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364 results on '"Kogure, Kazuhiro"'

6. Probe capture enrichment sequencing ofamoAgenes discloses diverse ammonia-oxidizing archaeal and bacterial populations

Author

Hiraoka, Satoshi, primary, Ijichi, Minoru, additional, Takeshima, Hirohiko, additional, Kumagai, Yohei, additional, Yang, Ching-Chia, additional, Makabe-Kobayashi, Yoko, additional, Fukuda, Hideki, additional, Yoshizawa, Susumu, additional, Iwasaki, Wataru, additional, Kogure, Kazuhiro, additional, and Shiozaki, Takuhei, additional

Published
2023
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7. Diversity of culturable heterotrophic bacteria from the Mariana Trench and their ability to degrade macromolecules

Author

Zhao, Xiuxiu, Liu, Jiwen, Zhou, Shun, Zheng, Yanfen, Wu, Yanhong, Kogure, Kazuhiro, and Zhang, Xiao-Hua

Abstract

The Mariana Trench is the deepest location on earth and harbors unique microbial communities as evidenced by 16S rRNA gene amplicon and metagenomic sequencing. Obtaining culturable microorganisms from the Mariana Trench will contribute to a further understanding of hadal biogeochemical processes and act as a unique microbial reservoir with potential applications. Here, 825 bacterial strains, identified by 16S rRNA gene sequencing, were isolated from 12 water depths (0–10,400 m) of the Mariana Trench with 2216E and R2A media at 4 °C or 28 °C on four cruises during 2015–2017. These bacteria belong to four phyla, nine classes, 27 orders, 45 families and 108 genera. Alphaproteobacteria, Gammaproteobacteria, Actinobacteria_c, Bacilliand Flavobacteriiawere the most abundant classes, accounting for 37.9%, 33.0%, 11.8%, 8.6% and 8.0% of the total bacterial isolates, respectively. 2216E and R2A media were found to have a better selectivity to Bacilliand Flavobacteriia, respectively. Fifty strains were potential novel bacterial species with a 16S rRNA gene similarity < 98.65%, and a higher percentage of novel strains were obtained from R2A than 2216E medium. Additionally, 301 (150 species) out of 354 strains (178 species) selected from each depth could degrade at least one of the ten kinds of macromolecules tested. These results indicate that there is a high diversity of culturable bacteria in the Mariana Trench and they can produce a variety of extracellular enzymes. Our study provides a valuable resource of microorganisms for investigating their biogeochemical roles in the Mariana Trench and for industrial applications.

Published
2024
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10. The Family Rhodothermaceae

Author

Park, Sanghwa, Akira, Yokota, Kogure, Kazuhiro, Rosenberg, Eugene, editor, DeLong, Edward F., editor, Lory, Stephen, editor, Stackebrandt, Erko, editor, and Thompson, Fabiano, editor

Published
2014
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11. Identification of important marine areas around the Japanese Archipelago: Establishment of a protocol for evaluating a broad area using ecologically and biologically significant areas selection criteria

Author

Yamakita, Takehisa, Yamamoto, Hiroyuki, Nakaoka, Masahiro, Yamano, Hiroya, Fujikura, Katsunori, Hidaka, Kiyotaka, Hirota, Yuichi, Ichikawa, Tadafumi, Kakehi, Shigeho, Kameda, Takahiko, Kitajima, Satoshi, Kogure, Kazuhiro, Komatsu, Teruhisa, Kumagai, Naoki H., Miyamoto, Hiroomi, Miyashita, Kazushi, Morimoto, Haruyuki, Nakajima, Ryota, Nishida, Shuhei, Nishiuchi, Kou, Sakamoto, Shingo, Sano, Masayoshi, Sudo, Kenji, Sugisaki, Hiroya, Tadokoro, Kazuaki, Tanaka, Katsuhiko, Jintsu-Uchifune, Yoshie, Watanabe, Kentaro, Watanabe, Hiromi, Yara, Yumiko, Yotsukura, Norishige, and Shirayama, Yoshihisa

Published
2015
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16. Structural basis for [Na.sup.+] transport mechanism by a light-driven [Na.sup.+] pump

