Advertisement

pp 1-35 | Cite as

Applications of Fluorescent Protein-Based Sensors in Bioimaging

  • Uday Kumar Sukumar
  • Arutselvan Natarajan
  • Tarik F. Massoud
  • Ramasamy PaulmuruganEmail author
Chapter
  • 16 Downloads
Part of the Topics in Medicinal Chemistry book series

Abstract

In the last two decades, there have been enormous developments in the area of reporter gene imaging for various bioimaging applications, especially to track cellular events that are occurring in intact cells and cells within living animals. As part of this process, there has been a significant interest in identifying new reporters or developing new substrates that can allow us to image multiple cellular events simultaneously without any signal overlap between the targets. Even though chemical dyes are useful for some of these applications, reporter proteins which mimic biological properties of proteins when tagged directly with the target proteins are very useful. Although molecular imaging has significantly advanced through use of different imaging probes (radiolabeled ligands, MR contrast agents, CT contrast agents, fluorescent dyes, fluorescent and bioluminescent proteins) and techniques (PET, SPECT, MRI, CT, optical, ultrasound, and photoacoustic imaging), optical imaging, such as fluorescence and bioluminescence imaging, has shown promising applications in various preclinical settings, especially in imaging cellular pathways and studies involving drug development. This is mainly owing to its simple and easy nature in performing the assay and also its high-throughput and cost-effective applications. In this chapter, we review the evolution of optical imaging with specific emphasis on fluorescent proteins, as well as an introduction regarding the general approach of optical imaging in in vitro and in vivo applications. We explain this by briefly introducing different optical imaging methods and fluorescent assays developed based on fluorescent dyes and fluorescent proteins followed by a detailed review of different fluorescent proteins currently used for various assay developments and applications.

Keywords

BRET Fluorescence dyes Fluorescent proteins FRET In vivo imaging 

Notes

Acknowledgments

We would like to thank the Canary Center at Stanford, Department of Radiology, for providing facility and resources. We also thank SCi3 Small Animal Imaging Service Center, Stanford University School of Medicine, for providing imaging facilities and data analysis support. We acknowledge Dr. Sanjiv Sam Gambhir, Chair of the Department of Radiology, Stanford University, for his constant support and help.

Compliance with Ethical Standards

Conflicts of Interest

There are no actual or potential conflicts of interest in regard to this chapter.

Funding

This research was supported by NIH R01CA209888 and NIH R21EB022298. This work was also in part supported by the Center for Cancer Nanotechnology Excellence for Translational Diagnostics (CCNE-TD) at Stanford University through an award (grant no. U54 CA199075) from the National Cancer Institute (NCI) of the National Institutes of Health (NIH).

Ethical Approval

All applicable international, national, and/or institutional guidelines for the care and use of animals were followed.

