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Trofimova AM, Amakhin DV, Postnikova TY, Tiselko VS, Alekseev A, Podoliak E, Gordeliy VI, Chizhov AV, Zaitsev AV. Light-Driven Sodium Pump as a Potential Tool for the Control of Seizures in Epilepsy. Mol Neurobiol 2024; 61:4691-4704. [PMID: 38114761 DOI: 10.1007/s12035-023-03865-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 12/06/2023] [Indexed: 12/21/2023]
Abstract
The marine flavobacterium Krokinobactereikastus light-driven sodium pump (KR2) generates an outward sodium ion current under 530 nm light stimulation, representing a promising optogenetic tool for seizure control. However, the specifics of KR2 application to suppress epileptic activity have not yet been addressed. In the present study, we investigated the possibility of KR2 photostimulation to suppress epileptiform activity in mouse brain slices using the 4-aminopyrindine (4-AP) model. We injected the adeno-associated viral vector (AAV-PHP.eB-hSyn-KR2-YFP) containing the KR2 sodium pump gene enhanced with appropriate trafficking tags. KR2 expression was observed in the lateral entorhinal cortex and CA1 hippocampus. Using whole-cell patch clamp in mouse brain slices, we show that KR2, when stimulated with LED light, induces a substantial hyperpolarization of entorhinal neurons. However, continuous photostimulation of KR2 does not interrupt ictal discharges in mouse entorhinal cortex slices induced by a solution containing 4-AP. KR2-induced hyperpolarization strongly activates neuronal HCN channels. Consequently, turning off photostimulation resulted in HCN channel-mediated rebound depolarization accompanied by a transient increase in spontaneous network activity. Using low-frequency pulsed photostimulation, we induced the generation of short HCN channel-mediated discharges that occurred in response to the light stimulus being turned off; these discharges reliably interrupt ictal activity. Thus, low-frequency pulsed photostimulation of KR2 can be considered as a potential tool for controlling epileptic seizures.
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Affiliation(s)
- Alina M Trofimova
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Saint Petersburg, Russia
| | - Dmitry V Amakhin
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Saint Petersburg, Russia
| | - Tatyana Y Postnikova
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Saint Petersburg, Russia
| | - Vasilii S Tiselko
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Saint Petersburg, Russia
| | - Alexey Alekseev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
| | - Elizaveta Podoliak
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
- Department of Ophthalmology, Universitäts-Augenklinik Bonn, University of Bonn, Bonn, Germany
| | - Valentin I Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Anton V Chizhov
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Saint Petersburg, Russia
- MathNeuro Team, Inria Centre at Université Côte d'Azur, Sophia Antipolis, France
| | - Aleksey V Zaitsev
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Saint Petersburg, Russia.
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2
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Yang Q, Chen D. Na + Binding and Transport: Insights from Light-Driven Na +-Pumping Rhodopsin. Molecules 2023; 28:7135. [PMID: 37894614 PMCID: PMC10608830 DOI: 10.3390/molecules28207135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/07/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Na+ plays a vital role in numerous physiological processes across humans and animals, necessitating a comprehensive understanding of Na+ transmembrane transport. Among the various Na+ pumps and channels, light-driven Na+-pumping rhodopsin (NaR) has emerged as a noteworthy model in this field. This review offers a concise overview of the structural and functional studies conducted on NaR, encompassing ground/intermediate-state structures and photocycle kinetics. The primary focus lies in addressing key inquiries: (1) unraveling the translocation pathway of Na+; (2) examining the role of structural changes within the photocycle, particularly in the O state, in facilitating Na+ transport; and (3) investigating the timing of Na+ uptake/release. By delving into these unresolved issues and existing debates, this review aims to shed light on the future direction of Na+ pump research.
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Affiliation(s)
- Qifan Yang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Deliang Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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3
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Xu J, Yang Q, Ma B, Li L, Kong F, Xiao L, Chen D. K +-Dependent Photocycle and Photocurrent Reveal the Uptake of K + in Light-Driven Sodium Pump. Int J Mol Sci 2023; 24:14414. [PMID: 37833864 PMCID: PMC10572131 DOI: 10.3390/ijms241914414] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 09/16/2023] [Accepted: 09/18/2023] [Indexed: 10/15/2023] Open
Abstract
Engineering light-controlled K+ pumps from Na+-pumping rhodopsins (NaR) greatly expands the scope of optogenetic applications. However, the limited knowledge regarding the kinetic and selective mechanism of K+ uptake has significantly impeded the modification and design of light-controlled K+ pumps, as well as their practical applications in various fields, including neuroscience. In this study, we presented K+-dependent photocycle kinetics and photocurrent of a light-driven Na+ pump called Nonlabens dokdonensis rhodopsin 2 (NdR2). As the concentration of K+ increased, we observed the accelerated decay of M intermediate in the wild type (WT) through flash photolysis. In 100 mM KCl, the lifetime of the M decay was approximately 1.0 s, which shortened to around 0.6 s in 1 M KCl. Additionally, the K+-dependent M decay kinetics were also observed in the G263W/N61P mutant, which transports K+. In 100 mM KCl, the lifetime of the M decay was approximately 2.5 s, which shortened to around 0.2 s in 1 M KCl. According to the competitive model, in high KCl, K+ may be taken up from the cytoplasmic surface, competing with Na+ or H+ during M decay. This was further confirmed by the K+-dependent photocurrent of WT liposome. As the concentration of K+ increased to 500 mM, the amplitude of peak current significantly dropped to approximately ~60%. Titration experiments revealed that the ratio of the rate constant of H+ uptake (kH) to that of K+ uptake (kK) is >108. Compared to the WT, the G263W/N61P mutant exhibited a decrease of approximately 40-fold in kH/kK. Previous studies focused on transforming NaR into K+ pumps have primarily targeted the intracellular ion uptake region of Krokinobacter eikastus rhodopsin 2 (KR2) to enhance K+ uptake. However, our results demonstrate that the naturally occurring WT NdR2 is capable of intracellular K+ uptake without requiring structural modifications on the intracellular region. This discovery provides diverse options for future K+ pump designs. Furthermore, we propose a novel photocurrent-based approach to evaluate K+ uptake, which can serve as a reference for similar studies on other ion pumps. In conclusion, our research not only provides new insights into the mechanism of K+ uptake but also offers a valuable point of reference for the development of optogenetic tools and other applications in this field.
