Comprehensive RNA, protein interaction and SNP analysis of CAX۱ in the Arabidopsis thaliana: integrated systems biology approach

Calcium exchanger ۱ (CAX۱) is the encoder of vacuolar Ca۲+/۳H+ antiporter. This protein involvesregulating Ca۲+ levels in the Arabidopsis thaliana. In this study, we performed a protein-protein networkanalysis to demonstrate the possible regulatory gene network of the transporter Ca۲+/۳H+ in the ArabidopsisThaliana. After literature mining, we indicated the protein-protein interaction network of the CAX۱ gene inthe Arabidopsis by STRING online software. The miRNA-mRNA interactions analysis of the selected geneswas performed by the miRWalk ۲.۰ online database. The analysis of single nucleotide polymorphism (SNP)was performed by miRNASNP-v۳. Based on this network analysis, the CAX۱ has significant proteininteractions with CAX۳, TPC۱, CAX۱۱, ACA۱۱, CXIP۴, SOS۲, SSE۱, NHX۱, T۲۲C۵.۲۳, and ECA. Thereis no possible Arabidopsis microRNA interaction with the selected genes. However, there is a significantmicroRNA interaction with hsa-miR-۶۸۹۴-۳p and SOS۲ in the ۳UTR position (Score: ۱.۰۰). Amongmentioned genes, TPC۱ is a key regulatory network in the conductance of sodium and calcium ions and theintravascular pH. ACA۱۱ is a ATPase in the mature vacuole membrane expressed in transgenic plants andvisualized in root cells. Based on miRNA SNP, rs۱۳۱۴۱۷۹۱۰۵ is an innovative and significant SNP on the۳UTR region of the SOS۲ gene (۱۴ gains and ۱۵ losses). The expression level and RNA interactions of thementioned genes are highly recommended to be evaluated in the Arabidopsis thaliana, bioinformatically andexperimentally.

کلیدواژه ها:

Arabidopsis Thaliana ، protein interaction ، gene network ، SNP ، CAX۱