Abstract
Since the last decade, a lot of advancement has been made to understand biological processes involving complex intracellular pathways. The major challenge faced was monitoring and trafficking of metabolites in real time. Although a range of quantitative and imaging techniques have been developed so far, the discovery of green fluorescent proteins (GFPs) has revolutionized the advancement in the field of metabolomics. GFPs and their variants have enabled researchers to ‘paint’ a wide range of biological molecules. Fluorescence resonance energy transfer (FRET)-based genetically encoded sensors is a promising technology to decipher the real-time monitoring of the cellular events inside living cells. GFPs and their variants, due to their intrinsic fluorescence properties, are extensively being used nowadays in cell-based assays. This review focuses on structure and function of GFP and its derivatives, mechanism emission and their use in the development of FRET-based sensors for metabolites.
Similar content being viewed by others
References
Ahmad M, Mohsin M, Iqrar S, Manzoor O, Siddiqi TO and Ahmad A 2018 Live cell imaging of vitamin B12 dynamics by genetically encoded fluorescent nanosensor. Sens. Actuators B Chem. 257 866–874
Ai HW, Hazelwood KL, Davidson MW and Campbell RE 2008 Fluorescent protein FRET pairs for ratiometric imaging of dual biosensors. Nat. Methods 5 401–403
Ameen S, Ahmad M, Mohsin M, Qureshi MI, Ibrahim MM, Abdin MZ and Ahmad A 2016 Designing, construction and characterization of genetically encoded FRET-based nanosensor for real time monitoring of lysine flux in living cells. J. Nanobiotechnol. 14 49
Ananthanarayanan B, Fosbrink M, Rahdar M and Zhang J 2007 Live-cell molecular analysis of Akt activation reveals roles for activation loop phosphorylation. J. Biol. Chem. 282 36634–36641
Ando R, Hama H, Yamamoto-Hino M, Mizuno H and Miyawaki A 2002 An optical marker based on the UV-induced green-to-red photoconversion of a fluorescent protein. Proc. Natl. Acad. Sci. USA 99 12651–12656
Awaji T, Hirasawa A, Shirakawa H, Tsujimoto G and Miyazaki S 2001 Novel green fluorescent protein-based ratiometric indicators for monitoring pH in defined intracellular microdomains. Biochem. Biophys. Res. Commun. 289 457–462
Badura A, Sun XR, Giovannucci A, Lynch LA and Wang SSH 2014 Fast calcium sensor proteins for monitoring neural activity. Neurophotonics 1 025008.
Baird GS, Zacharias DA and Tsien RY 1999 Circular permutation and receptor insertion within green fluorescent proteins. Proc. Natl. Acad. Sci. USA 96 11241–11246
Bajar BT, Wang ES, Lam AJ, Kim BB, Jacobs CL, Howe ES, Davidson MW, Lin MZ and Chu J 2016 Improving brightness and photostability of green and red fluorescent proteins for live cell imaging and FRET reporting. Sci. Rep. 6 20889
Bishop B, Raymond K, Rieger S and Held P 2013 Fluorescent proteins—filters, mirrors and wavelengths. Biotek.