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Affiliation(s)
- Jikang Xu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (B.M.)
| | - Qifan Yang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (B.M.)
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Baofu Ma
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (B.M.)
| | - Longjie Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (B.M.)
| | - Fei Kong
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (B.M.)
| | - Lan Xiao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (B.M.)
| | - Deliang Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (B.M.)
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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4
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Asido M, Wachtveitl J. Photochemistry of the Light-Driven Sodium Pump Krokinobacter eikastus Rhodopsin 2 and Its Implications on Microbial Rhodopsin Research: Retrospective and Perspective. J Phys Chem B 2023; 127:3766-3773. [PMID: 36919947 DOI: 10.1021/acs.jpcb.2c08933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
The discovery of the light-driven sodium pump Krokinobacter eikastus rhodopsin 2 (KR2) in 2013 has changed the paradigm that cation transport in microbial rhodopsins is restricted to the translocation of protons. Even though this finding is already remarkable by itself, it also reignited more general discussions about the functional mechanism of ion transport. The unique composition of the retinal binding pocket in KR2 with a tight interaction between the retinal Schiff base and its respective counterion D116 also has interesting implications on the photochemical pathway of the chromophore. Here, we discuss the most recent advances in our understanding of the KR2 functionality from the primary event of photon absorption by all-trans retinal up to the actual protein response in the later phases of the photocycle, mainly from the point of view of optical spectroscopy. In this context, we furthermore highlight some of the ongoing debates on the photochemistry of microbial rhodopsins and give some perspectives for promising future directions in this field of research.
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Affiliation(s)
- Marvin Asido
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Straße 7, 60438 Frankfurt am Main, Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Straße 7, 60438 Frankfurt am Main, Germany
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5
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Bogachev AV, Baykov AA, Bertsova YV, Mamedov MD. Mechanism of Ion Translocation by Na+-Rhodopsin. BIOCHEMISTRY (MOSCOW) 2022; 87:731-741. [DOI: 10.1134/s0006297922080053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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6
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Nakamizo Y, Fujisawa T, Kikukawa T, Okamura A, Baba H, Unno M. Low-temperature Raman spectroscopy of sodium-pump rhodopsin from Indibacter alkaliphilus: insight of Na + binding for active Na + transport. Phys Chem Chem Phys 2021; 23:2072-2079. [PMID: 33433533 DOI: 10.1039/d0cp05652a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We carried out the low-temperature Raman measurement of a sodium pump rhodopsin from Indibacter alkaliphilus (IaNaR) and examined the primary structural change for the light-driven Na+ pump. We observed that photoexcitation of IaNaR produced the distorted 13-cis retinal chromophore in the presence of Na+, while the structural distortion was significantly relaxed in the absence of Na+. This structural difference of the chromophore with/without Na+ was attributed to the Na+ binding to the protein, which alters the active site. Using the spectral sensitivity to the ion binding, we found that IaNaR had a second Na+ binding site in addition to the one already specified on the extracellular surface. To date, the Na+ binding has not been considered as a prerequisite for Na+ transport. However, this study provides insight that the protein structural change induced by the ion binding involved the formation of an R108-D250 salt bridge, which has critical importance in the active transport of Na+.
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Affiliation(s)
- Yushi Nakamizo
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan.
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7
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Muntyan MS, Morozov DA, Leonova YF, Ovchinnikova TV. Identification of Na+-Pumping Cytochrome Oxidase in the Membranes of Extremely Alkaliphilic Thioalkalivibrio Bacteria. BIOCHEMISTRY (MOSCOW) 2021; 85:1631-1639. [PMID: 33705300 DOI: 10.1134/s0006297920120147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
For the first time, the functioning of the oxygen reductase Na+-pump (Na+-pumping cytochrome c oxidase of the cbb3-type) was demonstrated by examining the respiratory chain of the extremely alkaliphilic bacterium Thioalkalivibrio versutus [Muntyan, M. S., et al. (2015) Cytochrome cbb3 of Thioalkalivibrio is a Na+-pumping cytochrome oxidase, Proc. Natl. Acad. Sci. USA, 112, 7695-7700], a product of the ccoNOQP operon. In this study, we detected and identified this enzyme using rabbit polyclonal antibody against the predicted C-terminal amino acid sequence of its catalytic subunit. We found that this cbb3-type oxidase is synthesized in bacterial cells, where it is located in the membranes. The 48-kDa oxidase subunit (CcoN) is catalytic, while subunits CcoO and CcoP with molecular masses of 29 and 34 kDa, respectively, are cytochromes c. The theoretical pI values of the CcoN, CcoO, and CcoP subunits were determined. It was shown that parts of the CcoO and CcoP subunits exposed to the aqueous phase on the cytoplasmic membrane P-side are enriched with negatively charged amino acid residues, in contrast to the parts of the integral subunit CcoN adjacent to the aqueous phase. Thus, the Na+-pumping cytochrome c oxidase of T. versutus, both in function and in structure, demonstrates adaptation to extremely alkaline conditions.
