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Iqbal MM, Nishimura M, Tsukamoto Y, Yoshizawa S. Changes in microbial community structure related to biodegradation of eelgrass (Zostera marina). Sci Total Environ 2024; 930:172798. [PMID: 38688366 DOI: 10.1016/j.scitotenv.2024.172798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 04/21/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024]
Abstract
Seagrass meadows produce organic carbon and deposit it on the seabed through the decaying process. Microbial activity is closely related to the process of eelgrass death and collapse. We investigated the microbial community structure of eelgrass during the eelgrass decomposition process by using a microcosm containing raw seawater and excised eelgrass leaves collected from a Zostera marina bed in Futtsu, Chiba Prefecture, Japan. The fast-growing microbes (i.e., Alphaproteobacteria, Gammaproteobacteria, and Flavobacteriia) rapidly adhered to the eelgrass leaf surface and proliferated in the first two weeks but gradually decreased the relative abundance as the months moved on. On the other hand, the slow-growing microbes (i.e., Cytophagia, Anaerolineae, Thaumarchaeota, and Actinobacteria) became predominant over the eelgrass surface late in the culture experiment (120, 180 days). The fast-growing groups of Gammaproteobacteria and Flavobacteriia appear to be closely related to the initial decomposition of eelgrass, especially the rapid decomposition of leaf-derived biopolymers. Changes in nitrogen content due to the bacterial rapid consumption of readily degradable organic carbon induced changes in the community structure at the early stage of eelgrass decomposition. In addition, shifts in the C/N ratio were driven by microbial community changes during later decomposition phases.
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Affiliation(s)
- Md Mehedi Iqbal
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan; Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8563, Japan.
| | - Masahiko Nishimura
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
| | - Yuya Tsukamoto
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan; Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8563, Japan.
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2
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Takada M, Jiang C, Sugai Y, Hasegawa-Takano M, Fujiwara T, Tsukamoto Y, Nakajima Y, Nishimura Y, Yoshizawa S. Draft genome sequences of three rhodopsin possessing Croceitalea sp. strains, isolated from the sea surface microlayer in Japan. Microbiol Resour Announc 2024; 13:e0003824. [PMID: 38364092 DOI: 10.1128/mra.00038-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/06/2024] [Indexed: 02/18/2024] Open
Abstract
Here, we present the draft genome sequences of three Croceitalea sp. strains containing microbial rhodopsins, isolated from the Japanese coastal sea surface microlayer, which is exposed to intense sunlight. This study will contribute to the understanding of the genus Croceitalea and the diversity of microbial rhodopsins.
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Affiliation(s)
- Mako Takada
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
- Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Chunqi Jiang
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Youta Sugai
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Masumi Hasegawa-Takano
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa, Japan
| | - Takayoshi Fujiwara
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
- Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Yuya Tsukamoto
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Yu Nakajima
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa, Japan
| | - Yosuke Nishimura
- Research Center for Bioscience and Nanoscience (CeBN), Research Institute for Marine Resources Utilization, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
- Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
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3
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Andrew SM, Moreno CM, Plumb K, Hassanzadeh B, Gomez-Consarnau L, Smith SN, Schofield O, Yoshizawa S, Fujiwara T, Sunda WG, Hopkinson BM, Septer AN, Marchetti A. Widespread use of proton-pumping rhodopsin in Antarctic phytoplankton. Proc Natl Acad Sci U S A 2023; 120:e2307638120. [PMID: 37722052 PMCID: PMC10523587 DOI: 10.1073/pnas.2307638120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 08/13/2023] [Indexed: 09/20/2023] Open
Abstract
Photosynthetic carbon (C) fixation by phytoplankton in the Southern Ocean (SO) plays a critical role in regulating air-sea exchange of carbon dioxide and thus global climate. In the SO, photosynthesis (PS) is often constrained by low iron, low temperatures, and low but highly variable light intensities. Recently, proton-pumping rhodopsins (PPRs) were identified in marine phytoplankton, providing an alternate iron-free, light-driven source of cellular energy. These proteins pump protons across cellular membranes through light absorption by the chromophore retinal, and the resulting pH energy gradient can then be used for active membrane transport or for synthesis of adenosine triphosphate. Here, we show that PPR is pervasive in Antarctic phytoplankton, especially in iron-limited regions. In a model SO diatom, we found that it was localized to the vacuolar membrane, making the vacuole a putative alternative phototrophic organelle for light-driven production of cellular energy. Unlike photosynthetic C fixation, which decreases substantially at colder temperatures, the proton transport activity of PPR was unaffected by decreasing temperature. Cellular PPR levels in cultured SO diatoms increased with decreasing iron concentrations and energy production from PPR photochemistry could substantially augment that of PS, especially under high light intensities, where PS is often photoinhibited. PPR gene expression and high retinal concentrations in phytoplankton in SO waters support its widespread use in polar environments. PPRs are an important adaptation of SO phytoplankton to growth and survival in their cold, iron-limited, and variable light environment.
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Affiliation(s)
- Sarah M. Andrew
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Carly M. Moreno
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Kaylie Plumb
- Department of Marine Sciences, University of Georgia, Athens, GA30602
| | - Babak Hassanzadeh
- Department of Biological Sciences, University of Southern California, Log Angeles, CA90089
| | - Laura Gomez-Consarnau
- Department of Biological Sciences, University of Southern California, Log Angeles, CA90089
- Departamento de Oceanografía Biológica, Centro de Investigación Científca y de Educación Superior de Ensenada, Ensenada, Baja California22860, Mexico
| | - Stephanie N. Smith
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Oscar Schofield
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ08901
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba277-8564, Japan
| | - Takayoshi Fujiwara
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba277-8564, Japan
| | - William G. Sunda
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | | | - Alecia N. Septer
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Adrian Marchetti
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
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Sato T, Yamaguchi T, Aoki K, Kajiwara C, Kimura S, Maeda T, Yoshizawa S, Sasaki M, Murakami H, Hisatsune J, Sugai M, Ishii Y, Tateda K, Urita Y. Whole-genome sequencing analysis of molecular epidemiology and silent transmissions causing meticillin-resistant Staphylococcus aureus bloodstream infections in a university hospital. J Hosp Infect 2023; 139:141-149. [PMID: 37301229 DOI: 10.1016/j.jhin.2023.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND The emergence of novel genomic-type clones, such as community-associated meticillin-resistant Staphylococcus aureus (MRSA) and livestock-associated MRSA, and their invasion into hospitals have become major concerns worldwide; however, little information is available regarding the prevalence of MRSA in Japan. Whole-genome sequencing (WGS) has been conducted to analyse various pathogens worldwide. Therefore, it is important to establish a genome database of clinical MRSA isolates available in Japan. AIM A molecular epidemiological analysis of MRSA strains isolated from bloodstream-infected patients in a Japanese university hospital was conducted using WGS and single-nucleotide polymorphism (SNP) analysis. Additionally, through a review of patients' clinical characteristics, the effectiveness of SNP analysis as a tool for detecting silent nosocomial transmission that may be missed by other methods was evaluated in diverse settings and various time points of detection. METHODS Polymerase-chain-reaction-based staphylococcal cassette chromosome mec (SCCmec) typing was performed using 135 isolates obtained between 2014 and 2018, and WGS was performed using 88 isolates obtained between 2015 and 2017. FINDINGS SCCmec type II strains, prevalent in 2014, became rare in 2018, whereas the prevalence of SCCmec type IV strains increased from 18.75% to 83.87% of the population, and became the dominant clones. Clonal complex (CC) 5 CC8 and CC1 were detected between 2015 and 2017, with CC1 being dominant. In 88 cases, SNP analyses revealed nosocomial transmissions among 20 patients which involved highly homologous strains. CONCLUSIONS Routine monitoring of MRSA by whole-genome analysis is effective not only for gaining knowledge regarding molecular epidemiology, but also for detecting silent nosocomial transmission.
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Affiliation(s)
- T Sato
- Department of General Medicine and Emergency Care, Toho University Graduate School of Medicine, Tokyo, Japan; Department of General Medicine and Emergency Care, Toho University Omori Medical Centre, Tokyo, Japan.
| | - T Yamaguchi
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan.
| | - K Aoki
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - C Kajiwara
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - S Kimura
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - T Maeda
- Department of General Medicine and Emergency Care, Toho University Omori Medical Centre, Tokyo, Japan
| | - S Yoshizawa
- Department of Clinical Laboratories, Toho University Omori Medical Centre, Tokyo, Japan
| | - M Sasaki
- Department of Clinical Laboratories, Toho University Omori Medical Centre, Tokyo, Japan
| | - H Murakami
- Department of Clinical Laboratories, Toho University Omori Medical Centre, Tokyo, Japan
| | - J Hisatsune
- National Institute of Infectious Diseases, Tokyo, Japan
| | - M Sugai
- National Institute of Infectious Diseases, Tokyo, Japan
| | - Y Ishii
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - K Tateda
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan; Department of Clinical Laboratories, Toho University Omori Medical Centre, Tokyo, Japan
| | - Y Urita
- Department of General Medicine and Emergency Care, Toho University Omori Medical Centre, Tokyo, Japan
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5
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Shiozaki T, Nishimura Y, Yoshizawa S, Takami H, Hamasaki K, Fujiwara A, Nishino S, Harada N. Correction: Distribution and survival strategies of endemic and cosmopolitan diazotrophs in the Arctic Ocean. ISME J 2023:10.1038/s41396-023-01444-7. [PMID: 37264154 DOI: 10.1038/s41396-023-01444-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Affiliation(s)
- Takuhei Shiozaki
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan.
| | - Yosuke Nishimura
- Research Centre for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, 237-0061, Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan
| | - Hideto Takami
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan
- Center for Mathematical Science and Advanced Technology, JAMSTEC, Yokohama, 236-0001, Japan
| | - Koji Hamasaki
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8564, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, 113-8657, Japan
| | - Amane Fujiwara
- Research Institute for Global Change, JAMSTEC, Yokosuka, 237-0061, Japan
| | - Shigeto Nishino
- Research Institute for Global Change, JAMSTEC, Yokosuka, 237-0061, Japan
| | - Naomi Harada
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan
- Research Institute for Global Change, JAMSTEC, Yokosuka, 237-0061, Japan
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6
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Takuhei S, Nishimura Y, Yoshizawa S, Takami H, Hamasaki K, Fujiwara A, Nishino S, Harada N. Distribution and survival strategies of endemic and cosmopolitan diazotrophs in the Arctic Ocean. ISME J 2023:10.1038/s41396-023-01424-x. [PMID: 37217593 DOI: 10.1038/s41396-023-01424-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 04/18/2023] [Accepted: 04/25/2023] [Indexed: 05/24/2023]
Abstract
Dinitrogen (N2) fixation is the major source of reactive nitrogen in the ocean and has been considered to occur specifically in low-latitude oligotrophic oceans. Recent studies have shown that N2 fixation also occurs in the polar regions and thus is a global process, although the physiological and ecological characteristics of polar diazotrophs are not yet known. Here, we successfully reconstructed diazotroph genomes, including that of cyanobacterium UCYN-A (Candidatus 'Atelocyanobacterium thalassa'), from metagenome data corresponding to 111 samples isolated from the Arctic Ocean. These diazotrophs were highly abundant in the Arctic Ocean (max., 1.28% of the total microbial community), suggesting that they have important roles in the Arctic ecosystem and biogeochemical cycles. Further, we show that diazotrophs within genera Arcobacter, Psychromonas, and Oceanobacter are prevalent in the <0.2 µm fraction in the Arctic Ocean, indicating that current methods cannot capture their N2 fixation. Diazotrophs in the Arctic Ocean were either Arctic-endemic or cosmopolitan species from their global distribution patterns. Arctic-endemic diazotrophs, including Arctic UCYN-A, were similar to low-latitude-endemic and cosmopolitan diazotrophs in genome-wide function, however, they had unique gene sets (e.g., diverse aromatics degradation genes), suggesting adaptations to Arctic-specific conditions. Cosmopolitan diazotrophs were generally non-cyanobacteria and commonly had the gene that encodes the cold-inducible RNA chaperone, which presumably makes their survival possible even in deep, cold waters of global ocean and polar surface waters. This study shows global distribution pattern of diazotrophs with their genomes and provides clues to answering the question of how diazotrophs can inhabit polar waters.