Buckley AM, Petersen J, Roe AJ, Douce GR and Christie JM 2015 LOV-based reporters for fluorescence imaging. Curr. Opin. Chem Biol. 27 39–45
Carrillo LD, Krishnamoorthy L and Mahal LK 2006 A cellular FRET-based sensor for beta-O-GlcNAc, a dynamic carbohydrate modification involved in signalling. J. Am. Chem. Soc. 128 14768–14769
Chalfie M and Kain S 1998 Green fluorescent protein: properties, applications, and protocols 2nd edition (New York: Wiley-Liss)
Chalfie M, Tu Y, Euskirchen G, Ward WW and Prasher DC 1994 Green fluorescent protein as a marker for gene expression. Science. 263 802–805
Chattoraj M, King BA, Bublitz GU and Boxer SG 1996 Ultra-fast excited state dynamics in green fluorescent protein: multiple states and proton transfer. Proc. Natl. Acad. Sci. USA 93 8362–8367
Chudakov DM, Belousov VV and Zaraisky AG 2003 Kindling fluorescent proteins for precise in vivo photolabeling. Nat. Biotechnol. 21 191–194
Cody CW, Prasher DC, Westler WM, Prendergast FG and Ward WW. 1993 Chemical structure of the hexapeptide chromophore of the Aequorea green-fluorescent protein. Biochemistry 32 1212–1218
Conn PM 1999 Green fluorescent protein: methods in enzymology (London, New York: Academic Press) vol. 302
Cormack BP, Valdivia R and Falkow S 1996 FACS-optimized mutants of the green fluorescent protein (GFP). Gene. 173 33–38
Cranfill PJ, Sell BR, Baird MA, Allen JR, Lavagnino Z, de Gruiter HM, Kremers GJ, Davidson, MW, Ustione A and Piston DW 2016 Quantitative assessment of fluorescent proteins. Nat. Methods. 13 557–562
Cubitt AB, Woollenweber LA and Heim R 1999 Understanding structure-function relationships in the Aequorea victoria green fluorescent protein. Methods. Cell. Biol. 58 19–30
De S, Macara IG and Lannigan DA 2005 Novel biosensors for the detection of estrogen receptor ligands. J. Steroid. Biochem. Mol. Biol. 96 235–244
Delagrave S, Hawtin RE, Silva CM, Yang MM and Youvan DC 1995 Red-shifted excitation mutants of the green fluorescent protein. Biotechnology (N Y). 13 151–154
Deuschle K, Okumoto S, Fehr M, Looger LL, Kozhukh L and Frommer WB 2005 Construction and optimization of a family of genetically encoded metabolite sensors by semirational protein engineering. Protein Sci. 14 2304–2314
Dittmer PJ, Miranda JG, Gorski JA and Palmer AE 2009 Genetically encoded sensors to elucidate spatial distribution of cellular zinc. J. Biol. Chem. 284 16289–16297
Doucette J, Zhao Z, Geyer RJ, Barra MM, Balunas MJ and Zweifach A 2016 Flow cytometry enables multiplexed measurements of genetically encoded intramolecular FRET sensors suitable for screening. J. Biomol. Screen. 21 535–547
Eisenstein M 2005 New fluorescent protein includes handy on-off switch. Nat. Methods. 2 8–9
Ellenberg J, Lippincott-Schwartz J and Presley JF 1998 Two-color green fluorescent protein time-lapse imaging. Biotechniques. 25 838–842, 844–846
Förster T 1965 Delocalized excitation and excitation transfer; in Modern quantum chemistry (ed) T Forster (London, New York: Academic Press) vol. 3, pp 93–137
Fujioka A, Terai K, Itoh RE, Aoki K, Nakamura T, Kuroda S, Nishida E and Matsuda M 2006 Dynamics of the Ras/ERK MAPK cascade as monitored by fluorescent probes. J. Biol. Chem. 281 8917–8926
Gavet O and Pines J 2010 Progressive activation of CyclinB1-Cdk1 coordinates entry to mitosis. Dev. Cell. 18 533–543
González-Vera JA and Morris MC 2015 Fluorescent reporters and biosensors for probing the dynamic behavior of protein kinases. Proteomes. 3 369–410
Gu H, Lalonde S, Okumoto S, Looger LL, Scharff-Poulsen AM, Grossman AR, Kossmann J, Jakobsen I and Frommer WB 2006 A novel analytical method for in vivo phosphate tracking. FEBS Lett. 580 5885–5893
Gu Z, Zhao M, Sheng Y, Bentolila LA and Tang Y 2011 Detection of mercury ion by infrared fluorescent protein and its hydrogel-based paper assay. Anal. Chem. 83 2324–2329
