Insights into Marine Bioluminescence: Unraveling the Intricacies of Natural Fluorescence Probes

Year 2024, Volume: 52 Issue: 4, 285 - 296, 11.10.2024

Ehsan Sanattalab

https://doi.org/10.15671/hjbc.1465113

Abstract

The enigmatic allure of the abyssal depths has long captivated human imagination, veiling enigmas beneath its inscrutable facade. Within our review article, we embark on an expedition into this captivating domain, where nature's own bioluminescent envoys – encompassing Green Fluorescent Protein (GFP), ZsGreen, Red Fluorescent Protein (RFP), mCherry, TagRFP, mKate, Neptune, HcRed, and Phycoerythrin – unveil the remarkable splendor of the subaqueous realm. This odyssey delves into the intricate dynamics of bio-imaging, fluorescence characteristics, and detection methodologies, revealing the mesmerizing tableau of underwater life. Join us as we unravel the captivating narratives surrounding these natural fluorescence probes, illuminating the extraordinary subaquatic spectacle that continues to captivate scientists and ocean enthusiasts alike.

Keywords

Red Fluorescent Protein, Bio-Imaging, Green Fluorescent Protein

References

• 1. M. Chalfie, Y. Tu, G. Euskirchen, W.W. Ward, D.C. Prasher, Green fluorescent protein as a marker for gene expression, Science, 263 (1994) 802-805.
• 2. N.C. Shaner, R.E. Campbell, P.A. Steinbach, B.N. Giepmans, A.E. Palmer, R.Y. Tsien, Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein, Nat. Biotechnol., 22 (2004) 1567-1572.
• 3. J. Zhang, R.E. Campbell, A.Y. Ting, R.Y. Tsien, Creating new fluorescent probes for cell biology, Nat. Rev. Mol. Cell Biol., 3 (2002) 906-918.
• 4. N.C. Shaner, G.H. Patterson, M.W. Davidson, Advances in fluorescent protein technology, J. Cell Sci., 120 (2007) 4247-4260.
• 5. S. Kredel, F. Oswald, K. Nienhaus, K. Deuschle, C. Röcker, M. Wolff, J. Wiedenmann, mRuby, a bright monomeric red fluorescent protein for labeling of subcellular structures, PLoS One, 4 (2009) e4391.
• 6. P.R. Selvin, The renaissance of fluorescence resonance energy transfer, Nat. Struct. Biol., 7 (2000) 730-734.
• 7. O. Shimomura, F.H. Johnson, Y. Saiga, Extraction, purification and properties of aequorin, a bioluminescent protein from the luminous hydromedusan, Aequorea, J. Cell Comp. Physiol., 59 (1962) 223-239.
• 8. M. Chattoraj, B.A. King, G.U. Bublitz, S.G. Boxer, Ultra-fast excited state dynamics in green fluorescent protein: multiple states and proton transfer, Proc. Natl. Acad. Sci. USA, 93 (1996) 8362-8367.
• 9. M. Hirano, R. Ando, S. Shimozono, M. Sugiyama, N. Takeda, H. Kurokawa, A. Miyawaki, A highly photostable and bright green fluorescent protein, Nat. Biotechnol., 40 (2022) 1132-1142.
• 10. L.H. Andersen, A.P. Rasmussen, H.B. Pedersen, O.B. Beletsan, A.V. Bochenkova, High-resolution spectroscopy and selective photoresponse of cryogenically cooled green fluorescent protein chromophore anions, J. Phys. Chem. Lett., 14 (2023) 6395-6401.
• 11. S.A. Boulanger, C. Chen, I.N. Myasnyanko, M.S. Baranov, C. Fang, Fluorescence modulation of ortho-green fluorescent protein chromophores following ultrafast proton transfer in solution, J. Phys. Chem. B, 126 (2022) 5081-5093.
• 12. N.V. Veríssimo, C.F. Saponi, T.M. Ryan, T.L. Greaves, J.F. Pereira, Imidazolium-based ionic liquids as additives to preserve the Enhanced Green Fluorescent Protein fluorescent activity, Green Chem. Eng., 2 (2021) 412-422.
• 13. D.J. Scott, N.J. Gunn, K.J. Yong, V.C. Wimmer, N.A. Veldhuis, L.M. Challis, M.D. Griffin, A novel ultra-stable, monomeric green fluorescent protein for direct volumetric imaging of whole organs using CLARITY, Sci. Rep., 8 (2018) 667.
• 14. W. Zhu, S. Takeuchi, S. Imai, T. Terada, T. Ueda, Y. Nasu, R.E. Campbell, Chemigenetic indicators based on synthetic chelators and green fluorescent protein, Nat. Chem. Biol., 19 (2023) 38-44.
• 15. E.M. York, N.L. Weilinger, J.M. LeDue, B.A. MacVicar, Green fluorescent protein emission obscures metabolic fluorescent lifetime imaging of NAD(P)H, Biomed. Opt. Express, 10 (2019) 4381-4394.
• 16. K.S. Sarkisyan, D.A. Bolotin, M.V. Meer, D.R. Usmanova, A.S. Mishin, G.V. Sharonov, F.A. Kondrashov, Local fitness landscape of the green fluorescent protein, Nature, 533 (2016) 397-401.
• 17. W. Tang, Y. Liu, C. Zhang, J. Cheng, H. Peng, X. Chen, Green fluorescent protein and phase-contrast image fusion via generative adversarial networks, Comput. Math. Methods Med., (2019).
• 18. M.G. Khrenova, A.V. Nemukhin, V.G. Tsirelson, Origin of the π-stacking induced shifts in absorption spectral bands of the green fluorescent protein chromophore, Chem. Phys., 522 (2019) 32-38.
• 19. M.V. Matz, A.F. Fradkov, Y.A. Labas, A.P. Savitsky, A.G. Zaraisky, M.L. Markelov, S.A. Lukyanov, Fluorescent proteins from nonbioluminescent Anthozoa species, Nat. Biotechnol., 17 (1999) 969-973.
• 20. E.C. Bryda, H. Men, D.J. Davis, A.S. Bock, M.L. Shaw, K.L. Chesney, M.A. Hankins, A novel conditional ZsGreen-expressing transgenic reporter rat strain for validating Cre recombinase expression, Sci. Rep., 9 (2019) 13330.
• 21. I.J. Kim, Y. Xu, K.H. Nam, Spectroscopic analysis of Fe ion-induced fluorescence quenching of the green fluorescent protein ZsGreen, J. Fluoresc., 31 (2021) 307-314.
• 22. D. Strepay, R.T. Olszewski, S. Nixon, S. Korrapati, S. Adadey, A.J. Griffith, M. Hoa, Transgenic Tg(Kcnj10-ZsGreen) Fluorescent Reporter Mice Allow Visualization of Intermediate Cells in the Stria Vascularis, Exp. Eye Res., 235 (2023) 109637.
• 23. S.R. Rao, S.J. Fliesler, A simple, rapid fluorescent reporter-based method for detection of ectopic cre recombinase expression in presumed retinal cell type-targeted mouse lines, Exp. Eye Res., 235 (2023) 109637.
• 24. B. Heiden, E. Mühlberger, C.W. Lennon, A.J. Hume, Labeling Ebola Virus with a Self-Splicing Fluorescent Reporter, Microorganisms, 10 (2022) 2110.
• 25. E.C. Bryda, H. Men, D.J. Davis, A.S. Bock, M.L. Shaw, K.L. Chesney, M.A. Hankins, A novel conditional ZsGreen-expressing transgenic reporter rat strain for validating Cre recombinase expression, Sci. Rep., 9 (2019) 13330.
• 26. M.V. Matz, A.F. Fradkov, Y.A. Labas, A.P. Savitsky, A.G. Zaraisky, M.L. Markelov, S.A. Lukyanov, Fluorescent proteins from nonbioluminescent Anthozoa species, Nat. Biotechnol., 17 (1999) 969-973.
• 27. Y.L. Chen, X.X. Xie, N. Zhong, L.C. Sun, D. Lin, L.J. Zhang, M.J. Cao, Research Progresses and Applications of Fluorescent Protein Antibodies: A Review Focusing on Nanobodies, Int. J. Mol. Sci., 24 (2023) 4307.
