1
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Matsunami-Nakamura R, Tamogami J, Takeguchi M, Ishikawa J, Kikukawa T, Kamo N, Nara T. Key determinants for signaling in the sensory rhodopsin II/transducer complex are different between Halobacterium salinarum and Natronomonas pharaonis. FEBS Lett 2023; 597:2334-2344. [PMID: 37532685 DOI: 10.1002/1873-3468.14711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 08/04/2023]
Abstract
The cell membrane of Halobacterium salinarum contains a retinal-binding photoreceptor, sensory rhodopsin II (HsSRII), coupled with its cognate transducer (HsHtrII), allowing repellent phototaxis behavior for shorter wavelength light. Previous studies on SRII from Natronomonas pharaonis (NpSRII) pointed out the importance of the hydrogen bonding interaction between Thr204NpSRII and Tyr174NpSRII in signal transfer from SRII to HtrII. Here, we investigated the effect on phototactic function by replacing residues in HsSRII corresponding to Thr204NpSRII and Tyr174NpSRII . Whereas replacement of either residue altered the photocycle kinetics, introduction of any mutations at Ser201HsSRII and Tyr171HsSRII did not eliminate negative phototaxis function. These observations imply the possibility of the presence of an unidentified molecular mechanism for photophobic signal transduction differing from NpSRII-NpHtrII.
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Affiliation(s)
| | - Jun Tamogami
- College of Pharmaceutical Sciences, Matsuyama University, Japan
| | - Miki Takeguchi
- College of Pharmaceutical Sciences, Matsuyama University, Japan
| | - Junya Ishikawa
- College of Pharmaceutical Sciences, Matsuyama University, Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Naoki Kamo
- College of Pharmaceutical Sciences, Matsuyama University, Japan
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Toshifumi Nara
- College of Pharmaceutical Sciences, Matsuyama University, Japan
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2
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Petrovskaya LE, Lukashev EP, Lyukmanova EN, Shulepko MA, Kryukova EA, Ziganshin RH, Dolgikh DA, Maksimov EG, Rubin AB, Kirpichnikov MP, Lanyi JK, Balashov SP. Expression of Xanthorhodopsin in Escherichia coli. Protein J 2023:10.1007/s10930-023-10109-5. [DOI: 10.1007/s10930-023-10109-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2023] [Indexed: 04/03/2023]
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3
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Otsuka K, Seike T, Toya Y, Ishii J, Hirono-Hara Y, Hara KY, Matsuda F. Evolutionary approach for improved proton pumping activity of heterologous rhodopsin expressed in Escherichia coli. J Biosci Bioeng 2022; 134:484-490. [PMID: 36171161 DOI: 10.1016/j.jbiosc.2022.08.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/29/2022] [Accepted: 08/17/2022] [Indexed: 12/13/2022]
Abstract
A light-driven ATP regeneration system using rhodopsin has been utilized as a method to improve the production of useful substances by microorganisms. To enable the industrial use of this system, the proton pumping rate of rhodopsin needs to be enhanced. Nonetheless, a method for this enhancement has not been established. In this study, we attempted to develop an evolutionary engineering method to improve the proton-pumping activity of rhodopsins. We first introduced random mutations into delta-rhodopsin (dR) from Haloterrigena turkmenica using error-prone PCR to generate approximately 7000 Escherichia coli strains carrying the mutant dR genes. Rhodopsin-expressing E. coli with enhanced proton pumping activity have significantly increased survival rates in prolonged saline water. Considering this, we enriched the mutant E. coli cells with higher proton pumping rates by selecting populations able to survive starvation under 50 μmol m-2 s-1 at 37 °C. As a result, we successfully identified two strains, in which proton pumping activity was enhanced two-fold by heterologous expression in E. coli in comparison to wild-type strains. The combined approach of survival testing using saline water and evolutionary engineering methods used in this study will contribute greatly to the discovery of a novel rhodopsin with improved proton pumping activity. This will facilitate the utilization of rhodopsin in industrial applications.
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Affiliation(s)
- Kensuke Otsuka
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Taisuke Seike
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Jun Ishii
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo 657-8501, Japan; Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo 657-8501, Japan
| | - Yoko Hirono-Hara
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga, Shizuoka 422-8526, Japan
| | - Kiyotaka Y Hara
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga, Shizuoka 422-8526, Japan; Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga, Shizuoka 422-8526, Japan
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
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4
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Toya Y, Hirono-Hara Y, Hirayama H, Kamata K, Tanaka R, Sano M, Kitamura S, Otsuka K, Abe-Yoshizumi R, Tsunoda SP, Kikukawa H, Kandori H, Shimizu H, Matsuda F, Ishii J, Hara KY. Optogenetic reprogramming of carbon metabolism using light-powering microbial proton pump systems. Metab Eng 2022; 72:227-236. [PMID: 35346842 DOI: 10.1016/j.ymben.2022.03.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/06/2022] [Accepted: 03/23/2022] [Indexed: 12/27/2022]
Abstract
In microbial fermentative production, ATP regeneration, while crucial for cellular processes, conflicts with efficient target chemical production because ATP regeneration exhausts essential carbon sources also required for target chemical biosynthesis. To wrestle with this dilemma, we harnessed the power of microbial rhodopsins with light-driven proton pumping activity to supplement with ATP, thereby facilitating the bioproduction of various chemicals. We first demonstrated a photo-driven ATP supply and redistribution of metabolic carbon flows to target chemical synthesis by installing already-known delta rhodopsin (dR) in Escherichia coli. In addition, we identified novel rhodopsins with higher proton pumping activities than dR, and created an engineered cell for in vivo self-supply of the rhodopsin-activator, all-trans-retinal. Our concept exploiting the light-powering ATP supplier offers a potential increase in carbon use efficiency for microbial productions through metabolic reprogramming.
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Affiliation(s)
- Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yoko Hirono-Hara
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Hidenobu Hirayama
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Kentaro Kamata
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Ryo Tanaka
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Mikoto Sano
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Sayaka Kitamura
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kensuke Otsuka
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Rei Abe-Yoshizumi
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi, 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi, 466-8555, Japan
| | - Satoshi P Tsunoda
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi, 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi, 466-8555, Japan
| | - Hiroshi Kikukawa
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan; Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi, 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi, 466-8555, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Jun Ishii
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan; Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Kiyotaka Y Hara
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan; Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan.
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5
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Abstract
Research on type 1 rhodopsins spans now a history of 50 years. Originally, just archaeal ion pumps and sensors have been discovered. However, with modern genetic techniques and gene sequencing tools, more and more proteins were identified in all kingdoms of life. Spectroscopic and other biophysical studies revealed quite diverse functions. Ion pumps, sensors, and channels are imprinted in the same seven-helix transmembrane protein scaffold carrying a retinal prosthetic group. In this review, molecular biology methods are described, which enabled the elucidation of their function and structure leading to optogenetic applications.
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Affiliation(s)
- Martin Engelhard
- Department Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
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6
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Kikuchi M, Kojima K, Nakao S, Yoshizawa S, Kawanishi S, Shibukawa A, Kikukawa T, Sudo Y. Functional expression of the eukaryotic proton pump rhodopsin OmR2 in Escherichia coli and its photochemical characterization. Sci Rep 2021; 11:14765. [PMID: 34285294 PMCID: PMC8292405 DOI: 10.1038/s41598-021-94181-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/07/2021] [Indexed: 01/05/2023] Open
Abstract
Microbial rhodopsins are photoswitchable seven-transmembrane proteins that are widely distributed in three domains of life, archaea, bacteria and eukarya. Rhodopsins allow the transport of protons outwardly across the membrane and are indispensable for light-energy conversion in microorganisms. Archaeal and bacterial proton pump rhodopsins have been characterized using an Escherichia coli expression system because that enables the rapid production of large amounts of recombinant proteins, whereas no success has been reported for eukaryotic rhodopsins. Here, we report a phylogenetically distinct eukaryotic rhodopsin from the dinoflagellate Oxyrrhis marina (O. marina rhodopsin-2, OmR2) that can be expressed in E. coli cells. E. coli cells harboring the OmR2 gene showed an outward proton-pumping activity, indicating its functional expression. Spectroscopic characterization of the purified OmR2 protein revealed several features as follows: (1) an absorption maximum at 533 nm with all-trans retinal chromophore, (2) the possession of the deprotonated counterion (pKa = 3.0) of the protonated Schiff base and (3) a rapid photocycle through several distinct photointermediates. Those features are similar to those of known eukaryotic proton pump rhodopsins. Our successful characterization of OmR2 expressed in E. coli cells could build a basis for understanding and utilizing eukaryotic rhodopsins.
