Identification of GCC Box in the Promoter region of Ubiquinol Cytochrome C Chaperone Gene using Molecular Beacon Probe and its in silico Protein-DNA interaction study in Rice (Oryza sativa L.)

Rice is the primary staple food for more than half of the world’s population but very sensitive to various abiotic stresses (submergence) causing crop loss. During abiotic stresses various genes are differentially expressed to cope up with the stress conditions. The identification of Sub1A gene was a major breakthrough for the submergence tolerance which often regulates other genes by binding to their consensus promoter motifs such as GCC box. It was observed that Ubiquinol Cytochrome C chaperone (UCCC) gene was among many up-regulated differentially co-expressed genes having GCC box as a conserved motif. The primary role of UCCC gene is oxidative respiration but also has imperative secondary functions in plants. Therefore, UCCC gene was selected for the identification of GCC Box in the promoter region using Molecular Beacon Probe based Real Time PCR and their interaction with Sub1A protein. Real Time PCR analysis confirmed the presence of GCC box. Subsequently, the interaction of Sub1A with GCC box was studied through HADDOCK server. Protein-DNA interaction thus, suggested significant binding affinity of Sub1A towards GCC box present in the promoter region of UCCC gene.