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Podoliak E, Lamm GHU, Marin E, Schellbach AV, Fedotov DA, Stetsenko A, Asido M, Maliar N, Bourenkov G, Balandin T, Baeken C, Astashkin R, Schneider TR, Bateman A, Wachtveitl J, Schapiro I, Busskamp V, Guskov A, Gordeliy V, Alekseev A, Kovalev K. A subgroup of light-driven sodium pumps with an additional Schiff base counterion. Nat Commun 2024; 15:3119. [PMID: 38600129 PMCID: PMC11006869 DOI: 10.1038/s41467-024-47469-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 04/01/2024] [Indexed: 04/12/2024] Open
Abstract
Light-driven sodium pumps (NaRs) are unique ion-transporting microbial rhodopsins. The major group of NaRs is characterized by an NDQ motif and has two aspartic acid residues in the central region essential for sodium transport. Here we identify a subgroup of the NDQ rhodopsins bearing an additional glutamic acid residue in the close vicinity to the retinal Schiff base. We thoroughly characterize a member of this subgroup, namely the protein ErNaR from Erythrobacter sp. HL-111 and show that the additional glutamic acid results in almost complete loss of pH sensitivity for sodium-pumping activity, which is in contrast to previously studied NaRs. ErNaR is capable of transporting sodium efficiently even at acidic pH levels. X-ray crystallography and single particle cryo-electron microscopy reveal that the additional glutamic acid residue mediates the connection between the other two Schiff base counterions and strongly interacts with the aspartic acid of the characteristic NDQ motif. Hence, it reduces its pKa. Our findings shed light on a subgroup of NaRs and might serve as a basis for their rational optimization for optogenetics.
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Affiliation(s)
- E Podoliak
- Department of Ophthalmology, University Hospital Bonn, Medical Faculty, Bonn, Germany
| | - G H U Lamm
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - E Marin
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG, Groningen, the Netherlands
| | - A V Schellbach
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- School of Chemistry, University of Edinburgh, Edinburgh, EH9 3FJ, UK
| | - D A Fedotov
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - A Stetsenko
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG, Groningen, the Netherlands
| | - M Asido
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - N Maliar
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - G Bourenkov
- European Molecular Biology Laboratory, EMBL Hamburg c/o DESY, 22607, Hamburg, Germany
| | - T Balandin
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - C Baeken
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - R Astashkin
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000, Grenoble, France
| | - T R Schneider
- European Molecular Biology Laboratory, EMBL Hamburg c/o DESY, 22607, Hamburg, Germany
| | - A Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - J Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - I Schapiro
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - V Busskamp
- Department of Ophthalmology, University Hospital Bonn, Medical Faculty, Bonn, Germany
| | - A Guskov
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG, Groningen, the Netherlands
| | - V Gordeliy
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000, Grenoble, France
| | - A Alekseev
- University Medical Center Göttingen, Institute for Auditory Neuroscience and InnerEarLab, Robert-Koch-Str. 40, 37075, Göttingen, Germany.
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.
| | - K Kovalev
- European Molecular Biology Laboratory, EMBL Hamburg c/o DESY, 22607, Hamburg, Germany.
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Maliar N, Okhrimenko IS, Petrovskaya LE, Alekseev AA, Kovalev KV, Soloviov DV, Popov PA, Rokitskaya TI, Antonenko YN, Zabelskii DV, Dolgikh DA, Kirpichnikov MP, Gordeliy VI. Erratum to: Novel pH-Sensitive Microbial Rhodopsin from Sphingomonas paucimobilis. DOKL BIOCHEM BIOPHYS 2021; 497:158. [PMID: 33895933 DOI: 10.1134/s1607672921020198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 01/28/2021] [Accepted: 01/28/2021] [Indexed: 11/23/2022]
Affiliation(s)
- N Maliar
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow oblast, Russia
| | - I S Okhrimenko
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow oblast, Russia
| | - L E Petrovskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - A A Alekseev
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow oblast, Russia.,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.,Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - K V Kovalev
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow oblast, Russia.,Institut de Biologie Structurale (IBS), University 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.,Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - D V Soloviov
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow oblast, Russia.,Institute for Safety Problems of Nuclear Power Plants, National Academy of Sciences of Ukraine, Kyiv, Ukraine.,Joint Institute for Nuclear Research, Dubna, Russia
| | - P A Popov
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow oblast, Russia.,Skolkovo Institute of Science and Technology, Moscow, Russia
| | - T I Rokitskaya
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Y N Antonenko
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - D V Zabelskii
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow oblast, Russia.,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
| | - D A Dolgikh
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Biological Faculty, Moscow State University, Moscow, Russia
| | - M P Kirpichnikov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Biological Faculty, Moscow State University, Moscow, Russia
| | - V I Gordeliy
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow oblast, Russia. .,Institut de Biologie Structurale (IBS), University 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.
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Maliar N, Okhrimenko IS, Petrovskaya LE, Alekseev AA, Kovalev KV, Soloviov DV, Popov PA, Rokitskaya TI, Antonenko YN, Zabelskii DV, Dolgikh DA, Kirpichnikov MP, Gordeliy VI. Novel pH-Sensitive Microbial Rhodopsin from Sphingomonas paucimobilis. DOKL BIOCHEM BIOPHYS 2020; 495:342-346. [PMID: 33368048 DOI: 10.1134/s1607672920060162] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/07/2020] [Accepted: 09/07/2020] [Indexed: 11/23/2022]
Abstract
This work provides the first characteristics of the rhodopsin SpaR from Sphingomonas paucimobilis, aerobic bacteria associated with opportunistic infections. The sequence analysis of SpaR has shown that this protein has unusual DTS motif which has never reported in rhodopsins from Proteobacteria. We report that SpaR operates as an outward proton pump at low pH; however, proton pumping is almost absent at neutral and alkaline pH. The photocycle of this rhodopsin in detergent micelles slows down with an increase in pH because of longer Schiff base reprotonation. Our results show that the novel microbial ion transporter SpaR of interest both as an object for basic research of membrane proteins and as a promising optogenetic tool.
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Affiliation(s)
- N Maliar
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow oblast, Russia
| | - I S Okhrimenko
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow oblast, Russia
| | - L E Petrovskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - A A Alekseev
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow oblast, Russia.,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.,Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - K V Kovalev
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow oblast, Russia.,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.,Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - D V Soloviov
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow oblast, Russia.,Institute for Safety Problems of Nuclear Power Plants, National Academy of Sciences of Ukraine, Kyiv, Ukraine.,Joint Institute for Nuclear Research, Dubna, Russia
| | - P A Popov
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow oblast, Russia.,Skolkovo Institute of Science and Technology, Moscow, Russia
| | - T I Rokitskaya
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Y N Antonenko
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - D V Zabelskii
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow oblast, Russia.,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
| | - D A Dolgikh
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Biological Faculty, Moscow State University, Moscow, Russia
| | - M P Kirpichnikov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Biological Faculty, Moscow State University, Moscow, Russia
| | - V I Gordeliy
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow oblast, Russia. .,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.
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