1
|
Nikolaev D, Mironov VN, Metelkina EM, Shtyrov AA, Mereshchenko AS, Demidov NA, Vyazmin SY, Tennikova TB, Moskalenko SE, Bondarev SA, Zhouravleva GA, Vasin AV, Panov MS, Ryazantsev MN. Rational Design of Far-Red Archaerhodopsin-3-Based Fluorescent Genetically Encoded Voltage Indicators: from Elucidation of the Fluorescence Mechanism in Archers to Novel Red-Shifted Variants. ACS PHYSICAL CHEMISTRY AU 2024; 4:347-362. [PMID: 39069984 PMCID: PMC11274289 DOI: 10.1021/acsphyschemau.3c00073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 04/07/2024] [Accepted: 04/08/2024] [Indexed: 07/30/2024]
Abstract
Genetically encoded voltage indicators (GEVIs) have found wide applications as molecular tools for visualization of changes in cell membrane potential. Among others, several classes of archaerhodopsin-3-based GEVIs have been developed and have proved themselves promising in various molecular imaging studies. To expand the application range for this type of GEVIs, new variants with absorption band maxima shifted toward the first biological window and enhanced fluorescence signal are required. Here, we integrate computational and experimental strategies to reveal structural factors that distinguish far-red bright archaerhodopsin-3-based GEVIs, Archers, obtained by directed evolution in a previous study (McIsaac et al., PNAS, 2014) and the wild-type archaerhodopsin-3 with an extremely dim fluorescence signal, aiming to use the obtained information in subsequent rational design. We found that the fluorescence can be enhanced by stabilization of a certain conformation of the protein, which, in turn, can be achieved by tuning the pK a value of two titratable residues. These findings were supported further by introducing mutations into wild-type archeorhodopsin-3 and detecting the enhancement of the fluorescence signal. Finally, we came up with a rational design and proposed previously unknown Archers variants with red-shifted absorption bands (λmax up to 640 nm) and potential-dependent bright fluorescence (quantum yield up to 0.97%).
Collapse
Affiliation(s)
- Dmitrii
M. Nikolaev
- Institute
of Chemistry, Saint Petersburg State University, 26 Universitetskii pr, St. Petersburg 198504, Russia
- Institute
of Biomedical Systems and Biotechnologies, Peter the Great St. Petersburg Polytechnic University, 29 Polytechnicheskaya Str., St. Petersburg 195251, Russia
| | - Vladimir N. Mironov
- Saint
Petersburg Academic University, 8/3 Khlopina Street, St.
Petersburg 194021, Russia
| | - Ekaterina M. Metelkina
- Institute
of Chemistry, Saint Petersburg State University, 26 Universitetskii pr, St. Petersburg 198504, Russia
| | - Andrey A. Shtyrov
- Institute
of Chemistry, Saint Petersburg State University, 26 Universitetskii pr, St. Petersburg 198504, Russia
| | - Andrey S. Mereshchenko
- Institute
of Chemistry, Saint Petersburg State University, 26 Universitetskii pr, St. Petersburg 198504, Russia
| | - Nikita A. Demidov
- Saint
Petersburg Academic University, 8/3 Khlopina Street, St.
Petersburg 194021, Russia
| | - Sergey Yu. Vyazmin
- Saint
Petersburg Academic University, 8/3 Khlopina Street, St.
Petersburg 194021, Russia
| | - Tatiana B. Tennikova
- Institute
of Chemistry, Saint Petersburg State University, 26 Universitetskii pr, St. Petersburg 198504, Russia
| | - Svetlana E. Moskalenko
- Department
of Genetics and Biotechnology, Saint Petersburg
State University, 7/9
Universitetskaya emb, St. Petersburg 199034, Russia
- Vavilov
Institute of General Genetics, St. Petersburg
Branch, Russian Academy of Sciences, St. Petersburg 199034, Russia
| | - Stanislav A. Bondarev
- Department
of Genetics and Biotechnology, Saint Petersburg
State University, 7/9
Universitetskaya emb, St. Petersburg 199034, Russia
- Laboratory
of Amyloid Biology, Saint Petersburg State
University, St. Petersburg 199034, Russia
| | - Galina A. Zhouravleva
- Department
of Genetics and Biotechnology, Saint Petersburg
State University, 7/9
Universitetskaya emb, St. Petersburg 199034, Russia
- Laboratory
of Amyloid Biology, Saint Petersburg State
University, St. Petersburg 199034, Russia
| | - Andrey V. Vasin
- Institute
of Biomedical Systems and Biotechnologies, Peter the Great St. Petersburg Polytechnic University, 29 Polytechnicheskaya Str., St. Petersburg 195251, Russia
| | - Maxim S. Panov
- Institute
of Chemistry, Saint Petersburg State University, 26 Universitetskii pr, St. Petersburg 198504, Russia
- St.
Petersburg State Chemical Pharmaceutical University, Professor Popov str., 14, lit. A, St. Petersburg 197022, Russia
| | - Mikhail N. Ryazantsev
- Institute
of Chemistry, Saint Petersburg State University, 26 Universitetskii pr, St. Petersburg 198504, Russia
| |
Collapse
|
2
|
Li G, Meng J, Yu S, Bai X, Dai J, Song Y, Peng X, Zhao Q. Excited-State Dynamics of a CRABPII-Based Microbial Rhodopsin Mimic. J Phys Chem B 2024. [PMID: 38940335 DOI: 10.1021/acs.jpcb.4c01296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
Microbial rhodopsin, a pivotal photoreceptor protein, has garnered widespread application in diverse fields such as optogenetics, biotechnology, biodevices, etc. However, current microbial rhodopsins are all transmembrane proteins, which both complicates the investigation on the photoreaction mechanism and limits their further applications. Therefore, a specific mimic for microbial rhodopsin can not only provide a better model for understanding the mechanism but also can extend the applications. The human protein CRABPII turns out to be a good template for design mimics on rhodopsin due to the convenience in synthesis and the stability after mutations. Recently, Geiger et al. designed a new CRABPII-based mimic M1-L121E on microbial rhodopsin with the 13-cis, syn (13C) isomerization after irradiation. However, it still remains a question as to how similar it is compared with the natural microbial rhodopsin, in particular, in the aspect of the photoreaction dynamics. In this article, we investigate the excited-state dynamics of this mimic by measuring its transient absorption spectra. Our results reveal that there are two components in the solution of mimic M1-L121E at pH 8, known as protonated Schiff base (PSB) and unprotonated Schiff base (USB) states. In both states, the photoreaction process from 13-cis, syn(13C) to all-trans,anti (AT) is faster than that from the inverse direction. In addition, the photoreaction process in the PSB state is faster than that in the USB state. We compared the isomerization time of the PSB state to that of microbial rhodopsin. Our findings indicate that M1-L121E exhibits behaviors similar to those of microbial rhodopsins in the general pattern of PSB isomerization, where the isomerization from 13C to AT is much faster than its inverse direction. However, our results also reveal significant differences in the excited-state dynamics of the mimic relative to the native microbial rhodopsin, including the slower PSB isomerization rates as well as the unusual USB photoreaction dynamics at pH = 8. By elucidating the distinctive characteristics of mimics M1-L121E, this study enhances our understanding of microbial rhodopsin mimics and their potential applications.
