-ku, Japan

Biomedicinal Information Research Center

Kōtō-ku, Japan
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Khan S. T.,Biomedicinal Information Research Center | Komaki H.,Biomedicinal Information Research Center | Komaki H.,Chiba Institute of Technology | Motohashi K.,Biomedicinal Information Research Center | And 4 more authors.
Environmental Microbiology | Year: 2011

Terrestrial actinobacteria have served as a primary source of bioactive compounds; however, a rapid decrease in the discovery of new compounds strongly necessitates new investigational approaches. One approach is the screening of actinobacteria from marine habitats, especially the members of the genus Streptomyces. Presence of this genus in a marine sponge, Haliclona sp., was investigated using culture-dependent and -independent techniques. 16S rRNA gene clone library analysis showed the presence of diverse Streptomyces in the sponge sample. In addition to the dominant genus Streptomyces, members of six different genera were isolated using four different media. Five phylogenetically new strains, each representing a novel species in the genus Streptomyces were also isolated. Polyphasic study suggesting the classification of two of these strains as novel species is presented. Searching the strains for the production of novel compounds and the presence of biosynthetic genes for secondary metabolites revealed seven novel compounds and biosynthetic genes with unique sequences. In these compounds, JBIR-43 exhibited cytotoxic activity against cancer cell lines. JBIR-34 and -35 were particularly interesting because of their unique chemical skeleton. To our knowledge, this is the first comprehensive study detailing the isolation of actinobacteria from a marine sponge and novel secondary metabolites from these strains. © 2010 Society for Applied Microbiology and Blackwell Publishing Ltd.


Khan S.T.,Biomedicinal Information Research Center | Tamura T.,Chiba Institute of Technology | Takagi M.,Biomedicinal Information Research Center | Shin-ya K.,Japan National Institute of Advanced Industrial Science and Technology
International Journal of Systematic and Evolutionary Microbiology | Year: 2010

Three Gram-positive, NaCl-requiring actinobacteria were isolated from a marine sponge, Haliclona sp., collected from the coast of Tateyama City, Japan. Comparison of 16S rRNA gene sequences indicated that these strains represent novel members of the genus Streptomyces, exhibiting low 16S rRNA gene sequence similarities of 98.3-97.4% with recognized members of the genus. The cell hydrolysates contained the LL-isomer of diaminopimelic acid and the predominant quinones were MK-9 (H6 and/or H8). The DNA G+C contents were in the range 72-75 mol%. A polyphasic study of the strains and comparison of the characters with related species of the genus show that these strains represent three novel species of the genus Streptomyces. Therefore, the names Streptomyces tateyamensis sp. nov., Streptomyces haliclonae sp. nov. and Streptomyces marinus sp. nov. are proposed for strains Sp080513SC-30T (=NBRC 105048T =DSM 41969T), Sp080513SC-31T (=NBRC 105049T =DSM 41970T) and Sp080513GE-26T (=NBRC 105047T =DSM 41968T), respectively. © 2010 IUMS.


Khan S.T.,Biomedicinal Information Research Center | Khan S.T.,King Saud University | Takagi M.,Biomedicinal Information Research Center | Shin-Ya K.,Japan National Institute of Advanced Industrial Science and Technology
Microbes and Environments | Year: 2011

Actinobacteria associated with 3 marine sponges, Cinachyra sp., Petrosia sp., and Ulosa sp., were investigated. Analyses of 16S rRNA gene clone libraries revealed that actinobacterial diversity varied greatly and that Ulosa sp. was most diverse, while Cinachyra sp. was least diverse. Culture-based approaches failed to isolate actinobacteria from Petrosia sp. or Ulosa sp., but strains belonging to 10 different genera and 3 novel species were isolated from Cinachyra sp.


Izumikawa M.,Biomedicinal Information Research Center | Takagi M.,Biomedicinal Information Research Center | Shin-Ya K.,Japan National Institute of Advanced Industrial Science and Technology
Journal of Natural Products | Year: 2012

The search for metabolites of Kibdelosporangium sp. AK-AA56 resulted in the discovery of novel N-phenylacetylated peptides, JBIR-78 (1) and JBIR-95 (2). Compounds 1 and 2 were established to be N-phenylacetylated heptapeptides by extensive NMR and HRESIMS analyses. The absolute configuration of the standard amino acids including a cysteic acid moiety was determined using Marfey's method on the acid hydrolysates of 1 and 2. The relative and absolute configurations of a nonstandard amino acid, β-hydroxyleucine, were elucidated using the J-based and modified Mosher's methods, respectively. In an antimicrobial test, 1 showed antibacterial activity against Micrococcus luteus. © 2012 The American Chemical Society and American Society of Pharmacognosy.


Gyobu N.,Biomedicinal Information Research Center
Methods in molecular biology (Clifton, N.J.) | Year: 2013

Once 2D crystals suitable for electron crystallography have been obtained, grid preparation for cryo-EM is a critical step in obtaining high-resolution structural information. Specimens have to be prepared in a manner that prevents dehydration and disruption of the crystals in the vacuum of the electron microscope. Sugar embedding is an effective way to preserve specimens in the native and hydrated state. Preparation of almost perfectly flat specimens is another prerequisite. Imperfect specimen flatness is a crucial problem in the recording of images and diffraction patterns at higher tilt angles because it causes the blurring of spots perpendicular to the tilt axis. In this chapter, we describe the protocols of preparing 2D crystal specimen for electron crystallographical data collection. These protocols cover preparation of a flat carbon support film by sparkless carbon evaporation, sugar embedding using back injection, and the recently developed carbon sandwich technique.