References

  1. 1.
    Bu L, Shen B, Cheng Z (2014) Fluorescent imaging of cancerous tissues for targeted surgery. Adv Drug Deliv Rev 76:21–38Google Scholar
  2. 2.
    Lavis LD, Raines RT (2008) Bright ideas for chemical biology. ACS Chem Biol 3(3):142–155Google Scholar
  3. 3.
    Tsien RY (2010) Nobel lecture: constructing and exploiting the fluorescent protein paintbox. Integr Biol 2(2–3):77–93Google Scholar
  4. 4.
    Vigneshvar S et al (2016) Recent advances in biosensor technology for potential applications – an overview. Front Bioeng Biotechnol 4:11Google Scholar
  5. 5.
    Shimomura O, Johnson FH, Saiga Y (1962) Extraction, purification and properties of aequorin, a bioluminescent protein from the luminous hydromedusan, Aequorea. J Cell Comp Physiol 59:223–239Google Scholar
  6. 6.
    Gong Z, Ju B, Wan H (2001) Green fluorescent protein (GFP) transgenic fish and their applications. Genetica 111(1–3):213–225Google Scholar
  7. 7.
    Lai L et al (2002) Transgenic pig expressing the enhanced green fluorescent protein produced by nuclear transfer using colchicine-treated fibroblasts as donor cells. Mol Reprod Dev 62(3):300–306Google Scholar
  8. 8.
    Dhandayuthapani S et al (1995) Green fluorescent protein as a marker for gene expression and cell biology of mycobacterial interactions with macrophages. Mol Microbiol 17(5):901–912Google Scholar
  9. 9.
    Zacharias DA et al (2002) Partitioning of lipid-modified monomeric GFPs into membrane microdomains of live cells. Science 296(5569):913–916Google Scholar
  10. 10.
    McCombs JE, Palmer AE (2008) Measuring calcium dynamics in living cells with genetically encodable calcium indicators. Methods 46(3):152–159Google Scholar
  11. 11.
    Mank M, Griesbeck O (2008) Genetically encoded calcium indicators. Chem Rev 108(5):1550–1564Google Scholar
  12. 12.
    Xiao T et al (2017) In vivo analysis with electrochemical sensors and biosensors. Anal Chem 89(1):300–313Google Scholar
  13. 13.
    Takanaga H, Chaudhuri B, Frommer WB (2008) GLUT1 and GLUT9 as major contributors to glucose influx in HepG2 cells identified by a high sensitivity intramolecular FRET glucose sensor. Biochim Biophys Acta 1778(4):1091–1099Google Scholar
  14. 14.
    Ha JS et al (2007) Design and application of highly responsive fluorescence resonance energy transfer biosensors for detection of sugar in living Saccharomyces cerevisiae cells. Appl Environ Microbiol 73(22):7408–7414Google Scholar
  15. 15.
    Hires SA, Zhu Y, Tsien RY (2008) Optical measurement of synaptic glutamate spillover and reuptake by linker optimized glutamate-sensitive fluorescent reporters. Proc Natl Acad Sci U S A 105(11):4411–4416Google Scholar
  16. 16.
    Tainaka K et al (2010) Design strategies of fluorescent biosensors based on biological macromolecular receptors. Sensors 10(2):1355–1376Google Scholar
  17. 17.
    Mehrotra P (2016) Biosensors and their applications – a review. J Oral Biol Craniofac Res 6(2):153–159Google Scholar
  18. 18.
    Bajar BT et al (2016) A guide to fluorescent protein FRET pairs. Sensors 16(9):1488Google Scholar
  19. 19.
    Laverdant J et al (2011) Experimental determination of the fluorescence quantum yield of semiconductor nanocrystals. Materials 4(7):1182–1193Google Scholar
  20. 20.
    Rurack K, Spieles M (2011) Fluorescence quantum yields of a series of red and near-infrared dyes emitting at 600-1000 nm. Anal Chem 83(4):1232–1242Google Scholar
  21. 21.
    Verma D, Grigoryan G, Bailey-Kellogg C (2015) Structure-based design of combinatorial mutagenesis libraries. Protein Sci 24(5):895–908Google Scholar
  22. 22.
    Saito Y et al (2018) Machine-learning-guided mutagenesis for directed evolution of fluorescent proteins. ACS Synth Biol 7(9):2014–2022Google Scholar
  23. 23.
    Mitchell JA et al (2016) Rangefinder: a semisynthetic FRET sensor design algorithm. ACS Sensors 1(11):1286–1290Google Scholar
  24. 24.
    Malakauskas SM, Mayo SL (1998) Design, structure and stability of a hyperthermophilic protein variant. Nat Struct Biol 5(6):470–475Google Scholar
  25. 25.
    Looger LL et al (2003) Computational design of receptor and sensor proteins with novel functions. Nature 423(6936):185–190Google Scholar
  26. 26.
    Jiang L et al (2008) De novo computational design of retro-aldol enzymes. Science 319(5868):1387–1391Google Scholar
  27. 27.
    Rothlisberger D et al (2008) Kemp elimination catalysts by computational enzyme design. Nature 453(7192):190–195Google Scholar
  28. 28.
    Kuhlman B et al (2003) Design of a novel globular protein fold with atomic-level accuracy. Science 302(5649):1364–1368Google Scholar
  29. 29.
    Yang F, Moss LG, Phillips Jr GN (1996) The molecular structure of green fluorescent protein. Nat Biotechnol 14(10):1246–1251Google Scholar
