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Rhodopsin-Based Optogenetics: Basics and Applications

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Rhodopsin

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2501))

Abstract

Optogenetics has revolutionized not only neuroscience but also had an impact on muscle physiology and cell biology. Rhodopsin-based optogenetics started with the discovery of the light-gated cation channels, called channelrhodopsins. Together with the light-driven ion pumps, these channels allow light-mediated control of electrically excitable cells in culture tissue and living animals. They can be activated (depolarized) or silenced (hyperpolarized) by light with incomparably high spatiotemporal resolution. Optogenetics allows the light manipulation of cells under electrode-free conditions in a minimally invasive manner. Through modern genetic techniques, virus-induced transduction can be performed with extremely high cell specificity in tissue and living animals, allowing completely new approaches for analyzing neural networks, behavior studies, and investigations of neurodegenerative diseases. First clinical trials for the optogenetic recovery of vision are underway.

This chapter provides a comprehensive description of the structure and function of the different light-gated channels and some new light-activated ion pumps. Some of them already play an essential role in optogenetics while others are supposed to become important tools for more specialized applications in the future.

At the moment, a large number of publications are available concerning intrinsic mechanisms of microbial rhodopsins. Mostly they describe CrChR2 and its variants, as CrChR2 is still the most prominent optogenetic tool. Therefore, many biophysically and biochemically oriented groups contributed to the overwhelming mass of information on this unique ion channel’s molecular mechanism. In this context, the function of new optogenetic tools is discussed, which is essential for rational optimization of the optogenetic approach for an eventual biomedical application. The comparison of the effectivity of ion pumps versus ion channels is discussed as well.

Applications of rhodopsins-based optogenetic tools are also discussed in the chapter. Because of the enormous number of these applications in neuroscience, only exemplary studies on cell culture neural tissue, muscle physiology, and remote control of animal behavior are presented.

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References

  1. Zemelman BV, Lee GA, Ng M et al (2002) Selective photostimulation of genetically ChARGed neurons. Neuron 33:15–22

    Article  CAS  PubMed  Google Scholar 

  2. Foster KW, Saranak J, Patel N et al (1984) A rhodopsin is the functional photoreceptor for phototaxis in the unicellular eukaryote Chlamydomonas. Nature 311:756–759

    Article  CAS  PubMed  Google Scholar 

  3. Sineshchekov OA, Litvin FF, Keszthelyi L (1990) Two components of photoreceptor potential in phototaxis of the flagellated green alga Haematococcus pluvialis. Biophys J 57:33–39

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Harz H, Hegemann P (1991) Rhodopsin-regulated calcium currents in Chlamydomonas. Nature 351:489–491

    Article  CAS  Google Scholar 

  5. Holland EM, Braun FJ, Nonnengässer C et al (1996) The nature of rhodopsin-triggered photocurrents in Chlamydomonas. I. Kinetics and influence of divalent ions. Biophys J 70:924–931

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Nonnengässer C, Holland EM, Harz H et al (1996) The nature of rhodopsin-triggered photocurrents in Chlamydomonas. II. Influence of monovalent ions. Biophys J 70:932–938

    Article  PubMed  PubMed Central  Google Scholar 

  7. Hildebrandt V, Fendler K, Heberle J et al (1993) Bacteriorhodopsin expressed in Schizosaccharomyces pombe pumps protons through the plasma membrane. Proc Natl Acad Sci 90:3578–3582

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Hoffmann A, Hildebrandt V, Heberle J et al (1994) Photoactive mitochondria: in vivo transfer of a light-driven proton pump into the inner mitochondrial membrane of Schizosaccharomyces pombe. Proc Natl Acad Sci 91:9367–9371

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Nagel G, Möckel B, Büldt G et al (1995) Functional expression of bacteriorhodopsin in oocytes allows direct measurement of voltage dependence of light induced H+ pumping. FEBS Lett 377:263–266

    Article  CAS  PubMed  Google Scholar 

  10. Geibel S, Friedrich T, Ormos P et al (2001) The voltage-dependent proton pumping in bacteriorhodopsin is characterized by optoelectric behavior. Biophys J 81:2059–2068

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Nagel G, Szellas T, Huhn W et al (2003) Channelrhodopsin-2, a directly light-gated cation-selective membrane channel. Proc Natl Acad Sci 100:13940–13945

