Updated on 2022/10/26

写真a

 
IHARA Kunio
 
Organization
Center for Gene Research Associate professor
Graduate School
Graduate School of Science
Title
Associate professor
Contact information
メールアドレス

Degree 1

  1. PhD ( Osaka University ) 

Research Interests 11

  1. Classification

  2. Archaea

  3. Energy Transfer System

  4. Evolution

  5. Biological Membrane

  6. Structual Biology

  7. Classification

  8. Retinal Proteins

  9. System Biology

  10. Genome

  11. Bioinformatics

Research Areas 6

  1. Others / Others  / Genomic microbiology

  2. Life Science / System genome science  / System Genome Biology

  3. Others / Others  / Microbial physiology

  4. Life Science / Structural biochemistry  / Functional Biochemistry

  5. Life Science / Biophysics  / Biophysics

  6. Life Science / Molecular biology  / Molecular Biology

▼display all

Current Research Project and SDGs 3

  1. Application and development of next-generation sequencer technology

  2. Evolutionary Biology of the three Domain comparison

  3. Realization of Population Microbiology and Analysis of Interactions between Organisms

Research History 4

  1. Nagoya University   Center for Gene Research   Associate professor

    2012.6

  2. Nagoya University   Center for Gene Research   Assistant Professor

    2007.4 - 2012.5

  3. Nagoya University   Center for Gene Research   Assistant

    1999.12 - 2007.3

  4. Nagoya University   School of Science, Department of Biology   Assistant

    1990.4 - 1999.11

Education 2

  1. Osaka University   Graduate School, Division of Natural Science   Phisyology

    1985.4 - 1989

      More details

    Country: Japan

  2. Osaka University   Faculty of Science   Department of Bilogy

    1981.4 - 1985.3

      More details

    Country: Japan

Professional Memberships 7

  1. 日本ゲノム微生物学会

  2. Japan Society for Archaea

  3. 極限生物学会

  4. 日本生物物理学会

  5. 日本微生物生態学会

  6. 好塩微生物研究会

  7. Japan Bioenergerics Group

▼display all

Committee Memberships 2

  1. 遺伝子実験施設連絡協議会   組換え生物等安全委員会委員長  

    2018.12 - 2020.11   

      More details

    Committee type:Academic society

    組換え生物等委員会 委員長

  2. 遺伝子実験施設連絡協議会   幹事  

    2017.12   

      More details

    Committee type:Academic society

Awards 1

  1. 科研費審査委員表彰

    2014   文部科学省  

 

Papers 96

  1. Existence of two substates in the O intermediate of the bacteriorhodopsin photocycle Reviewed

    Kouyama Tsutomu, Ihara Kunio

    BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES   Vol. 1864 ( 10 ) page: 183998   2022.10

     More details

    Language:Japanese   Publishing type:Research paper (scientific journal)   Publisher:Biochimica et Biophysica Acta - Biomembranes  

    The proton pumping cycle of bacteriorhodopsin (bR) is initiated when the retinal chromophore with the 13-trans configuration is photo-isomerized into the 13-cis configuration. To understand the recovery processes of the initial retinal configuration that occur in the late stage of the photocycle, we have performed a comprehensive analysis of absorption kinetics data collected at various pH levels and at different salt concentrations. The result of analysis revealed the following features of the late stages of the trans photocycle. i) Two substates occur in the O intermediate. ii) The visible absorption band of the first substate (O1) appears at a much shorter wavelength than that of the late substate (O2). iii) O1 is in rapid equilibrium with the preceding state (N), but O1 becomes less stable than N when an ionizable residue (X1) with a pKa value of 6.5 (in 2 M KCl) is deprotonated. iv) At a low pH and at a low salt concentration, the decay time constant of O2 is longer than those of the preceding states, but the relationship between these time constants is altered when the medium pH or the salt concentration is increased. On the basis of the present observations and previous studies on the structure of the chromophore in O, we suspect that the retinal chromophore in O1 takes on a distorted 13-cis configuration and the O1-to-O2 transition is accompanied by cis-to-trans isomerization about C13[dbnd]C14 bond.

    DOI: 10.1016/j.bbamem.2022.183998

    Web of Science

    Scopus

    PubMed

  2. Two substates in the O intermediate of the light-driven proton pump archaerhodopsin-2 Reviewed

    Kouyama Tsutomu, Ihara Kunio

    BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES   Vol. 1864 ( 7 ) page: 183919   2022.7

     More details

    Language:Japanese   Publishing type:Research paper (scientific journal)   Publisher:Biochimica et Biophysica Acta - Biomembranes  

    The proton pumping cycle of archaerhodopsin-2 (aR2) was investigated over a wide pH range and at different salt concentrations. We have found that two substates, which are spectroscopically and kinetically distinguishable, occur in the O intermediate. The first O-intermediate (O1) absorbs maximumly at ~580 nm, whereas the late O-intermediate (O2) absorbs maximumly at 605 nm. At neutral pH, O1 is in rapid equilibrium with the N intermediate. When the medium pH is increased, O1 becomes less stable than N and, in proportion to the amount of O1 in the dynamic equilibrium between N and O1, the formation rate of O2 decreases. By contrast, the decay rate of O2 increases ~100 folds when the pH of a low-salt membrane suspension is increased from 5.5 to 7.5 or when the salt concentration is increased to 2 M KCl. Together with our recent study on two substates in the O intermediate of bacteriorhodopsin (bR), the present study suggests that the thermally activated re-isomerization of the retinylidene chromophore into the initial all-trans configuration takes place in the O1-to-O2 transition; that is, O1 contains a distorted 13-cis chromophore. It is also found that the pKa value of the key ionizable residue (Asp101aR2, Asp96bR) in the proton uptake channel is elevated in the O1 state of aR2 as compared to the O1 state of bR. This implies that the structural property of O1 in the aR2 photocycle can be investigated over a wide pH range.

    DOI: 10.1016/j.bbamem.2022.183919

    Web of Science

    Scopus

    PubMed

  3. Mutations in the stator protein PomA affect switching of rotational direction in bacterial flagellar motor Reviewed

    Hiroyuki Terashima, Kiyoshiro Hori, Kunio Ihara, Michio Homma, Seiji Kojima

    Scientific Reports   Vol. 12 ( 1 ) page: 2979   2022.2

     More details

    Language:Japanese   Publishing type:Research paper (scientific journal)   Publisher:Springer Science and Business Media LLC  

    Abstract

    The flagellar motor rotates bi-directionally in counter-clockwise (CCW) and clockwise (CW) directions. The motor consists of a stator and a rotor. Recent structural studies have revealed that the stator is composed of a pentameric ring of A subunits and a dimer axis of B subunits. Highly conserved charged and neighboring residues of the A subunit interacts with the rotor, generating torque through a gear-like mechanism. The rotational direction is controlled by chemotaxis signaling transmitted to the rotor, with less evidence for the stator being involved. In this study, we report novel mutations that affect the switching of the rotational direction at the putative interaction site of the stator to generate rotational force. Our results highlight an aspect of flagellar motor function that appropriate switching of the interaction states between the stator and rotor is critical for controlling the rotational direction.

    DOI: 10.1038/s41598-022-06947-5

    Web of Science

    Scopus

    PubMed

    Other Link: https://www.nature.com/articles/s41598-022-06947-5

  4. Identification of ksg1 mutation showing long-lived phenotype in fission yeast Reviewed

    Matsui Kotaro, Okamoto Keisuke, Hasegawa Tomoka, Ohtsuka Hokuto, Shimasaki Takafumi, Ihara Kunio, Goto Yuhei, Aoki Kazuhiro, Aiba Hirofumi

    GENES TO CELLS   Vol. 26 ( 12 ) page: 967 - 978   2021.12

     More details

    Language:Japanese   Publishing type:Research paper (scientific journal)   Publisher:Genes to Cells  

    Fission yeast is a good model organism for the study of lifespan. To elucidate the mechanism, we screened for long-lived mutants. We found a nonsense mutation in the ksg1+ gene, which encodes an ortholog of mammalian PDK1 (phosphoinositide-dependent protein kinase). The mutation was in the PH domain of Ksg1 and caused defect in membrane localization and protein stability. Analysis of the ksg1 mutant revealed that the reduced amounts and/or activity of the Ksg1 protein are responsible for the increased lifespan. Ksg1 is essential for growth and known to phosphorylate multiple substrates, but the substrate responsible for the long-lived phenotype of ksg1 mutation is not yet known. Genetic analysis showed that deletion of pck2 suppressed the long-lived phenotype of ksg1 mutant, suggesting that Pck2 might be involved in the lifespan extension caused by ksg1 mutation.

    DOI: 10.1111/gtc.12897

    Web of Science

    Scopus

    PubMed

  5. A slight bending of an alpha-helix in FliM creates a counterclockwise-locked structure of the flagellar motor in Vibrio Reviewed

    Takekawa Norihiro, Nishikino Tatsuro, Yamashita Toshiki, Hori Kiyoshiro, Onoue Yasuhiro, Ihara Kunio, Kojima Seiji, Homma Michio, Imada Katsumi

    JOURNAL OF BIOCHEMISTRY   Vol. 170 ( 4 ) page: 531 - 538   2021.10

     More details

    Language:Japanese   Publishing type:Research paper (scientific journal)   Publisher:Journal of Biochemistry  

    Many bacteria swim by rotating flagella. The chemotaxis system controls the direction of flagellar rotation. Vibrio alginolyticus, which has a single polar flagellum, swims smoothly by rotating the flagellar motor counterclockwise (CCW) in response to attractants. In response to repellents, the motor frequently switches its rotational direction between CCW and clockwise (CW). We isolated a mutant strain that swims with a CW-locked rotation of the flagellum, which pulls rather than pushes the cell. This CW phenotype arises from a R49P substitution in FliM, which is the component in the C-ring of the motor that binds the chemotaxis signalling protein, phosphorylated CheY. However, this phenotype is independent of CheY, indicating that the mutation produces a CW conformation of the C-ring in the absence of CheY. The crystal structure of FliM with the R49P substitution showed a conformational change in the N-terminal α-helix of the middle domain of FliM (FliMM). This helix should mediates FliM-FliM interaction. The structural models of wild type and mutant C-ring showed that the relatively small conformational change in FliMM induces a drastic rearrangement of the conformation of the FliMM domain that generates a CW conformation of the C-ring.

    DOI: 10.1093/jb/mvab074

    Web of Science

    Scopus

    PubMed

  6. Identification of sur2 mutation affecting the lifespan of fission yeast Reviewed

    Kurauchi Tatsuhiro, Matsui Kotaro, Shimasaki Takafumi, Ohtsuka Hokuto, Tsubouchi Satoshi, Ihara Kunio, Tani Motohiro, Aiba Hirofumi

    FEMS MICROBIOLOGY LETTERS   Vol. 368 ( 12 )   2021.6

     More details

    Language:Japanese   Publishing type:Research paper (scientific journal)   Publisher:FEMS Microbiology Letters  

    Yeast is a suitable model system to analyze the mechanism of lifespan. In this study, to identify novel factors involved in chronological lifespan, we isolated a mutant with a long chronological lifespan and found a missense mutation in the sur2+ gene, which encodes a homolog of Saccharomyces cerevisiae sphingolipid C4-hydroxylase in fission yeast. Characterization of the mutant revealed that loss of sur2 function resulted in an extended chronological lifespan. The effect of caloric restriction, a well-known signal for extending lifespan, is thought to be dependent on the sur2+ gene.

    DOI: 10.1093/femsle/fnab070

    Web of Science

    Scopus

    PubMed

  7. Randomized phase II study comparing the efficacy and safety of SOX versus mFOLFOX6 as neoadjuvant chemotherapy without radiotherapy for locally advanced rectal cancer (KSCC1301) Reviewed

    Miwa Keisuke, Oki Eiji, Enomoto Masanobu, Ihara Keisuke, Ando Koji, Fujita Fumihiko, Tominaga Masahiro, Mori Shinichiro, Nakayama Goro, Shimokawa Mototsugu, Saeki Hiroshi, Baba Hideo, Mori Masaki, Akagi Yoshito

    BMC CANCER   Vol. 21 ( 1 )   2021.1

     More details

    Language:Japanese   Publishing type:Research paper (scientific journal)   Publisher:BMC Cancer  

    Background: Preoperative chemoradiotherapy (CRT), the current standard of care for locally advanced rectal cancer (LARC), is associated with many radiotherapy (RT)-related side effects. We aimed to evaluate whether S-1 and oxaliplatin (SOX) or folinic acid, 5-FU, and oxaliplatin (mFOLFOX6) can be as effective as neoadjuvant chemotherapy (NAC) regimens for LARC without RT. Methods: Patients with untreated resectable LARC were randomly assigned to receive SOX or mFOLFOX6. The NAC protocol period was 3 months. The primary endpoint was 3-year disease-free survival (DFS), and the secondary endpoints included pathological effects, surgical completion rate, 3-year survival, and safety. Results: From September 2013 to October 2015, 56 and 54 patients were enrolled in the SOX and mFOLFOX6 arms, respectively. The 3-year DFS rates were 69.4% (95% confidence interval [CI] 54.9–83.6) and 73.4% (95% CI 58.7–83.6) in the SOX and mFOLFOX6 arms, respectively; no significant differences were found between the arms (log-rank test; P = 0.5315, hazard ratio: 0.808, 95% CI 0.414–1.578). The 3-year survival rates were 92.3 and 91.8% in the SOX and mFOLFOX6 arms, respectively. The surgical completion rate was 98.1% overall, 100% in the SOX arm, and 96.0% in the mFOLFOX6 arm. The incidences of pathological response rates ≥grade 1b were 41.5 and 43.8% in the SOX and mFOLFOX6 arms, respectively. Both treatments were manageable and tolerable. Conclusion: We demonstrated the effectiveness and safety of SOX and mFOLFOX6, both of which may be new neoadjuvant treatment candidates in previously untreated LARC cases. Trial registration: Date of enrolment of the first participant to the trial: 3rd Oct 2013; This study was registered in the UMIN clinical trials registry on 14th Aug, 2013. (Prospectively registered, UMIN-CTR number UMIN000011486). https://upload.umin.ac.jp/cgi-open-bin/ctr/ctr.cgi?function=brows&recptno=R000013441&language=J

