Cloning, in silico characterization and expression analysis of TIP subfamily from rice (Oryza sativa L.)

Tonoplast Intrinsic Proteins (TIPs) constitute a significant class of the aquaporins. The TIPs control water trade among cytosolic and vacuolar compartments and can also transport glycerol, ammonia, urea, hydrogen peroxide, metals/metalloids, and so forth. Additionally, TIPs are engaged with different abiotic stress responses and developmental processes like leaf expansion, root elongation and seed germination. In this study, ten TIP genes in the rice genome were identified from Oryza sativa ssp indica. Among these, representative groups of TIP genes were cloned and sequenced whilst some TIP sequences showed stop codons in the coding region. The secondary structure analysis represented six conserved transmembrane helices along with the inter-helical regions having conserved motifs. The representative three-dimensional tetrameric design of protein sequence of TIP1;1 displayed key features like NPA motifs, aromatic/arginine (ar/R) selectivity filters, and Froger's residues. The vacuolar localization, transmembrane topological properties, and conserved motif analysis of the cloned genes altogether supported their identity as TIPs. An unrooted phylogenetic tree delineated the relatedness of TIPs from Oryza with different species and bunched them into five clades. The promoter analysis uncovered key regulons associated with administering abiotic stress responses. Gene expression studies showed thatTIPsare differentially regulated under salt and drought stress at various time points in shoots and roots of rice. Also, the pattern of expression was found to be significantly variable in five different rice tissues. The heat-map based tissue and stress- specific expression analysis supported the experimental findings. In conclusion, the identification and transcript-level expression studies of TIPs significantly contribute towards the comprehension of their utilitarian significance in the abiotic stress response.