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Light-Activated Ion Pumps and Channels for Temporally Precise Optical Control of Activity in Genetically Targeted Neurons

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Photosensitive Molecules for Controlling Biological Function

Part of the book series: Neuromethods ((NM,volume 55))

Abstract

The ability to turn on and off specific cell types and neural pathways in the brain, in a temporally precise fashion, has begun to enable the ability to test the sufficiency and necessity of particular neural activity patterns, and particular neural circuits, in the generation of normal and abnormal neural computations and behaviors by the brain. Over the last 5 years, a number of naturally occurring light-activated ion pumps and light-gated ion channels have been shown, upon genetic expression in specific neuron classes, to enable the voltage (and internal ionic composition) of those neurons to be controlled by light in a temporally precise fashion, without the need for chemical co-factors. In this chapter, we review three major classes of such genetically encoded “optogenetic” microbial opsins – light-gated ion channels such as channelrhodopsins, light-driven chloride pumps such as halorhodopsins, and light-driven proton pumps such as archaerhodopsins – that are in widespread use for mediating optical activation and silencing of neurons in species from C. elegans to nonhuman primate. We discuss the properties of these molecules – including their membrane expression, conductances, photocycle properties, ion selectivity, and action spectra – as well as genetic strategies for delivering these genes to neurons in different species, and hardware for performing light delivery in a diversity of settings. In the future, these molecules will not only continue to enable cutting-edge science, but may also support a new generation of optical prosthetics for treating brain disorders.

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References

  1. Nagel G et al (2003) Channelrhodopsin-2, a directly light-gated cation-selective membrane channel. Proc Natl Acad Sci U S A 100:13940–13945

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  3. Boyden ES, Zhang F, Bamberg E, Nagel G, Deisseroth K (2005) Millisecond-timescale, genetically targeted optical control of neural activity. Nat Neurosci 8:1263–1268

    PubMed  CAS  Google Scholar 

  4. Li X et al (2005) Fast noninvasive activation and inhibition of neural and network activity by vertebrate rhodopsin and green algae channelrhodopsin. Proc Natl Acad Sci U S A 102:17816–17821

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  6. Wang H et al (2009) Molecular determinants differentiating photocurrent properties of two channelrhodopsins from Chlamydomonas. J Biol Chem 284:5685–5696

    PubMed  CAS  Google Scholar 

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

    PubMed  Google Scholar 

  8. Berndt A, Yizhar O, Gunaydin LA, Hegemann P, Deisseroth K (2009) Bi-stable neural state switches. Nat Neurosci 12:229–234

    PubMed  CAS  Google Scholar 

  9. Lewis TL Jr, Mao T, Svoboda K, Arnold DB (2009) Myosin-dependent targeting of transmembrane proteins to neuronal dendrites. Nat Neurosci 12:568–576

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  11. Lanyi JK, Duschl A, Hatfield GW, May K, Oesterhelt D (1990) The primary structure of a halorhodopsin from Natronobacterium pharaonis. Structural, functional and evolutionary implications for bacterial rhodopsins and halorhodopsins. J Biol Chem 265:1253–1260

    PubMed  CAS  Google Scholar 

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

    PubMed  Google Scholar 

  13. Zhang F et al (2007) Multimodal fast optical interrogation of neural circuitry. Nature 446:633–639

    PubMed  CAS  Google Scholar 

  14. Bamberg E, Tittor J, Oesterhelt D (1993) Light-driven proton or chloride pumping by halorhodopsin. Proc Natl Acad Sci U S A 90:639–643

    PubMed  CAS  Google Scholar 

  15. Chow BY, Han X, Dobry AS, Qian X, Chuong AS, Li M, Henninger MA, Belfort GM, Lin Y, Monahan PE, Boyden ES (2010) High-performance genetically targetable optical neural silencing by light-driven proton pumps. Nature 463:98–102

    PubMed  CAS  Google Scholar 

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

    PubMed  Google Scholar 

  17. Zhao S et al (2008) Improved expression of halorhodopsin for light-induced silencing of neuronal activity. Brain Cell Biol 36:141–154