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Affiliation(s)
- Shiozaki Takuhei
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan.
| | - Yosuke Nishimura
- Research Centre for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, 237-0061, Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan
| | - Hideto Takami
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan
- Center for Mathematical Science and Advanced Technology, JAMSTEC, Yokohama, 236-0001, Japan
| | - Koji Hamasaki
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 277-8564, Kashiwa, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 113-8657, Bunkyo-ku, Japan
| | - Amane Fujiwara
- Research Institute for Global Change, JAMSTEC, Yokosuka, 237-0061, Japan
| | - Shigeto Nishino
- Research Institute for Global Change, JAMSTEC, Yokosuka, 237-0061, Japan
| | - Naomi Harada
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan
- Research Institute for Global Change, JAMSTEC, Yokosuka, 237-0061, Japan
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7
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Kojima K, Kawanishi S, Nishimura Y, Hasegawa M, Nakao S, Nagata Y, Yoshizawa S, Sudo Y. A blue-shifted anion channelrhodopsin from the Colpodellida alga Vitrella brassicaformis. Sci Rep 2023; 13:6974. [PMID: 37117398 PMCID: PMC10147648 DOI: 10.1038/s41598-023-34125-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 04/25/2023] [Indexed: 04/30/2023] Open
Abstract
Microbial rhodopsins, a family of photoreceptive membrane proteins containing the chromophore retinal, show a variety of light-dependent molecular functions. Channelrhodopsins work as light-gated ion channels and are widely utilized for optogenetics, which is a method for controlling neural activities by light. Since two cation channelrhodopsins were identified from the chlorophyte alga Chlamydomonas reinhardtii, recent advances in genomic research have revealed a wide variety of channelrhodopsins including anion channelrhodopsins (ACRs), describing their highly diversified molecular properties (e.g., spectral sensitivity, kinetics and ion selectivity). Here, we report two channelrhodopsin-like rhodopsins from the Colpodellida alga Vitrella brassicaformis, which are phylogenetically distinct from the known channelrhodopsins. Spectroscopic and electrophysiological analyses indicated that these rhodopsins are green- and blue-sensitive pigments (λmax = ~ 550 and ~ 440 nm) that exhibit light-dependent ion channeling activities. Detailed electrophysiological analysis revealed that one of them works as a monovalent anion (Cl-, Br- and NO3-) channel and we named it V. brassicaformis anion channelrhodopsin-2, VbACR2. Importantly, the absorption maximum of VbACR2 (~ 440 nm) is blue-shifted among the known ACRs. Thus, we identified the new blue-shifted ACR, which leads to the expansion of the molecular diversity of ACRs.
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Affiliation(s)
- Keiichi Kojima
- Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan.
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan.
| | - Shiho Kawanishi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Yosuke Nishimura
- Research Center for Bioscience and Nanoscience (CeBN), Research Institute for Marine Resources Utilization, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa, 237-0061, Japan
| | - Masumi Hasegawa
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-Star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa, 237-0061, Japan
| | - Shin Nakao
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Yuya Nagata
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan
| | - Yuki Sudo
- Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan.
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan.
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8
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Chazan A, Das I, Fujiwara T, Murakoshi S, Rozenberg A, Molina-Márquez A, Sano FK, Tanaka T, Gómez-Villegas P, Larom S, Pushkarev A, Malakar P, Hasegawa M, Tsukamoto Y, Ishizuka T, Konno M, Nagata T, Mizuno Y, Katayama K, Abe-Yoshizumi R, Ruhman S, Inoue K, Kandori H, León R, Shihoya W, Yoshizawa S, Sheves M, Nureki O, Béjà O. Phototrophy by antenna-containing rhodopsin pumps in aquatic environments. Nature 2023; 615:535-540. [PMID: 36859551 DOI: 10.1038/s41586-023-05774-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 01/31/2023] [Indexed: 03/03/2023]
Abstract
Energy transfer from light-harvesting ketocarotenoids to the light-driven proton pump xanthorhodopsins has been previously demonstrated in two unique cases: an extreme halophilic bacterium1 and a terrestrial cyanobacterium2. Attempts to find carotenoids that bind and transfer energy to abundant rhodopsin proton pumps3 from marine photoheterotrophs have thus far failed4-6. Here we detected light energy transfer from the widespread hydroxylated carotenoids zeaxanthin and lutein to the retinal moiety of xanthorhodopsins and proteorhodopsins using functional metagenomics combined with chromophore extraction from the environment. The light-harvesting carotenoids transfer up to 42% of the harvested energy in the violet- or blue-light range to the green-light absorbing retinal chromophore. Our data suggest that these antennas may have a substantial effect on rhodopsin phototrophy in the world's lakes, seas and oceans. However, the functional implications of our findings are yet to be discovered.
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Affiliation(s)
- Ariel Chazan
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Ishita Das
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, Israel
| | - Takayoshi Fujiwara
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
| | - Shunya Murakoshi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Andrey Rozenberg
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Ana Molina-Márquez
- Laboratory of Biochemistry and Molecular Biology, Faculty of Experimental Sciences, Marine International Campus of Excellence (CEIMAR), University of Huelva, Huelva, Spain
| | - Fumiya K Sano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Tatsuki Tanaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Patricia Gómez-Villegas
- Laboratory of Biochemistry and Molecular Biology, Faculty of Experimental Sciences, Marine International Campus of Excellence (CEIMAR), University of Huelva, Huelva, Spain
| | - Shirley Larom
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Alina Pushkarev
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Partha Malakar
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Masumi Hasegawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa, Japan
| | - Yuya Tsukamoto
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
| | - Tomohiro Ishizuka
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan
| | - Masae Konno
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan
| | - Takashi Nagata
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan
| | - Yosuke Mizuno
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan
| | - Kota Katayama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Japan
| | - Rei Abe-Yoshizumi
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan
| | - Sanford Ruhman
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Japan
| | - Rosa León
- Laboratory of Biochemistry and Molecular Biology, Faculty of Experimental Sciences, Marine International Campus of Excellence (CEIMAR), University of Huelva, Huelva, Spain
| | - Wataru Shihoya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan.
| | - Mordechai Sheves
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, Israel.
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
| | - Oded Béjà
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel.
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Kurihara M, Thiel V, Takahashi H, Kojima K, Ward DM, Bryant DA, Sakai M, Yoshizawa S, Sudo Y. Identification of a Functionally Efficient and Thermally Stable Outward Sodium-Pumping Rhodopsin (BeNaR) from a Thermophilic Bacterium. Chem Pharm Bull (Tokyo) 2023; 71:154-164. [PMID: 36724978 DOI: 10.1248/cpb.c22-00774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Rhodopsins are transmembrane proteins with retinal chromophores that are involved in photo-energy conversion and photo-signal transduction in diverse organisms. In this study, we newly identified and characterized a rhodopsin from a thermophilic bacterium, Bellilinea sp. Recombinant Escherichia coli cells expressing the rhodopsin showed light-induced alkalization of the medium only in the presence of sodium ions (Na+), and the alkalization signal was enhanced by addition of a protonophore, indicating an outward Na+ pump function across the cellular membrane. Thus, we named the protein Bellilinea Na+-pumping rhodopsin, BeNaR. Of note, its Na+-pumping activity is significantly greater than that of the known Na+-pumping rhodopsin, KR2. We further characterized its photochemical properties as follows: (i) Visible spectroscopy and HPLC revealed that BeNaR has an absorption maximum at 524 nm with predominantly (>96%) the all-trans retinal conformer. (ii) Time-dependent thermal denaturation experiments revealed that BeNaR showed high thermal stability. (iii) The time-resolved flash-photolysis in the nanosecond to millisecond time domains revealed the presence of four kinetically distinctive photointermediates, K, L, M and O. (iv) Mutational analysis revealed that Asp101, which acts as a counterion, and Asp230 around the retinal were essential for the Na+-pumping activity. From the results, we propose a model for the outward Na+-pumping mechanism of BeNaR. The efficient Na+-pumping activity of BeNaR and its high stability make it a useful model both for ion transporters and optogenetics tools.
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Affiliation(s)
- Marie Kurihara
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University
| | - Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Hirona Takahashi
- Department of Chemistry, Graduate School of Science, Okayama University of Science
| | - Keiichi Kojima
- Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University
| | - David M Ward
- Department of Land Resources and Environmental Sciences, Montana State University
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University
| | - Makoto Sakai
- Department of Chemistry, Graduate School of Science, Okayama University of Science
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo
| | - Yuki Sudo
- Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University
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10
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Iqbal MM, Nishimura M, Haider MN, Yoshizawa S. Microbial communities on eelgrass ( Zostera marina) thriving in Tokyo Bay and the possible source of leaf-attached microbes. Front Microbiol 2023; 13:1102013. [PMID: 36687565 PMCID: PMC9853538 DOI: 10.3389/fmicb.2022.1102013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 12/15/2022] [Indexed: 01/07/2023] Open
Abstract
Zostera marina (eelgrass) is classified as one of the marine angiosperms and is widely distributed throughout much of the Northern Hemisphere. The present study investigated the microbial community structure and diversity of Z. marina growing in Futtsu bathing water, Chiba prefecture, Japan. The purpose of this study was to provide new insight into the colonization of eelgrass leaves by microbial communities based on leaf age and to compare these communities to the root-rhizome of Z. marina, and the surrounding microenvironments (suspended particles, seawater, and sediment). The microbial composition of each sample was analyzed using 16S ribosomal gene amplicon sequencing. Each sample type was found to have a unique microbial community structure. Leaf-attached microbes changed in their composition depending on the relative age of the eelgrass leaf. Special attention was given to a potential microbial source of leaf-attached microbes. Microbial communities of marine particles looked more like those of eelgrass leaves than those of water samples. This finding suggests that leaf-attached microbes were derived from suspended particles, which could allow them to go back and forth between eelgrass leaves and the water column.
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Affiliation(s)
- Md Mehedi Iqbal
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan,Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan,*Correspondence: Md Mehedi Iqbal,
| | - Masahiko Nishimura
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Md. Nurul Haider
- Faculty of Fisheries, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan,Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan,Susumu Yoshizawa,
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11
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Yoshizawa S, Azuma T, Kojima K, Inomura K, Hasegawa M, Nishimura Y, Kikuchi M, Armin G, Tsukamoto Y, Miyashita H, Ifuku K, Yamano T, Marchetti A, Fukuzawa H, Sudo Y, Kamikawa R. Light-driven Proton Pumps as a Potential Regulator for Carbon Fixation in Marine Diatoms. Microbes Environ 2023; 38:n/a. [PMID: 37344444 DOI: 10.1264/jsme2.me23015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2023] Open
Abstract
Diatoms are a major phytoplankton group responsible for approximately 20% of carbon fixation on Earth. They perform photosynthesis using light-harvesting chlo-rophylls located in plastids, an organelle obtained through eukaryote-eukaryote endosymbiosis. Microbial rhodopsin, a photoreceptor distinct from chlo-rophyll-based photosystems, was recently identified in some diatoms. However, the physiological function of diatom rhodopsin remains unclear. Heterologous expression techniques were herein used to investigate the protein function and subcellular localization of diatom rhodopsin. We demonstrated that diatom rhodopsin acts as a light-driven proton pump and localizes primarily to the outermost membrane of four membrane-bound complex plastids. Using model simulations, we also examined the effects of pH changes inside the plastid due to rhodopsin-mediated proton transport on photosynthesis. The results obtained suggested the involvement of rhodopsin-mediated local pH changes in a photosynthetic CO2-concentrating mechanism in rhodopsin-possessing diatoms.