    DOI: 10.1186/s12885-020-07766-5

    Web of Science

    Scopus

  8. Loss of cell wall integrity genes cpxA and mrcB causes flocculation in Escherichia coli. Reviewed International journal

    Keita Sugawara, Hayato Toyoda, Mami Kimura, Shunsuke Hayasaka, Hiromi Saito, Hiroshi Kobayashi, Kunio Ihara, Tomoaki Ida, Takaaki Akaike, Eiji Ando, Mamoru Hyodo, Yoshihiro Hayakawa, Shin Hamamoto, Nobuyuki Uozumi

    The Biochemical journal   Vol. 478 ( 1 ) page: 41 - 59   2021.1

     More details

    Language:Japanese   Publishing type:Research paper (scientific journal)  

    Flocculation has been recognized for hundreds of years as an important phenomenon in brewing and wastewater treatment. However, the underlying molecular mechanisms remain elusive. The lack of a distinct phenotype to differentiate between slow-growing mutants and floc-forming mutants prevents the isolation of floc-related gene by conventional mutant screening. To overcome this, we performed a two-step Escherichia coli mutant screen. The initial screen of E. coli for mutants conferring floc production during high salt treatment yielded a mutant containing point mutations in 61 genes. The following screen of the corresponding single-gene mutants identified two genes, mrcB, encoding a peptidoglycan-synthesizing enzyme and cpxA, encoding a histidine kinase of a two-component signal transduction system that contributed to salt tolerance and flocculation prevention. Both single mutants formed flocs during high salt shock, these flocs contained cytosolic proteins. ΔcpxA exhibited decreased growth with increasing floc production and addition of magnesium to ΔcpxA suppressed floc production effectively. In contrast, the growth of ΔmrcB was inconsistent under high salt conditions. In both strains, flocculation was accompanied by the release of membrane vesicles containing inner and outer membrane proteins. Of 25 histidine kinase mutants tested, ΔcpxA produced the highest amount of proteins in floc. Expression of cpxP was up-regulated by high salt in ΔcpxA, suggesting that high salinity and activation of CpxR might promote floc formation. The finding that ΔmrcB or ΔcpxA conferred floc production indicates that cell envelope stress triggered by unfavorable environmental conditions cause the initiation of flocculation in E. coli.

    DOI: 10.1042/BCJ20200723

    Web of Science

    Scopus

    PubMed

  9. Energetics and kinetics of substrate analog-coupled staphylococcal nuclease folding revealed by a statistical mechanical approach. Reviewed

    Mizukami T, Furuzawa S, Itoh SG, Segawa S, Ikura T, Ihara K, Okumura H, Roder H, Maki K

    Proceedings of the National Academy of Sciences of the United States of America   Vol. 117 ( 33 ) page: 19953 - 19962   2020.8

     More details

    Language:Japanese   Publishing type:Research paper (scientific journal)   Publisher:NATL ACAD SCIENCES  

    Protein conformational changes associated with ligand binding, especially those involving intrinsically disordered proteins, are mediated by tightly coupled intra-and intermolecular events. Such reactions are often discussed in terms of two limiting kinetic mech-anisms, conformational selection (CS), where folding precedes binding, and induced fit (IF), where binding precedes folding. It has been shown that coupled folding/binding reactions can pro-ceed along both CS and IF pathways with the flux ratio depending on conditions such as ligand concentration. However, the struc-tural and energetic basis of such complex reactions remains poorly understood. Therefore, we used experimental, theoretical, and computational approaches to explore structural and energetic as-pects of the coupled-folding/binding reaction of staphylococcal nuclease in the presence of the substrate analog adenosine-3 ',5 '-diphosphate. Optically monitored equilibrium and kinetic data, combined with a statistical mechanical model, gave deeper insight into the relative importance of specific and Coulombic protein- ligand interactions in governing the reaction mechanism. We also investigated structural aspects of the reaction at the residue level using NMR and all-atom replica-permutation molecular dynamics simulations. Both approaches yielded clear evidence for accumula-tion of a transient protein-ligand encounter complex early in the reaction under IF-dominant conditions. Quantitative analysis of the equilibrium/kinetic folding revealed that the ligand-dependent CS-to-IF shift resulted from stabilization of the compact transition state primarily by weakly ligand-dependent Coulombic interactions with smaller contributions from specific binding energies. At a more macroscopic level, the CS-to-IF shift was represented as a displace-ment of the reaction "route" on the free energy surface, which was consistent with a flux analysis.

    DOI: 10.1073/pnas.1914349117

    Web of Science

    Scopus

    PubMed

  10. The role of ROC75 as a daytime component of the circadian oscillator in Chlamydomonas reinhardtii Reviewed

    Matsuo Takuya, Iida Takahiro, Ohmura Ayumi, Gururaj Malavika, Kato Daisaku, Mutoh Risa, Ihara Kunio, Ishiura Masahiro

    PLOS GENETICS   Vol. 16 ( 6 ) page: e1008814 - e1008814   2020.6

     More details

    Language:Japanese   Publishing type:Research paper (scientific journal)   Publisher:Public Library of Science (PLoS)  

    DOI: 10.1371/journal.pgen.1008814

    Web of Science

    Scopus

    PubMed

  11. Presynaptic MAST kinase controls opposing postsynaptic responses to convey stimulus valence in Caenorhabditis elegans. Reviewed International journal

    Shunji Nakano, Muneki Ikeda, Yuki Tsukada, Xianfeng Fei, Takamasa Suzuki, Yusuke Niino, Rhea Ahluwalia, Ayana Sano, Rumi Kondo, Kunio Ihara, Atsushi Miyawaki, Koichi Hashimoto, Tetsuya Higashiyama, Ikue Mori

    Proceedings of the National Academy of Sciences of the United States of America   Vol. 117 ( 3 ) page: 1638 - 1647   2020.1

     More details

    Language:Japanese   Publishing type:Research paper (scientific journal)  

    Presynaptic plasticity is known to modulate the strength of synaptic transmission. However, it remains unknown whether regulation in presynaptic neurons can evoke excitatory and inhibitory postsynaptic responses. We report here that the Caenorhabditis elegans homologs of MAST kinase, Stomatin, and Diacylglycerol kinase act in a thermosensory neuron to elicit in its postsynaptic neuron an excitatory or inhibitory response that correlates with the valence of thermal stimuli. By monitoring neural activity of the valence-coding interneuron in freely behaving animals, we show that the alteration between excitatory and inhibitory responses of the interneuron is mediated by controlling the balance of two opposing signals released from the presynaptic neuron. These alternative transmissions further generate opposing behavioral outputs necessary for the navigation on thermal gradients. Our findings suggest that valence-encoding interneuronal activity is determined by a presynaptic mechanism whereby MAST kinase, Stomatin, and Diacylglycerol kinase influence presynaptic outputs.

    DOI: 10.1073/pnas.1909240117

    Web of Science

    Scopus

    PubMed

  12. Haloarcula mannanilytica sp. nov., a galactomannan-degrading haloarchaeon isolated from commercial salt Reviewed

    Shigeaki Enomoto, Yasuhiro Shimane, Kunio Ihara, Masahiro Kamekura, Takashi Itoh, Moriya Ohkuma, Naoko Takahashi-Ando, Yasumasa Fukushima, Yasuhiko Yoshida, Ron Usami, Ken Takai, Hiroaki Minegishi

    International Journal of Systematic and Evolutionary Microbiology   Vol. 70 ( 12 ) page: 6331 - 6337   2020

     More details

    Language:Japanese   Publishing type:Research paper (scientific journal)  

    © 2020 The Authors. A mannan-degrading halophilic archaeal strain, MD130-1T, was isolated from a commercial salt sample. Cells were motile, rod-shaped, and stained Gram-negative. Colonies were pink pigmented. Strain MD130-1T was able to grow at 1.5–4.6 M NaCl (optimum, 3.6 M) at pH 6.0–8.0 (optimum, pH 7.0) and at 25–50 °C (optimum, 40 °C). The DNA G+C content was 62.1 mol% (genome). The orthologous 16S rRNA gene sequence showed the highest similarity (99.4%) to those of Haloarcula japonica JCM 7785T and Haloarcula hispanica JCM 8911T. The values of genome relatedness between strain MD130-1T and Haloarcula species were 84.33–85.96% in ANIb and 30.4–32.9% using GGDC formula 2. The polar lipids of strain MD130-1T were phosphatidylg-lycerol, phosphatidylglycerol phosphate methyl ester and triglycosyl diether-2. Based on the results of phenotypic and phylogenetic analyses, the strain represents a new species of the genus Haloarcula, for which the name Haloarcula mannanilytica sp. nov. is proposed. The type strain is MD130-1T (=JCM 33835T=KCTC 4287T) isolated from commercial salt made in Ishikawa prefecture, Japan.

    DOI: 10.1099/ijsem.0.004535

    Web of Science

    Scopus

    PubMed

  13. gas1 mutation extends chronological lifespan via Pmk1 and Sty1 MAPKs in Schizosaccharomyces pombe Reviewed

    Imai Yuki, Shimasaki Takafumi, Enokimura Chihiro, Ohtsuka Hokuto, Tsubouchi Satoshi, Ihara Kunio, Aiba Hirofumi

    BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY     page: 1-8   2019.10

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1080/09168451.2019.1676695

    Web of Science

    PubMed

  14. The mechanosensitive channel YbdG from <i>Escherichia coli</i> has a role in adaptation to osmotic up-shock. Reviewed

    Amemiya S, Toyoda H, Kimura M, Saito H, Kobayashi H, Ihara K, Kamagata K, Kawabata R, Kato S, Nakashimada Y, Furuta T, Hamamoto S, Uozumi N

    The Journal of biological chemistry     2019.6

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1074/jbc.RA118.007340

    PubMed

  15. Cholecystokinin induces crowing in chickens Reviewed International journal

    Shimmura Tsuyoshi, Tamura Mai, Ohashi Shosei, Sasaki Asuka, TakamichiYamanaka, Nakao Nobuhiro, Ihara Kunio, Okamura Shinsaku, TakashiYoshimura

    SCIENTIFIC REPORTS   Vol. 9 ( 1 ) page: 3978   2019.3

     More details

    Language:Japanese   Publishing type:Research paper (scientific journal)  

    DOI: 10.1038/s41598-019-40746-9

    Web of Science

    Scopus

    PubMed

  16. Comprehensive investigation of the gene expression system regulated by an Aspergillus oryzae transcription factor XlnR using integrated mining of gSELEX-Seq and microarray data. Reviewed

    Oka H, Kojima T, Ihara K, Kobayashi T, Nakano H

    BMC genomics   Vol. 20 ( 1 ) page: 16   2019.1

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1186/s12864-018-5375-5

    Scopus

    PubMed

  17. Obesity and mental health improvement following nutritional education focusing on gut microbiota composition in Japanese women: a randomised controlled trial. Reviewed

    Uemura M, Hayashi F, Ishioka K, Ihara K, Yasuda K, Okazaki K, Omata J, Suzutani T, Hirakawa Y, Chiang C, Aoyama A, Ohira T

    European journal of nutrition     2018.12

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1007/s00394-018-1873-0

    PubMed

  18. Three-Step Isomerization of the Retinal Chromophore during the Anion Pumping Cycle of Halorhodopsin Reviewed International journal

    Kouyama Tsutomu, Ihara Kunio, Maki Kosuke, Chan Siu Kit

    BIOCHEMISTRY   Vol. 57 ( 41 ) page: 6013 - 6026   2018.10

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1021/acs.biochem.8b00631

    Web of Science

    Scopus

    PubMed

  19. Draft Genome Sequence of Burkholderia vietnamiensis Strain RS1, a Nitrogen-Fixing Endophyte Isolated from Sweet Potato. Reviewed International journal

    Rina Shinjo, Kazuma Uesaka, Kunio Ihara, Shunsuke Sakazaki, Katsuya Yano, Motohiko Kondo, Aiko Tanaka

    Microbiology resource announcements   Vol. 7 ( 3 )   2018.7

     More details

    Language:Japanese   Publishing type:Research paper (scientific journal)  

    Burkholderia vietnamiensis strain RS1 is an endophytic bacterium with nitrogen-fixing ability that was isolated from tuberous roots of sweet potato. Here, we present its draft genome of 6,542,727 bases that contains a cluster of genes associated with nitrogen fixation. This genome sequence will provide important insights into the plant growth-promoting potential of endophytic bacteria.

