Visualizing dynamic activities of signaling enzymes using genetically encodable FRET-based biosensors: From designs to applications

Methods in Enzymology

Volumn 504, Issue , 2012, Pages 317-340

  Zhou, Xin ^a   Herbst Robinson, Katie J ^a   Zhang, Jin ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

fluorescence imaging; GTPases; Keywords; kinases

Indexed keywords

FLUORESCENT DYE; FLUORESCENT PROTEIN; GUANOSINE TRIPHOSPHATASE; PROTEIN KINASE; UNCLASSIFIED DRUG;

AKAR REPORTER GENE; ARTICLE; BIOSENSOR; CELL MIGRATION; DATA ANALYSIS; ENZYME ACTIVATION; ENZYME ACTIVITY; FLUORESCENCE RESONANCE ENERGY TRANSFER; FLUORESCENT BIOSENSOR; MICROSCOPY; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN EXPRESSION; REGULATORY MECHANISM; REPORTER GENE;

EID: 84862950678     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/B978-0-12-391857-4.00016-1     Document Type: Chapter

References (69)

1. H.W. Ai Fluorescent protein FRET pairs for ratiometric imaging of dual biosensors Nat. Methods 5 2008 401 403
2. R.D. Airan Temporally precise in vivo control of intracellular signalling Nature 458 2009 1025 1029
3. A. Aitken 14-3-3 proteins: Biological function and domain structure Biochem. Soc. Trans. 23 1995 605 611
4. L. Albertazzi Quantitative FRET analysis with the EGFP-mCherry fluorescent protein pair Photochem. Photobiol. 85 2009 287 297
5. M.D. Allen Reading dynamic kinase activity in living cells for high-throughput screening ACS Chem Biol. 1 2006 371 376
6. M.D. Allen, and J. Zhang Subcellular dynamics of protein kinase A activity visualized by FRET-based reporters Biochem. Biophys. Res. Commun. 348 2006 716 721 (Pubitemid 44188622)
7. B. Ananthanarayanan Signal propagation from membrane messengers to nuclear effectors revealed by reporters of phosphoinositide dynamics and Akt activity Proc. Natl. Acad. Sci. USA 102 2005 15081 15086 (Pubitemid 41513338)
8. B. Ananthanarayanan Live-cell molecular analysis of Akt activation reveals roles for activation loop phosphorylation J. Biol. Chem. 282 2007 36634 36641
9. K. Aoki, and M. Matsuda Visualization of small GTPase activity with fluorescence resonance energy transfer-based biosensors Nat. Protoc. 4 2009 1623 1631
10. N.N. Aye-Han Fluorescent biosensors for real-time tracking of post-translational modification dynamics Curr. Opin. Chem. Biol. 13 2009 392 397
11. M.J. Berridge Calcium signalling: Dynamics, homeostasis and remodelling Nat. Rev. Mol. Cell Biol. 4 2003 517 529 (Pubitemid 36773404)
12. V. Calleja Intramolecular and intermolecular interactions of protein kinase B define its activation in vivo PLoS Biol. 5 2007 e95
13. L.D. Carrillo A cellular FRET-based sensor for beta-O-GlcNAc, a dynamic carbohydrate modification involved in signaling J. Am. Chem. Soc. 128 2006 14768 14769 (Pubitemid 44851591)
14. M. Chalfie Green fluorescent protein as a marker for gene expression Science 263 1994 802 805 (Pubitemid 24093206)
15. D.E. Clapham Calcium signaling Cell 131 2007 1047 1058 (Pubitemid 350258556)
16. L.B. Cohen Changes in axon fluorescence during activity: Molecular probes of membrane potential J. Membr. Biol. 19 1974 1 36
17. A.B. Cubitt Understanding, improving and using green fluorescent proteins Trends Biochem. Sci. 20 1995 448 455
18. R.N. Day, and F. Schaufele Fluorescent protein tools for studying protein dynamics in living cells: A review J. Biomed. Opt. 13 2008 031202