    PubMed  CAS  Google Scholar 

  18. Chow B, Han X, Qian X, Boyden ES (2009) High-performance halorhodopsin variants for improved genetically-targetable optical neural silencing. Front Syst Neurosci. Conference abstract: computational and systems neuroscience. doi:10.3389/conf.neuro.10.2009.03.347

    Google Scholar 

  19. Han X, Qian X, Stern P, Chuong AS, Boyden ES (2009) Informational lesions: optical perturbation of spike timing and neural synchrony via microbial opsin gene fusions. Front Mol Neurosci 2:12. doi:10.3389/neuro.02.012.2009

    PubMed  Google Scholar 

  20. Henderson R, Schertler GF (1990) The structure of bacteriorhodopsin and its relevance to the visual opsins and other seven-helix G-protein coupled receptors. Philos Trans R Soc Lond B Biol Sci 326:379–389

    PubMed  CAS  Google Scholar 

  21. Palczewski KG (2006) Protein-coupled receptor rhodopsin. Annu Rev Biochem 75:743–767. doi:10.1146/annurev.bio­chem.75.103004.142743

    PubMed  CAS  Google Scholar 

  22. Lanyi JK (2004) Bacteriorhodopsin. Annu Rev Physiol 66:665–688. doi:10.1146/annurev.physiol.66.032102.150049

    PubMed  CAS  Google Scholar 

  23. Lanyi JK (1986) Halorhodopsin: a light-driven chloride ion pump. Annu Rev Biophys Biophys Chem 15:11–28. doi:10.1146/annurev.bb.15.060186.000303

    PubMed  CAS  Google Scholar 

  24. Essen LO (2002) Halorhodopsin: light-driven ion pumping made simple? Curr Opin Struct Biol 12:516–522

    PubMed  CAS  Google Scholar 

  25. Zemelman BV, Lee GA, Ng M, Miesenbock G (2002) Selective photostimulation of genetically chARGed neurons. Neuron 33:15–22

    PubMed  CAS  Google Scholar 

  26. Lin B, Koizumi A, Tanaka N, Panda S, Masland RH (2008) Restoration of visual function in retinal degeneration mice by ectopic expression of melanopsin. Proc Natl Acad Sci U S A 105:16009–16014

    PubMed  CAS  Google Scholar 

  27. Kolbe M, Besir H, Essen LO, Oesterhelt D (2000) Structure of the light-driven chloride pump halorhodopsin at 1.8  Å resolution. Science 288:1390–1396

    PubMed  CAS  Google Scholar 

  28. Luecke H, Schobert B, Richter HT, Cartailler JP, Lanyi JK (1999) Structure of bacteriorhodopsin at 1.55  Å resolution. J Mol Biol 291:899–911

    PubMed  CAS  Google Scholar 

  29. Braiman MS, Stern LJ, Chao BH, Khorana HG (1987) Structure–function studies on bacteriorhodopsin. IV. Purification and renaturation of bacterio-opsin polypeptide expressed in Escherichia coli. J Biol Chem 262:9271–9276

    PubMed  CAS  Google Scholar 

  30. Gilles-Gonzalez MA, Engelman DM, Khorana HG (1991) Structure–function studies of bacteriorhodopsin XV. Effects of deletions in loops B-C and E-F on bacteriorhodopsin chromophore and structure. J Biol Chem 266:8545–8550

    PubMed  CAS  Google Scholar 

  31. Mogi T, Stern LJ, Chao BH, Khorana HG (1989) Structure–function studies on bacteriorhodopsin. VIII. Substitutions of the membrane-embedded prolines 50, 91, and 186: the effects are determined by the substituting amino acids. J Biol Chem 264:14192–14196

    PubMed  CAS  Google Scholar 

  32. Mogi T, Marti T, Khorana HG (1989) Structure–function studies on bacteriorhodopsin. IX. Substitutions of tryptophan residues affect protein-retinal interactions in bacteriorhodopsin. J Biol Chem 264:14197–14201