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Affiliation(s)
- Masuzu Kikuchi
- Division of Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Keiichi Kojima
- Division of Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan.,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Shin Nakao
- Division of Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan
| | - Shiho Kawanishi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Atsushi Shibukawa
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, 060-0810, Japan.,Global Station for Soft Matter, GI-CoRE, Hokkaido University, Sapporo, 001-0021, Japan
| | - Yuki Sudo
- Division of Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan. .,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan.
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7
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Voskoboynikova N, Margheritis EG, Kodde F, Rademacher M, Schowe M, Budke-Gieseking A, Psathaki OE, Steinhoff HJ, Cosentino K. Evaluation of DIBMA nanoparticles of variable size and anionic lipid content as tools for the structural and functional study of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183588. [PMID: 33662362 DOI: 10.1016/j.bbamem.2021.183588] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 12/16/2022]
Abstract
Amphiphilic maleic acid-containing polymers allow for the direct extraction of membrane proteins into stable, homogenous, water-soluble copolymer/lipid nanoparticles without the use of detergents. By adjusting the polymer/lipid ratio, the size of the nanoparticles can be tuned at convenience for the incorporation of protein complexes of different size. However, an increase in the size of the lipid nanoparticles may correlate with increased sample heterogeneity, thus hampering their application to spectroscopic and structural techniques where highly homogeneous samples are desirable. In addition, size homogeneity can be affected by low liposome solubilization efficiency by DIBMA, which carries a negative charge, in the presence of high lipid charge density. In this work, we apply biophysical tools to characterize the size and size heterogeneity of large (above 15 nm) lipid nanoparticles encased by the diisobutylene/maleic acid (DIBMA) copolymer at different DIBMA/lipid ratios and percentages of anionic lipids. Importantly, for nanoparticle preparations in the diameter range of 40 nm or below, the size homogeneity of the DIBMA/lipid nanoparticles (DIBMALPs) remains unchanged. In addition, we show that anionic lipids do not affect the production, size and size homogeneity of DIBMALPs. Furthermore, they do not affect the overall lipid dynamics in the membrane, and preserve the functionality of an enclosed membrane protein. This work strengthens the suitability of DIBMALPs as universal, native-like lipid environments for functional studies of membrane proteins and provide useful insight on the suitability of these systems for those structural techniques requiring highly homogeneous sample preparations.
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Affiliation(s)
| | | | - Felix Kodde
- Department of Physics, University of Osnabrück, 49069 Osnabrück, Germany
| | - Malte Rademacher
- Department of Physics, University of Osnabrück, 49069 Osnabrück, Germany
| | - Maurice Schowe
- Department of Physics, University of Osnabrück, 49069 Osnabrück, Germany
| | - Annette Budke-Gieseking
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Germany
| | - Olympia-Ekaterini Psathaki
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Germany
| | | | - Katia Cosentino
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Germany.
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8
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Mosslehy W, Voskoboynikova N, Colbasevici A, Ricke A, Klose D, Klare JP, Mulkidjanian AY, Steinhoff HJ. Conformational Dynamics of Sensory Rhodopsin II in Nanolipoprotein and Styrene-Maleic Acid Lipid Particles. Photochem Photobiol 2019; 95:1195-1204. [PMID: 30849183 DOI: 10.1111/php.13096] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/03/2019] [Indexed: 02/01/2023]
Abstract
Styrene-maleic acid lipid particles (SMALPs) provide stable water-soluble nanocontainers for lipid-encased membrane proteins. Possible effects of the SMA-stabilized lipid environment on the interaction dynamics between functionally coupled membrane proteins remain to be elucidated. The photoreceptor sensory rhodopsin II, NpSRII and its cognate transducer, NpHtrII, of Natronomonas pharaonis form a transmembrane complex, NpSRII2 /NpHtrII2 that plays a key role in negative phototaxis and provides a unique model system to study the light-induced transfer of a conformational signal between two integral membrane proteins. Photon absorption induces transient structural changes in NpSRII comprising an outward movement of helix F that cause further conformational alterations in NpHtrII. We applied site-directed spin labeling and time-resolved optical and EPR spectroscopy to compare the conformational dynamics of NpSRII2 /NpHtrII2 reconstituted in SMALPs with that of nanolipoprotein particle and liposome preparations. NpSRII and NpSRII2 /NpHtrII2 show similar photocycles in liposomes and nanolipoprotein particles. An accelerated decay of the M photointermediate found for SMALPs can be explained by a high local proton concentration provided by the carboxylic groups of the SMA polymer. Light-induced large-scale conformational changes of NpSRII2 /NpHtrII2 observed in liposomes and nanolipoprotein particles are affected in SMALPs, indicating restrictions of the protein's conformational freedom.
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Affiliation(s)
- Wageiha Mosslehy
- Department of Physics, University of Osnabrück, Osnabrück, Germany
| | | | | | - Adrian Ricke
- Department of Physics, University of Osnabrück, Osnabrück, Germany
| | - Daniel Klose
- Department of Physics, University of Osnabrück, Osnabrück, Germany.,Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | - Johann P Klare
- Department of Physics, University of Osnabrück, Osnabrück, Germany
| | - Armen Y Mulkidjanian
- Department of Physics, University of Osnabrück, Osnabrück, Germany.,School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
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9
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Orekhov P, Bothe A, Steinhoff HJ, Shaitan KV, Raunser S, Fotiadis D, Schlesinger R, Klare JP, Engelhard M. Sensory Rhodopsin I and Sensory Rhodopsin II Form Trimers of Dimers in Complex with their Cognate Transducers. Photochem Photobiol 2018; 93:796-804. [PMID: 28500714 DOI: 10.1111/php.12763] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 03/02/2017] [Indexed: 12/28/2022]
Abstract
Archaeal photoreceptors consist of sensory rhodopsins in complex with their cognate transducers. After light excitation, a two-component signaling chain is activated, which is homologous to the chemotactic signaling cascades in enterobacteria. The latter system has been studied in detail. From structural and functional studies, a picture emerges which includes stable signaling complexes, which assemble to receptor arrays displaying hexagonal structural elements. At this higher order structural level, signal amplification and sensory adaptation occur. Here, we describe electron microscopy data, which show that also the archaeal phototaxis receptors sensory rhodopsin I and II in complex with their cognate transducers can form hexagonal lattices even in the presence of a detergent. This result could be confirmed by molecular dynamics calculations, which revealed similar structural elements. Calculations of the global modes of motion displayed one mode, which resembles the "U"-"V" transition of the NpSRII:NpHtrII complex, which was previously argued to represent a functionally relevant global conformational change accompanying the activation process [Ishchenko et al. (2013) J. Photochem. Photobiol. B 123, 55-58]. A model of cooperativity at the transmembrane level is discussed.
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Affiliation(s)
- Philipp Orekhov
- Department of Physics, University of Osnabrück, Osnabrück, Germany.,Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Arne Bothe
- Department Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | | | | | - Stefan Raunser
- Department Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Ramona Schlesinger
- Department of Physics, Institute of Experimental Physics, Genetic Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Johann P Klare
- Department of Physics, University of Osnabrück, Osnabrück, Germany
| | - Martin Engelhard
- Department Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
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10
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Engelhard C, Chizhov I, Siebert F, Engelhard M. Microbial Halorhodopsins: Light-Driven Chloride Pumps. Chem Rev 2018; 118:10629-10645. [DOI: 10.1021/acs.chemrev.7b00715] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | - Igor Chizhov
- Institute for Biophysical Chemistry, Hannover Medical School, OE8830 Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Friedrich Siebert
- Institut für Molekulare Medizin und Zellforschung, Sektion Biophysik, Albert-Ludwigs-Universität Freiburg, Hermann-Herderstr. 9, 79104 Freiburg, Germany
| | - Martin Engelhard
- Max Planck Institute for Molecular Physiology, Otto Hahn Str. 11, 44227 Dortmund, Germany
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11
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Honda N, Tsukamoto T, Sudo Y. Comparative evaluation of the stability of seven-transmembrane microbial rhodopsins to various physicochemical stimuli. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.05.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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12
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Voskoboynikova N, Mosslehy W, Colbasevici A, Ismagulova TT, Bagrov DV, Akovantseva AA, Timashev PS, Mulkidjanian AY, Bagratashvili VN, Shaitan KV, Kirpichnikov MP, Steinhoff HJ. Characterization of an archaeal photoreceptor/transducer complex from Natronomonas pharaonis assembled within styrene–maleic acid lipid particles. RSC Adv 2017. [DOI: 10.1039/c7ra10756k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The archaeal receptor/transducer complex NpSRII/NpHtrII retains its integrity upon reconstitution in styrene–maleic acid lipid particles.