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Affiliation(s)
- Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo
- Graduate School of Frontier Sciences, The University of Tokyo
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
| | - Tomonori Azuma
- Graduate School of Human and Environmental Studies, Kyoto University
| | - Keiichi Kojima
- School of Pharmaceutical Sciences, Okayama University
- Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University
| | | | - Masumi Hasegawa
- Atmosphere and Ocean Research Institute, The University of Tokyo
- Graduate School of Frontier Sciences, The University of Tokyo
| | - Yosuke Nishimura
- Atmosphere and Ocean Research Institute, The University of Tokyo
| | | | | | - Yuya Tsukamoto
- Atmosphere and Ocean Research Institute, The University of Tokyo
| | - Hideaki Miyashita
- Graduate School of Human and Environmental Studies, Kyoto University
| | | | | | - Adrian Marchetti
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill
| | | | - Yuki Sudo
- School of Pharmaceutical Sciences, Okayama University
- Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University
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12
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Iqbal MM, Nishimura M, Sano M, Yoshizawa S. Particle-attached Microbes in Eelgrass Vegetation Areas Differ in Community Structure Depending on the Distance from the Eelgrass Bed. Microbes Environ 2023; 38:ME23013. [PMID: 37661422 PMCID: PMC10522840 DOI: 10.1264/jsme2.me23013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 06/01/2023] [Indexed: 09/05/2023] Open
Abstract
Zostera marina (eelgrass) is a submerged flowering plant often found in the coastal areas of Japan. Large amounts of suspended particles form in highly productive environments, such as eelgrass beds, and the behavior of these particles is expected to affect the surrounding microbial community. We investigated the microbial community structure of suspended particles in three eelgrass fields (Ikuno-Shima Is., Mutsu Bay, and Nanao Bay) and inferred the formation and dynamics of suspended particles from a microbial community structure ana-lysis. Seawater samples were collected directly above each eelgrass bed (eelgrass-covering) and from locations dozens of meters away from the eelgrass bed (bare-ground). In consideration of the two different lifestyles of marine microbes, microbial communities were obtained from particle-attached (PA) and free-living (FL) states. Differences in microbial diversity and community structures were observed between PA and FL in all eelgrass beds. The FL microbial community was similar between the two sampling points (eelgrass-covering and bare-ground), whereas a significant difference was noted in the microbial community structure of suspended particles between the two sampling points. This difference appeared to be due to the supply of organic matter from the eelgrass sea ground and leaf-attached detritus produced by microbial activity. In addition, the classes Flavobacteriia, Alphaproteobacteria, and Gammaproteobacteria were abundant in the PA and FL fractions. Furthermore, many sequences of the key groups (e.g., Planctomycetes and Verrucomicrobia) were exclusively detected in the PA fraction, in which they may circulate nutrients. The present results provide insights into the microbial communities of suspended particles and provide the first step towards understanding their biogeochemical impact on the eelgrass bed.
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Affiliation(s)
- Md Mehedi Iqbal
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5–1–5 Kashiwanoha, Kashiwa, Chiba 277–8564, Japan
- Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, 5–1–5 Kashiwanoha, Kashiwa, Chiba 277–8563, Japan
| | - Masahiko Nishimura
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5–1–5 Kashiwanoha, Kashiwa, Chiba 277–8564, Japan
| | - Masayoshi Sano
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5–1–5 Kashiwanoha, Kashiwa, Chiba 277–8564, Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5–1–5 Kashiwanoha, Kashiwa, Chiba 277–8564, Japan
- Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, 5–1–5 Kashiwanoha, Kashiwa, Chiba 277–8563, Japan
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13
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Yu Z, Ito SI, Wong MKS, Yoshizawa S, Inoue J, Itoh S, Yukami R, Ishikawa K, Guo C, Ijichi M, Hyodo S. Comparison of species-specific qPCR and metabarcoding methods to detect small pelagic fish distribution from open ocean environmental DNA. PLoS One 2022; 17:e0273670. [PMID: 36070298 PMCID: PMC9451083 DOI: 10.1371/journal.pone.0273670] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 08/13/2022] [Indexed: 11/18/2022] Open
Abstract
Environmental DNA (eDNA) is increasingly used to noninvasively monitor aquatic animals in freshwater and coastal areas. However, the use of eDNA in the open ocean (hereafter referred to OceanDNA) is still limited because of the sparse distribution of eDNA in the open ocean. Small pelagic fish have a large biomass and are widely distributed in the open ocean. We tested the performance of two OceanDNA analysis methods—species-specific qPCR (quantitative polymerase chain reaction) and MiFish metabarcoding using universal primers—to determine the distribution of small pelagic fish in the open ocean. We focused on six small pelagic fish species (Sardinops melanostictus, Engraulis japonicus, Scomber japonicus, Scomber australasicus, Trachurus japonicus, and Cololabis saira) and selected the Kuroshio Extension area as a testbed, because distribution of the selected species is known to be influenced by the strong frontal structure. The results from OceanDNA methods were compared to those of net sampling to test for consistency. Then, we compared the detection performance in each target fish between the using of qPCR and MiFish methods. A positive correlation was evident between the qPCR and MiFish detection results. In the ranking of the species detection rates and spatial distribution estimations, comparable similarity was observed between results derived from the qPCR and MiFish methods. In contrast, the detection rate using the qPCR method was always higher than that of the MiFish method. Amplification bias on non-target DNA and low sample DNA quantity seemed to partially result in a lower detection rate for the MiFish method; the reason is still unclear. Considering the ability of MiFish to detect large numbers of species and the quantitative nature of qPCR, the combined usage of the two methods to monitor quantitative distribution of small pelagic fish species with information of fish community structures was recommended.
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Affiliation(s)
- Zeshu Yu
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Shin-ichi Ito
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
- * E-mail:
| | - Marty Kwok-Shing Wong
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Jun Inoue
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Sachihiko Itoh
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Ryuji Yukami
- Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Kazuo Ishikawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Chenying Guo
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Minoru Ijichi
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Susumu Hyodo
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
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14
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Iqbal MM, Nishimura M, Sano M, Yoshizawa S. Diversity and dynamics of particle-associated and free-living bacteria in eelgrass (Zostera marina) bed along the coast of Japan. Access Microbiol 2022. [DOI: 10.1099/acmi.ac2021.po0237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
As the seagrass leaves remain underwater, the primary source of leaf microbes is considered to be seawater heterotrophic bacterioplankton, which possess the ability to degrade biopolymers and are known to attach to surface and form biofilms. In this study, 16S rRNA gene amplicon sequencing was used to assess bacterial diversity and dynamics of the particle associated (PA) and free-living (FL) fraction of the seagrass-covering seawater (inside) and bulk seawater (outside) among different seagrass bed around Japan. Samples were collected from the three Zostera marinabeds (Ikuno-shima Is., Hiroshima; Nanao Bay, Ishikawa; Mutsu Bay, Aomori Prefecture) around Japan during summer (June-August 2015; July 2016). Prokaryotic DNA was extracted from samples using a FastDNA spin kit according to the manufacturer’s protocol. After extracting DNA, 16S ribosomal RNA (16S rRNA) genes were sequenced by Illumina Miseq platform. The Results showed that PA bacterial communities had a higher (p <0.001) diversity than FL ones. Compared to the outside of the seagrass bed, the inside had lower diversity both in PA and FL fraction. Taxonomic analysis revealed a different community composition between lifestyle (PA vs FL) and sampling point (inside vs outside). Differential abundance analysis showed that PA were significantly enriched in a diversity of Cyanobacteria (Synechococcaceae), Saprospiraceae and Hyphomonadaceae. Conversely, FL were more abundant in Gammaproteobacteria (including Halomonadaceae, Alteromonadaceae), Microbacteriaceae, Campylobacteraceae, Pelagibacteraceae,Acidimicrobiia(OCS155). The present data provide a comprehensive description of the PA and FL microbial community in the seagrass bed and can be useful for better understanding the seagrass microbe interactions.
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Affiliation(s)
| | | | - Masayoshi Sano
- National Institute of Polar Research, Japan
- The University of Tokyo, Japan
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15
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Iqbal MM, Nishimura M, Haider MN, Sano M, Ijichi M, Kogure K, Yoshizawa S. Diversity and Composition of Microbial Communities in an Eelgrass (Zostera marina) Bed in Tokyo Bay, Japan. Microbes Environ 2021; 36. [PMID: 34645731 PMCID: PMC8674447 DOI: 10.1264/jsme2.me21037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Zostera marina (eelgrass) is a widespread seagrass species that forms diverse and productive habitats along coast lines throughout much of the northern hemisphere. The present study investigated the microbial consortia of Z. marina growing at Futtsu clam-digging beach, Chiba prefecture, Japan. The following environmental samples were collected: sediment, seawater, plant leaves, and the root-rhizome. Sediment and seawater samples were obtained from three sampling points: inside, outside, and at the marginal point of the eelgrass bed. The microbial composition of each sample was analyzed using 16S ribosomal gene amplicon sequencing. Microbial communities on the dead (withered) leaf surface markedly differed from those in sediment, but were similar to those in seawater. Eelgrass leaves and surrounding seawater were dominated by the bacterial taxa Rhodobacterales (Alphaproteobacteria), whereas Rhodobacterales were a minor group in eelgrass sediment. Additionally, we speculated that the order Sphingomonadales (Alphaproteobacteria) acts as a major degrader during the decomposition process and constantly degrades eelgrass leaves, which then spread into the surrounding seawater. Withered eelgrass leaves did not accumulate on the surface sediment because they were transported out of the eelgrass bed by wind and residual currents unique to the central part of Tokyo Bay.
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Affiliation(s)
- Md Mehedi Iqbal
- Atmosphere and Ocean Research Institute, The University of Tokyo.,Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo
| | | | - Md Nurul Haider
- Atmosphere and Ocean Research Institute, The University of Tokyo.,Department of Fisheries Technology, Faculty of Fisheries, Bangladesh Agricultural University
| | - Masayoshi Sano
- Atmosphere and Ocean Research Institute, The University of Tokyo.,National Institute of Polar Research
| | - Minoru Ijichi
- Atmosphere and Ocean Research Institute, The University of Tokyo
| | - Kazuhiro Kogure
- Atmosphere and Ocean Research Institute, The University of Tokyo
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo.,Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo
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16
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Kikuchi M, Kojima K, Nakao S, Yoshizawa S, Kawanishi S, Shibukawa A, Kikukawa T, Sudo Y. Functional expression of the eukaryotic proton pump rhodopsin OmR2 in Escherichia coli and its photochemical characterization. Sci Rep 2021; 11:14765. [PMID: 34285294 PMCID: PMC8292405 DOI: 10.1038/s41598-021-94181-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/07/2021] [Indexed: 01/05/2023] Open
Abstract
Microbial rhodopsins are photoswitchable seven-transmembrane proteins that are widely distributed in three domains of life, archaea, bacteria and eukarya. Rhodopsins allow the transport of protons outwardly across the membrane and are indispensable for light-energy conversion in microorganisms. Archaeal and bacterial proton pump rhodopsins have been characterized using an Escherichia coli expression system because that enables the rapid production of large amounts of recombinant proteins, whereas no success has been reported for eukaryotic rhodopsins. Here, we report a phylogenetically distinct eukaryotic rhodopsin from the dinoflagellate Oxyrrhis marina (O. marina rhodopsin-2, OmR2) that can be expressed in E. coli cells. E. coli cells harboring the OmR2 gene showed an outward proton-pumping activity, indicating its functional expression. Spectroscopic characterization of the purified OmR2 protein revealed several features as follows: (1) an absorption maximum at 533 nm with all-trans retinal chromophore, (2) the possession of the deprotonated counterion (pKa = 3.0) of the protonated Schiff base and (3) a rapid photocycle through several distinct photointermediates. Those features are similar to those of known eukaryotic proton pump rhodopsins. Our successful characterization of OmR2 expressed in E. coli cells could build a basis for understanding and utilizing eukaryotic rhodopsins.
