Abstract
Ion-transporting microbial rhodopsins are widely used as major molecular tools in optogenetics. They are categorized into light-gated ion channels and light-driven ion pumps. While the former passively transport various types of cations and anions in a light-dependent manner, light-driven ion pumps actively transport specific ions, such as H+, Na+, Cl−, against electrophysiological potential by using light energy. Since the ion transport by these pumps induces hyperpolarization of membrane potential and inhibit neural firing, light-driven ion-pumping rhodopsins are mostly applied as inhibitory optogenetics tools. Recent progress in genome and metagenome sequencing identified more than several thousands of ion-pumping rhodopsins from a wide variety of microbes, and functional characterization studies has been revealing many new types of light-driven ion pumps one after another. Since light-gated channels were reviewed in other chapters in this book, here the rapid progress in functional characterization, molecular mechanism study, and optogenetic application of ion-pumping rhodopsins were reviewed.
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Abbreviations
- AntR:
-
Inward H+ pumping Antarctic rhodopsin
- AR:
-
Acetabularia rhodopsin
- Arch or AR3:
-
Archaerhodopsin-3
- ASR:
-
Anabaena sensory rhodopsin
- ASRT :
-
Anabaena sensory rhodopsin transducer
- ATR-FTIR:
-
Attenuated total reflection-Fourier transform infrared
- BacHR:
-
Bacterial halorhodopsin
- BR:
-
Bacteriorhodopsin
- ChR:
-
Channelrhodopsin
- ClR:
-
Bacterial Cl− pump rhodopsin
- CP:
-
Cytoplasmic
- cryoEM:
-
Cryo-electron microscopy
- CsR:
-
Coccomyxa subellipsoidea rhodopsin
- DNP:
-
Dynamic nuclear-polarization
- DsNaR:
-
Dokdonia sp. PRO95 Na+ pump rhodopsin
- EPR:
-
Paramagnetic electron resonance
- ER:
-
Endoplasmic reticulum
- ESR:
-
Exiguobacterium sibiricum rhodopsin
- FdNaR:
-
Flagellimonas sp_DIK Na+ pump rhodopsin
- FR:
-
Fulvimarina pelagi rhodopsin
- FTIR:
-
Fourier transform infrared
- GlNaR:
-
Gillisia limnaea Na+ pump rhodopsin
- GPCR:
-
G-protein coupled receptor
- GR:
-
Gloeobacter rhodopsin
- HKR:
-
Histidine kinase rhodopsin
- HR:
-
Halorhodopsin
- HS-AFM:
-
High-speed atomic force microscopy
- HsHR:
-
Halobacterium salinarum halorhodopsin
- IAA:
-
Indole-3-acetic acid
- IaNaR:
-
Indibacter alkaliphilus Na+ pump rhodopsin
- IC:
-
Internal cavity
- KR2 or DeNaR:
-
Krokinobacter eikastus rhodopsin 2
- LR:
-
Leptosphaeria rhodopsin
- MrHR:
-
Mastigocladopsis repens halorhodopsin
- NaR:
-
Na+ pump rhodopsin
- NMR:
-
Nuclear magnetic resonance
- NM-R3 or NmClR:
-
Nonlabens marinus bacterial Cl− pump rhodopsin
- NR:
-
Neurospora rhodopsin
- NsXeR:
-
Nanosalina xenorhodopsin
- NyNaR:
-
Nonlabens sp. YIK_SED-11 Na+ pump rhodopsin
- OLPVRII:
-
Organic Lake Phycodnavirus rhodopsin II
- ORP:
-
Opsin-related proteins
- PaR:
-
DTG rhodopsins from Pantoea ananatis
- PhaeoRD:
-
Phaeosphaeria rhodopsin
- pHR or NpHR:
-
Natronomonas pharaonis halorhodopsin
- PoClR:
-
Parvularcula oceani bacterial Cl− pump rhodopsin
- PoXeR:
-
Parvularcula oceani xenorhodopsin
- PR:
-
Proteorhodopsin
- PRG:
-
Proton release group
- PspR:
-
DTG rhodopsins from Pseudomonas putida
- PvR:
-
DTG rhodopsins from Pantoea vagans
- QM/MM:
-
Quantum mechanics/molecular mechanics
- RhGC:
-
Rhodopsin guanylyl cyclase
- Rh-PDE:
-
Rhodopsin phosphodiesterase
- RmXeR:
-
Rubricoccus marinus xenorhodopsin
- RSB:
-
Retinal Schiff base
- RxR:
-
Rubrobacter xylanophilus rhodopsin
- SFX:
-
Serial femtosecond crystallography
- SyHR:
-
Synechocystis sp. PCC 7509 halorhodopsin
- SzR:
-
Schizorhodopsin
- TM:
-
Transmembrane
- TR:
-
Thermophilic rhodopsin
- TR-SFX:
-
Time-resolved serial femtosecond crystallography
- XeR:
-
Xenorhodopsin
- XFEL:
-
X-ray free electron laser.
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Acknowledgments
The author would like to thank Drs. Leonid S. Brown and Oded Béjà for their careful reading of the manuscript and insightful comments.  I apologize to all authors whose research could not be cited because of space limitations. This work was supported by grants from the Japanese Ministry of Education, Culture, Sports, Science and Technology (17H03007), Takeda Science Foundation, The Mitsubishi Foundation, and Yamada Science Foundation.
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Inoue, K. (2021). Diversity, Mechanism, and Optogenetic Application of Light-Driven Ion Pump Rhodopsins. In: Yawo, H., Kandori, H., Koizumi, A., Kageyama, R. (eds) Optogenetics. Advances in Experimental Medicine and Biology, vol 1293. Springer, Singapore. https://doi.org/10.1007/978-981-15-8763-4_6
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