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Affiliation(s)
| | - W. Mosslehy
- Department of Physics
- University of Osnabrück
- Osnabrück
- Germany
| | - A. Colbasevici
- Department of Physics
- University of Osnabrück
- Osnabrück
- Germany
| | - T. T. Ismagulova
- Department of Bioengineering
- Faculty of Biology
- Lomonosov Moscow State University
- Moscow
- Russia
| | - D. V. Bagrov
- Department of Bioengineering
- Faculty of Biology
- Lomonosov Moscow State University
- Moscow
- Russia
| | - A. A. Akovantseva
- Institute of Photonic Technologies of Research Center “Crystallography and Photonics” of RAS
- Moscow
- Russia
| | - P. S. Timashev
- Institute for Regenerative Medicine of I. M. Sechenov First Moscow State Medical University
- Moscow
- Russia
- Institute of Photonic Technologies of Research Center “Crystallography and Photonics” of RAS
- Moscow
| | | | - V. N. Bagratashvili
- Institute of Photonic Technologies of Research Center “Crystallography and Photonics” of RAS
- Moscow
- Russia
| | - K. V. Shaitan
- Department of Bioengineering
- Faculty of Biology
- Lomonosov Moscow State University
- Moscow
- Russia
| | - M. P. Kirpichnikov
- Department of Bioengineering
- Faculty of Biology
- Lomonosov Moscow State University
- Moscow
- Russia
| | - H.-J. Steinhoff
- Department of Physics
- University of Osnabrück
- Osnabrück
- Germany
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13
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Bagrov DV, Voskoboynikova N, Armeev GA, Mosslehy W, Gluhov GS, Ismagulova TT, Mulkidjanian AY, Kirpichnikov MP, Steinhoff HJ, Shaitan KV. Characterization of lipodisc nanoparticles containing sensory rhodopsin II and its cognate transducer from Natronomonas pharaonis. Biophysics (Nagoya-shi) 2016. [DOI: 10.1134/s0006350916060063] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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14
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Doi S, Mori A, Tsukamoto T, Reissig L, Ihara K, Sudo Y. Structural and functional roles of the N- and C-terminal extended modules in channelrhodopsin-1. Photochem Photobiol Sci 2015; 14:1628-36. [PMID: 26098533 DOI: 10.1039/c5pp00213c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Channelrhodopsins have become a focus of interest because of their ability to control neural activity by light, used in a technology called optogenetics. The channelrhodopsin in the eukaryote Chlamydomonas reinhardtii (CrChR-1) is a light-gated cation channel responsible for motility changes upon photo-illumination and a member of the membrane-embedded retinal protein family. Recent crystal structure analysis revealed that CrChR-1 has unique extended modules both at its N- and C-termini compared to other microbial retinal proteins. This study reports the first successful expression of a ChR-1 variant in Escherichia coli as a holoprotein: the ChR-1 variant lacking both the N- and C-termini (CrChR-1_82-308). However, compared to ChR-1 having the extended modules (CrChR-1_1-357), truncation of the termini greatly altered the absorption maximum and photochemical properties, including the pKa values of its charged residues around the chromophore, the reaction rates in the photocycle and the photo-induced ion channeling activity. The results of some experiments regarding ion transport activity suggest that CrChR-1_82-308 has a proton channeling activity even in the dark. On the basis of these results, we discuss the structural and functional roles of the N- and C-terminal extended modules in CrChR-1.
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Affiliation(s)
- Satoko Doi
- Division of Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan.
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Bratanov D, Balandin T, Round E, Shevchenko V, Gushchin I, Polovinkin V, Borshchevskiy V, Gordeliy V. An Approach to Heterologous Expression of Membrane Proteins. The Case of Bacteriorhodopsin. PLoS One 2015; 10:e0128390. [PMID: 26046789 PMCID: PMC4457421 DOI: 10.1371/journal.pone.0128390] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 04/24/2015] [Indexed: 12/02/2022] Open
Abstract
Heterologous overexpression of functional membrane proteins is a major bottleneck of structural biology. Bacteriorhodopsin from Halobium salinarum (bR) is a striking example of the difficulties in membrane protein overexpression. We suggest a general approach with a finite number of steps which allows one to localize the underlying problem of poor expression of a membrane protein using bR as an example. Our approach is based on constructing chimeric proteins comprising parts of a protein of interest and complementary parts of a homologous protein demonstrating advantageous expression. This complementary protein approach allowed us to increase bR expression by two orders of magnitude through the introduction of two silent mutations into bR coding DNA. For the first time the high quality crystals of bR expressed in E. Coli were obtained using the produced protein. The crystals obtained with in meso nanovolume crystallization diffracted to 1.67 Å.
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Affiliation(s)
- Dmitry Bratanov
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany
- Institute of Crystallography, University of Aachen (RWTH), Jägerstrasse 17–19, Aachen, Germany
| | - Taras Balandin
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany
| | - Ekaterina Round
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany
- Univ. Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
| | - Vitaly Shevchenko
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany
- Research-Educational Centre “Bionanophysics”, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
| | - Ivan Gushchin
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany
- Univ. Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
- Research-Educational Centre “Bionanophysics”, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
| | - Vitaly Polovinkin
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany
- Univ. Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
- Research-Educational Centre “Bionanophysics”, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
| | - Valentin Borshchevskiy
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany
- Research-Educational Centre “Bionanophysics”, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
| | - Valentin Gordeliy
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany
- Univ. Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
- Research-Educational Centre “Bionanophysics”, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
- * E-mail:
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Heterologous expression of proteorhodopsin enhances H2 production in Escherichia coli when endogenous Hyd-4 is overexpressed. J Biotechnol 2015; 206:52-7. [PMID: 25913175 DOI: 10.1016/j.jbiotec.2015.04.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 04/09/2015] [Accepted: 04/11/2015] [Indexed: 11/23/2022]
Abstract
Proteorhodopsin (PR) is a light harvesting protein widely distributed among bacterioplankton that plays an integral energetic role in a new pathway of marine light capture. The conversion of light into chemical energy in non-chlorophyll-based bacterial systems could contribute to overcoming thermodynamic and metabolic constraints in biofuels production. In an attempt to improve biohydrogen production yields, H2 evolution catalyzed by endogenous hydrogenases, Hyd-3 and/or Hyd-4, was measured when recombinant proteorhodopsin (PR) was concomitantly expressed in Escherichia coli cells. Higher amounts of H2 were obtained with recombinant cells in a light and chromophore dependent manner. This effect was only observed when HyfR, the specific transcriptional activator of the hyf operon encoding Hyd-4 was overexpressed in E. coli, suggesting that an excess of protons generated by PR activity could increase hydrogen production by Hyd-4 but not by Hyd-3. Although many of the subunits of Hyd-3 and Hyd-4 are very similar, Hyd-4 possesses three additional proton-translocating NADH-ubiquinone oxidoreductase subunits, suggesting that it is dependent upon ΔμH(+). Altogether, these results suggest that protons generated by proteorhodopsin in the periplasm can only enhance hydrogen production by hydrogenases with associated proton translocating subunits.
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Orban-Glaß I, Voskoboynikova N, Busch KB, Klose D, Rickert C, Mosslehy W, Roder F, Wilkens V, Piehler J, Engelhard M, Steinhoff HJ, Klare JP. Clustering and dynamics of phototransducer signaling domains revealed by site-directed spin labeling electron paramagnetic resonance on SRII/HtrII in membranes and nanodiscs. Biochemistry 2014; 54:349-62. [PMID: 25489970 DOI: 10.1021/bi501160q] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In halophilic archaea the photophobic response is mediated by the membrane-embedded 2:2 photoreceptor/-transducer complex SRII/HtrII, the latter being homologous to the bacterial chemoreceptors. Both systems bias the rotation direction of the flagellar motor via a two-component system coupled to an extended cytoplasmic signaling domain formed by a four helical antiparallel coiled-coil structure. For signal propagation by the HAMP domains connecting the transmembrane and cytoplasmic domains, it was suggested that a two-state thermodynamic equilibrium found for the first HAMP domain in NpSRII/NpHtrII is shifted upon activation, yet signal propagation along the coiled-coil transducer remains largely elusive, including the activation mechanism of the coupled kinase CheA. We investigated the dynamic and structural properties of the cytoplasmic tip domain of NpHtrII in terms of signal transduction and putative oligomerization using site-directed spin labeling electron paramagnetic resonance spectroscopy. We show that the cytoplasmic tip domain of NpHtrII is engaged in a two-state equilibrium between a dynamic and a compact conformation like what was found for the first HAMP domain, thus strengthening the assumption that dynamics are the language of signal transfer. Interspin distance measurements in membranes and on isolated 2:2 photoreceptor/transducer complexes in nanolipoprotein particles provide evidence that archaeal photoreceptor/-transducer complexes analogous to chemoreceptors form trimers-of-dimers or higher-order assemblies even in the absence of the cytoplasmic components CheA and CheW, underlining conservation of the overall mechanistic principles underlying archaeal phototaxis and bacterial chemotaxis systems. Furthermore, our results revealed a significant influence of the NpHtrII signaling domain on the NpSRII photocycle kinetics, providing evidence for a conformational coupling of SRII and HtrII in these complexes.