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Boyden ES, Zhang F, Bamberg E et al (2005) Millisecond-timescale, genetically targeted optical control of neural activity. Nat Neurosci 8:1263–1268

    Article  CAS  PubMed  Google Scholar 

  13. Nagel G, Brauner M, Liewald JF et al (2005) Light activation of channelrhodopsin-2 in excitable cells of Caenorhabditis elegans triggers rapid behavioral responses. Curr Biol 15:2279–2284

    Article  CAS  PubMed  Google Scholar 

  14. Li X, Gutierrez DV, Hanson MG et al (2005) Fast noninvasive activation and inhibition of neural and network activity by vertebrate rhodopsin and green algae channelrhodopsin. Proc Natl Acad Sci 102:17816–17821

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Zhang F, Wang L-P, Brauner M et al (2007) Multimodal fast optical interrogation of neural circuitry. Nature 446:633–639

    Article  CAS  PubMed  Google Scholar 

  16. Kralj JM, Douglass AD, Hochbaum DR et al (2012) Optical recording of action potentials in mammalian neurons using a microbial rhodopsin. Nat Methods 9:90–95

    Article  CAS  Google Scholar 

  17. Hochbaum DR, Zhao Y, Farhi SL et al (2014) All-optical electrophysiology in mammalian neurons using engineered microbial rhodopsins. Nat Methods 11:825–833

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Miyawaki A, Llopis J, Heim R et al (1997) Fluorescent indicators for Ca2+ based on green fluorescent proteins and calmodulin. Nature 388:882–887

    Article  CAS  PubMed  Google Scholar 

  19. Ishizuka T, Kakuda M, Araki R et al (2006) Kinetic evaluation of photosensitivity in genetically engineered neurons expressing green algae light-gated channels. Neurosci Res 54:85–94

    Article  CAS  PubMed  Google Scholar 

  20. Feldbauer K, Zimmermann D, Pintschovius V et al (2009) Channelrhodopsin-2 is a leaky proton pump. Proc Natl Acad Sci 106:12317–12322

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Oesterhelt D, Stoeckenius W (1973) Functions of a new photoreceptor membrane. Proc Natl Acad Sci 70:2853–2857

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Oesterhelt D, Stoeckenius W (1971) Rhodopsin-like protein from the purple membrane of Halobacterium halobium. Nat New Biol 233:149–152

    Article  CAS  PubMed  Google Scholar 

  23. Lanyi JK (2004) Bacteriorhodopsin. Annu Rev Physiol 66:665–688

    Article  CAS  PubMed  Google Scholar 

  24. Béjà O, Aravind L, Koonin EV et al (2000) Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289:1902–1906

    Article  PubMed  Google Scholar 

  25. Hegemann P, Fuhrmann M, Kateriya S (2001) Algal sensory photoreceptors. J Phycol 37:668–676

    Article  CAS  Google Scholar 

  26. Sineshchekov OA, Jung K-H, Spudich JL (2002) Two rhodopsins mediate phototaxis to low- and high-intensity light in Chlamydomonas reinhardtii. Proc Natl Acad Sci 99:8689–8694

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Suzuki T, Yamasaki K, Fujita S et al (2003) Archaeal-type rhodopsins in Chlamydomonas: model structure and intracellular localization. Biochem Biophys Res Commun 301:711–717

    Article  CAS  PubMed  Google Scholar 

  28. Nagel G, Ollig D, Fuhrmann M et al (2002) Channelrhodopsin-1: a light-gated proton channel in green algae. Science 296:2395–2398

    Article  CAS  PubMed  Google Scholar 

  29. Berndt A, Schoenenberger P, Mattis J et al (2011) High-efficiency channelrhodopsins for fast neuronal stimulation at low light levels. Proc Natl Acad Sci 108:7595–7600

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Lin JY, Lin MZ, Steinbach P et al (2009) Characterization of engineered channelrhodopsin variants with improved properties and kinetics. Biophys J 96:1803–1814

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Zhang F, Prigge M, Beyrière F et al (2008) Red-shifted optogenetic excitation: a tool for fast neural control derived from Volvox carteri. Nat Neurosci 11:631–633

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  32. Yizhar O, Fenno LE, Prigge M et al (2011) Neocortical excitation/inhibition balance in information processing and social dysfunction. Nature 477:171–178

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Lin JY, Knutsen PM, Muller A et al (2013) ReaChR: a red-shifted variant of channelrhodopsin enables deep transcranial optogenetic excitation. Nat Neurosci 16:1499–1508

