Structural Characterization of a Novel Luciferase-Like-Monooxygenase from Pseudomonas meliae – An in-Silico Approach Structural characterization of luciferase-like-monooxygenase
Trends in Peptide and Protein Sciences,
Vol. 8 No. 1 (2023),
4 November 2023
,
Page 1-12(e3)
https://doi.org/10.22037/tpps.v8i1.41854
Abstract
Luciferase is a well-known oxidative enzyme that produces bioluminescence. The Pseudomonas meliae is a plant pathogen that causes wood to rot on nectarine and peach and possesses a luciferase-like monooxygenase. After activation, it produces bioluminescence, and the pathogen’s bioluminescence is a visual indicator of contaminated plants. The present study aims to model and characterize the luciferase-like monooxygenase protein in P. meliae for its similarity to well-established luciferase. In this study, the luciferase-like monooxygenase from P. meliae infects chinaberry plants has been first modeled and then, studied by comparing it with existing known luciferase. In addition, the similarities between uncharacterized luciferase from P. meliae and the template from Geobacillus thermodenitrificans were analyzed. The results suggest that the absence of bioluminescence in P. meliae could be critical for the production of the luciferin substrate and the catalytic activity of the enzyme due to the evolutionary mutation in positions 138 and 311. The active site remains identical except for two amino acids. Therefore, mutation of the residues 138 and 311 in P. meliae Luciferase-like monooxygenase may restore luciferase light-emitting ability.
HIGHLIGHTS
- Structural characterization of luciferase-like monooxygenase in P. meliae.
- Bioluminescence can be used to evaluate antimicrobial efficacy by releasing light emissions.
- Luciferase-like monooxygenase: a potential therapeutic candidate for clinical applications.
- Bioluminescence
- Luciferase
- Luciferase-like monooxygenase
- Plant pathogens
- Pseudomonas meliae

How to Cite
References
Aeini, M. and S.M. Taghavi, (2014). ″Genotypic characteristics of the causal agent of chinaberry gall.″ Archives of Phytopathology and Plant Protection, 47(12): 1466–1474. DOI: https://doi.org/10.1080/03235408.2013.845997.
Chatzou, M., Magis, C., Chang, J.M., Kemena, C., Bussotti, G., Erb, I. and C. Notredame, (2016). ″Multiple sequence alignment modeling: Methods and applications. ″ Briefings in Bioinformatics, 17(6): 1009–1023. DOI: https://doi.org/10.1093/BIB/BBV099.
Dartnell, L.R., Roberts, T.A., Moore, G., Ward, J.M. and J.P. Muller, (2013). ″Fluorescence characterization of clinically important bacteria.″ PLoS ONE, 8(9): e75270. DOI: https://doi.org/10.1371/journal.pone.0075270.
England, C.G., Ehlerding, E.B. and W. Cai, (2016). ″NanoLuc: A small luciferase is brightening up the field of bioluminescence.″ Bioconjugate Chemistry, 27(5): 1175–1187. DOI: https://doi.org/10.1021/acs.bioconjchem.6b00112.
Feeney, K.A., Putker, M., Brancaccio, M. and J.S. O’Neill, (2016). ″In-depth characterization of firefly luciferase as a reporter of circadian gene expression in mammalian cells.″ Journal of Biological Rhythms, 31(6): 540–550. DOI: https://doi.org/10.1177/0748730416668898.
Fleiss, A. and K.S. Sarkisyan, (2019). ″A brief review of bioluminescent systems.″ Current Genetics, 65(4): 877–882. DOI: https://doi.org/10.1007/s00294-019-00951-5.
Fodje, M.N. and S. Al-Karadaghi, (2002). ″Occurrence, conformational features and amino acid propensities for the π-helix.″ Protein Engineering, 15(5): 353–358. DOI: https://doi.org/10.1093/protein/15.5.353.
Galet, J., Deveau, A., Hôtel, L., Frey-Klett, P., Leblond, P. and B. Aigle, (2015). ″Pseudomonas fluorescens pirates both ferrioxamine and ferricoelichelin siderophores from Streptomyces ambofaciens.″ Applied and Environmental Microbiology, 81(9): 3132–3141. DOI: https://doi.org/10.1128/AEM.03520-14.
