Molecular Spies for Bioimaging-Fluorescent Protein-Based Probes

Molecular Cell

Volumn 58, Issue 4, 2015, Pages 632-643

  Miyawaki, Atsushi ^a,b   Niino, Yusuke ^a  

^a RIKEN BRAIN SCIENCE INSTITUTE   (Japan)

^b Institute of Physical and Chemical Research   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CYAN FLUORESCENT PROTEIN; FLUORESCENT DYE; YELLOW FLUORESCENT PROTEIN; PHOTOPROTEIN;

BIOLUMINESCENCE RESONANCE ENERGY TRANSFER; BRAIN MAPPING; CELL FUNCTION; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; ELECTROENCEPHALOGRAM; FLUORESCENCE IMAGING; FLUORESCENCE RESONANCE ENERGY TRANSFER; MOLECULAR IMAGING; MOLECULAR PROBE; NONHUMAN; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; REVIEW; SIGNAL NOISE RATIO; SIGNAL TRANSDUCTION; ZEBRA FISH; ANIMAL; FLUORESCENCE; FLUORESCENCE MICROSCOPY; GENETICS; HUMAN; LUMINESCENCE; METABOLISM; PROCEDURES;

ANIMALS; FLUORESCENCE; FLUORESCENCE RESONANCE ENERGY TRANSFER; FLUORESCENT DYES; HUMANS; LUMINESCENT MEASUREMENTS; LUMINESCENT PROTEINS; MICROSCOPY, FLUORESCENCE; MOLECULAR IMAGING;

EID: 84929666621     PISSN: 10972765     EISSN: 10974164     Source Type: Journal    
DOI: 10.1016/j.molcel.2015.03.002     Document Type: Review

References (62)