Collapse
Affiliation(s)
- Gaoshang Li
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
| | - Jiajia Meng
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
| | - Shuang Yu
- MIIT Key Laboratory of Complex-field Intelligent Exploration, School of Optics and Photonics, Beijing Institute of Technology, Beijing 100081, China
| | - Xiaolu Bai
- MIIT Key Laboratory of Complex-field Intelligent Exploration, School of Optics and Photonics, Beijing Institute of Technology, Beijing 100081, China
| | - Jin Dai
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
| | - Yin Song
- MIIT Key Laboratory of Complex-field Intelligent Exploration, School of Optics and Photonics, Beijing Institute of Technology, Beijing 100081, China
| | - Xubiao Peng
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
- Beijing Academy of Quantum Information Sciences, Beijing 100081, China
| | - Qing Zhao
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
- Beijing Academy of Quantum Information Sciences, Beijing 100081, China
| |
Collapse
|
3
|
Okhrimenko IS, Kovalev K, Petrovskaya LE, Ilyinsky NS, Alekseev AA, Marin E, Rokitskaya TI, Antonenko YN, Siletsky SA, Popov PA, Zagryadskaya YA, Soloviov DV, Chizhov IV, Zabelskii DV, Ryzhykau YL, Vlasov AV, Kuklin AI, Bogorodskiy AO, Mikhailov AE, Sidorov DV, Bukhalovich S, Tsybrov F, Bukhdruker S, Vlasova AD, Borshchevskiy VI, Dolgikh DA, Kirpichnikov MP, Bamberg E, Gordeliy VI. Mirror proteorhodopsins. Commun Chem 2023; 6:88. [PMID: 37130895 PMCID: PMC10154332 DOI: 10.1038/s42004-023-00884-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/12/2023] [Indexed: 05/04/2023] Open
Abstract
Proteorhodopsins (PRs), bacterial light-driven outward proton pumps comprise the first discovered and largest family of rhodopsins, they play a significant role in life on the Earth. A big remaining mystery was that up-to-date there was no described bacterial rhodopsins pumping protons at acidic pH despite the fact that bacteria live in different pH environment. Here we describe conceptually new bacterial rhodopsins which are operating as outward proton pumps at acidic pH. A comprehensive function-structure study of a representative of a new clade of proton pumping rhodopsins which we name "mirror proteorhodopsins", from Sphingomonas paucimobilis (SpaR) shows cavity/gate architecture of the proton translocation pathway rather resembling channelrhodopsins than the known rhodopsin proton pumps. Another unique property of mirror proteorhodopsins is that proton pumping is inhibited by a millimolar concentration of zinc. We also show that mirror proteorhodopsins are extensively represented in opportunistic multidrug resistant human pathogens, plant growth-promoting and zinc solubilizing bacteria. They may be of optogenetic interest.
Collapse
Affiliation(s)
- Ivan S Okhrimenko
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | | | - Lada E Petrovskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow, Russia
| | - Nikolay S Ilyinsky
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Alexey A Alekseev
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Egor Marin
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Tatyana I Rokitskaya
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Yuri N Antonenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Sergey A Siletsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Petr A Popov
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- iMolecule, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Yuliya A Zagryadskaya
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | | | - Igor V Chizhov
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | | | - Yury L Ryzhykau
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Alexey V Vlasov
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Alexander I Kuklin
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Andrey O Bogorodskiy
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Anatolii E Mikhailov
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Daniil V Sidorov
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Siarhei Bukhalovich
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Fedor Tsybrov
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Sergey Bukhdruker
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Anastasiia D Vlasova
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Valentin I Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Dmitry A Dolgikh
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow, Russia
- Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail P Kirpichnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow, Russia
- Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Ernst Bamberg
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Valentin I Gordeliy
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CNRS, CEA, Grenoble, France.
| |
Collapse
|
4
|
Marín MDC, Jaffe AL, West PT, Konno M, Banfield JF, Inoue K. Biophysical characterization of microbial rhodopsins with DSE motif. Biophys Physicobiol 2023; 20:e201023. [PMID: 38362324 PMCID: PMC10865882 DOI: 10.2142/biophysico.bppb-v20.s023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/07/2023] [Indexed: 03/09/2023] Open
Abstract
Microbial rhodopsins are photoreceptive transmembrane proteins that transport ions or regulate other intracellular biological processes. Recent genomic and metagenomic analyses found many microbial rhodopsins with unique sequences distinct from known ones. Functional characterization of these new types of microbial rhodopsins is expected to expand our understanding of their physiological roles. Here, we found microbial rhodopsins having a DSE motif in the third transmembrane helix from members of the Actinobacteria. Although the expressed proteins exhibited blue-green light absorption, either no or extremely small outward H+ pump activity was observed. The turnover rate of the photocycle reaction of the purified proteins was extremely slow compared to typical H+ pumps, suggesting these rhodopsins would work as photosensors or H+ pumps whose activities are enhanced by an unknown regulatory system in the hosts. The discovery of this rhodopsin group with the unique motif and functionality expands our understanding of the biological role of microbial rhodopsins.