    DOI: 10.1128/MRA.00820-18

    Web of Science

    Scopus

    PubMed

  20. In vivo transposon tagging in the nonheterocystous nitrogen-fixing cyanobacterium Leptolyngbya boryana

    Tomatsu Chie, Uesaka Kazuma, Yamakawa Hisanori, Tsuchiya Tohru, Ihara Kunio, Fujita Yuichi

    FEBS LETTERS   Vol. 592 ( 10 ) page: 1634-1642   2018.5

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1002/1873-3468.13079

    Web of Science

    PubMed

  21. Co-expression of the calcitonin receptor gene in the hypothalamic kisspeptin neurons in female rats Reviewed

    Assadullah, Nahoko Ieda, Narumi Kawai, Hirotaka Ishii, Kunio Ihara, Naoko Inoue, Yoshihisa Uenoyama, Hiroko Tsukamura

    Reprod. Med. Biol.     2018

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1002/rmb2.12085

  22. SLO potassium channels antagonize premature decision making in <i>C. elegans</i>. Reviewed

    Aoki I, Tateyama M, Shimomura T, Ihara K, Kubo Y, Nakano S, Mori I

    Communications biology   Vol. 1   page: 123   2018

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1038/s42003-018-0124-5

    PubMed

  23. Salinarchaeum chitinilyticum sp nov., a chitin-degrading haloarchaeon isolated from commercial salt

    Minegishi Hiroaki, Enomoto Shigeaki, Echigo Akinobu, Shimane Yasuhiro, Kondo Yusuke, Inoma Ayumi, Kamekura Masahiro, Takai Ken, Itoh Takashi, Ohkuma Moriya, Ihara Kunio, Takahashi-Ando Naoko, Fukushima Yasumasa, Ishii Shigeru, Yoshida Yasuhiko, Usami Ron

    INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY   Vol. 67 ( 7 ) page: 2274-2278   2017.7

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1099/ijsem.0.001941

    Web of Science

    PubMed

  24. Complete Chloroplast Genome Sequence of the Early Diverging Green Alga <i>Palmophyllum crassum</i>.

    Furukawa R, Kunugi M, Ihara K, Takabayashi A, Tanaka A

    Genome announcements   Vol. 5 ( 10 )   2017.3

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1128/genomeA.01745-16

    PubMed

  25. Transcriptional regulation of CmpR, the LysR family protein involved in CO2-responsive gene regulation in the cyanobacterium Synechococcus elongatus Reviewed

    Lu-Lu Pan1, Kiyoshi Onai2, Kazuma Uesaka1, Kunio Ihara2, Takumi Natsume1, Nobuyuki Takatani1, Masahiro Ishiura2 and Tatsuo Omata1*

    Biomedical Genetics and Genomics   Vol. 1 ( 5 ) page: 1-6   2017.1

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: : 10.15761/BGG.1000123

  26. Identification of a novel protein kinase that affects the chronological lifespan in fission yeast

    Kurauchi Tatsuhiro, Hashizume Aya, Imai Yuki, Hayashi Kanako, Tsubouchi Satoshi, Ihara Kunio, Ohtsuka Hokuto, Aiba Hirofumi

    FEMS MICROBIOLOGY LETTERS   Vol. 364 ( 2 )   2017.1

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1093/femsle/fnw257

    Web of Science

    PubMed

  27. Exome-wide association study identifies clec3b missense variant p.s106g as being associated with extreme longevity in east asian populations Reviewed

    Tanisawa K.

    Journals of Gerontology - Series A Biological Sciences and Medical Sciences   Vol. 72 ( 3 ) page: 309-318   2017

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1093/gerona/glw074

    Scopus

  28. Photochemical characterization of actinorhodopsin and its functional existence in the natural host. Reviewed

    Nakamura S, Kikukawa T, Tamogami J, Kamiya M, Aizawa T, Hahn MW, Ihara K, Kamo N, Demura M.

    Biochim Biophys Acta.   Vol. 1857 ( 12 ) page: 1900-1908   2016.12

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1016/j.bbabio.2016.09.006.

  29. A simple method for isolation and construction of markerless cyanobacterial mutants defective in acyl-acyl carrier protein synthetase. Reviewed

    Kojima K, Keta S, Uesaka K, Kato A, Takatani N, Ihara K, Omata T, Aichi M.

    Appl Microbiol Biotechnol.   Vol. 100 ( 23 ) page: 10107-10113   2016.12

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

  30. Haloparvum alkalitolerans sp. nov., alkali-tolerant haloarchaeon isolated from commercial salt. Reviewed

    Kondo Y, Minegishi H, Echigo A, Shimane Y, Kamekura M, Itoh T, Ohkuma M, Tanaka A, Takahashi-Ando N, Fukushima Y, Yoshida Y, Ihara K, Usami R.

    Int J Syst Evol Microbiol.   Vol. 66 ( 12 ) page: 5314-5319   2016.12

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1099/ijsem.0.001513.

  31. Shifting transcriptional machinery is required for long-term memory maintenance and modification in Drosophila mushroom bodies. Reviewed

    Hirano Y, Ihara K, Masuda T, Yamamoto T, Iwata I, Takahashi A, Awata H, Nakamura N, Takakura M, Suzuki Y, Horiuchi J, Okuno H, Saitoe M.

    Nat Commun.   Vol. 7   page: 13471   2016.11

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1038/ncomms13471.

  32. Complete Genome Sequence of Kosakonia sacchari Strain BO-1, an Endophytic Diazotroph Isolated from a Sweet Potato. Reviewed

    Shinjo R, Uesaka K, Ihara K, Loshakova K, Mizuno Y, Yano K, Tanaka A.

    Genome Announc.   Vol. 4 ( 5 ) page: e00868-16   2016.9

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1128/genomeA.00868-16.

  33. A Robust Analytical Pipeline for Genome-Wide Identification of the Genes Regulated by a Transcription Factor: Combinatorial Analysis Performed Using gSELEX-Seq and RNA-Seq. Reviewed

    Kojima T, Kunitake E, Ihara K, Kobayashi T, Nakano H.

    PLoS One.   Vol. 11 ( 7 ) page: e0159011   2016.7

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1371/journal.pone.0159011.

  34. Crystal Structure of the 11-cis Isomer of Pharaonis Halorhodopsin: Structural Constraints on Interconversions among Different Isomeric States. Reviewed

    Chan SK, Kawaguchi H, Kubo H, Murakami M, Ihara K, Maki K, Kouyama T.

    Biochemistry.   Vol. 55 ( 29 ) page: 4092-4104   2016.7

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1021/acs.biochem.6b00277.

  35. FliH and FliI ensure efficient energy coupling of flagellar type III protein export in Salmonella. Reviewed

    Minamino T, Kinoshita M, Inoue Y, Morimoto YV, Ihara K, Koya S, Hara N, Nishioka N, Kojima S, Homma M, Namba K.

    Microbiologyopen   Vol. 5 ( 3 ) page: 424-435   2016.6

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1002/mbo3.340.

  36. Evolution of Green Plants Accompanied Changes in Light-Harvesting Systems. Reviewed

    Kunugi M, Satoh S, Ihara K, Shibata K, Yamagishi Y, Kogame K, Obokata J, Takabayashi A, Tanaka A.

    Plant Cell Physiol.   Vol. 57 ( 6 ) page: 1231-1243   2016.6

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1093/pcp/pcw071.

  37. Identification of a Cyanobacterial RND-Type Efflux System Involved in Export of Free Fatty Acids. Reviewed

    Kato A, Takatani N, Use K, Uesaka K, Ikeda K, Chang Y, Kojima K, Aichi M, Ihara K, Nakahigashi K, Maeda S, Omata T.

    Plant Cell Physiol.   Vol. 56 ( 12 ) page: 2467-2477   2015.12

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1093/pcp/pcv150

  38. Structural and functional roles of the N- and C-terminal extended modules in channelrhodopsin-1. Reviewed

    Doi S, Mori A, Tsukamoto T, Reissig L, Ihara K, Sudo Y.

    Photochem Photobiol Sci.   Vol. 14 ( 9 ) page: 1628-36   2015.9

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

  39. Microbial rhodopsins of Halorubrum species isolated from Ejinoor salt lake in Inner Mongolia of China.

    Chaoluomeng, Dai G, Kikukawa T, Ihara K, Iwasa T.

    Photochem Photobiol Sci.     page: Epub ahead of print   2015.8

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    PubMed

  40. Probing the Cl--pumping photocycle of pharaonis halorhodopsin: Examinations with bacterioruberin, an intrinsic dye, and membrane potential-induced modulation of the photocycle. Reviewed

    Kikukawa T, Kusakabe C, Kokubo A, Tsukamoto T, Kamiya M, Aizawa T, Ihara K, Kamo N, Demura M.

    Biochim Biophys Acta.   Vol. 1847 ( 8 ) page: 748-758   2015.8

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    PubMed

  41. A genetic mechanism for female-limited Batesian mimicry in Papilio butterfly. Reviewed

    Nishikawa H, Iijima T, Kajitani R, Yamaguchi J, Ando T, Suzuki Y, Sugano S, Fujiyama A, Kosugi S, Hirakawa H, Tabata S, Ozaki K, Morimoto H, Ihara K, Obara M, Hori H, Itoh T, Fujiwara H.

    Nat Genet.   Vol. 47 ( 4 ) page: 405-409   2015.4

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1038/ng.3241

    PubMed

  42. Loss of cytochrome cM stimulates cyanobacterial heterotrophic growth in the dark Reviewed

    Yuto Hiraide, Kenshiro Oshima, Takatomo Fujisawa, Kazuma Uesaka, Yuu Hirose, Ryoma Tsujimoto, Haruki Yamamoto, Shinobu Okamoto, Yasukazu Nakamura, Kazuki Terauchi, Tatsuo Omata, Kunio Ihara, Masahira Hattori, and Yuichi Fujita

    Plant and Cell Physiology     2014.11

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    Although cyanobacteria are photoautotrophs, they have heterotrophic metabolism that enables them to survive in their natural habitat. However, cyanobacterial species that grow heterotrophically in the dark are rare. It remains largely unknown how cyanobacteria regulate heterotrophic activity. The cyanobacterium Leptolyngbya boryana grows heterotrophically with glucose in the dark. A dark-adapted variant dg5 isolated from the wild-type (WT) exhibits enhanced heterotrophic growth in the dark. We sequenced the genomes of dg5 and WT to identify the mutation(s) of dg5. The WT genome consists of a circular chromosome (6,176,364 bp), a circular plasmid pLBA (77,793 bp), and two linear plasmids pLBX (504,942 bp) and pLBY (44,369 bp). Genome comparison revealed three mutation sites. Phenotype analysis of mutants isolated from WT by introducing these mutations individually revealed that the relevant mutation is a single adenine insertion causing a frameshift of cytM encoding cytochrome cM. The respiratory oxygen consumption of the cytM-lacking mutant grown in the dark was significantly higher than that of WT. We isolated a cytM-lacking mutant, ΔcytM, from another cyanobacterium Synechocystis sp. PCC 6803, and ΔcytM grew in the dark with a doubling time of 33 h in contrast to no growth of WT. The respiratory oxygen consumption of ΔcytM grown in the dark was about 2-fold higher than that of wild type. These results suggest a suppressive role(s) of cytochrome cM in regulation of heterotrophic activity.

    DOI: 10.1093/pcp/pcu165

  43. Crystal Structure of Cruxrhodopsin-3 from Haloarcula vallismortis. Reviewed

    Chan SK, Kitajima-Ihara T, Fujii R, Gotoh T, Murakami M, Ihara K, Kouyama T.

    PLoS One   Vol. 9 ( 9 ) page: e108362   2014.9

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    Cruxrhodopsin-3 (cR3), a retinylidene protein found in the claret membrane of Haloarcula vallismortis, functions as a light-driven proton pump. In this study, the membrane fusion method was applied to crystallize cR3 into a crystal belonging to space group P321. Diffraction data at 2.1 Å resolution show that cR3 forms a trimeric assembly with bacterioruberin bound to the crevice between neighboring subunits. Although the structure of the proton-release pathway is conserved among proton-pumping archaeal rhodopsins, cR3 possesses the following peculiar structural features: 1) The DE loop is long enough to interact with a neighboring subunit, strengthening the trimeric assembly; 2) Three positive charges are distributed at the cytoplasmic end of helix F, affecting the higher order structure of cR3; 3) The cytoplasmic vicinity of retinal is more rigid in cR3 than in bacteriorhodopsin, affecting the early reaction step in the proton-pumping cycle; 4) the cytoplasmic part of helix E is greatly bent, influencing the proton uptake process. Meanwhile, it was observed that the photobleaching of retinal, which scarcely occurred in the membrane state, became significant when the trimeric assembly of cR3 was dissociated into monomers in the presence of an excess amount of detergent. On the basis of these observations, we discuss structural factors affecting the photostabilities of ion-pumping rhodopsins.

    DOI: 10.1371/journal.pone.0108362. eCollection 2014.

  44. Transcriptome Analysis of Reaction Wood in Gymnosperms by Next-Generation Sequencing Reviewed

    Saori Sato, Masato Yoshida, Hideto Hiraide, Kunio Ihara, Hiroyuki Yamamoto

    American Journal of Plant Sciences   Vol. 5   page: 2785-2798   2014.8

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    Special xylem tissue called compression wood is formed on the lower side of inclined stems
    when gymnosperms grow on a slope. We investigated the molecular mechanism of compression
    wood formation. Transcriptome analysis by next-generation sequencing (NGS) was applied to the
    xylem of Chamaecyparis obtusa to develop a catalog of general gene expression in differentiating
    xylem during compression and normal wood formation. The sequencing output generated
    234,924,605 reads and 40,602 contigs (mean size = 529 bp). Based on a sequence similarity
    search with known proteins, 54.2% (22,005) of the contigs showed homology with sequences in
    the databases. Of these annotated contigs, 19,293 contigs were assigned to Gene Ontology categories.
    Differential gene expression between the compression and normal wood libraries was
    analyzed by mapping the reads from each library to the assembled contigs. In total, 2875 contigs
    were identified as differentially expressed, including 1207 that were up-regulated and 1668 that
    were down-regulated in compression wood. We selected 30 genes and compared the transcript
    abundance between compression and normal wood by quantitative polymerase chain reaction
    analysis to validate the NGS results. We found that 27 of the 30 genes showed the same expression
    patterns as the original NGS results.

    DOI: 10.4236/ajps.2014.518295

  45. Searching for genomic region of high-fat diet-induced type 2 diabetes in mouse chromosome 2 by analysis of congenic strains. Reviewed

    Kobayashi M, Ohno T, Ihara K, Murai A, Kumazawa M, Hoshino H, Iwanaga K, Iwai H, Hamana Y, Ito M, Ohno K, Horio F.

