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6 - Sodium and Engineered Potassium Light-Driven Pumps

from Part II - Opsin Biology, Tools, and Technology Platform

Published online by Cambridge University Press:  28 April 2017

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Optogenetics
From Neuronal Function to Mapping and Disease Biology
, pp. 79 - 92
Publisher: Cambridge University Press
Print publication year: 2017

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References

Balashov, S.P., Imasheva, E.S., Boichenko, V.A., Antón, J., Wang, J.M., Lanyi, J.K., (2005). Xanthorhodopsin: a proton pump with a light-harvesting carotenoid antenna. Science 309, 20612064.CrossRefGoogle ScholarPubMed
Balashov, S.P., Imasheva, E.S., Dioumaev, A.K., Wang, J.M., Jung, K.-H., Lanyi, J.K., (2014). Light-driven Na+ pump from Gillisia limnaea: a high-affinity Na+ binding site is formed transiently in the photocycle. Biochem. (Mosc.) 53, 75497561.CrossRefGoogle Scholar
Balashov, S.P., Petrovskaya, L.E., Imasheva, E.S., Lukashev, E.P., Dioumaev, A.K., Wang, J.M., Sychev, S.V., Dolgikh, D.A., Rubin, A.B., Kirpichnikov, M.P., Lanyi, J.K., (2013). Breaking the carboxyl rule lysine 96 facilitates reprotonation of the Schiff base in the photocycle of a retinal protein from Exiguobacterium sibiricum. J. Biol. Chem. 288, 2125421265.CrossRefGoogle ScholarPubMed
Béjà, O., Aravind, L., Koonin, E.V., Suzuki, M.T., Hadd, A., Nguyen, L.P., Jovanovich, S.B., Gates, C.M., Feldman, R.A., Spudich, J.L., Spudich, E.N., DeLong, E.F., (2000). Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289, 19021906.CrossRefGoogle ScholarPubMed
Bertsova, Y.V., Bogachev, A.V., Skulachev, V.P., (2015). Proteorhodopsin from Dokdonia sp. PRO95 is a light-driven Na+-pump. Biochem. Mosc. 80, 449454.CrossRefGoogle ScholarPubMed
Bogomolni, R.A., Spudich, J.L., (1982). Identification of a third rhodopsin-like pigment in phototactic Halobacterium halobium. Proc. Natl. Acad. Sci. 79, 62506254.CrossRefGoogle ScholarPubMed
de la Torre, J.R. Christianson, L.M., Béjà, O., Suzuki, M.T., Karl, D.M., Heidelberg, J., DeLong, E.F., (2003). Proteorhodopsin genes are distributed among divergent marine bacterial taxa. Proc. Natl. Acad. Sci. 100, 1283012835.CrossRefGoogle ScholarPubMed
DeLong, E.F., Karl, D.M., (2005). Genomic perspectives in microbial oceanography. Nature 437, 336342.CrossRefGoogle ScholarPubMed
Ernst, O.P., Lodowski, D.T., Elstner, M., Hegemann, P., Brown, L.S., Kandori, H., (2014). Microbial and animal rhodopsins: structures, functions, and molecular mechanisms. Chem. Rev. 114, 126163.CrossRefGoogle ScholarPubMed
Gordeliy, V.I., Labahn, J., Moukhametzianov, R., Efremov, R., Granzin, J., Schlesinger, R., Büldt, G., Savopol, T., Scheidig, A.J., Klare, J.P., Engelhard, M., (2002). Molecular basis of transmembrane signalling by sensory rhodopsin II–transducer complex. Nature 419, 484487.CrossRefGoogle ScholarPubMed
Greene, R.V., Lanyi, J.K., (1979). Proton movements in response to a light-driven electrogenic pump for sodium ions in Halobacterium halobium membranes. J. Biol. Chem. 254, 1098610994.CrossRefGoogle ScholarPubMed
Gushchin, I., Chervakov, P., Kuzmichev, P., Popov, A.N., Round, E., Borshchevskiy, V., Ishchenko, A., Petrovskaya, L., Chupin, V., Dolgikh, D.A., Arseniev, A.S., Kirpichnikov, M., Gordeliy, V., (2013). Structural insights into the proton pumping by unusual proteorhodopsin from nonmarine bacteria. Proc. Natl. Acad. Sci. 110, 1263112636.CrossRefGoogle ScholarPubMed
Gushchin, I., Shevchenko, V., Polovinkin, V., Borshchevskiy, V., Buslaev, P., Bamberg, E., Gordeliy, V., (2015a). Structure of the light-driven sodium pump KR2 and its implications for optogenetics. FEBS J. 283, 12321238.CrossRefGoogle ScholarPubMed
