Tracking single molecules at work in living cells

Nature Chemical Biology

Volumn 10, Issue 7, 2014, Pages 524-532

  Kusumi, Akihiro ^a,b   Tsunoyama, Taka A ^a,b   Hirosawa, Kohichiro M ^a   Kasai, Rinshi S ^a,b   Fujiwara, Takahiro K ^a  

^a KYOTO UNIVERSITY   (Japan)

^b KYOTO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

FLUORESCENT DYE; G PROTEIN COUPLED RECEPTOR; HOMODIMER; MESSENGER RNA; OLIGOMER; RNA POLYMERASE; TRANSCRIPTION FACTOR;

CELL INTERACTION; CELL TRACKING; FOCAL ADHESION; GENE CONTROL; IMAGING; MICROSCOPY; PRIORITY JOURNAL; REVIEW; SIGNAL TRANSDUCTION; STOICHIOMETRY;

ADAPTOR PROTEINS, SIGNAL TRANSDUCING; ANIMALS; BIOLOGICAL TRANSPORT; CELL TRACKING; EUKARYOTIC CELLS; FLUORESCENT DYES; GENE EXPRESSION REGULATION; GPI-LINKED PROTEINS; HUMANS; MEMBRANE PROTEINS; MICROSCOPY, FLUORESCENCE; PHOTONS; RECEPTORS, G-PROTEIN-COUPLED; SIGNAL TRANSDUCTION; STOCHASTIC PROCESSES;

EID: 84902772267     PISSN: 15524450     EISSN: 15524469     Source Type: Journal    
DOI: 10.1038/nchembio.1558     Document Type: Review

References (121)

