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Goncharuk MV, Vasileva EV, Ananiev EA, Gorokhovatsky AY, Bocharov EV, Mineev KS, Goncharuk SA. Facade-Based Bicelles as a New Tool for Production of Active Membrane Proteins in a Cell-Free System. Int J Mol Sci 2023; 24:14864. [PMID: 37834312 PMCID: PMC10573531 DOI: 10.3390/ijms241914864] [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: 08/26/2023] [Revised: 09/18/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
Integral membrane proteins are important components of a cell. Their structural and functional studies require production of milligram amounts of proteins, which nowadays is not a routine process. Cell-free protein synthesis is a prospective approach to resolve this task. However, there are few known membrane mimetics that can be used to synthesize active membrane proteins in high amounts. Here, we present the application of commercially available "Facade" detergents for the production of active rhodopsin. We show that the yield of active protein in lipid bicelles containing Facade-EM, Facade-TEM, and Facade-EPC is several times higher than in the case of conventional bicelles with CHAPS and DHPC and is comparable to the yield in the presence of lipid-protein nanodiscs. Moreover, the effects of the lipid-to-detergent ratio, concentration of detergent in the feeding mixture, and lipid composition of the bicelles on the total, soluble, and active protein yields are discussed. We show that Facade-based bicelles represent a prospective membrane mimetic, available for the production of membrane proteins in a cell-free system.
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Affiliation(s)
- Marina V. Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
| | - Ekaterina V. Vasileva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
| | - Egor A. Ananiev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
| | - Andrey Y. Gorokhovatsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
| | - Eduard V. Bocharov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Konstantin S. Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
| | - Sergey A. Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
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2
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Petrovskaya LE, Siletsky SA, Mamedov MD, Lukashev EP, Balashov SP, Dolgikh DA, Kirpichnikov MP. Features of the Mechanism of Proton Transport in ESR, Retinal Protein from Exiguobacterium sibiricum. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1544-1554. [PMID: 38105023 DOI: 10.1134/s0006297923100103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 12/19/2023]
Abstract
Retinal-containing light-sensitive proteins - rhodopsins - are found in many microorganisms. Interest in them is largely explained by their role in light energy storage and photoregulation in microorganisms, as well as the prospects for their use in optogenetics to control neuronal activity, including treatment of various diseases. One of the representatives of microbial rhodopsins is ESR, the retinal protein of Exiguobacterium sibiricum. What distinguishes ESR from homologous proteins is the presence of a lysine residue (Lys96) as a proton donor for the Schiff base. This feature, along with the hydrogen bond of the proton acceptor Asp85 with the His57 residue, determines functional characteristics of ESR as a proton pump. This review examines the results of ESR studies conducted using various methods, including direct electrometry. Comparison of the obtained data with the results of structural studies and with other retinal proteins allows us to draw conclusions about the mechanisms of transport of hydrogen ions in ESR and similar retinal proteins.
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Affiliation(s)
- Lada E Petrovskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - Sergei A Siletsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Mahir D Mamedov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Eugene P Lukashev
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Sergei P Balashov
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697
| | - Dmitry A Dolgikh
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Mikhail P Kirpichnikov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
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3
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Belikov NE, Petrovskaya LE, Kryukova EA, Dolgikh DA, Lukashev EP, Lukin AY, Demina OV, Varfolomeev SD, Chupin VV, Khodonov AA. Interaction of the Fluorophenyl Analog of Retinal with Proteorhodopsin from Exiguobacterium sibiricum. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1068162022060073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Abstract—
We have developed an alternative method for the synthesis of an analog of natural retinal, which contains the p-fluorophenyl fragment instead of the trimethylcyclohexene ring. The proposed scheme for the synthesis of the target all-E-isomer of the target retinoid consists of using C5-phosphonate that contains the terminal nitrile group under Horner–Emmons reaction conditions. It has been shown that this scheme is more efficient and provides a higher total yield of the target product than the previously described variant. The procedure has been developed for the preparation of an analog of microbial proteorhodopsin ESRh from Exiguobacterium sibiricum, which contains a modified chromophore. It has been found that, as in the case of bacterioopsin from Halobacterium salinarum, the replacement of the trimethylcyclohexene ring in the natural chromophore by the p-fluorophenyl fragment does not prevent the formation of the artificial pigment F-Phe-ESRh from proteorhodopsin ESRh, which preserves the cycle of photochemical reactions. Certain differences have been found between the properties of native recombinant ESRh and its analog F-Phe-ESRh including a shift in the absorption maximum to the short-wavelength region, the formation of M intermediate at lower pH values, the presence of “long-lived M,” and a general slowdown in the photocycle. The reduced stability of the resulting proteorhodopsin analog F-Phe-ESRh to prolonged exposure to visible light has been also demonstrated.