    PLoS One   Vol. 9 ( 5 ) page: e96271   2014.5

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1371/journal.pone.0096271

  46. Mutation in the a-subunit of F(1)F(O)-ATPase causes an increased motility phenotype through the sodium-driven flagella of Vibrio.

    Terashima H, Terauchi T, Ihara K, Nishioka N, Kojima S, Homma M.

    J Biochem.   Vol. 154 ( 2 ) page: 177-184   2013.8

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1093/jb/mvt042

  47. A blue-shifted light-driven proton pump for neural silencing

    Sudo Y, Okazaki A, Ono H, Yagasaki J, Sugo S, Kamiya M, Reissig L, Inoue K, Ihara K, Kandori H, Takagi S, Hayashi S.

    J Biol Chem.   Vol. 288 ( 28 ) page: 20624-20632   2013.7

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

  48. Crystal structure of deltarhodopsin-3 from Haloterrigena thermotolerans

    Zhang J, Mizuno K, Murata Y, Koide H, Murakami M, Ihara K, Kouyama T.

    Proteins.   Vol. 81 ( 9 ) page: 1585-1592   2013.6

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

  49. Exome sequencing of senescence-accelerated mice (SAM) reveals deleterious mutations in degenerative disease-causing genes. Reviewed

    Tanisawa K, Mikami E, Fuku N, Honda Y, Honda S, Ohsawa I, Ito M, Endo S, Ihara K, Ohno K, Kishimoto Y, Ishigami A, Maruyama N, Sawabe M, Iseki H, Okazaki Y, Hasegawa-Ishii S, Takei S, Shimada A, Hosokawa M, Mori M, Higuchi K, Takeda T, Higuchi M, Tanaka M.

    BMC Genomics   Vol. 14   page: 248   2013.4

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1186/1471-2164-14-248

  50. Large deformation of helix F during the photoreaction cycle of Pharaonis halorhodopsin in complex with azide. Reviewed

    Nakanishi T, Kanada S, Murakami M, Ihara K, Kouyama T.

    Biophys J.   Vol. 104 ( 2 ) page: 377-385   2013.2

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1128/JB.01850-12

  51. A Novel dnaJ Family Gene, sflA, Encodes an Inhibitor of Flagellation in Marine Vibrio Species.

    Kitaoka M, Nishigaki T, Ihara K, Nishioka N, Kojima S, Homma M.

    Journal of Bacteriology   Vol. 195 ( 4 ) page: 816-822   2013.2

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1128/JB.01850-12.

  52. Crystal structure of the O intermediate of the Leu93->Ala mutant of bacteriorhodopsin.

    Zhang J, Yamazaki Y, Hikake M, Murakami M, Ihara K, Kouyama T.

    Proteins   Vol. 80 ( 10 ) page: 2384-2396   2012.10

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

  53. MarR-type transcriptional regulator ChlR activates expression of tetrapyrrole biosynthesis genes in response to low-oxygen conditions in cyanobacteria.

    Aoki R, Takeda T, Omata T, Ihara K, Fujita Y.

    Journal of Biological Chemistry   Vol. 287 ( 16 ) page: 13500-13507   2012.4

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

  54. Crystal structures of an O-like blue form and an anion-free yellow form of pharaonis halorhodopsin. Reviewed

    Kanada S, Takeguchi Y, Murakami M, Ihara K, Kouyama T.

    Journal of Molecular Biology   Vol. 413 ( 1 ) page: 162-176   2011.10

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1016/j.jmb.2011.08.021.

  55. Gene orders in the upstream of 16S rRNA genes divide genera of the family Halobacteriaceae into two groups Reviewed

    Minegishi, H. Kamekura, M. Kitajima-Ihara, T. Nakasone, K. Echigo, A. Shimane, Y. Usami, R. Itoh, T. Ihara, K.

    Int J Syst Evol Microbiol     2011.3

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    In many prokaryotic species, 16S rRNA genes are present in multiple copies, and their sequences in general do not differ significantly owing to the concerted evolution. The genus Haloarcula of the family Halobacteriaceae comprises nine validly published species, and all of them possess two to four, highly heterogeneous, 16S rRNA genes. Existence of heterogeneous multiple 16S rRNA genes makes it difficult to reconstruct a biological phylogenetic tree using their sequences data. If the orthologous gene is able to be discriminated from paralogous genes, a tree reconstructed from orthologous genes will reflect a simple biological phylogenetic relationship. At present, however, we have no means to distinguish the orthologous rRNA operon from paralogous one in the members of Halobacteriaceae.In this paper, we found that dihydroorotate oxidase gene, pyrD, was present in the immediate upstream of one 16S rRNA gene, in ten strains of Halobacteriaceae whose genome sequences have been determined, and the direction of pyrD was the opposite of that of the 16S rRNA genes. In two other strains whose genome sequences have been determined, the pyrD was present in far separated positions. We designed PCR primer sets to amplify DNA fragments encompassing from the conserved region of pyrD to a conserved region of tRNA-Ala genes or 23S rRNA genes to determine the 16S rRNA gene sequences preceded by pyrD, and to see if the pyrD is conserved in the immediate upstream of rRNA operon(s) in the type strains of the types species of 28 genera of Halobacteriaceae. Seventeen type strains, including the ten strains mentioned above, gave amplified DNA fragments of approximately 4,000 bp, while eleven type strains including the two strains mentioned above, did not give any PCR products. These eleven strains are members of the Clade I, which was originally defined by Walsh et al. (2004) and expanded by Minegishi et al. (2010). Analysis of contig sequences of three strains belonging to the Clade I also revealed the absence of the pyrD in the immediate upstream of any 16S rRNA genes. It may be scientifically sound to hypothesize that during the evolution of members of Halobacteriaceae, pyrD transposition event happened in one group, and this was followed by subsequent speciation processes in each group, yielding species/genera of the Clade I group and "the rest" of the present family Halobacteriaceae.

    DOI: ijs.0.031708-0 [pii] 10.1099/ijs.0.031708-0

  56. A Microbial Rhodopsin with a Unique Retinal Composition Shows Both Sensory Rhodopsin II and Bacteriorhodopsin-like Properties Reviewed

    Sudo, Y. Ihara, K. Kobayashi, S. Suzuki, D. Irieda, H. Kikukawa, T. Kandori, H. Homma, M.

    Journal of Biological Chemistry   Vol. 286 ( 8 ) page: 5967-5976   2011.2

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    Rhodopsins possess retinal chromophore surrounded by seven transmembrane alpha-helices, are widespread in prokaryotes and in eukaryotes, and can be utilized as optogenetic tools. Although rhodopsins work as distinctly different photo-receptors in various organisms, they can be roughly divided according to their two basic functions, light-energy conversion and light-signal transduction. In microbes, light-driven proton transporters functioning as light-energy converters have been modified by evolution to produce sensory receptors that relay signals to transducer proteins to control motility. In this study, we cloned and characterized two newly identified microbial rhodopsins from Haloquadratum walsbyi. One of them has photochemical properties and a proton pumping activity similar to the well known proton pump bacteriorhodopsin (BR). The other, named middle rhodopsin (MR), is evolutionarily transitional between BR and the phototactic sensory rhodopsin II (SRII), having an SRII-like absorption maximum, a BR-like photocycle, and a unique retinal composition. The wild-type MR does not have a light-induced proton pumping activity. On the other hand, a mutant MR with two key hydrogen-bonding residues located at the interaction surface with the transducer protein HtrII shows robust phototaxis responses similar to SRII, indicating that MR is potentially capable of the signaling. These results demonstrate that color tuning and insertion of the critical threonine residue occurred early in the evolution of sensory rhodopsins. MR may be a missing link in the evolution from type 1 rhodopsins (microorganisms) to type 2 rhodopsins (animals), because it is the first microbial rhodopsin known to have 11-cis-retinal similar to type 2 rhodopsins.

    DOI: 10.1074/jbc.M110.190058

  57. Photochemistry of a putative new class of sensory rhodopsin (SRIII) coded by xop2 of Haloarcular marismortui Reviewed

    Nakao, Y. Kikukawa, T. Shimono, K. Tamogami, J. Kimitsuki, N. Nara, T. Unno, M. Ihara, K. Kamo, N.

    Journal of Photochemistry and Photobiology B-Biology   Vol. 102 ( 1 ) page: 45-54   2011.1

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    Baliga et al. (2004) [1] reported the existence of a functionally unpredictable opsin gene, named xop2, in Haloarcula marismortui, a holophilic archaeon. Ihara et al. [38] performed molecular phylogenetic analysis and determined that the product of xop2 belonged to a new class of opsins in the sensory rhodopsins. This microbial rhodopsin was therefore named H. marismortui sensory rhodopsin III (HmSRIII). Here, we functionally expressed HmSRIII in Escherichia coli cell membranes to examine the photochemistry. The wavelength of maximum absorption (lambda(max)) for HmSRIII was 506 nm. We observed a very slow photocycle that completed in similar to 50 s. Intermediates were defined as M (lambda(max) similar to 380 nm), N (lambda(max) similar to 460 nm) and O (lambda(max) similar to 530 nm) 0.01 s after the flash excitation. The nomenclature for these intermediates was based on their locations along the absorption maxima of bacteriorhodopsin. Analysis of laser-flash-photolysis data in the presence and absence of azide gave the following results: (1) an equilibrium between N and 0 was attained, (2) the direct product of the M-decay was 0 but not N, and (3) the last photo-intermediate (HmSRIII') had a lambda(max) similar to that of the original, and its decay rate was very slow. Resonance Raman spectroscopy revealed that this N-intermediate had 13-cis retinal conformation. Proton uptake occurred during the course of M-decay, whereas proton release occurred during the course of O-decay (or exactly N-O equilibrium). Very weak proton-pumping activity was observed whose direction is the same as that of bacteriorhodopsin, a typical light-driven proton pump. (C) 2010 Elsevier B.V. All rights reserved.

    DOI: 10.1016/j.jphotobiol.2010.09.004

  58. Spectroscopic studies of a sensory rhodopsin I homologue from the archaeon Haloarcula vallismortis. Reviewed

    Yagasaki J, Suzuki D, Ihara K, Inoue K, Kikukawa T, Sakai M, Fujii M, Homma M, Kandori H, Sudo Y.

    Biochemistry   Vol. 49 ( 6 ) page: 1183-1190   2010.2

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    Sensory rhodopsin I (SRI) functions as a dual receptor regulating both negative and positive phototaxis. It transmits light signals through changes in protein-protein interactions with its transducer protein, HtrI. The phototaxis function of Halobacterium salinarum SRI (HsSRI) has been well characterized using genetic and molecular techniques, whereas that of Salinibacter ruber SRI (SrSRI) has not. SrSRI has the advantage of high protein stability compared with HsSRI and, therefore, provided new information about structural changes and Cl(-) binding of SRI. However, nothing is known about the functional role of SrSRI in phototaxis behavior. In this study, we expressed a SRI homologue from the archaeon Haloarcula vallismortis (HvSRI) as a recombinant protein which uses all-trans-retinal as a chromophore. Functionally important residues of HsSRI are completely conserved in HvSRI (unlike in SrSRI), and HvSRI is extremely stable in buffers without Cl(-). Taking advantage of the high stability, we characterized the photochemical properties of HvSRI under acidic and basic conditions and observed the effects of Cl(-) on the protein under both conditions. Fourier transform infrared results revealed that the structural changes in HvSRI were quite similar to those in HsSRI and SrSRI. Thus, HvSRI can become a useful protein model for improving our understanding of the molecular mechanism of the dual photosensing by SRI.

  59. *Crystal structure of the light-driven chloride pump halorhodopsin from Natronomonas pharaonis Reviewed

    Tsutomu Kouyama; Soun Kanada; Yu Takeguchi; Akihiro Narusawa; Midori Murakami; Kunio Ihara

    J. Mol. Biology   Vol. 396 ( 3 ) page: 564-579   2010.2

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    The light-driven chloride pump halorhodopsin from Natronomonas pharaonis (phR) crystallised into the monoclinic space group C2, with a phR trimer per the asymmetric unit. Diffraction data at 2.0-A resolution showed that the carotenoid bacterioruberin binds to crevices between adjacent protein subunits in the trimeric assembly. Besides seven transmembrane helices (A to G) that characterise archaeal rhodopsins, the phR protomer possesses an amphipathic alpha-helix (A') at the N-terminus. This helix, together with a long loop between helices B and C, forms a hydrophobic cap that covers the extracellular surface and prevents a rapid ion exchange between the active centre and the extracellular medium. The retinal bound to Lys256 in helix G takes on an all-trans configuration with the Schiff base being hydrogen-bonded to a water molecule. The Schiff base also interacts with Asp252 and a chloride ion, the latter being fixed by two polar groups (Thr126 and Ser130) in helix C. In the anion uptake pathway, four ionisable residues (Arg123, Glu234, Arg176 and His100) and seven water molecules are aligned to form a long hydrogen-bonding network. Conversely, the cytoplasmic half is filled mostly by hydrophobic residues, forming a large energetic barrier against the transport of anion. The height of this barrier would be lowered substantially if the cytoplasmic half functions as a proton/HCl antiporter. Interestingly, there is a long cavity extending from the main-chain carbonyl of Lys256 to Thr71 in helix B. This cavity, which is commonly seen in halobacterial light-driven proton pumps, is one possible pathway that is utilised for a water-mediated proton transfer from the cytoplasmic medium to the anion, which is relocated to the cytoplasmic channel during the photocycle. Copyright (c) 2009. Elsevier Ltd. All rights reserved.

  60. *Halorubrum chaoviator sp. nov., a haloarchaeon isolated from sea salt in Baja California, Mexico, Western Australia and Naxos, Greece. Reviewed

    Mancinelli R. L., Landheim R., Sanchez-Porro C., Dornmayr-Pfaffenhuemer M., Gruber C., Legat A., Ventosa A., Radax C., Ihara K., White M. R. andStan-Lotter H.

