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de Grip WJ, Ganapathy S. Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering. Front Chem 2022; 10:879609. [PMID: 35815212 PMCID: PMC9257189 DOI: 10.3389/fchem.2022.879609] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 05/16/2022] [Indexed: 01/17/2023] Open
Abstract
The first member and eponym of the rhodopsin family was identified in the 1930s as the visual pigment of the rod photoreceptor cell in the animal retina. It was found to be a membrane protein, owing its photosensitivity to the presence of a covalently bound chromophoric group. This group, derived from vitamin A, was appropriately dubbed retinal. In the 1970s a microbial counterpart of this species was discovered in an archaeon, being a membrane protein also harbouring retinal as a chromophore, and named bacteriorhodopsin. Since their discovery a photogenic panorama unfolded, where up to date new members and subspecies with a variety of light-driven functionality have been added to this family. The animal branch, meanwhile categorized as type-2 rhodopsins, turned out to form a large subclass in the superfamily of G protein-coupled receptors and are essential to multiple elements of light-dependent animal sensory physiology. The microbial branch, the type-1 rhodopsins, largely function as light-driven ion pumps or channels, but also contain sensory-active and enzyme-sustaining subspecies. In this review we will follow the development of this exciting membrane protein panorama in a representative number of highlights and will present a prospect of their extraordinary future potential.
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Affiliation(s)
- Willem J. de Grip
- Leiden Institute of Chemistry, Department of Biophysical Organic Chemistry, Leiden University, Leiden, Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Srividya Ganapathy
- Department of Imaging Physics, Delft University of Technology, Netherlands
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2
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Tamogami J, Kikukawa T, Nara T, Demura M, Kimura-Someya T, Shirouzu M, Yokoyama S, Miyauchi S, Shimono K, Kamo N. Existence of two O-like intermediates in the photocycle of Acetabularia rhodopsin II, a light-driven proton pump from a marine alga. Biophys Physicobiol 2017; 14:49-55. [PMID: 28560129 PMCID: PMC5437830 DOI: 10.2142/biophysico.14.0_49] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/02/2017] [Indexed: 12/01/2022] Open
Abstract
A spectrally silent change is often observed in the photocycle of microbial rhodopsins. Here, we suggest the presence of two O intermediates in the photocycle of Acetabularia rhodopsin II (ARII or also called Ace2), a light-driven algal proton pump from Acetabularia acetabulum. ARII exhibits a photocycle including a quasi-equilibrium state of M, N, and O (M⇄N⇄O→) at near neutral and above pH values. However, acidification of the medium below pH ~5.5 causes no accumulation of N, resulting in that the photocycle of ARII can be described as an irreversible scheme (M→O→). This may facilitate the investigation of the latter part of the photocycle, especially the rise and decay of O, during which molecular events have not been sufficiently understood. Thus we analyzed the photocycle under acidic conditions (pH ≤ 5.5). Analysis of the absorbance change at 610 nm, which mainly monitors the fractional concentration changes of K and O, was performed and revealed a photocycle scheme containing two sequential O-states with the different molar extinction coefficients. These photoproducts, termed O1 and O2, may be even produced at physiological pH, although they are not clearly observed under this condition due to the existence of a long M-N-O equilibrium.
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Affiliation(s)
- Jun Tamogami
- College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan.,Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo 001-0021, Japan
| | - Toshifumi Nara
- College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan
| | - Makoto Demura
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan.,Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo 001-0021, Japan
| | - Tomomi Kimura-Someya
- RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan
| | - Mikako Shirouzu
- RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan
| | - Shigeyuki Yokoyama
- RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.,RIKEN Structural Biology Laboratory, Yokohama 230-0045, Japan
| | - Seiji Miyauchi
- College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan.,Graduate School of Pharmaceutical Sciences, Toho University, Funabashi, Chiba 274-8510, Japan
| | - Kazumi Shimono
- College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan.,Graduate School of Pharmaceutical Sciences, Toho University, Funabashi, Chiba 274-8510, Japan
| | - Naoki Kamo
- College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan.,Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
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3
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Inoue K. The Study and Application of Photoreceptive Membrane Protein, Rhodopsin. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2016. [DOI: 10.1246/bcsj.20160235] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Yomoda H, Makino Y, Tomonaga Y, Hidaka T, Kawamura I, Okitsu T, Wada A, Sudo Y, Naito A. Color-Discriminating Retinal Configurations of Sensory Rhodopsin I by Photo-Irradiation Solid-State NMR Spectroscopy. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Yomoda H, Makino Y, Tomonaga Y, Hidaka T, Kawamura I, Okitsu T, Wada A, Sudo Y, Naito A. Color-discriminating retinal configurations of sensory rhodopsin I by photo-irradiation solid-state NMR spectroscopy. Angew Chem Int Ed Engl 2014; 53:6960-4. [PMID: 24846351 DOI: 10.1002/anie.201309258] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 02/17/2014] [Indexed: 12/20/2022]
Abstract
SRI (sensory rhodopsin I) can discriminate multiple colors for the attractant and repellent phototaxis. Studies aimed at revealing the color-dependent mechanism show that SRI is a challenging system not only in photobiology but also in photochemistry. During the photoreaction of SRI, an M-intermediate (attractant) transforms into a P-intermediate (repellent) by absorbing blue light. Consequently, SRI then cycles back to the G-state. The photoreactions were monitored with the (13)C NMR signals of [20-(13)C]retnal-SrSRI using in situ photo-irradiation solid-state NMR spectroscopy. The M-intermediate was trapped at -40 °C by illumination at 520 nm. It was transformed into the P-intermediate by subsequent illumination at 365 nm. These results reveal that the G-state could be directly transformed to the P-intermediate by illumination at 365 nm. Thus, the stationary trapped M- and P-intermediates are responsible for positive and negative phototaxis, respectively.