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Affiliation(s)
- Ioan Orban-Glaß
- Macromolecular Structure Group, Department of Physics, University of Osnabrück , Barbarastrasse 7, 49076 Osnabrück, Germany
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18
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Dittmann M, Seidel R, Chizhov I, Engelhard M. Total chemical synthesis of a membrane protein domain analogue containing two transmembrane helices: functional reconstitution of the semisynthetic sensory rhodopsin/transducer complex. J Pept Sci 2014; 20:137-44. [DOI: 10.1002/psc.2605] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 11/25/2013] [Accepted: 11/25/2013] [Indexed: 12/15/2022]
Affiliation(s)
- Marc Dittmann
- Max Planck Institute of Molecular Physiology; Otto Hahn Str. 11 44227 Dortmund Germany
| | - Ralf Seidel
- Max Planck Institute of Molecular Physiology; Otto Hahn Str. 11 44227 Dortmund Germany
| | - Igor Chizhov
- Medizinische Hochschule Hannover; Carl-Neuberg-Str. 1 30625 Hannover Germany
| | - Martin Engelhard
- Max Planck Institute of Molecular Physiology; Otto Hahn Str. 11 44227 Dortmund Germany
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Hopper JT, Yu YTC, Li D, Raymond A, Bostock M, Liko I, Mikhailov V, Laganowsky A, Benesch JL, Caffrey M, Nietlispach D, Robinson CV. Detergent-free mass spectrometry of membrane protein complexes. Nat Methods 2013; 10:1206-8. [PMID: 24122040 PMCID: PMC3868940 DOI: 10.1038/nmeth.2691] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 08/29/2013] [Indexed: 02/02/2023]
Abstract
We developed a method that allows release of intact membrane protein complexes from amphipols, bicelles and nanodiscs in the gas phase for observation by mass spectrometry (MS). Current methods involve release of membrane protein complexes from detergent micelles, which reveals subunit composition and lipid binding. We demonstrated that oligomeric complexes or proteins requiring defined lipid environments are stabilized to a greater extent in the absence of detergent.
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Affiliation(s)
- Jonathan T.S. Hopper
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ
| | - Yvonne Ting-Chun Yu
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA
| | - Dianfan Li
- School of Medicine Trinity College Dublin, Dublin, Ireland
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Alison Raymond
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ
| | - Mark Bostock
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA
| | - Idlir Liko
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ
| | - Victor Mikhailov
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ
| | - Arthur Laganowsky
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ
| | - Justin L.P. Benesch
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ
| | - Martin Caffrey
- School of Medicine Trinity College Dublin, Dublin, Ireland
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Daniel Nietlispach
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA
| | - Carol V. Robinson
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ
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Grote M, Engelhard M, Hegemann P. Of ion pumps, sensors and channels - perspectives on microbial rhodopsins between science and history. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:533-45. [PMID: 23994288 DOI: 10.1016/j.bbabio.2013.08.006] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 08/20/2013] [Accepted: 08/22/2013] [Indexed: 10/26/2022]
Abstract
We present a historical overview of research on microbial rhodopsins ranging from the 1960s to the present date. Bacteriorhodopsin (BR), the first identified microbial rhodopsin, was discovered in the context of cell and membrane biology and shown to be an outward directed proton transporter. In the 1970s, BR had a big impact on membrane structural research and bioenergetics, that made it to a model for membrane proteins and established it as a probe for the introduction of various biophysical techniques that are widely used today. Halorhodopsin (HR), which supports BR physiologically by transporting negatively charged Cl⁻ into the cell, is researched within the microbial rhodopsin community since the late 1970s. A few years earlier, the observation of phototactic responses in halobacteria initiated research on what are known today as sensory rhodopsins (SR). The discovery of the light-driven ion channel, channelrhodopsin (ChR), serving as photoreceptors for behavioral responses in green alga has complemented inquiries into this photoreceptor family. Comparing the discovery stories, we show that these followed quite different patterns, albeit the objects of research being very similar. The stories of microbial rhodopsins present a comprehensive perspective on what can nowadays be considered one of nature's paradigms for interactions between organisms and light. Moreover, they illustrate the unfolding of this paradigm within the broader conceptual and instrumental framework of the molecular life sciences. 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)
- Mathias Grote
- Institut für Philosophie, Literatur-, Wissenschafts- und Technikgeschichte, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany.
| | - Martin Engelhard
- Max Planck Institut für Molekulare Physiologie, Otto Hahn Str. 11, 44227 Dortmund, Germany
| | - Peter Hegemann
- Institute of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
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21
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Inoue K, Tsukamoto T, Sudo Y. Molecular and evolutionary aspects of microbial sensory rhodopsins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:562-77. [PMID: 23732219 DOI: 10.1016/j.bbabio.2013.05.005] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 05/14/2013] [Accepted: 05/16/2013] [Indexed: 02/03/2023]
Abstract
Retinal proteins (~rhodopsins) are photochemically reactive membrane-embedded proteins, with seven transmembrane α-helices which bind the chromophore retinal (vitamin A aldehyde). They are widely distributed through all three biological kingdoms, eukarya, bacteria and archaea, indicating the biological significance of the retinal proteins. Light absorption by the retinal proteins triggers a photoisomerization of the chromophore, leading to the biological function, light-energy conversion or light-signal transduction. This article reviews molecular and evolutionary aspects of the light-signal transduction by microbial sensory receptors and their related proteins. 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)
- Keiichi Inoue
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; Japan Science and Technology Agency (JST), PRESTO, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Takashi Tsukamoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
| | - Yuki Sudo
- Japan Science and Technology Agency (JST), PRESTO, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan; Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan; Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki, Japan.
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Kim S, Yoon Y, Lee H, Choi AR, Jung KH, Babajanyan A, Abrahamyan T, Yoo H, Lee JH, Cha D, Berthiau G, Friedman B, Lee K. Application of a sensitive near-field microwave microprobe to the nondestructive characterization of microbial rhodopsin. JOURNAL OF BIOPHOTONICS 2013; 6:163-170. [PMID: 22517728 DOI: 10.1002/jbio.201100143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Revised: 03/17/2012] [Accepted: 03/19/2012] [Indexed: 05/31/2023]
Abstract
We study the opto-electrical properties of Natronomonas pharaonis sensory rhodopsin II (NpSRII) by using a near-field microwave microprobe (NFMM) under external light illumination. To investigate the possibility of application of NFMM to biological macromolecules, we used time dependent properties of NPSRII before/after light activation which has three distinct states - ground-state, M-state, and O-state. The diagnostic ability of NFMM is demonstrated by measuring the microwave reflection coefficient (S(11)) spectrum of NpSRII under steady-state illumination in the wavelength range of 350-650 nm. Moreover, we present microwave reflection coefficient S(11) spectra in the same wavelength range for two fast-photocycling rhodopsins: green light-absorbing proteorhodopsin (GPR) and Gloeobacter rhodopsin (GR). In addition the frequency sweep shift can be detected completely even for tiny amounts of sample (∼10(-3) OD of rhodopsin). Based on these results NFMM shows both very high sensitivity for detecting conformational changes and produces a good time-resolved spectrum.
