SpringerLink
Log in

Molecular Biology of Microbial Rhodopsins

  • Protocol
  • First Online:
Rhodopsin

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

Abstract

Research on type 1 rhodopsins spans now a history of 50 years. Originally, just archaeal ion pumps and sensors have been discovered. However, with modern genetic techniques and gene sequencing tools, more and more proteins were identified in all kingdoms of life. Spectroscopic and other biophysical studies revealed quite diverse functions. Ion pumps, sensors, and channels are imprinted in the same seven-helix transmembrane protein scaffold carrying a retinal prosthetic group. In this review, molecular biology methods are described, which enabled the elucidation of their function and structure leading to optogenetic applications.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Protocol
USD 49.95
Price excludes VAT (Canada)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (Canada)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (Canada)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free ship** worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (Canada)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free ship** worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Grote M (2019) Membranes to molecular machines: active matter and the remaking of life. The University of Chicago Press, Chicago, IL

    Book  Google Scholar 

  2. Boll F (1977) On the anatomy and physiology of the retina (Translated by Ruth Hubbard with the help of Helene Hoffmann). Vis Res 17(11–12):1249–1265. https://doi.org/10.1016/0042-6989(77)90112-2

    Article  CAS  PubMed  Google Scholar 

  3. Lanska DJ (2013) Chapter 4 - Optograms and criminology: science, news reporting, and fanciful novels. In: Stiles A, Finger S, Boller F (eds) Progress in brain research, vol 205. Elsevier, Amsterdam, pp 55–84. https://doi.org/10.1016/B978-0-444-63273-9.00004-6

    Chapter  Google Scholar 

  4. Kühne W (1977) Chemical processes in the retina (Translation by R. Hubbard and G. Wald.). Vis Res 17(11–12):1269–1316. https://doi.org/10.1016/0042-6989(77)90114-6

    Article  PubMed  Google Scholar 

  5. Tansley K (1931) The regeneration of visual purple: its relation to dark adaptation and night blindness. J Physiol 71(4):442–458. https://doi.org/10.1113/jphysiol.1931.sp002749

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Wald G (1938) On rhodopsin in solution. J Gen Physiol 21(6):795–832. https://doi.org/10.1085/jgp.21.6.795

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Wald G (1968) The molecular basis of visual excitation. Nature 219(5156):800–807. https://doi.org/10.1038/219800a0

    Article  CAS  PubMed  Google Scholar 

  8. Oesterhelt D, Stoeckenius W (1971) Rhodopsin-like protein from the purple membrane of Halobacterium halobium. Nat New Biol 233(39):149–152

    Article  CAS  PubMed  Google Scholar 

  9. Blaurock AE, Stoeckenius W (1971) Structure of the purple membrane. Nat New Biol 233(39):152–155

    Article  CAS  PubMed  Google Scholar 

  10. Siebert F, Mäntele W, Kreutz W (1980) Flash-induced kinetic infrared spectroscopy applied to biochemical systems. Biophys Struct Mech 6(2):139–146

    Article  CAS  PubMed  Google Scholar 

  11. Eisenstein L, Lin SL, Dollinger G, Odashima K, Ding WD, Nakanishi K (1987) FTIR difference studies on apoproteins; protonation states of aspartic- and glutamic acid residues during the photocycle of bacteriorhodopsin. J Am Chem Soc 109:6860–6862

    Article  CAS  Google Scholar 

  12. Mathies R, Freedman TB, Stryer L (1977) Resonance Raman studies of the conformation of retinal in rhodopsin and isorhodopsin. J Mol Biol 109(2):367–372

    Article  CAS  PubMed  Google Scholar 

  13. Aton B, Doukas AG, Callender RH, Becher B, Ebrey TG (1977) Resonance Raman studies of the purple membrane. Biochemistry 16(13):2995–2999

    Article  CAS  PubMed  Google Scholar 

  14. Harbison GS, Smith SO, Pardoen JA, Mulder PP, Lugtenburg J, Herzfeld J, Mathies R, Griffin RG (1984) Solid-state 13C NMR studies of retinal in bacteriorhodopsin. Biochemistry 23(12):2662–2667

    Article  CAS  PubMed  Google Scholar 

  15. Engelhard M, Hess B, Emeis D, Metz G, Kreutz W, Siebert F (1989) Magic angle sample spinning 13C nuclear magnetic resonance of isotopically labeled bacteriorhodopsin. Biochemistry 28:3967–3975

    Article  CAS  PubMed  Google Scholar 

  16. Altenbach C, Flitsch SL, Khorana HG, Hubbell WL (1989) Structural studies on transmembrane proteins. 2. Spin labeling of bacteriorhodopsin mutants at unique cysteines. Biochemistry 28:7806–7812

    Article  CAS  PubMed  Google Scholar 

  17. Mandal T, Hustedt EJ, Song L, Oh KJ (2019) CW EPR and DEER methods to determine BCL-2 family protein structure and interactions: application of site-directed spin labeling to BAK apoptotic pores. In: Gavathiotis E (ed) BCL-2 family proteins. Methods in molecular biology, vol 1877. Humana Press, New York, NY, pp 257–303. https://doi.org/10.1007/978-1-4939-8861-7_18

