Bioinformatic analyses of microRNA profiles and protein-protein interactions within leaves from Haberlea rhodopensis subjected to severe drought

Abstract

Drought is a major threat to crop production, and resurrection plants provide a unique model for understanding extreme desiccation tolerance. While Apostolova et al. (2020) identified microRNAs (miRNAs) responsive to dehydration in Haberlea rhodopensis, the downstream protein targets and regulatory interaction networks remain largely unknown. This study addresses that gap by integrating miRNA profiles with protein–protein interaction (PPI) networks to predict target genes, identify hub regulators, and uncover pathways that regulate desiccation tolerance. Using PsRNATarget to predict mRNA targets (converted to Arabidopsis thaliana homologs) and Cytoscape-based network analysis, we identified three hub genes (SPL7 AT5G43270.3, and AT1G76580) as central regulators of the drought response. Functional enrichment revealed that metabolic pathways and secondary metabolite biosynthesis were significantly overrepresented, highlighting processes critical for survival under water deficit. This integrative approach moves beyond miRNA identification to demonstrate, for the first time, how miRNA-mediated regulation intersects with protein networks to coordinate desiccation tolerance in H. rhodopensis. The identified hub genes (SPL7 AT5G43270.3, and AT1G76580) can be utilized for future genetic engineering of drought-tolerant crops.