Published Papers - SHINZATO Naoya

New antimalarial iromycin analogs produced by <i>Streptomyces</i> sp. RBL-0292

Kimura, SI; Watanabe, Y; Shibasaki, S; Shinzato, N; Inahashi, Y; Sunazuka, T; Hokari, R; Ishiyama, A; Iwatsuki, M

JOURNAL OF ANTIBIOTICS ( Journal of Antibiotics )  77 ( 5 ) 272 - 277   2024.03 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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Two new antimalarial compounds, named prenylpyridones A (1) and B (2), were discovered from the actinomycete cultured material of Streptomyces sp. RBL-0292 isolated from the soil on Hamahiga Island in Okinawa prefecture. The structures of 1 and 2 were elucidated as new iromycin analogs having α-pyridone ring by MS and NMR analyses. Compounds 1 and 2 showed moderate in vitro antimalarial activity against chloroquine-sensitive and chloroquine-resistant Plasmodium falciparum strains, with IC50 values ranging from 80.7 to 106.7 µM.

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Precezomycin, a novel antibiotic biosynthetic precursor of cezomycin, from actinomycete <i>Kitasatospora putterlickiae</i> 10-13

Mao, D; Yu, PW; Shinzato, N; Zhang, L; Zheng, WP; Lu, S; Kakeya, H

JOURNAL OF ANTIBIOTICS ( Journal of Antibiotics )  77 ( 3 ) 182 - 184   2024.03 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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A novel antibiotic biosynthetic precursor of cezomycin, named precezomycin (1), was isolated from culture broth of actinomycete Kitasatospora putterlickiae 10-13. The planar structure was determined by 1D/2D NMR and HR(ESI)MS data analyses, and the absolute configurations were established by TDDFT calculation of ECD spectra. Precezomycin (1) exhibited moderate antibacterial activity against gram-positive bacteria including Staphylococcus aureus and Bacillus subtilis. The discovery of 1 extends the natural product family of cezomycin and provides a new insight into understanding the biosynthetic process of these polyether ionophore metabolites.

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Effect of Bagasse on the Activity of Alkane-Degrading Bacteria Isolated from Waste Oil

SARAYAMA Kae, FUJII Yuta, HINO Ryota, ONISHI Kenji, NISHIKAWA Naohito, OGATA Hiroki, HIROSE Kosaburo, SHINZATO Naoya, MATSUBARA Hitoshi

Journal of the Society of Materials Science, Japan ( The Society of Materials Science, Japan )  73 ( 1 ) 58 - 63   2024.01 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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<p>This study investigates the effects of bagasse addition on the activity of alkane-degrading bacteria derived from waste oil. Bagasse, a fibrous residue of sugarcane after juice extraction, has potential as a substrate for various microbial process. In this experiment, alkane-degrading bacteria were isolated from waste oil samples in Okinawa, Japan and their activity in tetracosane and triacontane, which are alkanes constituting machine oils, was evaluated in the presence of dried bagasse, bagasse ash, and carbonized bagasse. The results indicate that addition of dried bagasse and bagasse ash significantly enhances the activity of the bacteria, leading to improved alkane degradation of tetracosane and triacontane. The findings suggests that bagasse can serve as a promising co-substrate for enhancing the efficiency of microbial remediation of oil-contaminated environments.</p>

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Amoxetamide A, a new anoikis inducer, produced by combined-culture of Amycolatopsis sp. and Tsukamurella pulmonis

Pan, CQ; Ikeda, H; Minote, M; Tokuda, T; Kuranaga, T; Taniguchi, T; Shinzato, N; Onaka, H; Kakeya, H

JOURNAL OF ANTIBIOTICS ( Journal of Antibiotics )  77 ( 1 ) 66 - 70   2023.10 [ Peer Review Accepted ]

Type of publication: Research paper (other science council materials etc.)

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Cancer cells including colorectal cancer cells are resistant to anoikis, an anchorage-independent programmed death, which enables metastasis and subsequent survival in a new tumor microenvironment. In this study, we identified a new anoikis inducer, amoxetamide A (1) with a β-lactone moiety, that was produced by combined-culture of Amycolatopsis sp. 26-4 and mycolic acid-containing bacteria (MACB) Tsukamurella pulmonis TP-B0596. The structure of 1 including the stereochemistry of C8 was determined by MS and NMR spectroscopy and modified Mosher's method, and the absolute configurations of C11 and C12 were suggested as 11R and 12S, respectively, by GIAO NMR calculations. Amoxetamide A (1) exhibited anoikis-inducing activity in human colorectal cancer HT-29 cells in anchorage-independent culture conditions.