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Affiliation(s)
- Masuzu Kikuchi
- Division of Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Keiichi Kojima
- Division of Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan.,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Shin Nakao
- Division of Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan
| | - Shiho Kawanishi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Atsushi Shibukawa
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, 060-0810, Japan.,Global Station for Soft Matter, GI-CoRE, Hokkaido University, Sapporo, 001-0021, Japan
| | - Yuki Sudo
- Division of Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan. .,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan.
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17
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Nakajima Y, Kojima K, Kashiyama Y, Doi S, Nakai R, Sudo Y, Kogure K, Yoshizawa S. Bacterium Lacking a Known Gene for Retinal Biosynthesis Constructs Functional Rhodopsins. Microbes Environ 2021; 35. [PMID: 33281127 PMCID: PMC7734400 DOI: 10.1264/jsme2.me20085] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Microbial rhodopsins, comprising a protein moiety (rhodopsin apoprotein) bound to the light-absorbing chromophore retinal, function as ion pumps, ion channels, or light sensors. However, recent genomic and metagenomic surveys showed that some rhodopsin-possessing prokaryotes lack the known genes for retinal biosynthesis. Since rhodopsin apoproteins cannot absorb light energy, rhodopsins produced by prokaryotic strains lacking genes for retinal biosynthesis are hypothesized to be non-functional in cells. In the present study, we investigated whether Aurantimicrobium minutum KNCT, which is widely distributed in terrestrial environments and lacks any previously identified retinal biosynthesis genes, possesses functional rhodopsin. We initially measured ion transport activity in cultured cells. A light-induced pH change in a cell suspension of rhodopsin-possessing bacteria was detected in the absence of exogenous retinal. Furthermore, spectroscopic analyses of the cell lysate and HPLC-MS/MS analyses revealed that this strain contained an endogenous retinal. These results confirmed that A. minutum KNCT possesses functional rhodopsin and, hence, produces retinal via an unknown biosynthetic pathway. These results suggest that rhodopsin-possessing prokaryotes lacking known retinal biosynthesis genes also have functional rhodopsins.
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Affiliation(s)
- Yu Nakajima
- Microbial and Genetic Resources Research Group, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST).,Atmosphere and Ocean Research Institute (AORI), The University of Tokyo
| | - Keiichi Kojima
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University
| | | | - Satoko Doi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University
| | - Ryosuke Nakai
- Microbial Ecology and Technology Research Group, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Yuki Sudo
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University
| | - Kazuhiro Kogure
- Atmosphere and Ocean Research Institute (AORI), The University of Tokyo
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute (AORI), The University of Tokyo
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18
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Kato T, Yoshizawa A, Manabe S, Takanashi S, Kawamura A, Yoshizawa S, Kuwaki K. Xenoimmune Response Can Elicit Postoperative Bioprosthetic Valve Degeneration. J Heart Lung Transplant 2021. [DOI: 10.1016/j.healun.2021.01.848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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19
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Yoshizawa S, Ikemoto E, Kogure K. Visualization of Bacteria ( Vibrio alginolyticus) as They Really Are by Atomic Force Microscopy. CYTOLOGIA 2020. [DOI: 10.1508/cytologia.85.261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo
- Graduate School of Frontier Sciences, The University of Tokyo
| | - Eiko Ikemoto
- Atmosphere and Ocean Research Institute, The University of Tokyo
| | - Kazuhiro Kogure
- Atmosphere and Ocean Research Institute, The University of Tokyo
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20
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Hasegawa M, Hosaka T, Kojima K, Nishimura Y, Nakajima Y, Kimura-Someya T, Shirouzu M, Sudo Y, Yoshizawa S. A unique clade of light-driven proton-pumping rhodopsins evolved in the cyanobacterial lineage. Sci Rep 2020; 10:16752. [PMID: 33028840 PMCID: PMC7541481 DOI: 10.1038/s41598-020-73606-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 09/15/2020] [Indexed: 11/09/2022] Open
Abstract
Microbial rhodopsin is a photoreceptor protein found in various bacteria and archaea, and it is considered to be a light-utilization device unique to heterotrophs. Recent studies have shown that several cyanobacterial genomes also include genes that encode rhodopsins, indicating that these auxiliary light-utilizing proteins may have evolved within photoautotroph lineages. To explore this possibility, we performed a large-scale genomic survey to clarify the distribution of rhodopsin and its phylogeny. Our surveys revealed a novel rhodopsin clade, cyanorhodopsin (CyR), that is unique to cyanobacteria. Genomic analysis revealed that rhodopsin genes show a habitat-biased distribution in cyanobacterial taxa, and that the CyR clade is composed exclusively of non-marine cyanobacterial strains. Functional analysis using a heterologous expression system revealed that CyRs function as light-driven outward H+ pumps. Examination of the photochemical properties and crystal structure (2.65 Å resolution) of a representative CyR protein, N2098R from Calothrix sp. NIES-2098, revealed that the structure of the protein is very similar to that of other rhodopsins such as bacteriorhodopsin, but that its retinal configuration and spectroscopic characteristics (absorption maximum and photocycle) are distinct from those of bacteriorhodopsin. These results suggest that the CyR clade proteins evolved together with chlorophyll-based photosynthesis systems and may have been optimized for the cyanobacterial environment.
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Affiliation(s)
- Masumi Hasegawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan.,Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8563, Japan
| | - Toshiaki Hosaka
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Kanagawa, 230-0045, Japan
| | - Keiichi Kojima
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Yosuke Nishimura
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan
| | - Yu Nakajima
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Ibaraki, 305-8766, Japan
| | - Tomomi Kimura-Someya
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Kanagawa, 230-0045, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Kanagawa, 230-0045, Japan
| | - Yuki Sudo
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan. .,Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8563, Japan. .,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, 113-8657, Japan.
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21
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Matsuoka H, Kabata D, Taura A, Matsui T, Takahi K, Hirano F, Katayama M, Okamoto A, Suenaga Y, Suematsu E, Yoshizawa S, Ohmura K, Ito S, Takaoka H, Oguro E, Kuzuya K, Okita Y, Udagawa C, Yoshimura M, Teshigawara S, Harada Y, Isoda K, Yoshida Y, Ohshima S, Tohma S, Saeki Y. Lack of association between a disease-susceptible single-nucleotide polymorphism, rs2230926 of TNFAIP3, and tumour necrosis factor inhibitor therapeutic failure in Japanese patients with rheumatoid arthritis. Scand J Rheumatol 2020; 49:253-255. [PMID: 32406335 DOI: 10.1080/03009742.2020.1716992] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- H Matsuoka
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano, Japan.,Department of Clinical Research, NHO Osaka Minami Medical Center, Kawachinagano, Japan
| | - D Kabata
- Department of Medical Statics, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - A Taura
- Department of Clinical Research, NHO Osaka Minami Medical Center, Kawachinagano, Japan
| | - T Matsui
- Department of Rheumatology, NHO Sagamihara National Hospital, Sagamihara, Japan
| | - K Takahi
- Department of Orthopedics and Rheumatology, NHO Osaka Toneyama Medical Center, Toyonaka, Japan
| | - F Hirano
- Department of Internal Medicine, NHO Asahikawa Medical Center, Asahikawa, Japan
| | - M Katayama
- Department of Rheumatology, NHO Nagoya Medical Center, Nagoya, Japan
| | - A Okamoto
- Department of Rheumatology, NHO Himeji Medical Center, Himeji, Japan
| | - Y Suenaga
- Department of Rheumatology, NHO Beppu Medical Center, Beppu, Japan
| | - E Suematsu
- Department of Rheumatology, NHO Kyushu Medical Center, Fukuoka, Japan
| | - S Yoshizawa
- Department of Rheumatology, NHO Fukuoka National Hospital, Fukuoka, Japan
| | - K Ohmura
- Department of Rheumatology and Clinical Immunology, Kyoto University, Kyoto, Japan
| | - S Ito
- Department of Rheumatology, Niigata Rheumatic Center, Niigata, Japan
| | - H Takaoka
- Section of Internal Medicine and Rheumatology, Kumamoto Shinto General Hospital, Kumamoto, Japan
| | - E Oguro
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano, Japan
| | - K Kuzuya
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano, Japan
| | - Y Okita
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano, Japan
| | - C Udagawa
- Department of Clinical Research, NHO Osaka Minami Medical Center, Kawachinagano, Japan.,Department of Molecular Chemistry, Faculty of Pharmacy, Osaka Ohtani University, Tondabayashi, Osaka, Japan
| | - M Yoshimura
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano, Japan
| | - S Teshigawara
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano, Japan
| | - Y Harada
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano, Japan
| | - K Isoda
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano, Japan
| | - Y Yoshida
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano, Japan
| | - S Ohshima
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano, Japan
| | - S Tohma
- Department of Rheumatology, NHO Tokyo National Hospital, Tokyo, Japan
| | - Y Saeki
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano, Japan.,Department of Clinical Research, NHO Osaka Minami Medical Center, Kawachinagano, Japan
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22
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Marshel JH, Kim YS, Machado TA, Quirin S, Benson B, Kadmon J, Raja C, Chibukhchyan A, Ramakrishnan C, Inoue M, Shane JC, McKnight DJ, Yoshizawa S, Kato HE, Ganguli S, Deisseroth K. Cortical layer-specific critical dynamics triggering perception. Science 2019; 365:science.aaw5202. [PMID: 31320556 PMCID: PMC6711485 DOI: 10.1126/science.aaw5202] [Citation(s) in RCA: 300] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 07/02/2019] [Indexed: 12/24/2022]
Abstract
Perceptual experiences may arise from neuronal activity patterns in mammalian neocortex. We probed mouse neocortex during visual discrimination using a red-shifted channelrhodopsin (ChRmine, discovered through structure-guided genome mining) alongside multiplexed multiphoton-holography (MultiSLM), achieving control of individually specified neurons spanning large cortical volumes with millisecond precision. Stimulating a critical number of stimulus-orientation-selective neurons drove widespread recruitment of functionally related neurons, a process enhanced by (but not requiring) orientation-discrimination task learning. Optogenetic targeting of orientation-selective ensembles elicited correct behavioral discrimination. Cortical layer-specific dynamics were apparent, as emergent neuronal activity asymmetrically propagated from layer 2/3 to layer 5, and smaller layer 5 ensembles were as effective as larger layer 2/3 ensembles in eliciting orientation discrimination behavior. Population dynamics emerging after optogenetic stimulation both correctly predicted behavior and resembled natural internal representations of visual stimuli at cellular resolution over volumes of cortex.
