In silico PREDICTION, CHARACTERIZATION AND MOLECULAR DOCKING STUDY ON Tetranychus urticae KOCH PROTEINS AS A NOVEL TARGETS TO EXPLORING THE MECHANISM OF MITES DEALING

Main Article Content

BASSEM A. SOUDY
https://orcid.org/0000-0002-5301-7266
ISRAA. M. SHAMKH
SALLY F. M. ALLAM
MOURAD F. HASSAN
NASR. S. KHALIL

Abstract

Tetranychus urticae Koch is phytophagous in nature that can be the reason for major yield losses in many crops, fruits vegetables and ornamentals plants. Thus far, more than 3000 host species have been noted around the world in both outdoor crops and greenhouses. Our study explores the mechanisms of T. urticae dialing to provide a new understanding of the mechanism of controlling this pest including mentha plants (extracts and essential oils) which have an inhibitory effect on T. urticae. Even as mentha plants have been generally used to control T. urticae, in recent years, the interest in pesticides derived from plants has increased considerably as a result of environmental concerns and pest population resistance to conventional pesticides. Some pesticides can be easily produced but to study the mechanisms of their compounds against pests, are comparatively able against pests and with exceptions, their mammalian mortality and determination in the environment are undersized. Thus, the application of plant extracts determined to be a talented alternative plan for pest management, but the mechanism of mentha plants is unfamiliar with the effect of the compounds of extract or essential oils which exert considerable after effects on protein sequence in the T. urticae. So we carried this study to explain and explore the interacting mechanism which lead to the death of the T. urticae. Software's were used to survey plant natural compounds for their binding ability with the T. urticae protein. Docking score for ligands beside each protein was intended to estimate the binding open power. The compounds showed a strong ability to bind with the T. urticae proteins (the Caffeic acid, Cinnamic acid, Ferulic acid, Hesperidin, Naringin, and Rosmarinic acid) were used to predict its docking model and binding regions of T. urticae protein. The highest predicted ligand/protein affinity was with Hesperidin followed by A-Naringin. Molecular docking and protein-protein interaction also showed the probability of the six ligands to bind to the T. urticae proteins and the relationship of the proteins with the vital pathways in the T. urticae. The interaction residues and the binding energy for the bind complexes were identified. The strong binding ability of the six compounds to the T. urticae proteins. The selected proteins participate in vital pathways in the T. urticae confirm our previous study and identify the compounds of extract and essential oils of mentha plants and their interaction and which compounds are responsible for causing the death of the T. urticae.

Keywords:
Docking, mites activity, Tetranychus urticae, Monoterpenes

Article Details

How to Cite
SOUDY, B. A., SHAMKH, I. M., ALLAM, S. F. M., HASSAN, M. F., & KHALIL, N. S. (2021). In silico PREDICTION, CHARACTERIZATION AND MOLECULAR DOCKING STUDY ON Tetranychus urticae KOCH PROTEINS AS A NOVEL TARGETS TO EXPLORING THE MECHANISM OF MITES DEALING. PLANT CELL BIOTECHNOLOGY AND MOLECULAR BIOLOGY, 22(41-42), 109-124. Retrieved from https://ikpresse.com/index.php/PCBMB/article/view/6693
Section
Original Research Article

References

Riga M, Tsakireli D, Ilias A, Morou E, Myridakis A, Stephanou EG, et al. Abamectin is metabolized by CYP392A16, a cytochrome P450 associated with high levels of acaricide resistance in Tetranychus urticae. Insect Biochem Mol Biol. 2014;46:43–53.

Bhattacharya D, Cheng J. i3Drefine software for protein 3D structure refinement and its assessment in CASP10. PLOS ONE. 2013;8(7):e69648.

Bhattacharya D, Nowotny J, Cao R, Cheng J. 3Drefine: An interactive web server for efficient protein structure refinement. Nucleic Acids Research. Web Server Issue; 2016.
DOI: 10.1093/nar/gkw336.

Çağatay NS, Menault P, Riga M, Vontas J, Ay R. Identification and characterization of abamectin resistance in Tetranychus urticae Koch populations from greenhouses in Turkey. Crop Prot. 2018;112:112– 117.

Dunse KM, Stevens JA, Lay FT, Gaspar YM, Heath RL, Anderson MA. Coexpression of potato type I and II proteinase inhibitors gives cotton plants protection against insect damage in the field. Proc Natl Acad Sci USA. 2010;107: 15011-5.
PMID:20696895;
Available:http://dx.doi.org/10.1073/pnas.1009241107.

Ilias A, Vontas J, Tsagkarakou A. Global distribution and origin of target site insecticide resistance mutations in Tetranychus urticae. Insect Biochem Mol Biol. 2014;48:17–28.

Lawrence PK, Koundal KR. Plant protease inhibitors in control of phytophagous insects. Electron J Biotechnol. 2002;5:93-109.
Available:http://dx.doi.org/10.2225/vol5issue1-fulltext-3.

Roche DB, Buenavista MT, McGuffin LJ. The FunFOLD2 server for the prediction of protein-ligand interactions. Nucleic Acids Res. 2013;41:303–307.