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Affiliation(s)
- Songhui Kim
- Department of Physics, Kunsan National University, Gunsan 573-701, Korea
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Tamogami J, Kikukawa T, Ikeda Y, Demura M, Nara T, Kamo N. Photo-induced bleaching of sensory rhodopsin II (phoborhodopsin) from Halobacterium salinarum by hydroxylamine: identification of the responsible intermediates. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2012; 106:87-94. [PMID: 22104601 DOI: 10.1016/j.jphotobiol.2011.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 10/18/2011] [Accepted: 10/21/2011] [Indexed: 05/31/2023]
Abstract
Sensory rhodopsin II from Halobacterium salinarum (HsSRII) is a retinal protein in which retinal binds to a specific lysine residue through a Schiff base. Here, we investigated the photobleaching of HsSRII in the presence of hydroxylamine. For identification of intermediate(s) attacked by hydroxylamine, we employed the flash-induced bleaching method. In order to change the concentration of intermediates, such as M- and O-intermediates, experiments were performed under varying flashlight intensities and concentrations of azide that accelerated only the M-decay. We found the proportional relationship between the bleaching rate and area under the concentration-time curve of M, indicating a preferential attack of hydroxylamine on M. Since hydroxylamine is a water-soluble reagent, we hypothesize that for M, hydrophilicity or water-accessibility increases specifically in the moiety of Schiff base. Thus, hydroxylamine bleaching rates may be an indication of conformational changes near the Schiff base. We also considered the possibility that azide may induce a small conformational change around the Schiff base. We compared the hydroxylamine susceptibility between HsSRII and NpSRII (SRII from Natronomonas pharaonis) and found that the M of HsSRII is about three times more susceptible than that of the stable NpSRII. In addition, long illumination to HsSRII easily produced M-like photoproduct, P370. We thus infer that the instability of HsSRII under illumination may be related to this increase of hydrophilicity at M and P370.
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Affiliation(s)
- Jun Tamogami
- College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime, Japan
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Nannenga BL, Baneyx F. Enhanced expression of membrane proteins in E. coli with a P(BAD) promoter mutant: synergies with chaperone pathway engineering strategies. Microb Cell Fact 2011; 10:105. [PMID: 22151946 PMCID: PMC3265434 DOI: 10.1186/1475-2859-10-105] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Accepted: 12/09/2011] [Indexed: 11/10/2022] Open
Abstract
Background Membrane proteins (MPs) populate 20-30% of genomes sequenced to date and hold potential as therapeutic targets as well as for practical applications in bionanotechnology. However, MP toxicity and low yields in normally robust expression hosts such as E. coli has curtailed progress in our understanding of their structure and function. Results Using the seven transmembrane segments H. turkmenica deltarhodopsin (HtdR) as a reporter, we isolated a spontaneous mutant in the arabinose-inducible PBAD promoter leading to improved cell growth and a twofold increase in the recovery of active HtdR at 37°C. A single transversion in a conserved region of the cyclic AMP receptor protein binding site caused the phenotype by reducing htdR transcript levels by 65%. When the mutant promoter was used in conjunction with a host lacking the molecular chaperone Trigger Factor (Δtig cells), toxicity was further suppressed and the amount of correctly folded HtdR was 4-fold that present in the membranes of control cells. More importantly, while improved growth barely compensated for the reduction in transcription rates when another polytopic membrane protein (N. pharonis sensory rhodopsin II) was expressed under control of the mutant promoter in wild type cells, a 4-fold increase in productivity could be achieved in a Δtig host. Conclusions Our system, which combines a downregulated version of the tightly repressed PBAD promoter with a TF-deficient host may prove a valuable alternative to T7-based expression for the production of membrane proteins that have so far remained elusive targets.
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Affiliation(s)
- Brent L Nannenga
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195-1750, USA
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25
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Yamashita Y, Kikukawa T, Tsukamoto T, Kamiya M, Aizawa T, Kawano K, Miyauchi S, Kamo N, Demura M. Expression of salinarum halorhodopsin in Escherichia coli cells: solubilization in the presence of retinal yields the natural state. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:2905-12. [PMID: 21925140 DOI: 10.1016/j.bbamem.2011.08.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 08/27/2011] [Accepted: 08/30/2011] [Indexed: 11/29/2022]
Abstract
Salinarum halorhodopsin (HsHR), a light-driven chloride ion pump of haloarchaeon Halobacterium salinarum, was heterologously expressed in Escherichia coli. The expressed HsHR had no color in the E. coli membrane, but turned purple after solubilization in the presence of all-trans retinal. This colored HsHR was purified by Ni-chelate chromatography in a yield of 3-4 mg per liter culture. The purified HsHR showed a distinct chloride pumping activity by incorporation into the liposomes, and showed even in the detergent-solubilized state, its typical behaviors in both the unphotolyzed and photolyzed states. Upon solubilization, HsHR expressed in the E. coli membrane attains the proper folding and a trimeric assembly comparable to those in the native membranes.
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Affiliation(s)
- Yasutaka Yamashita
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
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26
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Gushchin I, Reshetnyak A, Borshchevskiy V, Ishchenko A, Round E, Grudinin S, Engelhard M, Bldt G, Gordeliy V. Active State of Sensory Rhodopsin II: Structural Determinants for Signal Transfer and Proton Pumping. J Mol Biol 2011; 412:591-600. [DOI: 10.1016/j.jmb.2011.07.022] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 06/23/2011] [Accepted: 07/13/2011] [Indexed: 10/17/2022]
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Nakatsuma A, Yamashita T, Sasaki K, Kawanabe A, Inoue K, Furutani Y, Shichida Y, Kandori H. Chimeric microbial rhodopsins containing the third cytoplasmic loop of bovine rhodopsin. Biophys J 2011; 100:1874-82. [PMID: 21504723 DOI: 10.1016/j.bpj.2011.02.054] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Revised: 02/12/2011] [Accepted: 02/17/2011] [Indexed: 10/18/2022] Open
Abstract
G-protein-coupled receptors transmit stimuli (light, taste, hormone, neurotransmitter, etc.) to the intracellular signaling systems, and rhodopsin (Rh) is the most-studied G-protein-coupled receptor. Rh possesses an 11-cis retinal as the chromophore, and 11-cis to all-trans photoisomerization leads to the protein structural changes in the cytoplasmic loops to activate G-protein. Microbial rhodopsins are similar heptahelical membrane proteins that function as bacterial sensors, light-driven ion-pumps, or light-gated channels. Microbial rhodopsins possess an all-trans retinal, and all-trans to 13-cis photoisomerization triggers protein structural changes for each function. Despite these similarities, there is no sequence homology between visual and microbial rhodopsins, and microbial rhodopsins do not activate G-proteins. However, it was reported that bacteriorhodopsin (BR) chimeras containing the third cytoplasmic loop of bovine Rh are able to activate G-protein, suggesting a common mechanism of protein structural changes. Here we design chimeric proteins for Natronomonas pharaonis sensory rhodopsin II (SRII, also called pharaonis phoborhodopsin), which has a two-orders-of-magnitude slower photocycle than BR. Light-dependent transducin activation was observed for most of the nine SRII chimeras containing the third cytoplasmic loop of bovine Rh (from Y223, G224, Q225 to T251, R252, and M253), but the activation level was 30,000-140,000 times lower than that of bovine Rh. The BR chimera, BR/Rh223-253, activates a G-protein transducin, whereas the activation level was 37,000 times lower than that of bovine Rh. We interpret the low activation by the chimeric proteins as reasonable, because bovine Rh must have been optimized for activating a G-protein transducin during its evolution. On the other hand, similar activation level of the SRII and BR chimeras suggests that the lifetime of the M intermediates is not the simple determinant of activation, because SRII chimeras have two-orders-of-magnitude's slower photocycle than the BR chimera. Activation mechanism of visual and microbial rhodopsins is discussed on the basis of these results.
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Affiliation(s)
- Aya Nakatsuma
- Department of Frontier Materials, Nagoya Institute of Technology, Nagoya, Japan
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Nannenga BL, Baneyx F. Reprogramming chaperone pathways to improve membrane protein expression in Escherichia coli. Protein Sci 2011; 20:1411-20. [PMID: 21633988 DOI: 10.1002/pro.669] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 05/22/2011] [Indexed: 11/10/2022]
Abstract
Because membrane proteins are difficult to express, our understanding of their structure and function is lagging. In Escherichia coli, α-helical membrane protein biogenesis usually involves binding of a nascent transmembrane segment (TMS) by the signal recognition particle (SRP), delivery of the SRP-ribosome nascent chain complexes (RNC) to FtsY, a protein that serves as SRP receptor and docks to the SecYEG translocon, cotranslational insertion of the growing chain into the translocon, and lateral transfer, packing and folding of TMS in the lipid bilayer in a process that may involve chaperone YidC. Here, we explored the feasibility of reprogramming this pathway to improve the production of recombinant membrane proteins in exponentially growing E. coli with a focus on: (i) eliminating competition between SRP and chaperone trigger factor (TF) at the ribosome through gene deletion; (ii) improving RNC delivery to the inner membrane via SRP overexpression; and (iii) promoting substrate insertion and folding in the lipid bilayer by increasing YidC levels. Using a bitopic histidine kinase and two heptahelical rhodopsins as model systems, we show that the use of TF-deficient cells improves the yields of membrane-integrated material threefold to sevenfold relative to the wild type, and that whereas YidC coexpression is beneficial to the production of polytopic proteins, higher levels of SRP have the opposite effect. The implications of our results on the interplay of TF, SRP, YidC, and SecYEG in membrane protein biogenesis are discussed.