    Chapter  Google Scholar 

  18. Engelhard M, Gerwert K, Hess B, Kreutz W, Siebert F (1985) Light-driven protonation changes of internal aspartic acids of bacteriorhodopsin: an investigation by static and time-resolved infrared difference spectroscopy using [4-13C] aspartic acid labeling purple membrane. Biochemistry 24:400–407

    Article  CAS  PubMed  Google Scholar 

  19. Bamberg E, Apell H-J, Dencher NA, Sperling W, Stieve H, Läuger P (1979) Photocurrents generated by bacteriorhodopsin on planar bilayer membranes. Biophys Struct Mech 5:277–292

    Article  CAS  Google Scholar 

  20. Nagel G, Möckel B, Büldt G, Bamberg E (1995) Functional expression of bacteriorhodopsin in oocytes allows direct measurement of voltage dependence of light induced H+ pum**. FEBS Lett 377:263–266

    Article  CAS  PubMed  Google Scholar 

  21. Unwin PN, Henderson R (1975) Molecular structure determination by electron microscopy of unstained crystalline specimens. J Mol Biol 94(3):425–440. https://doi.org/10.1016/0022-2836(75)90212-0

    Article  CAS  PubMed  Google Scholar 

  22. Henderson R, Unwin PN (1975) Three-dimensional model of purple membrane obtained by electron microscopy. Nature 257(5521):28–32. https://doi.org/10.1038/257028a0

    Article  CAS  PubMed  Google Scholar 

  23. Hargrave PA, McDowell JH, Curtis DR, Wang JK, Juszczak E, Fong SL, Rao JK, Argos P (1983) The structure of bovine rhodopsin. Biophys Struct Mech 9(4):235–244. https://doi.org/10.1007/BF00535659

    Article  CAS  PubMed  Google Scholar 

  24. Pebay-Peyroula E, Rummel G, Rosenbusch JP, Landau EM (1997) X-ray structure of bacteriorhodopsin at 2.5 Ångstroms from microcrystals grown in lipidic cubic phases. Science 277(5332):1676–1681

    Article  CAS  PubMed  Google Scholar 

  25. Landau EM, Rosenbusch JP (1996) Lipidic cubic phases - a novel concept for the crystallization of membrane proteins. Proc Natl Acad Sci U S A 93(25):14532–14535

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Deniaud A, Moiseeva E, Gordeliy V, Pebay-Peyroula E (2010) Crystallography of membrane proteins: from crystallization to structure. Methods Mol Biol 654:79–103. https://doi.org/10.1007/978-1-60761-762-4_5

    Article  CAS  PubMed  Google Scholar 

  27. Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima H, Fox BA, Le Trong I, Teller DC, Okada T, Stenkamp RE, Yamamoto M, Miyano M (2000) Crystal structure of rhodopsin: a G protein-coupled receptor. Science 289(5480):739–745

    Article  CAS  PubMed  Google Scholar 

  28. Ovchinnikov Iu A, Abdulaev NG, Feigina M, Artamonov ID, Bogachuk AS (1983) Visual rhodopsin. III. Complete amino acid sequence and topography in a membrane. Bioorg Khim 9(10):1331–1340

    CAS  PubMed  Google Scholar 

  29. Ovchinnikov YA, Abdulaev NG, Feigina MY, Kiselev AV, Lobanov NA (1979) The structural basis of the functioning of bacteriorhodopsin: an overview. FEBS Lett 100(2):219–224. https://doi.org/10.1016/0014-5793(79)80338-5

    Article  CAS  PubMed  Google Scholar 

  30. Gerber GE, Anderegg RJ, Herlihy WC, Gray CP, Biemann K, Khorana HG (1977) Partial primary structure of bacteriorhodopsin: sequencing methods for membrane proteins. Proc Natl Acad Sci U S A 76:227–231

    Article  Google Scholar 

  31. Nathans J, Hogness DS (1983) Isolation, sequence analysis, and intron-exon arrangement of the gene encoding bovine rhodopsin. Cell 34(3):807–814. https://doi.org/10.1016/0092-8674(83)90537-8

    Article  CAS  PubMed  Google Scholar 

  32. Dunn R, McCoy J, Simsek M, Majumdar A, Chang SH, Rajbhandary UL, Khorana HG (1981) The bacteriorhodopsin gene. Proc Natl Acad Sci U S A 78(11):6744–6748. https://doi.org/10.1073/pnas.78.11.6744

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Dassarma S, Rajbhandary UL, Khorana HG (1984) Bacterio-opsin mRNA in wild-type and bacterio-opsin-deficient Halobacterium halobium strains. Proc Natl Acad Sci U S A 81(1):125–129. https://doi.org/10.1073/pnas.81.1.125

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Oesterhelt D, Stoeckenius W (1973) Functions of a new photoreceptor membrane. Proc Natl Acad Sci U S A 70(10):2853–2857

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Lozier RH, Bogomolni RA, Stoeckenius W (1975) Bacteriorhodopsin: a light-driven proton pump in Halobacterium halobium. Biophys J 15(9):955–962