Gushchin, I., Shevchenko, V., Polovinkin, V., Kovalev, K., Alekseev, A., Round, E., Borshchevskiy, V., Balandin, T., Popov, A., Gensch, T., Fahlke, C., Bamann, C., Willbold, D., Büldt, G., Bamberg, E., Gordeliy, V., (2015b). Crystal structure of a light-driven sodium pump. Nat. Struct. Mol. Biol. 22, 390395.CrossRefGoogle ScholarPubMed
Han, X., Chow, B.Y., Zhou, H., Klapoetke, N.C., Chuong, A., Rajimehr, R., Yang, A., Baratta, M.V., Winkle, J., Desimone, R., Boyden, E.S., (2011). A high-light sensitivity optical neural silencer: development and application to optogenetic control of non-human primate cortex. Front. Syst. Neurosci. 5, 18.CrossRefGoogle ScholarPubMed
Henderson, R., Baldwin, J.M., Ceska, T.A., Zemlin, F., Beckmann, E., Downing, K.H., (1990). Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. J. Mol. Biol. 213, 899929.CrossRefGoogle ScholarPubMed
Inoue, K., Konno, M., Abe-Yoshizumi, R., Kandori, H., (2015). The role of the NDQ motif in sodium-pumping rhodopsins. Angew. Chem. 127, 1169811701.CrossRefGoogle Scholar
Inoue, K., Ono, H., Abe-Yoshizumi, R., Yoshizawa, S., Ito, H., Kogure, K., Kandori, H., (2013). A light-driven sodium ion pump in marine bacteria. Nat. Commun. 4, 1678.CrossRefGoogle ScholarPubMed
Ivanova, N., Rohde, C., Munk, C., Nolan, M., Lucas, S., Del Rio, T.G., Tice, H., Deshpande, S., Cheng, J.-F., Tapia, R., Han, C., Goodwin, L., Pitluck, S., Liolios, K., Mavromatis, K., Mikhailova, N., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y.-J., Jeffries, C.D., Brambilla, E., Rohde, M., Göker, M., Tindall, B.J., Woyke, T., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H.-P., Lapidus, A., (2011). Complete genome sequence of Truepera radiovictrix type strain (RQ-24T). Stand. Genomic Sci. 4, 9199.CrossRefGoogle Scholar
Kanada, S., Takeguchi, Y., Murakami, M., Ihara, K., Kouyama, T., (2011). Crystal structures of an O-like blue form and an anion-free yellow form of pharaonis halorhodopsin. J. Mol. Biol. 413, 162176.CrossRefGoogle Scholar
Kato, H.E., Inoue, K., Abe-Yoshizumi, R., Kato, Y., Ono, H., Konno, M., Hososhima, S., Ishizuka, T., Hoque, M.R., Kunitomo, H., Ito, J., Yoshizawa, S., Yamashita, K., Takemoto, M., Nishizawa, T., Taniguchi, R., Kogure, K., Maturana, A.D., Iino, Y., Yawo, H., Ishitani, R., Kandori, H., Nureki, O., (2015). Structural basis for Na+ transport mechanism by a light-driven Na+ pump. Nature 521, 4853.CrossRefGoogle ScholarPubMed
Kato, Y., Inoue, K., Kandori, H., (2015). Kinetic analysis of H+–Na+ selectivity in a light-driven Na+-pumping rhodopsin. J. Phys. Chem. Lett. 6, 51115115.CrossRefGoogle Scholar
Kolbe, M., Besir, H., Essen, L.-O., Oesterhelt, D., (2000). Structure of the light-driven chloride pump halorhodopsin at 1.8 Å resolution. Science 288, 13901396.CrossRefGoogle ScholarPubMed
Konno, M., Kato, Y., Kato, H.E., Inoue, K., Nureki, O., Kandori, H., (2016). Mutant of a light-driven sodium ion pump can transport cesium ions. J. Phys. Chem. Lett. 7, 5155.CrossRefGoogle ScholarPubMed
Kouyama, T., Kanada, S., Takeguchi, Y., Narusawa, A., Murakami, M., Ihara, K., (2010). Crystal structure of the light-driven chloride pump halorhodopsin from Natronomonas pharaonis. J. Mol. Biol. 396, 564579.CrossRefGoogle ScholarPubMed
Kwon, Y.M., Kim, S.-Y., Jung, K.-H., Kim, S.-J., (2016). Diversity and functional analysis of light-driven pumping rhodopsins in marine Flavobacteria. Microbiologyopen 5, 212223.CrossRefGoogle ScholarPubMed
Lindley, E.V., MacDonald, R.E., (1979). A second mechanism for sodium extrusion in Halobacterium halobium: a light-driven sodium pump. Biochem. Biophys. Res. Commun. 88, 491499.CrossRefGoogle ScholarPubMed
Luecke, H., Schobert, B., Richter, H.-T., Cartailler, J.-P., Lanyi, J.K., (1999). Structure of bacteriorhodopsin at 1.55 Å resolution 1. J. Mol. Biol. 291, 899911.CrossRefGoogle Scholar
Luecke, H., Schobert, B., Stagno, J., Imasheva, E.S., Wang, J.M., Balashov, S.P., Lanyi, J.K., (2008). Crystallographic structure of xanthorhodopsin, the light-driven proton pump with a dual chromophore. Proc. Natl. Acad. Sci. 105, 1656116565.CrossRefGoogle ScholarPubMed