Collapse
Affiliation(s)
- María del Carmen Marín
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - Alexander L. Jaffe
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA
- Department of Earth System Science, Stanford University, Stanford, CA 94305-4216, USA
| | - Patrick T. West
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA
| | - Masae Konno
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Jillian F. Banfield
- Innovative Genomics Institute, University of California, Berkeley, CA 94720-2151, USA
- Department of Earth and Planetary Science, University of California, Berkeley, CA 94720-4767, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720-3114, USA
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| |
Collapse
|
5
|
He S, Linz AM, Stevens SLR, Tran PQ, Moya-Flores F, Oyserman BO, Dwulit-Smith JR, Forest KT, McMahon KD. Diversity, distribution, and expression of opsin genes in freshwater lakes. Mol Ecol 2023; 32:2798-2817. [PMID: 36799010 DOI: 10.1111/mec.16891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 01/28/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023]
Abstract
Microbial rhodopsins are widely distributed in aquatic environments and may significantly contribute to phototrophy and energy budgets in global oceans. However, the study of freshwater rhodopsins has been largely limited. Here, we explored the diversity, ecological distribution, and expression of opsin genes that encode the apoproteins of type I rhodopsins in humic and clearwater lakes with contrasting physicochemical and optical characteristics. Using metagenomes and metagenome-assembled genomes, we recovered opsin genes from a wide range of taxa, mostly predicted to encode green light-absorbing proton pumps. Viral opsin and novel bacterial opsin clades were recovered. Opsin genes occurred more frequently in taxa from clearwater than from humic water, and opsins in some taxa have nontypical ion-pumping motifs that might be associated with physicochemical conditions of these two freshwater types. Analyses of the surface layer of 33 freshwater systems revealed an inverse correlation between opsin gene abundance and lake dissolved organic carbon (DOC). In humic water with high terrestrial DOC and light-absorbing humic substances, opsin gene abundance was low and dramatically declined within the first few meters, whereas the abundance remained relatively high along the bulk water column in clearwater lakes with low DOC, suggesting opsin gene distribution is influenced by lake optical properties and DOC. Gene expression analysis confirmed the significance of rhodopsin-based phototrophy in clearwater lakes and revealed different diel expressional patterns among major phyla. Overall, our analyses revealed freshwater opsin diversity, distribution and expression patterns, and suggested the significance of rhodopsin-based phototrophy in freshwater energy budgets, especially in clearwater lakes.
Collapse
Affiliation(s)
- Shaomei He
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Department of Geoscience, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Alexandra M Linz
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Sarah L R Stevens
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Patricia Q Tran
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Francisco Moya-Flores
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ben O Oyserman
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jeffrey R Dwulit-Smith
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Program in Biophysics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Katrina T Forest
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Program in Biophysics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Katherine D McMahon
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| |
Collapse
|
6
|
Suzuki K, del Carmen Marín M, Konno M, Bagherzadeh R, Murata T, Inoue K. Structural characterization of proton-pumping rhodopsin lacking a cytoplasmic proton donor residue by X-ray crystallography. J Biol Chem 2022; 298:101722. [PMID: 35151692 PMCID: PMC8927995 DOI: 10.1016/j.jbc.2022.101722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/05/2022] [Accepted: 02/08/2022] [Indexed: 01/10/2023] Open
Abstract
DTG/DTS rhodopsin, which was named based on a three-residue motif (DTG or DTS) that is important for its function, is a light-driven proton-pumping microbial rhodopsin using a retinal chromophore. In contrast to other light-driven ion-pumping rhodopsins, DTG/DTS rhodopsin does not have a cytoplasmic proton donor residue, such as Asp, Glu, or Lys. Because of the lack of cytoplasmic proton donor residue, proton directly binds to the retinal chromophore from the cytoplasmic solvent. However, mutational experiments that showed the complicated effects of mutations were not able to clarify the roles played by each residue, and the detail of proton uptake pathway is unclear because of the lack of structural information. To understand the proton transport mechanism of DTG/DTS rhodopsin, here we report the three-dimensional structure of one of the DTG/DTS rhodopsins, PspR from Pseudomonas putida, by X-ray crystallography. We show that the structure of the cytoplasmic side of the protein is significantly different from that of bacteriorhodopsin, the best-characterized proton-pumping rhodopsin, and large cytoplasmic cavities were observed. We propose that these hydrophilic cytoplasmic cavities enable direct proton uptake from the cytoplasmic solvent without the need for a specialized cytoplasmic donor residue. The introduction of carboxylic residues homologous to the cytoplasmic donors in other proton-pumping rhodopsins resulted in higher pumping activity with less pH dependence, suggesting that DTG/DTS rhodopsins are advantageous for producing energy and avoiding intracellular alkalization in soil and plant-associated bacteria.
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Abstract
Rhodopsins are photoreceptive membrane proteins consisting of a common heptahelical transmembrane architecture that contains a retinal chromophore. Rhodopsin was first discovered in the animal retina in 1876, but a different type of rhodopsin, bacteriorhodopsin, was reported to be present in the cell membrane of an extreme halophilic archaeon, Halobacterium salinarum, 95 years later. Although these findings were made by physiological observation of pigmented tissue and cell bodies, recent progress in genomic and metagenomic analyses has revealed that there are more than 10,000 microbial rhodopsins and 9000 animal rhodopsins with large diversity and tremendous new functionality. In this Cell Science at a Glance article and accompanying poster, we provide an overview of the diversity of functions, structures, color discrimination mechanisms and optogenetic applications of these two rhodopsin families, and will also highlight the third distinctive rhodopsin family, heliorhodopsin.