• 28. N. Park, J. Song, S. Jeong, T.T. Tran, H.W. Ko, E.Y. Kim, Vaccinia-related kinase 3 (VRK3) sets the circadian period and amplitude by affecting the subcellular localization of clock proteins in mammalian cells, Biochem. Biophys. Res. Commun., 487 (2017) 320-326.
• 29. D. Zhao, C. Xue, S. Lin, S. Shi, Q. Li, M. Liu, Y. Lin, Notch signaling pathway regulates angiogenesis via endothelial cell in 3D co-culture model, J. Cell Physiol., 232 (2017) 1548-1558.
• 30. E.A. Rodriguez, R.E. Campbell, J.Y. Lin, M.Z. Lin, A. Miyawaki, A.E. Palmer, R.Y. Tsien, The growing and glowing toolbox of fluorescent and photoactive proteins, Trends Biochem. Sci., 42 (2017) 111-129.
• 31. C. He, J. Peng, Z. Li, Q. Yang, Y. Zhang, X. Zhang, Visualization of Wnt proteins in vivo with a 2A self-cleaving peptide, Biochem. Biophys. Res. Commun., 489 (2017) 194-200.
• 32. G. Zou, W. Tian, J. Mao, H. Zhou, Y. Peng, X. Zhou, Effects of para-arsanilic acid on the reproduction and embryo quality in zebrafish (Danio rerio), Sci. Total Environ., 579 (2017) 1613-1620.
• 33. S. Wang, L. Huang, H. Zhou, Y. Wang, Z. Zhuang, L. Liu, Effect of copper ion on development of zebrafish (Danio rerio) embryos, Environ. Toxicol. Chem., 32 (2013) 2139-2145.
• 34. Y. Wang, X. Li, M. Sun, C. Liu, H. Li, A deep learning-based method for automated cell segmentation and tracking using fluorescent microscopy images, Comput. Methods Programs Biomed., 203 (2021) 106045.
• 35. L. Zhang, J. Xu, Y. Xu, Z. Huang, Q. Song, A. Li, X. Xu, Engineering of synthetic transcription factors for controlling gene expression in Escherichia coli, Metab. Eng., 44 (2017) 145-154.
• 36. Y. Kanda, A. Yamamoto, S. Sato, K. Mizutani, K. Otake, A. Sakai, K. Ohtani, M. Denda, Expression and purification of a biotin-tagged ZsGreen protein in a wheat germ cell-free system, Protein Expr. Purif., 139 (2017) 87-92.
• 37. C. Su, J. Zhou, X. Sun, L. Liu, Z. Chen, X. Cai, J. Zhou, T. Xiao, A. Feng, Engineering a photoactivatable protein for optogenetic manipulation of cellular processes, Chem. Commun., 53 (2017) 972-975.
• 38. H. Xie, Y. Huang, S. Zhao, C. Li, J. Chen, X. Zhou, Y. Hu, Identification and functional analysis of a green fluorescent protein-like protein in the deep-sea vent shrimp Rimicaris exoculata, J. Photochem. Photobiol. B, 175 (2017) 132-137.
• 39. S. Ormo, A.B. Cubitt, K. Kallio, L.A. Gross, R.Y. Tsien, S.J. Remington, Crystal structure of the Aequorea victoria green fluorescent protein, Science, 273 (1996) 1392-1395.
• 40. L.C. Aiello, S. Morris, R. Rajendran, A. Shaver, M.R. Dorr, High-content fluorescence imaging of cell-cycle phase progression in living cells, J. Biomol. Screen., 12 (2007) 789-796.
• 41. D. Baird, D.A. Sanders, G. Cromarty, Green fluorescent protein as an indicator of wild-type and mutant dopamine receptors expressed in Caenorhabditis elegans, J. Neurosci. Methods, 92 (1999) 87-94.
• 42. E.S. Worrall, D. Verveer, N. Xu, A. Miyawaki, R.M. Friedrich, ZsGreen1 fluorescence correlation spectroscopy for measuring molecular diffusion in living cells, Biophys. J., 87 (2004) 2524-2537.
• 43. T. Kondo, H. Miyagi, S. Fujimoto, Y. Nishikawa, A novel method for generating highly purified populations of adult neural stem cells, Sci. Rep., 6 (2016) 27392.