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Affiliation(s)
- Brent L Nannenga
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195-1750, USA
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Sudo Y, Tanaka R, Kobayashi T, Kamo N, Kohno T, Kojima C. Functional expression of a two-transmembrane HtrII protein using cell-free synthesis. Biophysics (Nagoya-shi) 2011; 7:51-58. [PMID: 27857592 PMCID: PMC5036783 DOI: 10.2142/biophysics.7.51] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Accepted: 05/23/2011] [Indexed: 12/01/2022] Open
Abstract
An approach of cell-free synthesis is presented for the functional expression of transmembrane proteins without the need of refolding. The transmembrane region of the pharaonis halobacterial transducer protein, pHtrII, was translated with various large soluble tags added (thioredoxin, glutathione S-transferase, green fluorescent protein and maltose binding protein). In this system, all fusion pHtrII were translated in a soluble fraction, presumably, forming giant micelle-like structures. The detergent n-dodecyl-β-d-maltoside was added for enhancing the solubilization of the hydrophobic region of pHtrII. The activity of the expressed pHtrII, having various tags, was checked using a pull-down assay, using the fact that pHtrII forms a signaling complex with pharaonis phoborhodopsin (ppR) in the membrane, as also in the presence of a detergent. All tagged pHtrII showed a binding activity with ppR. Interestingly, the binding activity with ppR was positively correlated with the molecular weight of the soluble tags. Thus, larger soluble tags lead to higher binding activities. We could show, that our approach is beneficial for the preparation of active membrane proteins, and is also potentially applicable for larger membrane proteins, such as 7-transmembrane proteins.
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Affiliation(s)
- Yuki Sudo
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan; PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Rikou Tanaka
- Mitsubishi Kagaku Institute of Life Sciences, Machida, Tokyo 194-0031, Japan
| | - Toshitatsu Kobayashi
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan
| | - Naoki Kamo
- College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime 790-8578, Japan
| | - Toshiyuki Kohno
- Mitsubishi Kagaku Institute of Life Sciences, Machida, Tokyo 194-0031, Japan
| | - Chojiro Kojima
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan; Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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Tateishi Y, Abe T, Tamogami J, Nakao Y, Kikukawa T, Kamo N, Unno M. Spectroscopic Evidence for the Formation of an N Intermediate during the Photocycle of Sensory Rhodopsin II (Phoborhodopsin) from Natronobacterium pharaonis. Biochemistry 2011; 50:2135-43. [DOI: 10.1021/bi1019572] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yusuke Tateishi
- Department of Chemistry and Applied Chemistry, Graduate School of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Takayuki Abe
- Faculty of Advanced Life Science and Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Jun Tamogami
- Faculty of Advanced Life Science and Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0810, Japan
- College of Pharmaceutical Sciences, Matsuyama University, Bunkyo-cho, Matsuyama 790-8578, Japan
| | - Yutaka Nakao
- Faculty of Advanced Life Science and Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Takashi Kikukawa
- Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Naoki Kamo
- College of Pharmaceutical Sciences, Matsuyama University, Bunkyo-cho, Matsuyama 790-8578, Japan
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Graduate School of Science and Engineering, Saga University, Saga 840-8502, Japan
- PRESTO, JST, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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Tamogami J, Kikukawa T, Ikeda Y, Takemura A, Demura M, Kamo N. The photochemical reaction cycle and photoinduced proton transfer of sensory rhodopsin II (Phoborhodopsin) from Halobacterium salinarum. Biophys J 2010; 98:1353-63. [PMID: 20371336 DOI: 10.1016/j.bpj.2009.12.4288] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Revised: 12/08/2009] [Accepted: 12/09/2009] [Indexed: 10/19/2022] Open
Abstract
Sensory rhodopsin II (HsSRII, also called phoborhodopsin) is a negative phototaxis receptor of Halobacterium salinarum, a bacterium that avoids blue-green light. In this study, we expressed the protein in Escherichia coli cells, and reconstituted the purified protein with phosphatidylcholine. The reconstituted HsSRII was stable. We examined the photocycle by flash-photolysis spectroscopy in the time range of milliseconds to seconds, and measured proton uptake/release using a transparent indium-tin oxide electrode. The pKa of the counterion of the Schiff base, Asp(73), was 3.0. Below pH 3, the depleted band was observed on flash illumination, but the positive band in the difference spectra was not found. Above pH 3, the basic photocycle was HsSRII (490) --> M (350) --> O (520) --> Y (490) --> HsSRII, where the numbers in parentheses are the maximum wavelengths. The decay rate of O-intermediate and Y-intermediate were pH-independent, whereas the M-intermediate decay was pH-dependent. For 3 < pH < 4.5, the M-decay was one phase, and the rate decreased with an increase in pH. For 4.5 < pH < 6.5, the decay was one phase with pH-independent rates, and azide markedly accelerated the M-decay. These findings suggest the existence of a protonated amino acid residue (X-H) that may serve as a proton relay to reprotonate the Schiff base. Above pH 6.5, the M-decay showed two phases. The fast M-decay was pH-independent and originated from the molecule having a protonated X-H, and the slow M-decay originated from the molecule having a deprotonated X, in which the proton came directly from the outside. The analysis yielded a value of 7.5 for the pKa of X-H. The proton uptake and release occurred during M-decay and O-decay, respectively.
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Affiliation(s)
- Jun Tamogami
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan; Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
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Protein-protein interaction changes in an archaeal light-signal transduction. J Biomed Biotechnol 2010; 2010:424760. [PMID: 20671933 PMCID: PMC2910557 DOI: 10.1155/2010/424760] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2009] [Accepted: 05/05/2010] [Indexed: 11/18/2022] Open
Abstract
Negative phototaxis in Natronomonas pharaonis is initiated by transient interaction changes between photoreceptor and transducer. pharaonis phoborhodopsin (ppR; also called pharaonis sensory rhodopsin II, psR-II) and the cognate transducer protein, pHtrII, form a tight 2 : 2 complex in the unphotolyzed state, and the interaction is somehow altered during the photocycle of ppR. We have studied the signal transduction mechanism in the ppR/pHtrII system by means of low-temperature Fourier-transform infrared (FTIR) spectroscopy. In the paper, spectral comparison in the absence and presence of pHtrII provided fruitful information in atomic details, where vibrational bands were identified by the use of isotope-labeling and site-directed mutagenesis. From these studies, we established the two pathways of light-signal conversion from the receptor to the transducer; (i) from Lys205 (retinal) of ppR to Asn74 of pHtrII through Thr204 and Tyr199, and (ii) from Lys205 of ppR to the cytoplasmic loop region of pHtrII that links Gly83.
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Gautier A, Mott HR, Bostock MJ, Kirkpatrick JP, Nietlispach D. Structure determination of the seven-helix transmembrane receptor sensory rhodopsin II by solution NMR spectroscopy. Nat Struct Mol Biol 2010; 17:768-74. [PMID: 20512150 PMCID: PMC2923064 DOI: 10.1038/nsmb.1807] [Citation(s) in RCA: 178] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Accepted: 03/16/2010] [Indexed: 11/18/2022]
Abstract
Seven-helix membrane proteins represent a challenge for structural biology. Here we report the first NMR structure determination of a detergent-solubilized seven-helix transmembrane (7TM) protein, the phototaxis receptor sensory rhodopsin II (pSRII) from Natronomonas pharaonis, as a proof of principle. The overall quality of the structure ensemble is good (backbone r.m.s. deviation of 0.48 A) and agrees well with previously determined X-ray structures. Furthermore, measurements in more native-like small phospholipid bicelles indicate that the protein structure is the same as in detergent micelles, suggesting that environment-specific effects are minimal when using mild detergents. We use our case study as a platform to discuss the feasibility of similar solution NMR studies for other 7TM proteins, including members of the family of G protein-coupled receptors.
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Affiliation(s)
- Antoine Gautier
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Helen R. Mott
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Mark J. Bostock
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - John P. Kirkpatrick
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Daniel Nietlispach
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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Suzuki D, Irieda H, Homma M, Kawagishi I, Sudo Y. Phototactic and chemotactic signal transduction by transmembrane receptors and transducers in microorganisms. SENSORS 2010; 10:4010-39. [PMID: 22319339 PMCID: PMC3274258 DOI: 10.3390/s100404010] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Revised: 03/29/2010] [Accepted: 04/09/2010] [Indexed: 12/17/2022]
Abstract
Microorganisms show attractant and repellent responses to survive in the various environments in which they live. Those phototaxic (to light) and chemotaxic (to chemicals) responses are regulated by membrane-embedded receptors and transducers. This article reviews the following: (1) the signal relay mechanisms by two photoreceptors, Sensory Rhodopsin I (SRI) and Sensory Rhodopsin II (SRII) and their transducers (HtrI and HtrII) responsible for phototaxis in microorganisms; and (2) the signal relay mechanism of a chemoreceptor/transducer protein, Tar, responsible for chemotaxis in E. coli. Based on results mainly obtained by our group together with other findings, the possible molecular mechanisms for phototaxis and chemotaxis are discussed.