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Affiliation(s)
- James H Marshel
- CNC Department, Stanford University, Stanford, CA 94305, USA
| | - Yoon Seok Kim
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Timothy A Machado
- CNC Department, Stanford University, Stanford, CA 94305, USA.,Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Sean Quirin
- CNC Department, Stanford University, Stanford, CA 94305, USA
| | - Brandon Benson
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Jonathan Kadmon
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Cephra Raja
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | - Charu Ramakrishnan
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Masatoshi Inoue
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | | | - Susumu Yoshizawa
- Department of Natural Environmental Studies, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8564, Japan
| | - Hideaki E Kato
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
| | - Surya Ganguli
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Karl Deisseroth
- CNC Department, Stanford University, Stanford, CA 94305, USA. .,Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.,Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
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23
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Seo K, Ichizuka K, Okai T, Dohi S, Nakamura M, Hasegawa J, Matsuoka R, Yoshizawa S, Umemura SI, Nagatsuka M, Sekizawa A. Treatment of twin-reversed arterial perfusion sequence using high-intensity focused ultrasound. Ultrasound Obstet Gynecol 2019; 54:128-134. [PMID: 30136326 DOI: 10.1002/uog.20101] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 07/31/2018] [Accepted: 08/10/2018] [Indexed: 06/08/2023]
Abstract
We describe our experience of high-intensity focused ultrasound (HIFU) for fetal therapy in twin-reversed arterial perfusion (TRAP) sequence. Six pregnant women underwent HIFU therapy, five before 16 weeks and one at 26 weeks. Two types of HIFU system were used: the first-generation system, which comprised a biaxial transducer and continuous exposure pattern, and the second-generation system, which comprised a coaxial transducer and sequential exposure pattern. The first-generation apparatus was used in four cases and the second-generation apparatus was used in two. In three cases, occlusion of the blood vessels mediating flow to the acardiac twin was achieved by HIFU. Two cases experienced intrauterine fetal death despite vessel occlusion. The total survival rate of pump fetuses 2 years after HIFU was 67% and the efficiency rate (the proportion of cases with occlusion or reduced blood flow on ultrasound after HIFU) was 83%. After more than 2 years of follow-up, the surviving infants had no severe clinical complications and no postnatal developmental problems. There was no significant difference in survival rate compared with TRAP cases managed expectantly. Given that complete occlusion of the blood vessels was not achieved in half of the cases, we could not show that HIFU therapy is superior to other treatments. However, HIFU can reduce the cardiac load of the pump fetus and, as it does not require uterine puncture for fetal therapy, there were no fatal complications, such as bleeding, rupture of membranes or infection. Thus, HIFU therapy may represent a less-invasive treatment for TRAP sequence in early pregnancy. Copyright © 2018 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- K Seo
- Showa University, School of Medicine, Department of Obstetrics and Gynecology, Tokyo, Japan
| | - K Ichizuka
- Showa University, School of Medicine, Department of Obstetrics and Gynecology, Tokyo, Japan
| | - T Okai
- Showa University, School of Medicine, Department of Obstetrics and Gynecology, Tokyo, Japan
| | - S Dohi
- Showa University, School of Medicine, Department of Obstetrics and Gynecology, Tokyo, Japan
| | - M Nakamura
- Showa University, School of Medicine, Department of Obstetrics and Gynecology, Tokyo, Japan
| | - J Hasegawa
- St Marianna University, School of Medicine, Department of Obstetrics and Gynecology, Kanagawa, Japan
| | - R Matsuoka
- Showa University, School of Medicine, Department of Obstetrics and Gynecology, Tokyo, Japan
| | - S Yoshizawa
- Tohoku University, Graduate School of Biomedical Engineering, Miyagi, Japan
| | - S-I Umemura
- Tohoku University, Graduate School of Biomedical Engineering, Miyagi, Japan
| | - M Nagatsuka
- Showa University, School of Medicine, Department of Obstetrics and Gynecology, Tokyo, Japan
| | - A Sekizawa
- Showa University, School of Medicine, Department of Obstetrics and Gynecology, Tokyo, Japan
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24
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Shibukawa A, Kojima K, Nakajima Y, Nishimura Y, Yoshizawa S, Sudo Y. Photochemical Characterization of a New Heliorhodopsin from the Gram-Negative Eubacterium Bellilinea caldifistulae (BcHeR) and Comparison with Heliorhodopsin-48C12. Biochemistry 2019; 58:2934-2943. [DOI: 10.1021/acs.biochem.9b00257] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Atsushi Shibukawa
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Keiichi Kojima
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Yu Nakajima
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba 277-8564, Japan
| | - Yosuke Nishimura
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba 277-8564, Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba 277-8564, Japan
- Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8563, Japan
| | - Yuki Sudo
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
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25
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Zhang H, Yoshizawa S, Sun Y, Huang Y, Chu X, González JM, Pinhassi J, Luo H. Repeated evolutionary transitions of flavobacteria from marine to non-marine habitats. Environ Microbiol 2019; 21:648-666. [PMID: 30565818 DOI: 10.1111/1462-2920.14509] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 12/14/2018] [Accepted: 12/14/2018] [Indexed: 01/26/2023]
Abstract
The taxonomy of marine and non-marine organisms rarely overlap, but the mechanisms underlying this distinction are often unknown. Here, we predicted three major ocean-to-land transitions in the evolutionary history of Flavobacteriaceae, a family known for polysaccharide and peptide degradation. These unidirectional transitions were associated with repeated losses of marine signature genes and repeated gains of non-marine adaptive genes. This included various Na+ -dependent transporters, osmolyte transporters and glycoside hydrolases (GH) for sulfated polysaccharide utilization in marine descendants, and in non-marine descendants genes for utilizing the land plant material pectin and genes facilitating terrestrial host interactions. The K+ scavenging ATPase was repeatedly gained whereas the corresponding low-affinity transporter repeatedly lost upon transitions, reflecting K+ ions are less available to non-marine bacteria. Strikingly, the central metabolism Na+ -translocating NADH: quinone dehydrogenase gene was repeatedly gained in marine descendants, whereas the H+ -translocating counterpart was repeatedly gained in non-marine lineages. Furthermore, GH genes were depleted in isolates colonizing animal hosts but abundant in bacteria inhabiting other non-marine niches; thus relative abundances of GH versus peptidase genes among Flavobacteriaceae lineages were inconsistent with the marine versus non-marine dichotomy. We suggest that phylogenomic analyses can cast novel light on mechanisms explaining the distribution and ecology of key microbiome components.
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Affiliation(s)
- Hao Zhang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Ying Sun
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Yongjie Huang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Xiao Chu
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - José M González
- Department of Microbiology, University of La Laguna, La Laguna, ES-38200, Spain
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden
| | - Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
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26
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Takano T, Ijichi M, Itoh H, Fukuda H, Yoshizawa S. Complete mitochondrial genome sequences of a deep-sea holothurian species of the genus Scotoplanes (Elasipodida: Elpidiidae). Mitochondrial DNA B Resour 2018. [DOI: 10.1080/23802359.2018.1536462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Tsuyoshi Takano
- Meguro Parasitological Museum, Meguro, Tokyo, Japan
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Minoru Ijichi
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Hajime Itoh
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Hideki Fukuda
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
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27
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Wong SK, Yoshizawa S, Nakajima Y, Cuadra MJ, Nogi Y, Nakamura K, Takami H, Ogura Y, Hayashi T, Chiura HX, Hamasaki K. Amylibacter kogurei sp. nov., a novel marine alphaproteobacterium isolated from the coastal sea surface microlayer of a marine inlet. Int J Syst Evol Microbiol 2018; 68:2872-2877. [DOI: 10.1099/ijsem.0.002911] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- Shu-Kuan Wong
- 1Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Susumu Yoshizawa
- 1Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Yu Nakajima
- 1Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Marie Johanna Cuadra
- 2Division of Biological Sciences, College of Arts and Sciences, University of the Philippines Visayas, Iloilo, Philippines
| | - Yuichi Nogi
- 3Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Keiji Nakamura
- 4Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hideto Takami
- 3Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yoshitoshi Ogura
- 4Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tetsuya Hayashi
- 4Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroshi Xavier Chiura
- 1Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Koji Hamasaki
- 1Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
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28
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Ijichi M, Takano T, Hasegawa M, Yashiki H, Kogure K, Kojima S, Yoshizawa S. The complete mitochondrial genome of the longfin dragonfish Tactostoma macropus (Stomiiformes: Stomiidae). Mitochondrial DNA B Resour 2018; 3:486-487. [PMID: 33490517 PMCID: PMC7800359 DOI: 10.1080/23802359.2018.1464411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The complete mitochondrial genome (mitogenome) was determined for the longfin dragonfish Tactostoma macropus, which is the first for the genus and the third within the family Stomiidae. The mitogenome sequence is 17,690 bp in length containing 2 ribosomal RNA genes, 22 transfer RNA genes, 13 protein-coding genes, and a control region, as in most fishes. The gene order of T. macropus showed an unreported deviation from the typical vertebrate one. Phylogenetic reconstruction using the maximum likelihood method placed T. macropus in the monophyletic Stomiiformes. Three stomiid species were recovered as a moderately supported clade in the phylogenetic tree.
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Affiliation(s)
- Minoru Ijichi
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Tsuyoshi Takano
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Masumi Hasegawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Haruka Yashiki
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Kazuhiro Kogure
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Shigeaki Kojima
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
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29
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Nakajima Y, Tsukamoto T, Kumagai Y, Ogura Y, Hayashi T, Song J, Kikukawa T, Demura M, Kogure K, Sudo Y, Yoshizawa S. Presence of a Haloarchaeal Halorhodopsin-Like Cl - Pump in Marine Bacteria. Microbes Environ 2018; 33:89-97. [PMID: 29553064 PMCID: PMC5877348 DOI: 10.1264/jsme2.me17197] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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.
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Affiliation(s)
- Yu Nakajima
- Atmosphere and Ocean research Institute (AORI), The University of Tokyo.,Department of Natural Environmental Studies, Graduate School of Frontier Sciences, the University of Tokyo
| | - Takashi Tsukamoto
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University
| | - Yohei Kumagai
- Atmosphere and Ocean research Institute (AORI), The University of Tokyo.,Department of Natural Environmental Studies, Graduate School of Frontier Sciences, the University of Tokyo
| | - Yoshitoshi Ogura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University
| | - Jaeho Song
- Department of Biological Sciences, Inha University
| | - Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University.,Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University
| | - Makoto Demura
- Faculty of Advanced Life Science, Hokkaido University.,Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University
| | - Kazuhiro Kogure
- Atmosphere and Ocean research Institute (AORI), The University of Tokyo.,Department of Natural Environmental Studies, Graduate School of Frontier Sciences, the University of Tokyo
| | - Yuki Sudo
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University
| | - Susumu Yoshizawa
- Atmosphere and Ocean research Institute (AORI), The University of Tokyo.,Department of Natural Environmental Studies, Graduate School of Frontier Sciences, the University of Tokyo
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30
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Olson DK, Yoshizawa S, Boeuf D, Iwasaki W, DeLong EF. Proteorhodopsin variability and distribution in the North Pacific Subtropical Gyre. ISME J 2018; 12:1047-1060. [PMID: 29476140 PMCID: PMC5864233 DOI: 10.1038/s41396-018-0074-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/21/2017] [Accepted: 12/05/2017] [Indexed: 11/17/2022]
Abstract
Proteorhodopsin is a light-activated retinal-containing proton pump found in many marine bacteria. These photoproteins are globally distributed in the ocean’s photic zone and are capable of generating a proton motive force across the cell membrane. We investigated the phylogenetic diversity, distribution, and abundance of proteorhodopsin encoding genes in free-living bacterioplankton in the North Pacific Subtropical Gyre, leveraging a gene catalog derived from metagenomic samples from the ocean’s surface to 1000 m depth. Proteorhodopsin genes were identified at all depths sampled, but were most abundant at depths shallower than 200 m. The majority of proteorhodopsin gene sequences (60.9%) belonged to members of the SAR11 lineage, with remaining sequences distributed among other diverse taxa. We observed variations in the conserved residues involved in ion pumping and spectral tuning, and biochemically confirmed four different proton pumping proteorhodopsin motifs, including one unique to deep-water SAR11. We also identified a new group of putative proteorhodopsins having unknown function. Our results reveal a broad organismal and unexpected depth distribution for different proteorhodopsin types, as well as substantial within-taxon variability. These data provide a framework for exploring the ecological relevance of proteorhodopsins and their spatiotemporal variation and function in heterotrophic bacteria in the open ocean.