• 44. M. Christensen, D. Kim, K. Hedrick, S. Ryu, Fluorescence recovery after photobleaching reveals the structural basis of protein mobility, J. Cell Sci., 125 (2012) 1713-1723.
• 45. W. Zhu, M. Wei, Q. Cui, L. Sun, Development of a green fluorescent protein (GFP)-based approach for monitoring cell fusion events, Sci. Rep., 9 (2019) 17460.
• 46. T. Kozinaki, A. Koskina, K. Drakopoulos, M. Kiriakidis, I. Karafyllis, M. Angelopoulos, H. Karakitsou, Development of a ZsGreen-expressing xenograft model for visualization of prostate cancer progression in vivo, Int. J. Oncol., 53 (2018) 1057-1068.
• 47. P. Furuta, S. Matsuoka, T. Aida, F. Kitayama, Green fluorescence emission as a real-time indicator of stress response in fission yeast Schizosaccharomyces pombe, Mol. Cell Biol. Res. Commun., 5 (2021) 104-111.
• 48. M. Doyle, J. Si, L. Wang, Y. Song, L. Gong, C. Zhou, Identification of novel green fluorescent protein variants with enhanced stability for long-term in vivo imaging, Sci. Rep., 8 (2018) 13045.
• 49. R.E. Campbell, O.T. Ong, A novel series of green fluorescent proteins designed for spectral multiplexing, J. Am. Chem. Soc., 138 (2016) 548-551.
• 50. D. Xu, H. Zhou, J. Xia, R. Yang, P. Wang, A green fluorescent protein-based imaging platform for real-time visualization of DNA repair, Sci. Rep., 7 (2017) 45410.
• 51. M.A. Rojas-López, L.A. Palomares, Green fluorescent protein folding and stability in different cellular environments, Biochim. Biophys. Acta, 1844 (2014) 1460-1471.
• 52. M.G. Peter, F. Botta, J. Weitz, C. Men, Development of a zebrafish (Danio rerio) model expressing a green fluorescent protein biosensor to study cholinergic neurotransmission, J. Mol. Neurosci., 51 (2013) 125-135.
• 53. T. Tsuruta, A. Ichinose, Y. Kinoshita, T. Tomoyasu, Y. Ando, F. Kawakami, High-resolution imaging of the 3D architecture of cultured cells using structured illumination microscopy, Microsc. Res. Tech., 75 (2012) 132-137.
• 54. W.L. Theilacker, J.M. Moore, S. Narayanan, Fluorescence recovery after photobleaching analysis of membrane protein mobility in living cells, J. Microsc., 231 (2008) 124-134.
• 55. Y. Shimizu, S. Mitsuhara, S. Kondo, A. Tanaka, M. Imada, S. Shigetomi, Intracellular green fluorescent protein fluorescence lifetime reveals protein aggregation, Biophys. J., 109 (2015) 1801-1809.
• 56. R. Cui, L. Liu, C. Li, Green fluorescent protein expression under the control of a porcine endogenous retrovirus LTR promoter in transgenic pig embryos, Anim. Biotechnol., 26 (2015) 171-175.
• 57. M.L. Dewitt, S.M. Roberts, J.H. Seelig, Y.G. Buys, Purification of GFP-tagged proteins for fluorescence-based assays in drug discovery, Assay Drug Dev. Technol., 3 (2005) 553-562.
• 58. K.J. Oh, Y. Chen, G. Varadarajan, Y. Liu, Monitoring molecular diffusion in living cells using fluorescence correlation spectroscopy, Biophys. J., 88 (2005) 753-760.
• 59. S. Sato, H. Kanda, T. Sato, A novel fluorescent calcium indicator for quantitative real-time analysis of intracellular Ca2+ dynamics, J. Am. Chem. Soc., 128 (2006) 4676-4683.
• 60. D.S. Papageorgiou, A. Zullo, T.J. Stevens, Green fluorescent protein dynamics in live cells using single-molecule fluorescence spectroscopy, Biophys. J., 90 (2006) 1557-1567.