1932

Abstract

Superresolution fluorescence microscopy permits the study of biological processes at scales small enough to visualize fine subcellular structures that are unresolvable by traditional diffraction-limited light microscopy. Many superresolution techniques, including those applicable to live cell imaging, utilize genetically encoded photocontrollable fluorescent proteins. The fluorescence of these proteins can be controlled by light of specific wavelengths. In this review, we discuss the biochemical and photophysical properties of photocontrollable fluorescent proteins that are relevant to their use in superresolution microscopy. We then describe the recently developed photoactivatable, photoswitchable, and reversibly photoswitchable fluorescent proteins, and we detail their particular usefulness in single-molecule localization–based and nonlinear ensemble–based superresolution techniques. Finally, we discuss recent applications of photocontrollable proteins in superresolution imaging, as well as how these applications help to clarify properties of intracellular structures and processes that are relevant to cell and developmental biology, neuroscience, cancer biology and biomedicine.

Keyword(s): EosFPPAGFPPALMPAmCherryRESOLFT
Loading

Article metrics loading...

/content/journals/10.1146/annurev-biophys-051013-022836
2014-05-06
2024-06-17
Loading full text...

Full text loading...

/deliver/fulltext/biophys/43/1/annurev-biophys-051013-022836.html?itemId=/content/journals/10.1146/annurev-biophys-051013-022836&mimeType=html&fmt=ahah

Literature Cited

  1. Adam V, Lelimousin M, Boehme S, Desfonds G, Nienhaus K. 1.  et al. 2008. Structural characterization of IrisFP, an optical highlighter undergoing multiple photo-induced transformations. Proc. Natl. Acad. Sci. USA 105:18343–48 [Google Scholar]
  2. Adam V, Moeyaert B, David CC, Mizuno H, Lelimousin M. 2.  et al. 2011. Rational design of photoconvertible and biphotochromic fluorescent proteins for advanced microscopy applications. Chem. Biol. 18:1241–51 [Google Scholar]
  3. Ando R, Mizuno H, Miyawaki A. 3.  2004. Regulated fast nucleocytoplasmic shuttling observed by reversible protein highlighting. Science 306:1370–73 [Google Scholar]
  4. Andresen M, Stiel AC, Folling J, Wenzel D, Schonle A. 4.  et al. 2008. Photoswitchable fluorescent proteins enable monochromatic multilabel imaging and dual color fluorescence nanoscopy. Nat. Biotechnol. 26:1035–40 [Google Scholar]
  5. Annibale P, Vanni S, Scarselli M, Rothlisberger U, Radenovic A. 5.  2011. Quantitative photo activated localization microscopy: unraveling the effects of photoblinking. PLoS ONE 6:e22678 [Google Scholar]
  6. Betzig E, Patterson GH, Sougrat R, Lindwasser OW, Olenych S. 6.  et al. 2006. Imaging intracellular fluorescent proteins at nanometer resolution. Science 313:1642–45 [Google Scholar]
  7. Brakemann T, Stiel AC, Weber G, Andresen M, Testa I. 7.  et al. 2011. A reversibly photoswitchable GFP-like protein with fluorescence excitation decoupled from switching. Nat. Biotechnol. 29:942–47Dreiklang performs well in both PALM and RESOLFT owing to its fatigue resistance and photoswitching decoupled from excitation. [Google Scholar]
  8. Bulina ME, Verkhusha VV, Staroverov DB, Chudakov DM, Lukyanov KA. 8.  2003. Heterooligomeric tagging diminishes non-specific aggregation of target proteins fused with Anthozoa fluorescent proteins. Biochem. J. 371:109–114 [Google Scholar]