Author

Kato, Hideaki E., Inoue, Keiichi, Abe-Yoshizumi, Rei, Kato, Yoshitaka, Ono, Hikaru, Konno, Masae, Hososhima, Shoko, Ishizuka, Toru, Hoque, Mohammad Razuanul, Kunitomo, Hirofumi, Ito, Jumpei, Yoshizawa, Susumu, Yamashita, Keitaro, Takemoto, Mizuki, Nishizawa, Tomohiro, Taniguchi, Reiya, Kogure, Kazuhiro, Maturana, Andres D., Iino, Yuichi, Yawo, Hiromu, Ishitani, Ryuichiro, Kandori, Hideki, and Nureki, Osamu

Subjects
Biological transport, Active -- Identification and classification, Proteins -- Structure, Sodium channels -- Health aspects -- Identification and classification, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Krokinobacter eikastus rhodopsin 2 (KR2) is the first light-driven [Na.sup.+] pump discovered, and is viewed as a potential next-generation optogenetics tool. Since the positively charged Schiff base proton, located within the ion-conducting pathway of all light-driven ion pumps, was thought to prohibit the transport of a non-proton cation, the discovery of KR2 raised the question of how it achieves [Na.sup.+] transport. Here we present crystal structures of KR2 under neutral and acidic conditions, which represent the resting and M-like intermediate states, respectively. Structural and spectroscopic analyses revealed the gating mechanism, whereby the flipping of Asp116 sequesters the Schiff base proton from the conducting pathway to facilitate [Na.sup.+] transport. Together with the structure-based engineering of the first light-driven [K.sup.+] pumps, electrophysiological assays in mammalian neurons and behavioural assays in a nematode, our studies reveal the molecular basis for light-driven non-proton cation pumps and thus provide a framework that may advance the development of next-generation optogenetics., Many organisms capture light energy and information using the rhodopsin family of proteins, which comprise the heptahelical transmembrane (7-TM) proteins called opsins covalently linked to retinal. Based on their primary [...]

Published
2015
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18. EVOLUTIONARY BIOLOGY IN BIODIVERSITY SCIENCE, CONSERVATION, AND POLICY: A CALL TO ACTION

Author

Hendry, Andrew P., Lohmann, Lúcia G., Conti, Elena, Cracraft, Joel, Crandall, Keith A., Faith, Daniel P., Häuser, Christoph, Joly, Carlos A., Kogure, Kazuhiro, Larigauderie, Anne, Magallón, Susana, Moritz, Craig, Tillier, Simon, Zardoya, Rafael, Prieur-Richard, Anne-Hélène, Walther, Bruno A., Yahara, Tetsukazu, and Donoghue, Michael J.

Published
2010

37. Presence of a Haloarchaeal Halorhodopsin-Like Cl− Pump in Marine Bacteria

Author

Nakajima, Yu, Tsukamoto, Takashi, Kumagai, Yohei, Ogura, Yoshitoshi, Hayashi, Tetsuya, Song, Jaeho, Kikukawa, Takashi, Demura, Makoto, Kogure, Kazuhiro, Sudo, Yuki, and Yoshizawa, Susumu

Subjects
Rhodopsin, genetic structures, Gene Transfer, Horizontal, Light, family Rhodothermaceae, Articles, Ion Pumps, Cyanobacteria, Archaea, Evolution, Molecular, Chlorides, Escherichia coli, Seawater, sense organs, chloride ion pump, Halorhodopsins, Genome, Bacterial, Phylogeny, genome analysis
Abstract

