Generic placeholder image

Current Proteomics

Editor-in-Chief

ISSN (Print): 1570-1646
ISSN (Online): 1875-6247

Research Article

Evaluation of Luciferase Thermal Stability by Arginine Saturation in the Flexible Loops

Author(s): Farzane Kargar, Mojtaba Mortazavi*, Masoud Torkzadeh-Mahani, Safa Lotfi and Shahryar Shakeri

Volume 17, Issue 1, 2020

Page: [30 - 39] Pages: 10

DOI: 10.2174/1570164616666190320151005

Price: $65

Abstract

Background: The firefly luciferase enzyme is widely used in protein engineering and diverse areas of biotechnology, but the main problem with this enzyme is low-temperature stability. Previous reports indicated that surface areas of thermostable proteins are rich in arginine, which increased their thermal stability. In this study, this aspect of thermophilic proteins evaluated by mutations of surface residues to Arg. Here, we report the construction, purification, and studying of these mutated luciferases.

Methods: For mutagenesis, the QuikChange site-directed mutagenesis was used and the I108R, T156R, and N177R mutant luciferases were created. In the following, the expression and purification of wild-type and mutant luciferases were conducted and their kinetic and structural properties were analyzed. To analyze the role of these Arg in these loops, the 3D models of these mutants’ enzymes were constructed in the I-TASSER server and the exact situation of these mutants was studied by the SPDBV and PyMOL software.

Results: Overall, the optimum temperature of these mutated enzymes was not changed. However, after 30 min incubation of these mutated enzymes at 30°C, the I108R, T156R, N177R, and wild-type kept the 80%, 50%, 20%, and 20% of their original activity, respectively. It should be noted that substitution of these residues by Arg preserved the specific activity of firefly luciferase.

Conclusion: Based on these results, it can be concluded that T156R and N177R mutants by compacting local protein structure, increased the thermostability of luciferase. However, insertion of positively charged residues in these positions create the new hydrogen bonds that associated with a series of structural changes and confirmed by intrinsic and extrinsic fluorescence spectroscopy and homology modeling studies.

Keywords: Luciferase, thermostability, protein engineering, bioinformatics, arg, enzyme.