    PubMed  CAS  Google Scholar 

  33. Mogi T, Stern LJ, Hackett NR, Khorana HG (1987) Bacteriorhodopsin mutants containing single tyrosine to phenylalanine substitutions are all active in proton translocation. Proc Natl Acad Sci U S A 84:5595–5599

    PubMed  Google Scholar 

  34. Marti T et al (1991) Bacteriorhodopsin mutants containing single substitutions of serine or threonine residues are all active in proton translocation. J Biol Chem 266:6919–6927

    PubMed  CAS  Google Scholar 

  35. Marinetti T, Subramaniam S, Mogi T, Marti T, Khorana HG (1989) Replacement of aspartic residues 85, 96, 115, or 212 affects the quantum yield and kinetics of proton release and uptake by bacteriorhodopsin. Proc Natl Acad Sci U S A 86:529–533

    PubMed  CAS  Google Scholar 

  36. Mogi T, Stern LJ, Marti T, Chao BH, Khorana HG (1988) Aspartic acid substitutions affect proton translocation by bacteriorhodopsin. Proc Natl Acad Sci U S A 85:4148–4152

    PubMed  CAS  Google Scholar 

  37. Subramaniam S, Greenhalgh DA, Khorana HG (1992) Aspartic acid 85 in bacteriorhodopsin functions both as proton acceptor and negative counterion to the Schiff base. J Biol Chem 267:25730–25733

    PubMed  CAS  Google Scholar 

  38. Brown LS, Needleman R, Lanyi JK (1996) Interaction of proton and chloride transfer pathways in recombinant bacteriorhodopsin with chloride transport activity: implications for the chloride translocation mechanism. Biochemistry 35:16048–16054

    PubMed  CAS  Google Scholar 

  39. Hegemann P, Oesterhelt D, Steiner M (1985) The photocycle of the chloride pump halorhodopsin. I: Azide-catalyzed deprotonation of the chromophore is a side reaction of photocycle intermediates inactivating the pump. EMBO J 4:2347–2350

    PubMed  CAS  Google Scholar 

  40. Blanck A, Oesterhelt D (1987) The halo-opsin gene. II. Sequence, primary structure of halorhodopsin and comparison with bacteriorhodopsin. EMBO J 6:265–273

    PubMed  CAS  Google Scholar 

  41. Rudiger M, Oesterhelt D (1997) Specific arginine and threonine residues control anion binding and transport in the light-driven chloride pump halorhodopsin. EMBO J 16:3813–3821

    PubMed  CAS  Google Scholar 

  42. Varo G et al (1995) Light-driven chloride ion transport by halorhodopsin from Natronobacterium pharaonis. 1. The photochemical cycle. Biochemistry 34:14490–14499

    PubMed  CAS  Google Scholar 

  43. Tittor J et al (1997) Chloride and proton transport in bacteriorhodopsin mutant D85T: different modes of ion translocation in a retinal protein. J Mol Biol 271:405–416

    PubMed  CAS  Google Scholar 

  44. Tittor J, Oesterhelt D, Bamberg E (1995) Bacteriorhodopsin mutants D85N, D85T and D85,96N as proton pumps. Biophys Chem 56:153–157

    PubMed  CAS  Google Scholar 

  45. Varo G, Needleman R, Lanyi JK (1995) Light-driven chloride ion transport by halorhodopsin from Natronobacterium pharaonis. 2. Chloride release and uptake, protein conformation change, and thermodynamics. Biochemistry 34:14500–14507

    PubMed  CAS  Google Scholar 

  46. Berthold P et al (2008) Channelrhodopsin-1 initiates phototaxis and photophobic responses in Chlamydomonas by immediate light-induced depolarization. Plant Cell 20:1665–1677. doi:10.1105/tpc.108.057919

    PubMed  CAS  Google Scholar 

  47. Sineshchekov OA, Govorunova EG, Spudich JL (2009) Photosensory functions of channelrhodopsins in native algal cells. Photochem Photobiol 85:556–563