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Rajasethupathy P, Sankaran S, Marshel JH et al (2015) Projections from neocortex mediate top-down control of memory retrieval. Nature 526:653–659

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Berndt A, Yizhar O, Gunaydin LA et al (2009) Bi-stable neural state switches. Nat Neurosci 12:229–234

    Article  CAS  PubMed  Google Scholar 

  36. Gunaydin LA, Yizhar O, Berndt A et al (2010) Ultrafast optogenetic control. Nat Neurosci 13:387–392

    Article  CAS  PubMed  Google Scholar 

  37. Klapoetke NC, Murata Y, Kim SS et al (2014) Independent optical excitation of distinct neural populations. Nat Methods 11:338–346

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Mager T, Lopez de la Morena D, Senn V et al (2018) High frequency neural spiking and auditory signaling by ultrafast red-shifted optogenetics. Nat Commun 9:1750

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  39. Marshel JH, Kim YS, Machado TA et al (2019) Cortical layer–specific critical dynamics triggering perception. Science 365:eaaw5202

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Shevchenko V, Mager T, Kovalev K et al (2017) Inward H+ pump xenorhodopsin: mechanism and alternative optogenetic approach. Sci Adv 3:e1603187

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  41. Gradinaru V, Zhang F, Ramakrishnan C et al (2010) Molecular and cellular approaches for diversifying and extending optogenetics. Cell 141:154–165

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Berndt A, Lee SY, Ramakrishnan C et al (2014) Structure-guided transformation of channelrhodopsin into a light-activated chloride channel. Science 344:420–424

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Gong X, Mendoza-Halliday D, Ting JT et al (2020) An ultra-sensitive step-function opsin for minimally invasive optogenetic stimulation in mice and macaques. Neuron 107:38

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Wietek J, Wiegert JS, Adeishvili N et al (2014) Conversion of channelrhodopsin into a light-gated chloride channel. Science 344:409

    Article  CAS  PubMed  Google Scholar 

  45. Kleinlogel S, Feldbauer K, Dempski RE et al (2011) Ultra light-sensitive and fast neuronal activation with the Ca2+-permeable channelrhodopsin CatCh. Nat Neurosci 14:513–518

    Article  CAS  PubMed  Google Scholar 

  46. Keppeler D, Merino RM, Lopez de la Morena D et al (2018) Ultrafast optogenetic stimulation of the auditory pathway by targeting-optimized Chronos. EMBO J 37:e99649

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  47. Brown J, Behnam R, Coddington L et al (2018) Expanding the optogenetics toolkit by topological inversion of rhodopsins. Cell 175:1131–1140.e11

    Article  CAS  PubMed  Google Scholar 

  48. Govorunova EG, Sineshchekov OA, Spudich JL (2016) Structurally distinct cation channelrhodopsins from cryptophyte algae. Biophys J 110:2302–2304

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Sineshchekov OA, Govorunova EG, Li H et al (2017) Bacteriorhodopsin-like channelrhodopsins: alternative mechanism for control of cation conductance. Proc Natl Acad Sci 114:E9512–E9519

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Ugalde JA, Podell S, Narasingarao P et al (2011) Xenorhodopsins, an enigmatic new class of microbial rhodopsins horizontally transferred between archaea and bacteria. Biol Direct 6:52

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Inoue K, Ito S, Kato Y et al (2016) A natural light-driven inward proton pump. Nat Commun 7:1–10

    Google Scholar 

  52. Bulzu P-A, Andrei A-Ş, Salcher MM et al (2019) Casting light on Asgardarchaeota metabolism in a sunlit microoxic niche. Nat Microbiol 4:1129–1137

    Article  CAS  PubMed  Google Scholar 

  53. Inoue K, Tsunoda SP, Singh M et al (2020) Schizorhodopsins: a family of rhodopsins from Asgard archaea that function as light-driven inward H+ pumps. Sci Adv 6:eaaz2441

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Schobert B, Lanyi JK (1982) Halorhodopsin is a light-driven chloride pump. J Biol Chem 257:10306–10313

    Article  CAS  PubMed  Google Scholar 

  55. Han X, Boyden ES (2007) Multiple-color optical activation, silencing, and desynchronization of neural activity, with single-spike temporal resolution. PLoS One 2:e299