Graphical Abstract
[1]
Ettensohn, C.E.; Wessel, G.M.; Wray, G. Development of sea urchins, ascidians, and other invertebrate deuterostomes: Experimental approaches, 1st ed; Academic Press, 2004, Vol. 74, p. 92.
[2]
Viviani, V.R. The origin, diversity, and structure function relationships of insect luciferases. Cell. Mol. Life Sci., 2002, 59(11), 1833-1850.
[3]
Wilson, T.; Hastings, J.W. Bioluminescence. Annu. Rev. Cell Dev. Biol., 1998, 14(1), 197-230.
[4]
Wood, K. The bioluminescence advantage. Promega Notes, 2007, 96, 3-5.
[5]
Ando, Y.; Niwa, K.; Yamada, N.; Enomoto, T.; Irie, T.; Kubota, H.; Ohmiya, Y.; Akiyama, H. Firefly bioluminescence quantum yield and colour change by pH-sensitive green emission. Nat. Photonics, 2008, 2(1), 44-47.
[6]
Bünzli, J.C.G.; Piguet, C. Taking advantage of luminescent lanthanide ions. Chem. Soc. Rev., 2005, 34(12), 1048-1077.
[7]
Hosseinkhani, S. Expression and purification of the luciferase enzyme and in vivo ATP assay. Physiol. Pharmacol., 2008, 12(2), 109-114.
[8]
Gould, S.J.; Subramani, S. Firefly luciferase as a tool in molecular and cell biology. Anal. Biochem., 1988, 175(1), 5-13.
[9]
Ronaghi, M.; Karamohamed, S.; Pettersson, B.; Uhlén, M.; Nyrén, P. Real-time DNA sequencing using detection of pyrophosphate release. Anal. Biochem., 1996, 242(1), 84-89.
[10]
Kricka, L.J. Clinical and biochemical applications of luciferases and luciferins. Anal. Biochem., 1988, 175(1), 14-21.
[11]
Herschman, H.R. Noninvasive imaging of reporter gene expression in living subjects. Adv. Cancer Res., 2004, 92, 30-80.
[12]
White, P.; Squirrell, D.; Arnaud, P.; Lowe, C.; Murray, J. Improved thermostability of the North American firefly luciferase: saturation mutagenesis at position 354. Biochem. J., 1996, 319, 343-350.
[13]
Seliger, H.H.; McElroy, W.D. Spectral emission and quantum yield of firefly bioluminescence. Arch. Biochem. Biophys., 1960, 88(1), 136-141.
[14]
Seliger, H.; McElroy, W. The colors of firefly bioluminescence: Enzyme configuration and species specificity. Proc. Natl. Acad. Sci. USA, 1964, 52(1), 75.
[15]
Ueda, I.; Shinoda, F.; Kamaya, H. Temperature-dependent effects of high pressure on the bioluminescence of firefly luciferase. Biophys. J., 1994, 66(6), 2107-2110.
[16]
Haney, P.J.; Badger, J.H.; Buldak, G.L.; Reich, C.I.; Woese, C.R.; Olsen, G.J. Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species. Proc. Natl. Acad. Sci., 1999, 96(7), 3578-3583.
[17]
Kumar, S.; Tsai, C.J.; Nussinov, R. Factors enhancing protein thermostability. Protein Eng., 2000, 13(3), 179-191.
[18]
Argos, P.; Rossmann, M.G.; Grau, U.M.; Zuber, H.; Frank, G.; Tratschin, J.D. Thermal stability and protein structure. Biochem., 1979, 18(25), 5698-5703.
[19]
Zhou, X.X.; Wang, Y.B.; Pan, Y.J.; Li, W.F. Differences in amino acids composition and coupling patterns between mesophilic and thermophilic proteins. Amino Acids, 2008, 34(1), 25-33.
[20]
Catanzano, F.; Barone, G.; Graziano, G.; Capasso, S. Thermodynamic analysis of the effect of selective monodeamidation at asparagine 67 in ribonuclease A. Protein Sci., 1997, 6(8), 1682-1693.
[21]
Chakravarty, S.; Varadarajan, R. Elucidation of determinants of protein stability through genome sequence analysis. FEBS Lett., 2000, 470(1), 65-69.
[22]
Pack, S.P.; Yoo, Y.J. Packing-based difference of structural features between thermophilic and mesophilic proteins. Int. J. Biol. Macromol., 2005, 35(3-4), 169-174.
[23]
Dill, K.A. Dominant forces in protein folding. Biochem., 1990, 29(31), 7133-7155.
[24]
Vogt, G.; Woell, S.; Argos, P. Protein thermal stability, hydrogen bonds, and ion pairs. J. Mol. Biol., 1997, 269(4), 631-643.
[25]
Sadeghi, M.; Naderi-Manesh, H.; Zarrabi, M.; Ranjbar, B. Effective factors in thermostability of thermophilic proteins. Biophys. Chem., 2006, 119(3), 256-270.
[26]
Xiao, L.; Honig, B. Electrostatic contributions to the stability of hyperthermophilic proteins. J. Mol. Biol., 1999, 289(5), 1435-1444.
