1
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Noji T, Chiba Y, Saito K, Ishikita H. Energetics of the H-Bond Network in Exiguobacterium sibiricum Rhodopsin. Biochemistry 2024. [PMID: 38745402 DOI: 10.1021/acs.biochem.4c00182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Exiguobacterium sibiricum rhodopsin (ESR) functions as a light-driven proton pump utilizing Lys96 for proton uptake and maintaining its activity over a wide pH range. Using a combination of methodologies including the linear Poisson-Boltzmann equation and a quantum mechanical/molecular mechanical approach with a polarizable continuum model, we explore the microscopic mechanisms underlying its pumping activity. Lys96, the primary proton uptake site, remains deprotonated owing to the loss of solvation in the ESR protein environment. Asp85, serving as a proton acceptor group for Lys96, does not form a low-barrier H-bond with His57. Instead, deprotonated Asp85 forms a salt-bridge with protonated His57, and the proton is predominantly located at the His57 moiety. Glu214, the only acidic residue at the end of the H-bond network exhibits a pKa value of ∼6, slightly elevated due to solvation loss. It seems likely that the H-bond network [Asp85···His57···H2O···Glu214] serves as a proton-conducting pathway toward the protein bulk surface.
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Affiliation(s)
- Tomoyasu Noji
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Yoshihiro Chiba
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Keisuke Saito
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Hiroshi Ishikita
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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2
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Petrovskaya LE, Siletsky SA, Mamedov MD, Lukashev EP, Balashov SP, Dolgikh DA, Kirpichnikov MP. Features of the Mechanism of Proton Transport in ESR, Retinal Protein from Exiguobacterium sibiricum. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1544-1554. [PMID: 38105023 DOI: 10.1134/s0006297923100103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 12/19/2023]
Abstract
Retinal-containing light-sensitive proteins - rhodopsins - are found in many microorganisms. Interest in them is largely explained by their role in light energy storage and photoregulation in microorganisms, as well as the prospects for their use in optogenetics to control neuronal activity, including treatment of various diseases. One of the representatives of microbial rhodopsins is ESR, the retinal protein of Exiguobacterium sibiricum. What distinguishes ESR from homologous proteins is the presence of a lysine residue (Lys96) as a proton donor for the Schiff base. This feature, along with the hydrogen bond of the proton acceptor Asp85 with the His57 residue, determines functional characteristics of ESR as a proton pump. This review examines the results of ESR studies conducted using various methods, including direct electrometry. Comparison of the obtained data with the results of structural studies and with other retinal proteins allows us to draw conclusions about the mechanisms of transport of hydrogen ions in ESR and similar retinal proteins.
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Affiliation(s)
- Lada E Petrovskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - Sergei A Siletsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Mahir D Mamedov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Eugene P Lukashev
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Sergei P Balashov
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697
| | - Dmitry A Dolgikh
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Mikhail P Kirpichnikov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
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3
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Petrovskaya LE, Lukashev EP, Mamedov MD, Kryukova EA, Balashov SP, Dolgikh DA, Rubin AB, Kirpichnikov MP, Siletsky SA. Oriented Insertion of ESR-Containing Hybrid Proteins in Proteoliposomes. Int J Mol Sci 2023; 24:ijms24087369. [PMID: 37108532 PMCID: PMC10138546 DOI: 10.3390/ijms24087369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/13/2023] [Accepted: 04/15/2023] [Indexed: 04/29/2023] Open
Abstract
Microbial rhodopsins comprise a diverse family of retinal-containing membrane proteins that convert absorbed light energy to transmembrane ion transport or sensory signals. Incorporation of these proteins in proteoliposomes allows their properties to be studied in a native-like environment; however, unidirectional protein orientation in the artificial membranes is rarely observed. We aimed to obtain proteoliposomes with unidirectional orientation using a proton-pumping retinal protein from Exiguobacterium sibiricum, ESR, as a model. Three ESR hybrids with soluble protein domains (mCherry or thioredoxin at the C-terminus and Caf1M chaperone at the N-terminus) were obtained and characterized. The photocycle of the hybrid proteins incorporated in proteoliposomes demonstrated a higher pKa of the M state accumulation compared to that of the wild-type ESR. Large negative electrogenic phases and an increase in the relative amplitude of kinetic components in the microsecond time range in the kinetics of membrane potential generation of ESR-Cherry and ESR-Trx indicate a decrease in the efficiency of transmembrane proton transport. On the contrary, Caf-ESR demonstrates a native-like kinetics of membrane potential generation and the corresponding electrogenic stages. Our experiments show that the hybrid with Caf1M promotes the unidirectional orientation of ESR in proteoliposomes.
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Affiliation(s)
- Lada E Petrovskaya
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Evgeniy P Lukashev
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory, 1, 119234 Moscow, Russia
| | - Mahir D Mamedov
- Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Elena A Kryukova
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Sergei P Balashov
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA
| | - Dmitry A Dolgikh
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory, 1, 119234 Moscow, Russia
| | - Andrei B Rubin
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory, 1, 119234 Moscow, Russia
| | - Mikhail P Kirpichnikov
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory, 1, 119234 Moscow, Russia
| | - Sergey A Siletsky
- Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
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4
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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.
