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Lusiany T, Terada T, Kishikawa JI, Hirose M, Chen DV, Sugihara F, Ismanto HS, van Eerden FJ, Li S, Kato T, Arase H, Yoshiharu M, Okada M, Standley DM. Enhancement of SARS-CoV-2 Infection via Crosslinking of Adjacent Spike Proteins by N-Terminal Domain-Targeting Antibodies. Viruses 2023; 15:2421. [PMID: 38140662 PMCID: PMC10747171 DOI: 10.3390/v15122421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/08/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
The entry of SARS-CoV-2 into host cells is mediated by the interaction between the spike receptor-binding domain (RBD) and host angiotensin-converting enzyme 2 (ACE2). Certain human antibodies, which target the spike N-terminal domain (NTD) at a distant epitope from the host cell binding surface, have been found to augment ACE2 binding and enhance SARS-CoV-2 infection. Notably, these antibodies exert their effect independently of the antibody fragment crystallizable (Fc) region, distinguishing their mode of action from previously described antibody-dependent infection-enhancing (ADE) mechanisms. Building upon previous hypotheses and experimental evidence, we propose that these NTD-targeting infection-enhancing antibodies (NIEAs) achieve their effect through the crosslinking of neighboring spike proteins. In this study, we present refined structural models of NIEA fragment antigen-binding region (Fab)-NTD complexes, supported by molecular dynamics simulations and hydrogen-deuterium exchange mass spectrometry (HDX-MS). Furthermore, we provide direct evidence confirming the crosslinking of spike NTDs by NIEAs. Collectively, our findings advance our understanding of the molecular mechanisms underlying NIEAs and their impact on SARS-CoV-2 infection.
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Affiliation(s)
- Tina Lusiany
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan (H.S.I.); (S.L.)
| | - Tohru Terada
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Tokyo 113-8657, Japan;
| | - Jun-ichi Kishikawa
- Cryo-EM Structural Biology, Institute for Protein Research, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan; (J.-i.K.); (M.H.); (T.K.)
| | - Mika Hirose
- Cryo-EM Structural Biology, Institute for Protein Research, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan; (J.-i.K.); (M.H.); (T.K.)
| | - David Virya Chen
- Department of System Immunology, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan; (D.V.C.); (F.J.v.E.)
- Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan;
| | - Fuminori Sugihara
- Core Facility, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Osaka 565-0871, Japan;
| | - Hendra Saputra Ismanto
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan (H.S.I.); (S.L.)
| | - Floris J. van Eerden
- Department of System Immunology, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan; (D.V.C.); (F.J.v.E.)
| | - Songling Li
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan (H.S.I.); (S.L.)
- Department of System Immunology, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan; (D.V.C.); (F.J.v.E.)
| | - Takayuki Kato
- Cryo-EM Structural Biology, Institute for Protein Research, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan; (J.-i.K.); (M.H.); (T.K.)
| | - Hisashi Arase
- Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan;
- Department of Immunochemistry, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
| | - Matsuura Yoshiharu
- Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan;
| | - Masato Okada
- Center for Advanced Modalities and DDS, Osaka University, 2-8 Yamadaoka, Suita 565-0871, Japan;
| | - Daron M. Standley
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan (H.S.I.); (S.L.)
- Department of System Immunology, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan; (D.V.C.); (F.J.v.E.)