1. Adams S.R., Harootunian A.T., Buechler Y.J., Taylor S.S., Tsien R.Y. Fluorescence ratio imaging of cyclic AMP in single cells. Nature 1991, 349:694-697.
2. Ahrens M.B., Li J.M., Orger M.B., Robson D.N., Schier A.F., Engert F., Portugues R. Brain-wide neuronal dynamics during motor adaptation in zebrafish. Nature 2012, 485:471-477.
3. Akerboom J., Rivera J.D., Guilbe M.M., Malavé E.C., Hernandez H.H., Tian L., Hires S.A., Marvin J.S., Looger L.L., Schreiter E.R. Crystal structures of the GCaMP calcium sensor reveal the mechanism of fluorescence signal change and aid rational design. J.Biol. Chem. 2009, 284:6455-6464.
4. Akerboom J., Chen T.W., Wardill T.J., Tian L., Marvin J.S., Mutlu S., Calderón N.C., Esposti F., Borghuis B.G., Sun X.R., et al. Optimization of a GCaMP calcium indicator for neural activity imaging. J.Neurosci. 2012, 32:13819-13840.
5. Akerboom J., Carreras Calderón N., Tian L., Wabnig S., Prigge M., Tolö J., Gordus A., Orger M.B., Severi K.E., Macklin J.J., et al. Genetically encoded calcium indicators for multi-color neural activity imaging and combination with optogenetics. Front. Mol. Neurosci. 2013, 6:2.
6. Albeck J.G., Mills G.B., Brugge J.S. Frequency-modulated pulses of ERK activity transmit quantitative proliferation signals. Mol. Cell 2013, 49:249-261.
7. Aoki K., Kumagai Y., Sakurai A., Komatsu N., Fujita Y., Shionyu C., Matsuda M. Stochastic ERK activation induced by noise and cell-to-cell propagation regulates cell density-dependent proliferation. Mol. Cell 2013, 52:529-540.
8. Aoki T., Kinoshita M., Aoki R., Agetsuma M., Aizawa H., Yamazaki M., Takahoko M., Amo R., Arata A., Higashijima S., et al. Imaging of neural ensemble for the retrieval of a learned behavioral program. Neuron 2013, 78:881-894.
9. Baird G.S., Zacharias D.A., Tsien R.Y. Circular permutation and receptor insertion within green fluorescent proteins. Proc. Natl. Acad. Sci. USA 1999, 96:11241-11246.
10. Chalfie M., Tu Y., Euskirchen G., Ward W.W., Prasher D.C. Green fluorescent protein as a marker for gene expression. Science 1994, 263:802-805.
11. Chen Y., Song X., Ye S., Miao L., Zhu Y., Zhang R.G., Ji G. Structural insight into enhanced calcium indicator GCaMP3 and GCaMPJ to promote further improvement. Protein Cell 2013, 4:299-309.
12. Ding J., Luo A.F., Hu L., Wang D., Shao F. Structural basis of the ultrasensitive calcium indicator GCaMP6. Sci. China Life Sci. 2014, 57:269-274.
13. Förster T. Zwischenmolekulare energiewanderung und fluoreszenz. Ann. Phys. 1948, 437:55-75.
14. Freeman J., Vladimirov N., Kawashima T., Mu Y., Sofroniew N.J., Bennett D.V., Rosen J., Yang C.T., Looger L.L., Ahrens M.B. Mapping brain activity at scale with cluster computing. Nat. Methods 2014, 11:941-950.
15. Griesbeck O., Baird G.S., Campbell R.E., Zacharias D.A., Tsien R.Y. Reducing the environmental sensitivity of yellow fluorescent protein. Mechanism and applications. J.Biol. Chem. 2001, 276:29188-29194.
16. Haugh J.M. Live-cell fluorescence microscopy with molecular biosensors: what are we really measuring?. Biophys. J. 2012, 102:2003-2011.
17. Heim N., Griesbeck O. Genetically encoded indicators of cellular calcium dynamics based on troponin C and green fluorescent protein. J.Biol. Chem. 2004, 279:14280-14286.
18. Herbst K.J., Allen M.D., Zhang J. Luminescent kinase activity biosensors based on a versatile bimolecular switch. J.Am. Chem. Soc. 2011, 133:5676-5679.
19. Hoffmann C., Gaietta G., Bünemann M., Adams S.R., Oberdorff-Maass S., Behr B., Vilardaga J.-P., Tsien R.Y., Ellisman M.H., Lohse M.J. A FlAsH-based FRET approach to determine G protein-coupled receptor activation in living cells. Nat. Methods 2005, 2:171-176.
20. 2+) indicators, yellow Cameleon-Nano. Nat. Methods 2010, 7:729-732.
21. Inoue M., Takeuchi A., Horigane S., Ohkura M., Gengyo-Ando K., Fujii H., Kamijo S., Takemoto-Kimura S., Kano M., Nakai J., et al. Rational design of a high-affinity, fast, red calcium indicator R-CaMP2. Nat. Methods 2015, 12:64-70.
22. Inouye S., Tsuji F.I. Aequorea green fluorescent protein. Expression of the gene and fluorescence characteristics of the recombinant protein. FEBS Lett. 1994, 341:277-280.
23. Kim B., Lin M.Z. Optobiology: optical control of biological processes via protein engineering. Biochem. Soc. Trans. 2013, 41:1183-1188.
24. Komatsu N., Aoki K., Yamada M., Yukinaga H., Fujita Y., Kamioka Y., Matsuda M. Development of an optimized backbone of FRET biosensors for kinases and GTPases. Mol. Biol. Cell 2011, 22:4647-4656.
25. Kotera I., Iwasaki T., Imamura H., Noji H., Nagai T. Reversible dimerization of Aequorea victoria fluorescent proteins increases the dynamic range of FRET-based indicators. ACS Chem. Biol. 2010, 5:215-222.
26. Kubo F., Hablitzel B., Dal Maschio M., Driever W., Baier H., Arrenberg A.B. Functional architecture of an optic flow-responsive area that drives horizontal eye movements in zebrafish. Neuron 2014, 81:1344-1359.
27. Kuchibhotla K.V., Goldman S.T., Lattarulo C.R., Wu H.Y., Hyman B.T., Bacskai B.J. Abeta plaques lead to aberrant regulation of calcium homeostasis invivo resulting in structural and functional disruption of neuronal networks. Neuron 2008, 59:214-225.