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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
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5
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Petrovskaya LE, Lukashev EP, Siletsky SA, Imasheva ES, Wang JM, Mamedov MD, Kryukova EA, Dolgikh DA, Rubin AB, Kirpichnikov MP, Balashov SP, Lanyi JK. Proton transfer reactions in donor site mutants of ESR, a retinal protein from Exiguobacterium sibiricum. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2022; 234:112529. [PMID: 35878544 DOI: 10.1016/j.jphotobiol.2022.112529] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 07/04/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
Light-driven proton transport by microbial retinal proteins such as archaeal bacteriorhodopsin involves carboxylic residues as internal proton donors to the catalytic center which is a retinal Schiff base (SB). The proton donor, Asp96 in bacteriorhodopsin, supplies a proton to the transiently deprotonated Schiff base during the photochemical cycle. Subsequent proton uptake resets the protonated state of the donor. This two step process became a distinctive signature of retinal based proton pumps. Similar steps are observed also in many natural variants of bacterial proteorhodopsins and xanthorhodopsins where glutamic acid residues serve as a proton donor. Recently, however, an exception to this rule was found. A retinal protein from Exiguobacterium sibiricum, ESR, contains a Lys residue in place of Asp or Glu, which facilitates proton transfer from the bulk to the SB. Lys96 can be functionally replaced with the more common donor residues, Asp or Glu. Proton transfer to the SB in the mutants containing these replacements (K96E and K96D/A47T) is much faster than in the proteins lacking the proton donor (K96A and similar mutants), and in the case of K96D/A47T, comparable with that in the wild type, indicating that carboxylic residues can replace Lys96 as proton donors in ESR. We show here that there are important differences in the functioning of these residues in ESR from the way Asp96 functions in bacteriorhodopsin. Reprotonation of the SB and proton uptake from the bulk occur almost simultaneously during the M to N transition (as in the wild type ESR at neutral pH), whereas in bacteriorhodopsin these two steps are well separated in time and occur during the M to N and N to O transitions, respectively.
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Affiliation(s)
- Lada E Petrovskaya
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow 117997, Russia.
| | - Evgeniy P Lukashev
- M. V. Lomonosov Moscow State University, Department of Biology, Leninskie gory, 1, Moscow 119234, Russia
| | - Sergey A Siletsky
- Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russian Federation.
| | - Eleonora S Imasheva
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA
| | - Jennifer M Wang
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA
| | - Mahir D Mamedov
- Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russian Federation
| | - Elena A Kryukova
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow 117997, Russia; Emanuel Institute of Biochemical Physics, Kosygina str., 4, Moscow 119334, Russia
| | - Dmitriy A Dolgikh
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow 117997, Russia; M. V. Lomonosov Moscow State University, Department of Biology, Leninskie gory, 1, Moscow 119234, Russia; Emanuel Institute of Biochemical Physics, Kosygina str., 4, Moscow 119334, Russia
| | - Andrei B Rubin
- M. V. Lomonosov Moscow State University, Department of Biology, Leninskie gory, 1, Moscow 119234, Russia
| | - Mikhail P Kirpichnikov
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow 117997, Russia; M. V. Lomonosov Moscow State University, Department of Biology, Leninskie gory, 1, Moscow 119234, Russia
| | - Sergei P Balashov
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA.
| | - Janos K Lanyi
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA
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6
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Application of direct electrometry in studies of microbial rhodopsins reconstituted in proteoliposomes. Biophys Rev 2022; 14:771-778. [PMID: 36124261 PMCID: PMC9481854 DOI: 10.1007/s12551-022-00986-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 07/15/2022] [Indexed: 01/21/2023] Open
Abstract
Microbial rhodopsins are the family of retinal-containing proteins that perform primarily the light-driven transmembrane ion transport and sensory functions. They are widely distributed in nature and can be used for optogenetic control of the cellular activities by light. Functioning of microbial rhodopsins results in generation of the transmembrane electric potential in response to a flash that can be measured by direct time-resolved electrometry. This method was developed by L. Drachev and his colleagues at the Belozersky Institute and successfully applied in the functional studies of microbial rhodopsins. First measurements were performed using bacteriorhodopsin from Halobacterium salinarum-the prototype member of the microbial retinal protein family. Later, direct electrometric studies were conducted with proteorhodopsin from Exiguobacterium sibiricum (ESR), the sodium pump from Dokdonia, and other proteins. They allowed detailed characterization of the charge transfer steps during the photocycle of microbial rhodopsins and provided new insights for profound understanding of their mechanism of action.
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7
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Brown LS. Light-driven proton transfers and proton transport by microbial rhodopsins - A biophysical perspective. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183867. [PMID: 35051382 DOI: 10.1016/j.bbamem.2022.183867] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/30/2021] [Accepted: 01/10/2022] [Indexed: 12/31/2022]
Abstract
In the last twenty years, our understanding of the rules and mechanisms for the outward light-driven proton transport (and underlying proton transfers) by microbial rhodopsins has been changing dramatically. It transitioned from a very detailed atomic-level understanding of proton transport by bacteriorhodopsin, the prototypical proton pump, to a confounding variety of sequence motifs, mechanisms, directions, and modes of transport in its newly found homologs. In this review, we will summarize and discuss experimental data obtained on new microbial rhodopsin variants, highlighting their contribution to the refinement and generalization of the ideas crystallized in the previous century. In particular, we will focus on the proton transport (and transfers) vectoriality and their structural determinants, which, in many cases, remain unidentified.
