Araştırma Makalesi
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Development of a Fluorescent Protein Based FRET Biosensor for Determination of Protease Activity

Yıl 2021, Cilt: 25 Sayı: 5, 1235 - 1244, 30.10.2021

İbrahim İncir Özlem Kaplan Sema Bilgin İsa Gökçe

https://doi.org/10.16984/saufenbilder.961026
Cited By: 2

Öz

Proteases are closely associated with many pathological conditions. Efficient detection of protease activity may be useful for diagnosis, prognosis, and the development of new therapeutic biomolecules. Fluorescent Resonance Energy Transfer (FRET) is defined as the non-radioactive energy transfer that occurs between two fluorophores. Fluorescent proteins are widely used in FRET biosensors because they can be genetically encoded and compatible with cells. Fluorescent Protein based FRET (FP-FRET) biosensors are used to monitor biological processes such as enzyme activity, intracellular ion concentration, conformational changes, protein-protein interactions. In this study, it was aimed to detect protease activity using an FP-FRET biosensor and TEV protease was chosen as a model enzyme. The plasmid encoding the mNeonGreen-mRuby3 fluorescent protein-based FRET biosensor was constructed. The gene of the designed FP-FRET biosensor was expressed in Escherichia coli DH5α cells using recombinant DNA techniques and purified using Ni-NTA affinity chromatography. As a result, the activity of the TEV protease enzyme was determined by emission measurements performed in the spectrofluorometer using the produced FP-FRET biosensor. The usability of the designed FP-FRET biosensor in the determination of protease enzyme activity was demonstrated.

Anahtar Kelimeler

Recombinant DNA Technology Fluorescent Proteins Fluorescent Resonance Energy Transfer (FRET) Biosensor E. coli

Destekleyen Kurum

Tokat Gaziosmanpaşa University, Foundation of Scientific Researches Projects

Proje Numarası

2019/71

Kaynakça

  • [1] J. S. Bond, “Proteases: History, discovery, and roles in health and disease,” Journal of Biological Chemistry, vol. 294, no. 5, pp. 1643–1651, 2019, doi: 10.1074/jbc.TM118.004156.
  • [2] B. T. Bajar, E. S. Wang, S. Zhang, M. Z. Lin, and J. Chu, “A guide to fluorescent protein FRET pairs,” Sensors (Switzerland), vol. 16, no. 9, 2016, doi: 10.3390/s16091488.
  • [3] M. P. Maria-Chantal Chirio-Lebrun, “Fluorescence resonance energy transfer (FRET): theory and experiments,” Biochemical Education, vol. 26, no. 4, pp. 320–323, 1998.
  • [4] A. Kaur, P. Kaur, and S. Ahuja, “Förster resonance energy transfer (FRET) and applications thereof,” Analytical Methods, vol. 12, no. 46. Royal Society of Chemistry, pp. 5532–5550, Dec. 14, 2020. doi: 10.1039/d0ay01961e.
  • [5] A. Masharina, L. Reymond, D. Maurel, K. Umezawa, and K. Johnsson, “A Fluorescent Sensor for GABA and Synthetic GABA,” Journal of the American Chemical Society, vol. 134, pp. 19026–19034, 2012, doi: 10.1021/ja306320s.
  • [6] H. Wang, E. Nakata, and I. Hamachi, “Recent Progress in Strategies for the Creation of Protein-Based Fluorescent Biosensors,” ChemBioChem, vol. 10, no. 16, pp. 2560–2577, Nov. 2009, doi: 10.1002/cbic.200900249.
  • [7] V. Trümper et al., “Flow cytometry-based FRET identifies binding intensities in PPARγ1 protein-protein interactions in living cells,” Theranostics, vol. 9, no. 19, pp. 5444–5463, 2019, doi: 10.7150/thno.29367.
  • [8] D. Zhang, E. Redington, and Y. Gong, “Rational engineering of ratiometric calcium sensors with bright green and red fluorescent proteins,” Communications Biology, vol. 4, no. 1, Dec. 2021, doi: 10.1038/s42003-021-02452-z.
  • [9] D. W. Piston and G. J. Kremers, “Fluorescent protein FRET: the good, the bad and the ugly,” Trends in Biochemical Sciences, vol. 32, no. 9, pp. 407–414, 2007, doi: 10.1016/j.tibs.2007.08.003.
  • [10] D. M. Chudakov, M. V. Matz, S. Lukyanov, and K. A. Lukyanov, “Fluorescent Proteins and Their Applications in Imaging Living Cells and Tissues,” Physiological Reviews, vol. 90, no. 3, pp. 1103–1163, Jul. 2010, doi: 10.1152/physrev.00038.2009.
  • [11] N. C. Shaner et al., “A bright monomeric green fluorescent protein derived from Branchiostoma lanceolatum,” Nat Methods, vol. 10, no. 5, pp. 407–409, 2013, doi: 10.1038/nmeth.2413.A.
  • [12] I. Stockmar et al., “Optimization of sample preparation and green color imaging using the mNeonGreen fluorescent protein in bacterial cells for photoactivated localization microscopy,” Scientific Reports, vol. 8, no. 1, pp. 1–11, 2018, doi: 10.1038/s41598-018-28472-0.
  • [13] S. Kredel et al., “mRuby, a Bright Monomeric Red Fluorescent Protein for Labeling of Subcellular Structures,” PLoS ONE, vol. 4, no. 2, p. e4391, Feb. 2009, doi: 10.1371/journal.pone.0004391.
  • [14] K. D. Piatkevich and V. V Verkhusha, “Guide to red fluorescent proteins and biosensors for flow cytometry.,” Methods in cell biology, vol. 102, pp. 431–61, 2011, doi: 10.1016/B978-0-12-374912-3.00017- 1.
  • [15] B. T. Bajar et al., “Improving brightness and photostability of green and red fluorescent proteins for live cell imaging and FRET reporting,” Scientific Reports, vol. 6, no. October 2015, pp. 1–12, 2016, doi: 10.1038/srep20889.
  • [16] H. Kuduğ, B. Ataman, R. İmamoğlu, D. Düzgün, and İ. Gökçe, “Production of red fluorescent protein (mCherry) in an inducible E. coli expression system in a bioreactor, purification and characterization,” International Advanced Researches and Engineering Journal, vol. 3, no. 1, pp. 20–25, 2019.
  • [17] Ö. Kaplan, R. İmamoğlu, İ. Şahingöz, and İ. Gökçe, “Recombinant production of Thermus aquaticus single-strand binding protein for usage as PCR enhancer,” International Advanced Researches and Engineering Journal, vol. 5, no. 1, pp. 42– 46, 2021, doi: 10.35860/iarej.766741.
  • [18] S. Shimozono and A. Miyawaki, “Engineering FRET Constructs Using CFP and YFP,” Methods in Cell Biology, vol. 85, no. 08, pp. 381–393, 2008, doi: 10.1016/S0091-679X(08)85016-9.
  • [19] A. E. Palmer, Y. Qin, J. G. Park, and J. E. McCombs, “Design and application of genetically encoded biosensors,” Trends in Biotechnology, vol. 29, no. 3, pp. 144–152, 2011, doi: 10.1016/j.tibtech.2010.12.004.
  • [20] R. D. Mitra, C. M. Silva, and D. C. Youvan, “Fluorescence resonance energy transfer between blue-emitting and red-shifted excitation derivatives of the green fluorescent protein,” Gene, vol. 173, no. 1, pp. 13–17, 1996, doi: 10.1016/0378- 1119(95)00768-7.
  • [21] R. Heim and R. Y. Tsien, “Engineering green fluorescent protein for improved brightness, longer wavelengths and fluorescence resonance energy transfer,” Current Biology, vol. 6, no. 2, pp. 178–182, Feb. 1996, doi: 10.1016/S0960- 9822(02)00450-5.
  • [22] A. W. Nguyen and P. S. Daugherty, “Evolutionary optimization of fluorescent proteins for intracellular FRET,” Nature Biotechnology, vol. 23, no. 3, pp. 355–360, 2005, doi: 10.1038/nbt1066.
  • [23] J. Yang et al., “Detection of MMP activity in living cells by a genetically encoded surface-displayed FRET sensor,” Biochim Biophys Acta, vol. 1773, no. 3, pp. 400–407, 2007, doi: 10.1016/j.bbamcr.2006.11.002.
  • [24] T. W. McCullock, D. M. MacLean, and P. J. Kammermeier, “Comparing the performance of mScarlet-I, mRuby3, and mCherry as FRET acceptors for mNeonGreen,” PLoS ONE, vol. 15, no. 2, pp. 1–22, 2020, doi: 10.1371/journal.pone.0219886.
  • [25] M. Van Rosmalen, M. Krom, and M. Merkx, “Tuning the Flexibility of GlycineSerine Linkers to Allow Rational Design of Multidomain Proteins,” Biochemistry, vol. 56, no. 50, pp. 6565–6574, 2017, doi: 10.1021/acs.biochem.7b00902.
  • [26] H. Y. Hu et al., “FRET-based and other fluorescent proteinase probes,” Biotechnology Journal, vol. 9, no. 2, pp. 266–281, Feb. 2014, doi: 10.1002/biot.201300201.
  • [27] X. Qiu and N. Hildebrandt, “A clinical role for Förster resonance energy transfer in molecular diagnostics of disease,” Expert Review of Molecular Diagnostics, vol. 19, no. 9. Taylor and Francis Ltd, pp. 767–771, Sep. 02, 2019. doi: 10.1080/14737159.2019.1649144.
  • [28] A. Ibraheem and R. E. Campbell, “Designs and applications of fluorescent proteinbased biosensors,” Current Opinion in Chemical Biology, vol. 14, no. 1, pp. 30–36, 2010, doi: 10.1016/j.cbpa.2009.09.033.

Yıl 2021, Cilt: 25 Sayı: 5, 1235 - 1244, 30.10.2021

İbrahim İncir Özlem Kaplan Sema Bilgin İsa Gökçe

https://doi.org/10.16984/saufenbilder.961026
Cited By: 2

Öz

Proje Numarası

2019/71

Kaynakça

  • [1] J. S. Bond, “Proteases: History, discovery, and roles in health and disease,” Journal of Biological Chemistry, vol. 294, no. 5, pp. 1643–1651, 2019, doi: 10.1074/jbc.TM118.004156.
  • [2] B. T. Bajar, E. S. Wang, S. Zhang, M. Z. Lin, and J. Chu, “A guide to fluorescent protein FRET pairs,” Sensors (Switzerland), vol. 16, no. 9, 2016, doi: 10.3390/s16091488.
  • [3] M. P. Maria-Chantal Chirio-Lebrun, “Fluorescence resonance energy transfer (FRET): theory and experiments,” Biochemical Education, vol. 26, no. 4, pp. 320–323, 1998.
  • [4] A. Kaur, P. Kaur, and S. Ahuja, “Förster resonance energy transfer (FRET) and applications thereof,” Analytical Methods, vol. 12, no. 46. Royal Society of Chemistry, pp. 5532–5550, Dec. 14, 2020. doi: 10.1039/d0ay01961e.
  • [5] A. Masharina, L. Reymond, D. Maurel, K. Umezawa, and K. Johnsson, “A Fluorescent Sensor for GABA and Synthetic GABA,” Journal of the American Chemical Society, vol. 134, pp. 19026–19034, 2012, doi: 10.1021/ja306320s.
  • [6] H. Wang, E. Nakata, and I. Hamachi, “Recent Progress in Strategies for the Creation of Protein-Based Fluorescent Biosensors,” ChemBioChem, vol. 10, no. 16, pp. 2560–2577, Nov. 2009, doi: 10.1002/cbic.200900249.
  • [7] V. Trümper et al., “Flow cytometry-based FRET identifies binding intensities in PPARγ1 protein-protein interactions in living cells,” Theranostics, vol. 9, no. 19, pp. 5444–5463, 2019, doi: 10.7150/thno.29367.
  • [8] D. Zhang, E. Redington, and Y. Gong, “Rational engineering of ratiometric calcium sensors with bright green and red fluorescent proteins,” Communications Biology, vol. 4, no. 1, Dec. 2021, doi: 10.1038/s42003-021-02452-z.
  • [9] D. W. Piston and G. J. Kremers, “Fluorescent protein FRET: the good, the bad and the ugly,” Trends in Biochemical Sciences, vol. 32, no. 9, pp. 407–414, 2007, doi: 10.1016/j.tibs.2007.08.003.
  • [10] D. M. Chudakov, M. V. Matz, S. Lukyanov, and K. A. Lukyanov, “Fluorescent Proteins and Their Applications in Imaging Living Cells and Tissues,” Physiological Reviews, vol. 90, no. 3, pp. 1103–1163, Jul. 2010, doi: 10.1152/physrev.00038.2009.
  • [11] N. C. Shaner et al., “A bright monomeric green fluorescent protein derived from Branchiostoma lanceolatum,” Nat Methods, vol. 10, no. 5, pp. 407–409, 2013, doi: 10.1038/nmeth.2413.A.
  • [12] I. Stockmar et al., “Optimization of sample preparation and green color imaging using the mNeonGreen fluorescent protein in bacterial cells for photoactivated localization microscopy,” Scientific Reports, vol. 8, no. 1, pp. 1–11, 2018, doi: 10.1038/s41598-018-28472-0.
  • [13] S. Kredel et al., “mRuby, a Bright Monomeric Red Fluorescent Protein for Labeling of Subcellular Structures,” PLoS ONE, vol. 4, no. 2, p. e4391, Feb. 2009, doi: 10.1371/journal.pone.0004391.
  • [14] K. D. Piatkevich and V. V Verkhusha, “Guide to red fluorescent proteins and biosensors for flow cytometry.,” Methods in cell biology, vol. 102, pp. 431–61, 2011, doi: 10.1016/B978-0-12-374912-3.00017- 1.