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2
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Oyama R, Ishigame H, Tanaka H, Tateshita N, Itazawa M, Imai R, Nishiumi N, Kishikawa JI, Kato T, Anindita J, Nishikawa Y, Maeki M, Tokeshi M, Tange K, Nakai Y, Sakurai Y, Okada T, Akita H. An Ionizable Lipid Material with a Vitamin E Scaffold as an mRNA Vaccine Platform for Efficient Cytotoxic T Cell Responses. ACS Nano 2023; 17:18758-18774. [PMID: 37814788 PMCID: PMC10569098 DOI: 10.1021/acsnano.3c02251] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 08/17/2023] [Indexed: 10/11/2023]
Abstract
RNA vaccines based on lipid nanoparticles (LNPs) with in vitro transcribed mRNA (IVT-mRNA) encapsulated are now a currently successful but still evolving modality of vaccines. One of the advantages of RNA vaccines is their ability to induce CD8+ T-cell-mediated cellular immunity that is indispensable for excluding pathogen-infected cells or cancer cells from the body. In this study, we report on the development of LNPs with an enhanced capability for inducing cellular immunity by using an ionizable lipid with a vitamin E scaffold. An RNA vaccine that contained this ionizable lipid and an IVT-mRNA encoding a model antigen ovalbumin (OVA) induced OVA-specific cytotoxic T cell responses and showed an antitumor effect against an E.G7-OVA tumor model. Vaccination with the LNPs conferred protection against lethal infection by Toxoplasma gondii using its antigen TgPF. The vitamin E scaffold-dependent type I interferon response was important for effector CD8+ T cell differentiation induced by the mRNA-LNPs. Our findings also revealed that conventional dendritic cells (cDCs) were essential for achieving CD8+ T cell responses induced by the mRNA-LNPs, while the XCR1-positive subset of cDCs, cDC1 specialized for antigen cross-presentation, was not required. Consistently, the mRNA-LNPs were found to selectively transfect another subset of cDCs, cDC2 that had migrated from the skin to lymph nodes, where they could make vaccine-antigen-dependent contacts with CD8+ T cells. The findings indicate that the activation of innate immune signaling by the adjuvant activity of the vitamin E scaffold and the expression of antigens in cDC2 are important for subsequent antigen presentation and the establishment of antigen-specific immune responses.
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Affiliation(s)
- Ryotaro Oyama
- Laboratory
of DDS Design and Drug Disposition, Graduate School of Pharmaceutical
Sciences, Chiba University, 1-8-1 Inohana,
Chuo-ku, Chiba City, Chiba, 260-0856, Japan
| | - Harumichi Ishigame
- Laboratory
for Tissue Dynamics, RIKEN Center for Integrative
Medical Sciences, 1-7-22
Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan
| | - Hiroki Tanaka
- Laboratory
of DDS Design and Drug Disposition, Graduate School of Pharmaceutical
Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai City, Miyagi 980-8578, Japan
| | - Naho Tateshita
- Laboratory
of DDS Design and Drug Disposition, Graduate School of Pharmaceutical
Sciences, Chiba University, 1-8-1 Inohana,
Chuo-ku, Chiba City, Chiba, 260-0856, Japan
| | - Moeko Itazawa
- Laboratory
for Tissue Dynamics, RIKEN Center for Integrative
Medical Sciences, 1-7-22
Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan
| | - Ryosuke Imai
- Laboratory
for Tissue Dynamics, RIKEN Center for Integrative
Medical Sciences, 1-7-22
Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan
- Division
of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical
Sciences, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Naomasa Nishiumi
- Laboratory
of DDS Design and Drug Disposition, Graduate School of Pharmaceutical
Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai City, Miyagi 980-8578, Japan
| | - Jun-ichi Kishikawa
- Laboratory
for Cryo-EM Structural Biology, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takayuki Kato
- Laboratory
for Cryo-EM Structural Biology, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Jessica Anindita
- Laboratory
of DDS Design and Drug Disposition, Graduate School of Pharmaceutical
Sciences, Chiba University, 1-8-1 Inohana,
Chuo-ku, Chiba City, Chiba, 260-0856, Japan
| | - Yoshifumi Nishikawa
- National
Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Nishi 2-13, Inada-cho, Obihiro City, Hokkaido 080-8555, Japan
| | - Masatoshi Maeki
- Division
of Applied Chemistry, Faculty of Engineering, Hokkaido University, Kita 13 Nishi 8, Kita-ku, Sapporo City, Hokkaido 060-8628, Japan
| | - Manabu Tokeshi
- Division
of Applied Chemistry, Faculty of Engineering, Hokkaido University, Kita 13 Nishi 8, Kita-ku, Sapporo City, Hokkaido 060-8628, Japan
| | - Kota Tange
- DDS
Research Laboratory, NOF CORPORATION, 3-3 Chidori-cho, Kawasaki-ku, Kawasaki City, Kanagawa 210-0865, Japan