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Affiliation(s)
- Leonid S Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Ontario N1G 2W1, Canada.
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8
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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.
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9
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Bondar AN. Mechanisms of long-distance allosteric couplings in proton-binding membrane transporters. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 128:199-239. [PMID: 35034719 DOI: 10.1016/bs.apcsb.2021.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Membrane transporters that use proton binding and proton transfer for function couple local protonation change with changes in protein conformation and water dynamics. Changes of protein conformation might be required to allow transient formation of hydrogen-bond networks that bridge proton donor and acceptor pairs separated by long distances. Inter-helical hydrogen-bond networks adjust rapidly to protonation change, and ensure rapid response of the protein structure and dynamics. Membrane transporters with known three-dimensional structures and proton-binding groups inform on general principles of protonation-coupled protein conformational dynamics. Inter-helical hydrogen bond motifs between proton-binding carboxylate groups and a polar sidechain are observed in unrelated membrane transporters, suggesting common principles of coupling protonation change with protein conformational dynamics.
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Affiliation(s)
- Ana-Nicoleta Bondar
- University of Bucharest, Faculty of Physics, Măgurele, Romania; Forschungszentrum Jülich, Institute of Computational Biomedicine, Jülich, Germany.
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10
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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.
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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
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11
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Sasaki S, Tamogami J, Nishiya K, Demura M, Kikukawa T. Replaceability of Schiff base proton donors in light-driven proton pump rhodopsins. J Biol Chem 2021; 297:101013. [PMID: 34329681 PMCID: PMC8387761 DOI: 10.1016/j.jbc.2021.101013] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
Many H+-pump rhodopsins conserve “H+ donor” residues in cytoplasmic (CP) half channels to quickly transport H+ from the CP medium to Schiff bases at the center of these proteins. For conventional H+ pumps, the donors are conserved as Asp or Glu but are replaced by Lys in the minority, such as Exiguobacterium sibiricum rhodopsin (ESR). In dark states, carboxyl donors are protonated, whereas the Lys donor is deprotonated. As a result, carboxyl donors first donate H+ to the Schiff bases and then capture the other H+ from the medium, whereas the Lys donor first captures H+ from the medium and then donates it to the Schiff base. Thus, carboxyl and Lys-type H+ pumps seem to have different mechanisms, which are probably optimized for their respective H+-transfer reactions. Here, we examined these differences via replacement of donor residues. For Asp-type deltarhodopsin (DR), the embedded Lys residue distorted the protein conformation and did not act as the H+ donor. In contrast, for Glu-type proteorhodopsin (PR) and ESR, the embedded residues functioned well as H+ donors. These differences were further examined by focusing on the activation volumes during the H+-transfer reactions. The results revealed essential differences between archaeal H+ pump (DR) and eubacterial H+ pumps PR and ESR. Archaeal DR requires significant hydration of the CP channel for the H+-transfer reactions; however, eubacterial PR and ESR require the swing-like motion of the donor residue rather than hydration. Given this common mechanism, donor residues might be replaceable between eubacterial PR and ESR.
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Affiliation(s)
- Syogo Sasaki
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Jun Tamogami
- College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime, Japan.
| | - Koki Nishiya
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Makoto Demura
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan.
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12
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Smitienko OA, Feldman TB, Petrovskaya LE, Nekrasova OV, Yakovleva MA, Shelaev IV, Gostev FE, Cherepanov DA, Kolchugina IB, Dolgikh DA, Nadtochenko VA, Kirpichnikov MP, Ostrovsky MA. Comparative Femtosecond Spectroscopy of Primary Photoreactions of Exiguobacterium sibiricum Rhodopsin and Halobacterium salinarum Bacteriorhodopsin. J Phys Chem B 2021; 125:995-1008. [PMID: 33475375 DOI: 10.1021/acs.jpcb.0c07763] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The primary stages of the Exiguobacterium sibiricum rhodopsin (ESR) photocycle were investigated by femtosecond absorption laser spectroscopy in the spectral range of 400-900 nm with a time resolution of 25 fs. The dynamics of the ESR photoreaction were compared with the reactions of bacteriorhodopsin (bR) in purple membranes (bRPM) and in recombinant form (bRrec). The primary intermediates of the ESR photocycle were similar to intermediates I, J, and K in bacteriorhodopsin photoconversion. The CONTIN program was applied to analyze the characteristic times of the observed processes and to clarify the reaction scheme. A similar photoreaction pattern was observed for all studied retinal proteins, including two consecutive dynamic Stokes shift phases lasting ∼0.05 and ∼0.15 ps. The excited state decays through a femtosecond reactive pathway, leading to retinal isomerization and formation of product J, and a picosecond nonreactive pathway that leads only to the initial state. Retinal photoisomerization in ESR takes 0.69 ps, compared with 0.48 ps in bRPM and 0.74 ps in bRrec. The nonreactive excited state decay takes 5 ps in ESR and ∼3 ps in bR. We discuss the similarity of the primary reactions of ESR and other retinal proteins.