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Affiliation(s)
- M S Muntyan
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - D A Morozov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Y F Leonova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - T V Ovchinnikova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
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8
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Zabelskii D, Alekseev A, Kovalev K, Rankovic V, Balandin T, Soloviov D, Bratanov D, Savelyeva E, Podolyak E, Volkov D, Vaganova S, Astashkin R, Chizhov I, Yutin N, Rulev M, Popov A, Eria-Oliveira AS, Rokitskaya T, Mager T, Antonenko Y, Rosselli R, Armeev G, Shaitan K, Vivaudou M, Büldt G, Rogachev A, Rodriguez-Valera F, Kirpichnikov M, Moser T, Offenhäusser A, Willbold D, Koonin E, Bamberg E, Gordeliy V. Viral rhodopsins 1 are an unique family of light-gated cation channels. Nat Commun 2020; 11:5707. [PMID: 33177509 PMCID: PMC7659345 DOI: 10.1038/s41467-020-19457-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/07/2020] [Indexed: 11/09/2022] Open
Abstract
Phytoplankton is the base of the marine food chain as well as oxygen and carbon cycles and thus plays a global role in climate and ecology. Nucleocytoplasmic Large DNA Viruses that infect phytoplankton organisms and regulate the phytoplankton dynamics encompass genes of rhodopsins of two distinct families. Here, we present a functional and structural characterization of two proteins of viral rhodopsin group 1, OLPVR1 and VirChR1. Functional analysis of VirChR1 shows that it is a highly selective, Na+/K+-conducting channel and, in contrast to known cation channelrhodopsins, it is impermeable to Ca2+ ions. We show that, upon illumination, VirChR1 is able to drive neural firing. The 1.4 Å resolution structure of OLPVR1 reveals remarkable differences from the known channelrhodopsins and a unique ion-conducting pathway. Thus, viral rhodopsins 1 represent a unique, large group of light-gated channels (viral channelrhodopsins, VirChR1s). In nature, VirChR1s likely mediate phototaxis of algae enhancing the host anabolic processes to support virus reproduction, and therefore, might play a major role in global phytoplankton dynamics. Moreover, VirChR1s have unique potential for optogenetics as they lack possibly noxious Ca2+ permeability. Nucleocytoplasmic Large DNA Viruses (NCLDV) that infect algae encode two distinct families of microbial rhodopsins. Here, the authors characterise two proteins form the viral rhodopsin group 1 OLPVR1 and VirChR1, present the 1.4 Å crystal structure of OLPVR1 and show that viral rhodopsins 1 are light-gated cation channels.
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Affiliation(s)
- Dmitrii Zabelskii
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany.,Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Alexey Alekseev
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany.,Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - Kirill Kovalev
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany.,Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany.,Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Vladan Rankovic
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany.,Auditory Neuroscience and Optogenetics Laboratory, German Primate Center, Göttingen, Germany
| | - Taras Balandin
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Dmytro Soloviov
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Joint Institute for Nuclear Research, Dubna, Russia.,Institute for Safety Problems of Nuclear Power Plants, NAS of Ukraine, Kyiv, 03680, Ukraine
| | - Dmitry Bratanov
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Ekaterina Savelyeva
- Institute of Biological Information Processing (IBI-3: Bioelectronics), Forschungszentrum Jülich GmbH, Jülich, Germany.,Laboratory of Functional Materials and Devices for Nanoelectronics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Center of Shared Research Facilities, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Elizaveta Podolyak
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Dmytro Volkov
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Svetlana Vaganova
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Roman Astashkin
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Igor Chizhov
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Natalia Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Maksim Rulev
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany.,European Synchrotron Radiation Facility, Grenoble, France
| | | | - Ana-Sofia Eria-Oliveira
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Tatiana Rokitskaya
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Thomas Mager
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Yuri Antonenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Riccardo Rosselli
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Spain.,Department of Marine Microbiology and Biogeochemistry, Royal Netherland Institute for Sea Research (NIOZ), and Utrecht University, Den Burg, The Netherlands
| | - Grigoriy Armeev
- Biological Faculty, M. V. Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Konstantin Shaitan
- Biological Faculty, M. V. Lomonosov Moscow State University, Moscow, 119991, Russia.,N. N. Semenov Institute of Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Michel Vivaudou
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France.,Laboratories of Excellence, Ion Channel Science and Therapeutics, 06560, Valbonne, France
| | - Georg Büldt
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Andrey Rogachev
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Joint Institute for Nuclear Research, Dubna, Russia
| | - Francisco Rodriguez-Valera
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Spain
| | - Mikhail Kirpichnikov
- Biological Faculty, M. V. Lomonosov Moscow State University, Moscow, 119991, Russia.,M. M. Shemyakin-Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Tobias Moser
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany.,Auditory Neuroscience and Optogenetics Laboratory, German Primate Center, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Andreas Offenhäusser
- Institute of Biological Information Processing (IBI-3: Bioelectronics), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Dieter Willbold
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany.,Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Eugene Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Ernst Bamberg
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Valentin Gordeliy
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany. .,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany. .,Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia. .,Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany. .,Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France.