| | - Yuta Nakai
- DDS
Research Laboratory, NOF CORPORATION, 3-3 Chidori-cho, Kawasaki-ku, Kawasaki City, Kanagawa 210-0865, Japan
| | - Yu Sakurai
- Laboratory
of DDS Design and Drug Disposition, Graduate School of Pharmaceutical
Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai City, Miyagi 980-8578, Japan
| | - Takaharu Okada
- Laboratory
for Tissue Dynamics, RIKEN Center for Integrative
Medical Sciences, 1-7-22
Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan
- Graduate
School of Medical Life Science, Yokohama
City University, 1-7-29
Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan
| | - Hidetaka Akita
- Laboratory
of DDS Design and Drug Disposition, Graduate School of Pharmaceutical
Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai City, Miyagi 980-8578, Japan
- Center
for Advanced Modalities and DDS, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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Nakanishi A, Kishikawa JI, Mitsuoka K, Yokoyama K. Cryo-EM analysis of V/A-ATPase intermediates reveals the transition of the ground-state structure to steady-state structures by sequential ATP binding. J Biol Chem 2023; 299:102884. [PMID: 36626983 PMCID: PMC9971907 DOI: 10.1016/j.jbc.2023.102884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/09/2023] Open
Abstract
Vacuolar/archaeal-type ATPase (V/A-ATPase) is a rotary ATPase that shares a common rotary catalytic mechanism with FoF1 ATP synthase. Structural images of V/A-ATPase obtained by single-particle cryo-electron microscopy during ATP hydrolysis identified several intermediates, revealing the rotary mechanism under steady-state conditions. However, further characterization is needed to understand the transition from the ground state to the steady state. Here, we identified the cryo-electron microscopy structures of V/A-ATPase corresponding to short-lived initial intermediates during the activation of the ground state structure by time-resolving snapshot analysis. These intermediate structures provide insights into how the ground-state structure changes to the active, steady state through the sequential binding of ATP to its three catalytic sites. All the intermediate structures of V/A-ATPase adopt the same asymmetric structure, whereas the three catalytic dimers adopt different conformations. This is significantly different from the initial activation process of FoF1, where the overall structure of the F1 domain changes during the transition from a pseudo-symmetric to a canonical asymmetric structure (PNAS NEXUS, pgac116, 2022). In conclusion, our findings provide dynamical information that will enhance the future prospects for studying the initial activation processes of the enzymes, which have unknown intermediate structures in their functional pathway.
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Affiliation(s)
- Atsuko Nakanishi
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, Japan,Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, Osaka, Japan
| | - Jun-ichi Kishikawa
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, Japan,Institute for Protein Research, Osaka University, Osaka Japan
| | - Kaoru Mitsuoka
- Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, Osaka, Japan
| | - Ken Yokoyama
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, Japan.
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Nakano A, Kishikawa JI, Nakanishi A, Mitsuoka K, Yokoyama K. Structural basis of unisite catalysis of bacterial F 0F 1-ATPase. PNAS Nexus 2022; 1:pgac116. [PMID: 36741449 PMCID: PMC9896953 DOI: 10.1093/pnasnexus/pgac116] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/07/2022] [Indexed: 06/17/2023]
Abstract
Adenosine triphosphate (ATP) synthases (F0F1-ATPases) are crucial for all aerobic organisms. F1, a water-soluble domain, can catalyze both the synthesis and hydrolysis of ATP with the rotation of the central γε rotor inside a cylinder made of α 3 β 3 in three different conformations (referred to as β E, β TP, and β DP). In this study, we determined multiple cryo-electron microscopy structures of bacterial F0F1 exposed to different reaction conditions. The structures of nucleotide-depleted F0F1 indicate that the ε subunit directly forces β TP to adopt a closed form independent of the nucleotide binding to β TP. The structure of F0F1 under conditions that permit only a single catalytic β subunit per enzyme to bind ATP is referred to as unisite catalysis and reveals that ATP hydrolysis unexpectedly occurs on β TP instead of β DP, where ATP hydrolysis proceeds in the steady-state catalysis of F0F1. This indicates that the unisite catalysis of bacterial F0F1 significantly differs from the kinetics of steady-state turnover with continuous rotation of the shaft.