1. Toomre, D. & Bewersdorf, J. A new wave of cellular imaging. Annu. Rev. Cell Dev. Biol. 26, 285-314 (2010).
2. Kusumi, A., Shirai, Y.M., Koyama-Honda, I., Suzuki, K.G.N. & Fujiwara, T.K. Hierarchical organization of the plasma membrane: Investigations by singlemolecule tracking vs. fluorescence correlation spectroscopy. FEBS Lett. 584, 1814-1823 (2010).
3. Triller, A. & Choquet, D. New concepts in synaptic biology derived from single-molecule imaging. Neuron 59, 359-374 (2008).
4. Haw, M. Middle World: The Restless Heart of Matter and Life (Macmillan, New York, 2007).
5. Murakoshi, H. et al. Single-molecule imaging analysis of Ras activation in living cells. Proc. Natl. Acad. Sci. USA 101, 7317-7322 (2004).
6. Kasai, R.S. et al. Full characterization of GPCR monomer-dimer dynamic equilibrium by single molecule imaging. J. Cell Biol. 192, 463-480 (2011).
7. Suzuki, K.G.N. et al. GPI-Anchored receptor clusters transiently recruit Lyn and G for temporary cluster immobilization and Lyn activation: Single-molecule tracking study 1. J. Cell Biol. 177, 717-730 (2007).
8. Suzuki, K.G.N.K., Fujiwara, T.K., Edidin, M.M. & Kusumi, A. Dynamic recruitment of phospholipase C gamma at transiently immobilized GPIanchored receptor clusters induces IP3-Ca2+ signaling: Single-molecule tracking study 2. J. Cell Biol. 177, 731-742 (2007).
9. Kasai, R.S. & Kusumi, A. Single-molecule imaging revealed dynamic GPCR dimerization. Curr. Opin. Cell Biol. 27, 78-86 (2014).
10. Zhang, J., Campbell, R.E., Ting, A.Y. & Tsien, R.Y. Creating new fluorescent probes for cell biology. Nat. Rev. Mol. Cell Biol. 3, 906-918 (2002).
11. Hinner, M.J. & Johnsson, K. How to obtain labeled proteins and what to do with them. Curr. Opin. Biotechnol. 21, 766-776 (2010).
12. Nishimura, H. et al. Biocompatible fluorescent silicon nanocrystals for singlemolecule tracking and fluorescence imaging. J. Cell Biol. 202, 967-983 (2013).
13. Ha, T. & Tinnefeld, P. Photophysics of fluorescent probes for single-molecule biophysics and super-resolution imaging. Annu. Rev. Phys. Chem. 63, 595-617 (2012).
14. Zheng, Q. et al. Ultra-stable organic fluorophores for single-molecule research. Chem. Soc. Rev. 43, 1044-1056 (2014).
15. Tokunaga, M., Imamoto, N. & Sakata-Sogawa, K. Highly inclined thin illumination enables clear single-molecule imaging in cells. Nat. Methods 5, 159-161 (2008).
16. Gustafsson, M.G.L. Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy. J. Microsc. 198, 82-87 (2000).
17. Jaqaman, K. et al. Robust single-particle tracking in live-cell time-lapse sequences. Nat. Methods 5, 695-702 (2008).
18. Hell, S.W. & Wichmann, J. Breaking the diffraction resolution limit by stimulated emission: Stimulated-emission-depletion fluorescence microscopy. Opt. Lett. 19, 780-782 (1994).
19. Ries, J. & Schwille, P. Fluorescence correlation spectroscopy. Bioessays 34, 361-368 (2012).
20. Pampaloni, F., Reynaud, E.G. & Stelzer, E.H.K. The third dimension bridges the gap between cell culture and live tissue. Nat. Rev. Mol. Cell Biol. 8, 839-845 (2007).
21. Carlton, P.M. et al. Fast live simultaneous multiwavelength four-dimensional optical microscopy. Proc. Natl. Acad. Sci. USA 107, 16016-16022 (2010).
22. Oida, T., Sako, Y. & Kusumi, A. Fluorescence lifetime imaging microscopy (flimscopy). Methodology development and application to studies of endosome fusion in single cells. Biophys. J. 64, 676-685 (1993).
23. Betzig, E. et al. Imaging intracellular fluorescent proteins at nanometer resolution. Science 313, 1642-1645 (2006).
24. Hess, S.T., Girirajan, T.P.K. & Mason, M.D. Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. Biophys. J. 91, 4258-4272 (2006).
25. Rust, M.J., Bates, M. & Zhuang, X. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat. Methods 3, 793-795 (2006).
26. Sahl, S.J. & Moerner, W.E. Super-resolution fluorescence imaging with single molecules. Curr. Opin. Struct. Biol. 23, 778-787 (2013).
