Abstract
Chilli leaf curl Ahmedabad virus (ChiLCAV), a begomovirus belonging to the family Geminiviridae, has been reported for its occurrence in India, infecting chilli and tomato plants. The viral proteins associated with ChiLCAV involves in the primary pathogenesis and transmission of the virus by whitefly. Viral protein interactions with host proteins show the dynamics of structural binding and interaction in their infection cycle. At the same time, plants have multiple defence mechanisms against bacterial and viral infections. Secondary metabolites play a significant role in the inborne defence mechanism of plants. Host proteins are also the prime producers of secondary metabolites. In the present study, we evaluated the host protein SnRK1 interaction with all six viral proteins (V1, V2, C1, C2, C3 and C4). Apart from C4, all the other viral proteins showed appreciable binding and interaction with SnRK1. SnRK1 has the regulation mechanism for the accumulation of diterpenoids, secondary metabolites. Flavonoids are secondary metabolites produced by the plant under stress conditions. Further, we studied the binding and interaction of six selected flavonoids produced by Solanaceae family members with all the ChiLCAV proteins. All six selected flavonoids showed considerable binding energy with all viral proteins. Each flavonoid showed high binding energy with different viral proteins. Molecular docking is carried out for both flavonoids and the host protein SnRK1. These in silico interactions and docking studies could be useful for understanding the plants defence mechanism against viral infections at the molecular level.
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References
Brown CR (2005) Antioxidants in potato. Am J Potato Res 82:163–172. https://doi.org/10.1007/BF02853654
Chakraborti S, Chatterjee P, Das A (2019) Testing safer options to manage apical leaf curling in chilli. J Entomol Res 43:457–466. https://doi.org/10.5958/0974-4576.2019.00080.X
Daina A, Michielin O, Zoete V (2017) SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep 7:1–13. https://doi.org/10.1038/srep42717
Delatte H, Naze F, Cottineau JS et al (2006) Occurrence of tomato chlorosis virus on tomato in Réunion Island. Plant Pathol 55:289. https://doi.org/10.1111/j.1365-3059.2005.01279.x
Domingo LR, Ríos-Gutiérrez M, Pérez P (2016) Applications of the conceptual density functional theory indices to organic chemistry reactivity. Molecules 21(6):748
Doyle J (1991) CTAB Total DNA Isolation. Mol Tech Taxon, pp 283–293
Falcone Ferreyra ML, Rius SP, Casati P (2012) Flavonoids: biosynthesis, biological functions, and biotechnological applications. Front Plant Sci 3:1–15. https://doi.org/10.3389/fpls.2012.00222
Fondong VN (2013) Geminivirus protein structure and function. Mol Plant Pathol 14:635–649. https://doi.org/10.1111/mpp.12032
Geerlings P, De Proft F, Langenaeker W (2003) Conceptual density functional theory. Chem Rev 103:1793–1873. https://doi.org/10.1021/cr990029p
Hey SJ, Powers SJ, Beale MH et al (2006) Enhanced seed phytosterol accumulation through expression of a modified HMG-CoA reductase. Plant Biotechnol J 4:219–229. https://doi.org/10.1111/j.1467-7652.2005.00174.x
Hutchison CA III, Smith HO, Pfannkoch C, Venter JC (2005) Cell-free cloning using φ29 DNA polymerase. Proc Nat Acad Sci 102(48):17332–17336
Jansen MAK, Van den Noort RE, Adillah Tan MY et al (2001) Phenol-oxidizing peroxidases contribute to the protection of plants from ultraviolet radiation stress. Plant Physiol 126:1012–1023. https://doi.org/10.1104/pp.126.3.1012
