In silico identification of agriculturally important molecule(s) for defense induction against bacterial blight disease in Soybean (Glycine max)

Abstract

The productivity of Glycine max (Soybean), one of the economically important crops of India, is seriously affected by bacterial blight disease which is mainly caused by Psedomonas syringae. The disease results in significant yield losses in Soybean crops. Since no proven resistant source is available against bacterial blight, the only option remaining is to utilize biotechnological strategies which could lead to inhibition of pathogenic proteins of the Psedomonas syringae responsible for disease progression. Phytoalexins are well known to inhibit bacterial growth and trigger defense response against diseases in crop plants. The present study was conducted to identify the molecules which could inhibit the growth and development of bacteria. A few proteins were selected from literature analysis viz., Ornithine carbamoyl transferase 2, phaseolotoxin-insensitive, avirulence protein AvrRpt2, HarpinHrpZ, Sensor protein GacS, and Translation initiation factor IF-3 of Psedomonas syringae as possible molecular targets of phytoalexins. The molecular modeling of these proteins were done by using their amino acid sequence on Phyre2 and I-TASSER tool followed by model validation through energy minimization and Ramachandran plot analysis. Subsequently molecular docking was performed using some selected phytoalexins produced by members of Brassicaceae, Fabaceae, Solanaceae, Vitaceae and Poaceae family with each modeled protein structure by AutoDock vina. Based on the molecular docking study, we identified efficient defense molecules, which can be used for the development of agrochemicals for protection of G. max against infection of Psedomonas syringae.