27. Singer, S.J. & Nicolson, G.L. The fluid mosaic model of the structure of cell membranes. Science 175, 720-731 (1972).
28. Kusumi, A., Suzuki, K.G.N., Kasai, R.S., Ritchie, K. & Fujiwara, T.K. Hierarchical mesoscale domain organization of the plasma membrane. Trends Biochem. Sci. 36, 604-615 (2011).
29. Hiramoto-Yamaki, N. et al. Ultrafast diffusion of a fluorescent cholesterol analog in compartmentalized plasma membranes. Traffic 15, 583-612 (2014).
30. Kusumi, A. et al. Membrane mechanisms for signal transduction: The coupling of the meso-scale raft domains to membrane-skeleton-induced compartments and dynamic protein complexes. Semin. Cell Dev. Biol. 23, 126-144 (2012).
31. Morone, N. et al. Three-dimensional reconstruction of the membrane skeleton at the plasma membrane interface by electron tomography. J. Cell Biol. 174, 851-862 (2006).
32. Kalay, Z., Fujiwara, T.K. & Kusumi, A. Cellular Domains (ed. Nabi, I.R.) 3-22 (Wiley, New York, 2011).
33. Kusumi, A. et al. Dynamic organizing principles of the plasma membrane that regulate signal transduction: Commemorating the fortieth anniversary of Singer and Nicolson's fluid-mosaic model. Annu. Rev. Cell Dev. Biol. 28, 215-250 (2012).
34. Kalay, Z., Fujiwara, T.K. & Kusumi, A. Confining domains lead to reaction bursts: Reaction kinetics in the plasma membrane. PLoS ONE 7, e32948 (2012).
35. Jaqaman, K. & Grinstein, S. Regulation from within: The cytoskeleton in transmembrane signaling. Trends Cell Biol. 22, 515-526 (2012).
36. Oh, D., Yu, Y., Lee, H., Wanner, B.L. & Ritchie, K. Dynamics of the serine chemoreceptor in the Escherichia coli inner membrane: A high-speed singlemolecule tracking study. Biophys. J. 106, 145-153 (2014).
37. Murase, K. et al. Ultrafine membrane compartments for molecular diffusion as revealed by single molecule techniques. Biophys. J. 86, 4075-4093 (2004).
38. Jaqaman, K. et al. Cytoskeletal control of CD36 diffusion promotes its receptor and signaling function. Cell 146, 593-606 (2011).
39. Kusumi, A., Koyama-Honda, I. & Suzuki, K.G.N. Molecular dynamics and interactions for creation of stimulation-induced stabilized rafts from small unstable steady-state rafts. Traffic 5, 213-230 (2004).
40. Parton, R.G. Lipid rafts and plasma membrane microorganization: Insights from Ras. Trends Cell Biol. 14, 141-147 (2004).
41. Owen, D.M., Williamson, D., Rentero, C. & Gaus, K. Quantitative microscopy: Protein dynamics and membrane organisation. Traffic 10, 962-971 (2009).
42. Lingwood, D. & Simons, K. Lipid rafts as a membrane-organizing principle. Science 327, 46-50 (2010).
43. Simons, K. & Sampaio, J.L. Membrane organization and lipid rafts. Cold Spring Harb. Perspect. Biol. 3, a004697 (2011).
44. Viola, A. & Gupta, N. Tether and trap: Regulation of membrane-raft dynamics by actin-binding proteins. Nat. Rev. Immunol. 7, 889-896 (2007).
45. Eggeling, C. et al. Direct observation of the nanoscale dynamics of membrane lipids in a living cell. Nature 457, 1159-1162 (2009).
46. Sahl, S.J., Leutenegger, M., Hilbert, M., Hell, S.W. & Eggeling, C. Fast molecular tracking maps nanoscale dynamics of plasma membrane lipids. Proc. Natl. Acad. Sci. USA 107, 6829-6834 (2010).
47. Suzuki, K.G.N. et al. Transient GPI-Anchored protein homodimers are units for raft organization and function. Nat. Chem. Biol. 8, 774-783 (2012).
48. Chung, I. et al. Spatial control of EGF receptor activation by reversible dimerization on living cells. Nature 464, 783-787 (2010).
49. Hern, J.A. et al. Formation and dissociation of M1 muscarinic receptor dimers seen by total internal reflection fluorescence imaging of single molecules. Proc. Natl. Acad. Sci. USA 107, 2693-2698 (2010).
50. Calebiro, D. et al. Single-molecule analysis of fluorescently labeled G protein-coupled receptors reveals complexes with distinct dynamics and organization. Proc. Natl. Acad. Sci. USA 110, 743-748 (2013).