Johnson M, Zaretskaya I, Raytselis Y et al (2008) NCBI BLAST: a better web interface. Nucleic Acids Res 36:5–9. https://doi.org/10.1093/nar/gkn201
Kaul TN, Middleton E, Ogra PL (1985) Antiviral effect of flavonoids on human viruses. J Med Virol 15:71–79. https://doi.org/10.1002/jmv.1890150110
Khan A, Samad A (2014) A new isolate of eclipta yellow vein virus along with a betasatellite associated with yellow vein leaf curl disease of andrographis paniculata in India. Plant Dis 98:698. https://doi.org/10.1094/PDIS-08-13-0848-PDN
Khan A, Sharma P, Khan F et al (2016) In silico and in vitro studies on begomovirus induced andrographolide biosynthesis pathway in andrographis paniculata for combating inflammation and cancer. Mol Inform 35:253–261. https://doi.org/10.1002/minf.201501010
Kikuchi K, Matsushita N, Suzuki K, Hogetsu T (2007) Flavonoids induce germination of basidiospores of the ectomycorrhizal fungus Suillus bovinus. Mycorrhiza 17:563–570. https://doi.org/10.1007/s00572-007-0131-8
Kumar Y, Hallan V, Zaidi AA (2011) Chilli leaf curl Palampur virus is a distinct begomovirus species associated with a betasatellite. Plant Pathol 60(6):1040–1047
Kumar S, Stecher G, Li M et al (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549. https://doi.org/10.1093/molbev/msy096
Melgarejo TA, Kon T, Rojas MR et al (2013) Characterization of a new world monopartite begomovirus causing leaf curl disease of tomato in Ecuador and Peru reveals a new direction in geminivirus evolution. J Virol 87:5397–5413. https://doi.org/10.1128/jvi.00234-13
Miar M, Shiroudi A, Pourshamsian K et al (2021) Theoretical investigations on the HOMO–LUMO gap and global reactivity descriptor studies, natural bond orbital, and nucleus-independent chemical shifts analyses of 3-phenylbenzo[d]thiazole-2(3H)-imine and its para-substituted derivatives: solvent and subs. J Chem Res 45:147–158. https://doi.org/10.1177/1747519820932091
Mohannath G, Jackel JN, Lee YH et al (2014) A complex containing SNF1-related kinase (SnRK1) and adenosine kinase in arabidopsis. PLoS ONE. https://doi.org/10.1371/journal.pone.0087592
Nietzsche M, Schießl I, Börnke F (2014) The complex becomes more complex: protein–protein interactions of SnRK1 with DUF581 family proteins provide a framework for cell- and stimulus type-specific SnRK1 signaling in plants. Front Plant Sci 5:1–14. https://doi.org/10.3389/fpls.2014.00054
Nigam K, Srivastava S, Kumar D, et al. (2014) Detection and analysis of leaf curl virus from Jatropha. 4:1–6
Panche AN, Diwan AD, Chandra SR (2016) Flavonoids: an overview. J Nutr Sci. https://doi.org/10.1017/jns.2016.41
Parniske M, Ahlborn B, Werner D (1991) Isoflavonoid-inducible resistance to the phytoalexin glyceollin in soybean rhizobia. J Bacteriol 173:3432–3439. https://doi.org/10.1128/jb.173.11.3432-3439.1991
Rai VP, Kumar R, Singh SP et al (2014) Monogenic recessive resistance to pepper leaf curl virus in an interspecific cross of capsicum. Sci Hortic (amsterdam) 172:34–38. https://doi.org/10.1016/j.scienta.2014.03.039
Rojas MR, Jiang H, Salati R et al (2001) Functional analysis of proteins involved in movement of the monopartite begomovirus, tomato yellow leaf curl virus. Virology 291:110–125. https://doi.org/10.1006/viro.2001.1194
Rombel IT, Sykes KF, Rayner S, Johnston SA (2002) ORF-FINDER: a vector for high-throughput gene identification. Gene 282(1–2):33–41
Sanchez G (2013) Las instituciones de ciencia y tecnología en los procesos de aprendizaje de la producción agroalimentaria en Argentina. El Sist Argentino Innovación Inst Empres y Redes El Desafío La Creación y Apropiación Conoc 515:659–664. https://doi.org/10.1002/prot