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Affiliation(s)
- Hiroki Yomoda
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501 (Japan)
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Sudo Y, Mizuno M, Wei Z, Takeuchi S, Tahara T, Mizutani Y. The Early Steps in the Photocycle of a Photosensor Protein Sensory Rhodopsin I from Salinibacter ruber. J Phys Chem B 2014; 118:1510-8. [DOI: 10.1021/jp4112662] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Yuki Sudo
- 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 444-8585, Japan
| | - Misao Mizuno
- Department
of Chemistry, Graduate School of Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Zhengrong Wei
- Molecular
Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Satoshi Takeuchi
- Molecular
Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Tahei Tahara
- Molecular
Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
- RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
| | - Yasuhisa Mizutani
- Department
of Chemistry, Graduate School of Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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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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Furutani Y, Okitsu T, Reissig L, Mizuno M, Homma M, Wada A, Mizutani Y, Sudo Y. Large Spectral Change due to Amide Modes of a β-Sheet upon the Formation of an Early Photointermediate of Middle Rhodopsin. J Phys Chem B 2013; 117:3449-58. [DOI: 10.1021/jp308765t] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Yuji Furutani
- Department of Life and Coordination-Complex
Molecular Science, Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi,
Saitama, 332-0012, Japan
| | - Takashi Okitsu
- Graduate School of Organic Chemistry
for Life Science, Kobe Pharmaceutical University, Higashinada-ku, Kobe 658-8558, Japan
| | - Louisa Reissig
- Division of Biological Science,
Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate
School of Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Michio Homma
- Division of Biological Science,
Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
| | - Akimori Wada
- Graduate School of Organic Chemistry
for Life Science, Kobe Pharmaceutical University, Higashinada-ku, Kobe 658-8558, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate
School of Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yuki Sudo
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi,
Saitama, 332-0012, Japan
- Division of Biological Science,
Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
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Oren A. Salinibacter: an extremely halophilic bacterium with archaeal properties. FEMS Microbiol Lett 2013; 342:1-9. [PMID: 23373661 DOI: 10.1111/1574-6968.12094] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Revised: 01/29/2013] [Accepted: 01/29/2013] [Indexed: 12/17/2022] Open
Abstract
The existence of large number of a member of the Bacteroidetes in NaCl-saturated brines in saltern crystallizer ponds was first documented in 1999 based on fluorescence in situ hybridization studies. Isolation of the organism and its description as Salinibacter ruber followed soon. It is a rod-shaped, red-orange pigmented, extreme halophile that grows optimally at 20-30% salt. The genus is distributed worldwide in hypersaline environments. Today, the genus Salinibacter includes three species, and a somewhat less halophilic relative, Salisaeta longa, has also been documented. Although belonging to the Bacteria, Salinibacter shares many features with the Archaea of the family Halobacteriaceae that live in the same habitat. Both groups use KCl for osmotic adjustment of their cytoplasm, both mainly possess salt-requiring enzymes with a large excess of acidic amino acids, and both contain different retinal pigments: light-driven proton pumps, chloride pumps, and light sensors. Salinibacter produces an unusual carotenoid, salinixanthin that forms a light antenna and transfers energy to the retinal group of xanthorhodopsin, a light-driven proton pump. Other unusual features of Salinibacter and Salisaeta include the presence of novel sulfonolipids (halocapnine derivatives). Salinibacter has become an excellent model for metagenomic, biogeographic, ecological, and evolutionary studies.
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Affiliation(s)
- Aharon Oren
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
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10
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Reissig L, Iwata T, Kikukawa T, Demura M, Kamo N, Kandori H, Sudo Y. Influence of Halide Binding on the Hydrogen Bonding Network in the Active Site of Salinibacter Sensory Rhodopsin I. Biochemistry 2012; 51:8802-13. [DOI: 10.1021/bi3009592] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Louisa Reissig
- Division of
Biological Science,
Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
| | - Tatsuya Iwata
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555,
Japan
- Center for Fostering
Young and
Innovative Researchers, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Makoto Demura
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Naoki Kamo
- College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555,
Japan
| | - Yuki Sudo
- Division of
Biological Science,
Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi,
Saitama, 332-0012, Japan
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11
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Maiti TK, Yamada K, Inoue K, Kandori H. L105K Mutant of Proteorhodopsin. Biochemistry 2012; 51:3198-204. [DOI: 10.1021/bi201916a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tushar Kanti Maiti
- Department
of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555,
Japan
| | - Keisuke Yamada
- Department
of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555,
Japan
| | - Keiichi Inoue
- 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
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12
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Sudo Y, Homma M. [Photosensing by membrane-embedded receptors and its application for the life scientists]. YAKUGAKU ZASSHI 2012; 132:407-16. [PMID: 22465915 DOI: 10.1248/yakushi.132.407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Light is one of the most important energy sources and signals providing critical information to biological systems. The photoreceptor rhodopsin, which possesses retinal chromophore (vitamin A aldehyde) surrounded by seven transmembrane alpha-helices, is widely dispersed in prokaryotes and in eukaryotes. Although rhodopsin molecules work as distinctly different photoreceptors, they can be divided according to their two basic functions such as light-energy conversion and light-signal transduction. Thus rhodopsin molecules have great potential for controlling cellular activity by light. Indeed, a light-energy converter channel rhodopsin is used to control neural activity. From 2001, we have been working on various microbial sensory rhodopsins functioning as light-signal converters. In this review, we will introduce rhodopsin molecules from microbes, and will describe artificial and light-dependent protein expression system in Escherichia coli using Anabeana sensory rhodopsin (ASR). The newly developed tools would be widely useful for life scientists.
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Affiliation(s)
- Yuki Sudo
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan.
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