Collapse
Affiliation(s)
- Takashi Nagata
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan.,PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| |
Collapse
|
9
|
Multiple energy sources and metabolic strategies sustain microbial diversity in Antarctic desert soils. Proc Natl Acad Sci U S A 2021; 118:2025322118. [PMID: 34732568 DOI: 10.1073/pnas.2025322118] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2021] [Indexed: 12/11/2022] Open
Abstract
Numerous diverse microorganisms reside in the cold desert soils of continental Antarctica, though we lack a holistic understanding of the metabolic processes that sustain them. Here, we profile the composition, capabilities, and activities of the microbial communities in 16 physicochemically diverse mountainous and glacial soils. We assembled 451 metagenome-assembled genomes from 18 microbial phyla and inferred through Bayesian divergence analysis that the dominant lineages present are likely native to Antarctica. In support of earlier findings, metagenomic analysis revealed that the most abundant and prevalent microorganisms are metabolically versatile aerobes that use atmospheric hydrogen to support aerobic respiration and sometimes carbon fixation. Surprisingly, however, hydrogen oxidation in this region was catalyzed primarily by a phylogenetically and structurally distinct enzyme, the group 1l [NiFe]-hydrogenase, encoded by nine bacterial phyla. Through gas chromatography, we provide evidence that both Antarctic soil communities and an axenic Bacteroidota isolate (Hymenobacter roseosalivarius) oxidize atmospheric hydrogen using this enzyme. Based on ex situ rates at environmentally representative temperatures, hydrogen oxidation is theoretically sufficient for soil communities to meet energy requirements and, through metabolic water production, sustain hydration. Diverse carbon monoxide oxidizers and abundant methanotrophs were also active in the soils. We also recovered genomes of microorganisms capable of oxidizing edaphic inorganic nitrogen, sulfur, and iron compounds and harvesting solar energy via microbial rhodopsins and conventional photosystems. Obligately symbiotic bacteria, including Patescibacteria, Chlamydiae, and predatory Bdellovibrionota, were also present. We conclude that microbial diversity in Antarctic soils reflects the coexistence of metabolically flexible mixotrophs with metabolically constrained specialists.
Collapse
|
10
|
Cho SG, Shim JG, Choun K, Meas S, Kang KW, Kim JH, Cho HS, Jung KH. Discovery of a new light-driven Li +/Na +-pumping rhodopsin with DTG motif. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2021; 223:112285. [PMID: 34411952 DOI: 10.1016/j.jphotobiol.2021.112285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/31/2021] [Accepted: 08/10/2021] [Indexed: 11/17/2022]
Abstract
Microbial pumping rhodopsin is a seven-transmembrane retinal binding protein, which is light-driven ion pump with a functional key motif. Ion-pumping with the key motif and charged amino acids in the rhodopsin is biochemically important. The rhodopsins with DTG motif have been discovered in various eubacteria, and they function as H+ pump. Especially, the DTG motif rhodopsins transported H+ despite the replacement of a proton donor by Gly. We investigated Methylobacterium populi rhodopsin (MpR) in one of the DTG motif rhodopsin clades. To determine which ions the MpR transport, we tested with various monovalent ion solutions and determined that MpR transports Li+/Na+. By replacing the three negatively charged residues residues which are located in helix B, Glu32, Glu33, and Asp35, we concluded that the residues play a critical role in the transport of Li+/Na+. The MpR E33Q transported H+ in place of Li+/Na+, suggesting that Glu33 is a Li+/Na+ binding site on the cytoplasmic side. Gly93 in MpR was replaced by Asp to convert from the Li+/Na+ pump to the H+ pump, resulting in MpR G93D transporting H+. Dissociation constant (Kd) values of Na+ for MpR WT and E33Q were determined to be 4.0 and 72.5 mM, respectively. These results indicated the mechanism by which MpR E33Q transports H+. Up to now, various ion-pumping rhodopsins have been discovered, and Li+/Na+-pumping rhodopsins were only found in the NDQ motif in NaR. Here, we report a new light-driven Na+ pump MpR and have determined the important residues required for Li+/Na+-pumping different from previously known NaR.
Collapse
Affiliation(s)
- Shin-Gyu Cho
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul 04107, Republic of Korea
| | - Jin-Gon Shim
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul 04107, Republic of Korea
| | - Kimleng Choun
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul 04107, Republic of Korea
| | - Seanghun Meas
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul 04107, Republic of Korea; Department of Biology, Faculty of Science, Royal University of Phnom Penh, Phnom Penh 12000, Cambodia
| | - Kun-Wook Kang
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul 04107, Republic of Korea
| | - Ji-Hyun Kim
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul 04107, Republic of Korea
| | - Hyun-Suk Cho
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul 04107, Republic of Korea
| | - Kwang-Hwan Jung
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul 04107, Republic of Korea.
| |
Collapse
|
11
|
Konno M, Inoue K, Kandori H. Ion Transport Activity Assay for Microbial Rhodopsin Expressed in Escherichia coli Cells. Bio Protoc 2021; 11:e4115. [PMID: 34458409 DOI: 10.21769/bioprotoc.4115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/29/2021] [Accepted: 05/05/2021] [Indexed: 11/02/2022] Open
Abstract
Microbial rhodopsins have diverse functions, including roles as light-driven ion pumps, light-gated ion channels, photosensors, and light-regulated enzymes. As the number of rhodopsin-like genes identified has increased in recent years, so has the requirement for rapid identification of their functions. The patch-clamp method is often used to investigate the ion transport mechanism of microbial rhodopsins in mammalian cells; however, this requires a dedicated system and advanced techniques. The ion transport assay using the Escherichia coli expression system described here evaluates the ion transport capacity by monitoring the pH change in E. coli suspensions; if the target rhodopsin has a light-dependent ion transport activity, a light-dependent pH change is observed. The pH increase or decrease corresponds to proton release from the cell or proton uptake into the cell, respectively. This method can be used to evaluate ion transport capacity in a high-throughput manner using a combination of general-purpose equipment and common techniques. Graphic abstract: Schematic diagram of the ion transport assay in rhodopsin-expressing E. coli cells.
Collapse
Affiliation(s)
- Masae Konno
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581 Japan.,PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581 Japan
| | - Hideki Kandori
- Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| |
Collapse
|
12
|
Abstract
Microbial rhodopsins are diverse photoreceptive proteins containing a retinal chromophore and are found in all domains of cellular life and are even encoded in genomes of viruses. These rhodopsins make up two families: type 1 rhodopsins and the recently discovered heliorhodopsins. These families have seven transmembrane helices with similar structures but opposing membrane orientation. Microbial rhodopsins participate in a portfolio of light-driven energy and sensory transduction processes. In this review we present data collected over the last two decades about these rhodopsins and describe their diversity, functions, and biological and ecological roles. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Andrey Rozenberg
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel; ,
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa 277-8581, Japan;
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya 466-8555, Japan;
| | - Oded Béjà
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel; ,
| |
Collapse
|
13
|
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: 16] [Impact Index Per Article: 5.3] [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.