  30. 30.
    Heim R, Prasher DC, Tsien RY (1994) Wavelength mutations and posttranslational autoxidation of green fluorescent protein. Proc Natl Acad Sci U S A 91(26):12501–12504Google Scholar
  31. 31.
    Heim R, Tsien RY (1996) Engineering green fluorescent protein for improved brightness, longer wavelengths and fluorescence resonance energy transfer. Curr Biol 6(2):178–182Google Scholar
  32. 32.
    Tomosugi W et al (2009) An ultramarine fluorescent protein with increased photostability and pH insensitivity. Nat Methods 6(5):351–353Google Scholar
  33. 33.
    Kremers GJ et al (2006) Cyan and yellow super fluorescent proteins with improved brightness, protein folding, and FRET Forster radius. Biochemistry 45(21):6570–6580Google Scholar
  34. 34.
    Rizzo MA et al (2004) An improved cyan fluorescent protein variant useful for FRET. Nat Biotechnol 22(4):445–449Google Scholar
  35. 35.
    Cormack BP, Valdivia RH, Falkow S (1996) FACS-optimized mutants of the green fluorescent protein (GFP). Gene 173(1):33–38Google Scholar
  36. 36.
    Heim R, Cubitt AB, Tsien RY (1995) Improved green fluorescence. Nature 373(6516):663–664Google Scholar
  37. 37.
    Yang TT, Cheng L, Kain SR (1996) Optimized codon usage and chromophore mutations provide enhanced sensitivity with the green fluorescent protein. Nucleic Acids Res 24(22):4592–4593Google Scholar
  38. 38.
    Ormo M et al (1996) Crystal structure of the Aequorea victoria green fluorescent protein. Science 273(5280):1392–1395Google Scholar
  39. 39.
    Gittins JR et al (2015) Fluorescent protein-mediated colour polymorphism in reef corals: multicopy genes extend the adaptation/acclimatization potential to variable light environments. Mol Ecol 24(2):453–465Google Scholar
  40. 40.
    Lukyanov KA et al (2000) Natural animal coloration can be determined by a nonfluorescent green fluorescent protein homolog. J Biol Chem 275(34):25879–25882Google Scholar
  41. 41.
    Matz MV et al (1999) Fluorescent proteins from nonbioluminescent Anthozoa species. Nat Biotechnol 17(10):969–973Google Scholar
  42. 42.
    Shkrob MA et al (2005) Far-red fluorescent proteins evolved from a blue chromoprotein from Actinia equina. Biochem J 392(Pt 3):649–654Google Scholar
  43. 43.
    Evdokimov AG et al (2006) Structural basis for the fast maturation of Arthropoda green fluorescent protein. EMBO Rep 7(10):1006–1012Google Scholar
  44. 44.
    Shagin DA et al (2004) GFP-like proteins as ubiquitous metazoan superfamily: evolution of functional features and structural complexity. Mol Biol Evol 21(5):841–850Google Scholar
  45. 45.
    Germond A et al (2016) Design and development of genetically encoded fluorescent sensors to monitor intracellular chemical and physical parameters. Biophys Rev 8(2):121–138Google Scholar
  46. 46.
    Tavare JM, Fletcher LM, Welsh GI (2001) Using green fluorescent protein to study intracellular signalling. J Endocrinol 170(2):297–306Google Scholar
  47. 47.
    Palmer AE et al (2011) Design and application of genetically encoded biosensors. Trends Biotechnol 29(3):144–152Google Scholar
  48. 48.
    Day RN, Davidson MW (2009) The fluorescent protein palette: tools for cellular imaging. Chem Soc Rev 38(10):2887–2921Google Scholar
  49. 49.
    Song W, Strack RL, Jaffrey SR (2013) Imaging bacterial protein expression using genetically encoded RNA sensors. Nat Methods 10(9):873–875Google Scholar
  50. 50.
    Thorn K (2017) Genetically encoded fluorescent tags. Mol Biol Cell 28(7):848–857Google Scholar
  51. 51.
    Rowland CE et al (2015) Intracellular FRET-based probes: a review. Methods Appl Fluoresc 3(4):042006Google Scholar
  52. 52.
    Miesenbock G, De Angelis DA, Rothman JE (1998) Visualizing secretion and synaptic transmission with pH-sensitive green fluorescent proteins. Nature 394(6689):192–195Google Scholar
  53. 53.
    Johnson DE et al (2009) Red fluorescent protein pH biosensor to detect concentrative nucleoside transport. J Biol Chem 284(31):20499–20511Google Scholar
  54. 54.
    Tallini YN et al (2006) Imaging cellular signals in the heart in vivo: cardiac expression of the high-signal Ca2+ indicator GCaMP2. Proc Natl Acad Sci U S A 103(12):4753–4758Google Scholar
  55. 55.
    Souslova EA et al (2007) Single fluorescent protein-based Ca2+ sensors with increased dynamic range. BMC Biotechnol 7:37Google Scholar
  56. 56.
    Griesbeck O et al (2001) Reducing the environmental sensitivity of yellow fluorescent protein. Mechanism and applications. J Biol Chem 276(31):29188–29194Google Scholar
  57. 57.
    Belousov VV et al (2006) Genetically encoded fluorescent indicator for intracellular hydrogen peroxide. Nat Methods 3(4):281–286Google Scholar
  58. 58.