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Gordeliy V, Kovalev K, Bamberg E, Rodriguez-Valera F, Zinovev E, Zabelskii D, Alekseev A, Rosselli R, Gushchin I, Okhrimenko I. Microbial Rhodopsins. Methods Mol Biol 2022; 2501:1-52. [PMID: 35857221 DOI: 10.1007/978-1-0716-2329-9_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The first microbial rhodopsin, a light-driven proton pump bacteriorhodopsin from Halobacterium salinarum (HsBR), was discovered in 1971. Since then, this seven-α-helical protein, comprising a retinal molecule as a cofactor, became a major driver of groundbreaking developments in membrane protein research. However, until 1999 only a few archaeal rhodopsins, acting as light-driven proton and chloride pumps and also photosensors, were known. A new microbial rhodopsin era started in 2000 when the first bacterial rhodopsin, a proton pump, was discovered. Later it became clear that there are unexpectedly many rhodopsins, and they are present in all the domains of life and even in viruses. It turned out that they execute such a diversity of functions while being "nearly the same." The incredible evolution of the research area of rhodopsins and the scientific and technological potential of the proteins is described in the review with a focus on their function-structure relationships.
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Affiliation(s)
- Valentin Gordeliy
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France.
| | - Kirill Kovalev
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
- 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 (National Research University), Dolgoprudny, Russia
- Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - Ernst Bamberg
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Francisco Rodriguez-Valera
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Egor Zinovev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Dmitrii Zabelskii
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, 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
| | - Riccardo Rosselli
- Departamento de Fisiología, Genetica y Microbiología. Facultad de Ciencias, Universidad de Alicante, Alicante, Spain
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Ivan Okhrimenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
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Sasaki S, Tamogami J, Nishiya K, Demura M, Kikukawa T. Replaceability of Schiff base proton donors in light-driven proton pump rhodopsins. J Biol Chem 2021; 297:101013. [PMID: 34329681 PMCID: PMC8387761 DOI: 10.1016/j.jbc.2021.101013] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
Many H+-pump rhodopsins conserve “H+ donor” residues in cytoplasmic (CP) half channels to quickly transport H+ from the CP medium to Schiff bases at the center of these proteins. For conventional H+ pumps, the donors are conserved as Asp or Glu but are replaced by Lys in the minority, such as Exiguobacterium sibiricum rhodopsin (ESR). In dark states, carboxyl donors are protonated, whereas the Lys donor is deprotonated. As a result, carboxyl donors first donate H+ to the Schiff bases and then capture the other H+ from the medium, whereas the Lys donor first captures H+ from the medium and then donates it to the Schiff base. Thus, carboxyl and Lys-type H+ pumps seem to have different mechanisms, which are probably optimized for their respective H+-transfer reactions. Here, we examined these differences via replacement of donor residues. For Asp-type deltarhodopsin (DR), the embedded Lys residue distorted the protein conformation and did not act as the H+ donor. In contrast, for Glu-type proteorhodopsin (PR) and ESR, the embedded residues functioned well as H+ donors. These differences were further examined by focusing on the activation volumes during the H+-transfer reactions. The results revealed essential differences between archaeal H+ pump (DR) and eubacterial H+ pumps PR and ESR. Archaeal DR requires significant hydration of the CP channel for the H+-transfer reactions; however, eubacterial PR and ESR require the swing-like motion of the donor residue rather than hydration. Given this common mechanism, donor residues might be replaceable between eubacterial PR and ESR.
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Affiliation(s)
- Syogo Sasaki
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Jun Tamogami
- College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime, Japan.
| | - Koki Nishiya
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Makoto Demura
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan.
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6
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Pereira O, Hochart C, Boeuf D, Auguet JC, Debroas D, Galand PE. Seasonality of archaeal proteorhodopsin and associated Marine Group IIb ecotypes (Ca. Poseidoniales) in the North Western Mediterranean Sea. THE ISME JOURNAL 2021; 15:1302-1316. [PMID: 33288859 PMCID: PMC8115670 DOI: 10.1038/s41396-020-00851-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 11/09/2020] [Accepted: 11/18/2020] [Indexed: 01/04/2023]
Abstract
The Archaea Marine Group II (MGII) is widespread in the world's ocean where it plays an important role in the carbon cycle. Despite recent discoveries on the group's metabolisms, the ecology of this newly proposed order (Candidatus Poseidoniales) remains poorly understood. Here we used a combination of time-series metagenome-assembled genomes (MAGs) and high-frequency 16S rRNA data from the NW Mediterranean Sea to test if the taxonomic diversity within the MGIIb family (Candidatus Thalassarchaeaceae) reflects the presence of different ecotypes. The MAGs' seasonality revealed a MGIIb family composed of different subclades that have distinct lifestyles and physiologies. The vitamin metabolisms were notably different between ecotypes with, in some, a possible link to sunlight's energy. Diverse archaeal proteorhodopsin variants, with unusual signature in key amino acid residues, had distinct seasonal patterns corresponding to changing day length. In addition, we show that in summer, archaea, as opposed to bacteria, disappeared completely from surface waters. Our results shed light on the diversity and the distribution of the euryarchaeotal proteorhodopsin, and highlight that MGIIb is a diverse ecological group. The work shows that time-series based studies of the taxonomy, seasonality, and metabolisms of marine prokaryotes is critical to uncover their diverse role in the ocean.