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9
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Kwon SK, Jun SH, Kim JF. Omega Rhodopsins: A Versatile Class of Microbial Rhodopsins. J Microbiol Biotechnol 2020; 30:633-641. [PMID: 32482928 PMCID: PMC9728251 DOI: 10.4014/jmb.1912.12010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 03/27/2020] [Indexed: 12/15/2022]
Abstract
Microbial rhodopsins are a superfamily of photoactive membrane proteins with covalently bound retinal cofactor. Isomerization of the retinal chromophore upon absorption of a photon triggers conformational changes of the protein to function as ion pumps or sensors. After the discovery of proteorhodopsin in an uncultivated γ-proteobacterium, light-activated proton pumps have been widely detected among marine bacteria and, together with chlorophyll-based photosynthesis, are considered as an important axis responsible for primary production in the biosphere. Rhodopsins and related proteins show a high level of phylogenetic diversity; we focus on a specific class of bacterial rhodopsins containing the 3 omega motif. This motif forms a stack of three nonconsecutive aromatic amino acids that correlates with the B-C loop orientation, and is shared among the phylogenetically close ion pumps such as the NDQ motif-containing sodium-pumping rhodopsin, the NTQ motif-containing chloride-pumping rhodopsin, and some proton-pumping rhodopsins including xanthorhodopsin. Here, we reviewed the recent research progress on these omega rhodopsins, and speculated on their evolutionary origin of functional diversity..
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Affiliation(s)
- Soon-Kyeong Kwon
- Division of Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Sung-Hoon Jun
- Electron Microscopy Research Center, Korea Basic Science Institute, Cheongju 8119, Republic of Korea
| | - Jihyun F. Kim
- Department of Systems Biology, Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, Seoul 0722, Republic of Korea
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10
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Engineered Passive Potassium Conductance in the KR2 Sodium Pump. Biophys J 2019; 116:1941-1951. [PMID: 31036257 DOI: 10.1016/j.bpj.2019.04.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/31/2019] [Accepted: 04/03/2019] [Indexed: 11/23/2022] Open
Abstract
Light-driven sodium pumps (NaRs) are microbial rhodopsins that utilize light energy to actively transport sodium ions out of the cell. Here, we used targeted mutagenesis and electrophysiological methods in living cells to demonstrate that NaRs can be converted into light-activated cation channels by molecular engineering. Specifically, introduction of the R109Q mutation into the sodium ion pump of Dokdonia eikasta (KR2) results in passive ion conductance, with a high preference for potassium over sodium ions. However, in this mutant, residual active outward pumping of sodium ions competes with passive inward transport of potassium. Channel-like behavior could also be achieved by introduction of other mutations into the KR2 counterion complex, and further, these modifications were transferrable to other NaRs. Combining the R109Q replacement with modifications at position S70 removed the residual sodium pumping and greatly enhanced the channel-like activity. However, passive photocurrents were only observed in leak mutants if the KR2 counterions, D116 and D251, were deprotonated, which was only observed under alkaline conditions. Overall, our results reveal that interactions between R109 and the nearby residues, L75, S70, D116, and D251, prevent passive backflow during ion transport in NaRs.
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11
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Kovalev K, Polovinkin V, Gushchin I, Alekseev A, Shevchenko V, Borshchevskiy V, Astashkin R, Balandin T, Bratanov D, Vaganova S, Popov A, Chupin V, Büldt G, Bamberg E, Gordeliy V. Structure and mechanisms of sodium-pumping KR2 rhodopsin. SCIENCE ADVANCES 2019; 5:eaav2671. [PMID: 30989112 PMCID: PMC6457933 DOI: 10.1126/sciadv.aav2671] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 02/21/2019] [Indexed: 05/20/2023]
Abstract
Rhodopsins are the most universal biological light-energy transducers and abundant phototrophic mechanisms that evolved on Earth and have a remarkable diversity and potential for biotechnological applications. Recently, the first sodium-pumping rhodopsin KR2 from Krokinobacter eikastus was discovered and characterized. However, the existing structures of KR2 are contradictory, and the mechanism of Na+ pumping is not yet understood. Here, we present a structure of the cationic (non H+) light-driven pump at physiological pH in its pentameric form. We also present 13 atomic structures and functional data on the KR2 and its mutants, including potassium pumps, which show that oligomerization of the microbial rhodopsin is obligatory for its biological function. The studies reveal the structure of KR2 at nonphysiological low pH where it acts as a proton pump. The structure provides new insights into the mechanisms of microbial rhodopsins and opens the way to a rational design of novel cation pumps for optogenetics.
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Affiliation(s)
- Kirill Kovalev
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, Grenoble, France
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
- Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - Vitaly Polovinkin
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, Grenoble, France
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany
| | - Ivan Gushchin
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
| | - Alexey Alekseev
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
- Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - Vitaly Shevchenko
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
- Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | | | - Roman Astashkin
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, Grenoble, France
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
| | - Taras Balandin
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany
| | - Dmitry Bratanov
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, Grenoble, France
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany
| | - Svetlana Vaganova
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany
| | - Alexander Popov
- European Synchrotron Radiation Facility, 38043 Grenoble, France
| | - Vladimir Chupin
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
| | - Georg Büldt
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
| | - Ernst Bamberg
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Corresponding author. (V.G.); (E.B.)
| | - Valentin Gordeliy
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, Grenoble, France
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
- Corresponding author. (V.G.); (E.B.)