    Gallegos LL, Kunkel MT, Newton AC (2006) Targeting protein kinase C activity reporter to discrete intracellular regions reveals spatiotemporal differences in agonist-dependent signaling. J Biol Chem 281(41):30947–30956Google Scholar
  59. 59.
    Goedhart J et al (2007) Sensitive detection of p65 homodimers using red-shifted and fluorescent protein-based FRET couples. PLoS One 2(10):e1011Google Scholar
  60. 60.
    Miyawaki A et al (1997) Fluorescent indicators for Ca2+ based on green fluorescent proteins and calmodulin. Nature 388(6645):882–887Google Scholar
  61. 61.
    Berney C, Danuser G (2003) FRET or no FRET: a quantitative comparison. Biophys J 84(6):3992–4010Google Scholar
  62. 62.
    Hanson GT et al (2002) Green fluorescent protein variants as ratiometric dual emission pH sensors. 1. Structural characterization and preliminary application. Biochemistry 41(52):15477–15488Google Scholar
  63. 63.
    Kneen M et al (1998) Green fluorescent protein as a noninvasive intracellular pH indicator. Biophys J 74(3):1591–1599Google Scholar
  64. 64.
    Jayaraman S et al (2000) Mechanism and cellular applications of a green fluorescent protein-based halide sensor. J Biol Chem 275(9):6047–6050Google Scholar
  65. 65.
    DiPilato LM, Cheng X, Zhang J (2004) Fluorescent indicators of cAMP and Epac activation reveal differential dynamics of cAMP signaling within discrete subcellular compartments. Proc Natl Acad Sci U S A 101(47):16513–16518Google Scholar
  66. 66.
    Hanson GT et al (2004) Investigating mitochondrial redox potential with redox-sensitive green fluorescent protein indicators. J Biol Chem 279(13):13044–13053Google Scholar
  67. 67.
    Ashby MC, Ibaraki K, Henley JM (2004) It’s green outside: tracking cell surface proteins with pH-sensitive GFP. Trends Neurosci 27(5):257–261Google Scholar
  68. 68.
    Llopis J et al (1998) Measurement of cytosolic, mitochondrial, and Golgi pH in single living cells with green fluorescent proteins. Proc Natl Acad Sci U S A 95(12):6803–6808Google Scholar
  69. 69.
    Sankaranarayanan S et al (2000) The use of pHluorins for optical measurements of presynaptic activity. Biophys J 79(4):2199–2208Google Scholar
  70. 70.
    Henderson JN et al (2009) Excited state proton transfer in the red fluorescent protein mKeima. J Am Chem Soc 131(37):13212–13213Google Scholar
  71. 71.
    Violot S et al (2009) Reverse pH-dependence of chromophore protonation explains the large Stokes shift of the red fluorescent protein mKeima. J Am Chem Soc 131(30):10356–10357Google Scholar
  72. 72.
    Fang EF et al (2017) In vitro and in vivo detection of mitophagy in human cells, C. Elegans, and mice. J Vis Exp 129:e56301Google Scholar
  73. 73.
    Shinoda H, Shannon M, Nagai T (2018) Fluorescent proteins for investigating biological events in acidic environments. Int J Mol Sci 19(6):1543Google Scholar
  74. 74.
    Tantama M, Hung YP, Yellen G (2011) Imaging intracellular pH in live cells with a genetically encoded red fluorescent protein sensor. J Am Chem Soc 133(26):10034–10037Google Scholar
  75. 75.
    Shcherbakova DM, Subach OM, Verkhusha VV (2012) Red fluorescent proteins: advanced imaging applications and future design. Angew Chem Int Ed Engl 51(43):10724–10738Google Scholar
  76. 76.
    Horikawa K et al (2010) Spontaneous network activity visualized by ultrasensitive Ca(2+) indicators, yellow Cameleon-Nano. Nat Methods 7(9):729–732Google Scholar
  77. 77.
    Nagai T et al (2004) Expanded dynamic range of fluorescent indicators for Ca(2+) by circularly permuted yellow fluorescent proteins. Proc Natl Acad Sci U S A 101(29):10554–10559Google Scholar
  78. 78.
    Palmer AE et al (2004) Bcl-2-mediated alterations in endoplasmic reticulum Ca2+ analyzed with an improved genetically encoded fluorescent sensor. Proc Natl Acad Sci U S A 101(50):17404–17409Google Scholar
  79. 79.
    Palmer AE et al (2006) Ca2+ indicators based on computationally redesigned calmodulin-peptide pairs. Chem Biol 13(5):521–530Google Scholar
  80. 80.
    Mank M et al (2008) A genetically encoded calcium indicator for chronic in vivo two-photon imaging. Nat Methods 5(9):805–811Google Scholar
  81. 81.
    Vinkenborg JL et al (2009) Genetically encoded FRET sensors to monitor intracellular Zn2+ homeostasis. Nat Methods 6(10):737–740Google Scholar
  82. 82.
    Evers TH et al (2007) Ratiometric detection of Zn(II) using chelating fluorescent protein chimeras. J Mol Biol 374(2):411–425Google Scholar
  83. 83.
    Qin Y et al (2011) Measuring steady-state and dynamic endoplasmic reticulum and Golgi Zn2+ with genetically encoded sensors. Proc Natl Acad Sci U S A 108(18):7351–7356Google Scholar
  84. 84.