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Affiliation(s)
- Olivier Pereira
- Sorbonne Universités, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique, Banyuls sur Mer, France
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China
| | - Corentin Hochart
- Sorbonne Universités, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique, Banyuls sur Mer, France
| | - Dominique Boeuf
- Daniel K. Inouye Center for Microbial Oceanography, Research and Education, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, United States, Honolulu, HI, 96822, USA
| | - Jean Christophe Auguet
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Montpellier, France, Montpellier, France
| | - Didier Debroas
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Genome et Environnement, 63000, Clermont-Ferrand, France
| | - Pierre E Galand
- Sorbonne Universités, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique, Banyuls sur Mer, France.
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7
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Remeeva A, Nazarenko VV, Kovalev K, Goncharov IM, Yudenko A, Astashkin R, Gordeliy V, Gushchin I. Insights into the mechanisms of light-oxygen-voltage domain color tuning from a set of high-resolution X-ray structures. Proteins 2021; 89:1005-1016. [PMID: 33774867 DOI: 10.1002/prot.26078] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/16/2021] [Indexed: 01/01/2023]
Abstract
Light-oxygen-voltage (LOV) domains are widespread photosensory modules that can be used in fluorescence microscopy, optogenetics and controlled production of reactive oxygen species. All of the currently known LOV domains have absorption maxima in the range of ~440 to ~450 nm, and it is not clear whether they can be shifted significantly using mutations. Here, we have generated a panel of LOV domain variants by mutating the key chromophore-proximal glutamine aminoacid of a thermostable flavin based fluorescent protein CagFbFP (Gln148) to asparagine, aspartate, glutamate, histidine, lysine and arginine. Absorption spectra of all of the mutants are blue-shifted, with the maximal shift of 8 nm observed for the Q148H variant. While CagFbFP and its Q148N/D/E variants are not sensitive to pH, Q148H/K/R reveal a moderate red shift induced byacidic pH. To gain further insight, we determined high resolution crystal structures of all of the mutants studied at the resolutions from 1.07 Å for Q148D to 1.63 Å for Q148R. Whereas in some of the variants, the aminoacid 148 remains in the vicinity of the flavin, in Q148K, Q148R and partially Q148D, the C-terminus of the protein unlatches and the side chain of the residue 148 is reoriented away from the chromophore. Our results explain the absence of color shifts from replacing Gln148 with charged aminoacids and pave the way for rational design of color-shifted flavin based fluorescent proteins.
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Affiliation(s)
- Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Vera V Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Kirill Kovalev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Institute of Crystallography, RWTH Aachen University, Aachen, Germany
| | - Ivan M Goncharov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Anna Yudenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - 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 J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, Grenoble, France
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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8
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Smitienko OA, Feldman TB, Petrovskaya LE, Nekrasova OV, Yakovleva MA, Shelaev IV, Gostev FE, Cherepanov DA, Kolchugina IB, Dolgikh DA, Nadtochenko VA, Kirpichnikov MP, Ostrovsky MA. Comparative Femtosecond Spectroscopy of Primary Photoreactions of Exiguobacterium sibiricum Rhodopsin and Halobacterium salinarum Bacteriorhodopsin. J Phys Chem B 2021; 125:995-1008. [PMID: 33475375 DOI: 10.1021/acs.jpcb.0c07763] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The primary stages of the Exiguobacterium sibiricum rhodopsin (ESR) photocycle were investigated by femtosecond absorption laser spectroscopy in the spectral range of 400-900 nm with a time resolution of 25 fs. The dynamics of the ESR photoreaction were compared with the reactions of bacteriorhodopsin (bR) in purple membranes (bRPM) and in recombinant form (bRrec). The primary intermediates of the ESR photocycle were similar to intermediates I, J, and K in bacteriorhodopsin photoconversion. The CONTIN program was applied to analyze the characteristic times of the observed processes and to clarify the reaction scheme. A similar photoreaction pattern was observed for all studied retinal proteins, including two consecutive dynamic Stokes shift phases lasting ∼0.05 and ∼0.15 ps. The excited state decays through a femtosecond reactive pathway, leading to retinal isomerization and formation of product J, and a picosecond nonreactive pathway that leads only to the initial state. Retinal photoisomerization in ESR takes 0.69 ps, compared with 0.48 ps in bRPM and 0.74 ps in bRrec. The nonreactive excited state decay takes 5 ps in ESR and ∼3 ps in bR. We discuss the similarity of the primary reactions of ESR and other retinal proteins.
