Hisayuki Komaki

DoBISCUIT: a database of secondary metabolite biosynthetic gene clusters

This article introduces DoBISCUIT (Database of BIoSynthesis clusters CUrated and InTegrated, http://www.bio.nite.go.jp/pks/), a literature-based, manually curated database of gene clusters for secondary metabolite biosynthesis. Bacterial secondary metabolites often show pharmacologically important activities and can serve as lead compounds and/or candidates for drug development. Biosynthesis of each secondary metabolite is catalyzed by a number of enzymes, usually encoded by a gene cluster. Although many scientific papers describe such gene clusters, the gene information is not always described in a comprehensive manner and the related information is rarely integrated. DoBISCUIT integrates the latest literature information and provides standardized gene/module/domain descriptions related to the gene clusters.

Streptomyces associated with a marine sponge Haliclona sp.; biosynthetic genes for secondary metabolites and products.

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.

JBIR-31, a new teleocidin analog, produced by salt-requiring Streptomyces sp. NBRC 105896 isolated from a marine sponge.

JBIR-31, a new teleocidin analog, produced by salt-requiring Streptomyces sp. NBRC 105896 isolated from a marine sponge

New sesquiterpenes, JBIR-27 and -28, isolated from a tunicate-derived fungus, Penicillium sp. SS080624SCf1

In the course of our screening program for novel metabolites from tunicate-derived fungi, novel sesquiterpenoids, named JBIR-27 (1) and -28 (2), together with known sporogen-AO1 and phomenone, were isolated from the culture broth of Penicillium sp. SS080624SCf1. The structures of 1 and 2 were determined to be eremophilane analogs on the basis of extensive NMR and MS analyses. Sporogen-AO1, phomenone and 2 showed cytotoxicity against human cervical carcinoma cell line HeLa at IC50 values of 8.3, 19 and 92 μM, respectively, whereas 1 was inactive at a concentration of 80 μM.

PCR Detection of Type I Polyketide Synthase Genes in Myxobacteria

ABSTRACT The diversity of type I modular polyketide synthase (PKS) was explored by PCR amplification of DNA encoding ketosynthase and acyltransferase domains in myxobacteria. The sequencing of the amplicons revealed that many PKS genes were distantly related to the published sequences. Thus, myxobacteria may be excellent resources for novel and diverse polyketides.

New Aureothin Derivative, Alloaureothin, from Streptomyces sp. MM23

A new polypropionate alloaureothin (1) possessing a nitro group, together with a known polypropionate aureothin (2), was isolated from mycelium of Streptomyces sp. MM23. The structure was determined on the basis of spectroscopic data. 1 exhibited growth inhibitory effect against human fibrosarcoma HT1080 cells with an IC50 value of 30 μM.

JBIR-37 and -38, Novel Glycosyl Benzenediols, Isolated from the Sponge-Derived Fungus, Acremonium sp. SpF080624G1f01

In the course of our chemical screening program for new secondary metabolites, we isolated new compounds JBIR-37 (1) and -38 (2) from a culture broth of the marine sponge-derived fungus, Acremonium sp. SpF080624G1f01. The structures of 1 and 2 were determined to be di- and mono-O-β-D-glucopyranosyloxy-4-(1,1-dimethyl-2-propenyl)benzene on the basis of extensive NMR and MS spectroscopic data, respectively.

Discovery of a pimaricin analog JBIR-13, from Streptomyces bicolor NBRC 12746 as predicted by sequence analysis of type I polyketide synthase gene

Sequence analysis of ketosynthase domain amplicons from Streptomyces bicolor NBRC 12746T revealed the presence of previously unreported type I polyketide synthases (PKS-I) genes. The clustering of these genes with the reference PKS-1 sequences suggested the possibility to produce a polyene compound similar to pimaricin. Thus, the cultured sample from NBRC 12746T was analyzed for the production of polyene compounds. The strain produced an antifungal compound which displayed the UV absorption spectrum of tetraene macrolides. The structure determination based on the spectroscopic analysis of the purified compound resulted in the identification of a novel pimaricin analog JBIR-13 (1). This study therefore strongly suggested that a careful analysis of PKS-I genes can provide valuable information in the search of novel bioactive compounds within a class predicted from phylogenetic analysis.

Taxonomic distribution of Streptomyces species capable of producing bioactive compounds among strains preserved at NITE/NBRC

The taxonomic distribution of Streptomyces species capable of producing bioactive compounds was investigated. Nine hundred and six strains were tested for the following four biological activities: antimicrobial, anti-tyrosinase, antioxidant, and hemolytic. Approximately 30% of strains tested showed antimicrobial activities, except for anti-Escherichia coli activity, which was present in only a few strains, while the rates of positivity for the anti-tyrosinase, antioxidant, and hemolytic activities were much lower. The distribution of Streptomyces strains capable of producing bioactive compounds was analyzed by the taxonomy based on 16S rRNA gene sequences. Moreover, the strains of Streptomyces hygroscopicus tested were divided into two clades in the phylogenetic tree, and all of the strains belonging to one clade showed antibacterial and antifungal activities. For detection of polyenes, the UV–visible spectra of metabolic extracts in the strains showing antifungal activities were measured. It was suggested that Streptomyces strains produce universal active compounds under different growth conditions. Further information on the relationship between the microbial taxonomy and the bioactive compounds produced would be useful for the utilization of industrial microorganisms.

Draft Genome Sequence of Marine-Derived Streptomyces sp. TP-A0873, a Producer of a Pyrrolizidine Alkaloid Bohemamine

ABSTRACT Streptomyces sp. TP-A0873, isolated from deep-sea water, produces three different classes of secondary metabolites: antimycin, bohemamine, and alkylated butenolides. In order to assess the biosynthetic potential of this strain, draft genome sequencing was carried out. The genome contained at least 14 gene clusters for polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS).