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Guidelines for Photoreceptor Engineering

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Optogenetics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1408))

Abstract

Sensory photoreceptors underpin optogenetics by mediating the noninvasive and reversible perturbation of living cells by light with unprecedented temporal and spatial resolution. Spurred by seminal optogenetic applications of natural photoreceptors, the engineering of photoreceptors has recently garnered wide interest and has led to the construction of a broad palette of novel light-regulated actuators. Photoreceptors are modularly built of photosensors that receive light signals, and of effectors that carry out specific cellular functions. These modules have to be precisely connected to allow efficient communication, such that light stimuli are relayed from photosensor to effector. The engineering of photoreceptors benefits from a thorough understanding of the underlying signaling mechanisms. This chapter gives a brief overview of key characteristics and signal-transduction mechanisms of sensory photoreceptors. Adaptation of these concepts in photoreceptor engineering has enabled the generation of novel optogenetic tools that greatly transcend the repertoire of natural photoreceptors.

*The first two authors contributed euqally to this chapter.

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References

  1. Möglich A, Moffat K (2010) Engineered photoreceptors as novel optogenetic tools. Photochem Photobiol Sci 9:1286–1300

    Article  PubMed  Google Scholar 

  2. Schmidt D, Cho YK (2015) Natural photoreceptors and their application to synthetic biology. Trends Biotechnol 33:80–91

    Article  CAS  PubMed  Google Scholar 

  3. Ziegler T, Möglich A (2015) Photoreceptor engineering. Front Mol Biosci 2:30

    Article  PubMed  PubMed Central  Google Scholar 

  4. Ernst OP, Lodowski DT, Elstner M, Hegemann P, Brown LS, Kandori H (2014) Microbial and animal rhodopsins: structures, functions, and molecular mechanisms. Chem Rev 114:126–163

    Article  CAS  PubMed  Google Scholar 

  5. Fenno L, Yizhar O, Deisseroth K (2011) The development and application of optogenetics. Annu Rev Neurosci 34:389–412

    Article  CAS  PubMed  Google Scholar 

  6. Schneider F, Grimm C, Hegemann P (2015) Biophysics of channelrhodopsin. Annu Rev Biophys 44:167–186

    Article  CAS  PubMed  Google Scholar 

  7. Hegemann P (2008) Algal sensory photoreceptors. Annu Rev Plant Biol 59:167–189

    Article  CAS  PubMed  Google Scholar 

  8. Möglich A, Yang X, Ayers RA, Moffat K (2010) Structure and function of plant photoreceptors. Annu Rev Plant Biol 61:21–47

    Article  PubMed  Google Scholar 

  9. Rockwell NC, Su Y-S, Lagarias JC (2006) Phytochrome structure and signaling mechanisms. Annu Rev Plant Biol 57:837–858

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Brown BA, Cloix C, Jiang GH, Kaiserli E, Herzyk P, Kliebenstein DJ, Jenkins GI (2005) A UV-B-specific signaling component orchestrates plant UV protection. Proc Natl Acad Sci U S A 102:18225–18230

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Conrad KS, Manahan CC, Crane BR (2014) Photochemistry of flavoprotein light sensors. Nat Chem Biol 10:801–809

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Losi A, Mandalari C, Gärtner W (2015) The evolution and functional role of flavin-based prokaryotic photoreceptors. Photochem Photobiol 91:1021–1031. doi:10.1111/php.12489

    Google Scholar 

  13. Pudasaini A, El-Arab KK, Zoltowski BD (2015) LOV-based optogenetic devices: light-driven modules to impart photoregulated control of cellular signaling. Front Mol Biosci 2:18

    Article  PubMed  PubMed Central  Google Scholar 

  14. Rockwell NC, Duanmu D, Martin SS, Bachy C, Price DC, Bhattacharya D, Worden AZ, Lagarias JC (2014) Eukaryotic algal phytochromes span the visible spectrum. Proc Natl Acad Sci U S A 111:3871–3876

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Ikeuchi M, Ishizuka T (2008) Cyanobacteriochromes: a new superfamily of tetrapyrrole-binding photoreceptors in cyanobacteria. Photochem Photobiol Sci 7:1159–1167