Collapse
Affiliation(s)
- Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, Chiba, Japan.
- PRESTO, Japan Science and Technology Agency, Saitama, Japan.
| |
Collapse
|
14
|
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: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [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.
Collapse
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.
| |
Collapse
|
15
|
Consiglieri E, Xu QZ, Zhao KH, Gärtner W, Losi A. The first molecular characterisation of blue- and red-light photoreceptors from Methylobacterium radiotolerans. Phys Chem Chem Phys 2020; 22:12434-12446. [PMID: 32458860 DOI: 10.1039/d0cp02014a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Methylobacteria are facultative methylotrophic phytosymbionts of great industrial and agronomical interest, and they are considered as opportunistic pathogens posing a health threat to humans. So far only a few reports mention photoreceptor coding sequences in Methylobacteria genomes, but no investigation at the molecular level has been performed yet. We here present comprehensive in silico research into potential photoreceptors in this bacterial phylum and report the photophysical and photochemical characterisation of two representatives of the most widespread photoreceptor classes, a blue-light sensing LOV (light, oxygen, voltage) protein and a red/far red light sensing BphP (biliverdin-binding bacterial phytochrome) from M. radiotolerans JCM 2831. Overall, both proteins undergo the expected light-triggered reactions, but peculiar features were also identified. The LOV protein Mr4511 has an extremely long photocycle and lacks a tryptophan conserved in ca. 75% of LOV domains. Mutation I37V accelerates the photocycle by one order of magnitude, while the Q112W change underscores the ability of tryptophan in this position to perform efficient energy transfer to the flavin chromophore. Time-resolved photoacoustic experiments showed that Mr4511 has a higher triplet quantum yield than other LOV domains and that the formation of the photoproduct results in a volume expansion, in sharp contrast to other LOV proteins. Mr4511 was found to be astonishingly resistant to denaturation by urea, still showing light-triggered reactions after incubation in urea for more than 20 h. The phytochrome MrBphP1 exhibits the so far most red-shifted absorption maxima for its Pr- and Pfr forms (λmax = 707 nm and 764 nm for the Pr and Pfr forms). The light-driven conversions in both directions occur with relatively high quantum yields of 0.2. Transient ns absorption spectroscopy (μs-ms time range) identifies the decay of the instantaneously formed lumi-intermediate, followed by only one additional intermediate before the formation of the respective final photoproducts for Pr-to-Pfr or Pfr-to-Pr photoconversion, in contrast to other BphPs. The relatively simple photoconversion patterns suggest the absence of the shunt pathways reported for other bacterial phytochromes.
Collapse
Affiliation(s)
- Eleonora Consiglieri
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze 7/A, 43124 Parma, Italy.
| | - Qian-Zhao Xu
- Institute for Analytical Chemistry, University of Leipzig, Linnéstrasse 3, 04103 Leipzig, Germany and State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Kai-Hong Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Wolfgang Gärtner
- Institute for Analytical Chemistry, University of Leipzig, Linnéstrasse 3, 04103 Leipzig, Germany
| | - Aba Losi
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze 7/A, 43124 Parma, Italy.
| |
Collapse
|
16
|
Hasegawa M, Hosaka T, Kojima K, Nishimura Y, Nakajima Y, Kimura-Someya T, Shirouzu M, Sudo Y, Yoshizawa S. A unique clade of light-driven proton-pumping rhodopsins evolved in the cyanobacterial lineage. Sci Rep 2020; 10:16752. [PMID: 33028840 PMCID: PMC7541481 DOI: 10.1038/s41598-020-73606-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 09/15/2020] [Indexed: 11/09/2022] Open
Abstract
Microbial rhodopsin is a photoreceptor protein found in various bacteria and archaea, and it is considered to be a light-utilization device unique to heterotrophs. Recent studies have shown that several cyanobacterial genomes also include genes that encode rhodopsins, indicating that these auxiliary light-utilizing proteins may have evolved within photoautotroph lineages. To explore this possibility, we performed a large-scale genomic survey to clarify the distribution of rhodopsin and its phylogeny. Our surveys revealed a novel rhodopsin clade, cyanorhodopsin (CyR), that is unique to cyanobacteria. Genomic analysis revealed that rhodopsin genes show a habitat-biased distribution in cyanobacterial taxa, and that the CyR clade is composed exclusively of non-marine cyanobacterial strains. Functional analysis using a heterologous expression system revealed that CyRs function as light-driven outward H+ pumps. Examination of the photochemical properties and crystal structure (2.65 Å resolution) of a representative CyR protein, N2098R from Calothrix sp. NIES-2098, revealed that the structure of the protein is very similar to that of other rhodopsins such as bacteriorhodopsin, but that its retinal configuration and spectroscopic characteristics (absorption maximum and photocycle) are distinct from those of bacteriorhodopsin. These results suggest that the CyR clade proteins evolved together with chlorophyll-based photosynthesis systems and may have been optimized for the cyanobacterial environment.
Collapse
Affiliation(s)
- Masumi Hasegawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan.,Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8563, Japan
| | - Toshiaki Hosaka
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Kanagawa, 230-0045, Japan
| | - Keiichi Kojima
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Yosuke Nishimura
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan
| | - Yu Nakajima
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Ibaraki, 305-8766, Japan
| | - Tomomi Kimura-Someya
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Kanagawa, 230-0045, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Kanagawa, 230-0045, Japan
| | - Yuki Sudo
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan. .,Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8563, Japan. .,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, 113-8657, Japan.