51. Veatch, S.L. et al. Correlation functions quantify super-resolution images and estimate apparent clustering due to over-counting. PLoS ONE 7, e31457 (2012).
52. Maurice, P., Kamal, M. & Jockers, R. Asymmetry of GPCR oligomers supports their functional relevance. Trends Pharmacol. Sci. 32, 514-520 (2011).
53. James, J.R., Oliveira, M.I., Carmo, A.M., Iaboni, A. & Davis, S.J. A rigorous experimental framework for detecting protein oligomerization using bioluminescence resonance energy transfer. Nat. Methods 3, 1001-1006 (2006).
54. Meyer, B.H. et al. FRET imaging reveals that functional neurokinin-1 receptors are monomeric and reside in membrane microdomains of live cells. Proc. Natl. Acad. Sci. USA 103, 2138-2143 (2006).
55. Brameshuber, M. et al. Imaging of mobile long-lived nanoplatforms in the live cell plasma membrane. J. Biol. Chem. 285, 41765-41771 (2010).
56. Brodsky, F.M. Diversity of clathrin function: New tricks for an old protein. Annu. Rev. Cell Dev. Biol. 28, 309-336 (2012).
57. Ulbrich, M.H. & Isacoff, E.Y. Subunit counting in membrane-bound proteins. Nat. Methods 4, 319-321 (2007).
58. Das, S.K., Darshi, M., Cheley, S., Wallace, M.I. & Bayley, H. Membrane protein stoichiometry determined from the step-wise photobleaching of dye-labelled subunits. ChemBioChem 8, 994-999 (2007).
59. Soeller, C., Crossman, D., Gilbert, R. & Cannell, M.B. Analysis of ryanodine receptor clusters in rat and human cardiac myocytes. Proc. Natl. Acad. Sci. USA 104, 14958-14963 (2007).
60. Arant, R.J. & Ulbrich, M.H. Deciphering the subunit composition of multimeric proteins by counting photobleaching steps. ChemPhysChem 15, 600-605 (2014).
61. McMahon, H.T. & Boucrot, E. Molecular mechanism and physiological functions of clathrin-mediated endocytosis. Nat. Rev. Mol. Cell Biol. 12, 517-533 (2011).
62. Taylor, M.J., Perrais, D. & Merrifield, C.J. A high precision survey of the molecular dynamics of mammalian clathrin-mediated endocytosis. PLoS Biol. 9, e1000604 (2011).
63. Posor, Y. et al. Spatiotemporal control of endocytosis by phosphatidylinositol-3,4-bisphosphate. Nature 499, 233-237 (2013).
64. Cocucci, E., Aguet, F., Boulant, S. & Kirchhausen, T. The first five seconds in the life of a clathrin-coated pit. Cell 150, 495-507 (2012).
65. Jones, S.A., Shim, S.-H., He, J. & Zhuang, X. Fast, three-dimensional superresolution imaging of live cells. Nat. Methods 8, 499-508 (2011).
66. Rothberg, K.G., Heuser, J.E., Donzell, W.C. & Ying, Y.S. Caveolin, a protein component of caveolae membrane coats. Cell 68, 673-682 (1992).
67. Parton, R.G. & del Pozo, M.A. Caveolae as plasma membrane sensors, protectors and organizers. Nat. Rev. Mol. Cell Biol. 14, 98-112 (2013).
68. Gambin, Y. et al. Single-molecule analysis reveals self assembly and nanoscale segregation of two distinct cavin subcomplexes on caveolae. eLife 3, e01434 (2014).
69. Kanchanawong, P. et al. Nanoscale architecture of integrin-based cell adhesions. Nature 468, 580-584 (2010).
70. Shroff, H. et al. Dual-color superresolution imaging of genetically expressed probes within individual adhesion complexes. Proc. Natl. Acad. Sci. USA 104, 20308-20313 (2007).
71. Shibata, A.C.E.A. et al. Archipelago architecture of the focal adhesion: Membrane molecules freely enter and exit from the focal adhesion zone. Cytoskeleton (Hoboken) 69, 380-392 (2012).
72. Rossier, O. et al. Integrins ?1 and ?3 exhibit distinct dynamic nanoscale organizations inside focal adhesions. Nat. Cell Biol. 14, 1057-1067 (2012).
73. Shibata, A.C.E. et al. Rac1 recruitment to the archipelago structure of the focal adhesion through the fluid membrane as revealed by single-molecule analysis. Cytoskeleton (Hoboken) 70, 161-177 (2013).