    Emmanouilidou E et al (1999) Imaging Ca2+ concentration changes at the secretory vesicle surface with a recombinant targeted cameleon. Curr Biol 9(16):915–918Google Scholar
  85. 85.
    Palmer AE, Tsien RY (2006) Measuring calcium signaling using genetically targetable fluorescent indicators. Nat Protoc 1(3):1057–1065Google Scholar
  86. 86.
    Kerppola TK (2008) Bimolecular fluorescence complementation (BiFC) analysis as a probe of protein interactions in living cells. Annu Rev Biophys 37:465–487Google Scholar
  87. 87.
    Kerppola TK (2008) Bimolecular fluorescence complementation: visualization of molecular interactions in living cells. Methods Cell Biol 85:431–470Google Scholar
  88. 88.
    Kodama Y, Hu CD (2012) Bimolecular fluorescence complementation (BiFC): a 5-year update and future perspectives. Biotechniques 53(5):285–298Google Scholar
  89. 89.
    Kerppola TK (2006) Visualization of molecular interactions by fluorescence complementation. Nat Rev Mol Cell Biol 7(6):449–456Google Scholar
  90. 90.
    Magliery TJ et al (2005) Detecting protein-protein interactions with a green fluorescent protein fragment reassembly trap: scope and mechanism. J Am Chem Soc 127(1):146–157Google Scholar
  91. 91.
    Hu CD, Chinenov Y, Kerppola TK (2002) Visualization of interactions among bZIP and Rel family proteins in living cells using bimolecular fluorescence complementation. Mol Cell 9(4):789–798Google Scholar
  92. 92.
    Hu CD, Kerppola TK (2003) Simultaneous visualization of multiple protein interactions in living cells using multicolor fluorescence complementation analysis. Nat Biotechnol 21(5):539–545Google Scholar
  93. 93.
    Shyu YJ et al (2006) Identification of new fluorescent protein fragments for bimolecular fluorescence complementation analysis under physiological conditions. Biotechniques 40(1):61–66Google Scholar
  94. 94.
    Waadt R et al (2008) Multicolor bimolecular fluorescence complementation reveals simultaneous formation of alternative CBL/CIPK complexes in planta. Plant J 56(3):505–516Google Scholar
  95. 95.
    Fan JY et al (2008) Split mCherry as a new red bimolecular fluorescence complementation system for visualizing protein-protein interactions in living cells. Biochem Biophys Res Commun 367(1):47–53Google Scholar
  96. 96.
    Kodama Y, Wada M (2009) Simultaneous visualization of two protein complexes in a single plant cell using multicolor fluorescence complementation analysis. Plant Mol Biol 70(1–2):211–217Google Scholar
  97. 97.
    Chu J et al (2009) A novel far-red bimolecular fluorescence complementation system that allows for efficient visualization of protein interactions under physiological conditions. Biosens Bioelectron 25(1):234–239Google Scholar
  98. 98.
    Grinberg AV, Hu CD, Kerppola TK (2004) Visualization of Myc/Max/Mad family dimers and the competition for dimerization in living cells. Mol Cell Biol 24(10):4294–4308Google Scholar
  99. 99.
    Vidi PA et al (2008) Ligand-dependent oligomerization of dopamine D(2) and adenosine A(2A) receptors in living neuronal cells. Mol Pharmacol 74(3):544–551Google Scholar
  100. 100.
    Niu W, Guo J (2013) Expanding the chemistry of fluorescent protein biosensors through genetic incorporation of unnatural amino acids. Mol Biosyst 9(12):2961–2970Google Scholar
  101. 101.
    Ayyadurai N et al (2011) Development of a selective, sensitive, and reversible biosensor by the genetic incorporation of a metal-binding site into green fluorescent protein. Angew Chem Int Ed Engl 50(29):6534–6537Google Scholar
  102. 102.
    Niu W, Guo J (2017) Novel fluorescence-based biosensors incorporating unnatural amino acids. Methods Enzymol 589:191–219Google Scholar
  103. 103.
    Wang F et al (2012) Unnatural amino acid mutagenesis of fluorescent proteins. Angew Chem Int Ed Engl 51(40):10132–10135Google Scholar
  104. 104.
    Chen S et al (2012) Reaction-based genetically encoded fluorescent hydrogen sulfide sensors. J Am Chem Soc 134(23):9589–9592Google Scholar
  105. 105.
    Chen ZJ et al (2013) Genetically encoded fluorescent probe for the selective detection of peroxynitrite. J Am Chem Soc 135(40):14940–14943Google Scholar
  106. 106.
    Alford SC et al (2012) A fluorogenic red fluorescent protein heterodimer. Chem Biol 19(3):353–360Google Scholar
  107. 107.
    Alford SC et al (2012) Dimerization-dependent green and yellow fluorescent proteins. ACS Synth Biol 1(12):569–575Google Scholar
  108. 108.
    Thornton JM, Sibanda BL (1983) Amino and carboxy-terminal regions in globular proteins. J Mol Biol 167(2):443–460Google Scholar
  109. 109.
    Bliven S, Prlic A (2012) Circular permutation in proteins. PLoS Comput Biol 8(3):e1002445Google Scholar
  110. 110.