    Int. J. Syst. Evol. Microbiol.   Vol. 59   page: 1908-1913   2009.8

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    Three halophilic isolates, strains Halo-G*T, AUS-1 and Naxos II, were compared. Halo-G* was isolated from an evaporitic salt crystal from Baja California, Mexico, whereas AUS-1 and Naxos II were isolated from salt pools in Western Australia and the Greek island of Naxos, respectively. Halo-G*T had been exposed previously to conditions of outer space and survived 2 weeks on the Biopan facility. Chemotaxonomic and molecular comparisons suggested high similarity between the three strains. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the strains clustered with Halorubrum species, showing sequence similarities of 99.2-97.1%. The DNA-DNA hybridization values of strain Halo-G*T and strains AUS-1 and Naxos II are 73 and 75%, respectively, indicating that they constitute a single species. The DNA relatedness between strain Halo-G*T and the type strains of 13 closely related species of the genus Halorubrum ranged from 39 to 2%, suggesting that the three isolates constitute a different genospecies. The G+C content of the DNA of the three strains was 65.5-66.5 mol%. All three strains contained C20C20 derivatives of diethers of phosphatidylglycerol, phosphatidylglyceromethylphosphate and phosphatidylglycerolsulfate, together with a sulfated glycolipid. On the basis of these results, a novel species that includes the three strains is proposed, with the name Halorubrum chaoviator sp. nov. The type strain is strain Halo-G*T (=DSM 19316T=NCIMB 14426T=ATCC BAA-1602T).

  61. A photochromic photoreceptor from a eubacterium. Invited

    Suzuki D, Kitajima-Ihara T, Furutani Y, Ihara K, Kandori H, Homma M, Sudo Y.

    Commun. Integr. Biol.   Vol. 1   page: 150-152   2008.10

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    Sensory rhodopsin I (SRI) is one of the most interesting photo- sensory receptors because of its function in using the photochromic reaction to mediate opposing signals which depend on the color of light. It was initially thought that SRI exists only in the archaea, but we recently reported for the first time a newly functional SRI from a eubacterium, Salinibacter ruber (SrSRI). The amino acid sequence of SrSRI shows 43% identity with the well-known SRI (HsSRI) and contains most of the amino acid residues identified as necessary for SRI function. The photochemical properties of SrSRI are similar to those of HsSRI. In addition, SrSRI is a highly stable protein, even in dilute salt conditions. Thus, SrSRI could be a key protein for characterizing its association with the SrSRI transducer protein, SrHtrI, and for elucidating structural changes of SRI and HtrI that occur during their function. Recently, new approaches to manipulate cellular functions with rhodopsins have been established. SRI can activate and deactivate a kinase, CheA, by the photochromic reaction. Kinases are key molecules for signal transduction in various organisms, and SRI could potentially manipulate their cellular functions.

  62. Salinibacter sensory rhodopsin: sensory rhodopsin I-like protein from a eubacterium. Reviewed

    Kitajima-Ihara T, Furutani Y, Suzuki D, Ihara K, Kandori H, Homma M, Sudo Y.

    Journal of Biological Chemistry   Vol. 283   page: 23533-23541   2008.8

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    Halobacterium salinarum sensory rhodopsin I (HsSRI), a dual receptor regulating both negative and positive phototaxis in haloarchaea, transmits light signals through changes in protein-protein interactions with its transducer, halobacterial transducer protein I (HtrI). Haloarchaea also have another sensor pigment, sensory rhodopsin II (SRII), which functions as a receptor regulating negative phototaxis. Compared with HsSRI, the signal relay mechanism of SRII is well characterized because SRII from Natronomonus pharaonis (NpSRII) is much more stable than HsSRI and HsSRII, especially in dilute salt solutions and is much more resistant to detergents. Two genes encoding SRI homologs were identified from the genome sequence of the eubacterium Salinibacter ruber. Those sequences are distantly related to HsSRI ( approximately 40% identity) and contain most of the amino acid residues identified as necessary for its function. To determine whether those genes encode functional protein(s), we cloned and expressed them in Escherichia coli. One of them (SrSRI) was expressed well as a recombinant protein having all-trans retinal as a chromophore. UV-Vis, low-temperature UV-Vis, pH-titration, and flash photolysis experiments revealed that the photochemical properties of SrSRI are similar to those of HsSRI. In addition to the expression system, the high stability of SrSRI makes it possible to prepare large amounts of protein and enables studies of mutant proteins that will allow new approaches to investigate the photosignaling process of SRI-HtrI.

  63. *A halorhodopsin-overproducing mutant isolated from an extremely haloalkaliphilic archaeon Natronomonas pharaonis. Reviewed

    Ihara K, Narusawa A, Maruyama K, Takeguchi M, Kouyama T.

    FEBS Letter   Vol. 582   page: 2931-2936   2008.8

     More details

    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)  

    The halorhodopsin (hR)-overproducing mutant strain KM-1 was isolated from the extremely haloalkaliphilic archaeon Natronomonas pharaonis type strain DSM2160(T). hR-enriched membranes were easily obtained by washing the cells with distilled water. The membranes were claret colored owing to two pigments: hR and bacterioruberin. The hR component in the absorption spectra changed from blue to purple upon the addition of Cl(-) and had a K(m) value of 1.7 mM. Overexpression of hR in strain KM-1 might be caused by the point mutation Asp324-->Asn in the bacteriorhodopsin activator homologues of N. pharaonis. The mutation changed the hR-expression pattern from inducible to constitutive in the late exponential phase.

  64. Halide binding by the D212N mutant of Bacteriorhodopsin affects hydrogen bonding of water in the active site. Reviewed

    Shibata M, Yoshitsugu M, Mizuide N, Ihara K, Kandori H.

    Biochemistry   Vol. 46 ( 25 ) page: 7525-7535   2007.6

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

  65. Hydrogen-bonding interaction of the protonated schiff base with halides in a chloride-pumping bacteriorhodopsin mutant. Reviewed

    Shibata M,Ihara K,Kandori H.

    Biochemistry   Vol. 45 ( 35 ) page: 10633-10640   2006.9

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    Bacteriorhodopsin (BR) and halorhodopsin (HR) are light-driven proton and chloride ion pumps, respectively, in Halobacterium salinarum. The amino acid identity of these proteins is about 25%, suggesting that each has been optimized for their own functions during evolution. However, it is known that the BR mutants, D85T and D85S, can pump chloride ions. This fact implies that the Schiff base region is important in determining ionic selectivity. The X-ray crystallographic structure of D85S(Br(-)) showed the presence of a bromide ion in the Schiff base region (Facciotti, M. T., Cheung, V. S., Nguyen, D., Rouhani, S., and Glaeser, R. M. (2003) Biophys. J. 85, 451-458). In this article, we report on the study of hydrogen bonds of the Schiff base and water molecules in D85S in the absence and presence of various halides, assigning their N-D and O-D stretching vibrations in D(2)O, respectively, in low-temperature Fourier-transform infrared (FTIR) spectroscopy. We found that the hydrogen bond of the Schiff base in D85S(Cl(-)) is much stronger than that in HR, being as strong as that in wild-type BR. Similar halide dependence in D85S and in solution implies that the Schiff base forms a direct hydrogen bond with a halide, consistent with the X-ray structure. Photoisomerization causes a weakened hydrogen bond of the Schiff base, and halide dependence on the stretching frequency is lost. These spectral features are similar to those in the photocycle of proton-pumping BR, though the weakened hydrogen bond is more significant for BR. However, the spectral features of water bands in D85S are closer to chloride-pumping HR because O-D stretching vibrations of water are observed only at >2500 cm(-)(1). Unlike in BR, we did not observe strongly hydrogen-bonded water molecules for halide-pumping D85S mutants. This observation agrees with our recent hypothesis that strongly hydrogen-bonded water molecules are required for the proton-pumping activity of archaeal rhodopsins. Hydrogen-bond

  66. Comparative study of archaeal light driven proton pumps Invited

    Ihara K

    12th International Conference on Reinal Protein satellite meeting ; Structure, Fuction, and Evolution of Rhodopsins -Mechanism of proton transfer and color tuning     page: 10-11   2006.6

     More details

    Authorship:Lead author   Language:English  

  67. Comparative study of archaeal light driven proton pumps for functional expression in Escherichia coli. Invited

    Ihara K

    12th International Conference on Reinal Protein     page: p092b   2006.6

     More details

    Authorship:Lead author   Language:English  

  68. Crystal structure of archaerhodopsin-1 and -2: Common structural motif in archaeal light-driven proton pumps Reviewed

    Enami N, Yoshimura K, Murakami M., Okunmura H., Ihara K. and Kouyama T.

    J.Mol. Biol.   Vol. 358 ( 3 ) page: 675-685   2006.5

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    Archaerhodopsin-1 and -2 (aR-1 and aR-2) are light-driven proton pumps found in Halorubrum sp. aus-1 and -2, which share 55-58% sequence identity with bacteriorhodopsin (bR), a proton pump found in Halobacterium salinarum. In this study, aR-1 and aR-2 were crystallized into 3D crystals belonging to P4(3)2(1)2 (a = b = 128.1 A, c = 117.6 A) and C222(1) (a = 122.9 A, b = 139.5 A, c = 108.1 A), respectively. In both the crystals, the asymmetric unit contains two protein molecules with slightly different conformations. Each subunit is composed of seven helical segments as seen in bR but, unlike bR, aR-1 as well as aR-2 has a unique omega loop near the N terminus. It is found that the proton pathway in the extracellular half (i.e. the proton release channel) is more opened in aR-2 than in aR-1 or bR. This structural difference accounts for a large variation in the pKa of the acid purple-to-blue transition among the three proton pumps. All the aromatic residues surrounding the retinal polyene chain are conserved among the three proton pumps, confirming a previous argument that these residues are required for the stereo-specificity of the retinal isomerization. In the cytoplasmic half, the region surrounded by helices B, C and G is highly conserved, while the structural conservation is very low for residues extruded from helices E and F. Structural conservation of the hydrophobic residues located on the proton uptake pathway suggests that their precise arrangement is necessary to prevent a backward flow of proton in the presence of a large pH gradient and membrane potential. An empty cavity is commonly seen in the vicinity of Leu93 contacting the retinal C13 methyl. Existence of such a cavity is required to allow a large rotation of the side-chain of Leu93 at the early stage of the photocycle, which has been shown to accompany water translocation across the Schiff base.

  69. *A light-driven proton pump from Haloterrigene turkmenica: functional expression in Escherichia coli membrane and coupling with a H+ co-transporter. Reviewed

    Kamo N., Hashiba T., Kikukawa T., Araiso T., Ihara K. and Nara T.

    Biochem. Biophys. Res. Commun.   Vol. 341   page: 285-290   2006.1

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

  70. *Internal water molecules of light-driven chloride pump proteins. Reviewed

    Shibata M., Muneda N., Ihara K., Sasaki T., Demura M. , and Kandori H.

    Chem. Phys. Lett.   Vol. 392   page: 330-333   2004

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

  71. Search for the retinal-type photosynthetic microorganisms from the japanease sea. Invited

    K.Ihara, K. Sugiura, and S. Ito

    Ann. Report Interdiscipl. Res. Inst. Environ. Sci   Vol. 22   page: 51-60   2003

     More details

    Authorship:Lead author   Language:English   Publishing type:Research paper (bulletin of university, research institution)  

  72. Halomicrobium mukohataei gen. nov., comb. nov., and emended description of Halomicrobium mukoataei Reviewed

    Oren, A, R. Elevi, S. Watanabe, T. Tamura, and K.Ihara

    Int. J. System. Evol. Microbiol.   Vol. 52   page: 1831-1835   2002

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

  73. Cytochrom aa3 and its gene duplication in Haloferax volcanii. Reviewed

    Tanaka, M., Ogawa, N., Ihara, K., Sugiyama, Y. and Mukohata, Y.

    J. Bacteriol.   Vol. 184   page: 840-845   2002

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

  74. Gene clusters encoding ATP synthase of Haloarcula japonica strain TR-1.

    R. Yatsunami, M. Iwamoto, K. Ihara, and S.Nakamura

    Nuceic Acids. Symposium Series   Vol. 44   page: 51-52   2001

     More details

    Language:English   Publishing type:Research paper (bulletin of university, research institution)  

  75. Function of a kaiC homologus gene found in an extremely halophilic archaeon, Halobacterium salinarum.

    Ihara K, Yokota H, Ishiura M.