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  49. Feldbauer K et al (2009) Channelrhodopsin-2 is a leaky proton pump. Proc Natl Acad Sci U S A 106:12317–12322

    PubMed  CAS  Google Scholar 

  50. Nagel G et al (2002) Channelrhodopsin-1: a light-gated proton channel in green algae. Science 296:2395–2398

    PubMed  CAS  Google Scholar 

  51. Ernst OP et al (2008) Photoactivation of channelrhodopsin. J Biol Chem 283:1637–1643

    PubMed  CAS  Google Scholar 

  52. Zhang F, Wang LP, Boyden ES, Deisseroth K (2006) Channelrhodopsin-2 and optical control of excitable cells. Nat Methods 3:785–792

    PubMed  CAS  Google Scholar 

  53. Huber D et al (2008) Sparse optical microstimulation in barrel cortex drives learned behaviour in freely moving mice. Nature 451:61–64

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  55. Nikolic K, Degenaar P, Toumazou C (2006) Modeling and engineering aspects of channelrhodopsin-2 system for neural photostimulation. Conf Proc IEEE Eng Med Biol Soc 1:1626–1629

    PubMed  Google Scholar 

  56. Tsunoda SP, Hegemann P (2009) Glu 87 of channelrhodopsin-1 causes pH-dependent color tuning and fast photocurrent inactivation. Photochem Photobiol 85:564–569

    PubMed  CAS  Google Scholar 

  57. Ritter E, Stehfest K, Berndt A, Hegemann P, Bartl FJ (2008) Monitoring light-induced structural changes of channelrhodopsin-2 by UV-visible and Fourier transform infrared spectroscopy. J Biol Chem 283:35033–35041. doi:10.1074/jbc.M806353200

    PubMed  CAS  Google Scholar 

  58. Harwood JL, Guschina IA (2009) The versatility of algae and their lipid metabolism. Biochimie 91:679–684

    PubMed  CAS  Google Scholar 

  59. Zipfel WR, Williams RM, Webb WW (2003) Nonlinear magic: multiphoton microscopy in the biosciences. Nat Biotechnol 21:1369–1377

    PubMed  CAS  Google Scholar 

  60. Mohanty SK et al (2008) In-depth activation of channelrhodopsin 2-sensitized excitable cells with high spatial resolution using two-photon excitation with a near-infrared laser microbeam. Biophys J 95:3916–3926

    PubMed  CAS  Google Scholar 

  61. Rickgauer JP, Tank DW (2009) Two-photon excitation of channelrhodopsin-2 at saturation. Proc Natl Acad Sci U S A 106:15025–15030

    PubMed  CAS  Google Scholar 

  62. Sineshchekov OA et al (2005) Rhodopsin-mediated photoreception in cryptophyte flagellates. Biophys J 89:4310–4319

    PubMed  CAS  Google Scholar 

  63. 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

    PubMed  CAS  Google Scholar 

  64. Litvin FF, Sineshchekov OA, Sineshchekov VA (1978) Photoreceptor electric potential in the phototaxis of the alga Haematococcus pluvialis. Nature 271:476–478

    PubMed  CAS  Google Scholar 

  65. Gradinaru V et al (2007) Targeting and readout strategies for fast optical neural control in vitro and in vivo. J Neurosci 27:14231–14238

    PubMed  CAS  Google Scholar 

  66. Ihara K et al (1999) Evolution of the archaeal rhodopsins: evolution rate changes by gene duplication and functional differentiation. J Mol Biol 285:163–174

    PubMed  CAS  Google Scholar 

  67. Mukohata Y, Ihara K, Tamura T, Sugiyama Y (1999) Halobacterial rhodopsins. J Biochem 125:649–657

    PubMed  CAS  Google Scholar 

  68. Klare JP, Chizhov I, Engelhard M (2008) Microbial rhodopsins: scaffolds for ion pumps, channels, and sensors. Results Probl Cell Differ 45:73–122

    PubMed  CAS  Google Scholar 

  69. Antón J et al (2005) Salinibacter ruber: genomics and biogeography. In: Gunde-Cimerman N, Plemenitas A, Oren A (eds) Adaptation to life in high salt concentrations in archaea, bacteria and eukarya. Springer pp 257–266