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Affiliation(s)
- Atsuki Nakano
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto 603-8555, Japan
| | - Jun-ichi Kishikawa
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto 603-8555, Japan
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Atsuko Nakanishi
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto 603-8555, Japan
- Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, 7-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Kaoru Mitsuoka
- Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, 7-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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Tomie Y, Nakanishi A, Kishikawa JI, Yokoyama K, Mitsuoka K. 3aB_MB-2Trials for Higher Resolution Structural Analysis of Rotary H+-ATPase/Synthase. Microscopy (Oxf) 2018. [DOI: 10.1093/jmicro/dfy084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Yuya Tomie
- Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, Osaka, Japan
| | - Atsuoka Nakanishi
- Department of Molecular Biosciences, Kyoto Sangyo University, Kyoto, Japan
| | - Jun-ichi Kishikawa
- Department of Molecular Biosciences, Kyoto Sangyo University, Kyoto, Japan
| | - Ken Yokoyama
- Department of Molecular Biosciences, Kyoto Sangyo University, Kyoto, Japan
| | - Kaoru Mitsuoka
- Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, Osaka, Japan
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Kishikawa JI, Inoue Y, Fujikawa M, Nishimura K, Nakanishi A, Tanabe T, Imamura H, Yokoyama K. General anesthetics cause mitochondrial dysfunction and reduction of intracellular ATP levels. PLoS One 2018; 13:e0190213. [PMID: 29298324 PMCID: PMC5752027 DOI: 10.1371/journal.pone.0190213] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 12/11/2017] [Indexed: 12/29/2022] Open
Abstract
General anesthetics are indispensable for effective clinical care. Although, the mechanism of action of general anesthetics remains controversial, lipid bilayers and proteins have been discussed as their targets. In this study, we focused on the relationship between cellular ATP levels and general anesthetics. The ATP levels of nematodes and cultured mammalian cells were decreased by exposure to three general anesthetics: isoflurane, pentobarbital, and 1-phenoxy-2-propanol. Furthermore, these general anesthetics abolished mitochondrial membrane potential, resulting in the inhibition of mitochondrial ATP synthesis. These results suggest that the observed decrease of cellular ATP level is a common phenomenon of general anesthetics.
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Affiliation(s)
- Jun-ichi Kishikawa
- Department of Molecular Biosciences, Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, Japan
| | - Yuki Inoue
- Department of Molecular Biosciences, Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, Japan
| | - Makoto Fujikawa
- Departmet of Pharmacology Neurobiology, Graduate School of Medicine, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Kenji Nishimura
- Department of Molecular Biosciences, Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, Japan
| | - Atsuko Nakanishi
- Department of Molecular Biosciences, Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, Japan
| | - Tsutomu Tanabe
- Departmet of Pharmacology Neurobiology, Graduate School of Medicine, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Hiromi Imamura
- Graduate School of Biostudies, Kyoto University, Yoshida-konoe-cho, Sakyo-ku, Kyoto, Japan
- * E-mail: (HI); (KY)
| | - Ken Yokoyama
- Department of Molecular Biosciences, Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, Japan
- * E-mail: (HI); (KY)
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Mitsuoka K, Nakanishi A, Kishikawa JI, Yokoyama K. PB-08Structural Analysis of Rotary H + -ATPase/Synthase by Cryo-Electron Microscopy. Microscopy (Oxf) 2017. [DOI: 10.1093/jmicro/dfx109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Kaoru Mitsuoka
- Research Center for Ultra-High Voltage Microscopy, Osaka University, Osaka, Japan, and
| | - Atsuoka Nakanishi
