In silico prediction, phylogenetic and bioinformatic analysis of SoPCS gene, survey of its protein characterization and gene expression in response to cadmium in Saccharum officinarum

Ecotoxicology and Environmental Safety
M KolahiMohammad Reza Tabandeh

Abstract

Phytochelatin synthase isolated from microorganisms, yeasts, algae and plant, serve a fundamental role in reducing heavy metals. In this research the in silico PCS gene structure (SoPCS) of sugarcane, its secondary and 3D protein structure, physicochemical properties, cell localization and phylogenetic tree were predicted utilizing bioinformatics tools. SoPCS expression in the leaves and roots of sugarcane in tissue culture treated with cadmium was also studied utilizing real time PCR. The predicted SoPCS gene contains 1524 nucleotides, a protein encoded with 508 amino acids of which the molecular weight is 55953.3 Da, 6 exons and 5 introns. The subcellular position of the enzyme is mitochondrion or cytoplasmic. Two domains belonging to the phytochelatin synthase family with similar features was found in Pfam having more than 97% similarity with the predicted SoPCS protein. Phylogeny analyses of plant species were well isolated from other organisms. Ten disulfide-bonded cysteines were excluded from the structure of SoPCS. The predicted 3D structure of SoPCS showed that it is able to bind to L-gamma-glutamylcysteine as substrate. The binding site sequence of PCS included amino acids 52(Q),55(P),56(A),57(F), 58(C),103(G),104(I),1...Continue Reading

Citations

Jun 10, 2020·International Journal of Molecular Sciences·Mohamad Farhan Mohamad SobriNorhayati Ramli
Oct 24, 2020·Journal of Biomolecular Structure & Dynamics·Habeebat Adekilekun OyewusiRoswanira Abdul Wahab

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