    Google Scholar 

  70. Balashov SP et al (2005) Xanthorhodopsin: a proton pump with a light-harvesting carotenoid antenna. Science 309:2061–2064

    PubMed  CAS  Google Scholar 

  71. Beja O, Spudich EN, Spudich JL, Leclerc M, DeLong EF (2001) Proteorhodopsin phototrophy in the ocean. Nature 411:786–789

    PubMed  CAS  Google Scholar 

  72. Beja O et al (2000) Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289:1902–1906

    PubMed  CAS  Google Scholar 

  73. Friedrich T et al (2002) Proteorhodopsin is a light-driven proton pump with variable vectoriality. J Mol Biol 321:821–838

    PubMed  CAS  Google Scholar 

  74. Kelemen BR, Du M, Jensen RB (2003) Proteorhodopsin in living color: diversity of spectral properties within living bacterial cells. Biochim Biophys Acta 1618:25–32

    PubMed  CAS  Google Scholar 

  75. Kim SY, Waschuk SA, Brown LS, Jung KH (2008) Screening and characterization of proteorhodopsin color-tuning mutations in Escherichia coli with endogenous retinal synthesis. Biochim Biophys Acta 1777:504–513

    PubMed  CAS  Google Scholar 

  76. Brown LS (2004) Fungal rhodopsins and opsin-related proteins: eukaryotic homologues of bacteriorhodopsin with unknown functions. Photochem Photobiol Sci 3:555–565

    PubMed  CAS  Google Scholar 

  77. Waschuk SA, Bezerra AG, Shi L, Brown LS (2005) Leptosphaeria rhodopsin: bacteriorhodopsin-like proton pump from a eukaryote. Proc Natl Acad Sci U S A 102:6879–6883. doi:10.1073/pnas.0409659102

    PubMed  CAS  Google Scholar 

  78. Tsunoda SP et al (2006) H+-Pumping rhodopsin from the marine alga Acetabularia. Biophys J 91:1471–1479

    PubMed  CAS  Google Scholar 

  79. Yoshimura K, Kouyama T (2008) Structural role of bacterioruberin in the trimeric structure of archaerhodopsin-2. J Mol Biol 375:1267–1281

    PubMed  CAS  Google Scholar 

  80. Enami N et al (2006) Crystal structures of archaerhodopsin-1 and -2: common structural motif in archaeal light-driven proton pumps. J Mol Biol 358:675–685

    PubMed  CAS  Google Scholar 

  81. Seki A et al (2007) Heterologous expression of Pharaonis halorhodopsin in Xenopus laevis oocytes and electrophysiological characterization of its light-driven Cl pump activity. Biophys J 92:2559–2569

    PubMed  CAS  Google Scholar 

  82. Okuno D, Asaumi M, Muneyuki E (1999) Chloride concentration dependency of the electrogenic activity of halorhodopsin. Biochemistry 38:5422–5429

    PubMed  CAS  Google Scholar 

  83. Muneyuki E, Shibazaki C, Wada Y, Yakushizin M, Ohtani H (2002) Cl(−) concentration dependence of photovoltage generation by halorhodopsin from Halobacterium salinarum. Biophys J 83:1749–1759

    PubMed  CAS  Google Scholar 

  84. Baliga NS et al (2004) Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Res 14:2221–2234

    PubMed  CAS  Google Scholar 

  85. Tonnesen J, Sorensen AT, Deisseroth K, Lundberg C, Kokaia M (2009) Optogenetic control of epileptiform activity. Proc Natl Acad Sci U S A 106:12162–12167

    PubMed  CAS  Google Scholar 

  86. Bernstein JG et al (2008) Prosthetic systems for therapeutic optical activation and silencing of genetically-targeted neurons. Proc Soc Photo Opt Instrum Eng 6854:68540H

    PubMed  Google Scholar 

  87. Ludmann K, Ibron G, Lanyi JK, Varo G (2000) Charge motions during the photocycle of pharaonis halorhodopsin. Biophys J 78:959–966

