In silico analysis of high affinity potassium transporter (HKT) isoforms in different plants

Abstract

BackgroundHigh affinity potassium transporters (HKTs) are located in the plasma membrane of the vessels and have significant influence on salt tolerance in some plants. They exclude Na+ from the parenchyma cells to reduce Na+ concentration. Despite many studies, the underlying regulatory mechanisms and the exact functions of HKTs within different genomic backgrounds are relatively unknown. In this study, various bioinformatics techniques, including promoter analysis, identification of HKT-surrounding genes, and construction of gene networks, were applied to investigate the HKT regulatory mechanism.ResultsPromoter analysis showed that rice HKTs carry ABA response elements. Additionally, jasmonic acid response elements were detected on promoter region of TmHKT1;5. In silico synteny highlighted several unknown and new loci near rice, Arabidopsis thaliana and Physcomitrella patent HKTs, which may play a significant role in salt stress tolerance in concert with HKTs. Gene network prediction unravelled that crosstalk between jasmonate and ethylene reduces AtHKT1;1 expression. Furthermore, antiporter and transferase proteins were found in AtHKT1;1 gene network. Interestingly, regulatory elements on the promoter region of HKT in wild genotype (TmHKT1;5) were more frequent and variable than the ones in cultivated wheat (TaHKT1;5) which provides the possibility of rapid response and better understanding of environmental conditions for wild genotype.ConclusionDetecting ABA and jasmonic acid response elements on promoter regions of HKTs provide valuable clues on underlying regulatory mechanisms of HKTs. In silico synteny and pathway discovery indicated several candidates which act in concert with HKTs in stress condition. We highlighted different arrangement of regulatory elements on promoter region of wild wheat (TmHKT1;5) compared to bread wheat (TaHKT1;5) in this study.

Molecular cloning and induced expression of the plasma membrane intrinsic protein gene and promoter from mulberry (Morus multicaulis)

“…Such findings have also been made in sunflower by Manavella et al (2008). Skn-1_modif is a cis-acting regulatory element required for endosperm expression and MSA-like is required for cell cycle regulation (Babgohari et al 2014). Transcription factors could be found in the promoter region involved in shoot-specific expression and response to light (as-2-box) (Fig.…”

“…In plants, TFs have important impacts on developmental processes, cellular physiology, and responses to environmental signals (Chow et al 2016). The promoter regions regulating the MmPIP2 gene may be conserved, as it has been reported that there are two AP-1 binding sites (TATA-box) and one CAAT-box in common cis-acting elements in promoter and enhancer regions, and a greater number of TATA boxes in the promoter region can result in higher expression of the gene (Babgohari et al 2014) and the CAAT-box has been demonstrated to have a positive effect on frequency of transcriptional initiation Fig. 1.…”

Unified Transcriptomic Signature of Arbuscular Mycorrhiza Colonization in Roots of Medicago truncatula by Integration of Machine Learning, Promoter Analysis, and Direct Merging Meta-Analysis

“…The developed transcriptomic signature of successful AM colonization of roots of Medicago truncatula , obtained by integration of meta-analysis and machine learning (attribute weighting) models, was used for upstream regulatory analysis through common regulator discovery, as previously described (Deihimi et al, 2012 ; Babgohari et al, 2014 ; Bakhtiarizadeh et al, 2014b ; Shamloo-Dashtpagerdi et al, 2015 ). To this end, the top 20 highly upregulated meta-genes, which responded to AM inoculation, (Supplementary Table 5 ) were selected for promoter analysis and common transcription factor discovery.…”

A novel pairwise comparison method for in silico discovery of statistically significant cis-regulatory elements in eukaryotic promoter regions: Application to Arabidopsis

“…MYB binding sites are abundant in promoters of stress responsive genes, however there are some evidence that they work together with other proteins to confer light responsiveness (Babgohari et al, 2014). MYB15 is R2R3 type MYB transcription factor involved in cold regulation of number of genes (Mahdi et al, 2013).…”

“…Recently, we developed a new approach for gene discovery irrespective from gene coding (BLAST), based on identifying distinct organization and combination of CREs (in view of order and distance) on promoter regions and identification of the genes with similar promoter architecture within whole genome (Hosseinpour et al, 2013). Recently, it has been demonstrated that CREs on the promoter regions of genes in wild wheat are more variable and frequent than the cultivated wheat which contributes in fast response and better understanding of environmental conditions for wild genotype (Babgohari et al, 2014). Due to the unique characteristic of transcription factors in binding to CREs on promoter regions of different genes, a small number of transcription factors are enough to regulate a considerable number of genes and play the central role in functional genomics (Mahdi et al, 2013;Mahdi et al, 2014).…”