Lupenone, a wonder chemical obtained from Euphorbia segetalis to boost affinity for the transcriptional factor escalating drought-tolerance in Solanum Lycopersicum: A cutting-edge computational biology approach

Abstract

Drought is the single greatest abiotic factor influencing crop yield worldwide. Plants remain in one area for extended periods, making them vulnerable to natural and man-made influences. Understanding plant drought responses will help us develop strategies for breeding drought-resistant crops. Large proteome analysis revealed that leaf and root tissue proteins respond to drought differently depending on the plant's genotype. Commonly known as tomatoes, Solanum Lycopersicum is a globally important vegetable crop. However, drought stress is one of the most significant obstacles to tomato production, making the development of cultivars adapted to dry conditions an essential goal of agricultural biotechnology. Breeders have put quite a lot of time and effort into the tomato to increase its productivity, adaptability, and resistance to biotic and abiotic challenges. However, conventional tomato breeding has only improved drought resistance due to the complexity of drought traits. The resilience of tomatoes under drought stress has been the subject of extensive study. Using contemporary sequencing approaches like genomics, transcriptomics, proteomics, and metabolomics has dramatically aided in discovering drought-responsive genes. One of the most prominent families of plant transcription factors, WRKY genes, plays a crucial role in plant growth and development in response to natural and abiotic stimuli. To develop plants that can withstand both biotic and abiotic stress, understanding the relationships between WRKY-proteins (transcription factors) and other proteins and ligands in plant cells is essential. This is despite the fact that tomatoes have a long history of domestication. This research aims to utilize Lupenone, a hormone produced in plant roots in response to stress, to increase drought resistance in plants. Lupenone exhibits a strong affinity for the WRKY protein at -9.64 kcal/mol. Molecular docking and modeling studies show that these polyphenols have a significant role in making Solanum Lycopersicum drought-resistant and improving the quality of its fruit. As a result of climate change, droughts are occurring more frequently and persisting for more extended periods, making it necessary to breed crops resistant to drought. While considerable variability for tolerance exists in wild cousins, little is known about the processes and essential genes influencing drought tolerance in cultivated tomato species.

Fig 1

(a) Boosted lenience to drought & biotic pressure and genes in charge (Available from: https://pgsb.helmholtz-muenchen.de/droughtdb/drought_db.html); (b) A model for genes that regulate decreases water loss by upregulating cell wall and stomatal regulator genes during drought [17].

Fig 2. Analysis of the docked posture of 2AYD-643732; displayed the ligand bound at the pocket of the receptor 2AYD, and the binding pocket residues interacted with the ligand displayed.

Fig 3

(a) RMSD of 2AYD and ligand Lupenone for 100 ns; (b) RMSF of 2AYD and ligand Lupenone for 100 ns; (c) Number of Hydrogen bindings of 2AYD and ligand Lupenone for 100 ns; (d) Radius of gyration of 2AYD and ligand Lupenone for 100 ns.

Fig 4. Types of bonds formed in 100ns simulation run.

Fig 5

(a) The figure displayed shows ligand characteristics such as RMSD, the radius of gyration (rGyr), intramolecular hydrogen bond, molecular surface area (MolSA), solvent accessible surface area (SASA), and polar surface area (P.S.A.) of Lupenone; (b) Ligand torsion profile after 100 ns simulation.

Fig 6. Protein interactions with the ligand can be monitored throughout the simulation.

Fig 7. Free energy landscape displaying the achievement of global minima (ΔG, kj/mol) of 2AYD in presence of Lupenone with respect to their RMSD (nm) and radius of gyration (Rg, nm).