Geourjon, C. and G. Deleage, (1995). ″SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments.″ Bioinformatics, 11(6): 681-684. DOI: https://doi.org/10.1093/bioinformatics/11.6.681.
Gouet, P., Robert, X. and E. Courcelle, (2003). ″ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins.″ Nucleic Acids Research, 31(13): 3320–3323. DOI: https://doi.org/10.1093/nar/gkg556.
Guo, F., & Wang, L. (2012). ″Computing the protein binding sites.″ BMC Bioinformatics, 13 (Suppl 10): 25–26. DOI: https://doi.org/10.1186/1471-2105-13-S10-S2.
Hameduh, T., Haddad, Y., Adam, V. and Z. Heger, (2020). ″Homology modeling in the time of collective and artificial intelligence.″ Computational and Structural Biotechnology Journal, 18: 3494–3506. DOI: https://doi.org/10.1016/j.csbj.2020.11.007.
Inouye, S. (2010). ″Firefly luciferase: An adenylate-forming enzyme for multicatalytic functions.″ Cellular and Molecular Life Sciences, 67(3): 387–404. DOI: https://doi.org/10.1007/s00018-009-0170-8.
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., Bridgland, A., Meyer, C., Kohl, S. A. A., Ballard, A. J., Cowie, A., Romera-Paredes, B., Nikolov, S., Jain, R., Adler, J., Back, T., Petersen, S., Reiman, D., Clancy, E., Zielinski, M., Steinegger, M., Pacholska, M., Berghammer, T., Bodenstein, S., Silver, D., Vinyals, O., Senior, A.W., Kavukcuoglu, K., Kohli, P. and D. Hassabis, (2021). ″Highly accurate protein structure prediction with AlphaFold.″ Nature, 596(7873): 583–589. DOI: https://doi.org/10.1038/s41586-021-03819-2.
Khazanov, N.A. and H.A. Carlson, (2013). ″Exploring the composition of protein-ligand binding sites on a large scale.″ PLoS Computational Biology, 9(11): e1003321. DOI: https://doi.org/10.1371/journal.pcbi.1003321.
Kirkpatrick, A., Xu, T., Ripp, S., Sayler, G. and D. Close, (2019). ″Biotechnological advances in luciferase enzymes.″ In: Bioluminescence - Analytical Applications and Basic Biology, Suzuki, H. (Ed), IntechOpen, pp. 1-23. DOI: https://doi.org/10.5772/intechopen.85313.
Kyte, J. and R.F. Doolittle, (1982). ″A simple method for displaying the hydropathic character of a protein.″ Journal of Molecular Biology, 157(1): 105-132. DOI: https://doi.org/10.1016/0022-2836(82)90515-0.
Lefèvre, F., Rémy, M.H. and J.M. Masson, (1997). ″Alanine-stretch scanning mutagenesis: A simple and efficient method to probe protein structure and function.″ Nucleic Acids Research, 25(2): 447–448. DOI: https://doi.org/10.1093/nar/25.2.447.
Li, Y. (2013). ″Conformational sampling in template-free protein loop structure modeling: An overview.″ Computational and Structural Biotechnology Journal, 5(6): e201302003. DOI: https://doi.org/10.5936/csbj.201302003.
Ma, W., Whitley, K. D., Chemla, Y. R., Luthey-Schulten, Z. and K. Schulten, (2018). ″Free-energy simulations reveal molecular mechanism for functional switch of a DNA helicase.″ ELife, 7: 1–21. DOI: https://doi.org/10.7554/eLife.34186.
O’Malley, C.J., Montague, G.A., Martin, E.B., Liddell, J.M., Kara, B. and N.J. Titchener-Hooker, (2012). ″Utilisation of key descriptors from protein sequence data to aid bioprocess route selection.″ Food and Bioproducts Processing, 90(4): 755–761. DOI: https://doi.org/10.1016/j.fbp.2012.01.005.
Patel, C.N., Georrge, J.J., Modi, K.M., Narechania, M.B., Patel, D.P., Gonzalez, F.J. and H.A. Pandya, (2018). ″Pharmacophore-based virtual screening of catechol-o-methyltransferase (COMT) inhibitors to combat Alzheimer’s disease.″ Journal of Biomolecular Structure and Dynamics, 36(15): 3938-3957. DOI: https://doi.org/10.1080/07391102.2017.1404931.
