Cloning and In silico analysis of Casparian strip membrane domain protein (CASP) from rice

Casparian strip (CS) seals the adjacent endodermal cells to form a tight junction and thereby regulate the movement of water and salts across the endodermis. Casparian strip membrane domain proteins (CASPs) play an important role in the formation of the CS. Among the CASP proteins, the role of CASP1 was much emphasized in the making of a protein scaffold on the surface of endodermal cells that inturn leads to the formation of CS. In this study, full-length cDNA of CASP1 was cloned from the roots of salt-stressed rice cultivar ASD16 using specific primers derived from the corresponding reference gene sequence in GenBank. The cDNA fragment of 813 bp obtained through RT-PCR was cloned in an intermediary cloning vector pJET1.2. The recombinant clone carrying CASP1 was characterized by restriction analysis and sequencing. Further, in silico analysis of CASP1 revealed that it is a transmembrane protein consisting of five transverse helices as per secondary and tertiary structure analysis. 3D structure of CASP1 protein was obtained by I TASSER online server. The structure was validated using PROCHECK structural analysis tool..