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Affiliation(s)
| | - Tatiana B Feldman
- Emanuel Institute of Biochemical Physics, Moscow 119334, Russia.,Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Lada E Petrovskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Oksana V Nekrasova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | | | - Ivan V Shelaev
- Semenov Federal Research Center of Chemical Physics, Moscow 119991, Russia
| | - Fedor E Gostev
- Semenov Federal Research Center of Chemical Physics, Moscow 119991, Russia
| | | | - Irina B Kolchugina
- Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Dmitry A Dolgikh
- Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Victor A Nadtochenko
- Semenov Federal Research Center of Chemical Physics, Moscow 119991, Russia.,Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Mikhail P Kirpichnikov
- Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Mikhail A Ostrovsky
- Emanuel Institute of Biochemical Physics, Moscow 119334, Russia.,Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
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13
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Inoue K. Diversity, Mechanism, and Optogenetic Application of Light-Driven Ion Pump Rhodopsins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1293:89-126. [PMID: 33398809 DOI: 10.1007/978-981-15-8763-4_6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ion-transporting microbial rhodopsins are widely used as major molecular tools in optogenetics. They are categorized into light-gated ion channels and light-driven ion pumps. While the former passively transport various types of cations and anions in a light-dependent manner, light-driven ion pumps actively transport specific ions, such as H+, Na+, Cl-, against electrophysiological potential by using light energy. Since the ion transport by these pumps induces hyperpolarization of membrane potential and inhibit neural firing, light-driven ion-pumping rhodopsins are mostly applied as inhibitory optogenetics tools. Recent progress in genome and metagenome sequencing identified more than several thousands of ion-pumping rhodopsins from a wide variety of microbes, and functional characterization studies has been revealing many new types of light-driven ion pumps one after another. Since light-gated channels were reviewed in other chapters in this book, here the rapid progress in functional characterization, molecular mechanism study, and optogenetic application of ion-pumping rhodopsins were reviewed.
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Affiliation(s)
- Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, Chiba, Japan.
- PRESTO, Japan Science and Technology Agency, Saitama, Japan.
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14
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His57 controls the efficiency of ESR, a light-driven proton pump from Exiguobacterium sibiricum at low and high pH. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148328. [PMID: 33075275 DOI: 10.1016/j.bbabio.2020.148328] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/06/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022]
Abstract
ESR, a light-driven proton pump from Exiguobacterium sibiricum, contains a lysine residue (Lys96) in the proton donor site. Substitution of Lys96 with a nonionizable residue greatly slows reprotonation of the retinal Schiff base. The recent study of electrogenicity of the K96A mutant revealed that overall efficiency of proton transport is decreased in the mutant due to back reactions (Siletsky et al., BBA, 2019). Similar to members of the proteorhodopsin and xanthorhodopsin families, in ESR the primary proton acceptor from the Schiff base, Asp85, closely interacts with His57. To examine the role of His57 in the efficiency of proton translocation by ESR, we studied the effects of H57N and H57N/K96A mutations on the pH dependence of light-induced pH changes in suspensions of Escherichia coli cells, kinetics of absorption changes and electrogenic proton transfer reactions during the photocycle. We found that at low pH (<5) the proton pumping efficiency of the H57N mutant in E. coli cells and its electrogenic efficiency in proteoliposomes is substantially higher than in the WT, suggesting that interaction of His57 with Asp85 sets the low pH limit for H+ pumping in ESR. The electrogenic components that correspond to proton uptake were strongly accelerated at low pH in the mutant indicating that Lys96 functions as a very efficient proton donor at low pH. In the H57N/K96A mutant, a higher H+ pumping efficiency compared with K96A was observed especially at high pH, apparently from eliminating back reactions between Asp85 and the Schiff base by the H57N mutation.
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15
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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
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16
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Lukashev EP, Petrovskaya LE, Tretyak MV, Kryukova EA, Sizova SV, Oleinikov VA. Formation of an Efficient Energy Transfer Complex between Quantum Dots and Exiguobacterium sibiricum Retinal Protein via the Histidine-Cysteine Anchor. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2019. [DOI: 10.1134/s1068162018050114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Elimination of proton donor strongly affects directionality and efficiency of proton transport in ESR, a light-driven proton pump from Exiguobacterium sibiricum. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:1-11. [DOI: 10.1016/j.bbabio.2018.09.365] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 08/31/2018] [Accepted: 09/16/2018] [Indexed: 11/20/2022]
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18
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The effect of the chromophoric group modification on the optical properties of retinal proteins. MENDELEEV COMMUNICATIONS 2018. [DOI: 10.1016/j.mencom.2018.07.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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19
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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
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20
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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.
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Affiliation(s)
- Andrew Harris
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada.
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21
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Abstract
Microbial rhodopsins (MRs) are a large family of photoactive membrane proteins, found in microorganisms belonging to all kingdoms of life, with new members being constantly discovered. Among the MRs are light-driven proton, cation and anion pumps, light-gated cation and anion channels, and various photoreceptors. Due to their abundance and amenability to studies, MRs served as model systems for a great variety of biophysical techniques, and recently found a great application as optogenetic tools. While the basic aspects of microbial rhodopsins functioning have been known for some time, there is still a plenty of unanswered questions. This chapter presents and summarizes the available knowledge, focusing on the functional and structural studies.