  9. Chang H, Zhang M, Ji W, Chen J, Zhang Y. 9.  et al. 2012. A unique series of reversibly switchable fluorescent proteins with beneficial properties for various applications. Proc. Natl. Acad. Sci. USA 109:4455–60 [Google Scholar]
  10. Chmyrov A, Keller J, Grotjohann T, Ratz M, d'Este E. 10.  et al. 2013. Nanoscopy with more than 100,000 ‘doughnuts.’. Nat. Methods 10:737–40Parallelized RESOLFT allows substantially faster image-acquisition speed than does point-scanning RESOLFT. [Google Scholar]
  11. Chudakov DM, Verkhusha VV, Staroverov DB, Souslova EA, Lukyanov S, Lukyanov KA. 11.  2004. Photoswitchable cyan fluorescent protein for protein tracking. Nat. Biotechnol. 22:1435–39 [Google Scholar]
  12. Chudakov DM, Matz MV, Lukyanov S, Lukyanov KA. 12.  2010. Fluorescent proteins and their applications in imaging living cells and tissues. Physiol. Rev. 90:1103–63 [Google Scholar]
  13. Chudakov DM, Lukyanov S, Lukyanov KA. 13.  2007. Tracking intracellular protein movements using photoswitchable fluorescent proteins PS-CFP2 and Dendra2. Nat. Protoc. 2:2024–32 [Google Scholar]
  14. Cox S, Rosten E, Monypenny J, Jovanovic-Talisman T, Burnette DT. 14.  et al. 2012. Bayesian localization microscopy reveals nanoscale podosome dynamics. Nat. Methods 9:195–200 [Google Scholar]
  15. Dedecker P, Hotta J, Flors C, Sliwa M, Uji-i H. 15.  et al. 2007. Subdiffraction imaging through the selective donut-mode depletion of thermally stable photoswitchable fluorophores: numerical analysis and application to the fluorescent protein Dronpa. J. Am. Chem. Soc. 129:16132–41 [Google Scholar]
  16. Dedecker P, Mo GC, Dertinger T, Zhang J. 16.  2012. Widely accessible method for superresolution fluorescence imaging of living systems. Proc. Natl. Acad. Sci. USA 109:10909–14 [Google Scholar]
  17. Dickson RM, Cubitt AB, Tsien RY, Moerner WE. 17.  1997. On/off blinking and switching behaviour of single molecules of green fluorescent protein. Nature 388:355–58 [Google Scholar]
  18. Egner A, Geisler C, von Middendorff C, Bock H, Wenzel D. 18.  et al. 2007. Fluorescence nanoscopy in whole cells by asynchronous localization of photoswitching emitters. Biophys. J. 93:3285–90 [Google Scholar]
  19. Flors C, Hotta J, Uji-i H, Dedecker P, Ando R. 19.  et al. 2007. A stroboscopic approach for fast photoactivation-localization microscopy with Dronpa mutants. J. Am. Chem. Soc. 129:13970–71 [Google Scholar]
  20. Folling J, Bossi M, Bock H, Medda R, Wurm CA. 20.  et al. 2008. Fluorescence nanoscopy by ground-state depletion and single-molecule return. Nat. Methods 5:943–45 [Google Scholar]
  21. Fuchs J, Bohme S, Oswald F, Hedde PN, Krause M. 21.  et al. 2010. A photoactivatable marker protein for pulse-chase imaging with superresolution. Nat. Methods 7:627–30mIrisFP undergoes green-to-red irreversible and dark-to-fluorescent reversible photoswitching, allowing pulse-chase imaging in two-color PALM. [Google Scholar]
  22. Gould TJ, Gunewardene MS, Gudheti MV, Verkhusha VV, Yin SR. 22.  et al. 2008. Nanoscale imaging of molecular positions and anisotropies. Nat. Methods 5:1027–30 [Google Scholar]
  23. Gould TJ, Verkhusha VV, Hess ST. 23.  2009. Imaging biological structures with fluorescence photoactivation localization microscopy. Nat. Protoc. 4:291–308 [Google Scholar]