    PubMed  CAS  Google Scholar 

  88. Chizhov I, Engelhard M (2001) Temperature and halide dependence of the photocycle of halorhodopsin from Natronobacterium pharaonis. Biophys J 81:1600–1612

    PubMed  CAS  Google Scholar 

  89. Ming M et al (2006) pH dependence of light-driven proton pumping by an archaerhodopsin from Tibet: comparison with bacteriorhodopsin. Biophys J 90:3322–3332

    PubMed  CAS  Google Scholar 

  90. Lukashev EP et al (1994) pH dependence of the absorption spectra and photochemical transformations of the archaerhodopsins. Photochem Photobiol 60:69–75

    PubMed  CAS  Google Scholar 

  91. Lanyi JK (2006) Proton transfers in the bacteriorhodopsin photocycle. Biochim Biophys Acta – Bioenergetics 1757:1012–1018

    CAS  Google Scholar 

  92. Bevensee MO, Cummins TR, Haddad GG, Boron WF, Boyarsky G (1996) pH regulation in single CA1 neurons acutely isolated from the hippocampi of immature and mature rats. J Physiol 494(Pt 2):315–328

    PubMed  CAS  Google Scholar 

  93. Chesler M (2003) Regulation and modulation of pH in the brain. Physiol Rev 83:1183–1221

    PubMed  CAS  Google Scholar 

  94. Meyer TM, Munsch T, Pape HC (2000) Activity-related changes in intracellular pH in rat thalamic relay neurons. NeuroReport 11:33–37

    PubMed  CAS  Google Scholar 

  95. Trapp S, Luckermann M, Brooks PA, Ballanyi K (1996) Acidosis of rat dorsal vagal neurons in situ during spontaneous and evoked activity. J Physiol 496(Pt 3):695–710

    PubMed  CAS  Google Scholar 

  96. Brown LS et al (1995) Glutamic acid 204 is the terminal proton release group at the extracellular surface of bacteriorhodopsin. J Biol Chem 270:27122–27126

    PubMed  CAS  Google Scholar 

  97. Phatak P, Ghosh N, Yu H, Cui Q, Elstner M (2008) Amino acids with an intermolecular proton bond as proton storage site in bacteriorhodopsin. Proc Natl Acad Sci USA 105:19672–19677

    PubMed  CAS  Google Scholar 

  98. Henderson R et al (1990) Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. J Mol Biol 213:899–929

    PubMed  CAS  Google Scholar 

  99. Man-Aharonovich D et al (2004) Characterization of RS29, a blue-green proteorhodopsin variant from the Red Sea. Photochem Photobiol Sci 3:459–462

    PubMed  CAS  Google Scholar 

  100. Sasaki J et al (1995) Conversion of bacteriorhodopsin into a chloride ion pump. Science 269:73–75

    PubMed  CAS  Google Scholar 

  101. Iwamoto M et al (2004) Proton release and uptake of pharaonis phoborhodopsin (sensory rhodopsin II) reconstituted into phospholipids. Biochemistry 43:3195–3203

    PubMed  CAS  Google Scholar 

  102. Sudo Y, Iwamoto M, Shimono K, Sumi M, Kamo N (2001) Photo-induced proton transport of pharaonis phoborhodopsin (sensory rhodopsin II) is ceased by association with the transducer. Biophys J 80:916–922

    PubMed  CAS  Google Scholar 

  103. Boichenko VA, Wang JM, Antón J, Lanyi JK, Balashov SP (2006) Functions of carotenoids in xanthorhodopsin and archaerhodopsin, from action spectra of photoinhibition of cell respiration. Biochim Biophys Acta – Bioenergetics 1757:1649–1656

    CAS  Google Scholar 

  104. Serrano EE, Zeiger E, Hagiwara S (1988) Red light stimulates an electrogenic proton pump in Vicia guard cell protoplasts. Proc Natl Acad Sci U S A 85:436–440