    Halophiles 2001 International Conference on Halophilic Microorganisms     page: L49   2001

     More details

    Authorship:Lead author   Language:English  

  76. Evolution of the Archaeal Rhodopsins : Evolution Rate Changes by Gene Duplication and Functional Differentiation Reviewed

    Journal of Molecular Biology   Vol. 285   page: 163-174   1999

     More details

    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)  

  77. Molecular cloning of A1-ATPase gene from extremely halophilic archaeon Haloarcula japonica strain TR-1

    R.Yatsunami, M. Iwamoto, K. Ihara and S. Nakamura

    Nucleic Acids Symposium Series   Vol. 42   page: 75-76   1999

     More details

    Language:English   Publishing type:Research paper (bulletin of university, research institution)  

  78. Halobacterial Rhodopsins Reviewed

    Journal of Biochemistry   Vol. 125   page: 649-657   1999

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

  79. Haloarcula argentinensis sp. nov. and Haloarcula mukohataei sp. nov. Two new extremely halophilic archaea collected in Argentina. Reviewed

    Ihara K, Watanabe S, Tamura T

    International Journal of Systematic Bacteriology   Vol. 47 ( 1 ) page: 73-77   1997

     More details

    Authorship:Lead author   Language:Japanese   Publishing type:Research paper (scientific journal)  

  80. Identification of proteolipid from an extremely halophilic archaeon Halobacterium salinarum as an N, N'-dicyclohexyl-carbodiimide binding subunit of ATP synthase Reviewed

    Archives of Biochemistry and Biophysics   Vol. 341 ( 2 ) page: 267-272   1997

     More details

    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)  

  81. Novel Bacterial Rhodopsins from Holoarcula vallismortis Reviewed

    Biochemical and Biophysical Research Communications   Vol. 220   page: 341   1996

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

  82. 高度好塩性古細菌 Invited

    月刊 地球   Vol. 17 ( 7 ) page: 490   1995

     More details

    Authorship:Lead author   Language:Japanese   Publishing type:Research paper (scientific journal)  

  83. 蘇れ!2億年の眠りから Invited

    科学朝日   Vol. 55 ( 11 ) page: 100   1995

     More details

    Authorship:Lead author   Language:Japanese  

  84. Met-145 is a key residue in the dark adaptation of bacteriorhodopsin homologs. Reviewed

    Biophysical Journal   Vol. 67   page: 1187-1191   1994

     More details

    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)  

  85. The novel ion pump rhodopsins from Haloarcula form a family independent from both the bacteriorhodopsin and archae-rhodopsin families/tribes. Reviewed

    Archives of Biochemistry and Biophysics   Vol. 315 ( 1 ) page: 127-132   1994

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

  86. Halobacterial A-ATP synthase in relation to V-ATPase. Invited Reviewed

    J. exp. Biol.   Vol. 172   page: 475-485   1992

     More details

    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)  

  87. Photophosphorylation Elements in Halobacteria : An A-type ATP Synthase and Bacterial Rhodopsins. Invited

    J. Bioenerg. Biomembr.   Vol. 24 ( 6 ) page: 547-553   1992

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

  88. The ATP synthase of Halobacterium salinarium(halobium)is an archaebacterial type as revealed from the amino acid sequences of its two Reviewed

    K.Ihara and Y. Mukohata

    Arch. Biochem. Biophys.   Vol. 286   page: 111-116   1991

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

  89. "The ATP synthase in extreme halophilic archaebacteria and its relatives. " Invited Reviewed

    Mukohata, Y., K. Ihara, M. Yoshida, Y. Sugiyama

    New era of bioenergetics     page: 169-196   1991

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

  90. Australian Halobactreia and their retinal-protein ion pumps. Reviewed

    Photochem. and Photobiol.   Vol. 54   page: 1   1991

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

  91. Close evolutionary relatedness of archaebacteria with eukaryotes. Reviewed

    Proc. Jpn. Acad.   Vol. 66B   page: 4   1990

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

  92. An australian halobacterium contains a novel proton pump retinal protein archaerhodopsin. Reviewed

    Biochem. Biophys. Res. Commun.   Vol. 151   page: 3   1988

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

  93. Proteoliposomes with right-side-out oriented purple membrane/bacteriorhodopsin require cations inside for proton pumping. Reviewed

    FEBS Lett   Vol. 240 ( 1 ) page: 2   1988

     More details

    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)  

  94. The halobacterial proton-translocating ATP synthase relates to the eukaryotic anion-sensitive proton ATPase. Reviewed

    Arch. Biochem. Biophys.   Vol. 259   page: 2   1987

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

  95. Bacteriorhodopsin regenerated from the blue membrane and cationic dye.

    Mukohata Y., Ihara K.

    Retinal Proteins     page: 195-204   1987

     More details

    Language:English  

  96. A H+-translocating ATP synthase in H. halobium Invited

    Energy Transduction in ATPases     page: 481-488   1987

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

▼display all

Books 6

  1. ゼブラフィッシュ実験ガイド 第17 章

    日比正彦、清水貴史、橋本寿司、井原邦夫( Role: Joint author ,  第17章 実験に必要な手続き)

    朝倉書店  2020.11  ( ISBN:978-4-254-17173-0

     More details

    Total pages:135   Responsible for pages:8   Language:Japanese Book type:Textbook, survey, introduction

  2. オプトジェネティクス─光工学と遺伝学による行動制御技術の最前線

    井原邦夫、神山勉( Role: Sole author)

    株式会社エヌ・ティー・エス 刊  2013.4 

     More details

    Language:Japanese

  3. 古細菌の生物学 第13章、電子伝達系とATPアーゼ

    若木高善、井原邦夫( Role: Joint author)

    東京大学出版会  1998 

     More details

    Language:Japanese

  4. 古細菌の生物学 第12章、高度好塩菌のエナジェテイックス

    井原邦夫( Role: Joint author)

    東京大学出版会  1998 

     More details

    Language:Japanese

  5. 極限環境微生物ハンドブック・好塩性古細菌

    向畑恭男, 井原邦夫( Role: Joint author)

    サイエンスフォーラム  1990 

     More details

    Language:Japanese

  6. Situation of archaebacterial ATPase among ion-translocating ATPase.

    Bioenergetics ; molecular biology. biochemistry and pathology  1990 

     More details

    Language:English

▼display all

MISC 1

  1. Three-Step Isomerization of the Retinal Chromophore during the Anion Pumping Cycle of Halorhodopsin Reviewed

    Kouyama Tsutomu, Ihara Kunio, Maki Kosuke, Chan Siu Kit

    BIOCHEMISTRY   Vol. 57 ( 41 ) page: 6013-6026   2018.10

     More details

    Language:English   Publishing type:Rapid communication, short report, research note, etc. (scientific journal)  

    DOI: 10.1021/acs.biochem.8b00631

    PubMed

Presentations 54

  1. 大量ゲノム解析から見えてきた凍結保存試料におけるゲノム多様性

    松尾佳祐 、上坂一馬 、井原邦夫

    第34 回 日本Archaea研究会講演会  2022.7.15  日本Archaea研究会

     More details

    Event date: 2022.7

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:福岡県 九州大学 西新プラザ 大会議室   Country:Japan  

  2. シアノバクテリア Leptolyngbya boryana の光合成依存的な窒素固定⽣育に関わる遺伝子群の探索

    馬場真理、上坂一馬、戸松千映、山本治樹、井原邦夫、藤田祐一

    第16回 日本ゲノム微生物学会  2022.3.3 

     More details

    Event date: 2022.3

    Language:Japanese   Presentation type:Oral presentation (general)  

  3. ⼤量ゲノム解析に基づいた UVC 光照射法による変異導⼊効率の評価

    松尾佳祐、上坂一馬、井原邦夫

    第16回 日本ゲノム微生物学会  2022.3.3 

     More details

    Event date: 2022.3

    Language:Japanese   Presentation type:Oral presentation (general)  

  4. Tn挿入ライブラリからゲノム変異を網羅的に検出するワークフローの開発

    上坂一馬、馬場真理、藤田祐一、井原邦夫

    第16回 日本ゲノム微生物学会  2022.3.3 

     More details

    Event date: 2022.3

    Presentation type:Poster presentation  

  5. Is the introduction of genomic mutations by UVc irradiation an effective method?

    2021.11.25 

     More details

    Event date: 2021.11

    Language:English   Presentation type:Oral presentation (general)  

    Country:Japan  

  6. Existence of two substates in the O intermediate of the bacteriorhodopsin photocycle

    2021.11.26 

     More details

    Event date: 2021.11

    Language:English   Presentation type:Oral presentation (general)  

    Country:Japan  

  7. 高度好塩性好アルカリ性古細菌 Natronomonas pharaonisを用いた大量変異導入と全ゲノムシーケンスい解析の実験系の開発

    松尾佳祐、上坂一馬、井原邦夫

    日本Archaea研究会 第33回講演会  2021.7.17  日本Archaea研究会

     More details

    Event date: 2021.7

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:オンライン(理化学研究所バイオリソースセンター)   Country:Japan  

  8. 嫌気環境で生育不良を示すシアノバクテリアSynechocystis sp. PCC 6803 変異株の網羅的遺伝子発現解析

    藤島 百花、上坂 一馬 、平田 香織、藤田 祐一 、井原 邦 、寺内 一姫

    第15回日本ゲノム微生物学会年会  2021.3.6  日本ゲノム微生物学会

     More details

    Event date: 2021.3

    Language:Japanese   Presentation type:Poster presentation  

    Venue:名古屋  

  9. ゲノムから見直す微生物分類の再考—Vibrio alginolyticusの場合—

    上坂一馬1・西岡典子2、小嶋誠司2、本間道夫2、井原邦夫1

    第15回日本ゲノム微生物学会  2021.3.6  日本微生物ゲノム学会

     More details

    Event date: 2021.3

    Language:Japanese   Presentation type:Poster presentation  

    Venue:オンライン(九州大学)  

  10. 経時寿命が延長する分裂酵母変異株のスクリーニングと新規寿命関連因子の同定

    松井 滉太朗、岡本 啓佑、長谷川 朋香 、島崎 嵩史 、大塚 北斗、井原 邦夫 、 中村 彰伸、後藤 祐平 、青木 一洋 、饗場 浩文

    第14回日本ゲノム微生物学会年会  2021.3.6  日本ゲノム微生物学会

     More details

    Event date: 2021.3 - 2020.3

    Language:Japanese   Presentation type:Poster presentation  

    Venue:名古屋  

  11. 近縁微生物ゲノムが存在する場合の簡易ゲノムフィニッシング手法

    上坂 一馬、井原 邦夫

    第14回日本ゲノム微生物学会年会  2021.3.6  日本ゲノム微生物学会

     More details

    Event date: 2021.3 - 2020.3

    Language:Japanese   Presentation type:Poster presentation  

    Venue:名古屋  

  12. 微生物ゲノムライブラリーを手軽で格安に作る-1コインゲノム解析を目指して

    井原 邦夫 、上坂 一馬

    第14回日本ゲノム微生物学会年会  2020.3.6  日本ゲノム微生物学会

     More details

    Event date: 2020.3

    Language:Japanese   Presentation type:Poster presentation  

    Venue:名古屋   Country:Japan  

  13. ショートリードを活用した効率的な微生物ゲノムアセンブリワークフローの提案

    上坂 一馬、井原 邦夫

    第13回日本ゲノム微生物学会年会  2019.3.6  日本ゲノム微生物学会

     More details

    Event date: 2019.3

    Language:Japanese   Presentation type:Poster presentation  

    Venue:八王子市(東京都立大学)  

  14. 糸状性シアノバクテリアLeptolyngbya boryanaの運動性を制御する新たな因子

    戸井田 一磨、上坂 一馬、井原 邦夫、藤田 祐一 、岩崎 秀雄

    第13回日本ゲノム微生物学会年会  2019.3.6  日本ゲノム微生物学会

     More details

    Event date: 2019.3

    Language:Japanese   Presentation type:Poster presentation  

    Venue:八王子市(東京都立大学)  

  15. ゲノム構造変化を感度良く検出する方法:SV-Quest

    上坂一馬、井原邦夫

    第12回 日本ゲノム微生物学会年会 

     More details

    Event date: 2018.3

    Language:Japanese   Presentation type:Poster presentation  

    Country:Japan  

  16. ゲノムシーケンスにもとづく微生物分類手法;好塩性古細菌を例として

    井原邦夫、上坂一馬、谷村要、中邨真之、越後輝敦、峯岸宏明

    第30回 日本Archaea研究会 

     More details

    Event date: 2017.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:東北大学 川内北キャンパス   Country:Japan  

  17. 高度好塩菌Haloarcula属3株の完全ゲノム構造解析から原核生物における種分化を考える International conference

    谷村 要、越後 輝敦、 峯岸 宏明、井原 邦夫

    第11回日本ゲノム微生物学会年会 

     More details

    Event date: 2017.3

    Language:Japanese   Presentation type:Poster presentation  

    Venue:慶應義塾大学 湘南藤沢キャンパス   Country:Japan  

  18. IBBP(Inter Bio-Backup Project)を利用した微生物遺伝子資源の保存 International conference

    井原邦夫、中邨真之

    第11回日本ゲノム微生物学会年会 

     More details

    Event date: 2017.3

    Language:Japanese   Presentation type:Poster presentation  

    Country:Japan  

  19. ショートリードデータのアセンブルによる微生物ゲノム構造決定のワークフロー構築 International conference

    上坂一馬、藤田祐一、井原邦夫、小俣達男

    第11回日本ゲノム微生物学会年会 

     More details

    Event date: 2017.3

    Language:Japanese   Presentation type:Poster presentation  

    Country:Japan  

  20. 高度好塩性古細菌 Haloarcula argentinensis, Ha. tradensis, Ha. salaria のゲノム構造比較に基づいた”種”分化の理解

    谷村 要、越後 輝敦、 峯岸 宏明、井原 邦夫

    第29回日本Archaea研究会講演会 

     More details

    Event date: 2016.7

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:東洋大学 白山キャンパス 8号館7階 125記念ホール   Country:Japan  

  21. Folding or Not folding in the membrane of Escherichia coli International conference

     More details

    Event date: 2006.12

    Language:English   Presentation type:Poster presentation  

    Country:Japan  

  22. FTIR studies of the hydrogen-bonding interaction of the protonated Schiff base with halides in a chloride-punping bacteriorhodopsin mutant International conference