Vassiliou VA, Kitsis P. Acaricide resistance in Tetranychus urticae (Acari: Tetranychidae) populations from Cyprus. J Econ Entomol. 2013;106:1848–1854.

Tang XF, Zhang YJ, Wu QJ, Xie W, Wang SL. Stage-specific expression of resistance to different acaricides in four field populations of Tetranychus urticae (Acari: Tetranychidae). J Econ Entomol. 2014;107: 1900–1907.

Ilias A, Vassiliou VA, Vontas J, Tsagkarakou A. Molecular diagnostics for detecting pyrethroid and abamectin resistance mutations in Tetranychus urticae. Pest Biochem Physiol. 2017;135:9–14

Van Leeuwen T, Dermauw W. The molecular evolution of xenobiotic metabolism and resistance in cheliceratemites. Annu Rev Entomol. 2016; 61:475–498.

Ozoe Y.

Ffrench-Constant RH, Williamson MS, Davies TG, Bass C. Ion channels as insecticide targets. J Neurogenet. 2016;30: 163–177.

Holden-Dye L, Walker RJ. Avermectin and avermectin derivatives are antagonists at the 4-aminobutyric acid (GABA) receptor on the somatic muscle cells of Ascaris – Is this the site of anthelmintic action? Parasitology. 1990;101:265– 271.

Wolstenholme AJ, Rogers AT. Glutamate-gated chloride channels and the mode of action of the avermectin/milbemycin anthelmintics. Parasitology. 2005; 131(Suppl):S85–95.

Wolstenholme AJ. Recent progress in understanding the interaction between avermectins and ligand-gated ion channels: putting the pests to sleep. Invert Neurosci. 2010;10:5–10.

Wolstenholme AJ. Glutamate-gated chloride channels. J BiolChem. 2012;287:40232–40238.

Schapira AH. Mitochondrial disease. Lancet. 2006;368:70–82.

Allam SF, Soudy BA, Hassan SH, Ramadan MM, Abo Baker D. How do mentha plants induce resistance against Tetranychus urticae (Acari: Tetranychidae) in organic farming? Journal of Plant Protection Research. 2018;58(3):265–275.
DOI: 10.24425/122943

Usha Rani P, Jyothsna Y. Biochemical and enzymatic changes in rice as a mechanism of defense. Acta Physiol Plant. 2010;32: 695-701.
Available:http://dx.doi.org/10.1007/ s11738-009-0449-2.

Wang L, Zhang YJ, Xie W, Wu QJ, Wang SL. A bioassay for evaluation of the resistance of Tetranychus urticae (Acari: Tetranychidae) to selected acaricides. SystApplAcarol. 2015;20:579–590.

Wang L, Zhang YJ, Xie W, Wu QJ, Wang SL. Sublethal effects of spinetoram on the two-spotted spider mite, Tetranychus urticae (Acari: Tetranychidae). Pest Biochem Physiol. 2016;132:102–107.

War AR, Paulraj MG, War MY, Ignacimuthu S. Jasmonic acid-mediated induced resistance in groundnut (Arachis hypogaea L.) against Helicoverpa armigera (Hubner) (Lepidoptera: Noctuidae). J Plant Growth Regul. 2011a;30:512-23.
Available:http://dx.doi.org/10.1007/ s00344-011-9213-0.

Xu DD, He YY, Zhang YJ, Xie W, Wu QJ, Wang SL. Status of pesticide resistance and associated mutations in the two-spotted spider mite, Tetranychus urticae, in China. Pest Biochem Physiol. 2018;150:89–96.

Xue WX, Snoeck S, Njiru C, Inak E, Dermauw W, van Leeuwen T. Geographical distribution and molecular insights into abamectin and milbemycin cross-resistance in European field populations of Tetranychus urticae. Pest Manag Sci. 2020;76:2569–2581.

Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: Architecture and applications. BMC Bioinformatics. 2009;10:421-430.

Steinegger M, Meier M, Mirdita M, Vöhringer H, Haunsberger SJ, Söding J. HH-suite3 for fast remote homology detection and deep protein annotation. BMC Bioinformatics. 2019;20:473.

Bowie JU, Lüthy R, Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science. 1991;253(5016):164-70.
DOI: 10.1126/science.1853201
PMID: 1853201.

Lüthy R, Bowie JU, Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature. 1992; 356(6364):83-5.
DOI: 10.1038/356083a0

PMID: 1538787.

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. [PubMed] [Google Scholar]

Schmuth, M., Watson, R.E., Deplewski, D., Dubrac, S., Zouboulis, C.C., and Griffiths, C.E., 2007. Nuclear hormone receptors in human skin. Horm. Metab. Res. 39, 96-105.

Studer G, Rempfer C, Waterhouse AM, Gumienny G, Haas J, Schwede T. QMEANDisCo - distance constraints applied on model quality estimation. Bioinformatics. 2020;36:1765-1771.

Trott O, Olson AJ (2010) AutoDock vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31: 455– 461.

Bertoni M, Kiefer F, Biasini M, Bordoli L, Schwede T. Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology. Scientific Reports. 2017;7.

