Molecular cloning and in silico analysis of heat stress responsive gene ClpB1 from Ziziphus nummularia genotypes

Abstract

Heat stress is one of the most destructive abiotic stresses which adversely affect crop plants, resulting in reduced potential yield. Plants that are able to tolerate heat stress possess an intrinsic mechanism which needs to be unravelled at molecular level so as to decipher the role of gene and metabolic pathways involved in heat stress tolerance. To understand the molecular mechanism of heat stress tolerance, studies on isolation and characterization of gene for abiotic stress tolerance, ClpB1 were performed in Ziziphus nummularia (Burm. f.) Wight & Arn, an inherently abiotic stress tolerant plant. Differential expression studies of gene ClpB1 by qRT-PCR in contrasting genotypes of Z. nummularia (genotype Jaisalmer: heat tolerant and genotype Godhra: heat sensitive) was carried out. CDS (Coding DNA sequence) of gene ClpB1 from the genotypes Z. nummularia J and Z. nummularia G were cloned and characterized. These genes ZnJClpB1 (ACNO: MN398267) and ZnGClpB1 (ACNO: MN398268) showed 1.09 and 2.3% dissimilarity at nucleotide and amino acid level, respectively. Computational based analysis revealed the presence of larger functional AAA lid 9 domains in ZnJClpB1 as compared to ZnGClpB1. Phylogenetic relationship and structure modeling was performed to understand isoform type and basic molecular functioning and of gene ZnClpB1 from Z. nummularia genotypes. Possibly, it is the first report on cloning, characterization and comparative in silico based analysis of gene ZnClpB1 in Z. nummularia. Gene ZnClpB1 would be a prospective resource for developing abiotic stress tolerant crops by transgenic or breeding approach.