Identification and in silico functional characterization of a Ghnac29-like transcription factor in response to abiotic stress tolerance in cotton

Abstract

Abiotic stresses produce an adverse impact on plant growth and crop productivity. In most developing countries including Pakistan, economies are agriculture-based and are affected badly by extreme weather changes. These climate changes influence the development and yield of the cotton crop. Numerous stress-tolerant genes including transcription factor genes have been known over the past few years that can serve as a key to regulating the stress-associated gene expression in cotton. The NAC transcription factor, which has a significant function in plant production, growth, and reaction to different environmental stresses, is now one of the major groups of plant TFs. In the current study GhNAC29-like gene, an uncharacterized cotton-born member of the NAC gene family, was functionally characterized. To amplify the full-length sequence of GhNAC29-like gene, total RNA was isolated followed by cDNA synthesis. The GhNAC29-like sequence was characterized by in-silico analysis including similarity search, multiple sequence alignment and phylogenetic analysis. The result indicates that GhNAC29-like shows maximum similarity with GrNAC29-like which is 91 %. In-silico analysis through different software also shows that GhNAC29-like is a membrane-soluble protein that is found within the nucleus and membrane of the cell, having no signal peptide located on it. This protein contains no transmembrane helix and it doesn't go under post-translational modifications. Further analysis shows that the conserved domain (pfamNAM) is present in the GhNAC29-like protein structure and it has NAM (No apical meristem) superfamily. The expression analysis of the stress-related NAC29-like gene Gossypium hirsutum was also studied using the CottonFGD database. GhNAC29-like gene expression is maximum under cold stress and increases with time whereas, under heat, drought, and salt stress, gene expression increases at a certain level, and then it decreases. High temperatures above 40 completely cause the loss of activity of protein due to which the yield decreases in high-temperature areas of Pakistan. This analysis shows that low temperatures are good for the protein activity (GhNAC29-like) and can make better the yield production rate. Abiotic factors including heat, drought, and excessive salinity are among the major causes of yield loss around the globe. Hence, GhNAC29-like shows a significant increase in expression in various abiotic stresses. Furthermore In-silico promoter analysis has shown the presence of various putative stress reactive cis-regulatory motifs. These findings suggest that cotton GhNAC genes have a function in the transcriptional regulation of environmental stresses to plant response.