  24. Greenfield D, McEvoy AL, Shroff H, Crooks GE, Wingreen NS. 24.  et al. 2009. Self-organization of the Escherichia coli chemotaxis network imaged with super-resolution light microscopy. PLoS Biol. 7:e1000137 [Google Scholar]
  25. Grotjohann T, Testa I, Leutenegger M, Bock H, Urban NT. 25.  et al. 2011. Diffraction-unlimited all-optical imaging and writing with a photochromic GFP. Nature 478:204–8Discusses the high fatigue resistance of rsEGFP enables RESOLFT of live cells and provides a conceptual basis of RESOLFT. [Google Scholar]
  26. Grotjohann T, Testa I, Reuss M, Brakemann T, Eggeling C. 26.  et al. 2012. rsEGFP2 enables fast RESOLFT nanoscopy of living cells. eLIFE 1:e00248 [Google Scholar]
  27. Gunewardene MS, Subach FV, Gould TJ, Penoncello GP, Gudheti MV. 27.  et al. 2011. Superresolution imaging of multiple fluorescent proteins with highly overlapping emission spectra in living cells. Biophys. J. 101:1522–28 [Google Scholar]
  28. Gurskaya NG, Verkhusha VV, Shcheglov AS, Staroverov DB, Chepurnykh TV. 28.  et al. 2006. Engineering of a monomeric green-to-red photoactivatable fluorescent protein induced by blue light. Nat. Biotechnol. 24:461–65 [Google Scholar]
  29. Gustafsson MG. 29.  2005. Nonlinear structured-illumination microscopy: wide-field fluorescence imaging with theoretically unlimited resolution. Proc. Natl. Acad. Sci. USA 102:13081–86 [Google Scholar]
  30. Habuchi S, Ando R, Dedecker P, Verheijen W, Mizuno H. 30.  et al. 2005. Reversible single-molecule photoswitching in the GFP-like fluorescent protein Dronpa. Proc. Natl. Acad. Sci. USA 102:9511–16 [Google Scholar]
  31. Habuchi S, Tsutsui H, Kochaniak AB, Miyawaki A, van Oijen AM. 31.  2008. mKikGR, a monomeric photoswitchable fluorescent protein. PLoS ONE 3:e3944 [Google Scholar]
  32. Hell SW. 32.  2003. Toward fluorescence nanoscopy. Nat. Biotechnol. 21:1347–55 [Google Scholar]
  33. Hell SW. 33.  2007. Far-field optical nanoscopy. Science 316:1153–58 [Google Scholar]
  34. Hell SW. 34.  2009. Microscopy and its focal switch. Nat. Methods 6:24–32 [Google Scholar]
  35. Hell SW, Wichmann J. 35.  1994. Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy. Opt. Lett. 19:780–82 [Google Scholar]
  36. Hess ST, Girirajan TP, Mason MD. 36.  2006. Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. Biophys. J. 91:4258–72 [Google Scholar]
  37. Hess ST, Gould TJ, Gudheti MV, Maas SA, Mills KD, Zimmerberg J. 37.  2007. Dynamic clustered distribution of hemagglutinin resolved at 40 nm in living cell membranes discriminates between raft theories. Proc. Natl. Acad. Sci. USA 104:17370–75 [Google Scholar]
  38. Hofmann M, Eggeling C, Jakobs S, Hell SW. 38.  2005. Breaking the diffraction barrier in fluorescence microscopy at low light intensities by using reversibly photoswitchable proteins. Proc. Natl. Acad. Sci. USA 102:17565–69 [Google Scholar]
  39. Hoi H, Shaner NC, Davidson MW, Cairo CW, Wang J, Campbell RE. 39.  2010. A monomeric photoconvertible fluorescent protein for imaging of dynamic protein localization. J. Mol. Biol. 401:776–91 [Google Scholar]
  40. Holden SJ, Uphoff S, Kapanidis AN. 40.  2011. DAOSTORM: an algorithm for high-density super-resolution microscopy. Nat. Methods 8:279–80 [Google Scholar]
  41. Hoze N, Nair D, Hosy E, Sieben C, Manley S. 41.  et al. 2012. Heterogeneity of AMPA receptor trafficking and molecular interactions revealed by superresolution analysis of live cell imaging. Proc. Natl. Acad. Sci. USA 109:17052–57 [Google Scholar]