Light-driven ion-pumping rhodopsins are widely distributed among bacteria, archaea, and eukaryotes in the euphotic zone of the aquatic environment. H+-pumping rhodopsin (proteorhodopsin: PR), Na+-pumping rhodopsin (NaR), and Cl−-pumping rhodopsin (ClR) have been found in marine bacteria, which suggests that these genes evolved independently in the ocean. Putative microbial rhodopsin genes were identified in the genome sequences of marine Cytophagia. In the present study, one of these genes was heterologously expressed in Escherichia coli cells and the rhodopsin protein named Rubricoccus marinus halorhodopsin (RmHR) was identified as a light-driven inward Cl− pump. Spectroscopic assays showed that the estimated dissociation constant (Kd,int.) of this rhodopsin was similar to that of haloarchaeal halorhodopsin (HR), while the Cl−-transporting photoreaction mechanism of this rhodopsin was similar to that of HR, but different to that of the already-known marine bacterial ClR. This amino acid sequence similarity also suggested that this rhodopsin is similar to haloarchaeal HR and cyanobacterial HRs (e.g., SyHR and MrHR). Additionally, a phylogenetic analysis revealed that retinal biosynthesis pathway genes (blh and crtY) belong to a phylogenetic lineage of haloarchaea, indicating that these marine Cytophagia acquired rhodopsin-related genes from haloarchaea by lateral gene transfer. Based on these results, we concluded that inward Cl−-pumping rhodopsin is present in genera of the class Cytophagia and may have the same evolutionary origins as haloarchaeal HR.

Published
2018

43. Distribution of Dimethylsulfoniopropionate Degradation Genes Reflects Strong Water Current Dependencies in the Sanriku Coastal Region in Japan: From Mesocosm to Field Study

Author

Cui, Yingshun, primary, Wong, Shu-Kuan, additional, Kaneko, Ryo, additional, Mouri, Ayako, additional, Tada, Yuya, additional, Nagao, Ippei, additional, Chun, Seong-Jun, additional, Lee, Hyung-Gwan, additional, Ahn, Chi-Yong, additional, Oh, Hee-Mock, additional, Sato-Takabe, Yuki, additional, Suzuki, Koji, additional, Fukuda, Hideki, additional, Nagata, Toshi, additional, Kogure, Kazuhiro, additional, and Hamasaki, Koji, additional

Published
2020
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46. Attachment of Vibrio alginolyticus to glass surfaces is dependent on swimming speed

Author

Kogure, Kazuhiro, Ikemoto, Eiko, and Morisaki, Hisao

Subjects
Vibrio -- Research, Microorganisms -- Motility, Biological sciences
Abstract

Research as conducted to examine the role of the polar flagellum in the attachment of Vibrio alginolyticus to glass surfaces. This study requires the comparative analysis of the attachment behavior of various types of mutants. Results show that mutants with polar flagellum attach faster and that the attachment is affected by sodium concentrations. It is therefore concluded that attachment to glass surfaces is a function of swimming speed.

Published
1998

48. Preface

Author

Shirayama, Yoshihisa, Kogure, Kazuhiro, Brewer, Peter G., Ohsumi, Takashi, Ishizaka, Joji, Kita, Jun, and Watanabe, Yuji

Published
2004

49. Respiratory dependence of the CCCP-resistant luminescence of Vibrio harveyi

Author

Wada, Minoru, Kogure, Kazuhiro, Ohwada, Kouichi, and Simidu, Usio

Subjects
Microbial respiration -- Research, Luminescence -- Physiological aspects, Vibrio -- Physiological aspects, Biological sciences
Abstract

The correlation between luminescece and respiratory activity in Vibrio harveyi in the presence of carbonyl cyanide m-chlorophenylhydrazone (CCCP) was described. Both the luminescence and the oxygen uptake rate of V. harveyi were sensitive to the proton conductor CCCP. In the absence of CCCP, luminescence and oxygen uptake rate were almost constant over the pH range 6.5-8.5. Thus, it was concluded that the luminescence of V. harveyi is respiratory-dependent in the presence of CCCP.

Published
1992

50. Coupling between the respiratory chain and the luminescent system of Vibrio harveyi

Author

Wada, Minoru, Kogure, Kazuhiro, Ohwada, Kouichi, and Simidu, Usio

Subjects
Microbial respiration -- Research, Luminescence -- Research, Vibrio -- Research, Biological sciences
Abstract

The coupling between luminescence and the respiratory chain in Vibrio harveyi was investigated. V. harveyi showed maximum oxygen uptake, as well as maximum luminescence at alkaline pH, in the presence of sodium. Changes in luminescence and oxygen uptake depended on the respiratory activity, which was determined by the monovalent cation. The growth and luminescence, at alkaline pH, of V. harveyi in the presence of a proton conductor also suggested the presence of a sodium-motive force.

Published
1992

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