1932

Abstract

Optobiochemical control of protein activities allows the investigation of protein functions in living cells with high spatiotemporal resolution. Over the last two decades, numerous natural photosensory domains have been characterized and synthetic domains engineered and assembled into photoregulatory systems to control protein function with light. Here, we review the field of optobiochemistry, categorizing photosensory domains by chromophore, describing photoregulatory systems by mechanism of action, and discussing protein classes frequently investigated using optical methods. We also present examples of how spatial or temporal control of proteins in living cells has provided new insights not possible with traditional biochemical or cell biological techniques.

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2021-06-20
2024-04-16
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Literature Cited

  1. 1. 
    Heim R, Cubitt AB, Tsien RY 1995. Improved green fluorescence. Nature 373:663–64
    [Google Scholar]
  2. 2. 
    Tsien RY. 1998. The green fluorescent protein. Annu. Rev. Biochem. 67:509–44
    [Google Scholar]
  3. 3. 
    Giepmans BN, Adams SR, Ellisman MH, Tsien RY 2006. The fluorescent toolbox for assessing protein location and function. Science 312:217–24
    [Google Scholar]
  4. 4. 
    Rodriguez EA, Campbell RE, Lin JY, Lin MZ, Miyawaki A et al. 2017. The growing and glowing toolbox of fluorescent and photoactive proteins. Trends Biochem. Sci. 42:111–29
    [Google Scholar]
  5. 5. 
    Repina NA, Rosenbloom A, Mukherjee A, Schaffer DV, Kane RS 2017. At light speed: advances in optogenetic systems for regulating cell signaling and behavior. Annu. Rev. Chem. Biomol. Eng. 8:13–39
    [Google Scholar]
  6. 6. 
    Shcherbakova DM, Shemetov AA, Kaberniuk AA, Verkhusha VV 2015. Natural photoreceptors as a source of fluorescent proteins, biosensors, and optogenetic tools. Annu. Rev. Biochem. 84:519–50
    [Google Scholar]
  7. 7. 
    Zhou XX, Pan M, Lin MZ 2015. Investigating neuronal function with optically controllable proteins. Front. Mol. Neurosci. 8:37
    [Google Scholar]
  8. 8. 
    Kim B, Lin MZ. 2013. Optobiology: optical control of biological processes via protein engineering. Biochem. Soc. Trans. 41:1183–88
    [Google Scholar]
  9. 9. 
    Shimizu-Sato S, Huq E, Tepperman JM, Quail PH 2002. A light-switchable gene promoter system. Nat. Biotechnol. 20:1041–44
    [Google Scholar]
  10. 10. 
    Toettcher JE, Weiner OD, Lim WA 2013. Using optogenetics to interrogate the dynamic control of signal transmission by the Ras/Erk module. Cell 155:1422–34
    [Google Scholar]
  11. 11. 
    Wang X, He L, Wu YI, Hahn KM, Montell DJ 2010. Light-mediated activation reveals a key role for Rac in collective guidance of cell movement in vivo. Nat. Cell Biol. 12:591–97
    [Google Scholar]
  12. 12. 
    Deisseroth K, Feng G, Majewska AK, Miesenbock G, Ting A, Schnitzer MJ 2006. Next-generation optical technologies for illuminating genetically targeted brain circuits. J. Neurosci. 26:10380–86
    [Google Scholar]
  13. 13. 
    Fenno L, Yizhar O, Deisseroth K 2011. The development and application of optogenetics. Annu. Rev. Neurosci. 34:389–412
    [Google Scholar]
  14. 14. 
    Xu X, Mee T, Jia X 2020. New era of optogenetics: from the central to peripheral nervous system. Crit. Rev. Biochem. Mol. Biol. 55:1–16
    [Google Scholar]
  15. 15. 
    Huang CL, Ferenczi EA, Lei M 2020. Optogenetics: an emerging approach in cardiac electrophysiology. Front. Physiol. 11:414
    [Google Scholar]
  16. 16. 