Guerrero G, Siegel MS, Roska B, Loots E and Isacoff EY 2002 Tuning FlaSh: redesign of the dynamics, voltage range, and color of the genetically encoded optical sensor of membrane potential. Biophys. J. 83 3607–3618
Heim R, Cubitt AB and Tsien RY 1995 Improved green fluorescence. Nature. 373 663–664
Heim R and Tsien RY 1996 Engineering green fluorescent protein for improved brightness, longer wavelengths and fluorescence resonance energy transfer. Curr. Biol. 6 178–182
Hessels AM, Taylorb KM and Merkx M 2016 Monitoring cytosolic and ER Zn2+ in stimulated breast cancer cells using genetically encoded FRET sensors. Metallomics. 8 211–217
Hung YP, Albeck JG, Tantama M and Yellen G 2011 Imaging cytosolic NADH-NAD(+) redox state with a genetically encoded fluorescent biosensor. Cell. Metab. 14 545–554
Imamura H, Nhat KP, Togawa H, Saito K, Iino R, Kato-Yamada Y, Nagai T and Noji H 2006 Visualization of ATP levels inside single living cells with fluorescence resonance energy transfer-based genetically encoded indicators. Proc. Natl. Acad. Sci. USA 106 15651–15656
Ishikawa-Ankerhold HC, Ankerhold R and Drummen GPC 2012 Advanced fluorescence microscopy techniques—FRAP, FLIP, FLAP, FRET and FLIM. Molecules. 17 4047–4132
Ito T, Umehara T, Sasaki K, Nakamura Y, Nishino N, Terada T, Shirouzu M, Padmanabhan B, Yokoyama S, Ito A and Yoshida M 2011 Real-time imaging of histone H4K12-specific acetylation determines the modes of action of histone deacetylase and bromodomain inhibitors. Chem. Biol. 18 495–507
Ivanova EV, Figueroa RA, Gatsinzi T, Hallberg E and Iverfeldt K 2016 Anchoring of FRET sensors – a requirement for spatiotemporal resolution. Sensors. 16 703
Jares-Erijman EA and Jovin TM 2003 FRET imaging. Nat. Biotechnol. 21 1387–1395
Jensen EC 2012 Use of fluorescent probes: their effect on cell biology and limitations. Anat. Rec (Hoboken). 295 2031–2036
Kaper T, Lager I, Looger LL, Chermak D and Frommer WB 2008 Fluorescence resonance energy transfer sensors for quantitative monitoring of pentose and disaccharide accumulation in bacteria. Biotechnol. Biofuels. 1 11
Kremers GJ, Gilbert SG, Cranfill PJ, Davidson MW and Piston DW 2011 Fluorescent proteins at a glance. J. Cell. Sci. 124 157–160
Kunkel MT, Toker A, Tsien RY and Newton A 2007 Calcium-dependent regulation of protein kinase D revealed by a genetically encoded kinase activity reporter. J. Biol. Chem. 282 6733–6742
Kurokawa K, Mochizuki N, Ohba Y, Mizuno H, Miyawaki A and Matsuda M 2001 A pair of fluorescent resonance energy transfer-based probes for tyrosine phosphorylation of the CrkII adaptor protein in vivo. J. Biol. Chem. 276 31305–31310
Lager I, Looger LL, Hilpert M, Lalonde S and Frommer WB 2006 Conversion of a putative Agrobacterium sugar-binding protein into a FRET sensor with high selectivity for sucrose. J. Biol. Chem. 281 30875–30883
Lin CW, Jao CY and Ting AY 2004 Genetically encoded fluorescent reporters of histone methylation in living cells. J. Am. Chem. Soc. 126 5982–5983
Lindenburg LH, Vinkenborg JL, Oortwijn J, Aper SJA and Merkx M 2006 MagFRET: the first genetically encoded fluorescent Mg2+ sensor. PLoS ONE. 8 e82009
Lippincott-Schwartz J and Patterson GH 2003 Development and use of fluorescent protein markers in living cells. Science 300 87–91
Lippincott-Schwartz J and Patterson GH 2009 Photoactivatable fluorescent proteins for diffraction-limited and super-resolution imaging. Trends Cell Biol. 19 555–565
Lippincott-Schwartz J, Snapp E and Kenworthy A 2001 Studying protein dynamics in living cells. Nat. Rev. Mol. Cell. Biol. 2 444–456
Markova O, Mukhtarov M, Real E, Jacob Y and Bregestovski P 2007 Genetically encoded chloride indicator with improved sensitivity. J. Neurosci. Methods. 170 67–76
Martin AS, Ceballo S, Ruminot I, Lerchundi R, Frommer WB and Barros LF 2013 A genetically encoded FRET lactate sensor and its use to detect the Warburg effect in single cancer cells. PLOS ONE. 8 e57712