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Racker E, Stoeckenius W (1974) Reconstitution of purple membrane vesicles catalyzing light- driven proton uptake and adenosine triphosphate formation. J Biol Chem 249(2):662–663

    Article  CAS  PubMed  Google Scholar 

  37. Mitchell P (1979) Keilin’s respiratory chain concept and its chemiosmotic consequences. Science 206(4423):1148–1159

    Article  CAS  PubMed  Google Scholar 

  38. Hildebrand E, Dencher N (1975) Two photosystems controlling behavioural responses of Halobacterium halobium. Nature 257:46–48

    Article  CAS  PubMed  Google Scholar 

  39. Bogomolni RA, Spudich JL (1982) Identification of a third rhodopsin-like pigment in phototactic Halobacterium halobium. Proc Natl Acad Sci U S A 79:6250–6254

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Takahashi T, Tomioka H, Kamo N, Kobatake Y (1985) A photosystem other than PS370 also mediates the negative phototaxis of Halobacterium halobium. FEMS Microb Lett 28:161–164

    Article  CAS  Google Scholar 

  41. Yao VJ, Spudich JL (1992) Primary structure of an archaebacterial transducer, a methyl-accepting protein associated with sensory rhodopsin I. Proc Natl Acad Sci U S A 89:11915–11919

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Seidel R, Scharf B, Gautel M, Kleine K, Oesterhelt D, Engelhard M (1995) The primary structure of sensory rhodopsin II: a member of an additional retinal protein subgroup is coexpressed with its transducer, the halobacterial transducer of rhodopsin II. Proc Natl Acad Sci U S A 92:3036–3040

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Rudolph J, Nordmann B, Storch KF, Gruenberg H, Rodewald K, Oesterhelt D (1996) A family of halobacterial transducer proteins. FEMS Microbiol Lett 139(2–3):161–168

    Article  CAS  PubMed  Google Scholar 

  44. Matsuno-Yagi A, Mukohata Y (1977) Two possible roles of bacteriorhodopsin; a comparative study of strains of Halobacterium halobium differing in pigmentation. Biochem Biophys Res Commun 78(1):237–243

    Article  CAS  PubMed  Google Scholar 

  45. Mukohata Y, Kaji Y (1981) Light-induced membrane-potential increase, ATP synthesis, and proton uptake in Halobacterium halobium, R1mR catalyzed by halorhodopsin: effects of N,N′-dicyclohexylcarbodiimide, triphenyltin chloride, and 3,5-di-tert-butyl-4-hydroxybenzylidenemalononitrile (SF6847). Can J Chem 206(1):72–76

    CAS  Google Scholar 

  46. Schobert B, Lanyi JK (1982) Halorhodopsin is a light-driven chloride pump. J Biol Chem 257(17):10306–10313

    Article  CAS  PubMed  Google Scholar 

  47. Engelhard C, Chizhov I, Siebert F, Engelhard M (2018) Microbial halorhodopsins: light-driven chloride pumps. Chem Rev 118:10629. https://doi.org/10.1021/acs.chemrev.7b00715

    Article  CAS  PubMed  Google Scholar 

  48. Soliman GSH, Trüper HG (1982) Halobacterium pharaonis sp. nov., a new, extremely Haloalkaliphilic Archaebacterium with low magnesium requirement. Zentralblatt für Bakteriologie Mikrobiologie und Hygiene: I. Abt Originale C: Allgemeine, angewandte und ökologische Mikrobiologie 3(2):318–329

    Article  CAS  Google Scholar 

  49. Bivin DB, Stoeckenius W (1986) Photoactive retinal pigments in Haloalkaliphilic bacteria. J Gen Microbiol 132:2167–2177

    CAS  PubMed  Google Scholar 

  50. Shimono K, Iwamoto M, Sumi M, Kamo N (1997) Functional expression of pharaonis phoborhodopsin in Escherichia coli. FEBS Lett 420(1):54–56

    Article  CAS  PubMed  Google Scholar 

  51. Hohenfeld IP, Wegener AA, Engelhard M (1999) Purification of histidine tagged bacteriorhodopsin, pharaonis halorhodopsin and pharaonis sensory rhodopsin II functionally expressed in Escherichia coli. FEBS Lett 442(2–3):198–202

    Article  CAS  PubMed  Google Scholar 

  52. Béjà O, Aravind L, Koonin EV, Suzuki MT, Hadd A, Nguyen LP, Jovanovich S, Gates CM, Feldman RA, Spudich JL, Spudich EN, DeLong EF (2000) Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289(5486):1902–1906

    Article  PubMed  Google Scholar 

  53. Béjà O, Suzuki MT, Heidelberg JF, Nelson WC, Preston CM, Hamada T, Eisen JA, Fraser CM, DeLong EF (2002) Unsuspected diversity among marine aerobic anoxygenic phototrophs. Nature 415:630–633

    Article  PubMed  Google Scholar 

  54. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304(5667):66–74

    Article  CAS  PubMed  Google Scholar 

  55. Foster KW, Smyth RD (1980) Light Antennas in phototactic algae. Microbiol Rev 44(4):572–630

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Foster KW, Saranak J, Patel N, Zarilli G, Okabe M, Kline T, Nakanishi K (1984) A rhodopsin is the functional photoreceptor for phototaxis in the unicellular eukaryote Chlamydomonas. Nature 311(5988):756–759