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Microbial symbiosis in anaerobic ciliates

Naoya Shinzato

The CELL   55 ( 6 ) 37 - 41   2023.05

Type of publication: Research paper (scientific journal)

Complete Genome Sequence of "<i>Candidatus</i> Hydrogeosomobacter endosymbioticus," an Intracellular Bacterial Symbiont of the Anaerobic Ciliate Scuticociliate GW7.

Shiohama Y, Takeshita K, Hirakata Y, Nobu MK, Ito M, Shinzato N

Microbiology resource announcements ( Microbiology Resource Announcements )  11 ( 2 ) e0115021   2022.02 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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The bacterium “ <italic>Candidatus</italic> Hydrogenosomobacter endosymbioticus” is an intracellular symbiont of anaerobic scuticociliate GW7, which is associated with hydrogenosome together with methanogenic archaea. Here, we report a complete genome sequence of the symbiont consisting of 827 kbp. Knowing this sequence would contribute to the understanding of the metabolic interactions and evolution of the tripartite symbiosis.

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Amycolapeptins A and B, Cyclic Nonadepsipeptides Produced by Combined-culture of <i>Amycolatopsis</i> sp. and <i>Tsukamurella pulmonis</i>.

Pan C, Kuranaga T, Cao X, Suzuki T, Dohmae N, Shinzato N, Onaka H, Kakeya H

The Journal of organic chemistry ( Journal of Organic Chemistry )  86 ( 2 ) 1843 - 1849   2021.01 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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Two nonapeptide natural products, amycolapeptins A (1) and B (2) with a 22-membered cyclic depsipeptide skeleton, β-hydroxytyrosine, and a highly modified side chain, which were not produced in a monoculture of the rare actinomycete Amycolatopsis sp. 26-4, were discovered in broth of its combined-culture with Tsukamurella pulmonis TP-B0596. The planar structures were elucidated by spectroscopic analyses (extensive 2D-NMR and MALDI-TOF MS/MS). The absolute configurations of component amino acids were unambiguously determined by the highly sensitive advanced Marfey's method we recently developed. Additionally, the structures of unstable/unusual moieties were corroborated by chemical synthesis and CD analysis.

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Pseudoalteropeptide A, A Novel Lipopeptide from the Marine Bacterium Pseudoalteromonas piscicida SWA4_PA4 Isolated from Marine Seaweed

Reiko Ueoka, Naoya Shinzato, Noritaka Kagaya, Hikaru Suenaga, Kazuo Shin-ya

The Journal of Antibiotics   74   105 - 110   2020.10 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

Thioamycolamides A-E, Sulfur-Containing Cycliclipopeptides Produced by the Rare Actinomycete <i>Amycolatopsis</i> sp.

Pan C, Kuranaga T, Liu C, Lu S, Shinzato N, Kakeya H

Organic letters ( American Chemical Society (ACS) )  22 ( 8 ) 3014 - 3017   2020.04 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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Development of 22 Microsatellite Markers for Assessing Hybridization in the Genus <i>Gekko</i> (Squamata: Gekkonidae)

OKAMOTO KOTA, KURITA TAKAKI, NAGANO MASAHIRO, SATO YUKUTO, AOYAMA HIROAKI, SAITOH SEIKOH, SHINZATO NAOYA, TODA MAMORU

Current herpetology ( 日本爬虫両棲類学会 )  39 ( 1 ) 66 - 74   2020.02 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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<p><i>Gekko yakuensis</i> and <i>G. tawaensis</i>, both endemic to western Japan, are threatened by genetic introgression from <i>G. hokouensis</i> and <i>G. japonicus</i>, respectively. To know detailed situation of their hybridizations for planning relevant conservation measures, development of sensitive genetic markers is desired. We here developed microsatellite markers based on the sequences obtained from <i>G. hokouensis</i> using 454 GS Junior sequencer, and tested stability of PCR amplification and species-specificity of alleles at each locus using <i>G. hokouensis</i>, <i>G. yakuensis</i>, <i>G. japonicus</i>, and <i>G. tawaensis</i>. The results showed that 22 loci were almost constantly amplified in more than one species. We further confirmed that there were fixed or nearly fixed allelic displacement between <i>G. hokouensis</i> and <i>G. yakuensis</i>, and between <i>G. japonicus</i> and <i>G. tawaensis</i> at 14 loci. Thus, these 22 loci are considered to be useful for evaluation of hybridizations between these pairs of species.</p>

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Tripartite Symbiosis of an Anaerobic Scuticociliate with Two Hydrogenosome-Associated Endosymbionts, a <i>Holospora</i>-Related Alphaproteobacterium and a Methanogenic Archaeon.