[27]
Mrabet, N.T.; Van den Broeck, A.; Van den Brande, I.; Stanssens, P.; Laroche, Y.; Lambeir, A.M.; Matthijssens, G.; Jenkins, J.; Chiadmi, M. Arginine residues as stabilizing elements in proteins. Biochem., 1992, 31(8), 2239-2253.
[28]
Mortazavi, M.; Hosseinkhani, S. Design of thermostable luciferases through arginine saturation in solvent-exposed loops. Protein Eng. Des. Sel., 2011, 24(12), 893-903.
[29]
Mortazavi, M.; Hosseinkhani, S. Surface charge modification increases firefly luciferase rigidity without alteration in bioluminescence spectra. Enzyme Microb. Technol., 2017, 96, 47-59.
[30]
Kaplan, W.; Littlejohn, T.G. Swiss-PDB viewer (deep view). Brief. Bioinform., 2001, 2(2), 195-197.
[31]
DeLano, W.L. The PyMOL molecular graphics system. Delano Sci., San Carlos, 2002, 7(1)
[32]
Kheirabadi, M.; Sharafian, Z.; Naderi-Manesh, H.; Heineman, U.; Gohlke, U.; Hosseinkhani, S. Crystal structure of native and a mutant of Lampyris turkestanicus luciferase implicate in bioluminescence color shift. Biochim. Biophys. Acta. Proteins Proteomics, 2013, 1834(12), 2729-2735.
[33]
Wang, W.; Malcolm, B. Two-stage PCR protocol allowing introduction of multiple mutations, deletions and insertions using quikchange site-directed mutagenesis. Biotech., 1999, 26(4), 680-682.
[34]
Mortazavi, M.; Hosseinkhani, S.; Khajeh, K.; Ranjbar, B.; Emamzadeh, A.R. Spectroscopic and functional characterization of Lampyris turkestanicus luciferase: A comparative study. Acta Biochim. Biophys. Sin., 2008, 40(5), 365-374.
[35]
Bradford, M.M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem., 1976, 72(1-2), 248-254.
[36]
Alipour, B.S.; Hosseinkhani, S.; Ardestani, S.K.; Moradi, A. The effective role of positive charge saturation in bioluminescence color and thermostability of firefly luciferase. Photochem. Photobiol. Sci., 2009, 8(6), 847-855.
[37]
Yousefi, F.; Ataei, F.; Mortazavi, M.; Hosseinkhani, S. Bifunctional role of leucine 300 of firefly luciferase in structural rigidity. Int. J. Biol. Macromol., 2017, 101, 67-74.
[38]
Emamzadeh, A.R.; Hosseinkhani, S.; Sadeghizadeh, M.; Nikkhah, M.; Chaichi, M.J.; Mortazavi, M. cDNA cloning, expression and homology modeling of a luciferase from the firefly Lampyroidea maculata. BMB Rep., 2006, 39(5), 578-585.
[39]
Hosseinkhani, S.; Szittner, R.; Meighen, E. Random mutagenesis of bacterial luciferase: Critical role of Glu175 in the control of luminescence decay. Biochem. J., 2005, 385, 575-580.
[40]
Eftink, M.; Ghiron, C. Exposure of tryptophanyl residues and protein dynamics. Biochemistry, 1977, 16(25), 5546-5551.
[41]
Schwede, T.; Kopp, J.; Guex, N.; Peitsch, M.C. SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res., 2003, 31(13), 3381-3385.
[42]
Zhang, Y. I-Tasser server for protein 3D structure prediction. BMC BioI., 2008, 9(1), 40.
[43]
Tina, K.; Bhadra, R.; Srinivasan, N. PIC: Protein Interactions Calculator. Nucleic Acids Res., 2007, 35(Web Server issue), W473-W476.
[44]
Guex, N.; Peitsch, M. Swiss-PdbViewer: A fast and easy-to-use PDB viewer for Macintosh and PC. Protein Data Bank Quat. Newslett, 1996, 77(7)
[45]
Vriend, G. What If: A molecular modeling and drug design program. J. Mol. Graph., 1990, 8(1), 52-56.
[46]
Snider, C.; Jayasinghe, S.; Hristova, K.; White, S.H. MPEx: A tool for exploring membrane proteins. Protein Sci., 2009, 18(12), 2624-2628.
[47]
Yousefi-Nejad, M.; Hosseinkhani, S.; Khajeh, K.; Ranjbar, B. Expression, purification and immobilization of firefly luciferase on alkyl-substituted Sepharose 4B. Enzyme Microb. Technol., 2007, 40(4), 740-746.
[48]
LE1-IRER. S. Solute perturbation of protein fluorescence. The quenching of tryptophyl fluorescence of model compounds and of lysozyme by iodide ion. Biochem., 1971, 10, 3254-3263.
[49]
Lehrer, S. The selective quenching of tryptophan fluorescence in proteins by iodide ion: lysozyme in the presence and absence of substrate. Biochem. Biophys. Res. Commun., 1967, 29(5), 767-772.