    Miyawaki A et al (1999) Dynamic and quantitative Ca2+ measurements using improved cameleons. Proc Natl Acad Sci U S A 96(5):2135–2140Google Scholar
  111. 111.
    Tian L, Hires SA, Looger LL (2012) Imaging neuronal activity with genetically encoded calcium indicators. Cold Spring Harb Protoc 2012(6):647–656Google Scholar
  112. 112.
    Nakai J, Ohkura M, Imoto K (2001) A high signal-to-noise Ca(2+) probe composed of a single green fluorescent protein. Nat Biotechnol 19(2):137–141Google Scholar
  113. 113.
    Nausch LW et al (2008) Differential patterning of cGMP in vascular smooth muscle cells revealed by single GFP-linked biosensors. Proc Natl Acad Sci U S A 105(1):365–370Google Scholar
  114. 114.
    Mizuno T et al (2007) Metal-ion-dependent GFP emission in vivo by combining a circularly permutated green fluorescent protein with an engineered metal-ion-binding coiled-coil. J Am Chem Soc 129(37):11378–11383Google Scholar
  115. 115.
    Mao T et al (2008) Characterization and subcellular targeting of GCaMP-type genetically-encoded calcium indicators. PLoS One 3(3):e1796Google Scholar
  116. 116.
    Suzuki J, Kanemaru K, Iino M (2016) Genetically encoded fluorescent indicators for organellar calcium imaging. Biophys J 111(6):1119–1131Google Scholar
  117. 117.
    Baird GS, Zacharias DA, Tsien RY (1999) Circular permutation and receptor insertion within green fluorescent proteins. Proc Natl Acad Sci U S A 96(20):11241–11246Google Scholar
  118. 118.
    Nagai T et al (2001) Circularly permuted green fluorescent proteins engineered to sense Ca2+. Proc Natl Acad Sci U S A 98(6):3197–3202Google Scholar
  119. 119.
    Ohkura M et al (2005) Genetically encoded bright Ca2+ probe applicable for dynamic Ca2+ imaging of dendritic spines. Anal Chem 77(18):5861–5869Google Scholar
  120. 120.
    Kawai Y, Sato M, Umezawa Y (2004) Single color fluorescent indicators of protein phosphorylation for multicolor imaging of intracellular signal flow dynamics. Anal Chem 76(20):6144–6149Google Scholar
  121. 121.
    Gautam SG et al (2009) Exploration of fluorescent protein voltage probes based on circularly permuted fluorescent proteins. Front Neuroeng 2:14Google Scholar
  122. 122.
    Knopfel T et al (2003) Optical recordings of membrane potential using genetically targeted voltage-sensitive fluorescent proteins. Methods 30(1):42–48Google Scholar
  123. 123.
    Berg J, Hung YP, Yellen G (2009) A genetically encoded fluorescent reporter of ATP:ADP ratio. Nat Methods 6(2):161–166Google Scholar
  124. 124.
    Hernandez-Barrera A et al (2015) Hyper, a hydrogen peroxide sensor, indicates the sensitivity of the Arabidopsis root elongation zone to aluminum treatment. Sensors 15(1):855–867Google Scholar
  125. 125.
    Niethammer P et al (2009) A tissue-scale gradient of hydrogen peroxide mediates rapid wound detection in zebrafish. Nature 459(7249):996–999Google Scholar
  126. 126.
    Forster T (1946) Energiewanderung und Fluoreszenz. Naturwissenschaften 33(6):166–175Google Scholar
  127. 127.
    Ma L, Yang F, Zheng J (2014) Application of fluorescence resonance energy transfer in protein studies. J Mol Struct 1077:87–100Google Scholar
  128. 128.
    Tamura T, Hamachi I (2014) Recent progress in design of protein-based fluorescent biosensors and their cellular applications. ACS Chem Biol 9(12):2708–2717Google Scholar
  129. 129.
    Day RN, Davidson MW (2012) Fluorescent proteins for FRET microscopy: monitoring protein interactions in living cells. Bioessays 34(5):341–350Google Scholar
  130. 130.
    Nikolaev VO, Gambaryan S, Lohse MJ (2006) Fluorescent sensors for rapid monitoring of intracellular cGMP. Nat Methods 3(1):23–25Google Scholar
  131. 131.
    Wallace DJ et al (2008) Single-spike detection in vitro and in vivo with a genetic Ca2+ sensor. Nat Methods 5(9):797–804Google Scholar
  132. 132.
    Shcherbo D et al (2009) Practical and reliable FRET/FLIM pair of fluorescent proteins. BMC Biotechnol 9:24Google Scholar
  133. 133.
    Zhang J et al (2001) Genetically encoded reporters of protein kinase A activity reveal impact of substrate tethering. Proc Natl Acad Sci U S A 98(26):14997–15002Google Scholar
  134. 134.
    Tsutsui H et al (2008) Improving membrane voltage measurements using FRET with new fluorescent proteins. Nat Methods 5(8):683–685Google Scholar
  135. 135.
    Mutoh H et al (2009) Spectrally-resolved response properties of the three most advanced FRET based fluorescent protein voltage probes. PLoS One 4(2):e4555Google Scholar
  136. 136.
    Tyas L et al (2000) Rapid caspase-3 activation during apoptosis revealed using fluorescence-resonance energy transfer. EMBO Rep 1(3):266–270Google Scholar
  137. 137.
    Wu X et al (2006) Measurement of two caspase activities simultaneously in living cells by a novel dual FRET fluorescent indicator probe. Cytometry A 69(6):477–486Google Scholar
