Nishtha Lukhmana, Mohit Jain, Sayan Chatterjee
University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India.
Heavy metals such as Cu, Fe and Zn are essential for normal plant growth, although elevated concentration of both essential (Cu, Fe, Mn, Mo, Ni, Zn, Co) and non-essential metals (As, Cd, Cr, Hg, Pb) can result in growth inhibition and toxicity symptoms. Once the cytosolic metal concentration in plants turns out of control, phytotoxicity of heavy metals inhibits transpiration and photosynthesis, disturbs carbohydrate metabolism, and drives the secondary stresses like nutrition stress and oxidative stress, which collectively affects plant development. To identify some motifs responsible for heavy metal tolerance, few genes namely FRO1, FRO2, ZIP4, IRO2, DAMS1, IRT1, NAAT1 etc from Oryza sativa were chosen and their respective sequences were obtained from the NCBI database. Using Basic Local Alignment Search Tool (BLAST), similar genes from Oryza sativa, Hordeum vulgare, Zea mays, Sorghum bicolor and Triticum aestivum satisfying the criteria of cut off ‘evalue’= 0, maximum identity>80% and query coverage>70% were selected. Using ClustalW, the sequences were aligned. The genes were analysed for common signature sequences. A few of them were identified which can qualify as candidate motifs. Our study revealed some signature sequences which remained conserved in certain genes with heavy metal tolerance in the above mentioned plant species subjected to heavy metal stress. The analysis showed evidence from where it could be concluded that 25 signature sequences in FRO1, 6 in FRO2, 3 in ZIP4, 6 in IR02, 5 in DAMS1 and 20 in IRT1 could be recognised as candidate motifs, whereas no signature sequences were found in NAAT1 that could be recognised as candidate motifs associated with heavy metal tolerance in plants. The results were further validated by studying the phylogenetic relationship of the genes involved. These signature sequences can further be used to identify potential heavy metal tolerant genes, either silent or having a different ORF, in other plants which apparently may not possess a heavy metal tolerant character. Read More …