  42. Huang B, Wang W, Bates M, Zhuang X. 42.  2008. Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy. Science 319:810–13 [Google Scholar]
  43. Huang B, Babcock H, Zhuang X. 43.  2010. Breaking the diffraction barrier: super-resolution imaging of cells. Cell 143:1047–58 [Google Scholar]
  44. Huang F, Hartwich TM, Rivera-Molina FE, Lin Y, Duim WC. 44.  et al. 2013. Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms. Nat. Methods 10:653–58 [Google Scholar]
  45. Huang F, Schwartz SL, Byars JM, Lidke KA. 45.  2011. Simultaneous multiple-emitter fitting for single molecule super-resolution imaging. Biomed. Opt. Express 2:1377–93 [Google Scholar]
  46. Joo C, Balci H, Ishitsuka Y, Buranachai C, Ha T. 46.  2008. Advances in single-molecule fluorescence methods for molecular biology. Annu. Rev. Biochem. 77:51–76 [Google Scholar]
  47. Juette MF, Gould TJ, Lessard MD, Mlodzianoski MJ, Nagpure BS. 47.  et al. 2008. Three-dimensional sub–100 nm resolution fluorescence microscopy of thick samples. Nat. Methods 5:527–29 [Google Scholar]
  48. Kanchanawong P, Shtengel G, Pasapera AM, Ramko EB, Davidson MW. 48.  et al. 2010. Nanoscale architecture of integrin-based cell adhesions. Nature 468:580–84 [Google Scholar]
  49. Kopek BG, Shtengel G, Xu CS, Clayton DA, Hess HF. 49.  2012. Correlative 3D superresolution fluorescence and electron microscopy reveal the relationship of mitochondrial nucleoids to membranes. Proc. Natl. Acad. Sci. USA 109:6136–41 [Google Scholar]
  50. Lee SH, Shin JY, Lee A, Bustamante C. 50.  2012. Counting single photoactivatable fluorescent molecules by photoactivated localization microscopy (PALM). Proc. Natl. Acad. Sci. USA 109:17436–41 [Google Scholar]
  51. Manley S, Gillette JM, Patterson GH, Shroff H, Hess HF. 51.  et al. 2008. High-density mapping of single-molecule trajectories with photoactivated localization microscopy. Nat. Methods 5:155–57 [Google Scholar]
  52. Manley S, Gunzenhauser J, Olivier N. 52.  2011. A starter kit for point-localization super-resolution imaging. Curr. Opin. Chem. Biol. 15:813–21 [Google Scholar]
  53. McEvoy AL, Hoi H, Bates M, Platonova E, Cranfill PJ. 53.  et al. 2012. mMaple: a photoconvertible fluorescent protein for use in multiple imaging modalities. PLoS ONE 7:e51314 [Google Scholar]
  54. McKinney SA, Murphy CS, Hazelwood KL, Davidson MW, Looger LL. 54.  2009. A bright and photostable photoconvertible fluorescent protein. Nat. Methods 6:131–33 [Google Scholar]
  55. Mizuno H, Dedecker P, Ando R, Fukano T, Hofkens J, Miyawaki A. 55.  2010. Higher resolution in localization microscopy by slower switching of a photochromic protein. Photochem. Photobiol. Sci. 9:239–48 [Google Scholar]
  56. Nieuwenhuizen RP, Lidke KA, Bates M, Puig DL, Grunwald D. 56.  et al. 2013. Measuring image resolution in optical nanoscopy. Nat. Methods 10:557–62 [Google Scholar]
  57. Patterson G, Davidson M, Manley S, Lippincott-Schwartz J. 57.  2010. Superresolution imaging using single-molecule localization. Annu. Rev. Phys. Chem. 61:345–67 [Google Scholar]
  58. Patterson GH, Lippincott-Schwartz J. 58.  2002. A photoactivatable GFP for selective photolabeling of proteins and cells. Science 297:1873–77 [Google Scholar]
  59. Post JN, Lidke KA, Rieger B, Arndt-Jovin DJ. 59.  2005. One- and two-photon photoactivation of a paGFP-fusion protein in live Drosophila embryos. FEBS Lett. 579:325–30 [Google Scholar]