74. Ribrault, C., Sekimoto, K. & Triller, A. From the stochasticity of molecular processes to the variability of synaptic transmission. Nat. Rev. Neurosci. 12, 375-387 (2011).
75. Frost, N.A., Shroff, H., Kong, H., Betzig, E. & Blanpied, T.A. Single-molecule discrimination of discrete perisynaptic and distributed sites of actin filament assembly within dendritic spines. Neuron 67, 86-99 (2010).
76. Izeddin, I. et al. Super-resolution dynamic imaging of dendritic spines using a low-Affinity photoconvertible actin probe. PLoS ONE 6, e15611 (2011).
77. Opazo, P., Sainlos, M. & Choquet, D. Regulation of AMPA receptor surface diffusion by PSD-95 slots. Curr. Opin. Neurobiol. 22, 453-460 (2012).
78. Triller, A. & Sheng, M. Synaptic structure and function. Curr. Opin. Neurobiol. 22, 363-365 (2012).
79. Choquet, D. & Triller, A. The dynamic synapse. Neuron 80, 691-703 (2013).
80. Douglass, A.D. & Vale, R.D. Single-molecule microscopy reveals plasma membrane microdomains created by protein-protein networks that exclude or trap signaling molecules in T cells. Cell 121, 937-950 (2005).
81. Yokosuka, T. et al. Newly generated T cell receptor microclusters initiate and sustain T cell activation by recruitment of Zap70 and SLP-76. Nat. Immunol. 6, 1253-1262 (2005).
82. Lillemeier, B.F. et al. TCR and Lat are expressed on separate protein islands on T cell membranes and concatenate during activation. Nat. Immunol. 11, 90-96 (2010).
83. Sherman, E. et al. Functional nanoscale organization of signaling molecules downstream of the T cell antigen receptor. Immunity 35, 705-720 (2011).
84. Sengupta, P. et al. Probing protein heterogeneity in the plasma membrane using PALM and pair correlation analysis. Nat. Methods 8, 969-975 (2011).
85. Dustin, M.L. & Depoil, D. New insights into the T cell synapse from single molecule techniques. Nat. Rev. Immunol. 11, 672-684 (2011).
86. Purbhoo, M.A. et al. Dynamics of subsynaptic vesicles and surface microclusters at the immunological synapse. Sci. Signal. 3, ra36 (2010).
87. Williamson, D.J. et al. Pre-existing clusters of the adaptor Lat do not participate in early T cell signaling events. Nat. Immunol. 12, 655-662 (2011).
88. Larghi, P. et al. VAMP7 controls T cell activation by regulating the recruitment and phosphorylation of vesicular Lat at TCR-Activation sites. Nat. Immunol. 723-731 (2013).
89. Balagopalan, L., Barr, V.A., Kortum, R.L., Park, A.K. & Samelson, L.E. Cutting edge: Cell surface linker for activation of T cells is recruited to microclusters and is active in signaling. J. Immunol. 190, 3849-3853 (2013).
90. James, J.R. et al. Single-molecule level analysis of the subunit composition of the T cell receptor on live T cells. Proc. Natl. Acad. Sci. USA 104, 17662-17667 (2007).
91. Rossy, J., Owen, D.M., Williamson, D.J., Yang, Z. & Gaus, K. Conformational states of the kinase Lck regulate clustering in early T cell signaling. Nat. Immunol. 14, 82-89 (2013).
92. Manz, B.N., Jackson, B.L., Petit, R.S., Dustin, M.L. & Groves, J. T-cell triggering thresholds are modulated by the number of antigen within individual T-cell receptor clusters. Proc. Natl. Acad. Sci. USA 108, 9089-9094 (2011).
93. Kusumi, A. & Suzuki, K. Toward understanding the dynamics of membraneraft-based molecular interactions. Biochim. Biophys. Acta 1746, 234-251 (2005).
94. Grasberger, B., Minton, A.P., DeLisi, C. & Metzger, H. Interaction between proteins localized in membranes. Proc. Natl. Acad. Sci. USA 83, 6258-6262 (1986).
95. Pierce, S.K. & Liu, W. The tipping points in the initiation of B cell signalling: How small changes make big differences. Nat. Rev. Immunol. 10, 767-777 (2010).
96. Liu, W., Sohn, H.W., Tolar, P. & Pierce, S.K. It's all about change: The antigendriven initiation of B-cell receptor signaling. Cold Spring Harb. Perspect. Biol. 2, a002295 (2010).