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Affiliation(s)
- Daniel K Olson
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography, University of Hawaii, Honolulu, HI, 96822, USA
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan
| | - Dominique Boeuf
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography, University of Hawaii, Honolulu, HI, 96822, USA
| | - Wataru Iwasaki
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography, University of Hawaii, Honolulu, HI, 96822, USA.
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31
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Inoue S, Yoshizawa S, Nakajima Y, Kojima K, Tsukamoto T, Kikukawa T, Sudo Y. Spectroscopic characteristics ofRubricoccus marinusxenorhodopsin (RmXeR) and a putative model for its inward H+transport mechanism. Phys Chem Chem Phys 2018; 20:3172-3183. [DOI: 10.1039/c7cp05033j] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
On the basis of functional and spectroscopic characterization, we propose a model for the inward proton transport inRmXeR, a newly discovered microbial rhodopsin.
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Affiliation(s)
- Saki Inoue
- Graduate School of Medicine
- Dentistry and Pharmaceutical Sciences
- Okayama University
- Okayama 700-8530
- Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute
- The University of Tokyo
- Chiba 277-8564
- Japan
| | - Yu Nakajima
- Atmosphere and Ocean Research Institute
- The University of Tokyo
- Chiba 277-8564
- Japan
| | - Keiichi Kojima
- Graduate School of Medicine
- Dentistry and Pharmaceutical Sciences
- Okayama University
- Okayama 700-8530
- Japan
| | - Takashi Tsukamoto
- Graduate School of Medicine
- Dentistry and Pharmaceutical Sciences
- Okayama University
- Okayama 700-8530
- Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science
- Hokkaido University
- Sapporo 060-0810
- Japan
- Global Station for Soft Matter
| | - Yuki Sudo
- Graduate School of Medicine
- Dentistry and Pharmaceutical Sciences
- Okayama University
- Okayama 700-8530
- Japan
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32
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Nakazato Y, Takaba M, Abe Y, Yoshida Y, Ono Y, Yoshizawa S, Nakamura H, Kawana F, Suganuma T, Kato T, Baba K. Accuracy of newly developed portable PSG device for detection of sleep bruxism-related masseter EMG muscle activity. Sleep Med 2017. [DOI: 10.1016/j.sleep.2017.11.693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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33
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Kanayama Katsuse A, Takahashi H, Yoshizawa S, Tateda K, Nakanishi Y, Kaneko A, Kobayashi I. Public health and healthcare-associated risk of electric, warm-water bidet toilets. J Hosp Infect 2017; 97:296-300. [PMID: 28756169 DOI: 10.1016/j.jhin.2017.07.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 07/20/2017] [Indexed: 11/18/2022]
Abstract
BACKGROUND In recent years, installation of bidet toilets within hospitals in Japan has raised concerns regarding potential for cross-contamination by antimicrobial-resistant bacteria from patients who are hospitalized over an extended period. AIM To investigate the distribution of antimicrobial-resistant bacteria recovered from bidet toilets at a university-affiliated hospital in Japan. METHODS All 292 electric bidet toilets at a university hospital were sampled for contamination. Swabs for culture were used to sample water-jet nozzles and toilet seats. FINDINGS Of the 292 toilet seats sampled, warm-water nozzles of 254 (86.9%) were found to be contaminated by one or more of the following organisms: Staphylococcus aureus, Streptococcus spp., Enterococcus spp., Enterobacteriaceae and non-Enterobacteriaceae Gram-negative bacteria. S. aureus was recovered from one water-jet nozzle and nine toilet seats; of these, meticillin-resistant S. aureus was recovered from the water-jet nozzle and from one toilet seat. Both the water-jet nozzle and seat of the same toilet were contaminated with a CTX-M-9 group extended-spectrum β-lactamase-producing Escherichia coli. Of the Gram-negative isolates recovered from samples, the organism with the highest frequency of isolation was Stenotrophomonas maltophilia, which was recovered from 39 bidet toilets. CONCLUSION Warm-water nozzles of bidet toilets are contaminated with a wide range of bacteria, making them a potential vehicle for cross-infection. In the hospital setting, shared use of bidet toilets must consider the clinical background of patients. Based on these findings, these devices must be part of the risk management programme, and steps should be included for monitoring and disinfection.
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Affiliation(s)
- A Kanayama Katsuse
- Department of Infection Control and Prevention, Toho University Faculty of Nursing, Tokyo, Japan
| | - H Takahashi
- Department of Infection Control and Prevention, Toho University Faculty of Nursing, Tokyo, Japan
| | - S Yoshizawa
- Clinical Research Centre, Toho University School of Medicine, Tokyo, Japan; Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Kazuhiro Tateda
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Y Nakanishi
- Department of Oral and Maxillofacial Surgery, Tokai University School of Medicine, Kanagawa, Japan
| | - A Kaneko
- Department of Oral and Maxillofacial Surgery, Tokai University School of Medicine, Kanagawa, Japan
| | - I Kobayashi
- Department of Infection Control and Prevention, Toho University Faculty of Nursing, Tokyo, Japan.
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34
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Wong SK, Park S, Lee JS, Lee KC, Ogura Y, Hayashi T, Chiura HX, Yoshizawa S, Hamasaki K. Algibacter aquaticus sp. nov., a slightly alkaliphilic marine Flavobacterium isolated from coastal surface water. Int J Syst Evol Microbiol 2017; 67:2199-2204. [DOI: 10.1099/ijsem.0.001924] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Shu-Kuan Wong
- Department of Marine Ecosystem Dynamics, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Sanghwa Park
- Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, Japan
- Technology Research Association for the Next Generation Natural Products Chemistry.Aomi, Koto-ku, Tokyo, Japan
| | - Jung-Sook Lee
- Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Keun Chul Lee
- Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Yoshitoshi Ogura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka-shi, Fukuoka, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka-shi, Fukuoka, Japan
| | - Hiroshi Xavier Chiura
- Department of Marine Ecosystem Dynamics, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Susumu Yoshizawa
- Department of Marine Ecosystem Dynamics, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Koji Hamasaki
- Department of Marine Ecosystem Dynamics, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
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Ohyashiki K, Saito Y, Imanishi S, Umezu T, Yoshizawa S, Asano M, Fujimoto H, Akahane D, Kobayashi C, Ohyashiki J. Extracellular Vesicles (EVS) Released by Bone Marrow Stromal Cells Show a Distinct Mirna Profile in High-Risk MDS Patients. Leuk Res 2017. [DOI: 10.1016/s0145-2126(17)30310-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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36
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Niho A, Yoshizawa S, Tsukamoto T, Kurihara M, Tahara S, Nakajima Y, Mizuno M, Kuramochi H, Tahara T, Mizutani Y, Sudo Y. Demonstration of a Light-Driven SO42– Transporter and Its Spectroscopic Characteristics. J Am Chem Soc 2017; 139:4376-4389. [DOI: 10.1021/jacs.6b12139] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Akiko Niho
- Faculty
of Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Susumu Yoshizawa
- Atmosphere
and Ocean Research Institute, The University of Tokyo, Chiba 277-8564, Japan
| | - Takashi Tsukamoto
- Faculty
of Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
- Graduate
School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Marie Kurihara
- Graduate
School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Shinya Tahara
- Molecular
Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Yu Nakajima
- Atmosphere
and Ocean Research Institute, The University of Tokyo, Chiba 277-8564, Japan
| | - Misao Mizuno
- Department
of Chemistry, Graduate School of Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Hikaru Kuramochi
- Molecular
Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
- Ultrafast
Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
| | - Tahei Tahara
- Molecular
Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
- Ultrafast
Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
| | - Yasuhisa Mizutani
- Department
of Chemistry, Graduate School of Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yuki Sudo
- Faculty
of Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
- Graduate
School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
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37
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Kanehara K, Yoshizawa S, Tsukamoto T, Sudo Y. A phylogenetically distinctive and extremely heat stable light-driven proton pump from the eubacterium Rubrobacter xylanophilus DSM 9941 T. Sci Rep 2017; 7:44427. [PMID: 28290523 PMCID: PMC5349596 DOI: 10.1038/srep44427] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 02/07/2017] [Indexed: 11/13/2022] Open
Abstract
Rhodopsins are proteins that contain seven transmembrane domains with a chromophore retinal and that function as photoreceptors for light-energy conversion and light-signal transduction in a wide variety of organisms. Here we characterized a phylogenetically distinctive new rhodopsin from the thermophilic eubacterium Rubrobacter xylanophilus DSM 9941T that was isolated from thermally polluted water. Although R. xylanophilus rhodopsin (RxR) is from Actinobacteria, it is located between eukaryotic and archaeal rhodopsins in the phylogenetic tree. Escherichia coli cells expressing RxR showed a light-induced decrease in environmental pH and inhibition by a protonophore, indicating that it works as a light-driven outward proton pump. We characterized purified RxR spectroscopically, and showed that it has an absorption maximum at 541 nm and binds nearly 100% all-trans retinal. The pKa values for the protonated retinal Schiff base and its counterion were estimated to be 10.7 and 1.3, respectively. Time-resolved flash-photolysis experiments revealed the formation of a red-shifted intermediate. Of note, RxR showed an extremely high thermal stability in comparison with other proton pumping rhodopsins such as thermophilic rhodopsin TR (by 16-times) and bacteriorhodopsin from Halobacterium salinarum (HsBR, by 4-times).
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Affiliation(s)
- Kanae Kanehara
- Division of Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba 277-8564, Japan
| | - Takashi Tsukamoto
- Division of Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan.,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Yuki Sudo
- Division of Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan.,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
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38
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Tsukamoto T, Yoshizawa S, Kikukawa T, Demura M, Sudo Y. Implications for the Light-Driven Chloride Ion Transport Mechanism of Nonlabens marinus Rhodopsin 3 by Its Photochemical Characteristics. J Phys Chem B 2017; 121:2027-2038. [PMID: 28194973 DOI: 10.1021/acs.jpcb.6b11101] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Several new retinal-based photoreceptor proteins that act as light-driven electrogenic halide ion pumps have recently been discovered. Some of them, called "NTQ" rhodopsins, contain a conserved Asn-Thr-Gln motif in the third or C-helix. In this study, we investigated the photochemical characteristics of an NTQ rhodopsin, Nonlabens marinus rhodopsin 3 (NM-R3), which was discovered in the N. marinus S1-08T strain, using static and time-resolved spectroscopic techniques. We demonstrate that NM-R3 binds a Cl- in the vicinity of the retinal chromophore accompanied by a spectral blueshift from 568 nm in the absence of Cl- to 534 nm in the presence of Cl-. From the Cl- concentration dependence, we estimated the affinity (dissociation constant, Kd) for Cl- in the original state as 24 mM, which is ca. 10 times weaker than that of archaeal halorhodopsins but ca. 3 times stronger than that of a marine bacterial Cl- pumping rhodopsin (C1R). NM-R3 showed no dark-light adaptation of the retinal chromophore and predominantly possessed an all-trans-retinal, which is responsible for the light-driven Cl- pump function. Flash-photolysis experiments suggest that NM-R3 passes through five or six photochemically distinct intermediates (K, L(N), O1, O2, and NM-R3'). From these results, we assume that the Cl- is released and taken up during the L(N)-O1 transition from a transiently formed cytoplasmic (CP) binding site and the O2-NM-R3' or the NM-R3'-original NM-R3 transitions from the extracellular (EC) side, respectively. We propose a mechanism for the Cl- transport by NM-R3 based on our results and its recently reported crystal structure.