| |
Collapse
|
17
|
Harris A, Lazaratos M, Siemers M, Watt E, Hoang A, Tomida S, Schubert L, Saita M, Heberle J, Furutani Y, Kandori H, Bondar AN, Brown LS. Mechanism of Inward Proton Transport in an Antarctic Microbial Rhodopsin. J Phys Chem B 2020; 124:4851-4872. [DOI: 10.1021/acs.jpcb.0c02767] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Andrew Harris
- Department of Physics, University of Guelph, 50 Stone Rd. E., Guelph, Ontario N1G 2W1, Canada
| | - Michalis Lazaratos
- Theoretical Molecular Biophysics Group, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Malte Siemers
- Theoretical Molecular Biophysics Group, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Ethan Watt
- Department of Physics, University of Guelph, 50 Stone Rd. E., Guelph, Ontario N1G 2W1, Canada
| | - Anh Hoang
- Department of Physics, University of Guelph, 50 Stone Rd. E., Guelph, Ontario N1G 2W1, Canada
| | - Sahoko Tomida
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Luiz Schubert
- Experimental Molecular Biophysics Group, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Mattia Saita
- Experimental Molecular Biophysics Group, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Joachim Heberle
- Experimental Molecular Biophysics Group, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Yuji Furutani
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Ana-Nicoleta Bondar
- Theoretical Molecular Biophysics Group, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Leonid S. Brown
- Department of Physics, University of Guelph, 50 Stone Rd. E., Guelph, Ontario N1G 2W1, Canada
| |
Collapse
|
18
|
Kovalev K, Volkov D, Astashkin R, Alekseev A, Gushchin I, Haro-Moreno JM, Chizhov I, Siletsky S, Mamedov M, Rogachev A, Balandin T, Borshchevskiy V, Popov A, Bourenkov G, Bamberg E, Rodriguez-Valera F, Büldt G, Gordeliy V. High-resolution structural insights into the heliorhodopsin family. Proc Natl Acad Sci U S A 2020; 117:4131-4141. [PMID: 32034096 PMCID: PMC7049168 DOI: 10.1073/pnas.1915888117] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Rhodopsins are the most abundant light-harvesting proteins. A new family of rhodopsins, heliorhodopsins (HeRs), has recently been discovered. Unlike in the known rhodopsins, in HeRs the N termini face the cytoplasm. The function of HeRs remains unknown. We present the structures of the bacterial HeR-48C12 in two states at the resolution of 1.5 Å, which highlight its remarkable difference from all known rhodopsins. The interior of HeR's extracellular part is completely hydrophobic, while the cytoplasmic part comprises a cavity (Schiff base cavity [SBC]) surrounded by charged amino acids and containing a cluster of water molecules, presumably being a primary proton acceptor from the Schiff base. At acidic pH, a planar triangular molecule (acetate) is present in the SBC. Structure-based bioinformatic analysis identified 10 subfamilies of HeRs, suggesting their diverse biological functions. The structures and available data suggest an enzymatic activity of HeR-48C12 subfamily and their possible involvement in fundamental redox biological processes.
Collapse
Affiliation(s)
- K Kovalev
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-Commission for Atomic Energy (CEA)-CNRS, 38000 Grenoble, France
- Institute of Biological Information Processing (Institute of Biological Information Processing: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
- Research Center for Mechanisms of Aging and Age Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny 141701, Russia
- Institute of Crystallography, University of Aachen (Rheinisch-Westfälische Technische Hochschule Aachen [RWTH]), 52062 Aachen, Germany
| | - D Volkov
- Institute of Biological Information Processing (Institute of Biological Information Processing: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - R Astashkin
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-Commission for Atomic Energy (CEA)-CNRS, 38000 Grenoble, France
- Research Center for Mechanisms of Aging and Age Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny 141701, Russia
| | - A Alekseev
- Institute of Biological Information Processing (Institute of Biological Information Processing: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
- Research Center for Mechanisms of Aging and Age Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny 141701, Russia
- Institute of Crystallography, University of Aachen (Rheinisch-Westfälische Technische Hochschule Aachen [RWTH]), 52062 Aachen, Germany
| | - I Gushchin
- Research Center for Mechanisms of Aging and Age Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny 141701, Russia
| | - J M Haro-Moreno
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, 03202 San Juan de Alicante, Spain
| | - I Chizhov
- Institute for Biophysical Chemistry, Hannover Medical School, 30625 Hannover, Germany
| | - S Siletsky
- Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - M Mamedov
- Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - A Rogachev
- Research Center for Mechanisms of Aging and Age Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny 141701, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna 141980, Russia
| | - T Balandin
- Institute of Biological Information Processing (Institute of Biological Information Processing: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - V Borshchevskiy
- Research Center for Mechanisms of Aging and Age Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny 141701, Russia
| | - A Popov
- Structural Biology Group, European Synchrotron Radiation Facility, 38000 Grenoble, France
| | - G Bourenkov
- Hamburg Unit care of Deutsches Elektronen-Synchrotron (DESY), European Molecular Biology Laboratory, 22607 Hamburg, Germany
| | - E Bamberg
- Research Center for Mechanisms of Aging and Age Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny 141701, Russia
- Biophysical Chemistry, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - F Rodriguez-Valera
- Research Center for Mechanisms of Aging and Age Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny 141701, Russia
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, 03202 San Juan de Alicante, Spain
| | - G Büldt
- Research Center for Mechanisms of Aging and Age Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny 141701, Russia
| | - V Gordeliy
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-Commission for Atomic Energy (CEA)-CNRS, 38000 Grenoble, France;
- Institute of Biological Information Processing (Institute of Biological Information Processing: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
- Research Center for Mechanisms of Aging and Age Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny 141701, Russia
| |
Collapse
|
19
|
Abstract
This is a review of relevant Raman spectroscopy (RS) techniques and their use in structural biology, biophysics, cells, and tissues imaging towards development of various medical diagnostic tools, drug design, and other medical applications. Classical and contemporary structural studies of different water-soluble and membrane proteins, DNA, RNA, and their interactions and behavior in different systems were analyzed in terms of applicability of RS techniques and their complementarity to other corresponding methods. We show that RS is a powerful method that links the fundamental structural biology and its medical applications in cancer, cardiovascular, neurodegenerative, atherosclerotic, and other diseases. In particular, the key roles of RS in modern technologies of structure-based drug design are the detection and imaging of membrane protein microcrystals with the help of coherent anti-Stokes Raman scattering (CARS), which would help to further the development of protein structural crystallography and would result in a number of novel high-resolution structures of membrane proteins—drug targets; and, structural studies of photoactive membrane proteins (rhodopsins, photoreceptors, etc.) for the development of new optogenetic tools. Physical background and biomedical applications of spontaneous, stimulated, resonant, and surface- and tip-enhanced RS are also discussed. All of these techniques have been extensively developed during recent several decades. A number of interesting applications of CARS, resonant, and surface-enhanced Raman spectroscopy methods are also discussed.