97. Andrews, N.L. et al. Actin restricts Fc?RI diffusion and facilitates antigeninduced receptor immobilization. Nat. Cell Biol. 10, 955-963 (2008).
98. Andrews, N.L. et al. Small, mobile Fc?RI receptor aggregates are signaling competent. Immunity 31, 469-479 (2009).
99. Larson, D.R., Singer, R.H. & Zenklusen, D. A single molecule view of gene expression. Trends Cell Biol. 19, 630-637 (2009).
100. Li, G.-W. & Xie, X.S. Central dogma at the single-molecule level in living cells. Nature 475, 308-315 (2011).
101. Pitchiaya, S., Heinicke, L.A., Custer, T.C. & Walter, N.G. Single molecule fluorescence approaches shed light on intracellular RNAs. Chem. Rev. 114, 3224-3265 (2014).
102. Park, H.Y. et al. Visualization of dynamics of single endogenous mRNA labeled in live mouse. Science 343, 422-424 (2014).
103. Wu, B., Chao, J.A. & Singer, R.H. Fluorescence fluctuation spectroscopy enables quantitative imaging of single mRNAs in living cells. Biophys. J. 102, 2936-2944 (2012).
104. Hocine, S., Raymond, P., Zenklusen, D., Chao, J.A. & Singer, R.H. Singlemolecule analysis of gene expression using two-color RNA labeling in live yeast. Nat. Methods 10, 119-121 (2013).
105. Zhao, Z.W. et al. Spatial organization of RNA polymerase II inside a mammalian cell nucleus revealed by reflected light-sheet superresolution microscopy. Proc. Natl. Acad. Sci. USA 111, 681-686 (2014).
106. Yamagishi, M., Ishihama, Y., Shirasaki, Y., Kurama, H. & Funatsu, T. Singlemolecule imaging of b-Actin mRNAs in the cytoplasm of a living cell. Exp. Cell Res. 315, 1142-1147 (2009).
107. Buxbaum, A.R., Wu, B. & Singer, R.H. Single ?-Actin mRNA detection in neurons reveals a mechanism for regulating its translatability. Science 343, 419-422 (2014).
108. Elf, J., Li, G.-W. & Xie, X.S. Probing transcription factor dynamics at the single-molecule level in a living cell. Science 316, 1191-1194 (2007).
109. Gebhardt, J.C.M. et al. Single-molecule imaging of transcription factor binding to DNA in live mammalian cells. Nat. Methods 10, 421-426 (2013).
110. Eggeling, C., Willig, K.I. & Barrantes, F.J. STED microscopy of living cells-new frontiers in membrane and neurobiology. J. Neurochem. 126, 203-212 (2013).
111. Tanaka, K.A.K. et al. Membrane molecules mobile even after chemical fixation. Nat. Methods 7, 865-866 (2010).
112. Tokunaga, M., Kitamura, K., Saito, K., Iwane, A.H. & Yanagida, T. Single molecule imaging of fluorophores and enzymatic reactions achieved by objective-Type total internal reflection fluorescence microscopy. Biochem. Biophys. Res. Commun. 235, 47-53 (1997).
113. Ritter, J.G., Veith, R., Veenendaal, A., Siebrasse, J.P. & Kubitscheck, U. Light sheet microscopy for single molecule tracking in living tissue. PLoS ONE 5, e11639 (2010).
114. Schmidt, T., Schutz, G.J., Baumgartner, W., Gruber, H.J. & Schindler, H. Imaging of single molecule diffusion. Proc. Natl. Acad. Sci. USA 93, 2926-2929 (1996).
115. Hinterdorfer, P., Garcia-Parajo, M.F.M. & Dufrêne, Y.F.Y. Single-molecule imaging of cell surfaces using near-field nanoscopy. Acc. Chem. Res. 45, 327-336 (2012).
116. Chenouard, N. et al. Objective comparison of particle tracking methods. Nat. Methods 11, 281-289 (2014).
117. Deschout, H. et al. Precisely and accurately localizing single emitters in fluorescence microscopy. Nat. Methods 11, 253-266 (2014).
118. Yildiz, A. et al. Myosin V walks hand-over-hand: Single fluorophore imaging with 1.5-nm localization. Science 300, 2061-2065 (2003).
119. Pertsinidis, A., Zhang, Y. & Chu, S. Subnanometre single-molecule localization, registration and distance measurements. Nature 466, 647-651 (2010).
120. Sako, Y., Minoghchi, S. & Yanagida, T. Single-molecule imaging of EGFR signalling on the surface of living cells. Nat. Cell Biol. 2, 168-172 (2000).
121. Manley, S. et al. High-density mapping of single-molecule trajectories with photoactivated localization microscopy. Nat. Methods 5, 155-157 (2008).