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Affiliation(s)
- Ivan Gushchin
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia.
| | - Valentin Gordeliy
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia.
- University of Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France.
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany.
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22
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DeCoursey TE, Morgan D, Musset B, Cherny VV. Insights into the structure and function of HV1 from a meta-analysis of mutation studies. J Gen Physiol 2017; 148:97-118. [PMID: 27481712 PMCID: PMC4969798 DOI: 10.1085/jgp.201611619] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 06/30/2016] [Indexed: 01/26/2023] Open
Abstract
The voltage-gated proton channel (HV1) is a widely distributed, proton-specific ion channel with unique properties. Since 2006, when genes for HV1 were identified, a vast array of mutations have been generated and characterized. Accessing this potentially useful resource is hindered, however, by the sheer number of mutations and interspecies differences in amino acid numbering. This review organizes all existing information in a logical manner to allow swift identification of studies that have characterized any particular mutation. Although much can be gained from this meta-analysis, important questions about the inner workings of HV1 await future revelation.
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Affiliation(s)
- Thomas E DeCoursey
- Department of Molecular Biophysics and Physiology, Rush University, Chicago, IL 60612
| | - Deri Morgan
- Department of Molecular Biophysics and Physiology, Rush University, Chicago, IL 60612
| | - Boris Musset
- Institut für Physiologie, PMU Klinikum Nürnberg, 90419 Nürnberg, Germany
| | - Vladimir V Cherny
- Department of Molecular Biophysics and Physiology, Rush University, Chicago, IL 60612
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23
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Wiechert M, Beitz E. Mechanism of formate-nitrite transporters by dielectric shift of substrate acidity. EMBO J 2017; 36:949-958. [PMID: 28250043 DOI: 10.15252/embj.201695776] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 01/25/2017] [Accepted: 01/30/2017] [Indexed: 11/09/2022] Open
Abstract
Bacterial formate-nitrite transporters (FNTs) regulate the metabolic flow of small, weak mono-acids. Recently, the eukaryotic PfFNT was identified as the malaria parasite's lactate transporter and novel drug target. Despite crystal data, central mechanisms of FNT gating and transport remained unclear. Here, we show elucidation of the FNT transport mechanism by single-step substrate protonation involving an invariant lysine in the periplasmic vestibule. Opposing earlier gating hypotheses and electrophysiology reports, quantification of total uptake by radiolabeled substrate indicates a permanently open conformation of the bacterial formate transporter, FocA, irrespective of the pH Site-directed mutagenesis, heavy water effects, mathematical modeling, and simulations of solvation imply a general, proton motive force-driven FNT transport mechanism: Electrostatic attraction of the acid anion into a hydrophobic vestibule decreases substrate acidity and facilitates protonation by the bulk solvent. We define substrate neutralization by proton transfer for transport via a hydrophobic transport path as a general theme of the Amt/Mep/Rh ammonium and formate-nitrite transporters.
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Affiliation(s)
- Marie Wiechert
- Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Eric Beitz
- Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, Kiel, Germany
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24
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Electrogenic steps of light-driven proton transport in ESR, a retinal protein from Exiguobacterium sibiricum. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1741-1750. [DOI: 10.1016/j.bbabio.2016.08.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/06/2016] [Accepted: 08/11/2016] [Indexed: 02/01/2023]
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25
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Albarracín VH, Kraiselburd I, Bamann C, Wood PG, Bamberg E, Farias ME, Gärtner W. Functional Green-Tuned Proteorhodopsin from Modern Stromatolites. PLoS One 2016; 11:e0154962. [PMID: 27187791 PMCID: PMC4871484 DOI: 10.1371/journal.pone.0154962] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 04/21/2016] [Indexed: 11/18/2022] Open
Abstract
The sequenced genome of the poly-extremophile Exiguobacterium sp. S17, isolated from modern stromatolites at Laguna Socompa (3,570 m), a High-Altitude Andean Lake (HAAL) in Argentinean Puna revealed a putative proteorhodopsin-encoding gene. The HAAL area is exposed to the highest UV irradiation on Earth, making the microbial community living in the stromatolites test cases for survival strategies under extreme conditions. The heterologous expressed protein E17R from Exiguobacterium (248 amino acids, 85% sequence identity to its ortholog ESR from E. sibiricum) was assembled with retinal displaying an absorbance maximum at 524 nm, which makes it a member of the green-absorbing PR-subfamily. Titration down to low pH values (eventually causing partial protein denaturation) indicated a pK value between two and three. Global fitting of data from laser flash-induced absorption changes gave evidence for an early red-shifted intermediate (its formation being below the experimental resolution) that decayed (τ1 = 3.5 μs) into another red-shifted intermediate. This species decayed in a two-step process (τ2 = 84 μs, τ3 = 11 ms), to which the initial state of E17-PR was reformed with a kinetics of 2 ms. Proton transport capability of the HAAL protein was determined by BLM measurements. Additional blue light irradiation reduced the proton current, clearly identifying a blue light absorbing, M-like intermediate. The apparent absence of this intermediate is explained by closely matching formation and decay kinetics.