Patel, C. N., Jani, S. P., Jaiswal, D. G., Kumar, S. P., Mangukia, N., Parmar, R. M., Rawal, R. M. and H.A. Pandya, (2021). ″Identification of antiviral phytochemicals as a potential SARS-CoV-2 main protease (Mpro) inhibitor using docking and molecular dynamics simulations.″ Scientific Reports, 11(1): 1–13. DOI: https://doi.org/10.1038/s41598-021-99165-4.
Pettersen, E.F., Goddard, T.D., Huang, C.C., Meng, E.C., Couch, G.S., Croll, T.I., Morris, J.H. and T.E. Ferrin, (2021). ″UCSF ChimeraX: Structure visualization for researchers, educators, and developers.″ Protein Science, 30(1): 70–82. DOI: https://doi.org/10.1002/pro.3943.
Pozzo, T., Akter, F., Nomura, Y., Louie, A.Y. and Y. Yokobayashi, (2018). ″Firefly luciferase mutant with enhanced activity and thermostability.″ ACS Omega, 3(3): 2628–2633. DOI: https://doi.org/10.1021/acsomega.7b02068.
Roura, S., Gálvez-Montón, C. and A. Bayes-Genis, (2013). ″Bioluminescence imaging: A shining future for cardiac regeneration.″ Journal of Cellular and Molecular Medicine, 17(6): 693–703. DOI: https://doi.org/10.1111/jcmm.12018.
Scales, B.S., Dickson, R.P., Lipuma, J.J. and G.B. Huffnagle, (2014). ″Microbiology, genomics, and clinical significance of the Pseudomonas fluorescens species complex, an unappreciated colonizer of humans.″ Clinical Microbiology Reviews, 27(4): 927–948. DOI: https://doi.org/10.1128/CMR.00044-14.
Siepen, J.A., Radford, S.E. and D.R. Westhead, (2009). ″β Edge strands in protein structure prediction and aggregation.″ Protein Science, 12(10): 2348–2359. DOI: https://doi.org/10.1110/ps.03234503.
Sumitha, A., Devi, P.B., Hari, S. and R. Dhanasekaran, (2020). ″COVID-19 - In silico structure prediction and molecular docking studies with doxycycline and quinine.″ Biomedical and Pharmacology Journal, 13(3): 1185–1193. DOI: https://doi.org/10.13005/bpj/1986.
Thorne, N., Inglese, J. and D.S. Auld, (2010). ″Illuminating insights into firefly luciferase and other bioluminescent reporters used in chemical Biology.″ Chemistry and Biology, 17(6): 646–657. DOI: https://doi.org/10.1016/j.chembiol.2010.05.012.
Thorne, N., Shen, M., Lea, W.A., Simeonov, A., Lovell, S., Auld, D.S. and J. Inglese, (2012). ″Firefly luciferase in chemical biology: A compendium of inhibitors, mechanistic evaluation of chemotypes, and suggested use as a reporter.″ Chemistry and Biology, 19(8): 1060–1072. DOI: https://doi.org/10.1016/j.chembiol.2012.07.015.
Varadi, M., Anyango, S., Deshpande, M., Nair, S., Natassia, C., Yordanova, G., Yuan, D., Stroe, O., Wood, G., Laydon, A., Zídek, A., Green, T., Tunyasuvunakool, K., Petersen, S., Jumper, J., Clancy, E., Green, R., Vora, A., Lutfi, M., Figurnov, M., Cowie, A., Hobbs, N., Kohli, P., Kleywegt, G., Birney, E., Hassabis, D. and S. Velankar, (2022). ″AlphaFold Protein Structure Database: Massively expanding the structural coverage of protein-sequence space with high-accuracy models.″ Nucleic Acids Research, 50(D1): D439–D444. https://doi.org/10.1093/nar/gkab1061.
Wiederstein, M. and M.J. Sippl, (2007). ″ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins.″ Nucleic Acids Research, 35(suppl_2): W407-W410. DOI: https://doi.org/10.1093/nar/gkm290.
- Abstract Viewed: 182 times
- PDF Downloaded: 69 times