     More details

    Event date: 2006.6

    Language:English   Presentation type:Poster presentation  

    Country:Japan  

  23. Comparative study of archaeal light driven prton pumps for functional expression in Escherichia coli

     More details

    Event date: 2006.6

    Language:English   Presentation type:Poster presentation  

    Country:Japan  

  24. 新規光プロトンポンプ、デルタロドプシンを発現した大腸菌における光リン酸化反応

    井原 邦夫、橋場剛、奈良敏文,加茂直樹

    第31回 日本生体エネルギー研究会 

     More details

    Event date: 2005.12

    Language:Japanese   Presentation type:Poster presentation  

    Country:Japan  

  25. ロドプシンがプロトンをポンプするためには強い水素結合を形成した内部結合水が必要である

    神取秀樹、古谷祐詞、柴田幹大、住井昌代、水出紀子、宗田法和、池田大亮、川鍋 陽、加茂直樹、出村 誠、井原邦夫、K.-H. Jung、L. S. Brown

    第43回 生物物理学会 

     More details

    Event date: 2005.11

    Language:Japanese   Presentation type:Poster presentation  

    Country:Japan  

  26. 2.5Å分解能のアーキロドプシン-2結晶のX線結晶構造解析

    吉村恵子, 江波信生, 井原邦夫, 神山勉

    第43回 生物物理学会 

     More details

    Event date: 2005.11

    Language:Japanese   Presentation type:Poster presentation  

    Country:Japan  

  27. 好塩性アーキアにおけるアーキア型ロドプシン遺伝子群の分布と発現

    井原邦夫

    第43回 生物物理学会 

     More details

    Event date: 2005.11

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  28. クロライドイオンをポンプするバクテリオロドプシン変異体の低温赤外分光

    柴田幹大,井原邦夫,神取秀樹

    第43回 生物物理学会 

     More details

    Event date: 2005.11

    Language:Japanese   Presentation type:Oral presentation (general)  

    Country:Japan  

  29. Light-driven proton pump in H. turkmenica

    Naoki Kamo, Tsuyoshi Hashiba, Takashi Kikukawa, Tsunehisa Araiso, Kunio Ihara, Toshifumi Nara

     More details

    Event date: 2005.6

    Language:English   Presentation type:Oral presentation (general)  

    Country:Japan  

  30. バクテリオロドプシンと類似蛋白質の構造比較

    吉村恵子,江波信生,奥村英夫,村上緑,井原邦夫,神山勉

    第42回 生物物理学会 

     More details

    Event date: 2004.12

    Language:Japanese   Presentation type:Poster presentation  

    Country:Japan  

  31. アーキロドプシンとバクテリオロドプシンの構造比較

    吉村恵子,江波信生,奥村英夫,村上緑,井原邦夫,神山勉

    2004年日本物理学会秋期大会 

     More details

    Event date: 2004.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Country:Japan  

  32. 光駆動塩素イオンポンプタンパク質、ハロロドプシン( HR ) 中の内部結合水の構造解析

    柴田幹大、宗田法和、井原邦夫、佐々木貴規、出村誠、神取秀樹

    第31回生体分子科学討論会 

     More details

    Event date: 2004.7

    Language:Japanese   Presentation type:Oral presentation (general)  

    Country:Japan  

  33. 高度好塩性古細菌Haloarcula属のレチナールタンパク質ファミリー

    井原邦夫、下野和美、加茂直樹

    第17回 日本Archaea研究会 

     More details

    Event date: 2004.7

    Language:Japanese   Presentation type:Oral presentation (general)  

    Country:Japan  

  34. CRYSTAL STRUCTURE OF ARCHAERHODOPSIN-2 FROM HALORUBRUM sp. AUS-2 International conference

     More details

    Event date: 2004.6

    Language:English   Presentation type:Poster presentation  

  35. 好熱菌由来クエン酸合成酵素の熱安定化構造

    村上 緑、井原 邦夫、神山 勉

    第42回 生物物理学会 

     More details

    Event date: 2004.6

    Language:Japanese   Presentation type:Poster presentation  

    Country:Japan  

  36. 高度好塩性古細菌Haloarcula属のレチナールタンパク質ファミリー

    井原邦夫

    第42 生物物理学会 

     More details

    Event date: 2004.6

    Language:Japanese   Presentation type:Poster presentation  

    Country:Japan  

  37. Crystal Structures of Archaerhodopsin-1 and –2 International conference

     More details

    Event date: 2004.6

    Language:English   Presentation type:Poster presentation  

  38. 古細菌型レチナールタンパク質の比較解析

    井原邦夫

    第29回 日本生体エネルギー研究会 

     More details

    Event date: 2003.12

    Language:Japanese   Presentation type:Oral presentation (general)  

    Country:Japan  

  39. Phylogenetic Analysis of Archaeal Type Rhodopsins

     More details

    Event date: 2003.11

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  40. 古細菌型レチナールタンパク質の比較解析

    井原邦夫

    第41回 生物物理学会 

     More details

    Event date: 2003.9

    Language:Japanese   Presentation type:Poster presentation  

    Country:Japan  

  41. 古細菌型レチナールタンパク質ファミリーの比較解析

    井原邦夫

    分子研研究会 「ロドプシンの分子科学」 

     More details

    Event date: 2003.5

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  42. 海洋性起源のレチナール型光合成微生物の日本近海における分布と純粋培養法の確立

    井原邦夫

    環境総合科学研究所 招待講演 

     More details

    Event date: 2003.5

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  43. 古細菌ロドプシンの多様性と共通性

    井原邦夫

    名工大神取研セミナー 

     More details

    Event date: 2003.3

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  44. バクテリオロドプシンの145番目のメチオニンを小さな側鎖のアミノ酸に変化させると、115番目のアスパラギン酸のpK値が大きく減少する

    井原 邦夫, 伊藤 繁, 向畑 恭男

    第40回 生物物理学会 

     More details

    Event date: 2002.11

    Language:Japanese   Presentation type:Oral presentation (general)  

    Country:Japan  

  45. 高度好塩性古細菌Halobacterium salinarumに存在するA型ATPaseは、ATP合成酵素として機能している

    井原邦夫

    第15回 日本Archaea研究会 

     More details

    Event date: 2002.7

    Language:Japanese   Presentation type:Oral presentation (general)  

    Country:Japan  

  46. 高度好塩性古細菌に存在する藍藻時計遺伝子の機能推定

    井原 邦夫 , 横田はるみ、石浦正寛

    第39回 生物物理学会 

     More details

    Event date: 2001.11

    Language:Japanese   Presentation type:Poster presentation  

    Country:Japan  

  47. 高度好塩性古細菌に存在する藍藻時計遺伝子の機能推定

    井原 邦夫 , 横田はるみ、石浦正寛

    第14回 日本古細菌研究会 

     More details

    Event date: 2001.10

    Language:Japanese   Presentation type:Oral presentation (general)  

    Country:Japan  

  48. Function of a kaiC homologous gene found in an extremely halophilic archaeon, Halobacterium salinarum International conference

    Halophiles 2001 

     More details

    Event date: 2001.10

    Language:English   Presentation type:Oral presentation (general)  

  49. 高度好塩性古細菌に存在する藍藻時計遺伝子の機能推定

    井原 邦夫, 横田はるみ、石浦正寛

    第27回 日本生体エネルギー研究会 

     More details

    Event date: 2001.8

    Language:Japanese   Presentation type:Oral presentation (general)  

    Country:Japan  

  50. 高度好塩菌Haloarcula属3株の完全ゲノム構造解析から原核生物における種分化を考える

    谷村 要, 越後 輝敦, 峯岸 宏明, 井原 邦夫

    第11回日本ゲノム微生物学会年会  2017.3.2 

     More details

    Language:Japanese   Presentation type:Poster presentation  

    Venue:慶應義塾大学 湘南藤沢キャンパス  

  51. ショートリードデータのアセンブルによる微生物ゲノム構造決定のワークフロー構築

    上坂一馬, 藤田祐一, 井原邦夫, 小俣達男

    第11回日本ゲノム微生物学会年会  2017.3.2 

     More details

    Language:Japanese   Presentation type:Poster presentation  

  52. ゲノム構造変化を感度良く検出する方法:SV-Quest International conference

    上坂一馬, 井原邦夫

    第12回 日本ゲノム微生物学会年会  2018.3.5 

     More details

    Language:Japanese   Presentation type:Poster presentation  

  53. ゲノムシーケンスにもとづく微生物分類手法;好塩性古細菌を例として International conference

    井原邦夫, 上坂一馬, 谷村要, 中邨真之, 越後輝敦, 峯岸宏明

    第30回 日本Archaea研究会  2017.9.1 

     More details

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:東北大学 川内北キャンパス  

  54. IBBP(Inter Bio-Backup Project)を利用した微生物遺伝子資源の保存

    井原邦夫, 中邨真之

    第11回日本ゲノム微生物学会年会  2017.3.2 

     More details

    Language:Japanese   Presentation type:Poster presentation  

▼display all

KAKENHI (Grants-in-Aid for Scientific Research) 11

  1. 長期にわたる暗所従属栄養に適応したシアノバクテリアの光合成喪失の進化プロセス

    Grant number:22K19146  2022.6 - 2025.3

    科学研究費助成事業  挑戦的研究(萌芽)

    藤田 祐一, 井原 邦夫

      More details

    Authorship:Coinvestigator(s) 

    光合成独立栄養生物は、光合成によって生産者として地球の生態系を支えている。光合成生物の中には、寄生植物のように、光合成を喪失し従属栄養という栄養形態へと進化した“非光合成”生物が高い頻度で観察されるが、光合成がどのように失われるのか、光合成喪失に至る進化の過程を観察した例はない。Leptolyngbya boryanaはグルコースを炭素源として完全暗所でも生育できる糸状性シアノバクテリアである。研究代表者は、L. boryanaを完全暗所で従属栄養的に継続して培養している。本研究では、暗所適応株のゲノム解析を行い、光合成を失う進化プロセスの複数の具体像を得、光合成喪失過程の一般化を試みる。

  2. Experimental and theoretical survey of diverse far-red O2-evolving photosynthesis

    Grant number:20K06684  2020.4 - 2024.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (C)

      More details

    Authorship:Coinvestigator(s) 

  3. 細胞寿命制御基盤の解明

    Grant number:20H02898  2020.4 - 2023.3

    科学研究費助成事業  基盤研究(B)

    饗場 浩文, 井原 邦夫

      More details

    Authorship:Coinvestigator(s) 

    健康長寿社会の構築に向けて、「寿命がいかにして決まるのか?」を解明することは現代生物学が取り組むべき重要課題の1つである。ヒトに代表される高等動物の寿命を理解するためには、その前提として細胞レベルで寿命を理解することが必須であると考え、申請者は微生物の専門家の立場から、分裂酵母をモデルにこの問題に取り組む。とりわけ、新規な寿命制御シグナルの発見と作用機構の解明、ならびに未知の寿命制御因子の同定と機能解析に焦点を絞り、普遍的な細胞寿命制御機構に関する知見を得る。これらの解析を通して寿命の基本的理解を深め、将来的なヒトの寿命創薬に向けた基盤を確立する。

  4. 強力な直接遺伝学を駆使して微生物走性システムの全貌を見る

    Grant number:19K06627  2019.4 - 2022.3

    科学研究費助成事業  基盤研究(C)

    井原 邦夫

      More details

    Authorship:Principal investigator 

    Grant amount:\4290000 ( Direct Cost: \3300000 、 Indirect Cost:\990000 )

    様々な生物のゲノムが大量に読まれる時代が到来した。しかし、ゲノム中の遺伝子 (ORF)の機能は分かっていないものが多く、ゲノムから生命を理解する際の大きな課題の1つとなっている。次世代シーケンサー(NGS)解析で強化された順方向遺伝学は、ゲノム中の遺伝子 (ORF) を生物機能システムの構成要素として理解する強力な手法である。このパワフルな順遺伝学を微生物の走性システムに適用し、システムに関係するORFを推定すると同時に、新規に得られる関連遺伝子数から、走性システムのサイズ(関係する遺伝子数)を見積もる手法を構築する。
    令和2年度は、高度好塩性好アルカリ性古細菌ナトロノモナスを使用したUV照射変異実験を中心にプレート単位での大量培養、ゲノムDNA抽出とゲノムシーケンス解析を行った。
    UV照射実験では、照射位置におけるUV線量を正確に測定する目的で、UV照射光(クロスリンカーのUV蛍光管を1本に減らして使用)が安定化した後に、リモートで開閉する装置を作成した。この際に、UV変異を導入する菌懸濁液のセット位置付近にUV線量計を設置して、実際に照射したUV線量をエネルギー量(J/m2)として確認できるように工夫した。この装置を使って、未照射群(UV照射装置に入れて1分ほどおいたが、蓋を開かなかった試料)と大まかに3段階の異なるエネルギー群(15, 50, 100 J/m2)に分けて照射する実験を独立して30回程度繰り返し行った。4つの群それぞれから90サンプルをランダムに抽出して、合計360サンプルからゲノムライブラリー調製を行った。ここでは、96のディープウェル用の振盪培養装置(一昨年導入)使って効率的に培養すると同時に、効率的な培養液の量と振盪条件に工夫を行った。それに続くゲノムDNA調製も、96プレートのまま進められるプロトコルを更にチューニングした。さらに、昨年度に工夫したビーズ上でタグメンテーションを行うライブラリー調製法を96プレート単位で行ことで、効率的な大量ライブラリー調製方法が完成した。ゲノムDNAの段階とライブラリー作成の最後の段階で96サンプルすべてにおいて、そのDNA量をサイバーグリーンによる蛍光法で定量し、最後のライブラリーはキャピラリーシーケンサーを使用してDNAのサイズ分布も調べた。シーケンス結果は、まだ戻ってきていないので、解析できていない。
    令和2年度は、新型コロナウイルス感染防止対策による学生、研究員の実験制限による遅延と、申請者のエフォートの変化(リモート授業準備など)の影響が大きく出て、細かいトラブルシューティングに対して、迅速な対応ができなかった。また、経費節減のためシーケンス解析を外注しているが、サンプル輸送に関する時間が、これまでより長くかかっている。
    当初の予定の順序とは逆になるが、まず好塩性古細菌の変異体を大量に作成し、そのゲノム構造を1000株ほど決める作業を続けると同時に、続いて真正細菌(Vibrio)のUV変異導入ーゲノム解析の実験を行う。余裕があれば、真核微生物(Schizosaccharomyces pombe)も比較対象に加えたい。
    また、作成した変異体を保存する方法(グリセロール冷凍保管)を工夫すると同時に、すべての作成した古細菌変異株の走性に関するスクリーニング実験を行う。さらに、スクリーニング方法を工夫して、いくつかの表現型(抗生物質耐性、栄養要求性、窒素飢餓応答等)に対して、作成した同じ変異体ライブラリー(1000クローン)を使ってスクリーニングし、ゲノムシーケンス配列と直結した絞り込み作業を行う。これによって、それぞれの表現型が持つシステムサイズを見積もる。この段階では、各表現型の詳細には入り込まず、1000種類程度のランダム変異体ライブラリー(平均、10箇所程度に変異を持つ)のスクリーニング効率を検証することを第一目標にする。また、リソースの保存方法にも注意を払い、-80℃での保存でどの程度再生してくるのか?についても半年から1年ごとに調べ、これに関してもゲノム変異との相関を見る。
    ビーズ上で行うタグメンテーション法は、市販の試薬を準用しているが、これにコストがかかる。そのため、大腸菌で発現したTn5トランスポゼース(ここまでは構築済み)をアビジンビーズ上に固定化する作業までを自作しようと計画に加えた。現在、1サンプルのゲノム解析にトータル1200円程度かかっているが、この作業によって500円以下にできるので、少し回り道してでも自作Tn5-ビーズでのタグメンテーションライブラリー法を作成して、大量変異導入システム解析の基盤を作りたい。変異体リストは、データベース化し、公開する予定である。

