Systems Biology Approach to Identify miRNAs Regulating Defense Genes in TEV-Infected Arabidopsis thaliana

This study investigated the transcriptome response of the Arabidopsis thaliana WT-۱ ecotype to Tobacco etch virus (TEV) infection and explored the role of microRNAs in this response. Using GEO۲R, ۱۳۶۷ differentially expressed genes were identified, with ۱۱۸۶ upregulated and ۱۸۱ downregulated. Gene enrichment analysis through g:Profiler revealed molecular processes and pathways involving these genes. Protein-protein interaction (PPI) networks were reconstructed using STRING. Topological analysis in Cytoscape identified PER۱, PAL۴, and CCoAMT as key genes involved in crucial biological pathways like secondary metabolite biosynthesis and phenylpropanoid biosynthesis. These pathways contribute to the production of defense compounds such as lignin and flavonoids, strengthening cell walls and creating physical and chemical barriers against the virus. Interactions between miRNAs and hub gene CDS sequences were analyzed using psRNATarget. Results showed that miRNAs like ath-miR۴۰۸-۳p, ath-miR۱۸۸۶.۱, ath-miR۲۱۱۲-۵p, ath-miR۱۵۷c-۳p, and ath-miR۵۶۳۲-۵pinteracted with PAL۴, CCoAMT, and PER۱, respectively, playing a significant role in the plant's defense response. For instance, miRNAs targeting PER۱, involved in reducing oxidative stress, inhibited its expression, while PAL۴ and CCoAMT, involved in defense compoundbiosynthesis, were also regulated by miRNAs. The identified miRNAs hold potential for genetic engineering to create TEV-resistant plants. This study not only enhances our understanding of plant- virus interactions but also proposes strategies for developing resistant plants by manipulating miRNA expression or altering target gene sequences. Techniques like CRISPR/Cas۹ can be employed to create miRNA-resistant versions of these genes. Overall, this research highlights the critical role of miRNA regulatory networks in plant defense against viruses and their potential to improve food security and reduce pesticide use.

Keywords:

Arabidopsis thaliana , Tobacco Etch Virus (TEV) , microarray , microRNAs , protein- protein interaction network(PPI) , gene regulation , plant defense , genetic engineering ,