In-silico identification and functional analysis of cis-regulatory elements in selected protein phosphatase 2A (PP2A) gene promoters of Arabidopsis thaliana reveals 5′-AAAG-3′ as over-represented motif under abiotic stress condition

A strong gene regulation mechanism is essential to provide accurate temporal and spatial gene expression. This is facilitated by an exclusive arrangement of cis-regulatory elements (CREs) in the upstream regulatory regions of the genes, which collaborate with transcription factors (TFs) in regulating many biological processes, such as plant response to environmental stress. Here, we conducted a bioinformatics analysis in detail to find and profile CREs in the 1 kilobase (1Kbp) upstream regions of Arabidopsis thaliana protein phosphatase 2A (PP2A) genes. Through the plant-specific database newPLACE (SOGO), we found a broad spectrum of CREs involved in phytohormonal signaling, development, and stress responses. Furthermore, de novo motif discovery by the MEME suite identified a new and statistically significant motif, 5′-AAAG-3′, with a high enrichment throughout the PP2A promoters, indicating that it might play a role in regulating gene expression under different physiological conditions. To ascertain the functional significance of these genes further, we carried out a meta-analysis using Genevestigator, which illustrated differential expression of the PP2A genes—upregulation and downregulation—under a range of abiotic stress conditions. Overall, our results shed light on intricate PP2A gene transcriptional regulation and point out CREs as major factors governing plant development, growth, and stress acclimation.