    Article  CAS  PubMed  Google Scholar 

  57. Litvin FF, Sineshchekov OA, Sineshchekov VA (1978) Photoreceptor electric potential in the phototaxis of the alga Haematococcus pluvialis. Nature 271(5644):476–478. https://doi.org/10.1038/271476a0

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  Google Scholar 

  59. Braun FJ, Hegemann P (1999) Two light-activated conductances in the eye of the green alga Volvox carteri. Biophys J 76(3):1668–1678. https://doi.org/10.1016/S0006-3495(99)77326-1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Nagel G, Ollig D, Fuhrmann M, Kateriya S, Musti AM, Bamberg E, Hegemann P (2002) Channelrhodopsin-1: a light-gated proton channel in green algae. Science 296(5577):2395–2398

    Article  CAS  PubMed  Google Scholar 

  61. Sineshchekov OA, Jung KH, Spudich JL (2002) Two rhodopsins mediate phototaxis to low- and high-intensity light in Chlamydomonasreinhardtii. Proc Natl Acad Sci U S A 99(13):8689–8694

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. 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 U S A 100(24):13940–13945

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Kojima K, Shibukawa A, Sudo Y (2020) The unlimited potential of microbial rhodopsins as optical tools. Biochemistry 59(3):218–229. https://doi.org/10.1021/acs.biochem.9b00768

    Article  CAS  PubMed  Google Scholar 

  64. Oesterhelt D, Bräuchle C, Hampp N (1991) Bacteriorhodopsin: a biological material for information processing. Q Rev Biophys 24:425–478

    Article  CAS  PubMed  Google Scholar 

  65. Adamantidis A, Arber S, Bains JS, Bamberg E, Bonci A, Buzsaki G, Cardin JA, Costa RM, Dan Y, Goda Y, Graybiel AM, Hausser M, Hegemann P, Huguenard JR, Insel TR, Janak PH, Johnston D, Josselyn SA, Koch C, Kreitzer AC, Luscher C, Malenka RC, Miesenbock G, Nagel G, Roska B, Schnitzer MJ, Shenoy KV, Soltesz I, Sternson SM, Tsien RW, Tsien RY, Turrigiano GG, Tye KM, Wilson RI (2015) Optogenetics: 10 years after ChR2 in neurons--views from the community. Nat Neurosci 18(9):1202–1212. https://doi.org/10.1038/nn.4106

    Article  CAS  PubMed  Google Scholar 

  66. Oprian DD, Molday RS, Kaufman RJ, Khorana HG (1987) Expression of a synthetic bovine rhodopsin gene in monkey kidney cells. Proc Natl Acad Sci U S A 84(24):8874–8878. https://doi.org/10.1073/pnas.84.24.8874

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Nathans J, Weitz CJ, Agarwal N, Nir I, Papermaster DS (1989) Production of bovine rhodopsin by mammalian cell lines expressing cloned cDNA: spectrophotometry and subcellular localization. Vis Res 29(8):907–914. https://doi.org/10.1016/0042-6989(89)90105-3

    Article  CAS  PubMed  Google Scholar 

  68. Kesidis A, Dep** P, Lode A, Vaitsopoulou A, Bill RM, Goddard AD, Rothnie AJ (2020) Expression of eukaryotic membrane proteins in eukaryotic and prokaryotic hosts. Methods 180:3. https://doi.org/10.1016/j.ymeth.2020.06.006

    Article  CAS  PubMed  Google Scholar 

  69. Bratanov D, Balandin T, Round E, Shevchenko V, Gushchin I, Polovinkin V, Borshchevskiy V, Gordeliy V (2015) An approach to heterologous expression of membrane proteins. The case of bacteriorhodopsin. PLoS One 10(6):e0128390. https://doi.org/10.1371/journal.pone.0128390

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Tu CH, Yi HP, Hsieh SY, Lin HS, Yang CS (2018) Overexpression of different types of microbial rhodopsins with a highly expressible bacteriorhodopsin from Haloarcula marismortui as a single protein in E. coli. Sci Rep 8(1):14026. https://doi.org/10.1038/s41598-018-32399-x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Heymann J, Jäger R, Subramaniam S (1997) Expression of bacteriorhodopsin in sf9 and cos-1 cells. J Bioenerg Biomembr 29(1):55–59

    Article  CAS  PubMed  Google Scholar 

  72. Sineshchekov OA, Trivedi VD, Sasaki J, Spudich JL (2005) Photochromicity of anabaena sensory rhodopsin, an atypical microbial receptor with a cis-retinal light-adapted form. J Biol Chem 280(15):14663–14668

    Article  CAS  PubMed  Google Scholar 

  73. Shevchenko V, Mager T, Kovalev K, Polovinkin V, Alekseev A, Juettner J, Chizhov I, Bamann C, Vavourakis C, Ghai R, Gushchin I, Borshchevskiy V, Rogachev A, Melnikov I, Popov A, Balandin T, Rodriguez-Valera F, Manstein DJ, Bueldt G, Bamberg E, Gordeliy V (2017) Inward H+ pump xenorhodopsin: mechanism and alternative optogenetic approach. Sci Adv 3(9):e1603187. https://doi.org/10.1126/sciadv.1603187