  60. Rego EH, Shao L, Macklin JJ, Winoto L, Johansson GA. 60.  et al. 2012. Nonlinear structured-illumination microscopy with a photoswitchable protein reveals cellular structures at 50-nm resolution. Proc. Natl. Acad. Sci. USA 109:E135–43 [Google Scholar]
  61. Renz M, Daniels BR, Vamosi G, Arias IM, Lippincott-Schwartz J. 61.  2012. Plasticity of the asialoglycoprotein receptor deciphered by ensemble FRET imaging and single-molecule counting PALM imaging. Proc. Natl. Acad. Sci. USA 109:E2989–97 [Google Scholar]
  62. Rossi A, Moritz TJ, Ratelade J, Verkman AS. 62.  2012. Super-resolution imaging of aquaporin-4 orthogonal arrays of particles in cell membranes. J. Cell Sci. 125:4405–12 [Google Scholar]
  63. Rust MJ, Bates M, Zhuang X. 63.  2006. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat. Methods 3:793–95 [Google Scholar]
  64. Sengupta P, Jovanovic-Talisman T, Skoko D, Renz M, Veatch SL, Lippincott-Schwartz J. 64.  2011. Probing protein heterogeneity in the plasma membrane using PALM and pair correlation analysis. Nat. Methods 8:969–75Combination of PALM with pair-correlation analysis enables studies of protein clusters, their size, their density, and their abundance in plasma membrane. [Google Scholar]
  65. Sengupta P, Lippincott-Schwartz J. 65.  2012. Quantitative analysis of photoactivated localization microscopy (PALM) datasets using pair-correlation analysis. BioEssays 34:396–405 [Google Scholar]
  66. Sengupta P, Van Engelenburg S, Lippincott-Schwartz J. 66.  2012. Visualizing cell structure and function with point-localization superresolution imaging. Dev. Cell 23:1092–102 [Google Scholar]
  67. Shannon CE. 67.  1949. Communication in the presence of noise. Proc. IRE 37:10–21 [Google Scholar]
  68. Sherman E, Barr V, Manley S, Patterson G, Balagopalan L. 68.  et al. 2011. Functional nanoscale organization of signaling molecules downstream of the T cell antigen receptor. Immunity 35:705–20 [Google Scholar]
  69. Shroff H, Galbraith CG, Galbraith JA, Betzig E. 69.  2008. Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics. Nat. Methods 5:417–23 [Google Scholar]
  70. Shroff H, Galbraith CG, Galbraith JA, White H, Gillette J. 70.  et al. 2007. Dual-color superresolution imaging of genetically expressed probes within individual adhesion complexes. Proc. Natl. Acad. Sci. USA 104:20308–13 [Google Scholar]
  71. Shtengel G, Galbraith JA, Galbraith CG, Lippincott-Schwartz J, Gillette JM. 71.  et al. 2009. Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure. Proc. Natl. Acad. Sci. USA 106:3125–30 [Google Scholar]
  72. Smith CS, Joseph N, Rieger B, Lidke KA. 72.  2010. Fast, single-molecule localization that achieves theoretically minimum uncertainty. Nat. Methods 7:373–75 [Google Scholar]
  73. Stiel AC, Andresen M, Bock H, Hilbert M, Schilde J. 73.  et al. 2008. Generation of monomeric reversibly switchable red fluorescent proteins for far-field fluorescence nanoscopy. Biophys. J. 95:2989–97 [Google Scholar]
  74. Stiel AC, Trowitzsch S, Weber G, Andresen M, Eggeling C. 74.  et al. 2007. 1.8 A bright-state structure of the reversibly switchable fluorescent protein Dronpa guides the generation of fast switching variants. Biochem. J. 402:35–42 [Google Scholar]
  75. Subach FV, Patterson GH, Manley S, Gillette JM, Lippincott-Schwartz J, Verkhusha VV. 75.  2009. Photoactivatable mCherry for high-resolution two-color fluorescence microscopy. Nat. Methods 6:153–59 [Google Scholar]