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Affiliation(s)
- Virginia Helena Albarracín
- Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT, CONICET. Av. Belgrano y Pasaje Caseros. 4000- S. M. de Tucumán, Argentina
- Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, 4000, S. M. de Tucumán, Argentina
- * E-mail: (VHA); (WG)
| | - Ivana Kraiselburd
- Instituto de Biología Molecular y Celular de Rosario (IBR - CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas (FBIOYF - UNR), Suipacha 590, 2000, Rosario, Santa Fe, Argentina
| | - Christian Bamann
- Max-Planck-Institute for Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt am Main, Germany
| | - Phillip G. Wood
- Max-Planck-Institute for Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt am Main, Germany
| | - Ernst Bamberg
- Max-Planck-Institute for Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt am Main, Germany
| | - María Eugenia Farias
- Max-Planck-Institute for Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt am Main, Germany
| | - Wolfgang Gärtner
- Max-Planck-Institute for Chemical Energy Conversion, Stiftstrasse 34–36, D-45470 Mülheim, Germany
- * E-mail: (VHA); (WG)
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26
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Gushchin I, Shevchenko V, Polovinkin V, Borshchevskiy V, Buslaev P, Bamberg E, Gordeliy V. Structure of the light-driven sodium pump KR2 and its implications for optogenetics. FEBS J 2015; 283:1232-8. [DOI: 10.1111/febs.13585] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 10/22/2015] [Accepted: 10/30/2015] [Indexed: 01/27/2023]
Affiliation(s)
- Ivan Gushchin
- Institute of Complex Systems (ICS); ICS-6: Structural Biochemistry; Research Centre Jülich; Germany
- Moscow Institute of Physics and Technology; Dolgoprudniy Russia
| | - Vitaly Shevchenko
- Institute of Complex Systems (ICS); ICS-6: Structural Biochemistry; Research Centre Jülich; Germany
- Moscow Institute of Physics and Technology; Dolgoprudniy Russia
| | - Vitaly Polovinkin
- Institute of Complex Systems (ICS); ICS-6: Structural Biochemistry; Research Centre Jülich; Germany
- Moscow Institute of Physics and Technology; Dolgoprudniy Russia
- Institut de Biologie Structurale; Université Grenoble Alpes; France
- Institut de Biologie Structurale; Centre National de la Recherche Scientifique; Grenoble France
- Institut de Biologie Structurale; Direction des Sciences du Vivant; Commissariat à l'Énergie Atomique; Grenoble France
| | - Valentin Borshchevskiy
- Institute of Complex Systems (ICS); ICS-6: Structural Biochemistry; Research Centre Jülich; Germany
- Moscow Institute of Physics and Technology; Dolgoprudniy Russia
| | - Pavel Buslaev
- Moscow Institute of Physics and Technology; Dolgoprudniy Russia
| | - Ernst Bamberg
- Max Planck Institute of Biophysics; Frankfurt am Main Germany
| | - Valentin Gordeliy
- Institute of Complex Systems (ICS); ICS-6: Structural Biochemistry; Research Centre Jülich; Germany
- Moscow Institute of Physics and Technology; Dolgoprudniy Russia
- Institut de Biologie Structurale; Université Grenoble Alpes; France
- Institut de Biologie Structurale; Centre National de la Recherche Scientifique; Grenoble France
- Institut de Biologie Structurale; Direction des Sciences du Vivant; Commissariat à l'Énergie Atomique; Grenoble France
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Abstract
Rhodopsins are light-sensing proteins used in optogenetics. The word "rhodopsin" originates from the Greek words "rhodo" and "opsis," indicating rose and sight, respectively. Although the classical meaning of rhodopsin is the red-colored pigment in our eyes, the modern meaning of rhodopsin encompasses photoactive proteins containing a retinal chromophore in animals and microbes. Animal and microbial rhodopsins possess 11-cis and all-trans retinal, respectively, to capture light in seven transmembrane α-helices, and photoisomerizations into all-trans and 13-cis forms, respectively, initiate each function. Ion-transporting proteins can be found in microbial rhodopsins, such as light-gated channels and light-driven pumps, which are the main tools in optogenetics. Light-driven pumps, such as archaeal H(+) pump bacteriorhodopsin (BR) and Cl(-) pump halorhodopsin (HR), were discovered in the 1970s, and their mechanism has been extensively studied. On the other hand, different kinds of H(+) and Cl(-) pumps have been found in marine bacteria, such as proteorhodopsin (PR) and Fulvimarina pelagi rhodopsin (FR), respectively. In addition, a light-driven Na(+) pump was found, Krokinobacter eikastus rhodopsin 2 (KR2). These light-driven ion-pumping microbial rhodopsins are classified as DTD, TSA, DTE, NTQ, and NDQ rhodopsins for BR, HR, PR, FR, and KR2, respectively. Recent understanding of ion-pumping microbial rhodopsins is reviewed in this paper.