Takeshita K, Yamada T, Kawahara Y, Narihiro T, Ito M, Kamagata Y, Shinzato N

Applied and environmental microbiology ( Applied and Environmental Microbiology )  85 ( 24 ) e00854-19   2019.12 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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<i>Streptomyces</i> Strain 5-94, Obtained from the Subtropical Region in Okinawa, has Inhibitory Activity against <i>Colletotrichum orbiculare</i>

UENO Makoto, TAMURA Tomoko, YANO Yuka, ITO Michihiro, SHINZATO Naoya

Tropical Agriculture and Development ( 日本熱帯農業学会 )  63 ( 4 ) 192 - 197   2019.04 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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<p>We previously reported on the construction of a microbial library isolated from soils in Okinawa (Okinawa Microbial Library, OML, http://omlus.jimdo.com/), including the Yaeyama Archipelago, and validated its phylogenetic diversity. In the present study, we report that strain 5-94, obtained from soil samples collected from Ikei Island, Okinawa Prefecture, Japan, produced inhibitory compounds against <i>Colletotrichum orbiculare</i>, the causal agent of anthracnose disease. Mycelial growth of <i>C. orbiculare</i> was inhibited by strain 5-94 in a dual culture assay. Additionally, the use of culture filtrates of this strain significantly suppressed the spore germination in <i>C. orbicular</i>. The sequence analysis of the 16S rDNA region indicated that strain 5-94 was similar to the <i>Streptomyces</i> species. Anthracnose disease caused by <i>C. orbiculare</i> was suppressed by the strain 5-94 culture filtrate in cucumber leaves pretreated for 3 and 7 d. Furthermore, growth inhibition zones of <i>C. orbicular</i> in the culture filtrate of this strain were detected by a thin layer chromatography. These results, therefore, suggested that inhibitory compounds from the culture filtrate of <i>Streptomyces</i> strain 5-94 might be a promising source for the development of new chemical fungicides to prevent anthracnose disease caused by <i>C. orbiculare</i>.</p>

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Microbial secondary metabolite induction of abnormal appressoria formation mediates control of rice blast disease caused by Magnaporthe oryzae

Tamura T, Shinzato N, Ito M, Ueno M

Journal of phytopathology   167 ( 3 ) 156 - 162   2019.01 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

Population Connectivity in the Common Reef Zoantharian Zoanthus sansibaricus (Anthozoa: Hexacorallia) in Southern Japan.

Albinsky D, Wham D, Shinzato N, Reimer JD

Zoological science ( Zoological Science )  35 ( 4 ) 321 - 329   2018.08 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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Geochemical and Microbiological Evidence for Microbial Methane Production in Deep Aquifers of the Cretaceous Accretionary Prism.

Matsushita M, Magara K, Sato Y, Shinzato N, Kimura H

Microbes and environments   33 ( 2 ) 205 - 213   2018.07 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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Accretionary prisms are thick layers of sedimentary material piled up at convergent plate boundaries. Large amounts of anaerobic groundwater and methane (CH4) are contained in the deep aquifers associated with accretionary prisms. In order to identify microbial activity and CH4 production processes in the deep aquifers associated with the Cretaceous accretionary prism in Okinawa Island, Japan, we performed geochemical and microbiological studies using anaerobic groundwater and natural gas (mainly CH4) samples collected through four deep wells. Chemical and stable hydrogen and oxygen isotope analyses of groundwater samples indicated that the groundwater samples obtained from each site originated from ancient seawater and a mixture of rainwater and seawater, respectively. Additionally, the chemical and stable carbon isotopic signatures of groundwater and natural gas samples suggested that CH4 in the natural gas samples was of a biogenic origin or a mixture of biogenic and thermogenic origins. Microscopic observations and a 16S rRNA gene analysis targeting microbial communities in groundwater samples revealed the predominance of dihydrogen (H2)-producing fermentative bacteria and H2-utilizing methanogenic archaea. Moreover, anaerobic cultures using groundwater samples suggested a high potential for CH4 production by a syntrophic consortium of H2-producing fermentative bacteria and H2-utilizing methanogenic archaea through the biodegradation of organic substrates. Collectively, our geochemical and microbiological data support the conclusion that the ongoing biodegradation of organic matter widely contributes to CH4 production in the deep aquifers associated with the Cretaceous accretionary prism.