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Affiliation(s)
- Daisuke Suzuki
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan; E-Mails: (D.S.); (H.I.); (M.H.)
| | - Hiroki Irieda
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan; E-Mails: (D.S.); (H.I.); (M.H.)
| | - Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan; E-Mails: (D.S.); (H.I.); (M.H.)
| | - Ikuro Kawagishi
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, 184-8584, Japan; E-Mail: (I.K.)
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, 184-8584, Japan
| | - Yuki Sudo
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan; E-Mails: (D.S.); (H.I.); (M.H.)
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama, 332-0012, Japan
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +81-52-789-2993; Fax: +81-52-789-3001
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35
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Yagasaki J, Suzuki D, Ihara K, Inoue K, Kikukawa T, Sakai M, Fujii M, Homma M, Kandori H, Sudo Y. Spectroscopic studies of a sensory rhodopsin I homologue from the archaeon Haloarcula vallismortis. Biochemistry 2010; 49:1183-90. [PMID: 20067303 DOI: 10.1021/bi901824a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sensory rhodopsin I (SRI) functions as a dual receptor regulating both negative and positive phototaxis. It transmits light signals through changes in protein-protein interactions with its transducer protein, HtrI. The phototaxis function of Halobacterium salinarum SRI (HsSRI) has been well characterized using genetic and molecular techniques, whereas that of Salinibacter ruber SRI (SrSRI) has not. SrSRI has the advantage of high protein stability compared with HsSRI and, therefore, provided new information about structural changes and Cl(-) binding of SRI. However, nothing is known about the functional role of SrSRI in phototaxis behavior. In this study, we expressed a SRI homologue from the archaeon Haloarcula vallismortis (HvSRI) as a recombinant protein which uses all-trans-retinal as a chromophore. Functionally important residues of HsSRI are completely conserved in HvSRI (unlike in SrSRI), and HvSRI is extremely stable in buffers without Cl(-). Taking advantage of the high stability, we characterized the photochemical properties of HvSRI under acidic and basic conditions and observed the effects of Cl(-) on the protein under both conditions. Fourier transform infrared results revealed that the structural changes in HvSRI were quite similar to those in HsSRI and SrSRI. Thus, HvSRI can become a useful protein model for improving our understanding of the molecular mechanism of the dual photosensing by SRI.
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Affiliation(s)
- Jin Yagasaki
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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36
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Dai G, Ohno Y, Ikeda Y, Tamogami J, Kikukawa T, Kamo N, Iwasa T. Photoreaction Cycle of Phoborhodopsin (Sensory Rhodopsin II) from Halobacterium salinarum Expressed in Escherichia coli. Photochem Photobiol 2010; 86:571-9. [DOI: 10.1111/j.1751-1097.2009.00687.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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37
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Abe R, Caaveiro JMM, Kudou M, Tsumoto K. Solubilization of membrane proteins with novel N-acylamino acid detergents. MOLECULAR BIOSYSTEMS 2010; 6:677-9. [DOI: 10.1039/b925791h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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Sasaki T, Aizawa T, Kamiya M, Kikukawa T, Kawano K, Kamo N, Demura M. Effect of Chloride Binding on the Thermal Trimer−Monomer Conversion of Halorhodopsin in the Solubilized System. Biochemistry 2009; 48:12089-95. [DOI: 10.1021/bi901380c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Takanori Sasaki
- Faculty of Life Science, Hokkaido University, Sapporo 060-0810, Japan
- School of Science and Technology, Meiji University, Tama-ku, Kawasaki-shi, Kanagawa 214-8571, Japan
| | - Tomoyasu Aizawa
- Faculty of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Masakatsu Kamiya
- Faculty of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Takashi Kikukawa
- Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Keiichi Kawano
- Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Naoki Kamo
- College of Pharmaceutical Sciences, Matsuyama University, Bunkyo-cho, Matsuyama 790-8578, Japan
| | - Makoto Demura
- Faculty of Life Science, Hokkaido University, Sapporo 060-0810, Japan
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Sudo Y, Okada A, Suzuki D, Inoue K, Irieda H, Sakai M, Fujii M, Furutani Y, Kandori H, Homma M. Characterization of a Signaling Complex Composed of Sensory Rhodopsin I and Its Cognate Transducer Protein from the Eubacterium Salinibacter ruber. Biochemistry 2009; 48:10136-45. [DOI: 10.1021/bi901338d] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yuki Sudo
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Akiko Okada
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Daisuke Suzuki
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Keiichi Inoue
- Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Hiroki Irieda
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Makoto Sakai
- Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Masaaki Fujii
- Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Yuji Furutani
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
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40
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Kim YJ, Chizhov I, Engelhard M. Functional Expression of the Signaling Complex Sensory Rhodopsin II/Transducer II fromHalobacterium salinaruminEscherichia coli. Photochem Photobiol 2009; 85:521-8. [DOI: 10.1111/j.1751-1097.2008.00470.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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41
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Sasaki T, Kubo M, Kikukawa T, Kamiya M, Aizawa T, Kawano K, Kamo N, Demura M. Halorhodopsin fromNatronomonas pharaonisForms a Trimer Even in the Presence of a Detergent, Dodecyl-β-d-maltoside. Photochem Photobiol 2009; 85:130-6. [DOI: 10.1111/j.1751-1097.2008.00406.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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42
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Johnson ET, Schmidt-Dannert C. Light-energy conversion in engineered microorganisms. Trends Biotechnol 2008; 26:682-9. [PMID: 18951642 DOI: 10.1016/j.tibtech.2008.09.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2008] [Revised: 09/05/2008] [Accepted: 09/11/2008] [Indexed: 11/19/2022]
Abstract
Increasing interest in renewable resources by the energy and chemical industries has spurred new technologies both to capture solar energy and to develop biologically derived chemical feedstocks and fuels. Advances in molecular biology and metabolic engineering have provided new insights and techniques for increasing biomass and biohydrogen production, and recent efforts in synthetic biology have demonstrated that complex regulatory and metabolic networks can be designed and engineered in microorganisms. Here, we explore how light-driven processes may be incorporated into nonphotosynthetic microbes to boost metabolic capacity for the production of industrial and fine chemicals. Progress towards the introduction of light-driven proton pumping or anoxygenic photosynthesis into Escherichia coli to increase the efficiency of metabolically-engineered biosynthetic pathways is highlighted.
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Affiliation(s)
- Ethan T Johnson
- Department of Biochemistry, Molecular Biology and Biophysics, 1479 Gortner Avenue, 140 Gortner Laboratory, University of Minnesota, St. Paul, MN 55108, USA
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Doebber M, Bordignon E, Klare JP, Holterhues J, Martell S, Mennes N, Li L, Engelhard M, Steinhoff HJ. Salt-driven equilibrium between two conformations in the HAMP domain from Natronomonas pharaonis: the language of signal transfer? J Biol Chem 2008; 283:28691-701. [PMID: 18697747 PMCID: PMC2661416 DOI: 10.1074/jbc.m801931200] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Revised: 08/06/2008] [Indexed: 11/06/2022] Open
Abstract
HAMP domains (conserved in histidine kinases, adenylyl cyclases, methyl-accepting chemotaxis proteins, and phosphatases) perform their putative function as signal transducing units in diversified environments in a variety of protein families. Here the conformational changes induced by environmental agents, namely salt and temperature, on the structure and function of a HAMP domain of the phototransducer from Natronomonas pharaonis (NpHtrII) in complex with sensory rhodopsin II (NpSRII) were investigated by site-directed spin labeling electron paramagnetic resonance. A series of spin labeled mutants were engineered in NpHtrII157, a truncated analog containing only the first HAMP domain following the transmembrane helix 2. This truncated transducer is shown to be a valid model system for a signal transduction domain anchored to the transmembrane light sensor NpSRII. The HAMP domain is found to be engaged in a "two-state" equilibrium between a highly dynamic (dHAMP) and a more compact (cHAMP) conformation. The structural properties of the cHAMP as proven by mobility, accessibility, and intra-transducer-dimer distance data are in agreement with the four helical bundle NMR model of the HAMP domain from Archaeoglobus fulgidus.