  • [15] B. T. Bajar et al., “Improving brightness and photostability of green and red fluorescent proteins for live cell imaging and FRET reporting,” Scientific Reports, vol. 6, no. October 2015, pp. 1–12, 2016, doi: 10.1038/srep20889.
  • [16] H. Kuduğ, B. Ataman, R. İmamoğlu, D. Düzgün, and İ. Gökçe, “Production of red fluorescent protein (mCherry) in an inducible E. coli expression system in a bioreactor, purification and characterization,” International Advanced Researches and Engineering Journal, vol. 3, no. 1, pp. 20–25, 2019.
  • [17] Ö. Kaplan, R. İmamoğlu, İ. Şahingöz, and İ. Gökçe, “Recombinant production of Thermus aquaticus single-strand binding protein for usage as PCR enhancer,” International Advanced Researches and Engineering Journal, vol. 5, no. 1, pp. 42– 46, 2021, doi: 10.35860/iarej.766741.
  • [18] S. Shimozono and A. Miyawaki, “Engineering FRET Constructs Using CFP and YFP,” Methods in Cell Biology, vol. 85, no. 08, pp. 381–393, 2008, doi: 10.1016/S0091-679X(08)85016-9.
  • [19] A. E. Palmer, Y. Qin, J. G. Park, and J. E. McCombs, “Design and application of genetically encoded biosensors,” Trends in Biotechnology, vol. 29, no. 3, pp. 144–152, 2011, doi: 10.1016/j.tibtech.2010.12.004.
  • [20] R. D. Mitra, C. M. Silva, and D. C. Youvan, “Fluorescence resonance energy transfer between blue-emitting and red-shifted excitation derivatives of the green fluorescent protein,” Gene, vol. 173, no. 1, pp. 13–17, 1996, doi: 10.1016/0378- 1119(95)00768-7.
  • [21] R. Heim and R. Y. Tsien, “Engineering green fluorescent protein for improved brightness, longer wavelengths and fluorescence resonance energy transfer,” Current Biology, vol. 6, no. 2, pp. 178–182, Feb. 1996, doi: 10.1016/S0960- 9822(02)00450-5.
  • [22] A. W. Nguyen and P. S. Daugherty, “Evolutionary optimization of fluorescent proteins for intracellular FRET,” Nature Biotechnology, vol. 23, no. 3, pp. 355–360, 2005, doi: 10.1038/nbt1066.
  • [23] J. Yang et al., “Detection of MMP activity in living cells by a genetically encoded surface-displayed FRET sensor,” Biochim Biophys Acta, vol. 1773, no. 3, pp. 400–407, 2007, doi: 10.1016/j.bbamcr.2006.11.002.
  • [24] T. W. McCullock, D. M. MacLean, and P. J. Kammermeier, “Comparing the performance of mScarlet-I, mRuby3, and mCherry as FRET acceptors for mNeonGreen,” PLoS ONE, vol. 15, no. 2, pp. 1–22, 2020, doi: 10.1371/journal.pone.0219886.
  • [25] M. Van Rosmalen, M. Krom, and M. Merkx, “Tuning the Flexibility of GlycineSerine Linkers to Allow Rational Design of Multidomain Proteins,” Biochemistry, vol. 56, no. 50, pp. 6565–6574, 2017, doi: 10.1021/acs.biochem.7b00902.
  • [26] H. Y. Hu et al., “FRET-based and other fluorescent proteinase probes,” Biotechnology Journal, vol. 9, no. 2, pp. 266–281, Feb. 2014, doi: 10.1002/biot.201300201.
  • [27] X. Qiu and N. Hildebrandt, “A clinical role for Förster resonance energy transfer in molecular diagnostics of disease,” Expert Review of Molecular Diagnostics, vol. 19, no. 9. Taylor and Francis Ltd, pp. 767–771, Sep. 02, 2019. doi: 10.1080/14737159.2019.1649144.
  • [28] A. Ibraheem and R. E. Campbell, “Designs and applications of fluorescent proteinbased biosensors,” Current Opinion in Chemical Biology, vol. 14, no. 1, pp. 30–36, 2010, doi: 10.1016/j.cbpa.2009.09.033.
Toplam 28 adet kaynakça vardır.