    Article  PubMed  PubMed Central  Google Scholar 

  56. Gradinaru V, Thompson KR, Deisseroth K (2008) eNpHR: a Natronomonas halorhodopsin enhanced for optogenetic applications. Brain Cell Biol 36:129–139

    Article  PubMed  PubMed Central  Google Scholar 

  57. Kleinlogel S, Terpitz U, Legrum B et al (2011) A gene-fusion strategy for stoichiometric and co-localized expression of light-gated membrane proteins. Nat Methods 8:1083–1088

    Article  CAS  PubMed  Google Scholar 

  58. Chow BY, Han X, Dobry AS et al (2010) High-performance genetically targetable optical neural silencing by light-driven proton pumps. Nature 463:98–102

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Han X, Chow BY, Zhou H et al (2011) A high-light sensitivity optical neural silencer: development and application to optogenetic control of non-human primate cortex. Front Syst Neurosci 5:18

    Article  PubMed  PubMed Central  Google Scholar 

  60. Inoue K, Ono H, Abe-Yoshizumi R et al (2013) A light-driven sodium ion pump in marine bacteria. Nat Commun 4:1678

    Article  PubMed  CAS  Google Scholar 

  61. Gushchin I, Shevchenko V, Polovinkin V et al (2015) Crystal structure of a light-driven sodium pump. Nat Struct Mol Biol 22:390–395

    Article  CAS  PubMed  Google Scholar 

  62. Kato HE, Inoue K, Abe-Yoshizumi R et al (2015) Structural basis for Na+ transport mechanism by a light-driven Na+ pump. Nature 521:48–53

    Article  CAS  PubMed  Google Scholar 

  63. Grimm C, Silapetere A, Vogt A et al (2018) Electrical properties, substrate specificity and optogenetic potential of the engineered light-driven sodium pump eKR2. Sci Rep 8:9316

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  64. Vogt A, Silapetere A, Grimm C et al (2019) Engineered passive potassium conductance in the KR2 sodium pump. Biophys J 116:1941–1951

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Berndt A, Lee SY, Wietek J et al (2016) Structural foundations of optogenetics: determinants of channelrhodopsin ion selectivity. Proc Natl Acad Sci 113:822–829

    Article  CAS  PubMed  Google Scholar 

  66. Govorunova EG, Sineshchekov OA, Janz R et al (2015) Natural light-gated anion channels: a family of microbial rhodopsins for advanced optogenetics. Science 349:647–650

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Sineshchekov OA, Govorunova EG, Li H et al (2015) Gating mechanisms of a natural anion channelrhodopsin. Proc Natl Acad Sci 112:14236–14241

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Kato HE, Kim YS, Paggi JM et al (2018) Structural mechanisms of selectivity and gating in anion channelrhodopsins. Nature 561:349–354

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Oppermann J, Fischer P, Silapetere A et al (2019) MerMAIDs: a family of metagenomically discovered marine anion-conducting and intensely desensitizing channelrhodopsins. Nat Commun 10:1–13

    Article  CAS  Google Scholar 

  70. Rost BR, Schneider F, Grauel MK et al (2015) Optogenetic acidification of synaptic vesicles and lysosomes. Nat Neurosci 18:1845–1852

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Tkatch T, Greotti E, Baranauskas G et al (2017) Optogenetic control of mitochondrial metabolism and Ca2+ signaling by mitochondria-targeted opsins. Proc Natl Acad Sci 114:E5167–E5176

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Reyer A, Häßler M, Scherzer S et al (2020) Channelrhodopsin-mediated optogenetics highlights a central role of depolarization-dependent plant proton pumps. Proc Natl Acad Sci 117:20920–20925

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Luck M, Mathes T, Bruun S et al (2012) A photochromic histidine kinase rhodopsin (HKR1) that is bimodally switched by ultraviolet and blue light. J Biol Chem 287:40083–40090

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Avelar GM, Schumacher RI, Zaini PA et al (2014) A rhodopsin-guanylyl cyclase gene fusion functions in visual perception in a fungus. Curr Biol 24:1234–1240

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Yoshida K, Tsunoda SP, Brown LS et al (2017) A unique choanoflagellate enzyme rhodopsin exhibits light-dependent cyclic nucleotide phosphodiesterase activity. J Biol Chem 292:7531–7541

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Kim CK, Adhikari A, Deisseroth K (2017) Integration of optogenetics with complementary methodologies in systems neuroscience. Nat Rev Neurosci 18:222–235