  138. 138.
    Bozza WP et al (2014) The use of a stably expressed FRET biosensor for determining the potency of cancer drugs. PLoS One 9(9):e107010Google Scholar
  139. 139.
    Kominami K et al (2012) In vivo imaging of hierarchical spatiotemporal activation of caspase-8 during apoptosis. PLoS One 7(11):e50218Google Scholar
  140. 140.
    Sipieter F et al (2014) Shining light on cell death processes – a novel biosensor for necroptosis, a newly described cell death program. Biotechnol J 9(2):224–240Google Scholar
  141. 141.
    Li M et al (2012) A high-throughput FRET-based assay for determination of Atg4 activity. Autophagy 8(3):401–412Google Scholar
  142. 142.
    Lu P et al (2011) Extracellular matrix degradation and remodeling in development and disease. Cold Spring Harb Perspect Biol 3(12):a005058Google Scholar
  143. 143.
    Eichorst JP, Clegg RM, Wang Y (2012) Red-shifted fluorescent proteins monitor enzymatic activity in live HT-1080 cells with fluorescence lifetime imaging microscopy (FLIM). J Microsc 248(1):77–89Google Scholar
  144. 144.
    Hou BH et al (2011) Optical sensors for monitoring dynamic changes of intracellular metabolite levels in mammalian cells. Nat Protoc 6(11):1818–1833Google Scholar
  145. 145.
    Gavet O, Pines J (2010) Progressive activation of CyclinB1-Cdk1 coordinates entry to mitosis. Dev Cell 18(4):533–543Google Scholar
  146. 146.
    Miura H, Matsuda M, Aoki K (2014) Development of a FRET biosensor with high specificity for Akt. Cell Struct Funct 39(1):9–20Google Scholar
  147. 147.
    Yoshizaki H et al (2007) Akt-PDK1 complex mediates epidermal growth factor-induced membrane protrusion through Ral activation. Mol Biol Cell 18(1):119–128Google Scholar
  148. 148.
    Seong J et al (2013) Distinct biophysical mechanisms of focal adhesion kinase mechanoactivation by different extracellular matrix proteins. Proc Natl Acad Sci U S A 110(48):19372–19377Google Scholar
  149. 149.
    Wang Y et al (2005) Visualizing the mechanical activation of Src. Nature 434(7036):1040–1045Google Scholar
  150. 150.
    Vevea JD et al (2013) Ratiometric biosensors that measure mitochondrial redox state and ATP in living yeast cells. J Vis Exp 77:50633Google Scholar
  151. 151.
    Fehr M et al (2003) In vivo imaging of the dynamics of glucose uptake in the cytosol of COS-7 cells by fluorescent nanosensors. J Biol Chem 278(21):19127–19133Google Scholar
  152. 152.
    San Martin A et al (2013) A genetically encoded FRET lactate sensor and its use to detect the Warburg effect in single cancer cells. PLoS One 8(2):e57712Google Scholar
  153. 153.
    Nagai T, Miyawaki A (2004) A high-throughput method for development of FRET-based indicators for proteolysis. Biochem Biophys Res Commun 319(1):72–77Google Scholar
  154. 154.
    Mizutani T et al (2010) A novel FRET-based biosensor for the measurement of BCR-ABL activity and its response to drugs in living cells. Clin Cancer Res 16(15):3964–3975Google Scholar
  155. 155.
    Nobis M et al (2013) Intravital FLIM-FRET imaging reveals dasatinib-induced spatial control of src in pancreatic cancer. Cancer Res 73(15):4674–4686Google Scholar
  156. 156.
    Randriamampita C et al (2008) A novel ZAP-70 dependent FRET based biosensor reveals kinase activity at both the immunological synapse and the antisynapse. PLoS One 3(1):e1521Google Scholar
  157. 157.
    Paster W et al (2009) Genetically encoded Forster resonance energy transfer sensors for the conformation of the Src family kinase Lck. J Immunol 182(4):2160–2167Google Scholar
  158. 158.
    Grashoff C et al (2010) Measuring mechanical tension across vinculin reveals regulation of focal adhesion dynamics. Nature 466(7303):263–266Google Scholar
  159. 159.
    Conway DE et al (2013) Fluid shear stress on endothelial cells modulates mechanical tension across VE-cadherin and PECAM-1. Curr Biol 23(11):1024–1030Google Scholar
  160. 160.
    Borghi N et al (2012) E-cadherin is under constitutive actomyosin-generated tension that is increased at cell-cell contacts upon externally applied stretch. Proc Natl Acad Sci U S A 109(31):12568–12573Google Scholar
  161. 161.
    Potzkei J et al (2012) Real-time determination of intracellular oxygen in bacteria using a genetically encoded FRET-based biosensor. BMC Biol 10:28Google Scholar
  162. 162.
    Conway JR, Carragher NO, Timpson P (2014) Developments in preclinical cancer imaging: innovating the discovery of therapeutics. Nat Rev Cancer 14(5):314–328Google Scholar
  163. 163.
    Bernardini A et al (2015) Type I cell ROS kinetics under hypoxia in the intact mouse carotid body ex vivo: a FRET-based study. Am J Physiol Cell Physiol 308(1):C61–C67Google Scholar
