Regulatory Network Identification, Promoter and Expression Analysis of Arabidopsis thaliana NPR1 in Defense Responses against Stresses

Salicylic acid (SA) and jasmonic acid (JA) phytohormones have been known for their roles in plant defense behaviour against biotic and abiotic stresses. They regulate defense pathways by antagonistic interaction. NPR1 as a key regulatory factor in the cross-talk between SA and JA, signaling is essential for the inhibition of JA-responsive gene expression by SA. In silico promoter analysis of 1.5 kb promoter regions of NPR1 gene revealed that NPR1 contains 23 MYB and 20 WRKY transcription factor binding sites. Different cis-elements associated with various stress responses were identified in Arabidopsis thaliana NPR1. The most common element was allocated to the defense responses against biotic stresses. Based on gene network analysis, NPR1, TGA2 and TGA3 were predicted to have functional cooperation with each other. Affymetrix microarray data analysis of A. thaliana under SA treatment demonstrated that most genes involved in NPR1 network are up-regulated under SA treatment. Therefore, interaction and cooperation between these factors might serve to fine-tune regulation of defense and immune responses against biotic and abiotic stresses

analysis for Arabidopsis DREB-genes

Dehydration response element binding factors (DREBs) are one of the principal plant transcription factor subfamilies that regulate the expression of many abiotic stress-inducible genes. This sub-family belongs to AP2 transcription factor family and plays a considerable role in improving abiotic stresses tolerance in plants. Therefore, it is of interest to identify critical cis-acting elements involved in abiotic stress responses. In this study, we survey promoter cis-elements for ATDREBs genes (Arabidopsis thaliana DREBs). Regulatory networks based on ATDREB candidate genes were also generated to find other genes that are functionally similar to DREBs. The study was conducted on all 20 Arabidopsis thaliana non redundant DREB genes stored in RefSeq database. Promoter analysis and regulatory network prediction was accomplished by use of Plant CARE program and GeneMANIA web tool, respectively. The results indicated that among all genes, DREB1A, DREB1C, DREB2C, DREB2G and DEAR3 have the most type of diverse motifs involved in abiotic stress responses. It is implied that co-operation of abscisic acid, ethylene, salicylic acid and methyl jasmonate signaling is crucial for the regulation of the expression of drought and cold responses through DREB transcription factors. Gene network analysis showed different co-expressed but functionally similar genes that had physical and functional interactions with candidate DREB genes

A comprehensive meta-analysis to identify transcriptional signatures of abiotic stress responses in barley (Hordeum vulgare)

Barley, as one of the major cereals, possesses natural tolerance to major abiotic stresses such as drought and salinity, so that it is an outstanding model in abiotic stresses research. The study focuses on meta-analysis by combining different datasets of barley abiotic stress-related microarray data to identify stress-responsive genes and pathways. In addition to a thorough investigation to determine the up and downregulated gene sets under stress conditions, other analyses including gene ontology (GO) enrichment and protein–protein interaction network analysis were performed for a comprehensive study of differentially expressed genes under abiotic stresses. A total of 256 microarray samples from 14 different experiments were analyzed and 3723 probe sets were identified. The metabolic processes, cellular process, localization, biological regulation and regulation of biological process were the top enriched GO terms. Interestingly, the response to abiotic stress in the functional group contained the highest number of upregulated genes. In addition, the photosynthesis biological category included only downregulated genes. Fourteen genes in this category were related to photosystem II while only six genes belonged to photosystem I. Network analysis of DEGs revealed 52 and 57 genes as critical genes in down and upregulated networks, respectively; module analysis unveiled 28 and 23 clusters for up and downregulated networks. Regarding the GO analysis of modules, one upregulated cluster and two downregulated clusters exhibited a direct response to abiotic stress