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Paz JT, Davidson TJ, Frechette ES et al (2013) Closed-loop optogenetic control of thalamus as a tool for interrupting seizures after cortical injury. Nat Neurosci 16:64–70

    Article  CAS  PubMed  Google Scholar 

  78. Ji G, Feldman ME, Deng K-Y et al (2004) Ca2+-sensing transgenic mice postsynaptic signaling in smooth muscle. J Biol Chem 279:21461–21468

    Article  CAS  PubMed  Google Scholar 

  79. Vogt N (2015) Voltage sensors: challenging, but with potential. Nat Methods 12:921–924

    Article  CAS  PubMed  Google Scholar 

  80. Zhang H, Reichert E, Cohen AE (2016) Optical electrophysiology for probing function and pharmacology of voltage-gated ion channels. elife 5:e15202

    Article  PubMed  PubMed Central  Google Scholar 

  81. Gómez-Consarnau L, Raven JA, Levine NM et al (2019) Microbial rhodopsins are major contributors to the solar energy captured in the sea. Sci Adv 5:eaaw8855

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  82. Pushkarev A, Inoue K, Larom S et al (2018) A distinct abundant group of microbial rhodopsins discovered using functional metagenomics. Nature 558:595–599

    Article  CAS  PubMed  Google Scholar 

  83. Yutin N, Koonin EV (2012) Proteorhodopsin genes in giant viruses. Biol Direct 7:34

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Needham DM, Yoshizawa S, Hosaka T et al (2019) A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators. Proc Natl Acad Sci 116:20574–20583

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Bratanov D, Kovalev K, Machtens J-P et al (2019) Unique structure and function of viral rhodopsins. Nat Commun 10:4939

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  86. Zabelskii D, Alekseev A, Kovalev K et al (2020) Viral rhodopsins 1 are an unique family of light-gated cation channels. Nat Commun 11:5707

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Kato HE, Zhang F, Yizhar O et al (2012) Crystal structure of the channelrhodopsin light-gated cation channel. Nature 482:369–374

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Müller M, Bamann C, Bamberg E et al (2011) Projection structure of channelrhodopsin-2 at 6 Å resolution by electron crystallography. J Mol Biol 414:86–95

    Article  PubMed  CAS  Google Scholar 

  89. Müller M, Bamann C, Bamberg E et al (2015) Light-induced helix movements in channelrhodopsin-2. J Mol Biol 427:341–349

    Article  PubMed  CAS  Google Scholar 

  90. Volkov O, Kovalev K, Polovinkin V et al (2017) Structural insights into ion conduction by channelrhodopsin 2. Science 358:eaan8862

    Article  PubMed  CAS  Google Scholar 

  91. Oda K, Vierock J, Oishi S et al (2018) Crystal structure of the red light-activated channelrhodopsin Chrimson. Nat Commun 9:1–11

    Article  CAS  Google Scholar 

  92. Kim YS, Kato HE, Yamashita K et al (2018) Crystal structure of the natural anion-conducting channelrhodopsin Gt ACR1. Nature 561:343–348

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Lórenz-Fonfría VA, Resler T, Krause N et al (2013) Transient protonation changes in channelrhodopsin-2 and their relevance to channel gating. Proc Natl Acad Sci 110:E1273–E1281

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  94. Lórenz-Fonfría VA, Bamann C, Resler T et al (2015) Temporal evolution of helix hydration in a light-gated ion channel correlates with ion conductance. Proc Natl Acad Sci U S A 112:E5796–E5804

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  95. Bamann C, Kirsch T, Nagel G et al (2008) Spectral characteristics of the photocycle of channelrhodopsin-2 and its implication for channel function. J Mol Biol 375:686–694

    Article  CAS  PubMed  Google Scholar 

  96. Eisenhauer K, Kuhne J, Ritter E et al (2012) In channelrhodopsin-2 Glu-90 is crucial for ion selectivity and is deprotonated during the photocycle. J Biol Chem 287:6904–6911

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Ito S, Kato HE, Taniguchi R et al (2014) Water-containing hydrogen-bonding network in the active center of channelrhodopsin. J Am Chem Soc 136:3475–3482

    Article  CAS  PubMed  Google Scholar 

  98. Radu I, Bamann C, Nack M et al (2009) Conformational changes of channelrhodopsin-2. J Am Chem Soc 131:7313–7319

    Article  CAS  PubMed  Google Scholar 

  99. Kuhne J, Vierock J, Tennigkeit SA et al (2019) Unifying photocycle model for light adaptation and temporal evolution of cation conductance in channelrhodopsin-2. Proc Natl Acad Sci 116:9380–9389