28. Lam A.J., St-Pierre F., Gong Y., Marshall J.D., Cranfill P.J., Baird M.A., McKeown M.R., Wiedenmann J., Davidson M.W., Schnitzer M.J., et al. Improving FRET dynamic range with bright green and red fluorescent proteins. Nat. Methods 2012, 9:1005-1012.
29. Lin L.T., Wang B.S., Chen J.C., Liu C.H., Chou C., Chiu S.J., Chang W.Y., Liu R.S., Allen Chang C., Lee Y.J. mPlum-IFP 1.4 fluorescent fusion protein may display Förster resonance energy transfer associated properties that can be used for near-infrared based reporter gene imaging. J.Biomed. Opt. 2013, 18:126013.
30. Marshall C.J. Specificity of receptor tyrosine kinase signaling: transient versus sustained extracellular signal-regulated kinase activation. Cell 1995, 80:179-185.
31. Miyawaki A. Visualization of the spatial and temporal dynamics of intracellular signaling. Dev. Cell 2003, 4:295-305.
32. Miyawaki A. Development of probes for cellular functions using fluorescent proteins and fluorescence resonance energy transfer. Annu. Rev. Biochem. 2011, 80:357-373.
33. 2+ based on green fluorescent proteins and calmodulin. Nature 1997, 388:882-887.
34. 2+. Proc. Natl. Acad. Sci. USA 2001, 98:3197-3202.
35. 2+) by circularly permuted yellow fluorescent proteins. Proc. Natl. Acad. Sci. USA 2004, 101:10554-10559.
36. 2+) probe composed of a single green fluorescent protein. Nat. Biotechnol. 2001, 19:137-141.
37. 2+ indicator for detecting optically evoked action potentials. PLoS ONE 2012, 7:e39933.
38. Oldach L., Zhang J. Genetically encoded fluorescent biosensors for live-cell visualization of protein phosphorylation. Chem. Biol. 2014, 21:186-197.
39. 2+ indicators based on computationally redesigned calmodulin-peptide pairs. Chem. Biol. 2006, 13:521-530.
40. Palmer A.E., Qin Y., Park J.G., McCombs J.E. Design and application of genetically encoded biosensors. Trends Biotechnol. 2011, 29:144-152.
41. Portugues R., Feierstein C.E., Engert F., Orger M.B. Whole-brain activity maps reveal stereotyped, distributed networks for visuomotor behavior. Neuron 2014, 81:1328-1343.
42. Prasher D.C., Eckenrode V.K., Ward W.W., Prendergast F.G., Cormier M.J. Primary structure of the Aequorea victoria green-fluorescent protein. Gene 1992, 111:229-233.
43. Reymond L., Lukinavičius G., Umezawa K., Maurel D., Brun M.A., Masharina A., Bojkowska K., Mollwitz B., Schena A., Griss R., Johnsson K. Visualizing biochemical activities in living cells through chemistry. Chimia (Aarau) 2011, 65:868-871.
44. 2+-dependent changes in the fluorescence emission of an indicator composed of two green fluorescent protein variants linked by a calmodulin-binding sequence. A new class of fluorescent indicators. J.Biol. Chem. 1997, 272:13270-13274.
45. Rose T., Goltstein P.M., Portugues R., Griesbeck O. Putting a finishing touch on GECIs. Front. Mol. Neurosci. 2014, 7:88.
46. Sabouri-Ghomi M., Wu Y., Hahn K., Danuser G. Visualizing and quantifying adhesive signals. Curr. Opin. Cell Biol. 2008, 20:541-550.
47. Sample V., Mehta S., Zhang J. Genetically encoded molecular probes to visualize and perturb signaling dynamics in living biological systems. J.Cell Sci. 2014, 127:1151-1160.
48. Sasagawa S., Ozaki Y., Fujita K., Kuroda S. Prediction and validation of the distinct dynamics of transient and sustained ERK activation. Nat. Cell Biol. 2005, 7:365-373.
49. Shimomura O., Johnson F.H., Saiga Y. Extraction, purification and properties of aequorin, a bioluminescent protein from the luminous hydromedusan, Aequorea. J.Cell. Comp. Physiol. 1962, 59:223-239.
50. Stryer L. Fluorescence energy transfer as a spectroscopic ruler. Annu. Rev. Biochem. 1978, 47:819-846.
51. To T.-L., Fadul M.J., Shu X. Singlet oxygen triplet energy transfer-based imaging technology for mapping protein-protein proximity in intact cells. Nat. Commun. 2014, 5:4072.
52. Tsien R.Y. The green fluorescent protein. Annu. Rev. Biochem. 1998, 67:509-544.
53. Tsien R.Y. Building and breeding molecules to spy on cells and tumors. FEBS Lett. 2005, 579:927-932.
54. Wang Q., Shui B., Kotlikoff M.I., Sondermann H. Structural basis for calcium sensing by GCaMP2. Structure 2008, 16:1817-1827.
55. Weitzman M., Hahn K.M. Optogenetic approaches to cell migration and beyond. Curr. Opin. Cell Biol. 2014, 30:112-120.
56. 2± indicators and photophysical considerations for optogenetic applications. ACS Chem. Neurosci. 2013, 4:963-972.
57. Yao J.Z., Uttamapinant C., Poloukhtine A., Baskin J.M., Codelli J.A., Sletten E.M., Bertozzi C.R., Popik V.V., Ting A.Y. Fluorophore targeting to cellular proteins via enzyme-mediated azide ligation and strain-promoted cycloaddition. J.Am. Chem. Soc. 2012, 134:3720-3728.
58. Yasuda R., Murakoshi H. The mechanisms underlying the spatialspreading of signaling activity. Curr. Opin. Neurobiol. 2011, 21:313-321.
59. Zacharias D.A., Violin J.D., Newton A.C., Tsien R.Y. Partitioning of lipid-modified monomeric GFPs into membrane microdomains of live cells. Science 2002, 296:913-916.
60. Zhai S., Ark E.D., Parra-Bueno P., Yasuda R. Long-distance integration of nuclear ERK signaling triggered by activation of a few dendritic spines. Science 2013, 342:1107-1111.
61. Zhang J., Campbell R.E., Ting A.Y., Tsien R.Y. Creating new fluorescent probes for cell biology. Nat. Rev. Mol. Cell Biol. 2002, 3:906-918.
62. 2+ indicators. Science 2011, 333:1888-1891.