MacDonald, R.E., Greene, R.V., Clark, R.D., Lindley, E.V., (1979). Characterization of the light-driven sodium pump of Halobacterium halobium. J Biol Chem 254, 1183111838.CrossRefGoogle ScholarPubMed
Mongodin, E.F., Nelson, K.E., Daugherty, S., DeBoy, R.T., Wister, J., Khouri, H., Weidman, J., Walsh, D.A., Papke, R.T., Perez, G.S., Sharma, A.K., Nesbø, C.L., MacLeod, D., Bapteste, E., Doolittle, W.F., Charlebois, R.L., Legault, B., Rodriguez-Valera, F., (2005). The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea. Proc. Natl. Acad. Sci. 102, 1814718152.CrossRefGoogle ScholarPubMed
Moukhametzianov, R., Klare, J.P., Efremov, R., Baeken, C., Göppner, A., Labahn, J., Engelhard, M., Büldt, G., Gordeliy, V.I., (2006). Development of the signal in sensory rhodopsin and its transfer to the cognate transducer. Nature 440, 115119.CrossRefGoogle Scholar
Nagel, G., Szellas, T., Huhn, W., Kateriya, S., Adeishvili, N., Berthold, P., Ollig, D., Hegemann, P., Bamberg, E., (2003). Channelrhodopsin-2, a directly light-gated cation-selective membrane channel. Proc. Natl. Acad. Sci. 100, 1394013945.CrossRefGoogle ScholarPubMed
Nakanishi, M., Meirelles, P., Suzuki, R., Takatani, N., Mino, S., Suda, W., Oshima, K., Hattori, M., Ohkuma, M., Hosokawa, M., Miyashita, K., Thompson, F.L., Niwa, A., Sawabe, T., Sawabe, T., (2014). Draft genome sequences of marine flavobacterium nonlabens strains NR17, NR24, NR27, NR32, NR33, and Ara13. Genome Announc. 2, e01165-14.CrossRefGoogle ScholarPubMed
Oesterhelt, D., Stoeckenius, W., (1971). Rhodopsin-like protein from the purple membrane of Halobacterium halobium. Nature 233, 149152.Google ScholarPubMed
O’Malley, M.A., (2007). Exploratory experimentation and scientific practice: metagenomics and the proteorhodopsin case. Hist. Philos. Life Sci. 29, 337360.Google ScholarPubMed
Riedel, T., Held, B., Nolan, M., Lucas, S., Lapidus, A., Tice, H., Del Rio, T.G., Cheng, J.-F., Han, C., Tapia, R., Goodwin, L.A., Pitluck, S., Liolios, K., Mavromatis, K., Pagani, I., Ivanova, N., Mikhailova, N., Pati, A., Chen, A., Palaniappan, K., Land, M., Rohde, M., Tindall, B.J., Detter, J.C., Göker, M., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H.-P., Woyke, T., (2012). Genome sequence of the Antarctic rhodopsins-containing flavobacterium Gillisia limnaea type strain (R-8282(T)). Stand. Genomic Sci. 7, 107119.CrossRefGoogle Scholar
Schobert, B., Lanyi, J.K., (1982). Halorhodopsin is a light-driven chloride pump. J. Biol. Chem. 257, 1030610313.CrossRefGoogle ScholarPubMed
Singh, A., Kumar Jangir, P., Sharma, R., Singh, A., Kumar Pinnaka, A., Shivaji, S., (2013). Draft genome sequence of Indibacter alkaliphilus strain LW1T, isolated from Lonar Lake, a haloalkaline lake in the Buldana District of Maharashtra, India. Genome Announc. 1, e00515-13.CrossRefGoogle Scholar
Stoeckenius, W., Lozier, R.H., Bogomolni, R.A., (1979). Bacteriorhodopsin and the purple membrane of halobacteria. Biochim. Biophys. Acta BBA Rev. Bioenerg. 505, 215278.CrossRefGoogle ScholarPubMed
Wickstrand, C., Dods, R., Royant, A., Neutze, R., (2015). Bacteriorhodopsin: would the real structural intermediates please stand up? Biochim. Biophys. Acta 1850, 536553.CrossRefGoogle Scholar
Yoshizawa, S., Kumagai, Y., Kim, H., Ogura, Y., Hayashi, T., Iwasaki, W., DeLong, E.F., Kogure, K., (2014). Functional characterization of Flavobacteria rhodopsins reveals a unique class of light-driven chloride pump in bacteria. Proc. Natl. Acad. Sci. 111, 67326737.CrossRefGoogle ScholarPubMed
Zhao, S., Cunha, C., Zhang, F., Liu, Q., Gloss, B., Deisseroth, K., Augustine, G.J., Feng, G., (2008). Improved expression of halorhodopsin for light-induced silencing of neuronal activity. Brain Cell Biol. 36, 141154.CrossRefGoogle ScholarPubMed

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