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Seki A, Miyauchi S, Hayashi S, Kikukawa T, Kubo M, Demura M, Ganapathy V, Kamo N (2007) Heterologous expression of Pharaonis halorhodopsin in Xenopus laevis oocytes and electrophysiological characterization of its light-driven Cl- pump activity. Biophys J 92(7):2559–2569. https://doi.org/10.1529/biophysj.106.093153

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Kim K, Kwon SK, Jun SH, Cha JS, Kim H, Lee W, Kim JF, Cho HS (2016) Crystal structure and functional characterization of a light-driven chloride pump having an NTQ motif. Nat Commun 7:12677. https://doi.org/10.1038/ncomms12677

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Yoshizawa S, Kumagai Y, Kim H, Ogura Y, Hayashi T, Iwasaki W, DeLong EF, Kogure K (2014) Functional characterization of flavobacteria rhodopsins reveals a unique class of light-driven chloride pump in bacteria. Proc Natl Acad Sci U S A 111(18):6732–6737. https://doi.org/10.1073/pnas.1403051111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. 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):1–10. https://doi.org/10.1038/ncomms2689

    Article  CAS  Google Scholar 

  78. Volkov O, Kovalev K, Polovinkin V, Borshchevskiy V, Bamann C, Astashkin R, Marin E, Popov A, Balandin T, Willbold D, Büldt G, Bamberg E, Gordeliy V (2017) Structural insights into ion conduction by channelrhodopsin 2. Science 358(6366):eaan8862. https://doi.org/10.1126/science.aan8862

    Article  CAS  PubMed  Google Scholar 

  79. 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(50):35033–35041. https://doi.org/10.1074/jbc.M806353200. M806353200 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Marshel JH, Kim YS, Machado TA, Quirin S, Benson B, Kadmon J, Raja C, Chibukhchyan A, Ramakrishnan C, Inoue M, Shane JC, McKnight DJ, Yoshizawa S, Kato HE, Ganguli S, Deisseroth K (2019) Cortical layer-specific critical dynamics triggering perception. Science 365(6453):eaaw5202. https://doi.org/10.1126/science.aaw5202

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Wietek J, Broser M, Krause BS, Hegemann P (2016) Identification of a natural green light absorbing chloride conducting channelrhodopsin from Proteomonas sulcata. J Biol Chem 291(8):4121–4127. https://doi.org/10.1074/jbc.M115.699637

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Sugiyama Y, Inoue T, Ikematsu M, Iseki M, Sekiguchi T (1997) Controlling the orientation of purple membrane fragments on an air/water interface by a new method of direct electric field application during purple membrane spreading. Jpn J Appl Phys 36(9A):5674–5679

    Article  CAS  Google Scholar 

  83. Oppermann J, Fischer P, Silapetere A, Liepe B, Rodriguez-Rozada S, Flores-Uribe J, Peter E, Keidel A, Vierock J, Kaufmann J, Broser M, Luck M, Bartl F, Hildebrandt P, Wiegert JS, Beja O, Hegemann P, Wietek J (2019) MerMAIDs: a family of metagenomically discovered marine anion-conducting and intensely desensitizing channelrhodopsins. Nat Commun 10(1):3315. https://doi.org/10.1038/s41467-019-11322-6

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Schmies G, Chizhov I, Engelhard M (2000) Functional expression of His-tagged sensory rhodopsin I in Escherichia coli. FEBS Lett 466(1):67–69

    Article  CAS  PubMed  Google Scholar 

  85. Kitajima T, Hirayama J, Ihara K, Sugiyama Y, Kamo N, Mukohata Y (1996) Novel bacterial rhodopsins from Haloarcula vallismortis. Biochem Biophys Res Commun 220:341–345

    Article  CAS  PubMed  Google Scholar 

  86. Bratanov D, Kovalev K, Machtens JP, Astashkin R, Chizhov I, Soloviov D, Volkov D, Polovinkin V, Zabelskii D, Mager T, Gushchin I, Rokitskaya T, Antonenko Y, Alekseev A, Shevchenko V, Yutin N, Rosselli R, Baeken C, Borshchevskiy V, Bourenkov G, Popov A, Balandin T, Buldt G, Manstein DJ, Rodriguez-Valera F, Fahlke C, Bamberg E, Koonin E, Gordeliy V (2019) Unique structure and function of viral rhodopsins. Nat Commun 10(1):4939. https://doi.org/10.1038/s41467-019-12718-0