    Article  CAS  PubMed  Google Scholar 

  16. Rockwell NC, Lagarias JC (2010) A brief history of phytochromes. Chemphyschem 11:1172–1180

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Filonov GS, Piatkevich KD, Ting L-M, Zhang J, Kim K, Verkhusha VV (2011) Bright and stable near-infrared fluorescent protein for in vivo imaging. Nat Biotechnol 29:757–761

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Gasser C, Taiber S, Yeh C-M, Wittig CH, Hegemann P, Ryu S, Wunder F, Möglich A (2014) Engineering of a red-light-activated human cAMP/cGMP-specific phosphodiesterase. Proc Natl Acad Sci U S A 111:8803–8808

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Ryu M-H, Kang I-H, Nelson MD, Jensen TM, Lyuksyutova AI, Siltberg-Liberles J, Raizen DM, Gomelsky M (2014) Engineering adenylate cyclases regulated by near-infrared window light. Proc Natl Acad Sci U S A 111:10167–10172

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Shu X, Royant A, Lin MZ, Aguilera TA, Lev-Ram V, Steinbach PA, Tsien RY (2009) Mammalian expression of infrared fluorescent proteins engineered from a bacterial phytochrome. Science 324:804–807

    Article  PubMed  PubMed Central  Google Scholar 

  21. Alexandre MT, Arents JC, van Grondelle R, Hellingwerf KJ, Kennis JT (2007) A base-catalyzed mechanism for dark state recovery in the Avena sativa phototropin-1 LOV2 domain. Biochemistry 46:3129–3137

    Article  CAS  PubMed  Google Scholar 

  22. Zhou XX, Chung HK, Lam AJ, Lin MZ (2012) Optical control of protein activity by fluorescent protein domains. Science 338:810–814

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Lee J, Natarajan M, Nashine VC, Socolich M, Vo T, Russ WP, Benkovic SJ, Ranganathan R (2008) Surface sites for engineering allosteric control in proteins. Science 322:438–442

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Ohlendorf R, Vidavski RR, Eldar A, Moffat K, Möglich A (2012) From dusk till dawn: one-plasmid systems for light-regulated gene expression. J Mol Biol 416:534–542

    Article  CAS  PubMed  Google Scholar 

  25. Jansen V, Alvarez L, Balbach M, Strünker T, Hegemann P, Kaupp UB, Wachten D (2015) Controlling fertilization and cAMP signaling in sperm by optogenetics. eLife 4:e05161

    Google Scholar 

  26. Grusch M, Schelch K, Riedler R, Reichhart E, Differ C, Berger W, Inglés-Prieto Á, Janovjak H (2014) Spatio-temporally precise activation of engineered receptor tyrosine kinases by light. EMBO J 33:1713–1726

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Guntas G, Hallett RA, Zimmerman SP, Williams T, Yumerefendi H, Bear JE, Kuhlman B (2015) Engineering an improved light-induced dimer (iLID) for controlling the localization and activity of signaling proteins. Proc Natl Acad Sci U S A 112:112–117

    Article  CAS  PubMed  Google Scholar 

  28. Cosentino C, Alberio L, Gazzarrini S et al (2015) Optogenetics. Engineering of a light-gated potassium channel. Science 348:707–710

    Article  CAS  PubMed  Google Scholar 

  29. Goldsmith M, Tawfik DS (2012) Directed enzyme evolution: beyond the low-hanging fruit. Curr Opin Struct Biol 22:406–412

    Article  CAS  PubMed  Google Scholar 

  30. Bugaj LJ, Choksi AT, Mesuda CK, Kane RS, Schaffer DV (2013) Optogenetic protein clustering and signaling activation in mammalian cells. Nat Methods 10:249–252

    Article  CAS  PubMed  Google Scholar 

  31. Lamb JS, Zoltowski BD, Pabit SA, Crane BR, Pollack L (2008) Time-resolved dimerization of a PAS-LOV protein measured with photocoupled small angle X-ray scattering. J Am Chem Soc 130:12226–12227