Bourne,P., Berman,H.M., Watenpaugh,K., Westbrook,J.D. andFitzgerald,P.M.D. (1997) Methods Enzymol., 277, 571–590

Agrawal AA. Transgenerational consequences of plant responses to herbivory: An adaptive maternal effect? Am Nat; 2001;157:555-69.
PMID:18707262.

Mirdita M, von den Driesch L, Galvez C, Martin MJ, Söding J, Steinegger M. Uniclust databases of clustered and deeply annotated protein sequences and alignments. Nucleic Acids Research. 2016; 45:D170–D176.

Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, Gumienny R, Heer FT, de Beer TAP, Rempfer C, Bordoli L, Lepore R, Schwede T. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 2018; 46(W1):W296-W303.

Guex N, Peitsch MC, Schwede T. Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: A historical perspective. Electrophoresis. 2009;30:S162- S173.

Bienert S, Waterhouse A, de Beer TAP, Tauriello G, Studer G, Bordoli L, Schwede T. The SWISS-MODEL repository - new features and functionality. Nucleic Acids Res. 2017;45:D313-D319

Colovos C, Yeates TO. 1993. Verification

of protein structures: patterns of nonbonded atomic interactions. Protein Sci.2:1511–19

Bhattacharya D, Cheng J. 3drefine: consistent protein structure refinement by optimizing hydrogen bonding network and atomic level energy minimization. Proteins: Structure, Function, and Bioinformatics. 2012;81(1):119-131.

Boyko A, Blevins T, Yao Y, Golubov A, Bilichak A, Ilnytskyy Y, et al. Transgenerational adaptation of Arabidopsis to stress requires DNA methylation and the function of Dicer-like proteins. PLoS One. 2010;5:e9514.
Available:http://dx.doi.org/10.1371/journal. pone.0009514
PMID:20209086.

Roche DB, Buenavista MT, Tetchner SJ, McGuffin LJ. The infold server: An integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction, and ligand binding site prediction. Nucleic Acids Res. 2011;39: 171–176.

McGuffin LJ, Atkins JD, Saleh BR, Shuid AN, Roche DB. IntFOLD: An integrated server for modeling protein structures and functions from amino acid sequences. Nucleic Acids Res.; 2015.

Pavlidi N, Tseliou V, Riga M, Nauen R, Van Leeuwen T, Labrou NE, Vontas J. Functional characterization of glutathione S-transferases associated with insecticide resistance in Tetranychus urticae. Pestic. Biochem. Physiol. 2015;121:53–60.

Van Leeuwen T, Vontas J, Tsagkarakou A, Dermauw W, Tirry L. Acaricide resistance mechanisms in the two-spotted spider mite Tetranychus urticae and other important Acari: A review. Insect Biochem Mol Biol. 2010;40:563–572.

Casida JE, Durkin KA. Neuroactive insecticides: targets, selectivity, resistance, and secondary effects. Annu. Rev. Entomol. 2013;58:99.

Badawy MEI, Abdelgaleil SAM, Mahmoud NF, Marei AESM. Preparation and characterizations of essential oil and monoterpenena noemulsions and acaricidal activity against two-spotted spider mite (Tetranychus urticae Koch). Int. J. Acarol. 2018;44:330–340.

Melo SA, Moutinho C, Ropero S, Calin GA, Rossi S, Spizzo R, Fernandez AF, Davalos V, Villanueva A, Montoya G. A genetic defect in exportin-5 traps precursor microRNAs in the nucleus of cancer cells. Cancer Cell. 2010;18:303–315.

Rattan RS. Mechanism of action of insecticidal secondary metabolites of plant origin. Crop Prot. 2010;29:913–920.

Costa B, Da Pozzo E, Chelli B, Simola N, Morelli M, Luisi M, Maccheroni M, Taliani S, Simorini F, Da Settimo F. Anxiolytic properties of a 2-phenylindolglyoxylamide TSPO ligand: Stimulation of in vitro neurosteroid production affecting GABA A receptor activity. Psychoneuroendocrino-logy. 2011;36:463–472.

Khumalo G, Holechek J .2005. Relationship between Chihuahuan Desert perennial grass production and precipitation. Rangeland Ecology and Management 58, 239–246.

Davies K.W, Boyd CS, Beck J.L, Bates J.D, Svejcar T.J, Gregg M.A (2011) Saving the sagebrush sea, an ecosystem conservation plan for big sagebrush plant communities. Biological Conservation 144, 2573–2584.

Abdelgaleil SAM, Mohamed MIE, Shawir MS, Abou-Taleb HK. Chemical composition, insecticidal and biochemical effects of essential oils of different plant species from Northern Egypt on the rice weevil. Sitophilusoryzae L. J. Pest. Sci. 2016;89:219–229.

Allam SF, Soudy BA, Hassan SH. Insecticidal effects of essential oils of Mentha against Tetranychus urticae. Bioscience Research. 2017;14(4): 874- 878.

Pavela R, Stepanycheva E, Shchenikova A, Chermenskaya T, Petrova M. Essential oils as prospective fumigants against Tetranychus urticae Koch. Ind. Crop. Prod. 2016;94:755–761.