Miyawaki A, Llopis J, Heim R, McCaffery JM, Adams JA, Ikura M and Tsien RY 1997 Fluorescent indicators for Ca2+ based on green fluorescent proteins and calmodulin. Nature 388 882–887
Mochizuki N, Yamashita S, Kurokawa K, Ohba Y, Nagai T, Miyawaki A and Matsuda M 2001 Spatio-temporal images of growth-factor-induced activation of Ras and Rap1. Nature 411 1065–1068
Möckl L, Lamb DC and Bräuchle C 2014 Super-resolved fluorescence microscopy: Nobel Prize in Chemistry 2014 for Eric Betzig, Stefan Hell, and William E. Moerner. Angew. Chem., Int. Ed. Engl. 53 13972–13977
Mohsin M, Abdin MZ, Nischal L, Kardam H and Ahmad A 2013 Genetically encoded FRET-based nanosensor for in vivo measurement of leucine. Biosens. Bioelectron. 50 72–77
Mohsin M and Ahmad A 2014 Genetically-encoded nanosensor for quantitative monitoring of methionine in bacterial and yeast cells. Biosens. Bioelectron. 59 358–364
Mohsin M, Ahmad A and Iqbal M 2015 FRET-based genetically-encoded sensors for quantitative monitoring of metabolites. Biotechnol. Lett. 37 1919–1928
Nguyen AW and Daugherty PS 2005 Evolutionary optimization of fluorescent proteins for intracellular FRET. Nat. Biotechnol. 23 355–360
Nishioka T, Aoki K, Hikake K, Yoshizaki H, Kiyokawa E and Matsuda M 2008 Rapid turnover rate of phosphoinositides at the front of migrating MDCK cells. Mol. Biol. Cell. 19 4213–4223
Obeng EM, Dullah EC, Danquah MK, Budimana C and Ongkudon CM 2016 FRET spectroscopy—towards effective biomolecular probing. Anal. Methods 8 5323–5337
Offterdinger M, Georget V, Girod A and Bastiaens PI 2004 Imaging phosphorylation dynamics of the epidermal growth factor receptor. J. Biol. Chem. 279 36972–36981
Okada S, Ota K and Ito T 2009 Circular permutation of ligand-binding module improves dynamic range of genetically encoded FRET-based nanosensor. Protein Sci. 18 2518–2527
Okumoto S 2010 Imaging approach for monitoring cellular metabolites and ions using genetically encoded biosensors. Curr. Opin. Biotechnol. 21 45–54
Olenych SG, Claxton NS, Ottenberg GK and Davidson MW 2007 The fluorescent protein color palette. Curr. Protoc. Cell Biol. 36 1–34
Ormo M, Cubitt AB, Kallio K, Gross LA, Tsien RY and Remington SJ 1996 Crystal structure of the Aequorea victoria green fluorescent protein. Science 273 1392–1395
Palmer AE, Qin Y, Genevieve J and McCombs JE 2011 Design and application of genetically encoded biosensors. Trends Biotechnol. 29 144–152
Patterson GH and Lippincott-Schwartz J 2002 A photo-activatable GFP for selective photolabeling of proteins and cells. Science 297 1873–1877
Pearce LL, Gandley RE, Han W, Wasserloos K, Stitt M, Kanai AJ, McLaughlin MK, Pitt BR and Levitan ES 2000 Role of metallothionein in nitric oxide signaling as revealed by a green fluorescent fusion protein. Proc. Natl. Acad. Sci. USA 97 477–482
Piston DW, Patterson GH, Lippincott-Schwartz J, Claxton NS and Davidson MW 2012 Introduction to Fluorescent Proteins; Nikon. Available online at: http://www.microscopyu.com/articles/livecellimaging/fpintro.html
Prasher DC, Eckenrode VK, Ward WW, Prendergast FG and Cormier MJ 1992 Primary structure of the Aequorea victoria green-fluorescent protein. Gene. 11 229–233
Remington SJ 2011 Green fluorescent protein: a perspective. Protein Sci. 20 1509–1519
Rizzo MA, Springer GH, Granada B and Piston DW 2004 An improved cyan fluorescent protein variant useful for FRET. Nat. Biotechnol. 22 445–449
Rizzuto R, Brini M, De Giorgi F, Rossi R, Heim R, Tsien RY and Pozzan T 1996 Double labelling of subcellular structures with organelle-targeted GFP mutants in vivo. Curr Biol. 6 183–188
Sasaki K, Sato M and Umezawa Y 2003 Fluorescent indicators for Akt/protein kinase B and dynamics of Akt activity visualized in living cells. J. Biol. Chem. 278 30945–30951
Sato M, Ozawa T, Inukai K, Asano T and Umezawa Y 2002 Fluorescent indicators for imaging protein phosphorylation in single living cells. Nat. Biotechnol. 20 287–294