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Takahashi F, Yamagata D, Ishikawa M, Fukamatsu Y, Ogura Y, Kasahara M, Kiyosue T, Kikuyama M, Wada M, Kataoka H (2007) AUREOCHROME, a photoreceptor required for photomorphogenesis in stramenopiles. Proc Natl Acad Sci U S A 104:19625–19630

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Nash AI, McNulty R, Shillito ME, Swartz TE, Bogomolni RA, Luecke H, Gardner KH (2011) Structural basis of photosensitivity in a bacterial light-oxygen-voltage/helix-turn-helix (LOV-HTH) DNA-binding protein. Proc Natl Acad Sci U S A 108:9449–9454

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Christie JM, Arvai AS, Baxter KJ et al (2012) Plant UVR8 photoreceptor senses UV-B by tryptophan-mediated disruption of cross-dimer salt bridges. Science 335:1492–1496

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Kennedy MJ, Hughes RM, Peteya LA, Schwartz JW, Ehlers MD, Tucker CL (2010) Rapid blue-light-mediated induction of protein interactions in living cells. Nat Methods 7:973–975

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Yazawa M, Sadaghiani AM, Hsueh B, Dolmetsch RE (2009) Induction of protein-protein interactions in live cells using light. Nat Biotechnol 27:941–945

    Article  CAS  PubMed  Google Scholar 

  37. Levskaya A, Weiner OD, Lim WA, Voigt CA (2009) Spatiotemporal control of cell signalling using a light-switchable protein interaction. Nature 461:997–1001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Shimizu-Sato S, Huq E, Tepperman JM, Quail PH (2002) A light-switchable gene promoter system. Nat Biotechnol 20:1041–1044

    Article  CAS  PubMed  Google Scholar 

  39. Harper SM, Neil LC, Gardner KH (2003) Structural basis of a phototropin light switch. Science 301:1541–1544

    Article  CAS  PubMed  Google Scholar 

  40. Christie JM, Blackwood L, Petersen J, Sullivan S (2015) Plant flavoprotein photoreceptors. Plant Cell Physiol 56:401–413

    Article  PubMed  Google Scholar 

  41. Renicke C, Schuster D, Usherenko S, Essen L-O, Taxis C (2013) A LOV2 domain-based optogenetic tool to control protein degradation and cellular function. Chem Biol 20:619–626

    Article  CAS  PubMed  Google Scholar 

  42. Herman E, Kottke T (2015) Allosterically regulated unfolding of the A′α helix exposes the dimerization site of the blue-light-sensing aureochrome-LOV domain. Biochemistry 54:1484–1492

    Article  CAS  PubMed  Google Scholar 

  43. Conrad KS, Bilwes AM, Crane BR (2013) Light-induced subunit dissociation by a light-oxygen-voltage domain photoreceptor from Rhodobacter sphaeroides. Biochemistry 52:378–391

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Rubinstenn G, Vuister GW, Mulder FAA, Düx PE, Boelens R, Hellingwerf KJ, Kaptein R (1998) Structural and dynamic changes of photoactive yellow protein during its photocycle in solution. Nat Struct Mol Biol 5:568–570

    Article  CAS  Google Scholar 

  45. Rivera-Cancel G, Ko W, Tomchick DR, Correa F, Gardner KH (2014) Full-length structure of a monomeric histidine kinase reveals basis for sensory regulation. Proc Natl Acad Sci U S A 111:17839–17844

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Takala H, Björling A, Berntsson O et al (2014) Signal amplification and transduction in phytochrome photosensors. Nature 509:245–248

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Anders K, Gutt A, Gärtner W, Essen L-O (2014) Phototransformation of the red light sensor cyanobacterial phytochrome 2 from Synechocystis species depends on its tongue motifs. J Biol Chem 289:25590–25600

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Chang K-Y, Woo D, Jung H et al (2014) Light-inducible receptor tyrosine kinases that regulate neurotrophin signalling. Nat Commun 5:4057

    CAS  PubMed  Google Scholar 

  49. Kim N, Kim JM, Lee M, Kim CY, Chang K-Y, Heo WD (2014) Spatiotemporal control of fibroblast growth factor receptor signals by blue light. Chem Biol 21:903–912

