Identification and Characterization of miRNAs in Exosome-like Nanoparticles (ELNs) Derived from Nauclea officinalis

Abstract Plant-derived exosome-like nanoparticles (ELNPs) are cell-secreted extracellular vesicles (EVs), which contain miRNAs that regulate plant physiology and can be used for intercellular communication. In this study, the Nauclea officinalis-derived ELNPs (N-ELNPs) were isolated via ultracentrifugation and characterized by transmission electron microscopy. Their miRNAs were analyzed through high-throughput sequencing and target gene and function prediction was conducted using miRDeep, miRBase, miRanda, GO, and KEGG. The obtained results showed that N-ELNs (50–200 nm, vesicular) harbored 875 known and 62 novel miRNAs; top 10 expressed miRNAs belonged to MIR172, MIR1919, and MIR396 families. Conducted GO enrichment covered 10 major biological processes, 2 cellular components, and 8 molecular functions; KEGG enrichment involved 10 pathways linked to plant hormonal signal transduction, lipid metabolic reprogramming, branched-chain amino acid catabolism, energy homeostasis, and specialized metabolite production. The obtained data guide future research to identify specific targets for regulation via N-ELNPs and their miRNAs both within the plants themselves and in the potential regulation of gene expression in animal cells.