Collapse
|
20
|
A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators. Proc Natl Acad Sci U S A 2019; 116:20574-20583. [PMID: 31548428 PMCID: PMC6789865 DOI: 10.1073/pnas.1907517116] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Giant viruses are remarkable for their large genomes, often rivaling those of small bacteria, and for having genes thought exclusive to cellular life. Most isolated to date infect nonmarine protists, leaving their strategies and prevalence in marine environments largely unknown. Using eukaryotic single-cell metagenomics in the Pacific, we discovered a Mimiviridae lineage of giant viruses, which infects choanoflagellates, widespread protistan predators related to metazoans. The ChoanoVirus genomes are the largest yet from pelagic ecosystems, with 442 of 862 predicted proteins lacking known homologs. They are enriched in enzymes for modifying organic compounds, including degradation of chitin, an abundant polysaccharide in oceans, and they encode 3 divergent type-1 rhodopsins (VirR) with distinct evolutionary histories from those that capture sunlight in cellular organisms. One (VirRDTS) is similar to the only other putative rhodopsin from a virus (PgV) with a known host (a marine alga). Unlike the algal virus, ChoanoViruses encode the entire pigment biosynthesis pathway and cleavage enzyme for producing the required chromophore, retinal. We demonstrate that the rhodopsin shared by ChoanoViruses and PgV binds retinal and pumps protons. Moreover, our 1.65-Å resolved VirRDTS crystal structure and mutational analyses exposed differences from previously characterized type-1 rhodopsins, all of which come from cellular organisms. Multiple VirR types are present in metagenomes from across surface oceans, where they are correlated with and nearly as abundant as a canonical marker gene from Mimiviridae Our findings indicate that light-dependent energy transfer systems are likely common components of giant viruses of photosynthetic and phagotrophic unicellular marine eukaryotes.
Collapse
|
21
|
Faramarzi S, Feng J, Mertz B. Allosteric Effects of the Proton Donor on the Microbial Proton Pump Proteorhodopsin. Biophys J 2018; 115:1240-1250. [PMID: 30219284 DOI: 10.1016/j.bpj.2018.08.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 08/21/2018] [Accepted: 08/22/2018] [Indexed: 11/17/2022] Open
Abstract
Proteorhodopsin (PR) is a microbial proton pump that is ubiquitous in marine environments and may play an important role in the oceanic carbon cycle. Photoisomerization of the retinal chromophore in PR leads to a series of proton transfers between specific acidic amino acid residues and the Schiff base of retinal, culminating in a proton motive force to facilitate ATP synthesis. The proton donor in a similar retinal protein, bacteriorhodopsin, acts as a latch to allow the influx of bulk water. However, it is unclear if the proton donor in PR, E108, utilizes the same latch mechanism to become internally hydrated. Here, we used molecular dynamics simulations to model the changes in internal hydration of the blue variant of PR during photoactivation with the proton donor in protonated and deprotonated states. We find that there is a stark contrast in the levels of internal hydration of the cytoplasmic half of PR based on the protonation state of E108. Instead of a latch mechanism, deprotonation of E108 acts as a gate, taking advantage of a nearby polar residue (S61) to promote the formation of a stable water wire from bulk cytoplasm to the retinal-binding pocket over hundreds of nanoseconds. No large-scale conformational changes occur in PR over the microsecond timescale. This subtle yet clear difference in the effect of deprotonation of the proton donor in PR may help explain why the photointermediates that involve the proton donor (i.e., M and N states) have timescales that are orders of magnitude different from the archaeal proton pump, bacteriorhodopsin. In general, our study highlights the importance of understanding how structural fluctuations lead to differences in the way that retinal proteins accomplish the same task.
Collapse
Affiliation(s)
- Sadegh Faramarzi
- C. Eugene Department of Chemistry, West Virginia University, Morgantown, West Virginia
| | - Jun Feng
- C. Eugene Department of Chemistry, West Virginia University, Morgantown, West Virginia
| | - Blake Mertz
- C. Eugene Department of Chemistry, West Virginia University, Morgantown, West Virginia.
| |
Collapse
|
22
|
Inoue K, Tahara S, Kato Y, Takeuchi S, Tahara T, Kandori H. Spectroscopic Study of Proton-Transfer Mechanism of Inward Proton-Pump Rhodopsin, Parvularcula oceani Xenorhodopsin. J Phys Chem B 2018; 122:6453-6461. [DOI: 10.1021/acs.jpcb.8b01279] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Keiichi Inoue
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Shinya Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | | | - Satoshi Takeuchi
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | | |
Collapse
|
23
|
Harris A, Saita M, Resler T, Hughes-Visentin A, Maia R, Pranga-Sellnau F, Bondar AN, Heberle J, Brown LS. Molecular details of the unique mechanism of chloride transport by a cyanobacterial rhodopsin. Phys Chem Chem Phys 2018; 20:3184-3199. [PMID: 29057415 DOI: 10.1039/c7cp06068h] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Microbial rhodopsins are well known as versatile and ubiquitous light-driven ion transporters and photosensors. While the proton transport mechanism has been studied in great detail, much less is known about various modes of anion transport. Until recently, only two main groups of light-driven anion pumps were known, archaeal halorhodopsins (HRs) and bacterial chloride pumps (known as ClRs or NTQs). Last year, another group of cyanobacterial anion pumps with a very distinct primary structure was reported. Here, we studied the chloride-transporting photocycle of a representative of this new group, Mastigocladopsis repens rhodopsin (MastR), using time-resolved spectroscopy in the infrared and visible ranges and site-directed mutagenesis. We found that, in accordance with its unique amino acid sequence containing many polar residues in the transmembrane region of the protein, its photocycle features a number of unusual molecular events not known for other anion-pumping rhodopsins. It appears that light-driven chloride ion transfers by MastR are coupled with translocation of protons and water molecules as well as perturbation of several polar sidechains. Of particular interest is transient deprotonation of Asp-85, homologous to the cytoplasmic proton donor of light-driven proton pumps (such as Asp-96 of bacteriorhodopsin), which may serve as a regulatory mechanism.