    PubMed  CAS  Google Scholar 

  105. Moreau CJ, Dupuis JP, Revilloud J, Arumugam K, Vivaudou M (2008) Coupling ion channels to receptors for biomolecule sensing. Nat Nanotechnol 3:620–625

    PubMed  CAS  Google Scholar 

  106. Wang H et al (2007) High-speed mapping of synaptic connectivity using photostimulation in channelrhodopsin-2 transgenic mice. Proc Natl Acad Sci U S A 104:8143–8148

    PubMed  CAS  Google Scholar 

  107. Han X et al (2009) Millisecond-timescale optical control of neural dynamics in the nonhuman primate brain. Neuron 62:191–198

    PubMed  CAS  Google Scholar 

  108. Atasoy D, Aponte Y, Su HH, Sternson SM (2008) A FLEX switch targets channelrhodopsin-2 to multiple cell types for imaging and long-range circuit mapping. J Neurosci 28:7025–7030

    PubMed  CAS  Google Scholar 

  109. Kuhlman SJ, Huang ZJ (2008) High-resolution labeling and functional manipulation of specific neuron types in mouse brain by Cre-activated viral gene expression. PLoS ONE 3:e2005

    PubMed  Google Scholar 

  110. Petreanu L, Huber D, Sobczyk A, Svoboda K (2007) Channelrhodopsin-2-assisted circuit mapping of long-range callosal projections. Nat Neurosci 10:663–668

    PubMed  CAS  Google Scholar 

  111. Schroll C et al (2006) Light-induced activation of distinct modulatory neurons triggers appetitive or aversive learning in Drosophila larvae. Curr Biol 16:1741–1747

    PubMed  CAS  Google Scholar 

  112. Douglass AD, Kraves S, Deisseroth K, Schier AF, Engert F (2008) Escape behavior elicited by single, channelrhodopsin-2-evoked spikes in zebrafish somatosensory neurons. Curr Biol 18:1133–1137

    PubMed  CAS  Google Scholar 

  113. Yan W et al (2001) Cloning and characterization of a human beta, beta-carotene-15,15′-dioxygenase that is highly expressed in the retinal pigment epithelium. Genomics 72:193–202

    PubMed  CAS  Google Scholar 

  114. Dittgen T et al (2004) Lentivirus-based genetic manipulations of cortical neurons and their optical and electrophysiological monitoring in vivo. Proc Natl Acad Sci U S A 101:18206–18211

    PubMed  CAS  Google Scholar 

  115. Chhatwal JP, Hammack SE, Jasnow AM, Rainnie DG, Ressler KJ (2007) Identification of cell-type-specific promoters within the brain using lentiviral vectors. Gene Ther 14:575–583

    PubMed  CAS  Google Scholar 

  116. Adamantidis AR, Zhang F, Aravanis AM, Deisseroth K, de Lecea L (2007) Neural substrates of awakening probed with optogenetic control of hypocretin neurons. Nature 450:420–424

    PubMed  CAS  Google Scholar 

  117. Tan W et al (2008) Silencing preBotzinger complex somatostatin-expressing neurons induces persistent apnea in awake rat. Nat Neurosci 11:538–540

    PubMed  CAS  Google Scholar 

  118. Nathanson JL, Yanagawa Y, Obata K, Callaway EM (2009) Preferential labeling of inhibitory and excitatory cortical neurons by endogenous tropism of adeno-associated virus and lentivirus vectors. Neuroscience 161:441–450

    PubMed  CAS  Google Scholar 

  119. Wickersham IR, Finke S, Conzelmann KK, Callaway EM (2007) Retrograde neuronal tracing with a deletion-mutant rabies virus. Nat Methods 4:47–49

    PubMed  CAS  Google Scholar 

  120. Stachler MD, Chen I, Ting AY, Bartlett JS (2008) Site-specific modification of AAV vector particles with biophysical probes and targeting ligands using biotin ligase. Mol Ther 16:1467–1473

    PubMed  CAS  Google Scholar 

  121. Toni N et al (2008) Neurons born in the adult dentate gyrus form functional synapses with target cells. Nat Neurosci 11:901–907