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Affiliation(s)
- Hideki Kandori
- Department of Frontier Materials and OptoBioTechnology Research Center, Nagoya Institute of Technology Nagoya, Japan
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28
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Harris A, Ljumovic M, Bondar AN, Shibata Y, Ito S, Inoue K, Kandori H, Brown LS. A new group of eubacterial light-driven retinal-binding proton pumps with an unusual cytoplasmic proton donor. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1518-29. [PMID: 26260121 DOI: 10.1016/j.bbabio.2015.08.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/05/2015] [Accepted: 08/05/2015] [Indexed: 10/23/2022]
Abstract
One of the main functions of microbial rhodopsins is outward-directed light-driven proton transport across the plasma membrane, which can provide sources of energy alternative to respiration and chlorophyll photosynthesis. Proton-pumping rhodopsins are found in Archaea (Halobacteria), multiple groups of Bacteria, numerous fungi, and some microscopic algae. An overwhelming majority of these proton pumps share the common transport mechanism, in which a proton from the retinal Schiff base is first transferred to the primary proton acceptor (normally an Asp) on the extracellular side of retinal. Next, reprotonation of the Schiff base from the cytoplasmic side is mediated by a carboxylic proton donor (Asp or Glu), which is located on helix C and is usually hydrogen-bonded to Thr or Ser on helix B. The only notable exception from this trend was recently found in Exiguobacterium, where the carboxylic proton donor is replaced by Lys. Here we describe a new group of efficient proteobacterial retinal-binding light-driven proton pumps which lack the carboxylic proton donor on helix C (most often replaced by Gly) but possess a unique His residue on helix B. We characterize the group spectroscopically and propose that this histidine forms a proton-donating complex compensating for the loss of the carboxylic proton donor.
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Affiliation(s)
- Andrew Harris
- Department of Physics, University of Guelph, ON, Canada
| | | | | | - Yohei Shibata
- Department of Frontier Materials, Nagoya Institute of Technology, Nagoya, Japan
| | - Shota Ito
- Department of Frontier Materials, Nagoya Institute of Technology, Nagoya, Japan
| | - Keiichi Inoue
- Department of Frontier Materials, Nagoya Institute of Technology, Nagoya, Japan; PRESTO, Japan Science and Technology Agency, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Nagoya, Japan.
| | - Leonid S Brown
- Department of Physics, University of Guelph, ON, Canada.
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Petrovskaya LE, Balashov SP, Lukashev EP, Imasheva ES, Gushchin IY, Dioumaev AK, Rubin AB, Dolgikh DA, Gordeliy VI, Lanyi JK, Kirpichnikov MP. ESR — A retinal protein with unusual properties from Exiguobacterium sibiricum. BIOCHEMISTRY (MOSCOW) 2015; 80:688-700. [DOI: 10.1134/s000629791506005x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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30
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Martin-Cuadrado AB, Garcia-Heredia I, Moltó AG, López-Úbeda R, Kimes N, López-García P, Moreira D, Rodriguez-Valera F. A new class of marine Euryarchaeota group II from the Mediterranean deep chlorophyll maximum. ISME JOURNAL 2014; 9:1619-34. [PMID: 25535935 DOI: 10.1038/ismej.2014.249] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 11/14/2014] [Accepted: 11/19/2014] [Indexed: 11/09/2022]
Abstract
We have analyzed metagenomic fosmid clones from the deep chlorophyll maximum (DCM), which, by genomic parameters, correspond to the 16S ribosomal RNA (rRNA)-defined marine Euryarchaeota group IIB (MGIIB). The fosmid collections associated with this group add up to 4 Mb and correspond to at least two species within this group. From the proposed essential genes contained in the collections, we infer that large sections of the conserved regions of the genomes of these microbes have been recovered. The genomes indicate a photoheterotrophic lifestyle, similar to that of the available genome of MGIIA (assembled from an estuarine metagenome in Puget Sound, Washington Pacific coast), with a proton-pumping rhodopsin of the same kind. Several genomic features support an aerobic metabolism with diversified substrate degradation capabilities that include xenobiotics and agar. On the other hand, these MGIIB representatives are non-motile and possess similar genome size to the MGIIA-assembled genome, but with a lower GC content. The large phylogenomic gap with other known archaea indicates that this is a new class of marine Euryarchaeota for which we suggest the name Thalassoarchaea. The analysis of recruitment from available metagenomes indicates that the representatives of group IIB described here are largely found at the DCM (ca. 50 m deep), in which they are abundant (up to 0.5% of the reads), and at the surface mostly during the winter mixing, which explains formerly described 16S rRNA distribution patterns. Their uneven representation in environmental samples that are close in space and time might indicate sporadic blooms.
