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20222
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Subject: Biotechnology and molecular Biology × End date: 2022 × Type: Thesis × Thesis Type: M.Sc ×
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    ThesisItemOpen Access
    Molecular docking of Alternaria brassicae fungal proteins with phytoalexins of Brassica juncea and comparison with standard fungicides
    (G.B. Pant University of Agriculture and Technology, Pantnagar, District Udham Singh Nagar, Uttarakhand. PIN - 263145, 2022-08) Shivakumar R; Singh, B.R.
    Brassica juncea being one of the important oil seed crops in India as well as around the globe faces a major problem in imbalance between the production and consumption due to yield loss. This yield loss is accounted by several diseases and pests that infect the crop during its growth stages. The most important factor causing a reportable yield loss is due to a necrotrophic fungi Alternaria brassicae, of an average yield reduction of 30-40%. Therefore, mitigation strategies must be developed to resist the infection of this pathogen at molecular level. Though the fungicides do their role to an extent in controlling the infection, certain strategies must be developed to replace the fungicides, keeping in mind the harmful effects of fungicides towards environment, biodiversity and human well-being. In this study we attempt to use the molecular mechanism during the pathogenesis. Where the Alternaria brassicae aims in producing the proteins that actively take part in causing the disease and the intricate defense of the plants to combat the infection. Plant defense system involves the production of Pathogenesis Related proteins that inhibits the fungi and also it produces a wide range of secondary metabolites known as phytoalexins to neutralize the fungal proteins. Hence the interaction between the phytoalexins and fungal proteins are studied at in-silico level by performing molecular docking. The interactions of the selected proteins ABC transporter, Calmodulin and NRPS are analyzed by obtaining their docking scores in terms of binding energies against the Brassica’s phytoalexins such as Brassilexin, Cyclobrassinin, Indole-3-carboxyaldehyde, Methoxybrassitin and Rutalexin. The same docking analysis is also done with the standard fungicides that are recommended towards Alternaria blight infection to understand the advantages of phytoalexins over standard fungicides. The fungicides Azoxystrobin and Cyprodinil shows an effective performance against Alternaria brassicae proteins. Hence the results of docking exhibits that the phytoalexins such as Cyclobrassinin, Indole-3-carboxyaldehyde exhibits docking scores ranging from -5 Kcal/mol to -7 Kcal/mol, which is considered ideal and could be suggested as an alternative to fungicides selected in the study.
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    ThesisItemOpen Access
    Virtual screening of phytoalexin(s) of Brassica juncea as defense inducing molecule(s) against alternaria blight
    (G. B. Pant University of Agriculture and Technology, Pantnagar, 2022-08) Kurma, Devakrishna; Gohar Taj
    Brassica juncea is an important Rapeseed-mustard crop in India, accounting for more than 90% of the total area. It is used as sources of oil, vegetable and fodder. Brassica has a high potential yield in India, but there is a large gap between potential and actual yields, which is mostly due to biotic and abiotic stress. Alternaria blight is a serious disease among the biotic stresses. It causes huge economic losses in terms of both production and oil quality. Alternaria brassicae is the causal organism of Alternaria blight and can infect the host at any stage of development. Alternaria brassicae proteins MAT1, BETA-TUBULIN, and ALTA1 are involved in mating, motility, and spore germination activities respectively during the pathogenesis of Alternaria blight on Brassica spp. Physiochemical analysis through high Aliphatic Index (AI), Index of Instability and Grand Average of Hydropathy (GRAVY) reveals that all the three proteins were heat stable as well as hydrophobic proteins. In this study molecular docking-based approach was used to predict the above proteins of Alternaria brassicae as possible molecular target of phytoalexins during pathogenesis or defense response. I-TASSER was used to predict 3-D structures for above proteins which were subsequently docked with phytoalexins which included Camalexin, Glucobrassicin, Methoxybrassinin, Spirobrassinin, Indole- 3acetaldoxime N-oxide and also with the five standard fungicides. Among the phytoalexins, the results of docking of Glucobrassicin with the above target proteins showed good affinity as well as low docking score in the range of -8.57 to -3.97 whereas the fungicide Tebuconazole had docking score in the range of -5.47 to -1.24. Therefore, the phytoalexin Glucobrassicin could be used for the protection of Brassica plants against Alternaria blight. Further In-vitro studies and downstream validation would give way to use the Glucobrassicin phytoalexin(s) as a substitute for hazardous fungicides to control plant diseases.