  76. Subach FV, Patterson GH, Renz M, Lippincott-Schwartz J, Verkhusha VV. 76.  2010. Bright monomeric photoactivatable red fluorescent protein for two-color super-resolution sptPALM of live cells. J. Am. Chem. Soc. 132:6481–91PATagRFP demonstrates advanced PALM properties and enables two-color single-particle tracking PALM together with PAGFP in live cells. [Google Scholar]
  77. Subach FV, Piatkevich KD, Verkhusha VV. 77.  2011. Directed molecular evolution to design advanced red fluorescent proteins. Nat. Methods 8:1019–26 [Google Scholar]
  78. Subach FV, Zhang L, Gadella TW, Gurskaya NG, Lukyanov KA, Verkhusha VV. 78.  2010. Red fluorescent protein with reversibly photoswitchable absorbance for photochromic FRET. Chem. Biol. 17:745–55rsTagRFP is characterized by high contrast and photochromism, allowing its use in various applications including two-color pcSOFI. [Google Scholar]
  79. Subach OM, Entenberg D, Condeelis JS, Verkhusha VV. 79.  2012. A FRET-facilitated photoswitching using an orange fluorescent protein with the fast photoconversion kinetics. J. Am. Chem. Soc. 134:14789–99Orange-to-far-red PSmOrange2 is photoswitched by noncytotoxic blue-green light and awaits its application in multicolor PALM. [Google Scholar]
  80. Subach OM, Patterson GH, Ting LM, Wang Y, Condeelis JS, Verkhusha VV. 80.  2011. A photoswitchable orange-to-far-red fluorescent protein, PSmOrange. Nat. Methods 8:771–77 [Google Scholar]
  81. Testa I, Urban NT, Jakobs S, Eggeling C, Willig KI, Hell SW. 81.  2012. Nanoscopy of living brain slices with low light levels. Neuron 75:992–1000 [Google Scholar]
  82. Thompson RE, Larson DR, Webb WW. 82.  2002. Precise nanometer localization analysis for individual fluorescent probes. Biophys. J. 82:2775–83Derives the equation for a precision of localization of single molecules in fluorescence imaging. [Google Scholar]
  83. Verkhusha VV, Sorkin A. 83.  2005. Conversion of the monomeric red fluorescent protein into a photoactivatable probe. Chem. Biol. 12:279–85 [Google Scholar]
  84. Wiedenmann J, Ivanchenko S, Oswald F, Schmitt F, Rocker C. 84.  et al. 2004. EosFP, a fluorescent marker protein with UV-inducible green-to-red fluorescence conversion. Proc. Natl. Acad. Sci. USA 101:15905–10 [Google Scholar]
  85. Williamson DJ, Owen DM, Rossy J, Magenau A, Wehrmann M. 85.  et al. 2011. Pre-existing clusters of the adaptor Lat do not participate in early T cell signaling events. Nat. Immunol. 12:655–62 [Google Scholar]
  86. York AG, Ghitani A, Vaziri A, Davidson MW, Shroff H. 86.  2011. Confined activation and subdiffractive localization enables whole-cell PALM with genetically expressed probes. Nat. Methods 8:327–33 [Google Scholar]
  87. Zhang M, Chang H, Zhang Y, Yu J, Wu L. 87.  et al. 2012. Rational design of true monomeric and bright photoactivatable fluorescent proteins. Nat. Methods 9:727–29mEos3.1 and mEos3.2 are optimized for monomeric behavior, enabling PALM imaging of fused membrane proteins at high local density. [Google Scholar]
  88. Zhu L, Zhang W, Elnatan D, Huang B. 88.  2012. Faster STORM using compressed sensing. Nat. Methods 9:721–23 [Google Scholar]
/content/journals/10.1146/annurev-biophys-051013-022836
Loading
/content/journals/10.1146/annurev-biophys-051013-022836
Loading

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error