[50]
Emamzadeh, R.; Hosseinkhani, S.; Hemati, R.; Sadeghizadeh, M. RACE-based amplification of cDNA and expression of a Luciferin-Regenerating Enzyme (LRE): an attempt towards persistent bioluminescent signal. Enzyme Microb. Technol., 2010, 47(4), 159-165.
[51]
Gomi, K.; Hirokawa, K.; Kajiyama, N. Molecular cloning and expression of the cDNAs encoding luciferin-regenerating enzyme from Luciola cruciata and Luciola lateralis. Gene, 2002, 294(1), 157-166.
[52]
Hosseinkhani, S. Molecular enigma of multicolor bioluminescence of firefly luciferase. Cell. Mol. Life Sci., 2011, 68(7), 1167-1182.
[53]
Strub, C.; Alies, C.; Lougarre, A.; Ladurantie, C.; Czaplicki, J.; Fournier, D. Mutation of exposed hydrophobic amino acids to arginine to increase protein stability. BMC Biochem., 2004, 5(1), 9.
[54]
Tafreshi, N.K.; Hosseinkhani, S.; Sadeghizadeh, M.; Sadeghi, M.; Ranjbar, B.; Naderi-Manesh, H. The influence of insertion of a critical residue (Arg356) in structure and bioluminescence spectra of firefly luciferase. J. Biol. Chem., 2007, 282(12), 8641-8647.
[55]
Nowroozi-Nejad, Z.; Bahramian, B.; Hosseinkhani, S. Efficient immobilization of firefly luciferase in a metal organic framework: Fe-MIL-88 (NH2) as a mighty support for this purpose. Enzyme Microb. Technol., 2019, 121, 59-67.
[56]
Chu, Y.; Hou, J.; Boyer, C.; Richardson, J.J.; Liang, K.; Xu, J. Biomimetic synthesis of coordination network materials: Recent advances in MOFs and MPNs. Appl. Mater. Today, 2018, 10, 93-105.
[57]
Fattahi, M.; Malekpour, A.; Mortazavi, M.; Safarpour, A.; Naseri, N. The characteristics of rare codon clusters in the genome and proteins of hepatitis C virus; a bioinformatics look. Middle East J. Dig. Dis., 2014, 6(4), 214.
[58]
Ghorban, H.N.; Tebianian, M.; Farhadi, A.; Hossein, K.A.; Rahimi, A.; Mortazavi, M.; Hosseini, S.Y.; Taghizadeh, M.; Rezaei, M.; Mahdavi, M. In silico analysis of L1/L2 sequences of human papillomaviruses: implication for universal vaccine design. Viral Immunol., 2017, 30(3), 210-223.
[59]
Mortazavi, M.; Zarenezhad, M.; Alavian, S.M.; Gholamzadeh, S.; Malekpour, A.; Ghorbani, M.; Mahani, M.T.; Lotfi, S.; Fakhrzad, A. Bioinformatics analysis of codon usage and phylogenetic relationships in different genotypes of the hepatitis C virus. Hepat. Mon., 2016, 16(10)e39196
[60]
Kargar, F.; Mortazavi, M.; Savardashtaki, A.; Hosseinkhani, S.; Mahani, M.T.; Ghasemi, Y. Genomic and protein structure analysis of the luciferase from the Iranian bioluminescent beetle, Luciola sp. Int. J. Biol. Macromol., 2019, 124, 689-698.
[61]
Mortazavi, M.; Zarenezhad, M.; Gholamzadeh, S.; Alavian, S.M.; Ghorbani, M.; Dehghani, R.; Malekpour, A.; Meshkibaf, M.; Fakhrzad, A. Bioinformatics identification of rare codon clusters (RCCs) in HBV genome and evaluation of RCCs in proteins structure of hepatitis B virus. Hepat. Mon., 2016, 16(10)e39909
[62]
Mortazavi, M.; Nezafat, N.; Negahdaripour, M.; Gholami, A.; Torkzadeh-Mahani, M.; Lotfi, S.; Ghasemi, Y. In silico evaluation of rare codons and their positions in the structure of cytosine deaminase and substrate docking studies. Trends Pharmacol. Sci., 2016, 2(2), 117-130.
[63]
Malekpour, A.; Mortazavi, M.; Elyadrani, K.E.; Zahedi, S.; Ghorbani, M. Bioinformatics analysis of codon usage and phylogenetic relationships of different genotypes of hepatitis C virus: p23. J. Viral Hepat., 2015, 22, 33-34.
[64]
Daniel, E.; Weber, G. Cooperative effects in binding by bovine serum albumin. I. The binding of 1-anilino-8-naphthalenesulfonate. Fluorimetric titrations. Biochemistry, 1966, 5(6), 1893-1900.
[65]
Steinberg, I.Z. Long-range nonradiative transfer of electronic excitation energy in proteins and polypeptides. Annu. Rev. Biochem., 1971, 40(1), 83-114.

Rights & Permissions Print Cite
© 2024 Bentham Science Publishers | Privacy Policy