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Biotransformation of dibenzothiophene by resting cells of a newly isolated Serratia marscens sp. strain originated from industrial wastewater

El-Bassi L, Ouertani RN, Shinzato N, Ghrabi A

Journal of bioremediation and biodegradation   9 ( 3 ) 439   2018.05 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

Genome Sequence of Lactobacillus paracasei Strain LC-Ikematsu, Isolated from a Pineapple in Okinawa, Japan.

Tada I, Saitoh S, Aoyama H, Shinzato N, Yamamoto N, Arita M, Ikematsu S

Genome announcements ( American Society for Microbiology )  5 ( 5 )   2017.02 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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The draft genome sequence of Lactobacillus paracasei strain LCIkematsu, isolated from a pineapple in Okinawa, was determined. The total length of the 87 contigs was 3.08 Mb with a G+C content of 46.2% and 2,946 coding sequences. The genome analysis revealed its biosynthetic ability of 11 amino acids.

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Complete Genome Sequence of the Intracellular Bacterial Symbiont TC1 in the Anaerobic Ciliate Trimyema compressum.

Shinzato N, Aoyama H, Saitoh S, Nikoh N, Nakano K, Shimoji M, Shinzato M, Satou K, Teruya K, Hirano T, Yamada T, Nobu MK, Tamaki H, Shirai Y, Park S, Narihiro T, Liu WT, Kamagata Y

Genome announcements ( American Society for Microbiology )  4 ( 5 )   2016.09 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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A free-living ciliate, Trimyema compressum, found in anoxic freshwater environments harbors methanogenic archaea and a bacterial symbiont named TC1 in its cytoplasm. Here, we report the complete genome sequence of the TC1 symbiont, consisting of a 1.59-Mb chromosome and a 35.8-kb plasmid, which was determined using the PacBio RSII sequencer.

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Complete mitochondrial genome of <i>Cacospongia mycofijiensis</i> (Dictyoceratida: Demospongiae): the first report for the sponge family Thorectidae.

Aoyama H, Saitoh S, Park S, Shirai Y, Shinzato N

Mitochondrial DNA. Part B, Resources ( Mitochondrial DNA Part B: Resources )  1 ( 1 ) 477 - 478   2016.07 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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We sequenced a complete mitochondrial genome of the marine sponge, Cacospongia mycofijiensis, which is the first report for the family Thorectidae in the class Demospongiae. The mitogenome was obtained from a de novo assembly of shotgun genome sequencing using Illumina Miseq technology, which reconstructed a circular genome with 97 x of sequence coverage. The assembled mitochondrial genome consisting of 16,227 bp includes 14 protein-coding genes, 2 rRNAs and 2 tRNAs. This complete mitogenome sequence will be useful especially for the phylogenic studies of Demospongiae.

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A quantitative protocol for DNA metabarcoding of springtails (Collembola).

Saitoh S, Aoyama H, Fujii S, Sunagawa H, Nagahama H, Akutsu M, Shinzato N, Kaneko N, Nakamori T

Genome ( CANADIAN SCIENCE PUBLISHING, NRC RESEARCH PRESS )  59 ( 9 ) 705 - 23   2016.06 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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We developed a novel protocol with superior quantitative analysis results for DNA metabarcoding of Collembola, a major soil microarthropod order. Degenerate PCR primers were designed for conserved regions in the mitochondrial cytochrome c oxidase subunit I (mtCOI) and 16S ribosomal RNA (mt16S) genes based on published collembolan mitogenomes. The best primer pair was selected based on its ability to amplify each gene, irrespective of the species. DNA was extracted from 10 natural communities sampled in a temperate forest (with typically 25-30 collembolan species per 10 soil samples) and 10 mock communities (with seven cultured collembolan species). The two gene regions were then amplified using the selected primers, ligated with adapters for 454 technology, and sequenced. Examination of the natural community samples showed that 32 and 36 operational taxonomic units (defined at a 90% sequence similarity threshold) were recovered from the mtCOI and mt16S data, respectively, which were comparable to the results of the microscopic identification of 25 morphospecies. Further, sequence abundances for each collembolan species from the mtCOI and mt16S data of the mock communities, after normalization by using a species as the internal control, showed good correlation with the number of individuals in the samples (R = 0.91-0.99), although relative species abundances within a mock community sample estimated from sequences were skewed from community composition in terms of the number of individuals or biomass of the species. Thus, this protocol enables the comparison of collembolan communities in a quantitative manner by metabarcoding.

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