- Department of Molecular Biosciences, Kyoto Sangyo University, Kyoto, Japan
| | - Jun-ichi Kishikawa
- Department of Molecular Biosciences, Kyoto Sangyo University, Kyoto, Japan
| | - Ken Yokoyama
- Department of Molecular Biosciences, Kyoto Sangyo University, Kyoto, Japan
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Mitsuoka K, Nakanishi A, Takeuchi N, Kishikawa JI, Yokoyama K. C3-P-13Single Particle Analysis of Thermus ThermophilusV-ATPase by Cryo-Electron Microscopy. Microscopy (Oxf) 2015. [DOI: 10.1093/jmicro/dfv316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Nakanishi A, Kishikawa JI, Tamakoshi M, Yokoyama K. The ingenious structure of central rotor apparatus in VoV1; key for both complex disassembly and energy coupling between V1 and Vo. PLoS One 2015; 10:e0119602. [PMID: 25756791 PMCID: PMC4355294 DOI: 10.1371/journal.pone.0119602] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 01/14/2015] [Indexed: 11/25/2022] Open
Abstract
Vacuolar type rotary H+-ATPases (VoV1) couple ATP synthesis/hydrolysis by V1 with proton translocation by Vo via rotation of a central rotor apparatus composed of the V1-DF rotor shaft, a socket-like Vo-C (eukaryotic Vo-d) and the hydrophobic rotor ring. Reconstitution experiments using subcomplexes revealed a weak binding affinity of V1-DF to Vo-C despite the fact that torque needs to be transmitted between V1-DF and Vo-C for the tight energy coupling between V1 and Vo. Mutation of a short helix at the tip of V1-DF caused intramolecular uncoupling of VoV1, suggesting that proper fitting of the short helix of V1-D into the socket of Vo-C is required for tight energy coupling between V1 and Vo. To account for the apparently contradictory properties of the interaction between V1-DF and Vo-C (weak binding affinity but strict requirement for torque transmission), we propose a model in which the relationship between V1-DF and Vo-C corresponds to that between a slotted screwdriver and a head of slotted screw. This model is consistent with our previous result in which the central rotor apparatus is not the major factor for the association of V1 with Vo (Kishikawa and Yokoyama, J Biol Chem. 2012 24597-24603).
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Affiliation(s)
- Atsuko Nakanishi
- Department of Molecular Biosciences, Kyoto Sangyo University, Motoyama Kamigamo, Kita-ku, Kyoto, Japan
| | - Jun-ichi Kishikawa
- Department of Molecular Biosciences, Kyoto Sangyo University, Motoyama Kamigamo, Kita-ku, Kyoto, Japan
| | - Masatada Tamakoshi
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, Horinouchi, Hachioji, Tokyo, Japan
| | - Ken Yokoyama
- Department of Molecular Biosciences, Kyoto Sangyo University, Motoyama Kamigamo, Kita-ku, Kyoto, Japan
- * E-mail:
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10
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Kishikawa JI, Nakanishi A, Furuike S, Tamakoshi M, Yokoyama K. Molecular basis of ADP inhibition of vacuolar (V)-type ATPase/synthase. J Biol Chem 2013; 289:403-12. [PMID: 24247239 DOI: 10.1074/jbc.m113.523498] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Reduction of ATP hydrolysis activity of vacuolar-type ATPase/synthase (V0V1) as a result of ADP inhibition occurs as part of the normal mechanism of V0V1 of Thermus thermophilus but not V0V1 of Enterococcus hirae or eukaryotes. To investigate the molecular basis for this difference, domain-swapped chimeric V1 consisting of both T. thermophilus and E. hirae enzymes were generated, and their function was analyzed. The data showed that the interaction between the nucleotide binding and C-terminal domains of the catalytic A subunit from E. hirae V1 is central to increasing binding affinity of the chimeric V1 for phosphate, resulting in reduction of the ADP inhibition. These findings together with a comparison of the crystal structures of T. thermophilus V1 with E. hirae V1 strongly suggest that the A subunit adopts a conformation in T. thermophilus V1 different from that in E. hirae V1. This key difference results in ADP inhibition of T. thermophilus V1 by abolishing the binding affinity for phosphate during ATP hydrolysis.