    Josselyn SA. 2018. The past, present and future of light-gated ion channels and optogenetics. eLife7e42367
    [Google Scholar]
  17. 17. 
    Boyden ES. 2015. Optogenetics and the future of neuroscience. Nat. Neurosci. 18:1200–1
    [Google Scholar]
  18. 18. 
    Spangler SM, Bruchas MR. 2017. Optogenetic approaches for dissecting neuromodulation and GPCR signaling in neural circuits. Curr. Opin. Pharmacol. 32:56–70
    [Google Scholar]
  19. 19. 
    Kumar A, Ali AM, Woolley GA 2015. Photo-control of DNA binding by an engrailed homeodomain-photoactive yellow protein hybrid. Photochem. Photobiol. Sci. 14:1729–36
    [Google Scholar]
  20. 20. 
    Zhou XX, Chung HK, Lam AJ, Lin MZ 2012. Optical control of protein activity by fluorescent protein domains. Science 338:810–14
    [Google Scholar]
  21. 21. 
    Zhou XX, Fan LZ, Li P, Shen K, Lin MZ 2017. Optical control of cell signaling by single-chain photoswitchable kinases. Science 355:836–42
    [Google Scholar]
  22. 22. 
    Jenkins GI. 2014. The UV-B photoreceptor UVR8: from structure to physiology. Plant Cell 26:21–37
    [Google Scholar]
  23. 23. 
    Chen D, Gibson ES, Kennedy MJ 2013. A light-triggered protein secretion system. J. Cell Biol. 201:631–40
    [Google Scholar]
  24. 24. 
    Christie JM, Arvai AS, Baxter KJ, Heilmann M, Pratt AJ et al. 2012. Plant UVR8 photoreceptor senses UV-B by tryptophan-mediated disruption of cross-dimer salt bridges. Science 335:1492–96
    [Google Scholar]
  25. 25. 
    Wu D, Hu Q, Yan Z, Chen W, Yan C et al. 2012. Structural basis of ultraviolet-B perception by UVR8. Nature 484:214–19
    [Google Scholar]
  26. 26. 
    Tissot N, Ulm R. 2020. Cryptochrome-mediated blue-light signalling modulates UVR8 photoreceptor activity and contributes to UV-B tolerance in Arabidopsis. Nat. Commun. 11:1323
    [Google Scholar]
  27. 27. 
    Muller K, Engesser R, Timmer J, Zurbriggen MD, Weber W 2014. Orthogonal optogenetic triple-gene control in mammalian cells. ACS Synth. Biol. 3:796–801
    [Google Scholar]
  28. 28. 
    Kyndt JA, Vanrobaeys F, Fitch JC, Devreese BV, Meyer TE et al. 2003. Heterologous production of Halorhodospira halophila holo-photoactive yellow protein through tandem expression of the postulated biosynthetic genes. Biochemistry 42:965–70
    [Google Scholar]
  29. 29. 
    Hoff WD, van der Horst MA, Nudel CB, Hellingwerf KJ 2009. Prokaryotic phototaxis. Methods Mol. Biol. 571:25–49
    [Google Scholar]
  30. 30. 
    van der Horst MA, Laan W, Yeremenko S, Wende A, Palm P et al. 2005. From primary photochemistry to biological function in the blue-light photoreceptors PYP and AppA. Photochem. Photobiol. Sci. 4:688–93
    [Google Scholar]
  31. 31. 
    Glantz ST, Carpenter EJ, Melkonian M, Gardner KH, Boyden ES et al. 2016. Functional and topological diversity of LOV domain photoreceptors. PNAS 113:E1442–51
    [Google Scholar]
  32. 32. 
    Salomon M, Christie JM, Knieb E, Lempert U, Briggs WR 2000. Photochemical and mutational analysis of the FMN-binding domains of the plant blue light receptor, phototropin. Biochemistry 39:9401–10
    [Google Scholar]
  33. 33. 
    Harper SM, Neil LC, Gardner KH 2003. Structural basis of a phototropin light switch. Science 301:1541–44
    [Google Scholar]
  34. 34. 
    Briggs WR, Beck CF, Cashmore AR, Christie JM, Hughes J et al. 2001. The phototropin family of photoreceptors. Plant Cell 13:993–97
    [Google Scholar]
  35. 35. 
    Hart JE, Sullivan S, Hermanowicz P, Petersen J, Diaz-Ramos LA et al. 2019. Engineering the phototropin photocycle improves photoreceptor performance and plant biomass production. PNAS 116:12550–57
    [Google Scholar]
  36. 36. 
    Zoltowski BD, Schwerdtfeger C, Widom J, Loros JJ, Bilwes AM et al. 2007. Conformational switching in the fungal light sensor Vivid. Science 316:1054–57
    [Google Scholar]
  37. 37. 
    Zoltowski BD, Vaccaro B, Crane BR 2009. Mechanism-based tuning of a LOV domain photoreceptor. Nat. Chem. Biol. 5:827–34
    [Google Scholar]
  38. 38. 
    Grusch M, Schelch K, Riedler R, Reichhart E, Differ C et al. 2014. Spatio-temporally precise activation of engineered receptor tyrosine kinases by light. EMBO J 33:1713–26
    [Google Scholar]
  39. 39. 
    Nakasone Y, Zikihara K, Tokutomi S, Terazima M 2010. Kinetics of conformational changes of the FKF1-LOV domain upon photoexcitation. Biophys. J. 99:3831–39
    [Google Scholar]
  40. 40. 
    Yazawa M, Sadaghiani AM, Hsueh B, Dolmetsch RE 2009. Induction of protein-protein interactions in live cells using light. Nat. Biotechnol. 27:941–45
    [Google Scholar]
  41. 41. 
    Park SY, Tame JRH. 2017. Seeing the light with BLUF proteins. Biophys. Rev. 9:169–76
    [Google Scholar]
  42. 42. 
    Bonetti C, Mathes T, van Stokkum IH, Mullen KM, Groot ML et al. 2008. Hydrogen bond switching among flavin and amino acid side chains in the BLUF photoreceptor observed by ultrafast infrared spectroscopy. Biophys. J. 95:4790–802
    [Google Scholar]
  43. 43. 
    Ohki M, Sato-Tomita A, Matsunaga S, Iseki M, Tame JRH et al. 2017. Molecular mechanism of photoactivation of a light-regulated adenylate cyclase. PNAS 114:8562–67
    [Google Scholar]
  44. 44. 
    Fujisawa T, Masuda S. 2018. Light-induced chromophore and protein responses and mechanical signal transduction of BLUF proteins. Biophys. Rev. 10:327–37
    [Google Scholar]
  45. 45. 
    Blain-Hartung M, Rockwell NC, Moreno MV, Martin SS, Gan F et al. 2018. Cyanobacteriochrome-based photoswitchable adenylyl cyclases (cPACs) for broad spectrum light regulation of cAMP levels in cells. J. Biol. Chem. 293:8473–83
    [Google Scholar]
  46. 46. 
    Chaves I, Pokorny R, Byrdin M, Hoang N, Ritz T et al. 2011. The cryptochromes: blue light photoreceptors in plants and animals. Annu. Rev. Plant Biol. 62:335–64
    [Google Scholar]
  47. 47. 
    Liu H, Yu X, Li K, Klejnot J, Yang H et al. 2008. Photoexcited CRY2 interacts with CIB1 to regulate transcription and floral initiation in Arabidopsis. Science 322:1535–39
    [Google Scholar]
  48. 48. 
    Bugaj LJ, Choksi AT, Mesuda CK, Kane RS, Schaffer DV 2013. Optogenetic protein clustering and signaling activation in mammalian cells. Nat. Methods 10:249–52
    [Google Scholar]
  49. 49. 
    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 7:973–75
    [Google Scholar]
  50. 50. 
    Taslimi A, Zoltowski B, Miranda JG, Pathak GP, Hughes RM, Tucker CL 2016. Optimized second-generation CRY2-CIB dimerizers and photoactivatable Cre recombinase. Nat. Chem. Biol. 12:425–30
    [Google Scholar]
  51. 51. 
    Hughes RM, Vrana JD, Song J, Tucker CL 2012. Light-dependent, dark-promoted interaction between Arabidopsis cryptochrome 1 and phytochrome B proteins. J. Biol. Chem. 287:22165–72
    [Google Scholar]
  52. 52. 
    Briscoe AD. 2008. Reconstructing the ancestral butterfly eye: focus on the opsins. J. Exp. Biol. 211:1805–13
    [Google Scholar]
  53. 53. 
    Zhang F, Vierock J, Yizhar O, Fenno LE, Tsunoda S et al. 2011. The microbial opsin family of optogenetic tools. Cell 147:1446–57
    [Google Scholar]
  54. 54. 
    Spudich JL. 2006. The multitalented microbial sensory rhodopsins. Trends Microbiol 14:480–87
    [Google Scholar]
  55. 55. 
    Inoue K, Tsukamoto T, Sudo Y 2014. Molecular and evolutionary aspects of microbial sensory rhodopsins. Biochim. Biophys. Acta Bioenerg. 1837:562–77
    [Google Scholar]
  56. 56. 
    Deisseroth K. 2015. Optogenetics: 10 years of microbial opsins in neuroscience. Nat. Neurosci. 18:1213–25
    [Google Scholar]
  57. 57. 
    von Lintig J, Kiser PD, Golczak M, Palczewski K 2010. The biochemical and structural basis for trans-to-cis isomerization of retinoids in the chemistry of vision. Trends Biochem. Sci. 35:400–10
    [Google Scholar]
  58. 58. 
    Airan RD, Thompson KR, Fenno LE, Bernstein H, Deisseroth K 2009. Temporally precise in vivo control of intracellular signalling. Nature 458:1025–29
    [Google Scholar]
  59. 59. 
    Masseck OA, Spoida K, Dalkara D, Maejima T, Rubelowski JM et al. 2014. Vertebrate cone opsins enable sustained and highly sensitive rapid control of Gi/o signaling in anxiety circuitry. Neuron 81:1263–73
    [Google Scholar]
  60. 60. 
    Spoida K, Masseck OA, Deneris ES, Herlitze S 2014. Gq/5-HT2c receptor signals activate a local GABAergic inhibitory feedback circuit to modulate serotonergic firing and anxiety in mice. PNAS 111:6479–84
    [Google Scholar]
  61. 61. 
    van Wyk M, Pielecka-Fortuna J, Lowel S, Kleinlogel S 2015. Restoring the ON switch in blind retinas: Opto-mGluR6, a next-generation, cell-tailored optogenetic tool. PLOS Biol 13:e1002143
    [Google Scholar]
  62. 62. 
    Siuda ER, McCall JG, Al-Hasani R, Shin G, Park SI et al. 2015. Optodynamic simulation of β-adrenergic receptor signalling. Nat. Commun. 6:8480
    [Google Scholar]
  63. 63. 
    Ando R, Mizuno H, Miyawaki A 2004. Regulated fast nucleocytoplasmic shuttling observed by reversible protein highlighting. Science 306:1370–73
    [Google Scholar]
  64. 64. 
    Andresen M, Stiel AC, Trowitzsch S, Weber G, Eggeling C et al. 2007. Structural basis for reversible photoswitching in Dronpa. PNAS 104:13005–9
    [Google Scholar]
  65. 65. 
    Mizuno H, Mal TK, Walchli M, Kikuchi A, Fukano T et al. 2008. Light-dependent regulation of structural flexibility in a photochromic fluorescent protein. PNAS 105:9227–32
    [Google Scholar]
  66. 66. 
    Padmanabhan S, Jost M, Drennan CL, Elias-Arnanz M 2017. A new facet of vitamin B12: gene regulation by cobalamin-based photoreceptors. Annu. Rev. Biochem. 86:485–514
    [Google Scholar]
  67. 67. 
    Ortiz-Guerrero JM, Polanco MC, Murillo FJ, Padmanabhan S, Elias-Arnanz M 2011. Light-dependent gene regulation by a coenzyme B12-based photoreceptor. PNAS 108:7565–70
    [Google Scholar]
  68. 68. 
    Kainrath S, Stadler M, Reichhart E, Distel M, Janovjak H 2017. Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angew. Chem. Int. Ed. 56:4608–11
    [Google Scholar]
  69. 69. 
    Jost M, Fernandez-Zapata J, Polanco MC, Ortiz-Guerrero JM, Chen PY et al. 2015. Structural basis for gene regulation by a B12-dependent photoreceptor. Nature 526:536–41
    [Google Scholar]
  70. 70. 
    Levskaya A, Weiner OD, Lim WA, Voigt CA 2009. Spatiotemporal control of cell signalling using a light-switchable protein interaction. Nature 461:997–1001
    [Google Scholar]
  71. 71. 
    Kaberniuk AA, Shemetov AA, Verkhusha VV 2016. A bacterial phytochrome-based optogenetic system controllable with near-infrared light. Nat. Methods 13:591–97
    [Google Scholar]
  72. 72. 
    Rockwell NC, Martin SS, Feoktistova K, Lagarias JC 2011. Diverse two-cysteine photocycles in phytochromes and cyanobacteriochromes. PNAS 108:11854–59
    [Google Scholar]
  73. 73. 
    Uda Y, Miura H, Goto Y, Yamamoto K, Mii Y et al. 2020. Improvement of phycocyanobilin synthesis for genetically encoded phytochrome-based optogenetics. ACS Chem. Biol 15:2896–906
    [Google Scholar]
  74. 74. 
    Strickland D, Moffat K, Sosnick TR 2008. Light-activated DNA binding in a designed allosteric protein. PNAS 105:10709–14
    [Google Scholar]
  75. 75. 
    Wu YI, Frey D, Lungu OI, Jaehrig A, Schlichting I et al. 2009. A genetically encoded photoactivatable Rac controls the motility of living cells. Nature 461:104–8
    [Google Scholar]
  76. 76. 
    Murakoshi H, Shin ME, Parra-Bueno P, Szatmari EM, Shibata AC, Yasuda R 2017. Kinetics of endogenous CaMKII required for synaptic plasticity revealed by optogenetic kinase inhibitor. Neuron 94:3747.e5
    [Google Scholar]
  77. 77. 
    Lee J, Natarajan M, Nashine VC, Socolich M, Vo T et al. 2008. Surface sites for engineering allosteric control in proteins. Science 322:438–42
    [Google Scholar]
  78. 78. 
    Smart AD, Pache RA, Thomsen ND, Kortemme T, Davis GW, Wells JA 2017. Engineering a light-activated caspase-3 for precise ablation of neurons in vivo. PNAS 114:E8174–83
    [Google Scholar]
  79. 79. 
    Dagliyan O, Tarnawski M, Chu PH, Shirvanyants D, Schlichting I et al. 2016. Engineering extrinsic disorder to control protein activity in living cells. Science 354:1441–44
    [Google Scholar]
  80. 80. 
    Nakamura M, Chen L, Howes SC, Schindler TD, Nogales E, Bryant Z 2014. Remote control of myosin and kinesin motors using light-activated gearshifting. Nat. Nanotechnol. 9:693–97
    [Google Scholar]
  81. 81. 
    Levskaya A, Chevalier AA, Tabor JJ, Simpson ZB, Lavery LA et al. 2005. Synthetic biology: engineering Escherichia coli to see light. Nature 438:441–42
    [Google Scholar]
  82. 82. 
    Moglich A, Ayers RA, Moffat K 2009. Design and signaling mechanism of light-regulated histidine kinases. J. Mol. Biol. 385:1433–44
    [Google Scholar]
  83. 83. 
    Ryu MH, Kang IH, Nelson MD, Jensen TM, Lyuksyutova AI et al. 2014. Engineering adenylate cyclases regulated by near-infrared window light. PNAS 111:10167–72
    [Google Scholar]
  84. 84. 
    Gasser C, Taiber S, Yeh CM, Wittig CH, Hegemann P et al. 2014. Engineering of a red-light-activated human cAMP/cGMP-specific phosphodiesterase. PNAS 111:8803–8
    [Google Scholar]
  85. 85. 
    Ziegler T, Moglich A. 2015. Photoreceptor engineering. Front. Mol. Biosci. 2:30
    [Google Scholar]
  86. 86. 
    Wang X, Chen X, Yang Y 2012. Spatiotemporal control of gene expression by a light-switchable transgene system. Nat. Methods 9:266–69
    [Google Scholar]
  87. 87. 
    Chang KY, Woo D, Jung H, Lee S, Kim S et al. 2014. Light-inducible receptor tyrosine kinases that regulate neurotrophin signalling. Nat. Commun. 5:4057
    [Google Scholar]
  88. 88. 
    Kyung T, Lee S, Kim JE, Cho T, Park H et al. 2015. Optogenetic control of endogenous Ca2+ channels in vivo. Nat. Biotechnol. 33:1092–96
    [Google Scholar]
  89. 89. 
    Park H, Kim NY, Lee S, Kim N, Kim J, Heo WD 2017. Optogenetic protein clustering through fluorescent protein tagging and extension of CRY2. Nat. Commun. 8:30
    [Google Scholar]
  90. 90. 
    Duan L, Hope J, Ong Q, Lou HY, Kim N et al. 2017. Understanding CRY2 interactions for optical control of intracellular signaling. Nat. Commun. 8:547
    [Google Scholar]
  91. 91. 
    Zhang K, Duan L, Ong Q, Lin Z, Varman PM et al. 2014. Light-mediated kinetic control reveals the temporal effect of the Raf/MEK/ERK pathway in PC12 cell neurite outgrowth. PLOS ONE 9:e92917
    [Google Scholar]
  92. 92. 
    Sinnen BL, Bowen AB, Forte JS, Hiester BG, Crosby KC et al. 2017. Optogenetic control of synaptic composition and function. Neuron 93:64660.e5
    [Google Scholar]
  93. 93. 
    Lee S, Park H, Kyung T, Kim NY, Kim S et al. 2014. Reversible protein inactivation by optogenetic trapping in cells. Nat. Methods 11:633–36
    [Google Scholar]
  94. 94. 
    Dine E, Gil AA, Uribe G, Brangwynne CP, Toettcher JE 2018. Protein phase separation provides long-term memory of transient spatial stimuli. Cell Syst 6:65563.e5
    [Google Scholar]
  95. 95. 
    Morgan SA, Al-Abdul-Wahid S, Woolley GA 2010. Structure-based design of a photocontrolled DNA binding protein. J. Mol. Biol. 399:94–112
    [Google Scholar]
  96. 96. 
    Guntas G, Hallett RA, Zimmerman SP, Williams T, Yumerefendi H et al. 2015. Engineering an improved light-induced dimer (iLID) for controlling the localization and activity of signaling proteins. PNAS 112:112–17
    [Google Scholar]
  97. 97. 
    Strickland D, Lin Y, Wagner E, Hope CM, Zayner J et al. 2012. TULIPs: tunable, light-controlled interacting protein tags for cell biology. Nat. Methods 9:379–84
    [Google Scholar]
  98. 98. 
    Kawano F, Suzuki H, Furuya A, Sato M 2015. Engineered pairs of distinct photoswitches for optogenetic control of cellular proteins. Nat. Commun. 6:6256
    [Google Scholar]
  99. 99. 
    Kawano F, Okazaki R, Yazawa M, Sato M 2016. A photoactivatable Cre-loxP recombination system for optogenetic genome engineering. Nat. Chem. Biol. 12:1059–64
    [Google Scholar]
  100. 100. 
    Wang H, Vilela M, Winkler A, Tarnawski M, Schlichting I et al. 2016. LOVTRAP: an optogenetic system for photoinduced protein dissociation. Nat. Methods 13:755–58
    [Google Scholar]
  101. 101. 
    Stone OJ, Pankow N, Liu B, Sharma VP, Eddy RJ et al. 2019. Optogenetic control of cofilin and αTAT in living cells using Z-lock. Nat. Chem. Biol. 15:1183–90
    [Google Scholar]
  102. 102. 
    Morgan SA, Woolley GA. 2010. A photoswitchable DNA-binding protein based on a truncated GCN4-photoactive yellow protein chimera. Photochem. Photobiol. Sci. 9:1320–26
    [Google Scholar]
  103. 103. 
    Ali AM, Reis JM, Xia Y, Rashid AJ, Mercaldo V et al. 2015. Optogenetic inhibitor of the transcription factor CREB. Chem. Biol. 22:1531–39
    [Google Scholar]
  104. 104. 
    Ma G, Liu J, Ke Y, Liu X, Li M et al. 2018. Optogenetic control of voltage-gated calcium channels. Angew. Chem. Int. Ed. 57:7019–22
    [Google Scholar]
  105. 105. 
    Cosentino C, Alberio L, Gazzarrini S, Aquila M, Romano E et al. 2015. Optogenetics. Engineering of a light-gated potassium channel. Science 348:707–10
    [Google Scholar]
  106. 106. 
    Valon L, Marin-Llaurado A, Wyatt T, Charras G, Trepat X 2017. Optogenetic control of cellular forces and mechanotransduction. Nat. Commun. 8:14396
    [Google Scholar]
  107. 107. 
    Oakes PW, Wagner E, Brand CA, Probst D, Linke M et al. 2017. Optogenetic control of RhoA reveals zyxin-mediated elasticity of stress fibres. Nat. Commun. 8:15817
    [Google Scholar]
  108. 108. 
    Woo D, Seo Y, Jung H, Kim S, Kim N et al. 2019. Locally activating TrkB receptor generates actin waves and specifies axonal fate. Cell Chem. Biol. 26:165263.e4
    [Google Scholar]
  109. 109. 
    Kim N, Kim JM, Lee M, Kim CY, Chang KY, Heo WD 2014. Spatiotemporal control of fibroblast growth factor receptor signals by blue light. Chem. Biol. 21:903–12
    [Google Scholar]
  110. 110. 
    Huang P, Liu A, Song Y, Hope JM, Cui B, Duan L 2020. Optical activation of TrkB signaling. J. Mol. Biol. 432:3761–70
    [Google Scholar]
  111. 111. 
    Leopold AV, Chernov KG, Verkhusha VV 2018. Optogenetically controlled protein kinases for regulation of cellular signaling. Chem. Soc. Rev. 47:2454–84
    [Google Scholar]
  112. 112. 
    Hallett RA, Zimmerman SP, Yumerefendi H, Bear JE, Kuhlman B 2016. Correlating in vitro and in vivo activities of light-inducible dimers: a cellular optogenetics guide. ACS Synth. Biol. 5:53–64
    [Google Scholar]
  113. 113. 
    Motta-Mena LB, Reade A, Mallory MJ, Glantz S, Weiner OD et al. 2014. An optogenetic gene expression system with rapid activation and deactivation kinetics. Nat. Chem. Biol. 10:196–202
    [Google Scholar]
  114. 114. 
    Quejada JR, Park SE, Awari DW, Shi F, Yamamoto HE et al. 2017. Optimized light-inducible transcription in mammalian cells using Flavin Kelch-repeat F-box1/GIGANTEA and CRY2/CIB1. Nucleic Acids Res 45:e172
    [Google Scholar]
  115. 115. 
    Imayoshi I, Isomura A, Harima Y, Kawaguchi K, Kori H et al. 2013. Oscillatory control of factors determining multipotency and fate in mouse neural progenitors. Science 342:1203–8
    [Google Scholar]
  116. 116. 
    Polstein LR, Gersbach CA. 2015. A light-inducible CRISPR-Cas9 system for control of endogenous gene activation. Nat. Chem. Biol. 11:198–200
    [Google Scholar]
  117. 117. 
    Nihongaki Y, Kawano F, Nakajima T, Sato M 2015. Photoactivatable CRISPR-Cas9 for optogenetic genome editing. Nat. Biotechnol. 33:755–60
    [Google Scholar]
  118. 118. 
    Zhou XX, Zou X, Chung HK, Gao Y, Liu Y et al. 2017. A single-chain photoswitchable CRISPR-Cas9 architecture for light-inducible gene editing and transcription. ACS Chem. Biol.13:443–48
    [Google Scholar]
  119. 119. 
    Zhao J, Li B, Ma J, Jin W, Ma X 2020. Photoactivatable RNA N6-methyladenosine editing with CRISPR-Cas13. Small 16e1907301
    [Google Scholar]
  120. 120. 
    Mathony J, Hoffmann MD, Niopek D 2020. Optogenetics and CRISPR: a new relationship built to last. Methods Mol. Biol. 2173:261–81
    [Google Scholar]
  121. 121. 
    Morikawa K, Furuhashi K, de Sena-Tomas C, Garcia-Garcia AL, Bekdash R et al. 2020. Photoactivatable Cre recombinase 3.0 for in vivo mouse applications. Nat. Commun. 11:2141
    [Google Scholar]
  122. 122. 
    Meador K, Wysoczynski CL, Norris AJ, Aoto J, Bruchas MR, Tucker CL 2019. Achieving tight control of a photoactivatable Cre recombinase gene switch: new design strategies and functional characterization in mammalian cells and rodent. Nucleic Acids Res 47:e97
    [Google Scholar]
  123. 123. 
    Jung H, Kim SW, Kim M, Hong J, Yu D et al. 2019. Noninvasive optical activation of Flp recombinase for genetic manipulation in deep mouse brain regions. Nat. Commun. 10:314
    [Google Scholar]
  124. 124. 
    Goglia AG, Toettcher JE. 2019. A bright future: optogenetics to dissect the spatiotemporal control of cell behavior. Curr. Opin. Chem. Biol. 48:106–13
    [Google Scholar]
  125. 125. 
    van Bergeijk P, Hoogenraad CC, Kapitein LC 2016. Right time, right place: probing the functions of organelle positioning. Trends Cell Biol 26:121–34
    [Google Scholar]
  126. 126. 
    Shin Y, Brangwynne CP. 2017. Liquid phase condensation in cell physiology and disease. Science357:eaaf4382
    [Google Scholar]
  127. 127. 
    Duan L, Che D, Zhang K, Ong Q, Guo S, Cui B 2015. Optogenetic control of molecular motors and organelle distributions in cells. Chem. Biol. 22:671–82
    [Google Scholar]
  128. 128. 
    van Bergeijk P, Adrian M, Hoogenraad CC, Kapitein LC 2015. Optogenetic control of organelle transport and positioning. Nature 518:111–14
    [Google Scholar]
  129. 129. 
    Gil AA, Carrasco-López C, Zhu L, Zhao EM, Ravindran PT et al. 2020. Optogenetic control of protein binding using light-switchable nanobodies. Nat. Commun. 11:4044
    [Google Scholar]
  130. 130. 
    Pertz O, Hodgson L, Klemke RL, Hahn KM 2006. Spatiotemporal dynamics of RhoA activity in migrating cells. Nature 440:1069–72
    [Google Scholar]
  131. 131. 
    Krishnamurthy VV, Khamo JS, Mei W, Turgeon AJ, Ashraf HM et al. 2016. Reversible optogenetic control of kinase activity during differentiation and embryonic development. Development 143:4085–94
    [Google Scholar]
  132. 132. 
    Regev A, Shapiro E. 2002. Cellular abstractions: cells as computation. Nature 419:343
    [Google Scholar]
  133. 133. 
    Eungdamrong NJ, Iyengar R. 2004. Computational approaches for modeling regulatory cellular networks. Trends Cell Biol 14:661–69
    [Google Scholar]
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