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Needham DM, Yoshizawa S, Hosaka T, Poirier C, Choi CJ, Hehenberger E, Irwin NAT, Wilken S, Yung CM, Bachy C, Kurihara R, Nakajima Y, Kojima K, Kimura-Someya T, Leonard G, Malmstrom RR, Mende DR, Olson DK, Sudo Y, Sudek S, Richards TA, DeLong EF, Keeling PJ, Santoro AE, Shirouzu M, Iwasaki W, Worden AZ (2019) A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators. Proc Natl Acad Sci U S A 116(41):20574–20583. https://doi.org/10.1073/pnas.1907517116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Kovalev K, Volkov D, Astashkin R, Alekseev A, Gushchin I, Haro-Moreno JM, Chizhov I, Siletsky S, Mamedov M, Rogachev A, Balandin T, Borshchevskiy V, Popov A, Bourenkov G, Bamberg E, Rodriguez-Valera F, Buldt G, Gordeliy V (2020) High-resolution structural insights into the heliorhodopsin family. Proc Natl Acad Sci U S A 117(8):4131–4141. https://doi.org/10.1073/pnas.1915888117

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Lamarche LB, Kumar RP, Trieu MM, Devine EL, Cohen-Abeles LE, Theobald DL, Oprian DD (2017) Purification and characterization of RhoPDE, a Retinylidene/phosphodiesterase fusion protein and potential optogenetic tool from the Choanoflagellate Sal**oeca rosetta. Biochemistry 56(43):5812–5822. https://doi.org/10.1021/acs.biochem.7b00519

    Article  CAS  PubMed  Google Scholar 

  90. Yoshida K, Tsunoda SP, Brown LS, Kandori H (2017) A unique choanoflagellate enzyme rhodopsin exhibits light-dependent cyclic nucleotide phosphodiesterase activity. J Biol Chem 292(18):7531–7541. https://doi.org/10.1074/jbc.M117.775569

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Scheib U, Stehfest K, Gee CE, Korschen HG, Fudim R, Oertner TG, Hegemann P (2015) The rhodopsin-guanylyl cyclase of the aquatic fungus Blastocladiella emersonii enables fast optical control of cGMP signaling. Sci Signal 8(389):rs8. https://doi.org/10.1126/scisignal.aab0611

    Article  CAS  PubMed  Google Scholar 

  92. Luck M, Mathes T, Bruun S, Fudim R, Hagedorn R, Tran Nguyen TM, Kateriya S, Kennis JTM, Hildebrandt P, Hegemann P (2012) A photochromic histidine kinase rhodopsin (HKR1) that is bimodally switched by ultraviolet and blue light. J Biol Chem 287(47):40083–40090

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Hoffmann A, Hildebrandt V, Heberle J, Büldt G (1994) Photoactive mitochondria: in vivo transfer of a light- driven proton pump into the inner mitochondrial membrane of Schizosaccharomyces pombe. Proc Natl Acad Sci U S A 91(20):9367–9371

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Nirenberg MW, Matthaei JH (1961) The dependence of cell-free protein synthesis in E. coli upon naturally occurring or synthetic polyribonucleotides. Proc Natl Acad Sci U S A 47:1588–1602. https://doi.org/10.1073/pnas.47.10.1588

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Nirenberg M (2004) Historical review: deciphering the genetic code - a personal account. Trends Biochem Sci 29(1):46–54

    Article  CAS  PubMed  Google Scholar 

  96. Sonar S, Patel N, Fischer W, Rothschild KJ (1993) Cell-free synthesis, functional refolding, and spectroscopic characterization of bacteriorhodopsin, an integral membrane protein. Biochemistry 32:13777–13781

    Article  CAS  PubMed  Google Scholar 

  97. Kalmbach R, Chizhov I, Schumacher MC, Friedrich T, Bamberg E, Engelhard M (2007) Functional cell-free synthesis of a seven helix membrane protein: in situ insertion of bacteriorhodopsin into liposomes. J Mol Biol 371(3):639–648

    Article  CAS  PubMed  Google Scholar 

  98. Henrich E, Sormann J, Eberhardt P, Peetz O, Mezhyrova J, Morgner N, Fendler K, Dotsch V, Wachtveitl J, Bernhard F, Bamann C (2017) From gene to function: cell-free electrophysiological and optical analysis of ion pumps in nanodiscs. Biophys J 113(6):1331–1341. https://doi.org/10.1016/j.bpj.2017.03.026

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Baumann A, Kerruth S, Fitter J, Buldt G, Heberle J, Schlesinger R, Ataka K (2016) In-situ observation of membrane protein folding during cell-free expression. PLoS One 11(3):e0151051. https://doi.org/10.1371/journal.pone.0151051

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Engelman DM, Chen Y, Chin CN, Curran AR, Dixon AM, Dupuy AD, Lee AS, Lehnert U, Matthews EE, Reshetnyak YK, Senes A, Popot JL (2003) Membrane protein folding: beyond the two stage model. FEBS Lett 555(1):122–125. https://doi.org/10.1016/s0014-5793(03)01106-2

    Article  CAS  PubMed  Google Scholar 

  101. Tastan O, Dutta A, Booth P, Klein-Seetharaman J (2014) Retinal proteins as model systems for membrane protein folding. Biochim Biophys Acta 1837(5):656–663. https://doi.org/10.1016/j.bbabio.2013.11.021

    Article  CAS  PubMed  Google Scholar 

  102. Cornish VW, Benson DR, Altenbach CA, Hideg K, Hubbell WL, Schultz PG (1994) Site-specific incorporation of biophysical probes into proteins. Proc Natl Acad Sci U S A 91:2910–2914