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. El-Shamayleh Y, Horwitz GD (2019) Primate optogenetics: progress and prognosis. Proc Natl Acad Sci 116:26195–26203

    Article  CAS  PubMed Central  Google Scholar 

  101. Liu X, Ramirez S, Pang PT et al (2012) Optogenetic stimulation of a hippocampal engram activates fear memory recall. Nature 484:381–385

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Roy DS, Arons A, Mitchell TI et al (2016) Memory retrieval by activating engram cells in mouse models of early Alzheimer’s disease. Nature 531:508–512

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Ramirez S, Liu X, Lin P-A et al (2013) Creating a false memory in the hippocampus. Science 341:387–391

    Article  CAS  PubMed  Google Scholar 

  104. Denny CA, Kheirbek MA, Alba EL et al (2014) Hippocampal memory traces are differentially modulated by experience, time, and adult neurogenesis. Neuron 83:189–201

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. Jeschke M, Moser T (2015) Considering optogenetic stimulation for cochlear implants. Hear Res 322:224–234

    Article  PubMed  Google Scholar 

  106. Zeng F-G, Rebscher S, Harrison W et al (2008) Cochlear implants: system design, integration, and evaluation. IEEE Rev Biomed Eng 1:115–142

    Article  PubMed  PubMed Central  Google Scholar 

  107. Hernandez VH, Gehrt A, Reuter K et al (2014) Optogenetic stimulation of the auditory pathway. J Clin Invest 124:1114–1129

    Article  PubMed  PubMed Central  Google Scholar 

  108. Sahel J-A, Roska B (2013) Gene therapy for blindness. Annu Rev Neurosci 36:467–488

    Article  CAS  PubMed  Google Scholar 

  109. Bi A, Cui J, Ma Y-P et al (2006) Ectopic expression of a microbial-type rhodopsin restores visual responses in mice with photoreceptor degeneration. Neuron 50:23–33

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. Busskamp V, Picaud S, Sahel JA et al (2012) Optogenetic therapy for retinitis pigmentosa. Gene Ther 19:169–175

    Article  CAS  PubMed  Google Scholar 

  111. Busskamp V, Duebel J, Balya D et al (2010) Genetic reactivation of cone photoreceptors restores visual responses in retinitis pigmentosa. Science 329:413–417

    Article  CAS  PubMed  Google Scholar 

  112. Chuong AS, Miri ML, Busskamp V et al (2014) Noninvasive optical inhibition with a red-shifted microbial rhodopsin. Nat Neurosci 17:1123–1129

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. McGregor JE, Godat T, Dhakal KR et al (2020) Optogenetic restoration of retinal ganglion cell activity in the living primate. Nat Commun 11:1–9

    Article  CAS  Google Scholar 

  114. Sahel J-A, Boulanger-Scemama E, Pagot C et al (2021) Partial recovery of visual function in a blind patient after optogenetic therapy. Nat Med 1–7

    Google Scholar 

  115. Gradinaru V, Mogri M, Thompson KR et al (2009) Optical deconstruction of Parkinsonian neural circuitry. Science 324:354–359

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. Chen S, Weitemier AZ, Zeng X et al (2018) Near-infrared deep brain stimulation via upconversion nanoparticle–mediated optogenetics. Science 359:679

    Article  CAS  PubMed  Google Scholar 

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Acknowledgment

This work was supported by Russian Science Foundation (RSF) Project 21-64-00018.

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Authors and Affiliations

  1. Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia

    Alexey Alekseev

  2. Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France

    Valentin Gordeliy

  3. Max Planck Institute of Biophysics, Frankfurt am Main, Germany

    Ernst Bamberg

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  2. Valentin Gordeliy
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  3. Ernst Bamberg
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Correspondence to Ernst Bamberg .

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  1. Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France

    Valentin Gordeliy

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Alekseev, A., Gordeliy, V., Bamberg, E. (2022). Rhodopsin-Based Optogenetics: Basics and Applications. In: Gordeliy, V. (eds) Rhodopsin. Methods in Molecular Biology, vol 2501. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2329-9_3

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  • DOI: https://doi.org/10.1007/978-1-0716-2329-9_3

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2328-2

  • Online ISBN: 978-1-0716-2329-9

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