Ayrıntılar

Birincil Dil İngilizce
Konular Yapısal Biyoloji
Bölüm Araştırma Makalesi
Yazarlar

İbrahim İncir 0000-0003-4599-6908

Özlem Kaplan 0000-0002-3052-4556

Sema Bilgin 0000-0001-5921-5434

İsa Gökçe 0000-0002-5023-9947

Proje Numarası 2019/71
Yayımlanma Tarihi 30 Ekim 2021
Gönderilme Tarihi 2 Temmuz 2021
Kabul Tarihi 29 Eylül 2021
Yayımlandığı Sayı Yıl 2021 Cilt: 25 Sayı: 5

Kaynak Göster

APA İncir, İ., Kaplan, Ö., Bilgin, S., Gökçe, İ. (2021). Development of a Fluorescent Protein Based FRET Biosensor for Determination of Protease Activity. Sakarya University Journal of Science, 25(5), 1235-1244. https://doi.org/10.16984/saufenbilder.961026
AMA İncir İ, Kaplan Ö, Bilgin S, Gökçe İ. Development of a Fluorescent Protein Based FRET Biosensor for Determination of Protease Activity. SAUJS. Ekim 2021;25(5):1235-1244. doi:10.16984/saufenbilder.961026
Chicago İncir, İbrahim, Özlem Kaplan, Sema Bilgin, ve İsa Gökçe. “Development of a Fluorescent Protein Based FRET Biosensor for Determination of Protease Activity”. Sakarya University Journal of Science 25, sy. 5 (Ekim 2021): 1235-44. https://doi.org/10.16984/saufenbilder.961026.
EndNote İncir İ, Kaplan Ö, Bilgin S, Gökçe İ (01 Ekim 2021) Development of a Fluorescent Protein Based FRET Biosensor for Determination of Protease Activity. Sakarya University Journal of Science 25 5 1235–1244.
IEEE İ. İncir, Ö. Kaplan, S. Bilgin, ve İ. Gökçe, “Development of a Fluorescent Protein Based FRET Biosensor for Determination of Protease Activity”, SAUJS, c. 25, sy. 5, ss. 1235–1244, 2021, doi: 10.16984/saufenbilder.961026.
ISNAD İncir, İbrahim vd. “Development of a Fluorescent Protein Based FRET Biosensor for Determination of Protease Activity”. Sakarya University Journal of Science 25/5 (Ekim 2021), 1235-1244. https://doi.org/10.16984/saufenbilder.961026.
JAMA İncir İ, Kaplan Ö, Bilgin S, Gökçe İ. Development of a Fluorescent Protein Based FRET Biosensor for Determination of Protease Activity. SAUJS. 2021;25:1235–1244.
MLA İncir, İbrahim vd. “Development of a Fluorescent Protein Based FRET Biosensor for Determination of Protease Activity”. Sakarya University Journal of Science, c. 25, sy. 5, 2021, ss. 1235-44, doi:10.16984/saufenbilder.961026.
Vancouver İncir İ, Kaplan Ö, Bilgin S, Gökçe İ. Development of a Fluorescent Protein Based FRET Biosensor for Determination of Protease Activity. SAUJS. 2021;25(5):1235-44.

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