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Affiliation(s)
- Meike Doebber
- Fachbereich Physik, Universität Osnabrück, Barbarastrasse 7, 49076 Osnabrück, Germany
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44
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Gautier A, Kirkpatrick J, Nietlispach D. Solution-State NMR Spectroscopy of a Seven-Helix Transmembrane Protein Receptor: Backbone Assignment, Secondary Structure, and Dynamics. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200802783] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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45
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Gautier A, Kirkpatrick J, Nietlispach D. Solution-State NMR Spectroscopy of a Seven-Helix Transmembrane Protein Receptor: Backbone Assignment, Secondary Structure, and Dynamics. Angew Chem Int Ed Engl 2008; 47:7297-300. [DOI: 10.1002/anie.200802783] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Abstract
Pharaonis phoborhodopsin (ppR, also called pharaonis sensory rhodopsin II) is a seven transmembrane helical retinal protein. ppR forms a signaling complex with pharaonis Halobacterial transducer II (pHtrII) in the membrane that transmits a light signal to the sensory system in the cytoplasm. The M-state during the photocycle of ppR (lambda(max) = 386 nm) is one of the active (signaling) intermediates. However, progress in characterizing the M-state at physiological temperature has been slow because its lifetime is very short (decay half-time is approximately 1 s). In this study, we identify a highly stable photoproduct that can be trapped at room temperature in buffer solution containing n-octyl-beta-d-glucoside, with a decay half-time and an absorption maximum of approximately 2 h and 386 nm, respectively. HPLC analysis revealed that this stable photoproduct contains 13-cis-retinal as a chromophore. Previously, we reported that water-soluble hydroxylamine reacts selectively with the M-state, and we found that this stable photoproduct also reacts selectively with that reagent. These results suggest that the physical properties of the stable photoproduct (named the M-like state) are very similar with the M-state during the photocycle. By utilizing the high stability of the M-like state, we analyzed interactions of the M-like state and directly estimated the pK(a) value of the Schiff base in the M-like state. These results suggest that the dissociation constant of the ppR(M-like)/pHtrII complex greatly increases (to 5 muM) as the pK(a) value greatly decreases (from 12 to 1.5). The proton transfer reaction of ppR from the cytoplasmic to the extracellular side is proposed to be caused by this change in pK(a).
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47
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Kawamura I, Yoshida H, Ikeda Y, Yamaguchi S, Tuzi S, Saitô H, Kamo N, Naito A. Dynamics change of phoborhodopsin and transducer by activation: study using D75N mutant of the receptor by site-directed solid-state 13C NMR. Photochem Photobiol 2008; 84:921-30. [PMID: 18363620 DOI: 10.1111/j.1751-1097.2008.00326.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pharaonis phoborhodopsin (ppR or sensory rhodopsin II) is a negative phototaxis receptor of Natronomonas pharaonis, and forms a complex, which transmits the photosignal into cytoplasm, with its cognate transducer (pHtrII). We examined a possible local dynamics change of ppR and its D75N mutant complexed with pHtrII, using solid-state (13)C NMR of [3-(13)C]Ala- and [1-(13)C]Val-labeled preparations. We distinguished Ala C(beta) (13)C signals of relatively static stem (Ala221) in the C-terminus of the receptors from those of flexible tip (Ala228, 234, 236 and 238), utilizing a mutant with truncated C-terminus. The local fluctuation frequency at the C-terminal tip was appreciably decreased when ppR was bound to pHtrII, while it was increased when D75N, that mimics the signaling state because of disrupted salt bridge between C and G helices prerequisite for the signal transfer, was bound to pHtrII. This signal change may be considered with the larger dissociation constant of the complex between pHtrII and M-state of ppR. At the same time, it turned out that fluctuation frequency of cytoplasmic portion of pHtrII is lowered when ppR is replaced by D75N in the complex with pHtrII. This means that the C-terminal tip partly participates in binding with the linker region of pHtrII in the dark, but this portion might be released at the signaling state leading to mutual association of the two transducers in the cytoplasmic regions within the ppR/pHtrII complex.
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Affiliation(s)
- Izuru Kawamura
- Graduate School of Engineering, Yokohama National University, Hodogaya-ku, Yokohama, Japan
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48
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Kikukawa T, Saha CK, Balashov SP, Imasheva ES, Zaslavsky D, Gennis RB, Abe T, Kamo N. The lifetimes of Pharaonis phoborhodopsin signaling states depend on the rates of proton transfers--effects of hydrostatic pressure and stopped flow experiments. Photochem Photobiol 2008; 84:880-8. [PMID: 18346087 DOI: 10.1111/j.1751-1097.2008.00318.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pharaonis phoborhodopsin (ppR), a negative phototaxis receptor of Natronomonas pharaonis, undergoes photocycle similar to the light-driven proton pump bacteriorhodopsin (BR), but the turnover rate is much slower due to much longer lifetimes of the M and O intermediates. The M decay was shown to become as fast as it is in BR in the L40T/F86D mutant. We examined the effects of hydrostatic pressure on the decay of these intermediates. For BR, pressure decelerated M decay but slightly affected O decay. In contrast, with ppR and with its L40T/F86D mutant, pressure slightly affected M decay but accelerated O decay. Clearly, the pressure-dependent factors for M and O decay are different in BR and ppR. In order to examine the deprotonation of Asp75 in unphotolyzed ppR we performed stopped flow experiments. The pH jump-induced deprotonation of Asp75 occurred with 60 ms, which is at least 20 times slower than deprotonation of the equivalent Asp85 in BR and about 10-fold faster than the O decay of ppR. These data suggest that proton transfer is slowed not only in the cytoplasmic channel but also in the extracellular channel of ppR and that the light-induced structural changes in the O intermediate of ppR additionally decrease this rate.
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Affiliation(s)
- Takashi Kikukawa
- Creative Research Initiative Sosei, Hokkaido University, Sapporo, Japan.
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49
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Optimized in vitro and in vivo expression of proteorhodopsin: A seven-transmembrane proton pump. Protein Expr Purif 2008; 58:103-13. [DOI: 10.1016/j.pep.2007.10.017] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2007] [Revised: 10/15/2007] [Accepted: 10/18/2007] [Indexed: 11/19/2022]
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50
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Sudo Y, Furutani Y, Iwamoto M, Kamo N, Kandori H. Structural changes in the O-decay accelerated mutants of pharaonis phoborhodopsin. Biochemistry 2008; 47:2866-74. [PMID: 18247579 DOI: 10.1021/bi701885k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
pharaonis phoborhodopsin ( ppR, also called pharaonis sensory rhodopsin II, psRII) is a receptor for negative phototaxis in Natronomonas pharaonis. The X-ray crystallographic structure of ppR is very similar to those of the ion-pumping rhodopsins, bacteriorhodopsin (BR) and halorhodopsin (hR). However, the decay processes of the photocycle intermediates such as M and O are much slower than those of BR and hR, which is advantageous for the sensor function of ppR. Iwamoto et al. previously found that, in a quadruple mutant (P182S/P183E/V194T/T204C; denoted as SETC) of ppR, the decay of the O intermediate was accelerated by approximately 100 times ( t 1/2 approximately 6.6 ms vs 690 ms for the wild type of ppR), being almost equal to that of BR (Iwamoto, M., et al. (2005) Biophys. J. 88, 1215-1223). The mutated residues are located on the extracellular surface (Pro182, Pro183, and Val194) and near the Schiff base (Thr204). The present Fourier-transform infrared (FTIR) spectroscopy of SETC revealed that protein structural changes in the K and M states were similar to those of the wild type. In contrast, the ppR O minus ppR infrared difference spectra of SETC are clearly different from those of the wild type in amide-I (1680-1640 cm (-1)) and S-H stretching (2580-2520 cm (-1)) vibrations. The 1673 (+) and 1656 (-) cm (-1) bands newly appear for SETC in the frequency region typical for the amide-I vibration of the alpha II- and alpha I-helices, respectively. The intensities of the 1673 (+) cm (-1) band of various mutants were well correlated with their O-decay half-times. Since the alpha II-helix possesses a considerably distorted structure, the result implies that distortion of the helix is required for fast O-decay. In addition, the characteristic changes in the S-H stretching vibration of Cys204 were different between SETC and T204C, suggesting that structural change near the Schiff base was induced by mutations of the extracellular surface. We conclude that the lifetime of the O intermediate in ppR is regulated by the distorted alpha-helix and strengthened hydrogen bond of Cys204.
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Affiliation(s)
- Yuki Sudo
- Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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