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12
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Electrical properties, substrate specificity and optogenetic potential of the engineered light-driven sodium pump eKR2. Sci Rep 2018; 8:9316. [PMID: 29915394 PMCID: PMC6006383 DOI: 10.1038/s41598-018-27690-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/24/2018] [Indexed: 01/22/2023] Open
Abstract
A new microbial rhodopsin class that actively transports sodium out of the cell upon illumination was described in 2013. However, poor membrane targeting of the first-identified sodium pump KR2 in mammalian cells has hindered the direct electrical investigation of its transport mechanism and optogenetic application to date. Accordingly, we designed enhanced KR2 (eKR2), which exhibits improved membrane targeting and higher photocurrents in mammalian cells to facilitate molecular characterization and future optogenetic applications. Our selectivity measurements revealed that stationary photocurrents are primarily carried by sodium, whereas protons only play a minor role, if any. Combining laser-induced photocurrent and absorption measurements, we found that spectral changes were not necessarily related to changes in transport activity. Finally, we showed that eKR2 can be expressed in cultured hippocampal mouse neurons and induce reversible inhibition of action potential firing with millisecond precision upon illumination with moderate green-light. Hence, the light-driven sodium pump eKR2 is a reliable inhibitory optogenetic tool applicable to situations in which the proton and chloride gradients should not be altered.
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13
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Tomida S, Ito S, Inoue K, Kandori H. Hydrogen-bonding network at the cytoplasmic region of a light-driven sodium pump rhodopsin KR2. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:684-691. [PMID: 29852143 DOI: 10.1016/j.bbabio.2018.05.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 05/11/2018] [Accepted: 05/24/2018] [Indexed: 01/15/2023]
Abstract
Light-driven sodium-pumping rhodopsins are able to actively transport sodium ions. Structure/function studies of Krokinobacter eikastus rhodopsin 2 (KR2) identified N61 and G263 at the cytoplasmic surface constituting the "Ion-selectivity filter" for sodium ions, while retinal Schiff base acts as the light "Switch and Gate" for transport of sodium ions. Q123 is located between the two regions, and plays an important role for the pump function, which was implicated by functional, spectroscopic, X-ray crystallographic and computational studies. According to the atomic structure of KR2, Q123 is involved in the hydrogen-bonding network at the cytoplasmic region, together with S64, protein-bound waters, and peptide carbonyl of K255 bound to the chromophore. To gain the detailed structural information around Q123, here we compared light-induced difference Fourier-transform infrared (FTIR) spectra at 77 K between the wild-type (WT) and mutant proteins of KR2, such as Q123A, Q123V, and S64A. The obtained spectra were very similar between WT and these mutants, whereas the observed mutation effects enabled us to identify vibrations of the hydrogen-bonding network at the Q123 and S64 region. This is unique for KR2, not for the corresponding mutations in a light-driven proton-pump bacteriorhodopsin (BR). Hydrogen-bonding alteration is absent for the mutants of KR2, suggesting that proper inter-helical connectivity of helices B, C, and G is important for protein structural changes for sodium-pump function, which is controlled by the region around Q123.
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Affiliation(s)
- Sahoko Tomida
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Shota Ito
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Keiichi Inoue
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; Frontier Research Institute for Material Science, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan.
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14
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Mamedov AM, Bertsova YV, Anashkin VA, Mamedov MD, Baykov AA, Bogachev AV. Identification of the key determinant of the transport promiscuity in Na +-translocating rhodopsins. Biochem Biophys Res Commun 2018; 499:600-604. [PMID: 29601812 DOI: 10.1016/j.bbrc.2018.03.196] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 03/26/2018] [Indexed: 02/07/2023]
Abstract
Bacterial Na+-transporting rhodopsins convert solar energy into transmembrane ion potential difference. Typically, they are strictly specific for Na+, but some can additionally transport H+. To determine the structural basis of cation promiscuity in Na+-rhodopsins, we compared their primary structures and found a single position that harbors a cysteine in strictly specific Na+-rhodopsins and a serine in the promiscuous Krokinobacter eikastus Na+-rhodopsin (Kr2). A Cys253Ser variant of the strictly specific Dokdonia sp. PRO95 Na+-rhodopsin (NaR) was indeed found to transport both Na+ and H+ in a light-dependent manner when expressed in retinal-producing Escherichia coli cells. The dual specificity of the NaR variant was confirmed by analysis of its photocycle, which revealed an acceleration of the cation-capture step by comparison with the wild-type NaR in a Na+-deficient medium. The structural basis for the dependence of the Na+/H+ specificity in Na+-rhodopsin on residue 253 remains to be determined.
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Affiliation(s)
- Adalyat M Mamedov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Yulia V Bertsova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Viktor A Anashkin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Mahir D Mamedov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Alexander A Baykov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Alexander V Bogachev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia.
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15
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Kandori H, Inoue K, Tsunoda SP. Light-Driven Sodium-Pumping Rhodopsin: A New Concept of Active Transport. Chem Rev 2018. [DOI: 10.1021/acs.chemrev.7b00548] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
| | - Keiichi Inoue
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Satoshi P. Tsunoda
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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16
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Chen HF, Inoue K, Ono H, Abe-Yoshizumi R, Wada A, Kandori H. Time-resolved FTIR study of light-driven sodium pump rhodopsins. Phys Chem Chem Phys 2018; 20:17694-17704. [DOI: 10.1039/c8cp02599a] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Light-driven sodium ion pump rhodopsin (NaR) is a new functional class of microbial rhodopsin. Present step-scan time-resolved FTIR spectroscopy revealed that the K, L and O intermediates of NaRs contain 13-cis retinal with similar distortion.