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Affiliation(s)
- Takashi Tsukamoto
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University , 700-8530 Okayama, Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo , Chiba 277-8564, Japan
| | | | | | - Yuki Sudo
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University , 700-8530 Okayama, Japan
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Nagasawa K, Tada Y, Koarada S, Tsukamoto H, Horiuchi T, Yoshizawa S, Murai K, Ueda A, Haruta Y, Ohta A. Prevention of steroid-induced osteonecrosis of femoral head in systemic lupus erythematosus by anti-coagulant. Lupus 2016; 15:354-7. [PMID: 16830881 DOI: 10.1191/0961203306lu2311oa] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Although osteonecrosis of femoral head (ONF) is one of the serious complications in systemic lupus erythematosus (SLE) associated with corticosteroid therapy, there has been few trials of prevention of ONF described. We aimed to prevent ONF in steroid-treated SLE patients using anticoagulant, warfarin, conducting a multicenter prospective study. Sixty newly diagnosed SLE patients requiring 40 mg/day or more prednisolone were alternately assigned to either of two groups; a warfarin group and a control one. Warfarin (1 ∼ 5 mg/day) was started together with the beginning of steroid therapy and continued at least for three months. Patients were observed for the development of silent ONF by magnetic resonance imaging (MRI) and symptomatic ONF by plain radiography for over five years. The warfarin group consisted of 31 patients (62 hips) and the control one 29 patients (58 hips). Silent ONF developed in 13 hips (21%) and 19 hips (33%) in the warfarin group and the control group, respectively ( P = 0.13). On the other hand, warfarin tended to prevent symptomatic ONF; only three hips of 62 (4.8%) in the warfarin group and eight hips of 58 (14%) in the control group ( P = 0.08) developed silent ONF. It was also found that silent ONF developed, if it did, very early; within three months in 16 of 18 patients (89%). Among risk factors for silent ONF, steroid pulse therapy was most outstanding and it seemed to overcome the effect of warfarin. Taken together, for the time being, anticoagulant therapy, if not significantly sufficient, may be of use for the prevention of steroid-induced ONF in SLE. We consider that this study added to important evidence for the pathogenesis and prevention of ONF.
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Affiliation(s)
- K Nagasawa
- Department of Internal Medicine, Saga Medical School, Japan.
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40
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Nagasawa K, Tada Y, Koarada S, Horiuchi T, Tsukamoto H, Murai K, Ueda A, Yoshizawa S, Ohta A. Very early development of steroid-associated osteonecrosis of femoral head in systemic lupus erythematosus: prospective study by MRI. Lupus 2016; 14:385-90. [PMID: 15934439 DOI: 10.1191/0961203305lu2103oa] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The objective of this study was to define prospectively the early development of corticosteroid-induced osteonecrosis of femoral head (ONF) in patients with systemic lupus erythematosus (SLE) and to identify the association of initial steroid treatment with the development of early (silent) ONF. Forty-five patients who were newly diagnosed as having SLE and required 40 mg/day or more prednisolone were enrolled. To detect silent ONF, examinations using magnetic resonance imaging (MRI) were done three months after starting steroid therapy, followed by every year’s MRI and plain radiography for over five years. Clinical and laboratory data were compared between silent ONF and non-ONF groups. Of 45 patients, 15 (33%) developed silent ONF and five (11%) symptomatic ONF. It was of interest that MRI detected silent ONF very early (by three months) in 14 patients (93%). It should be noted that pulse therapy with 1000 mg/day methylprednisolone was found to be done very frequently (13 of 15, 87%) in the silent ONF group compared to non-ONF group (11 of 30, 37%) (P, 0.01) although other clinical features were not significantly different between both groups. High dose corticosteroids caused elevation of serum levels of total cholesterol, albumin, and leukocyte count in most of patients. The degree of elevation of those parameters at one or three months was more prominent in the silent ONF group. In particular, the change ratio of total cholesterol at one month was outstanding in the silent ONF group compared to non-ONF group (0.551 versus 0.374, P, 0.05). In conclusion, pathological ONF develops very early in one-third of SLE patients who received high dose corticosteroids and steroid pulse therapy could be a significant risk factor. An abrupt elevation of serum total cholesterol and/or sensitivity to steroids seem to be associated with the pathogenesis of ONF.
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Affiliation(s)
- K Nagasawa
- Department of Internal Medicine, Saga Medical School, Saga, Japan.
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41
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Hosaka T, Yoshizawa S, Nakajima Y, Ohsawa N, Hato M, DeLong EF, Kogure K, Yokoyama S, Kimura-Someya T, Iwasaki W, Shirouzu M. Structural Mechanism for Light-driven Transport by a New Type of Chloride Ion Pump, Nonlabens marinus Rhodopsin-3. J Biol Chem 2016; 291:17488-17495. [PMID: 27365396 DOI: 10.1074/jbc.m116.728220] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Indexed: 01/28/2023] Open
Abstract
The light-driven inward chloride ion-pumping rhodopsin Nonlabens marinus rhodopsin-3 (NM-R3), from a marine flavobacterium, belongs to a phylogenetic lineage distinct from the halorhodopsins known as archaeal inward chloride ion-pumping rhodopsins. NM-R3 and halorhodopsin have distinct motif sequences that are important for chloride ion binding and transport. In this study, we present the crystal structure of a new type of light-driven chloride ion pump, NM-R3, at 1.58 Å resolution. The structure revealed the chloride ion translocation pathway and showed that a single chloride ion resides near the Schiff base. The overall structure, chloride ion-binding site, and translocation pathway of NM-R3 are different from those of halorhodopsin. Unexpectedly, this NM-R3 structure is similar to the crystal structure of the light-driven outward sodium ion pump, Krokinobacter eikastus rhodopsin 2. Structural and mutational analyses of NM-R3 revealed that most of the important amino acid residues for chloride ion pumping exist in the ion influx region, located on the extracellular side of NM-R3. In contrast, on the opposite side, the cytoplasmic regions of K. eikastus rhodopsin 2 were reportedly important for sodium ion pumping. These results provide new insight into ion selection mechanisms in ion pumping rhodopsins, in which the ion influx regions of both the inward and outward pumps are important for their ion selectivities.
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Affiliation(s)
- Toshiaki Hosaka
- From the Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, and
| | - Susumu Yoshizawa
- the Atmosphere and Ocean Research Institute, University of Tokyo, Chiba 277-8564, Japan
| | - Yu Nakajima
- the Atmosphere and Ocean Research Institute, University of Tokyo, Chiba 277-8564, Japan
| | - Noboru Ohsawa
- From the Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, and
| | - Masakatsu Hato
- From the Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, and
| | - Edward F DeLong
- the Center for Microbial Oceanography, Research and Education, University of Hawaii, Honolulu, Hawaii 96822, and
| | - Kazuhiro Kogure
- the Atmosphere and Ocean Research Institute, University of Tokyo, Chiba 277-8564, Japan
| | | | - Tomomi Kimura-Someya
- From the Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, and
| | - Wataru Iwasaki
- the Atmosphere and Ocean Research Institute, University of Tokyo, Chiba 277-8564, Japan, .,the Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0032, Japan
| | - Mikako Shirouzu
- From the Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, and
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42
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Sudo Y, Yoshizawa S. Functional and Photochemical Characterization of a Light-Driven Proton Pump from the Gammaproteobacterium Pantoea vagans. Photochem Photobiol 2016; 92:420-7. [PMID: 26970049 DOI: 10.1111/php.12585] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 02/15/2016] [Indexed: 11/29/2022]
Abstract
Photoactive retinal proteins are widely distributed throughout the domains of the microbial world (i.e., bacteria, archaea, and eukarya). Here we describe three retinal proteins belonging to a phylogenetic clade with a unique DTG motif. Light-induced decrease in the environmental pH and its inhibition by carbonyl cyanide m-chlorophenylhydrazone revealed that these retinal proteins function as light-driven outward electrogenic proton pumps. We further characterized one of these proteins, Pantoea vagans rhodopsin (PvR), spectroscopically. Visible spectroscopy and high-performance liquid chromatography revealed that PvR has an absorption maximum at 538 nm with the retinal chromophore predominantly in the all-trans form (>90%) under both dark and light conditions. We estimated the pKa values of the protonated Schiff base of the retinal chromophore and its counterion as approximately 13.5 and 2.1, respectively, by using pH titration experiments, and the photochemical reaction cycle of PvR was measured by time-resolved flash-photolysis in the millisecond timeframe. We observed a blue-shifted and a red-shifted intermediate, which we assigned as M-like and O-like intermediates, respectively. Decay of the M-like intermediate was highly sensitive to environmental pH, suggesting that proton uptake is coupled to decay of the M-like intermediate. From these results, we propose a putative model for the photoreaction of PvR.
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Affiliation(s)
- Yuki Sudo
- Division of Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
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Hiraoka S, Machiyama A, Ijichi M, Inoue K, Oshima K, Hattori M, Yoshizawa S, Kogure K, Iwasaki W. Genomic and metagenomic analysis of microbes in a soil environment affected by the 2011 Great East Japan Earthquake tsunami. BMC Genomics 2016; 17:53. [PMID: 26764021 PMCID: PMC4712596 DOI: 10.1186/s12864-016-2380-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 01/06/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Great East Japan Earthquake of 2011 triggered large tsunami waves, which flooded broad areas of land along the Pacific coast of eastern Japan and changed the soil environment drastically. However, the microbial characteristics of tsunami-affected soil at the genomic level remain largely unknown. In this study, we isolated microbes from a soil sample using general low-nutrient and seawater-based media to investigate microbial characteristics in tsunami-affected soil. RESULTS As expected, a greater proportion of strains isolated from the tsunami-affected soil than the unaffected soil grew in the seawater-based medium. Cultivable strains in both the general low-nutrient and seawater-based media were distributed in the genus Arthrobacter. Most importantly, whole-genome sequencing of four of the isolated Arthrobacter strains revealed independent losses of siderophore-synthesis genes from their genomes. Siderophores are low-molecular-weight, iron-chelating compounds that are secreted for iron uptake; thus, the loss of siderophore-synthesis genes indicates that these strains have adapted to environments with high-iron concentrations. Indeed, chemical analysis confirmed the investigated soil samples to be rich in iron, and culture experiments confirmed weak cultivability of some of these strains in iron-limited media. Furthermore, metagenomic analyses demonstrated over-representation of denitrification-related genes in the tsunami-affected soil sample, as well as the presence of pathogenic and marine-living genera and genes related to salt-tolerance. CONCLUSIONS Collectively, the present results would provide an example of microbial characteristics of soil disturbed by the tsunami, which may give an insight into microbial adaptation to drastic environmental changes. Further analyses on microbial ecology after a tsunami are envisioned to develop a deeper understanding of the recovery processes of terrestrial microbial ecosystems.