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Affiliation(s)
- Jun-ichi Kishikawa
- From the Department of Molecular Biosciences, Kyoto Sangyo University, Motoyama Kamigamo, Kita-ku, Kyoto 603-8555, Japan
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Tsuyama T, Kishikawa JI, Han YW, Harada Y, Tsubouchi A, Noji H, Kakizuka A, Yokoyama K, Uemura T, Imamura H. In vivo fluorescent adenosine 5'-triphosphate (ATP) imaging of Drosophila melanogaster and Caenorhabditis elegans by using a genetically encoded fluorescent ATP biosensor optimized for low temperatures. Anal Chem 2013; 85:7889-96. [PMID: 23875533 DOI: 10.1021/ac4015325] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Adenosine 5'-triphosphate (ATP) is the major energy currency of all living organisms. Despite its important functions, the spatiotemporal dynamics of ATP levels inside living multicellular organisms is unclear. In this study, we modified the genetically encoded Förster resonance energy transfer (FRET)-based ATP biosensor ATeam to optimize its affinity at low temperatures. This new biosensor, AT1.03NL, detected ATP changes inside Drosophila S2 cells more sensitively than the original biosensor did, at 25 °C. By expressing AT1.03NL in Drosophila melanogaster and Caenorhabditis elegans, we succeeded in imaging the in vivo ATP dynamics of these model animals at single-cell resolution.
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Affiliation(s)
- Taiichi Tsuyama
- Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan
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Kishikawa JI, Ibuki T, Nakamura S, Nakanishi A, Minamino T, Miyata T, Namba K, Konno H, Ueno H, Imada K, Yokoyama K. Common evolutionary origin for the rotor domain of rotary ATPases and flagellar protein export apparatus. PLoS One 2013; 8:e64695. [PMID: 23724081 PMCID: PMC3665681 DOI: 10.1371/journal.pone.0064695] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 04/17/2013] [Indexed: 02/02/2023] Open
Abstract
The V1- and F1- rotary ATPases contain a rotor that rotates against a catalytic A3B3 or α3β3 stator. The rotor F1-γ or V1-DF is composed of both anti-parallel coiled coil and globular-loop parts. The bacterial flagellar type III export apparatus contains a V1/F1-like ATPase ring structure composed of FliI6 homo-hexamer and FliJ which adopts an anti-parallel coiled coil structure without the globular-loop part. Here we report that FliJ of Salmonella enterica serovar Typhimurium shows a rotor like function in Thermus thermophilus A3B3 based on both biochemical and structural analysis. Single molecular analysis indicates that an anti-parallel coiled-coil structure protein (FliJ structure protein) functions as a rotor in A3B3. A rotary ATPase possessing an F1-γ-like protein generated by fusion of the D and F subunits of V1 rotates, suggesting F1-γ could be the result of a fusion of the genes encoding two separate rotor subunits. Together with sequence comparison among the globular part proteins, the data strongly suggest that the rotor domains of the rotary ATPases and the flagellar export apparatus share a common evolutionary origin.