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Affiliation(s)
- Hui-Fen Chen
- Department of Medicinal and Applied Chemistry
- Kaohsiung Medical University
- Kaohsiung
- Taiwan
- Department of Life Science and Applied Chemistry
| | - Keiichi Inoue
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
- OptoBioTechnology Research Center
| | - Hikaru Ono
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
| | - Rei Abe-Yoshizumi
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
| | - Akimori Wada
- Laboratory of Organic Chemistry for Life Science
- Kobe Pharmaceutical University
- Kobe 658-8558
- Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
- OptoBioTechnology Research Center
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17
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Abstract
Microbial rhodopsins (MRs) are a large family of photoactive membrane proteins, found in microorganisms belonging to all kingdoms of life, with new members being constantly discovered. Among the MRs are light-driven proton, cation and anion pumps, light-gated cation and anion channels, and various photoreceptors. Due to their abundance and amenability to studies, MRs served as model systems for a great variety of biophysical techniques, and recently found a great application as optogenetic tools. While the basic aspects of microbial rhodopsins functioning have been known for some time, there is still a plenty of unanswered questions. This chapter presents and summarizes the available knowledge, focusing on the functional and structural studies.
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Affiliation(s)
- Ivan Gushchin
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia.
| | - Valentin Gordeliy
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia.
- University of Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France.
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany.
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18
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Schlesinger R. Do It Fast: Immediate Functional Testing of Membrane Pumps Expressed into Nanodiscs. Biophys J 2017; 113:1177-1178. [PMID: 28867509 DOI: 10.1016/j.bpj.2017.08.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 08/14/2017] [Indexed: 12/13/2022] Open
Affiliation(s)
- Ramona Schlesinger
- Department of Physics, Genetic Biophysics, Freie Universität Berlin, Berlin, Germany.
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19
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Tsunoda SP, Prigge M, Abe-Yoshizumi R, Inoue K, Kozaki Y, Ishizuka T, Yawo H, Yizhar O, Kandori H. Functional characterization of sodium-pumping rhodopsins with different pumping properties. PLoS One 2017; 12:e0179232. [PMID: 28749956 PMCID: PMC5531490 DOI: 10.1371/journal.pone.0179232] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/25/2017] [Indexed: 12/25/2022] Open
Abstract
Sodium pumping rhodopsins (NaRs) are a unique member of the microbial-type I rhodopsin family which actively transport Na+ and H+ depending on ionic condition. In this study, we surveyed 12 different NaRs from various sources of eubacteria for their electrophysiological as well as spectroscopic properties. In mammalian cells several of these NaRs exhibited a Na+ based pump photocurrent and four interesting candidates were chosen for further characterization. Voltage dependent photocurrent amplitudes revealed a membrane potential-sensitive turnover rate, indicating the presence of an electrically-charged intermediate(s) in the photocycle reaction. The NaR from Salinarimonas rosea DSM21201 exhibited a red-shifted absorption spectrum, and slower kinetics compared to the first described sodium pump, KR2. Although the ratio of Na+ to H+ ion transport varied among the NaRs we tested, the NaRs from Flagellimonas sp_DIK and Nonlabens sp_YIK_SED-11 showed significantly higher Na+ selectivity when compared to KR2. All four further investigated NaRs showed a functional expression in dissociated hippocampal neuron culture and hyperpolarizing activity upon light-stimulation. Additionally, all four NaRs allowed optical inhibition of electrically-evoked neuronal spiking. Although efficiency of silencing was 3–5 times lower than silencing with the enhanced version of the proton pump AR3 from Halorubrum sodomense, our data outlines a new approach for hyperpolarization of excitable cells without affecting the intracellular and extracellular proton environment.
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Affiliation(s)
- Satoshi P. Tsunoda
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Nagoya, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Japan
| | - Matthias Prigge
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Rei Abe-Yoshizumi
- Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Nagoya, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Japan
| | - Keiichi Inoue
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Nagoya, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Japan
- Department of Frontier Materials, Nagoya Institute of Technology, Nagoya, Japan
| | - Yuko Kozaki
- Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Nagoya, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Japan
| | - Toru Ishizuka
- Department of Developmental Biology and Neurosciences, Tohoku University Graduate School of Life Science, Sendai, Japan
| | - Hiromu Yawo
- Department of Developmental Biology and Neurosciences, Tohoku University Graduate School of Life Science, Sendai, Japan
| | - Ofer Yizhar
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Hideki Kandori
- Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Nagoya, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Japan
- * E-mail:
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20
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Govorunova EG, Sineshchekov OA, Li H, Spudich JL. Microbial Rhodopsins: Diversity, Mechanisms, and Optogenetic Applications. Annu Rev Biochem 2017; 86:845-872. [PMID: 28301742 PMCID: PMC5747503 DOI: 10.1146/annurev-biochem-101910-144233] [Citation(s) in RCA: 236] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Microbial rhodopsins are a family of photoactive retinylidene proteins widespread throughout the microbial world. They are notable for their diversity of function, using variations of a shared seven-transmembrane helix design and similar photochemical reactions to carry out distinctly different light-driven energy and sensory transduction processes. Their study has contributed to our understanding of how evolution modifies protein scaffolds to create new protein chemistry, and their use as tools to control membrane potential with light is fundamental to optogenetics for research and clinical applications. We review the currently known functions and present more in-depth assessment of three functionally and structurally distinct types discovered over the past two years: (a) anion channelrhodopsins (ACRs) from cryptophyte algae, which enable efficient optogenetic neural suppression; (b) cryptophyte cation channelrhodopsins (CCRs), structurally distinct from the green algae CCRs used extensively for neural activation and from cryptophyte ACRs; and
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Affiliation(s)
- Elena G Govorunova
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas 77030; , , ,
| | - Oleg A Sineshchekov
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas 77030; , , ,
| | - Hai Li
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas 77030; , , ,
| | - John L Spudich
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas 77030; , , ,
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21
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Zhao H, Ma B, Ji L, Li L, Wang H, Chen D. Coexistence of light-driven Na + and H + transport in a microbial rhodopsin from Nonlabens dokdonensis. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2017; 172:70-76. [PMID: 28527429 DOI: 10.1016/j.jphotobiol.2017.05.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 04/06/2017] [Accepted: 05/04/2017] [Indexed: 02/04/2023]
Abstract
Ion pumping microbial rhodopsins are photochemically active membrane proteins, converting light energy into ion-motive-force for ATP synthesis. Nonlabens dokdonensis rhodopsin 2 (NdR2), was recently identified as a light-driven Na+ pump. However, few functional studies on NdR2 have been conducted to elucidate its mechanism of ion transport. By reconstituting NdR2 into liposomes, we proved that NdR2 functions as a light-driven Na+/H+ pump. As Na+ concentration increased, the dominant H+ pump activity switched to the Na+ pump activity at neutral pH. The inversion of pH change by the addition of CCCP at low Na+ further suggested that the transport of Na+ and H+ should coexist in NdR2. By increasing H+ concentration, the affinity for Na+ lowered, which was indicated by an increase in KM from ~31mM at pH ~7.5, to ~74mM at pH ~6.5. These results demonstrated that Na+ transport competed with H+ transport in NdR2, which was confirmed by the dominant H+ pump activity at pH ~5.7. Kinetic experiments using pyranine uncovered a transient H+ uptake, followed by an H+ release at the millisecond time scale in both Na+ and K+ solutions. Therefore, these NdR2 results may provide functional and kinetic insights into the ion transport mechanism in light-driven Na+ pumps.