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Alexiev U, Farrens DL (2014) Fluorescence spectroscopy of rhodopsins: insights and approaches. Biochim Biophys Acta 1837(5):694–709. https://doi.org/10.1016/j.bbabio.2013.10.008

    Article  CAS  PubMed  Google Scholar 

  104. Kriegsmann J, Brehs M, Klare JP, Engelhard M, Fitter J (2009) Sensory rhodopsin II/transducer complex formation in detergent and in lipid bilayers studied with FRET. Biochim Biophys Acta 1788(2):522–531. https://doi.org/10.1016/j.bbamem.2008.11.011. S0005-2736(08)00376-3 [pii]

    Article  CAS  PubMed  Google Scholar 

  105. Wegener AA, Klare JP, Engelhard M, Steinhoff HJ (2001) Structural insights into the early steps of receptor-transducer signal transfer in archaeal phototaxis. EMBO J 20(19):5312–5319

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Klare JP, Bordignon E, Engelhard M, Steinhoff HJ (2004) Sensory rhodopsin II and bacteriorhodopsin: light activated helix F movement. Photochem Photobiol Sci 3(6):543–547

    Article  CAS  PubMed  Google Scholar 

  107. Hazard ES III, Govindjee R, Ebrey TG, Crouch RK (1992) Biosynthetic incorporation of M-fluorotyrosine into bacteriorhodopsin. Photochem Photobiol 56:929–934

    Article  CAS  PubMed  Google Scholar 

  108. Anthony-Cahill SJ, Griffith MC, Noren CJ, Suich DJ, Schultz PG (1989) Site-specific mutagenesis with unnatural amino acids. Trends Biochem Sci 14:400–403

    Article  CAS  PubMed  Google Scholar 

  109. Chemla Y, Ozer E, Algov I, Alfonta L (2018) Context effects of genetic code expansion by stop codon suppression. Curr Opin Chem Biol 46:146–155. https://doi.org/10.1016/j.cbpa.2018.07.012

    Article  CAS  PubMed  Google Scholar 

  110. Huber T, Naganathan S, Tian H, Ye S, Sakmar TP (2013) Unnatural amino acid mutagenesis of GPCRs using amber codon suppression and bioorthogonal labeling. Methods Enzymol 520:281–305. https://doi.org/10.1016/B978-0-12-391861-1.00013-7

    Article  CAS  PubMed  Google Scholar 

  111. Krause BS, Kaufmann JCD, Kuhne J, Vierock J, Huber T, Sakmar TP, Gerwert K, Bartl FJ, Hegemann P (2019) Tracking pore hydration in channelrhodopsin by site-directed infrared-active azido probes. Biochemistry 58(9):1275–1286. https://doi.org/10.1021/acs.biochem.8b01211

    Article  CAS  PubMed  Google Scholar 

  112. Ohtsuka T, Neki S, Kanai T, Akiyoshi K, Nomura SM, Ohtsuki T (2011) Synthesis and in situ insertion of a site-specific fluorescently labeled membrane protein into cell-sized liposomes. Anal Biochem 418(1):97–101. https://doi.org/10.1016/j.ab.2011.06.026

    Article  CAS  PubMed  Google Scholar 

  113. Boyden ES, Zhang F, Bamberg E, Nagel G, Deisseroth K (2005) Millisecond-timescale, genetically targeted optical control of neural activity. Nat Neurosci 8(9):1263–1268. https://doi.org/10.1038/nn1525

    Article  CAS  PubMed  Google Scholar 

  114. Nagel G, Brauner M, Liewald JF, Adeishvili N, Bamberg E, Gottschalk A (2005) Light activation of channelrhodopsin-2 in excitable cells of Caenorhabditis elegans triggers rapid behavioral responses. Curr Biol 15(24):2279–2284. https://doi.org/10.1016/j.cub.2005.11.032

    Article  CAS  PubMed  Google Scholar 

  115. Zemelman BV, Lee GA, Ng M, Miesenbock G (2002) Selective photostimulation of genetically chARGed neurons. Neuron 33(1):15–22. https://doi.org/10.1016/s0896-6273(01)00574-8

    Article  CAS  PubMed  Google Scholar 

  116. Zemelman BV, Nesnas N, Lee GA, Miesenbock G (2003) Photochemical gating of heterologous ion channels: remote control over genetically designated populations of neurons. Proc Natl Acad Sci U S A 100(3):1352–1357. https://doi.org/10.1073/pnas.242738899

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  117. Rost BR, Schneider-Warme F, Schmitz D, Hegemann P (2017) Optogenetic tools for subcellular applications in neuroscience. Neuron 96(3):572–603. https://doi.org/10.1016/j.neuron.2017.09.047

    Article  CAS  PubMed  Google Scholar 

  118. Venkatachalam V, Cohen Adam E (2014) Imaging GFP-based reporters in neurons with multiwavelength optogenetic control. Biophys J 107(7):1554–1563. https://doi.org/10.1016/j.bpj.2014.08.020