  164. 164.
    Awaji T et al (2001) Novel green fluorescent protein-based ratiometric indicators for monitoring pH in defined intracellular microdomains. Biochem Biophys Res Commun 289(2):457–462Google Scholar
  165. 165.
    Urra J et al (2008) A genetically encoded ratiometric sensor to measure extracellular pH in microdomains bounded by basolateral membranes of epithelial cells. Pflugers Arch 457(1):233–242Google Scholar
  166. 166.
    Heydorn A et al (2006) Protein translocation assays: key tools for accessing new biological information with high-throughput microscopy. Methods Enzymol 414:513–530Google Scholar
  167. 167.
    Knauer SK et al (2005) Translocation biosensors to study signal-specific nucleo-cytoplasmic transport, protease activity and protein-protein interactions. Traffic 6(7):594–606Google Scholar
  168. 168.
    Fetz V, Stauber RH, Knauer SK (2018) Translocation biosensors-versatile tools to probe protein functions in living cells. Methods Mol Biol 1683:195–210Google Scholar
  169. 169.
    Dieguez-Hurtado R et al (2011) A Cre-reporter transgenic mouse expressing the far-red fluorescent protein Katushka. Genesis 49(1):36–45Google Scholar
  170. 170.
    Yamaguchi Y et al (2011) Live imaging of apoptosis in a novel transgenic mouse highlights its role in neural tube closure. J Cell Biol 195(6):1047–1060Google Scholar
  171. 171.
    Audet M et al (2010) Protein-protein interactions monitored in cells from transgenic mice using bioluminescence resonance energy transfer. FASEB J 24(8):2829–2838Google Scholar
  172. 172.
    Hoffman RM (2005) The multiple uses of fluorescent proteins to visualize cancer in vivo. Nat Rev Cancer 5(10):796–806Google Scholar
  173. 173.
    Hara M et al (2004) Imaging endoplasmic reticulum calcium with a fluorescent biosensor in transgenic mice. Am J Physiol Cell Physiol 287(4):C932–C938Google Scholar
  174. 174.
    Zhang J et al (2005) Insulin disrupts beta-adrenergic signalling to protein kinase A in adipocytes. Nature 437(7058):569–573Google Scholar
  175. 175.
    Sun F et al (2018) A genetically encoded fluorescent sensor enables rapid and specific detection of dopamine in flies, fish, and mice. Cell 174(2):481–496.e19Google Scholar
  176. 176.
    Portugues R et al (2014) Whole-brain activity maps reveal stereotyped, distributed networks for visuomotor behavior. Neuron 81(6):1328–1343Google Scholar
  177. 177.
    Livet J et al (2007) Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system. Nature 450(7166):56–62Google Scholar
  178. 178.
    Nobis M et al (2017) A RhoA-FRET biosensor mouse for intravital imaging in normal tissue homeostasis and disease contexts. Cell Rep 21(1):274–288Google Scholar
  179. 179.
    Heppert JK et al (2016) Comparative assessment of fluorescent proteins for in vivo imaging in an animal model system. Mol Biol Cell 27(22):3385–3394Google Scholar
  180. 180.
    Hirayama T et al (2012) Near-infrared fluorescent sensor for in vivo copper imaging in a murine Wilson disease model. Proc Natl Acad Sci U S A 109(7):2228–2233Google Scholar
  181. 181.
    Giloh H, Sedat JW (1982) Fluorescence microscopy: reduced photobleaching of rhodamine and fluorescein protein conjugates by n-propyl gallate. Science 217(4566):1252–1255Google Scholar
  182. 182.
    White J, Stelzer E (1999) Photobleaching GFP reveals protein dynamics inside live cells. Trends Cell Biol 9(2):61–65Google Scholar
  183. 183.
    Dixit R, Cyr R (2003) Cell damage and reactive oxygen species production induced by fluorescence microscopy: effect on mitosis and guidelines for non-invasive fluorescence microscopy. Plant J 36(2):280–290Google Scholar
  184. 184.
    Niswender KD et al (1995) Quantitative imaging of green fluorescent protein in cultured cells: comparison of microscopic techniques, use in fusion proteins and detection limits. J Microsc 180(Pt 2):109–116Google Scholar
  185. 185.
    Shaner NC, Steinbach PA, Tsien RY (2005) A guide to choosing fluorescent proteins. Nat Methods 2(12):905–909Google Scholar
  186. 186.
    Shcherbakova DM, Verkhusha VV (2013) Near-infrared fluorescent proteins for multicolor in vivo imaging. Nat Methods 10(8):751–754Google Scholar
  187. 187.
    Nishihara R et al (2019) Highly bright and stable NIR-BRET with blue-shifted coelenterazine derivatives for deep-tissue imaging of molecular events in vivo. Theranostics 9(9):2646–2661Google Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Uday Kumar Sukumar
    • 1
  • Arutselvan Natarajan
    • 1
  • Tarik F. Massoud
    • 1
  • Ramasamy Paulmurugan
    • 1
    Email author
  1. 1.Molecular Imaging Program at Stanford, Department of RadiologyStanford University School of MedicineStanfordUSA

Personalised recommendations