Satya VK, Malathi VG, Renukadevi P, Sangeetha B (2022) Role of plant viral satellites association in geminivirus infection. In Geminivirus: Detection, Diagnosis and Management. Academic Press, pp 421–442
Senanayake DMJB, Mandal B, Lodha S, Varma A (2007) First report of chilli leaf curl virus affecting chilli in India. Plant Pathol 56:343. https://doi.org/10.1111/j.1365-3059.2007.01513.x
Senanayake DMJB, Varma A, Mandal B (2012) Virus-vector relationships, host range, detection and sequence comparison of chilli leaf curl virus associated with an epidemic of leaf curl disease of chilli in Jodhpur, India. J Phytopathol 160:146–155. https://doi.org/10.1111/j.1439-0434.2011.01876.x
Shen Q, Bao M, Zhou X (2012) A plant kinase plays roles in defense response against geminivirus by phosphorylation of a viral pathogenesis protein. Plant Signal Behav 7:888–892. https://doi.org/10.4161/psb.20646
Singh RP, Gu M, Agarwal R (2008) Silibinin inhibits colorectal cancer growth by inhibiting tumor cell proliferation and angiogenesis. Cancer Res 68:2043–2050. https://doi.org/10.1158/0008-5472.CAN-07-6247
Sukal AC, Kidanemariam DB, Dale JL et al (2019) Assessment and optimization of rolling circle amplification protocols for the detection and characterization of badnaviruses. Virology 529:73–80. https://doi.org/10.1016/j.virol.2019.01.013
Thakur H, Jindal S, Sharma A, Dhaliwal M (2018) Chilli leaf curl virus disease: a serious threat for chilli cultivation. J Plant Dis Prot 125:239–249. https://doi.org/10.1007/s41348-018-0146-8
Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680. https://doi.org/10.1093/nar/22.22.4673
Wang H, Hao L, Shung CY et al (2003) Adenosine kinase is inactivated by geminivirus AL2 and L2 proteins. Plant Cell 15:3020–3032. https://doi.org/10.1105/tpc.015180
Webb B, Sali A (2017) Protein structure modeling with MODELLER BT—functional genomics: methods and protocols. 1654:39–54. https://doi.org/10.1007/978-1-4939-7231-9
Williams CJ, Headd JJ, Moriarty NW, et al. (2017) Tools for protein science protein science. 3330:1–73
Yamasaki H, Sakihama Y, Ikehara N (1997) Flavonoid-peroxidase reaction as a detoxification mechanism of plant cells against H2O2. Plant Physiol 115:1405–1412. https://doi.org/10.1104/pp.115.4.1405
Zhu K, Day T, Warshaviak D, et al. (2017) Non-specificity_clearence.pdf. 82:1646–1655. https://doi.org/10.1002/prot.24551.Antibody
Zubair M, Shan-E-Ali Zaidi S, Shakir S et al (2017) An insight into cotton leaf curl multan betasatellite, the most important component of cotton leaf curl disease complex. Viruses 9:1–12. https://doi.org/10.3390/v9100280
Acknowledgements
This work has been performed through the DST; Early Career Research (ECR) project sanctioned by the Government of India. The authors thank the Department of Science and Technology (DST- SERB), Government of India, for the support.
Funding
Funded through the ECR-SERB project sanctioned by the Department of Science and Technology (DST), Government of India (File No. ECR/2017 /000562).
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Sravya, G., Jeyaraj, G., Vadivelu, A. et al. Molecular characterization of chilli leaf curl Ahmedabad virus: homology modelling and evaluation of viral proteins interacting with host protein SnRK1 and docking against flavonoids—an in silico approach. Theory Biosci. 142, 47–60 (2023). https://doi.org/10.1007/s12064-022-00383-9
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DOI: https://doi.org/10.1007/s12064-022-00383-9