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Glock C, Nagpal J, Gottschalk A (2015) Microbial rhodopsin optogenetic tools: application for analyses of synaptic transmission and of neuronal network activity in behavior. Methods Mol Biol 1327:87–103. https://doi.org/10.1007/978-1-4939-2842-2_8

    Article  CAS  PubMed  Google Scholar 

  120. Zhang K, Duan L, Ong Q, Lin Z, Varman PM, Sung K, Cui B (2014) Light-mediated kinetic control reveals the temporal effect of the Raf/MEK/ERK pathway in PC12 cell neurite outgrowth. PLoS One 9(3):e92917. https://doi.org/10.1371/journal.pone.0092917

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Henderson MJ, Baldwin HA, Werley CA, Boccardo S, Whitaker LR, Yan X, Holt GT, Schreiter ER, Looger LL, Cohen AE, Kim DS, Harvey BK (2015) A low affinity GCaMP3 variant (GCaMPer) for imaging the endoplasmic reticulum calcium store. PLoS One 10(10):e0139273. https://doi.org/10.1371/journal.pone.0139273

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. Wiegert JS, Mahn M, Prigge M, Printz Y, Yizhar O (2017) Silencing neurons: tools, applications, and experimental constraints. Neuron 95(3):504–529. https://doi.org/10.1016/j.neuron.2017.06.050

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Mühlhäuser WW, Fischer A, Weber W, Radziwill G (2017) Optogenetics - bringing light into the darkness of mammalian signal transduction. Biochim Biophys Acta 1864(2):280–292. https://doi.org/10.1016/j.bbamcr.2016.11.009

    Article  CAS  Google Scholar 

  124. Govorunova EG, Sineshchekov OA, Li H, Spudich JL (2017) Microbial rhodopsins: diversity, mechanisms, and optogenetic applications. Annu Rev Biochem 86:845–872. https://doi.org/10.1146/annurev-biochem-101910-144233

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Deisseroth K (2015) Optogenetics: 10 years of microbial opsins in neuroscience. Nat Neurosci 18:1213. https://doi.org/10.1038/nn.4091. https://www.nature.com/articles/nn.4091#supplementary-information

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Dagliyan O, Hahn KM (2019) Controlling protein conformation with light. Curr Opin Struct Biol 57:17–22. https://doi.org/10.1016/j.sbi.2019.01.012

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  127. Mansouri M, Strittmatter T, Fussenegger M (2019) Light-controlled mammalian cells and their therapeutic applications in synthetic biology. Adv Sci 6(1):1800952. https://doi.org/10.1002/advs.201800952

    Article  CAS  Google Scholar 

  128. Dombrowski T, Rankovic V, Moser T (2019) Toward the optical cochlear implant. Cold Spring Harb Perspect Med 9(8):a033225. https://doi.org/10.1101/cshperspect.a033225

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Simunovic MP, Shen W, Lin JY, Protti DA, Lisowski L, Gillies MC (2019) Optogenetic approaches to vision restoration. Exp Eye Res 178:15–26. https://doi.org/10.1016/j.exer.2018.09.003

    Article  CAS  PubMed  Google Scholar 

  130. Kichuk TC, Carrasco-Lopez C, Avalos JL (2020) Lights up on organelles: optogenetic tools to control subcellular structure and organization. Wiley Interdiscip Rev Syst Biol Med 13:e1500. https://doi.org/10.1002/wsbm.1500

    Article  CAS  Google Scholar 

  131. Hartmann J, Krueger D, De Renzis S (2020) Using optogenetics to tackle systems-level questions of multicellular morphogenesis. Curr Opin Cell Biol 66:19–27. https://doi.org/10.1016/j.ceb.2020.04.004

    Article  CAS  PubMed  Google Scholar 

  132. Zhang K, Cui B (2015) Optogenetic control of intracellular signaling pathways. Trends Biotechnol 33(2):92–100. https://doi.org/10.1016/j.tibtech.2014.11.007

    Article  CAS  PubMed  Google Scholar 

  133. Ye H, Fussenegger M (2019) Optogenetic medicine: synthetic therapeutic solutions precision-guided by light. Cold Spring Harb Perspect Med 9(9):a034371. https://doi.org/10.1101/cshperspect.a034371

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  134. Wickstrand C, Nogly P, Nango E, Iwata S, Standfuss J, Neutze R (2019) Bacteriorhodopsin: structural insights revealed using X-ray lasers and synchrotron radiation. Annu Rev Biochem 88:59–83. https://doi.org/10.1146/annurev-biochem-013118-111327

    Article  CAS  PubMed  Google Scholar 

  135. Mathony J, Hoffmann MD, Niopek D (2020) Optogenetics and CRISPR: a new relationship built to last. Methods Mol Biol 2173:261–281. https://doi.org/10.1007/978-1-0716-0755-8_18

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany

    Martin Engelhard

Authors
  1. Martin Engelhard
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Martin Engelhard .

Editor information

Editors and Affiliations

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

    Valentin Gordeliy

Rights and permissions

Reprints and permissions

Copyright information

© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Engelhard, M. (2022). Molecular Biology of Microbial Rhodopsins. 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_2

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-2329-9_2

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2328-2

  • Online ISBN: 978-1-0716-2329-9

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation