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Illuminating cell signalling with optogenetic tools

Nature Reviews Molecular Cell Biology volume 15, pages 551–558 (2014)Cite this article

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Abstract

The light-based control of ion channels has been transformative for the neurosciences, but the optogenetic toolkit does not stop there. An expanding number of proteins and cellular functions have been shown to be controlled by light, and the practical considerations in deciding between reversible optogenetic systems (such as systems that use light-oxygen-voltage domains, phytochrome proteins, cryptochrome proteins and the fluorescent protein Dronpa) are well defined. The field is moving beyond proof of concept to answering real biological questions, such as how cell signalling is regulated in space and time, that were difficult or impossible to address with previous tools.

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Figure 1: Different strategies for optogenetic inputs.
Figure 2: Optogenetics for in vivo biochemistry.
Figure 3: Optogenetic control of signals in space.
Figure 4: Optogenetic control of signals in time.

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References

  1. Kaplan, J. H., Forbush, B. & Hoffman, J. F. Rapid photolytic release of adenosine 5′-triphosphate from a protected analogue: utilization by the Na:K pump of human red blood cell ghosts. Biochemistry 17, 1929–1935 (1978).

    Article  CAS  PubMed  Google Scholar 

  2. Callaway, E. M. & Katz, L. C. Photostimulation using caged glutamate reveals functional circuitry in living brain slices. Proc. Natl Acad. Sci. USA 90, 7661–7665 (1993).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Zemelman, B. V., Lee, G. A., Ng, M. & Miesenbock, G. Selective photostimulation of genetically chARGed neurons. Neuron 33, 15–22 (2002).

    Article  CAS  PubMed  Google Scholar 

  4. Boyden, E. S., Zhang, F., Bamberg, E., Nagel, G. & Deisseroth, K. Millisecond-timescale, genetically targeted optical control of neural activity. Nature Neurosci. 8, 1263–1268 (2005).

    Article  CAS  PubMed  Google Scholar 

  5. Li, X. et al. Fast noninvasive activation and inhibition of neural and network activity by vertebrate rhodopsin and green algae channelrhodopsin. Proc. Natl Acad. Sci. USA 102, 17816–17821 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  7. Arrenberg, A. B., Stainier, D. Y., Baier, H. & Huisken, J. Optogenetic control of cardiac function. Science 330, 971–974 (2010).

    Article  CAS  PubMed  Google Scholar 

  8. Tsai, H. C. et al. Phasic firing in dopaminergic neurons is sufficient for behavioral conditioning. Science 324, 1080–1084 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Liu, H. et al. Photoexcited CRY2 interacts with CIB1 to regulate transcription and floral initiation in Arabidopsis. Science 322, 1535–1539 (2008).

    Article  CAS  PubMed  Google Scholar 

  10. Kennedy, M. J. et al. Rapid blue-light-mediated induction of protein interactions in living cells. Nature Methods 7, 973–975 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Bugaj, L. J., Choksi, A. T., Mesuda, C. K., Kane, R. S. & Schaffer, D. V. Optogenetic protein clustering and signaling activation in mammalian cells. Nature Methods 10, 249–252 (2013).

    Article  CAS  PubMed  Google Scholar 

  12. Christie, J. M., Salomon, M., Nozue, K., Wada, M. & Briggs, W. R. LOV (light, oxygen, or voltage) domains of the blue-light photoreceptor phototropin (nph1): binding sites for the chromophore flavin mononucleotide. Proc. Natl Acad. Sci. USA 96, 8779–8783 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Harper, S. M., Neil, L. C. & Gardner, K. H. Structural basis of a phototropin light switch. Science 301, 1541–1544 (2003).

    Article  CAS  PubMed  Google Scholar 

  14. Wu, Y. I. et al. A genetically encoded photoactivatable Rac controls the motility of living cells. Nature 461, 104–108 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Strickland, D. et al. TULIPs: tunable, light-controlled interacting protein tags for cell biology. Nature Methods 9, 379–384 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Ni, M., Tepperman, J. M. & Quail, P. H. Binding of phytochrome B to its nuclear signalling partner PIF3 is reversibly induced by light. Nature 400, 781–784 (1999).

    Article  CAS  PubMed  Google Scholar 

  17. Shimizu-Sato, S., Huq, E., Tepperman, J. M. & Quail, P. H. A light-switchable gene promoter system. Nature Biotech. 20, 1041–1044 (2002).

    Article  CAS  Google Scholar 

  18. Levskaya, A., Weiner, O. D., Lim, W. A. & Voigt, C. A. Spatiotemporal control of cell signalling using a light-switchable protein interaction. Nature 461, 997–1001 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Zhou, X. X., Chung, H. K., Lam, A. J. & Lin, M. Z. Optical control of protein activity by fluorescent protein domains. Science 338, 810–814 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Ando, R., Mizuno, H. & Miyawaki, A. Regulated fast nucleocytoplasmic shuttling observed by reversible protein highlighting. Science 306, 1370–1373 (2004).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Ryu, M. H., Moskvin, O. V., Siltberg-Liberles, J. & Gomelsky, M. Natural and engineered photoactivated nucleotidyl cyclases for optogenetic applications. J. Biol. Chem. 285, 41501–41508 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Stierl, M. et al. Light modulation of cellular cAMP by a small bacterial photoactivated adenylyl cyclase, bPAC, of the soil bacterium Beggiatoa. J. Biol. Chem. 286, 1181–1188 (2011).

    Article  CAS  PubMed  Google Scholar 

  24. Airan, R. D., Thompson, K. R., Fenno, L. E., Bernstein, H. & Deisseroth, K. Temporally precise in vivo control of intracellular signalling. Nature 458, 1025–1029 (2009).

    Article  CAS  PubMed  Google Scholar 

  25. Karunarathne, W. K., Giri, L., Patel, A. K., Venkatesh, K. V. & Gautam, N. Optical control demonstrates switch-like PIP3 dynamics underlying the initiation of immune cell migration. Proc. Natl Acad. Sci. USA 110, E1575–E1583 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  26. Chen, D., Gibson, E. S. & Kennedy, M. J. A light-triggered protein secretion system. J. Cell Biol. 201, 631–640 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Crefcoeur, R. P., Yin, R., Ulm, R. & Halazonetis, T. D. Ultraviolet-B-mediated induction of protein–protein interactions in mammalian cells. Nature Commun. 4, 1779 (2013).

    Article  Google Scholar 

  28. Yazawa, M., Sadaghiani, A. M., Hsueh, B. & Dolmetsch, R. E. Induction of protein-protein interactions in live cells using light. Nature Biotech. 27, 941–945 (2009).

    Article  CAS  Google Scholar 

  29. Bonger, K. M., Rakhit, R., Payumo, A. Y., Chen, J. K. & Wandless, T. J. General method for regulating protein stability with light. ACS Chem. Biol. 9, 111–115 (2014).

    Article  CAS  PubMed  Google Scholar 

  30. Gambetta, G. A. & Lagarias, J. C. Genetic engineering of phytochrome biosynthesis in bacteria. Proc. Natl Acad. Sci. USA 98, 10566–10571 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Muller, K. et al. Synthesis of phycocyanobilin in mammalian cells. Chem. Commun. (Camb.) 49, 8970–8972 (2013).

    Article  Google Scholar 

  32. Mas, P., Devlin, P. F., Panda, S. & Kay, S. A. Functional interaction of phytochrome B and cryptochrome 2. Nature 408, 207–211 (2000).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  34. Motta-Mena, L. B. et al. An optogenetic gene expression system with rapid activation and deactivation kinetics. Nature Chem. Biol. 10, 196–202 (2014).

    Article  CAS  Google Scholar 

  35. Idevall-Hagren, O., Dickson, E. J., Hille, B., Toomre, D. K. & De Camilli, P. Optogenetic control of phosphoinositide metabolism. Proc. Natl Acad. Sci. USA 109, E2316–E2323 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Wend, S. et al. Optogenetic control of protein kinase activity in mammalian cells. ACS Synth. Biol. 3, 280–285 (2013).

    Article  PubMed  Google Scholar 

  37. Leung, D. W., Otomo, C., Chory, J. & Rosen, M. K. Genetically encoded photoswitching of actin assembly through the Cdc42–WASP–Arp2/3 complex pathway. Proc. Natl Acad. Sci. USA 105, 12797–12802 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Yang, X., Jost, A. P., Weiner, O. D. & Tang, C. A light-inducible organelle targeting system for dynamically activating and inactivating signaling in budding yeast. Mol. Biol. Cell 24, 2419–2430 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Toettcher, J. E., Gong, D., Lim, W. A. & Weiner, O. D. Light-based feedback for controlling intracellular signaling dynamics. Nature Methods 8, 837–839 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Toettcher, J. E., Weiner, O. D. & Lim, W. A. Using optogenetics to interrogate the dynamic control of signal transmission by the Ras/Erk module. Cell 155, 1422–1434 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Konermann, S. et al. Optical control of mammalian endogenous transcription and epigenetic states. Nature 500, 472–476 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Lungu, O. I. et al. Designing photoswitchable peptides using the AsLOV2 domain. Chem. Biol. 19, 507–517 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Tyszkiewicz, A. B. & Muir, T. W. Activation of protein splicing with light in yeast. Nature Methods 5, 303–305 (2008).

    Article  CAS  PubMed  Google Scholar 

  44. Cao, J. et al. Light-inducible activation of target mRNA translation in mammalian cells. Chem. Commun. 49, 8338–8340 (2013).

    Article  CAS  Google Scholar 

  45. Lee, S. et al. Reversible protein inactivation by optogenetic trapping in cells. Nature Methods 11, 633–636 (2014).

    Article  CAS  PubMed  Google Scholar 

  46. Rao, M. V., Chu, P. H., Hahn, K. M. & Zaidel-Bar, R. An optogenetic tool for the activation of endogenous diaphanous-related formins induces thickening of stress fibers without an increase in contractility. Cytoskeleton 70, 394–407 (2013).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  48. Wang, X., He, L., Wu, Y. I., Hahn, K. M. & Montell, D. J. Light-mediated activation reveals a key role for Rac in collective guidance of cell movement in vivo. Nature Cell Biol. 12, 591–597 (2010).

    Article  CAS  PubMed  Google Scholar 

  49. Yoo, S. K. et al. Differential regulation of protrusion and polarity by PI3K during neutrophil motility in live zebrafish. Dev. Cell 18, 226–236 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Toettcher, J. E., Gong, D., Lim, W. A. & Weiner, O. D. Light control of plasma membrane recruitment using the Phy–PIF system. Methods Enzymol. 497, 409–423 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Spencer, S. L., Gaudet, S., Albeck, J. G., Burke, J. M. & Sorger, P. K. Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis. Nature 459, 428–432 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Haber, J. E. In vivo biochemistry: physical monitoring of recombination induced by site-specific endonucleases. Bioessays 17, 609–620 (1995).

    Article  CAS  PubMed  Google Scholar 

  53. Ferrell, J. E. Jr & Machleder, E. M. The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes. Science 280, 895–898 (1998).

    Article  CAS  PubMed  Google Scholar 

  54. Shimizu, T. S., Tu, Y. & Berg, H. C. A modular gradient-sensing network for chemotaxis in Escherichia coli revealed by responses to time-varying stimuli. Mol. Syst. Biol. 6, 382 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  55. Goentoro, L., Shoval, O., Kirschner, M. W. & Alon, U. The incoherent feedforward loop can provide fold-change detection in gene regulation. Mol. Cell 36, 894–899 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Wartlick, O. et al. Dynamics of Dpp signaling and proliferation control. Science 331, 1154–1159 (2011).

    Article  CAS  PubMed  Google Scholar 

  57. Devreotes, P. N. & Zigmond, S. H. Chemotaxis in eukaryotic cells: a focus on leukocytes and Dictyostelium. Annu. Rev. Cell Biol. 4, 649–686 (1988).

    Article  CAS  PubMed  Google Scholar 

  58. Hartline, H. K., Wagner, H. G. & Ratliff, F. Inhibition in the eye of Limulus. J. Gen. Physiol. 39, 651–673 (1956).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Purvis, J. E. & Lahav, G. Encoding and decoding cellular information through signaling dynamics. Cell 152, 945–956 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Santos, S. D., Verveer, P. J. & Bastiaens, P. I. Growth factor-induced MAPK network topology shapes Erk response determining PC-12 cell fate. Nature Cell Biol. 9, 324–330 (2007).

    Article  CAS  PubMed  Google Scholar 

  61. Purvis, J. E. et al. p53 dynamics control cell fate. Science 336, 1440–1444 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Zhang, K. et al. Light-mediated kinetic control reveals the temporal effect of the Raf/MEK/ERK pathway in PC12 cell neurite outgrowth. PLoS ONE 9, e92917 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  63. Takala, H. et al. Signal amplification and transduction in phytochrome photosensors. Nature 509, 245–248 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Kim, J. I. et al. Phytochrome phosphorylation modulates light signaling by influencing the protein–protein interaction. Plant Cell 16, 2629–2640 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Medzihradszky, M. et al. Phosphorylation of phytochrome B inhibits light-induced signaling via accelerated dark reversion in Arabidopsis. Plant Cell 25, 535–544 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Hughes, R. M., Vrana, J. D., Song, J. & Tucker, C. L. Light-dependent, dark-promoted interaction between Arabidopsis cryptochrome 1 and phytochrome B proteins. J. Biol. Chem. 287, 22165–22172 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Strickland, D. et al. Rationally improving LOV domain-based photoswitches. Nature Methods 7, 623–626 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Loewer, A., Karanam, K., Mock, C. & Lahav, G. The p53 response in single cells is linearly correlated to the number of DNA breaks without a distinct threshold. BMC Biol. 11, 114 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  69. Burgie, E. S., Bussell, A. N., Walker J.M., Dubiel K. & Vierstra R.D. Crystal structure of the photosensing module from a red/far-red light-absorbing plant phytochrome. Proc. Natl Acad. Sci. USA (in the press).

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Acknowledgements

The authors thank members of the Weiner laboratory for helpful discussions. This work was supported by a Genentech Fellowship (D.T.) and US National Institutes of Health (NIH) grants GM084040, GM096164 and GM109899 (O.D.W.).

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  1. Cardiovascular Research Institute and Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, 94158–9001, California, USA

    Doug Tischer & Orion D. Weiner

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Correspondence to Orion D. Weiner.

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Tischer, D., Weiner, O. Illuminating cell signalling with optogenetic tools. Nat Rev Mol Cell Biol 15, 551–558 (2014). https://doi.org/10.1038/nrm3837

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