  5. 遺伝子発現制御機構におけるシスエレメント機能の論理解析

    Grant number:19K05766  2019.4 - 2022.3

    科学研究費助成事業  基盤研究(C)

    兒島 孝明, 井原 邦夫

      More details

    Authorship:Coinvestigator(s) 

    微生物をセルファクトリーとして目的有用物質を効率よく生産するためには、関連遺伝子群の発現量バランスを合理的に最適化することが非常に重要となる。この発現制御の鍵となるのがDNA結合型転写因子と目的遺伝子コーディング領域上流に位置するプロモーターである。申請者らが開発した転写因子結合部位の解析システム、CaT-Seq法は、高精度かつ網羅的な転写因子制御下遺伝子の同定を可能とする。本申請研究は、このシステムと数理解析技術を融合させることにより、産業微生物Aspergillus oryzaeにおける転写因子による発現制御機構を包括的に理解する基盤技術構築を目的とする。
    Aspergillus oryzaeにおける転写因子による発現制御機構の解明と、A. oryzaeによる標的有用物質の高効率生産を目的として、以下のアプローチを実施した。
    1) A. oryzae転写因子KojRの結合部位の網羅的同定 昨年度実施したKojRを用いたgSELEX-Seqに関して、この転写因子に制御を受ける候補遺伝子162個を同定した。この中にはコウジ酸の生合成との関連性が報告されているトランスポーターも含まれていたものの、kojAやkojTなど先行研究でKojRによる発現制御が報告されている遺伝子は含まれていなかった。この要因として、結合配列の濃縮効率が当初想定していたよりも低かったことが挙げられる。現在、選択条件を再度検討した上でgSELEX-Seqを再度実施中である。
    2) A. oryzae kojR欠損株を用いたRNA-Seq
    昨年度取得したkojR欠損株を用いたRNA-Seqを実施した。この際、高速DNAシーケンシングのプラットフォームとしてナノポアシーケンサーを採用した。これにより、サンプル調製からRNA-Seqのデータ取得までのワークフローを確立した。一方でkojRに関連する遺伝子の有意な発現変動が観察されなかったため、A. oryzaeの培養条件を再検討の上、再度RNA-Seqを実施する予定である。
    3) A. oryzaeプロモーター機能の論理解析 昨年度構築したAoXlnRによる配列毎の発現制御の予測モデルのさらなる洗練化を試み、このモデルにより結合部位周辺の配列情報から下流に位置する遺伝子の発現変動を80%以上の精度で予測できることを示した。この成果に関して、3件の国内学会発表をを行い、近日中に論文を投稿する予定である。
    本研究の進捗状況がやや遅れていることに関して、KojRの結合部位の同定のためのgSELEX-Seqや発現変動遺伝子同定のためのRNA-Seqを実施したものの、いずれも想定した結果を取得できなかったことが主な要因として挙げられる。また、新型コロナウイルスの影響による研究活動の停止の影響も少ないとは言えない。その一方で、PCを用いたリモートワークでも作業できる A. oryzaeプロモーター機能の論理解析に関しては、昨年度に比べて顕著な進展が見られた。
    A. oryzae転写因子KojRの結合部位の同定および発現変動遺伝子に関して、これまでに遂行した解析条件をベースにより質や信頼性が改善されたデータの取得を試みる。また、そのほかのA. oryzae由来の転写因子に関して、NsdD(コウジ酸代謝)、AlcR(アルコール代謝)、AraR(アラビノース代謝)、ManR(β-マンナン代謝)、CreA (カーボンカタボライト抑制)の各DNA結合ドメイン配列を取得済みであり、順次gSELEX-SeqおよびRNA-Seqを実施する予定となっている。

  6. Structural analyses of reaction states of ion-pumping rhodopsin

    Grant number:19K06582  2019.4 - 2022.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (C)

      More details

    Authorship:Coinvestigator(s) 

  7. 光合成の喪失と従属栄養の促進:長期継代培養による栄養性の進化

    Grant number:18K19173  2018.6 - 2022.3

    科学研究費助成事業  挑戦的研究(萌芽)

    藤田 祐一, 井原 邦夫

      More details

    Authorship:Coinvestigator(s) 

    昨年度までの研究で、シアノバクテリアLeptolyngbya boryanaの長期暗所培養によって生じた変異の多くが特定の遺伝子rsbUに蓄積していたことから、RsbUがこのシアノバクテリアにおいて光合成と呼吸の調節に関わる情報伝達系に関わっていることが示唆された。長期培養で生じた形質(光合成生育能の喪失・暗所従属栄養能の促進)が本遺伝子の欠損に起因するのかどうかを確認するために、改めて野生型(元株としたdg5)からrsbUの単独欠損株を単離し、その形質を検討した。rsbU単独欠損株は、光独立栄養条件ではdg5に比べて有意に生育が遅かったのに対し、グルコースを添加した光混合栄養や暗所従属栄養条件では生育が有意に速かった。細胞の光合成活性(酸素発生量)と呼吸活性(暗所での酸素消費量)を比較すると、rsbU欠損株では光合成活性の低下と呼吸活性の向上が認められ、生育の差がこれらの活性の違いに起因すると推察された。この結果は、長期暗所培養に対する適応進化の原因遺伝子の一つがrsbUであることを支持している。さらに、グルコースを添加しない培地で暗所にてインキュベートするという炭素枯渇ストレス条件では、短期(30日まで)処理では野生型と変わらず耐性を示したが、30日以上の長期にわたると野生型に比べ有意に細胞が死滅した。好気明条件下で窒素源を添加しない窒素枯渇ストレスに対しては、両株ともにフィコビリン含量の減少が見られるがrsbU欠損株のフィコビリン減少は野生型よりも有意に速かった。14日間の窒素枯渇処理の後硝酸塩を添加し好気明条件で窒素枯渇からの回復を観察したところ、野生型が直ちに増殖を再開したのに対し、rsbUは2日間の遅滞期を経て増殖を再開した。これらの結果は、RsbUが関与する情報伝達系が炭素および窒素の枯渇ストレス応答に対して一定の役割を担っていることを示唆している。
    2020年度にはrsbU欠損株のトランスクリプトーム解析を行う予定であったが、新型コロナウィルス感染症蔓延に伴って名古屋大学の警戒レベルが最高となり学生の大学への入構が制限されたため実験の実施が困難な期間が約2ヶ月ほど続いた。加えて、トランスクリプトーム解析のために充分な質のRNA調製の条件検討に予想外に時間がかかったため、本研究課題を1年延長させていただくことにした。
    2021年度は、まず質的に充分なRNAを調製できる条件を確定し、そのRNA試料をもちいてRNA-seq解析を依頼する。その結果から、rsbUが関わる情報伝達系が発現を制御しているターゲット遺伝子群の全貌を明らかにする。

  8. Mechanisms of ultra-fast excitation energy dissipation in lichens, algae, mosses and plant under drought stress and its application

    Grant number:17K07440  2017.4 - 2022.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (C)

      More details

    Authorship:Coinvestigator(s) 

  9. Structural analyses of reaction states of ion-pumping rhodopsins

    Grant number:16K07267  2016.4 - 2020.3

    Kouyama Tsutomu

      More details

    Authorship:Coinvestigator(s) 

    The anion pumping cycle of halorhodopsin is initiated when the all-trans/15-anti isomer of retinal is photo-isomerized into the 13-cis/15-anti configuration. A previous study suggested that a reaction state with 13-cis/15-syn retinal occurred during the anion release process, i.e., after the N state with the 13-cis/15-anti retinal and before the O state with all-trans/15-anti retinal. In this study, we found that the 13-cis isomer (HR'), in which the absorption spectrum was blue-shifted by 8 nm as compared with that of the trans isomer (HR), accumulated significantly when pHR-rich claret membranes in 4 M NaBr was illuminated with continuous light. It was suggested that the branching of the trans photocycle into the 13-cis isomer (HR’) occurs during the decay of an O-like state (O’) with 13-cis/15-syn retinal. At a high bromide ion concentration, the anion pumping cycle is described by the scheme: HR -(hν)-> K -> L1 -> N -> N’ -> O’ -> HR’-> HR.

  10. 光駆動性塩素イオンポンプの構造・機能解析

    Grant number:21570164  2009.4 - 2012.3

    科学研究費補助金  基盤研究(C)

    井原 邦夫

      More details

    Authorship:Principal investigator 

  11. 光駆動性イオンポンプの時間分解構造解析

    Grant number:21023013  2009.4 - 2011.3

    科学研究費補助金  特定領域研

    井原 邦夫

      More details

    Authorship:Principal investigator 

▼display all

 

Teaching Experience (On-campus) 10

  1. 生物学基礎I

    2021

  2. 基礎生化学IIa

    2021

  3. 基礎生物学演習

    2021

  4. 現代の生命科学

    2021

  5. 生物学実験法および実験IV(分担)

    2020

     詳細を見る

    大腸菌を宿主としてオワンクラゲの蛍光タンパク質GFPを発現させ、それをt-ブタノール溶液と硫酸アンモニウム溶液を用いた3相分配法並びに疎水結合クロマトグラフィー法により精製し、精製した度合いを紫外ー可視領域の分光解析によって評価する。

  6. 基礎生化学II

    2016

  7. 現代の生命科学

    2016

  8. 基礎生物学演習I

    2016

  9. 現代の生命科学

    2014

  10. 基礎生物学演習I

    2014

▼display all

Teaching Experience (Off-campus) 3

  1. 基礎生化学II

    Nagoya University)

  2. 基礎生物学演習I

    Nagoya University)

  3. 現代の生命科学

    Nagoya University)

 

Social Contribution 10

  1. SSH事業 「 大腸菌とファージを用いた感染攻防の観察とPCR法とシーケンス技術を使った変異体検 出の理解」

    Role(s):Lecturer, Demonstrator

    一宮高校SSH  2021.8

  2. 社会人サポータ講習会 (名古屋西高校)

    Role(s):Lecturer

    2019.12

  3. SSH事業 「PCR法による品種推定 ーコメの品種判定を例に挙げて」

    Role(s):Lecturer

    2019.8

     More details

    Audience: High school students

    Type:Other

  4. SSH事業 「遺伝子実験の技術~DNA抽出とシーケンサー」

    Role(s):Lecturer

    2018.8

     More details

    Audience: High school students

    Type:Other

  5. SSH事業 「ワークショップ 髪からDNAを取り出す」

    Role(s):Lecturer

    2017.5 - 2017.8

     More details

    Audience: High school students

    Type:Other

  6. SSH重点枠事業「ワークショップ 乳製品に存在する発酵微生物を知る」

    2016.8

     More details

    高校の先生と生徒、計36 名に対して、乳製品を持ち寄ってもらい、(1)乳製品の一部を牛乳に接種することでヨーグルトができること、(2)乳製品の一部をMRS寒天培地にまくことで菌のコロニーを作らせること、(3)乳製品から直接DNAを取り出して、PCRにより16S rRNA遺伝子を増幅し、塩基配列を決めることで、菌を同定すること。
    を行い、研究の”考え方”を学んだ。

  7. SSH重点枠事業「実習:光タンパク質を取り出す」

    2015.8

     More details

    高校の先生と生徒、計20 名に遺伝子組換え大腸菌(GFPを導入)の作製と大腸菌で発現したGFPを精製する実験の指導を行った。同時に、組換えDNA実験の基本に関して学習した。

  8. 出前授業

    2013.6

     More details

    明和高校で大学の最先端研究の話を出来るだけ分かりやすく講義する。

  9. SSH「自然科学部交流会」

    Role(s):Lecturer

    2012.11

     More details

    Type:Lecture

    高校生の自然科学に関する研究発表会に参加し、色々なコメント、議論を通じて論理的な考え方を養い、問題解決の為の実験計画に対してアドバイスをする。
    次世代シーケンサーの話題に関して、基礎的な所から最先端の所までを簡単に講演した。

  10. Jr.サイエンス教室

    Role(s):Demonstrator

    2000.2

     More details

    Type:University open house

    小学生高学年、中学生を対象に、遺伝現象の担い手であるDNAが細胞のどこにあるのか?を顕微鏡で観察し、実際にDNAを取り出す作業をすることで、生命科学の片鱗に触れる。

▼display all

Academic Activities 1

  1. 第14回日本ゲノム微生物学会年会

    Role(s):Planning, management, etc.

    2020.3

     More details

    Type:Competition, symposium, etc.