The Enhanced Affinity of WRKY Reinforces Drought Tolerance in Solanum lycopersicum L.: An Innovative Bioinformatics Study

Abstract

In the scenario of global climate change, understanding how plants respond to drought is critical for developing future crops that face restricted water resources. This present study focuses on the role of WRKY transcription factors on drought tolerance in tomato, Solanum lycopersicum L., which is a significant vegetable crop. WRKY transcription factors are a group of proteins that regulate a wild range of growth and developmental processes in plants such as seed germination and dormancy and the stress response. These transcription factors are defined by the presence of a DNA-binding domain, namely, the WRKY domain. It is well-known that WRKY transcription factors can interact with a variety of proteins and therefore control downstream activities. It aims to simulate the effect of curcumin, a bioactive compound with regulatory capacity, on the protein–protein interaction events by WRKY transcription factors with an emphasis on drought stress. It was found that curcumin binds to WRKY with an energy of −11.43 kcal/mol with inhibitory concentration (Ki) 0.12 mM and has the potential to improve fruit quality and reinforce drought tolerance of S. lycopersicum, according to the results based on bioinformatics tools. The root means square deviation (RMSD) of the C-α, the backbone of 2AYD with ligand coupled complex, displayed a very stable structure with just a little variation of 1.89 Å. MD simulation trajectory of Cα atoms of 2AYD bound to Curcumin revealed more un-ordered orientation in PC1 and PC10 modes and more toward negative correlation from the initial 400 frames during PCA. Establishing the binding energies of the ligand–target interaction is essential in order to characterize the compound’s binding affinity to the drought transcription factor. We think we have identified a phyto-agent called curcumin that has the potential to enhance the drought tolerance. Compared to the part of the mismatch repair-base technique that can be used to fix drought related genes, curcumin performed better in a drop-in crop yield over time, and it was suggested that curcumin is a potential candidate factor for improving drought tolerance in tomatoes, and it needs future validation by experiments in laboratory and field.

Action of the plant-based essential oil-derived compound Taxol for improvising drought tolerance in Eucalyptus by modulating the VIT1 channel protein: a cutting-edge computational approach

“…The re-docking experiments demonstrated that Taxol and the 6IU4 protein formed a distinct binding pocket with a binding free energy of −10.23 kcal/ mol and an inhibitory concentration of 0.36 mM. This finding highlights the strong interaction between Taxol and the protein, which may contribute to the plant's ability to withstand drought conditions (Shivakumar et al, 2010;Debnath et al, 2023;Perveen et al, 2023). To further examine the stability and quality of the Taxol-6IU4 complex, a molecular dynamics simulation (MDS) was performed for a total time of 100 ns The results revealed that the complex was relatively stable throughout the simulation, with an average root-mean-square deviation (RMSD) of 1.2 Å for the Cα backbone of the VIT1 protein.…”

“…Eucalyptus species, including E. grandis, have developed strategies to cope with extreme drought conditions, such as adjusting stomatal functioning and consuming large amounts of organic solutes like proline (Snowdon et al, 2000;Graciano et al, 2005). However, these Drought is a significant challenge in agriculture and forestry as it affects crop yield and quality, as well as the overall health and survival of plants (Breda et al, 2006;Correia et al, 2018;Debnath et al, 2023). In this context, exploring the potential of essential oils to enhance drought resistance in plants represents a valuable contribution to both the scientific community and the agricultural sector.…”

QTL mapping and analysis for drought tolerance in rice by genome-wide association study

“…Breeding for abiotic conditions like drought remains challenging due to the complex nature of the genetic system and the risk of unexpected developments ( Debnath et al., 2023 ). To find the genes that control characteristics of drought tolerance, a modern molecular technique called QTL analysis was employed.…”

Enhancing drought tolerance in cauliflower (Brassica oleracea var. botrytis) by targeting LFY transcription factor modulation via the ethylene precursor, ACCA: an innovative computational approach

“…In molecular dynamics (MD) simulations, a commonly employed approach to monitor the temporal evolution of atomic motion involves the integration of the classical equation of motion. Docking provides a fixed representation of the conformation of a molecule’s binding pose within the active site of a protein ( Debnath et al., 2023b ; Jorgensen et al., 1996 ). Due to this factor, it is important to give careful thought to this matter.…”