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Affiliation(s)
- Jun-ichi Kishikawa
- Department of Molecular Biosciences, Kyoto Sangyo University, Motoyama Kamigamo, Kita-ku, Kyoto, Japan
| | - Tatsuya Ibuki
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Shuichi Nakamura
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
- Department of Applied Physics, Graduate School of Engineering, Tohoku University, Sendai, Miyagi, Japan
| | - Astuko Nakanishi
- Department of Molecular Biosciences, Kyoto Sangyo University, Motoyama Kamigamo, Kita-ku, Kyoto, Japan
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Tomoko Miyata
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
- Riken Quantitative Biology Center, Osaka, Japan
| | - Hiroki Konno
- Imaging Research Division, Bio-AFM Frontier Research Center, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Hiroshi Ueno
- Department of Physics, Faculty of Science and Engineering, Chuo University, Bunkyo-ku, Tokyo, Japan
| | - Katsumi Imada
- Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
- * E-mail: (KI); (KY)
| | - Ken Yokoyama
- Department of Molecular Biosciences, Kyoto Sangyo University, Motoyama Kamigamo, Kita-ku, Kyoto, Japan
- * E-mail: (KI); (KY)
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Abstract
Vacuolar-type rotary H+-ATPase/synthase (VoV1) from Thermus thermophilus, composed of nine subunits, A, B, D, F, C, E, G, I, and L, has been reconstituted from individually isolated V1 (A3B3D1F1) and Vo (C1E2G2I1L12) subcomplexes in vitro. A3B3D and A3B3 also reconstituted with Vo, resulting in a holoenzyme-like complexes. However, A3B3D-Vo and A3B3-Vo did not show ATP synthesis and dicyclohexylcarbodiimide-sensitive ATPase activity. The reconstitution process was monitored in real time by fluorescence resonance energy transfer (FRET) between an acceptor dye attached to subunit F or D in V1 or A3B3D and a donor dye attached to subunit C in Vo. The estimated dissociation constants Kd for VoV1 and A3B3D-Vo were ∼0.3 and ∼1 nm at 25 °C, respectively. These results suggest that the A3B3 domain tightly associated with the two EG peripheral stalks of Vo, even in the absence of the central shaft subunits. In addition, F subunit is essential for coupling of ATP hydrolysis and proton translocation and has a key role in the stability of whole complex. However, the contribution of the F subunit to the association of A3B3 with Vo is much lower than that of the EG peripheral stalks.
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Affiliation(s)
- Jun-ichi Kishikawa
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto 603-8555, Japan
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Kishikawa JI, Fujikawa M, Imamura H, Yasuda K, Noji H, Ishii N, Mitani S, Yokoyama K. MRT letter: Expression of ATP sensor protein in Caenorhabditis elegans. Microsc Res Tech 2011; 75:15-9. [PMID: 22038755 DOI: 10.1002/jemt.21103] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 09/08/2011] [Indexed: 11/08/2022]
Abstract
Adenosine 5'-triphosphate (ATP) is the major energy currency and is involved in many biological processes. The ATP-monitoring system for cells in animals can be helpful to study the relationship between energy metabolism and biological processes. The fluorescent ATP biosensor ATeam (ATP indicator based on Epsilon subunit for Analytical Measurements), which has been reported to monitor ATP levels in cultured cells on the basis of fluorescence resonance energy transfer (FRET), was introduced into nematodes by microinjection and UV-irradiation method. To confirm whether ATeam functions as an ATP sensor in nematode cells, the authors measured FRET of ATeam in cells of transgenic nematode. The ATeam was expressed in target cells in nematode. In vulva cells, ATP levels in the cytosol were higher than those in mitochondria. ATeam also sensed ATP level change in cultured cells from the transgenic nematode. These experiments indicated that ATeam is available for detection of changes in ATP levels in nematode cells.
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Affiliation(s)
- Jun-ichi Kishikawa
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-ku, Kyoto, Japan
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Kishikawa JI, Kabashima Y, Kurokawa T, Sakamoto J. The cytochrome bcc-aa3-type respiratory chain of Rhodococcus rhodochrous. J Biosci Bioeng 2010; 110:42-7. [PMID: 20541114 DOI: 10.1016/j.jbiosc.2009.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 12/12/2009] [Accepted: 12/14/2009] [Indexed: 10/19/2022]
Abstract
Rhodococcus rhodochrous is an active soil bacterium belonging to the Nocardia group of high GC gram-positive bacteria. It is rich in various enzymes and thus important in the industrial production of chemicals and bioremediation. In this work, the respiratory chain of this aerobic organism was investigated and characterized. Grown under highly aerobic conditions, the membrane fraction of R. rhodochrous cells only contained a-, b- and c-type cytochromes, suggesting that it is the cytochrome bcc-aa(3)-type pathway that mainly operates under these conditions. In contrast, the d-type cytochrome was also present under microaerobic conditions, indicating that the alternative pathway of the bd-type oxidase works in these circumstances. In addition, the results of H(+)/O ratio measurements indicate that these two pathways have different energy efficiencies.
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Affiliation(s)
- Jun-ichi Kishikawa
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Kawazu 680-4, Iizuka, Fukuoka, 820-8502, Japan
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