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Affiliation(s)
- Hongshen Zhao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baofu Ma
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liangliang Ji
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Longjie Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huanhuan Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Deliang Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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22
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From Gene to Function: Cell-Free Electrophysiological and Optical Analysis of Ion Pumps in Nanodiscs. Biophys J 2017; 113:1331-1341. [PMID: 28450130 DOI: 10.1016/j.bpj.2017.03.026] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 03/14/2017] [Accepted: 03/27/2017] [Indexed: 12/15/2022] Open
Abstract
Nanodiscs that hold a lipid bilayer surrounded by a boundary of scaffold proteins have emerged as a powerful tool for membrane protein solubilization and analysis. By combining nanodiscs and cell-free expression technologies, even completely detergent-free membrane protein characterization protocols can be designed. Nanodiscs are compatible with various techniques, and due to their bilayer environment and increased stability, they are often superior to detergent micelles or liposomes for membrane protein solubilization. However, transport assays in nanodiscs have not been conducted so far, due to limitations of the two-dimensional nature of nanodisc membranes that offers no compartmentalization. Here, we study Krokinobacter eikastus rhodopsin-2 (KR2), a microbial light-driven sodium or proton pump, with noncovalent mass-spectrometric, electrophysiological, and flash photolysis measurements after its cotranslational insertion into nanodiscs. We demonstrate the feasibility of adsorbing nanodiscs containing KR2 to an artificial bilayer. This allows us to record light-induced capacitive currents that reflect KR2's ion transport activity. The solid-supported membrane assay with nanodisc samples provides reliable control over the ionic condition and information of the relative ion activity of this promiscuous pump. Our strategy is complemented with flash photolysis data, where the lifetimes of different photointermediates were determined at different ionic conditions. The advantage of using identical samples to three complementary approaches allows for a comprehensive comparability. The cell-free synthesis in combination with nanodiscs provides a defined hydrophobic lipid environment minimizing the detergent dependence often seen in assays with membrane proteins. KR2 is a promising tool for optogenetics, thus directed engineering to modify ion selectivity can be highly beneficial. Our approach, using the fast generation of functional ion pumps incorporated into nanodiscs and their subsequent analysis by several biophysical techniques, can serve as a versatile screening and engineering platform. This may open new avenues for the study of ion pumps and similar electrogenic targets.
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23
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Kajimoto K, Kikukawa T, Nakashima H, Yamaryo H, Saito Y, Fujisawa T, Demura M, Unno M. Transient Resonance Raman Spectroscopy of a Light-Driven Sodium-Ion-Pump Rhodopsin from Indibacter alkaliphilus. J Phys Chem B 2017; 121:4431-4437. [DOI: 10.1021/acs.jpcb.7b02421] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kousuke Kajimoto
- Department
of Chemistry and Applied Chemistry, Graduate School of Science and
Engineering, Saga University, Saga 840-8502, Japan
| | - Takashi Kikukawa
- Faculty
of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
- Global
Station for Soft Matter, Global Institution for Collaborative Research
and Education, Hokkaido University, Sapporo 060-0810, Japan
| | - Hiroki Nakashima
- Department
of Chemistry and Applied Chemistry, Graduate School of Science and
Engineering, Saga University, Saga 840-8502, Japan
| | - Haruki Yamaryo
- Department
of Chemistry and Applied Chemistry, Graduate School of Science and
Engineering, Saga University, Saga 840-8502, Japan
| | - Yuta Saito
- Faculty
of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Tomotsumi Fujisawa
- Department
of Chemistry and Applied Chemistry, Graduate School of Science and
Engineering, Saga University, Saga 840-8502, Japan
| | - Makoto Demura
- Faculty
of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
- Global
Station for Soft Matter, Global Institution for Collaborative Research
and Education, Hokkaido University, Sapporo 060-0810, Japan
| | - Masashi Unno
- Department
of Chemistry and Applied Chemistry, Graduate School of Science and
Engineering, Saga University, Saga 840-8502, Japan
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24
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Li H, Sineshchekov OA, Wu G, Spudich JL. In Vitro Activity of a Purified Natural Anion Channelrhodopsin. J Biol Chem 2016; 291:25319-25325. [PMID: 27789708 DOI: 10.1074/jbc.c116.760041] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 10/26/2016] [Indexed: 12/29/2022] Open
Abstract
Natural anion channelrhodopsins (ACRs) recently discovered in cryptophyte algae are the most active rhodopsin channels known. They are of interest both because of their unique natural function of light-gated chloride conductance and because of their unprecedented efficiency of membrane hyperpolarization for optogenetic neuron silencing. Light-induced currents of ACRs have been studied in HEK cells and neurons, but light-gated channel conductance of ACRs in vitro has not been demonstrated. Here we report light-induced chloride channel activity of a purified ACR protein reconstituted in large unilamellar vesicles (LUVs). EPR measurements establish that the channels are inserted uniformly "inside-out" with their cytoplasmic surface facing the medium of the LUV suspension. We show by time-resolved flash spectroscopy that the photochemical reaction cycle of a functional purified ACR from Guillardia theta (GtACR1) in LUVs exhibits similar spectral shifts, indicating similar photocycle intermediates as GtACR1 in detergent micelles. Furthermore, the photocycle rate is dependent on electric potential generated by chloride gradients in the LUVs in the same manner as in voltage-clamped animal cells. We confirm with this system that, in contrast to cation-conducting channelrhodopsins, opening of the channel occurs prior to deprotonation of the Schiff base. However, the photointermediate transitions in the LUVs exhibit faster kinetics. The ACR-incorporated LUVs provide a purified defined system amenable to EPR, optical and vibrational spectroscopy, and fluorescence resonance energy transfer measurements of structural changes of ACRs with the molecules in a demonstrably functional state.