    PubMed  CAS  Google Scholar 

  122. Wickersham IR et al (2007) Monosynaptic restriction of transsynaptic tracing from single, genetically targeted neurons. Neuron 53:639–647

    PubMed  CAS  Google Scholar 

  123. Banfield BW, Kaufman JD, Randall JA, Pickard GE (2003) Development of pseudorabies virus strains expressing red fluorescent proteins: new tools for multisynaptic labeling applications. J Virol 77:10106–10112

    PubMed  CAS  Google Scholar 

  124. Foust KD et al (2009) Intravascular AAV9 preferentially targets neonatal neurons and adult astrocytes. Nat Biotechnol 27:59–65

    PubMed  CAS  Google Scholar 

  125. Chan SY, Bernstein JG, Boyden ES (2010) Scalable fluidic injector arrays for viral targeting of intact 3-D brain circuits. J Vis Exp 35:1489. doi:10.3791/1489, http://www.jove.com/index/details.stp?id=1489

    Google Scholar 

  126. (2007) Retracing events. Nat Biotechnol 25:949

    Google Scholar 

  127. Bi A et al (2006) Ectopic expression of a microbial-type rhodopsin restores visual responses in mice with photoreceptor degeneration. Neuron 50:23–33

    PubMed  CAS  Google Scholar 

  128. Lagali PS et al (2008) Light-activated channels targeted to ON bipolar cells restore visual function in retinal degeneration. Nat Neurosci 11:667–675

    PubMed  CAS  Google Scholar 

  129. Campagnola L, Wang H, Zylka MJ (2008) Fiber-coupled light-emitting diode for localized photostimulation of neurons expressing channelrhodopsin-2. J Neurosci Methods 169:27–33

    PubMed  CAS  Google Scholar 

  130. Rickgauer JP, Tank DW (2009) Two-photon excitation of channelrhodopsin-2 at saturation, PNAS 106(35):15025–30

    Google Scholar 

  131. Petreanu L, Mao T, Sternson SM, Svoboda K (2009) The subcellular organization of neocortical excitatory connections. Nature 457:1142–1145

    PubMed  CAS  Google Scholar 

  132. Farah N, Reutsky I, Shoham S (2007) Patterned optical activation of retinal ganglion cells. Conf Proc IEEE Eng Med Biol Soc 2007:6369–6371

    Google Scholar 

  133. Guo ZV, Hart AC, Ramanathan S (2009) Optical interrogation of neural circuits in Caenorhabditis elegans. Nat Methods 6:891–896

    PubMed  CAS  Google Scholar 

  134. Bernstein J et al (2008) A scalable toolbox for systematic, cell-specific optical control of entire 3-D neural circuits in the intact mammalian brain. Society for Neuroscience, online

    Google Scholar 

  135. Bernstein JG et al (2009) Modulation of fear behavior via optical fiber arrays targeted to bilateral prefrontal cortex. Society for Neuroscience, online

    Google Scholar 

  136. Ayling OG, Harrison TC, Boyd JD, Goroshkov A, Murphy TH (2009) Automated light-based mapping of motor cortex by photoactivation of channelrhodopsin-2 transgenic mice. Nat Methods 6:219–224

    PubMed  CAS  Google Scholar 

  137. Honda K (2004) Dawn of the evolution of photoelectrochemistry. J Photochem Photobiol A Chem 166:63–68

    CAS  Google Scholar 

  138. Gratzel M (2001) Photoelectrochemical cells. Nature 414:338–344

    PubMed  CAS  Google Scholar 

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Chow, B.Y., Han, X., Bernstein, J.G., Monahan, P.E., Boyden, E.S. (2011). Light-Activated Ion Pumps and Channels for Temporally Precise Optical Control of Activity in Genetically Targeted Neurons. In: Chambers, J., Kramer, R. (eds) Photosensitive Molecules for Controlling Biological Function. Neuromethods, vol 55. Humana Press. https://doi.org/10.1007/978-1-61779-031-7_6

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