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Affiliation(s)
- Ana-Belen Martin-Cuadrado
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Inmaculada Garcia-Heredia
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Aitor Gonzaga Moltó
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Rebeca López-Úbeda
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Nikole Kimes
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Purificación López-García
- Unité d'Ecologie, Systématique et Evolution, UMR CNRS 8079, Université Paris-Sud, Orsay Cedex, France
| | - David Moreira
- Unité d'Ecologie, Systématique et Evolution, UMR CNRS 8079, Université Paris-Sud, Orsay Cedex, France
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
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Balashov SP, Imasheva ES, Dioumaev A, Wang JM, Jung KH, Lanyi JK. Light-driven Na(+) pump from Gillisia limnaea: a high-affinity Na(+) binding site is formed transiently in the photocycle. Biochemistry 2014; 53:7549-61. [PMID: 25375769 PMCID: PMC4263435 DOI: 10.1021/bi501064n] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 10/17/2014] [Indexed: 02/06/2023]
Abstract
A group of microbial retinal proteins most closely related to the proton pump xanthorhodopsin has a novel sequence motif and a novel function. Instead of, or in addition to, proton transport, they perform light-driven sodium ion transport, as reported for one representative of this group (KR2) from Krokinobacter. In this paper, we examine a similar protein, GLR from Gillisia limnaea, expressed in Escherichia coli, which shares some properties with KR2 but transports only Na(+). The absorption spectrum of GLR is insensitive to Na(+) at concentrations of ≤3 M. However, very low concentrations of Na(+) cause profound differences in the decay and rise time of photocycle intermediates, consistent with a switch from a "Na(+)-independent" to a "Na(+)-dependent" photocycle (or photocycle branch) at ∼60 μM Na(+). The rates of photocycle steps in the latter, but not the former, are linearly dependent on Na(+) concentration. This suggests that a high-affinity Na(+) binding site is created transiently after photoexcitation, and entry of Na(+) from the bulk to this site redirects the course of events in the remainder of the cycle. A greater concentration of Na(+) is needed for switching the reaction path at lower pH. The data suggest therefore competition between H(+) and Na(+) to determine the two alternative pathways. The idea that a Na(+) binding site can be created at the Schiff base counterion is supported by the finding that upon perturbation of this region in the D251E mutant, Na(+) binds without photoexcitation. Binding of Na(+) to the mutant shifts the chromophore maximum to the red like that of H(+), which occurs in the photocycle of the wild type.
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Affiliation(s)
- Sergei P. Balashov
- Department
of Physiology and Biophysics, University
of California, Irvine, California 92697, United States
| | - Eleonora S. Imasheva
- Department
of Physiology and Biophysics, University
of California, Irvine, California 92697, United States
| | - Andrei
K. Dioumaev
- Department
of Physiology and Biophysics, University
of California, Irvine, California 92697, United States
| | - Jennifer M. Wang
- Department
of Physiology and Biophysics, University
of California, Irvine, California 92697, United States
| | - Kwang-Hwan Jung
- Department
of Life Science and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Shinsu-Dong 1, Mapo-Gu, Seoul 121-742, Korea
| | - Janos K. Lanyi
- Department
of Physiology and Biophysics, University
of California, Irvine, California 92697, United States
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33
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Bamann C, Bamberg E, Wachtveitl J, Glaubitz C. Proteorhodopsin. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:614-25. [PMID: 24060527 DOI: 10.1016/j.bbabio.2013.09.010] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 09/11/2013] [Accepted: 09/13/2013] [Indexed: 10/26/2022]
Abstract
Proteorhodopsins are the most abundant retinal based photoreceptors and their phototrophic function might be relevant in marine ecosystems. Here, we describe their remarkable molecular properties with a special focus on the green absorbing variant. Its distinct features include a high pKa value of the primary proton acceptor stabilized through an interaction with a conserved histidine, a long-range interaction between the cytoplasmic EF loop and the chromophore entailing a particular mode of color tuning and a variable proton pumping vectoriality with complex voltage-dependence. The proteorhodopsin family represents a profound example for structure-function relationships. Especially the development of a biophysical understanding of green proteorhodopsin is an excellent example for the unique opportunities offered by a combined approach of advanced spectroscopic and electrophysiological methods. This article is part of a Special Issue entitled: Retinal Proteins-You can teach an old dog new tricks.
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Affiliation(s)
- Christian Bamann
- Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany.
| | - Ernst Bamberg
- Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Josef Wachtveitl
- Johann Wolfgang Goethe University, Institute for Physical and Theoretical Chemistry, Max-von-Laue Straße 7, 60438 Frankfurt am Main, Germany
| | - Clemens Glaubitz
- Johann Wolfgang Goethe University, Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance, Max-von-Laue Straße 9, 60438 Frankfurt am Main, Germany
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Dioumaev AK, Petrovskaya LE, Wang JM, Balashov SP, Dolgikh DA, Kirpichnikov MP, Lanyi JK. Photocycle of Exiguobacterium sibiricum rhodopsin characterized by low-temperature trapping in the IR and time-resolved studies in the visible. J Phys Chem B 2013; 117:7235-53. [PMID: 23718558 DOI: 10.1021/jp402430w] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The photocycle of the retinal protein from Exiguobacterium sibiricum, which differs from bacteriorhodopsin in both its primary donor and acceptor, is characterized by visible and infrared spectroscopy. At pH above pKa ~6.5, we find a bacteriorhodopsin-like photocycle, which originates from excitation of the all-trans retinal chromophore with K-, L-, M-, and N-like intermediates. At pH below pKa ~6.5, the M state, which reflects Schiff base deprotonation during proton pumping, is not accumulated. However, using the infrared band at ~1760 cm(-1) as a marker for transient protonation of the primary acceptor, we find that Schiff base deprotonation must have occurred at pH not only above but also below the pKa ~6.5. Thus, the M state is formed but not accumulated for kinetic reasons. Further, chromophore reisomerization from the 13-cis to the all-trans conformation occurs very late in the photocycle. The strongly red-shifted states that dominate the second half of the cycle are produced before the reisomerization step, and by this criterion, they are not O-like but rather N-like states. The assignment of photocycle intermediates enables reevaluation of the photocycle; its specific features are discussed in relation to the general mechanism of proton transport in retinal proteins.
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Affiliation(s)
- Andrei K Dioumaev
- Department of Physiology and Biophysics, University of California, Irvine, California 92697, USA.
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