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Affiliation(s)
- Hai Li
- From the Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center, McGovern Medical School, Houston, Texas 77030 and
| | - Oleg A Sineshchekov
- From the Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center, McGovern Medical School, Houston, Texas 77030 and
| | - Gang Wu
- From the Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center, McGovern Medical School, Houston, Texas 77030 and.,the Department of Internal Medicine, University of Texas Health Science Center, McGovern Medical School, Houston, Texas 77030
| | - John L Spudich
- From the Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center, McGovern Medical School, Houston, Texas 77030 and
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Marine Bacterial and Archaeal Ion-Pumping Rhodopsins: Genetic Diversity, Physiology, and Ecology. Microbiol Mol Biol Rev 2016; 80:929-54. [PMID: 27630250 DOI: 10.1128/mmbr.00003-16] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The recognition of a new family of rhodopsins in marine planktonic bacteria, proton-pumping proteorhodopsin, expanded the known phylogenetic range, environmental distribution, and sequence diversity of retinylidene photoproteins. At the time of this discovery, microbial ion-pumping rhodopsins were known solely in haloarchaea inhabiting extreme hypersaline environments. Shortly thereafter, proteorhodopsins and other light-activated energy-generating rhodopsins were recognized to be widespread among marine bacteria. The ubiquity of marine rhodopsin photosystems now challenges prior understanding of the nature and contributions of "heterotrophic" bacteria to biogeochemical carbon cycling and energy fluxes. Subsequent investigations have focused on the biophysics and biochemistry of these novel microbial rhodopsins, their distribution across the tree of life, evolutionary trajectories, and functional expression in nature. Later discoveries included the identification of proteorhodopsin genes in all three domains of life, the spectral tuning of rhodopsin variants to wavelengths prevailing in the sea, variable light-activated ion-pumping specificities among bacterial rhodopsin variants, and the widespread lateral gene transfer of biosynthetic genes for bacterial rhodopsins and their associated photopigments. Heterologous expression experiments with marine rhodopsin genes (and associated retinal chromophore genes) provided early evidence that light energy harvested by rhodopsins could be harnessed to provide biochemical energy. Importantly, some studies with native marine bacteria show that rhodopsin-containing bacteria use light to enhance growth or promote survival during starvation. We infer from the distribution of rhodopsin genes in diverse genomic contexts that different marine bacteria probably use rhodopsins to support light-dependent fitness strategies somewhere between these two extremes.
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Kato Y, Inoue K, Kandori H. Kinetic Analysis of H(+)-Na(+) Selectivity in a Light-Driven Na(+)-Pumping Rhodopsin. J Phys Chem Lett 2015; 6:5111-5115. [PMID: 26673197 DOI: 10.1021/acs.jpclett.5b02371] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Krokinobacter eikastus rhodopsin 2 (KR2) is a recently identified light-driven Na(+) pump from a marine bacterium. KR2 pumps Na(+) in NaCl solution but pumps H(+) in the absence of Na(+) and Li(+). The Na(+) transport mechanism in KR2 has been extensively studied, whereas understanding of the H(+) transport mechanism is very limited. Here we studied ion uptake mechanisms and H(+)-Na(+) selectivity using flash photolysis. The results show that decay of the blue-shifted M intermediate is dependent on both [Na(+)] and [H(+)], indicating that KR2 competitively uptakes Na(+) or H(+) upon M decay. Comprehensive concentration dependence of Na(+) and H(+) revealed that the rate constant of H(+) uptake (kH) was much larger than that of Na(+) uptake (kNa) with a ratio (kH/kNa) of >10(3). Therefore, KR2 pumps only H(+) when Na(+) and H(+) concentrations are similar. On the contrary, KR2 pumps Na(+) exclusively under physiological conditions in which [Na(+)] is much greater than [H(+)].
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Affiliation(s)
- Yoshitaka Kato
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Keiichi Inoue
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
- PRESTO, Japan Science and Technology Agency (JST) , 4-1-8 Honcho Kawaguchi, Saitama, 332-0012, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
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