19. C. Depry Visualization of PKA activity in plasma membrane microdomains Mol Biosyst. 7 2011 52 58
20. L.M. DiPilato Fluorescent indicators of cAMP and Epac activation reveal differential dynamics of cAMP signaling within discrete subcellular compartments Proc. Natl. Acad. Sci. USA 101 2004 16513 16518
21. T.A. Dunn Imaging of cAMP levels and protein kinase A activity reveals that retinal waves drive oscillations in second-messenger cascades J. Neurosci. 26 2006 12807 12815 (Pubitemid 44904576)
22. T. Forster Intermolecular energy migration and fluorescence Ann. Phys. 2 1948 55 75
23. M. Fosbrink Visualization of JNK activity dynamics with a genetically encoded fluorescent biosensor Proc. Natl. Acad. Sci. USA 107 2010 5459 5464
24. M.W. Friedrich Imaging CREB activation in living cells J. Biol. Chem. 285 2010 23285 23295
25. H. Fu 14-3-3 proteins: Structure, function, and regulation Annu. Rev. Pharmacol. Toxicol. 40 2000 617 647 (Pubitemid 30340695)
26. A. Fujioka Dynamics of the Ras/ERK MAPK cascade as monitored by fluorescent probes J. Biol. Chem. 281 2006 8917 8926 (Pubitemid 43847999)
27. X. Gao, and J. Zhang Spatiotemporal analysis of differential Akt regulation in plasma membrane microdomains Mol. Biol. Cell 19 2008 4366 4373
28. G. Grynkiewicz A new generation of Ca2+ indicators with greatly improved fluorescence properties J. Biol. Chem. 260 1985 3440 3450 (Pubitemid 15114340)
29. C.D. Harvey A genetically encoded fluorescent sensor of ERK activity Proc. Natl. Acad. Sci. USA 105 2008 19264 19269
30. J.N. Henderson Structural basis for reversible photobleaching of a green fluorescent protein homologue Proc. Natl. Acad. Sci. USA 104 2007 6672 6677 (Pubitemid 47175559)
31. K.J. Herbst Luminescent kinase activity biosensors based on a versatile bimolecular switch J. Am. Chem. Soc. 133 2011 5676 5679
32. L. Hodgson Design and optimization of genetically encoded fluorescent biosensors: GTPase biosensors Methods Cell Biol. 85 2008 63 81
33. S. Karasawa Cyan-emitting and orange-emitting fluorescent proteins as a donor/acceptor pair for fluorescence resonance energy transfer Biochem. J. 381 2004 307 312 (Pubitemid 38932237)
34. V.S. Kraynov Localized Rac activation dynamics visualized in living cells Science 290 2000 333 337
35. A. Levskaya Spatiotemporal control of cell signalling using a light-switchable protein interaction Nature 461 2009 997 1001
36. C.J. Lim Integrin-mediated protein kinase A activation at the leading edge of migrating cells Mol. Biol. Cell 19 2008 4930 4941
37. C.W. Lin Genetically encoded fluorescent reporters of histone methylation in living cells J. Am. Chem. Soc. 126 2004 5982 5983
38. S. Lu The spatiotemporal pattern of Src activation at lipid rafts revealed by diffusion-corrected FRET imaging PLoS Comput. Biol. 4 2008 e1000127
39. M. Machacek Coordination of Rho GTPase activities during cell protrusion Nature 461 2009 99 103
40. M.L. Markwardt An improved cerulean fluorescent protein with enhanced brightness and reduced reversible photoswitching PLoS One 6 2011 e17896
41. A. Miyawaki Visualization of the spatial and temporal dynamics of intracellular signaling Dev. Cell 4 2003 295 305 (Pubitemid 36342356)
42. A. Miyawaki Fluorescent indicators for Ca2+ based on green fluorescent proteins and calmodulin Nature 388 1997 882 887 (Pubitemid 27377061)
43. N. Mochizuki Spatio-temporal images of growth-factor-induced activation of Ras and Rap1 Nature 411 2001 1065 1068 (Pubitemid 32612332)