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Affiliation(s)
- Satoshi Hiraoka
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Chiba, 277-8568, Japan.
| | - Asako Machiyama
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Tokyo, 113-0032, Japan.
| | - Minoru Ijichi
- Atmosphere and Ocean Research Institute, the University of Tokyo, Chiba, 277-8564, Japan.
| | - Kentaro Inoue
- Atmosphere and Ocean Research Institute, the University of Tokyo, Chiba, 277-8564, Japan.
| | - Kenshiro Oshima
- Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan.
| | - Masahira Hattori
- Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan.
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, the University of Tokyo, Chiba, 277-8564, Japan.
| | - Kazuhiro Kogure
- Atmosphere and Ocean Research Institute, the University of Tokyo, Chiba, 277-8564, Japan.
| | - Wataru Iwasaki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Chiba, 277-8568, Japan. .,Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Tokyo, 113-0032, Japan. .,Atmosphere and Ocean Research Institute, the University of Tokyo, Chiba, 277-8564, Japan.
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Urabe N, Ishii Y, Hyodo Y, Aoki K, Yoshizawa S, Saga T, Murayama SY, Sakai K, Homma S, Tateda K. Molecular epidemiologic analysis of a Pneumocystis pneumonia outbreak among renal transplant patients. Clin Microbiol Infect 2015; 22:365-371. [PMID: 26724988 DOI: 10.1016/j.cmi.2015.12.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 12/11/2015] [Accepted: 12/14/2015] [Indexed: 10/22/2022]
Abstract
Between 18 November and 3 December 2011, five renal transplant patients at the Department of Nephrology, Toho University Omori Medical Centre, Tokyo, were diagnosed with Pneumocystis pneumonia (PCP). We used molecular epidemiologic methods to determine whether the patients were infected with the same strain of Pneumocystis jirovecii. DNA extracted from the residual bronchoalveolar lavage fluid from the five outbreak cases and from another 20 cases of PCP between 2007 and 2014 were used for multilocus sequence typing to compare the genetic similarity of the P. jirovecii. DNA base sequencing by the Sanger method showed some regions where two bases overlapped and could not be defined. A next-generation sequencer was used to analyse the types and ratios of these overlapping bases. DNA base sequences of P. jirovecii in the bronchoalveolar lavage fluid from four of the five PCP patients in the 2011 outbreak and from another two renal transplant patients who developed PCP in 2013 were highly homologous. The Sanger method revealed 14 genomic regions where two differing DNA bases overlapped and could not be identified. Analyses of the overlapping bases by a next-generation sequencer revealed that the differing types of base were present in almost identical ratios. There is a strong possibility that the PCP outbreak at the Toho University Omori Medical Centre was caused by the same strain of P. jirovecii. Two different types of base present in some regions may be due to P. jirovecii's being a diploid species.
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Affiliation(s)
- N Urabe
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Japan
| | - Y Ishii
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Japan.
| | - Y Hyodo
- Department of Nephrology Medicine, Japan
| | - K Aoki
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Japan
| | - S Yoshizawa
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Japan
| | - T Saga
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Japan
| | - S Y Murayama
- Laboratory of Molecular Cell Biology, School of Pharmacy, Nihon University, Funabashi, Chiba, Japan
| | - K Sakai
- Department of Nephrology Medicine, Japan
| | - S Homma
- Department of Respiratory Medicine, Toho University Omori Medical Centre, Otaku, Tokyo, Japan
| | - K Tateda
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Japan
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Song J, Choi A, Im M, Joung Y, Yoshizawa S, Cho JC, Kogure K. Aurantivirga profunda gen. nov., sp. nov., isolated from deep-seawater, a novel member of the family Flavobacteriaceae. Int J Syst Evol Microbiol 2015; 65:4850-4856. [PMID: 26443199 DOI: 10.1099/ijsem.0.000662] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, proteorhodopsin-containing, orange, rod-shaped bacterium, designated SAORIC-234T, was isolated from deep seawater in the Pacific Ocean. 16S rRNA gene sequence analysis revealed that the strain could be affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and shared less than 94.6 % similarity with other species of the family with validly published names. The phenotypic characteristics of this novel isolate, such as growth properties and enzyme activities, could be differentiated from those of other species. The strain was non-motile, oxidase-positive and catalase-negative. The G+C content of the genomic DNA was determined to be 34.8 mol% and menaquinone-6 (MK-6) was the predominant isoprenoid quinone. The predominant fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C16 : 0 3-OH, iso-C17 : 0 3-OH and iso-C15 : 0 3-OH. The major polar lipids comprised phosphatidylethanolamine, three unknown aminolipids and three unknown lipids. On the basis of the taxonomic data collected in this study, it was concluded that strain SAORIC-234T represents a novel genus and species in the family Flavobacteriaceae, for which the name Aurantivirga profunda gen. nov., sp. nov. is proposed. The type strain of the type species, Aurantivirga profunda sp. nov., is SAORIC-234T ( = NBRC 110606T = KACC 18400T).
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Affiliation(s)
- Jaeho Song
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
| | - Ahyoung Choi
- Department of Biological Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Mihye Im
- Department of Biological Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Yochan Joung
- Department of Biological Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
| | - Jang-Cheon Cho
- Department of Biological Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Kazuhiro Kogure
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
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Yoshimura S, Miyazu M, Yoshizawa S, So M, Kusama N, Hirate H, Sobue K. Efficacy of an enteral feeding protocol for providing nutritional support after paediatric cardiac surgery. Anaesth Intensive Care 2015; 43:587-93. [PMID: 26310408 DOI: 10.1177/0310057x1504300506] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Enteral nutrition (EN) is considered to be a more appropriate method than parenteral feeding for providing nutrition to critically ill children. However, children who undergo cardiac surgery are at high risk of postoperative gastrointestinal complications during EN. The purpose of this study was to demonstrate the safety and efficacy of our EN feeding protocol after paediatric cardiac surgery through comparison between a single-centre prospective case series and historical cases. Forty-seven children who were admitted to the ICU after cardiac surgery were enrolled ('post group'). Data for these children were compared with a similar cohort of children who were admitted before the implementation of the feeding protocol (n=62; 'pre group'). The incidence of complications including vomiting, necrotising enterocolitis and hypoglycaemia; the time until the initiation of EN; and the changes in calories provided were compared between the groups. The frequency of vomiting was significantly lower in the post group than in the pre group (36.2% versus 58.0%, P=0.038), and necrotising enterocolitis did not occur in either group. The time until the initiation of EN and the total calories provided did not differ significantly; however, in the post group the proportion of energy provided by parenteral nutrition was significantly smaller (P <0.001), and provided by EN was significantly larger (P=0.003), than in the pre group. The frequency of hypoglycaemia was similar in both groups. This study showed that our EN protocol resulted in adjustments to calories provided via EN versus parenteral nutrition after paediatric cardiac surgery, and reduced the frequency of vomiting.
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Affiliation(s)
- S Yoshimura
- Anaesthetist, Department of Anesthesiology and Medical Crisis Management, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - M Miyazu
- Anaesthetist, Department of Anesthesiology and Medical Crisis Management, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - S Yoshizawa
- Research Assistant, Department of Anesthesiology and Medical Crisis Management, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - M So
- Anaesthetist, Department of Anesthesiology and Medical Crisis Management, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - N Kusama
- Assistant Professor, Department of Anesthesiology and Medical Crisis Management, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - H Hirate
- Assistant Professor, Department of Anesthesiology and Medical Crisis Management, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - K Sobue
- Professor, Department of Anesthesiology and Medical Crisis Management, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
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Katayama M, Miyamura T, Suenaga Y, Suematsu E, Urata Y, Matsui T, Kaneko A, Kida D, Sato T, Kawabe Y, Yoshizawa S, Tsunoda S, Sano H, Saisho K, Takahi K, Nishino J, Tohma S. AB0365 Prevalence and Factors Associated with Depression and Anxiety in Patients with Rheumatoid Arthritis Using Data from a Large Japanese Cohort Database in 2013 (Ninja 2013 Database). Ann Rheum Dis 2015. [DOI: 10.1136/annrheumdis-2015-eular.4265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Moriuchi S, Yoshizawa S, Mizuno K, Hosoya N, Noda S, Kubota K. Effect of 1,25-dihydroxycholecalciferol on the duodenal villi and alkaline phosphatase in the developing chick embryo. Contrib Nephrol 2015; 22:9-17. [PMID: 6893176 DOI: 10.1159/000385982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Administration of 1,25-(OH)2D3 to developing 14-day chick embryo gave precocious induction of alkaline phosphatase in 20-day chick embryonic duodenum. 1,25-(OH)-2D3-induced alkaline phosphase involved in changes in Km and Vmax values. Furthermore, polyacrylamide gel disc electrophoresis of n-butanol-solubilized alkaline phosphatase from control and 1,25-(OH)2D3-treated chick embryonic duodenum revealed that 1,25-(OH)2D3 involved the transformation of neuraminidase-resistant fast migrating form to the neuraminidase-sensitive faster migrating one. Scanning electron microscopic data showed that the injection of 1,25-(OH)2D3 stimulated the elongation of duodenal microvilli, although there was no effect on the duodenal absorptive epithelial cell height.
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Kato HE, Inoue K, Abe-Yoshizumi R, Kato Y, Ono H, Konno M, Hososhima S, Ishizuka T, Hoque MR, Kunitomo H, Ito J, Yoshizawa S, Yamashita K, Takemoto M, Nishizawa T, Taniguchi R, Kogure K, Maturana AD, Iino Y, Yawo H, Ishitani R, Kandori H, Nureki O. Structural basis for Na(+) transport mechanism by a light-driven Na(+) pump. Nature 2015; 521:48-53. [PMID: 25849775 DOI: 10.1038/nature14322] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 02/11/2015] [Indexed: 02/06/2023]
Abstract
Krokinobacter eikastus rhodopsin 2 (KR2) is the first light-driven Na(+) 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(+) 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(+) transport. Together with the structure-based engineering of the first light-driven K(+) 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.
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Affiliation(s)
- Hideaki E Kato
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Keiichi Inoue
- 1] Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan [2] OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan [3] PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Rei Abe-Yoshizumi
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Yoshitaka Kato
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Hikaru Ono
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Masae Konno
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Shoko Hososhima
- 1] Department of Developmental Biology and Neuroscience, Tohoku University Graduate School of Life Sciences, Sendai 980-8577, Japan [2] CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Toru Ishizuka
- 1] Department of Developmental Biology and Neuroscience, Tohoku University Graduate School of Life Sciences, Sendai 980-8577, Japan [2] CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Mohammad Razuanul Hoque
- 1] Department of Developmental Biology and Neuroscience, Tohoku University Graduate School of Life Sciences, Sendai 980-8577, Japan [2] CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Hirofumi Kunitomo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Jumpei Ito
- Department of Bioengineering Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
| | | | - Mizuki Takemoto
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Tomohiro Nishizawa
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Reiya Taniguchi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Kazuhiro Kogure
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
| | - Andrés D Maturana
- Department of Bioengineering Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Yuichi Iino
- 1] Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan [2] CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Hiromu Yawo
- 1] Department of Developmental Biology and Neuroscience, Tohoku University Graduate School of Life Sciences, Sendai 980-8577, Japan [2] CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Ryuichiro Ishitani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hideki Kandori
- 1] Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan [2] OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
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Lee H, Yoshizawa S, Kogure K, Kim HS, Yoon J. Pelagitalea pacifica gen. nov., sp. nov., a New Marine Bacterium Isolated from Seawater. Curr Microbiol 2014; 70:514-9. [DOI: 10.1007/s00284-014-0750-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 10/30/2014] [Indexed: 11/24/2022]
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