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Affiliation(s)
| | - Tatiana B Feldman
- Emanuel Institute of Biochemical Physics, Moscow 119334, Russia.,Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Lada E Petrovskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Oksana V Nekrasova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | | | - Ivan V Shelaev
- Semenov Federal Research Center of Chemical Physics, Moscow 119991, Russia
| | - Fedor E Gostev
- Semenov Federal Research Center of Chemical Physics, Moscow 119991, Russia
| | | | - Irina B Kolchugina
- Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Dmitry A Dolgikh
- Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Victor A Nadtochenko
- Semenov Federal Research Center of Chemical Physics, Moscow 119991, Russia.,Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Mikhail P Kirpichnikov
- Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Mikhail A Ostrovsky
- Emanuel Institute of Biochemical Physics, Moscow 119334, Russia.,Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
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9
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Inoue K. Diversity, Mechanism, and Optogenetic Application of Light-Driven Ion Pump Rhodopsins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1293:89-126. [PMID: 33398809 DOI: 10.1007/978-981-15-8763-4_6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ion-transporting microbial rhodopsins are widely used as major molecular tools in optogenetics. They are categorized into light-gated ion channels and light-driven ion pumps. While the former passively transport various types of cations and anions in a light-dependent manner, light-driven ion pumps actively transport specific ions, such as H+, Na+, Cl-, against electrophysiological potential by using light energy. Since the ion transport by these pumps induces hyperpolarization of membrane potential and inhibit neural firing, light-driven ion-pumping rhodopsins are mostly applied as inhibitory optogenetics tools. Recent progress in genome and metagenome sequencing identified more than several thousands of ion-pumping rhodopsins from a wide variety of microbes, and functional characterization studies has been revealing many new types of light-driven ion pumps one after another. Since light-gated channels were reviewed in other chapters in this book, here the rapid progress in functional characterization, molecular mechanism study, and optogenetic application of ion-pumping rhodopsins were reviewed.
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Affiliation(s)
- Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, Chiba, Japan.
- PRESTO, Japan Science and Technology Agency, Saitama, Japan.
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10
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The effect of the chromophoric group modification on the optical properties of retinal proteins. MENDELEEV COMMUNICATIONS 2018. [DOI: 10.1016/j.mencom.2018.07.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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11
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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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12
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Electrogenic steps of light-driven proton transport in ESR, a retinal protein from Exiguobacterium sibiricum. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1741-1750. [DOI: 10.1016/j.bbabio.2016.08.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/06/2016] [Accepted: 08/11/2016] [Indexed: 02/01/2023]
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Nakamura S, Kikukawa T, Tamogami J, Kamiya M, Aizawa T, Hahn MW, Ihara K, Kamo N, Demura M. Photochemical characterization of actinorhodopsin and its functional existence in the natural host. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1900-1908. [PMID: 27659506 DOI: 10.1016/j.bbabio.2016.09.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 09/13/2016] [Accepted: 09/17/2016] [Indexed: 11/29/2022]
Abstract
Actinorhodopsin (ActR) is a light-driven outward H+ pump. Although the genes of ActRs are widely spread among freshwater bacterioplankton, there are no prior data on their functional expression in native cell membranes. Here, we demonstrate ActR phototrophy in the native actinobacterium. Genome analysis showed that Candidatus Rhodoluna planktonica, a freshwater actinobacterium, encodes one microbial rhodopsin (RpActR) belonging to the ActR family. Reflecting the functional expression of RpActR, illumination induced the acidification of the actinobacterial cell suspension and then elevated the ATP content inside the cells. The photochemistry of RpActR was also examined using heterologously expressed RpActR in Escherichia coli membranes. The purified RpActR showed λmax at 534nm and underwent a photocycle characterized by the very fast formation of M intermediate. The subsequent intermediate, named P620, could be assigned to the O intermediate in other H+ pumps. In contrast to conventional O, the accumulation of P620 remains prominent, even at high pH. Flash-induced absorbance changes suggested that there exists only one kind of photocycle at any pH. However, above pH7, RpActR shows heterogeneity in the H+ transfer sequences: one first captures H+ and then releases it during the formation and decay of P620, while the other first releases H+ prior to H+ uptake during P620 formation.
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Affiliation(s)
- Shintaro Nakamura
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan.
| | - Jun Tamogami
- College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Japan
| | - Masakatsu Kamiya
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Tomoyasu Aizawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Martin W Hahn
- Research Institute for Limnology, University of Innsbruck, Mondsee, Austria
| | - Kunio Ihara
- Center for Gene Research, Nagoya University, Nagoya, Japan
| | - Naoki Kamo
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Makoto Demura
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
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