44. T. Nagai Expanded dynamic range of fluorescent indicators for Ca(2+) by circularly permuted yellow fluorescent proteins Proc. Natl. Acad. Sci. USA 101 2004 10554 10559 (Pubitemid 38955780)
45. P. Nalbant Activation of endogenous Cdc42 visualized in living cells Science 305 2004 1615 1619 (Pubitemid 39296355)
46. R.H. Newman, and J. Zhang Visualization of phosphatase activity in living cells with a FRET-based calcineurin activity sensor Mol. Biosyst. 4 2008 496 501 (Pubitemid 351706288)
47. R.H. Newman Genetically encodable fluorescent biosensors for tracking signaling dynamics in living cells Chem. Rev. 111 2011 3614 3666
48. A.W. Nguyen, and P.S. Daugherty Evolutionary optimization of fluorescent proteins for intracellular FRET Nat. Biotechnol. 23 2005 355 360 (Pubitemid 41094425)
49. Q. Ni Analyzing protein kinase dynamics in living cells with FRET reporters Methods 40 2006 279 286 (Pubitemid 44635295)
50. 2+ -cAMP-PKA oscillatory circuit Nat. Chem. Biol. 7 2011 34 40
51. J. Perroy Real-time monitoring of ubiquitination in living cells by BRET Nat. Methods 1 2004 203 208
52. O. Pertz Spatiotemporal dynamics of RhoA activity in migrating cells Nature 440 2006 1069 1072
53. A.J. Ridley Cell migration: Integrating signals from front to back Science 302 2003 1704 1709 (Pubitemid 37505725)
54. M.A. Rizzo An improved cyan fluorescent protein variant useful for FRET Nat. Biotechnol. 22 2004 445 449 (Pubitemid 38451376)
55. W.N. Ross A large change in dye absorption during the action potential Biophys. J. 14 1974 983 986
56. K. Sasaki Real-time imaging of histone H4 hyperacetylation in living cells Proc. Natl. Acad. Sci. USA 106 2009 16257 16262
57. A. Schleifenbaum Genetically encoded FRET probe for PKC activity based on pleckstrin J. Am. Chem. Soc. 126 2004 11786 11787 (Pubitemid 39298316)
58. N.C. Shaner A guide to choosing fluorescent proteins Nat. Methods 2 2005 905 909 (Pubitemid 43108726)
59. E. Tkachenko Protein kinase A governs a RhoA-RhoGDI protrusion-retraction pacemaker in migrating cells Nat. Cell Biol. 13 2011 661 668
60. R.Y. Tsien The green fluorescent protein Annu. Rev. Biochem. 67 1998 509 544 (Pubitemid 28411137)
61. J.D. Violin A genetically encoded fluorescent reporter reveals oscillatory phosphorylation by protein kinase C J. Cell Biol. 161 2003 899 909 (Pubitemid 36718423)
62. S.A. Walker, and P.J. Lockyer Visualizing Ras signalling in real-time J. Cell Sci. 117 2004 2879 2886 (Pubitemid 39117663)
63. Y.I. Wu A genetically encoded photoactivatable Rac controls the motility of living cells Nature 461 2009 104 108
64. M. Zaccolo A genetically encoded, fluorescent indicator for cyclic AMP in living cells Nat. Cell Biol. 2 2000 25 29
65. D.A. Zacharias Partitioning of lipid-modified monomeric GFPs into membrane microdomains of live cells Science 296 2002 913 916 (Pubitemid 34464897)
66. J. Zhang, and M.D. Allen FRET-based biosensors for protein kinases: Illuminating the kinome Mol. Biosyst. 3 2007 759 765 (Pubitemid 47587185)
67. J. Zhang Genetically encoded reporters of protein kinase A activity reveal impact of substrate tethering Proc. Natl. Acad. Sci. USA 98 2001 14997 15002 (Pubitemid 34013958)
68. J. Zhang Creating new fluorescent probes for cell biology Nat. Rev. Mol. Cell Biol. 3 2002 906 918 (Pubitemid 35477369)
69. J. Zhang Insulin disrupts beta-adrenergic signalling to protein kinase A in adipocytes Nature 437 2005 569 573 (Pubitemid 41613556)