Hosoya T.,Biomedicinal Information Research Center | Hirokawa T.,Japan National Institute of Advanced Industrial Science and Technology | Takagi M.,Biomedicinal Information Research Center | Shin-Ya K.,Japan National Institute of Advanced Industrial Science and Technology
Journal of Natural Products | Year: 2012

Three new trichostatin analogues, JBIR-109 (1), JBIR-110 (2), and JBIR-111 (3), were isolated from the culture of the marine sponge-derived Streptomyces sp. strain RM72, together with trichostatin A (4) and trichostatic acid (5). The planar structures of 1-3 were determined on the basis of extensive NMR and MS analyses. In addition, the absolute configurations of the amino acid residues were determined by Marfey's method. The histone deacetylase inhibitory activities of 1-5 were examined, and their structure-activity relationships are discussed. © 2012 The American Chemical Society and American Society of Pharmacognosy.


Izumikawa M.,Biomedicinal Information Research Center | Tabrez Khan S.,Biomedicinal Information Research Center | Takagi M.,Biomedicinal Information Research Center | Shin-ya K.,Japan National Institute of Advanced Industrial Science and Technology
Journal of Natural Products | Year: 2010

In the course of our screening program for isoprenoids of marine actinobacterial origin, 523 actinobacterial strains were isolated from marine samples. Actinobacteria usually use the 2-C-methyl-D-erythritol 4-phosphate pathway for the production of primary metabolites, but some have been reported to use the mevalonate (MVA) pathway for the production of isoprenoids as secondary metabolites. 3-Hydroxy-3-methyl glutaryl coenzyme A reductase (HMGR) is a key enzyme and plays an important role in the MVA pathway. Therefore, we screened strains possessing the HMGR gene from the 523 strains mentioned above and also investigated isoprenoid compounds from cultures of strains possessing HMGR genes. As a result, Streptomyces sp. SpC080624SC-11 isolated from a marine sponge, Cinachyra sp., was shown to possess the HMGR gene and produce novel isoprenoids, JBIR-46 (1), -47 (2), and -48 (3). On the basis of extensive NMR and MS analyses, the structures of 1-3 were determined to be phenazine derivatives harboring dimethylallyl moieties. Furthermore, the isoprene units of 2 and 3 were confirmed to be synthesized via the MVA pathway in a feeding experiment using [1-13C]acetate. © 2010 American Chemical Society and American Society of Pharmacognosy.


Motohashi K.,Biomedicinal Information Research Center | Takagi M.,Biomedicinal Information Research Center | Shin-ya K.,Japan National Institute of Advanced Industrial Science and Technology
Journal of Natural Products | Year: 2010

Two new modified indole-containing peptides, JBIR-34 (1) and JBIR-35 (2), were isolated from the fermentation broth of a sponge-derived actinomycete identified by phylogenetic methods as a Streptomyces sp. (strain Sp080513GE-23). The planar structures of 1 and 2 were assigned on the basis of ID and 2D NMR spectroscopy and MS analyses. Further, the absolute configurations of the amino acid residues were determined using Marfey's method. © 2010 American Chemical Society and American Society of Pharmacognosy.


Motohashi K.,Biomedicinal Information Research Center | Takagi M.,Biomedicinal Information Research Center | Shin-Ya K.,Japan National Institute of Advanced Industrial Science and Technology
Journal of Natural Products | Year: 2010

Two new anthracyclines, tetracenoquinocin (1) and 5-iminoaranciamycin (2), together with the known compounds aranciamycin (3) and antibiotic SM 173B were isolated from the culture of Streptomyces sp. Sp080513GE-26 associated with a marine sponge, Haliclona sp. The structures of 1 and 2 were established on the basis of extensive NMR and MS analyses along with 13C-labeling experiments. The compounds 1-3 were evaluated for cytotoxicity against two cancer cell lines. © 2010 The American Chemical Society and American Society of Pharmacognosy.


Hwang J.-H.,Japan National Institute of Advanced Industrial Science and Technology | Takagi M.,Biomedicinal Information Research Center | Murakami H.,Aichi Cancer Center Research Institute | Sekido Y.,Aichi Cancer Center Research Institute | And 2 more authors.
Cancer Letters | Year: 2011

Malignant pleural mesothelioma (MPM) is a highly aggressive tumor with a poor prognosis. Thus, novel therapeutic agents need to be developed for treating it. We recently reported the isolation of the novel anti-MPM compound designated as JBIR-23 from Streptomyces sp. AK-AB27. In this study, JBIR-23 exerted its cytotoxic effect on MPM cells by promotion of tubulin polymerization and G 2/M arrest, which was followed by apoptosis induction via the caspase pathway through phosphorylation of p38 mitogen-activated protein kinase and c-jun N-terminal kinase. Furthermore, in vivo analysis demonstrated that JBIR-23 prevented tumor growth in tumor-bearing nude mice without evident side effects. © 2010 Elsevier Ireland Ltd.

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