Collapse
Affiliation(s)
- Andrew Harris
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada.
| | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Nomura Y, Ito S, Teranishi M, Ono H, Inoue K, Kandori H. Low-temperature FTIR spectroscopy provides evidence for protein-bound water molecules in eubacterial light-driven ion pumps. Phys Chem Chem Phys 2018; 20:3165-3171. [DOI: 10.1039/c7cp05674e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The present FTIR study showed that eubacterial light-driven H+, Na+ and Cl− pump rhodopsins contain strongly hydrogen-bonded water molecule, the functional determinant of light-driven proton pump. This explains well the asymmetric functional conversions of light-driven ion pumps.
Collapse
Affiliation(s)
- Yurika Nomura
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Showa-ku
- Japan
| | - Shota Ito
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Showa-ku
- Japan
| | - Miwako Teranishi
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Showa-ku
- Japan
| | - Hikaru Ono
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Showa-ku
- Japan
| | - Keiichi Inoue
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Showa-ku
- Japan
- OptoBioTechnology Research Center
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Showa-ku
- Japan
- OptoBioTechnology Research Center
| |
Collapse
|
25
|
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.
Collapse
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.
| |
Collapse
|
26
|
Inoue K. The Study and Application of Photoreceptive Membrane Protein, Rhodopsin. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2016. [DOI: 10.1246/bcsj.20160235] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
27
|
Kottke T, Lórenz-Fonfría VA, Heberle J. The Grateful Infrared: Sequential Protein Structural Changes Resolved by Infrared Difference Spectroscopy. J Phys Chem B 2016; 121:335-350. [PMID: 28100053 DOI: 10.1021/acs.jpcb.6b09222] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The catalytic activity of proteins is a function of structural changes. Very often these are as minute as protonation changes, hydrogen bonding changes, and amino acid side chain reorientations. To resolve these, a methodology is afforded that not only provides the molecular sensitivity but allows for tracing the sequence of these hierarchical reactions at the same time. This feature article showcases results from time-resolved IR spectroscopy on channelrhodopsin (ChR), light-oxygen-voltage (LOV) domain protein, and cryptochrome (CRY). All three proteins are activated by blue light, but their biological role is drastically different. Channelrhodopsin is a transmembrane retinylidene protein which represents the first light-activated ion channel of its kind and which is involved in primitive vision (phototaxis) of algae. LOV and CRY are flavin-binding proteins acting as photoreceptors in a variety of signal transduction mechanisms in all kingdoms of life. Beyond their biological relevance, these proteins are employed in exciting optogenetic applications. We show here how IR difference absorption resolves crucial structural changes of the protein after photonic activation of the chromophore. Time-resolved techniques are introduced that cover the time range from nanoseconds to minutes along with some technical considerations. Finally, we provide an outlook toward novel experimental approaches that are currently developed in our laboratories or are just in our minds ("Gedankenexperimente"). We believe that some of them have the potential to provide new science.
Collapse
Affiliation(s)
- Tilman Kottke
- Department of Chemistry, Physical and Biophysical Chemistry, Bielefeld University , Universitätsstraße 25, 33615 Bielefeld, Germany
| | | | - Joachim Heberle
- Experimental Molecular Biophysics, Freie Universität Berlin , Arnimalle 14, 14195 Berlin, Germany
| |
Collapse
|
28
|
Maresca JA, Keffer JL, Miller KJ. Biochemical Analysis of Microbial Rhodopsins. ACTA ACUST UNITED AC 2016; 41:1F.4.1-1F.4.18. [PMID: 27153387 DOI: 10.1002/cpmc.5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Ion-pumping rhodopsins transfer ions across the microbial cell membrane in a light-dependent fashion. As the rate of biochemical characterization of microbial rhodopsins begins to catch up to the rate of microbial rhodopsin identification in environmental and genomic sequence data sets, in vitro analysis of their light-absorbing properties and in vivo analysis of ion pumping will remain critical to characterizing these proteins. As we learn more about the variety of physiological roles performed by microbial rhodopsins in different cell types and environments, observing the localization patterns of the rhodopsins and/or quantifying the number of rhodopsin-bearing cells in natural environments will become more important. Here, we provide protocols for purification of rhodopsin-containing membranes, detection of ion pumping, and observation of functional rhodopsins in laboratory and environmental samples using total internal reflection fluorescence microscopy. © 2016 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- Julia A Maresca
- University of Delaware, Department of Civil and Environmental Engineering, Newark, Delaware
| | - Jessica L Keffer
- University of Delaware, Department of Civil and Environmental Engineering, Newark, Delaware
| | - Kelsey J Miller
- University of Delaware, Department of Biological Sciences, Newark, Delaware
| |
Collapse
|
29
|
Sudo Y, Yoshizawa S. Functional and Photochemical Characterization of a Light-Driven Proton Pump from the Gammaproteobacterium Pantoea vagans. Photochem Photobiol 2016; 92:420-7. [PMID: 26970049 DOI: 10.1111/php.12585] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 02/15/2016] [Indexed: 11/29/2022]
Abstract
Photoactive retinal proteins are widely distributed throughout the domains of the microbial world (i.e., bacteria, archaea, and eukarya). Here we describe three retinal proteins belonging to a phylogenetic clade with a unique DTG motif. Light-induced decrease in the environmental pH and its inhibition by carbonyl cyanide m-chlorophenylhydrazone revealed that these retinal proteins function as light-driven outward electrogenic proton pumps. We further characterized one of these proteins, Pantoea vagans rhodopsin (PvR), spectroscopically. Visible spectroscopy and high-performance liquid chromatography revealed that PvR has an absorption maximum at 538 nm with the retinal chromophore predominantly in the all-trans form (>90%) under both dark and light conditions. We estimated the pKa values of the protonated Schiff base of the retinal chromophore and its counterion as approximately 13.5 and 2.1, respectively, by using pH titration experiments, and the photochemical reaction cycle of PvR was measured by time-resolved flash-photolysis in the millisecond timeframe. We observed a blue-shifted and a red-shifted intermediate, which we assigned as M-like and O-like intermediates, respectively. Decay of the M-like intermediate was highly sensitive to environmental pH, suggesting that proton uptake is coupled to decay of the M-like intermediate. From these results, we propose a putative model for the photoreaction of PvR.
Collapse
Affiliation(s)
- Yuki Sudo
- Division of Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
| |
Collapse
|