    Article  CAS  PubMed  Google Scholar 

  50. Nihongaki Y, Suzuki H, Kawano F, Sato M (2014) Genetically engineered photoinducible homodimerization system with improved dimer-forming efficiency. ACS Chem Biol 9:617–621

    Article  CAS  PubMed  Google Scholar 

  51. Wang X, Chen X, Yang Y (2012) Spatiotemporal control of gene expression by a light-switchable transgene system. Nat Methods 9:266–269

    Article  CAS  PubMed  Google Scholar 

  52. Aoki K, Kumagai Y, Sakurai A, Komatsu N, Fujita Y, Shionyu C, Matsuda M (2013) Stochastic ERK activation induced by noise and cell-to-cell propagation regulates cell density-dependent proliferation. Mol Cell 52:529–540

    Article  CAS  PubMed  Google Scholar 

  53. Wu YI, Frey D, Lungu OI, Jaehrig A, Schlichting I, Kuhlman B, Hahn KM (2009) A genetically encoded photoactivatable Rac controls the motility of living cells. Nature 461:104–108

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Schmidt D, Tillberg PW, Chen F, Boyden ES (2014) A fully genetically encoded protein architecture for optical control of peptide ligand concentration. Nat Commun 5:3019

    PubMed  PubMed Central  Google Scholar 

  55. Bonger KM, Rakhit R, Payumo AY, Chen JK, Wandless TJ (2014) General method for regulating protein stability with light. ACS Chem Biol 9:111–115

    Article  CAS  PubMed  Google Scholar 

  56. Anantharaman V, Balaji S, Aravind L (2006) The signaling helix: a common functional theme in diverse signaling proteins. Biol Direct 1:25

    Article  PubMed  PubMed Central  Google Scholar 

  57. Möglich A, Ayers RA, Moffat K (2009) Design and signaling mechanism of light-regulated histidine kinases. J Mol Biol 385:1433–1444

    Article  PubMed  Google Scholar 

  58. Möglich A, Ayers RA, Moffat K (2010) Addition at the molecular level: signal integration in designed Per-ARNT-Sim receptor proteins. J Mol Biol 400:477–486

    Article  PubMed  Google Scholar 

  59. Rockwell NC, Ohlendorf R, Möglich A (2013) Cyanobacteriochromes in full color and three dimensions. Proc Natl Acad Sci U S A 110:806–807

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Levskaya A, Chevalier AA, Tabor JJ et al (2005) Synthetic biology: sngineering Escherichia coli to see light. Nature 438:441–442

    Article  CAS  PubMed  Google Scholar 

  61. Losi A, Polverini E, Quest B, Gärtner W (2002) First evidence for phototropin-related blue-light receptors in prokaryotes. Biophys J 82:2627–2634

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Avelar GM, Schumacher RI, Zaini PA, Leonard G, Richards TA, Gomes SL (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 

  63. Yoshihara S, Suzuki F, Fujita H, Geng XX, Ikeuchi M (2000) Novel putative photoreceptor and regulatory genes required for the positive phototactic movement of the unicellular motile Cyanobacterium Synechocystis sp. PCC 6803. Plant Cell Physiol 41:1299–1304

    Article  CAS  PubMed  Google Scholar 

  64. Davis SJ, Vener AV, Vierstra RD (1999) Bacteriophytochromes: phytochrome-like photoreceptors from nonphotosynthetic eubacteria. Science 286:2517–2520

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

Research in our laboratory is generously supported through a Sofja-Kovalevskaya Award by the Alexander-von-Humboldt Foundation (to A.M.) and by the Deutsche Forschungsgemeinschaft within the Cluster of Excellence ‘Unicat—Unifying Concepts in Catalysis’.

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Correspondence to Andreas Möglich .

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Ziegler, T., Schumacher, C.H., Möglich, A. (2016). Guidelines for Photoreceptor Engineering. In: Kianianmomeni, A. (eds) Optogenetics. Methods in Molecular Biology, vol 1408. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3512-3_27

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  • DOI: https://doi.org/10.1007/978-1-4939-3512-3_27

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