Sattarzadeh A, Saberianfar R, Zipfel WR, Menassa R and Hanson MR 2015 Green to red photoconversion of GFP for protein tracking in vivo. Sci. Rep. 5 11771
Schulenburg C, Faccio G, Jankowska D, Maniura-Weberr K and Richterr M 2016 A FRET-based biosensor for the detection of neutrophil elastase. Analyst. 141 1645–1648
Shaner NC, Campbell RE, Steinbach PA, Giepmans BN, Palmer AE and Tsien RY 2004 Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein. Nat. Biotechnol. 22 1567–1572
Shaner NC, Patterson JH and Davidson MW 2007 Advances in fluorescent protein technology. J. Cell Sci. 120 4247–4260
Shimomura O 2005 The discovery of aequorin and green fluorescent protein. J. Microsc. 217 3–15
Snapp E 2005 Design and use of fluorescent fusion proteins in cell biology. Curr. Protoc. Cell Biol. 21, p. 21
Tsien RY 1998 The green fluorescent protein. Annu. Rev. Biochem. 67509–544
Van Roessel P and Brand AH 2002 Imaging into the future: visualizing gene expression and protein interactions with fluorescent proteins. Nat. Cell Biol. 4 E15–E20
Veetil JV, Jin S and Ye K 2010 A glucose sensor protein for continuous glucose monitoring. Biosens. Bioelectron. 26 1650–1655
Vinkenborg JL, van Duijnhoven SM and Merkx M 2011 Reengineering of a fluorescent zinc sensor protein yields the first genetically encoded cadmium probe. Chem. Commun. (Camb). 47 11879–11881
Wang Y, Botvinick EL, Zhao Y, Berns MW, Usami S, Tsien RY and Chien S 2005 Visualizing the mechanical activation of Src. Nature 434 1040–1050
Ward WW, Prentice HJ, Roth AF, Cody CW and Reeves SC 1982 Spectral perturbations of the Aequorea green-fluorescent protein. Photochem. Photobiol. 35 803–808
Waypa GB, Guzy R, Mungai PT, Mack MM, Marks JD, Roe MW and Schumacker PT 2006 Increases in mitochondrial reactive oxygen species trigger hypoxia-induced calcium responses in pulmonary artery smooth muscle cells. Circ. Res. 99 970–978
Wegner SV, Sun F, Hernandez N and He C 2011 The tightly regulated copper window in yeast. Chem. Commun. (Camb). 47 2571–2573
Wong KA and O’Bryan JP 2011 Bimolecular fluorescence complementation. J. Vis. Exp. 50 2643
Xu X, Gerard AL, Huang BC, Anderson DC, Payan DG and Luo Y 1998 Detection of programmed cell death using fluorescence energy transfer. Nucleic Acids Res. 26 2034–2035
Yang F, Moss LG, Phillips GN J 1996 The molecular structure of green fluorescent protein. Nat. Biotechnol. 14 1246–1251
Yoshizaki H, Aoki K, Nakamura T and Matsuda M 2006 Regulation of RalA GTPase by phosphatidylinositol 3-kinase as visualized by FRET probes. Biochem. Soc. Trans. 34 851–854
Zacharias DA, Violin JD, Newton AC and Tsien RY 2002 Partitioning of lipid-modified monomeric GFPs into membrane microdomains of live cells. Science 296 913–916
Zhang J, Campbell RE, Ting AY and Tsien RY 2002 Creating new fluorescent probes for cell biology. Nat. Rev. Mol. Cell Biol. 12 906–918
Zimmer M 2002 Green fluorescent protein (GFP): applications, structure and related photophysical behaviour. Chem. Rev. 102 759–781
Acknowledgements
The first author (NS) is thankful to University Grants Commission for a Junior Research Fellowship. Financial assistance in the form of a start-up research grant (Grant No. YSS/2014/000393/LS) from SERB, Department of Science and Technology, Government of India for conducting this research work is gratefully acknowledged.
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by AMITABHA CHATTOPADHYAY.
Corresponding editor: Amitabha Chattopadhyay
Rights and permissions
About this article
Cite this article
Soleja, N., Manzoor, O., Khan, I. et al. Role of green fluorescent proteins and their variants in development of FRET-based sensors. J Biosci 43, 763–784 (2018). https://doi.org/10.1007/s12038-018-9783-0
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12038-018-9783-0