Genome-Wide Identification of Phenylacetaldehyde Reductase Genes and Molecular Docking Simulation Study of OePAR1 in Olives

Hydroxytyrosol is a natural phenolic compound found in olives. Phenylacetaldehyde reductase (PAR) is a key enzyme in the final step of the hydroxytyrosol biosynthesis pathway in olives. However, genome-wide studies on the PAR gene family in olives have not been reported. In this study, 21 genes were identified through a genome-wide analysis. Phylogenetic analysis classified these genes into three subgroups: PAR, CCR (Cinnamoyl-CoA reductase), and DFR (Dihydroflavonol 4-reductase). Expression pattern analysis suggested that genes within these subfamilies may play crucial roles in the biosynthesis of polyphenols, lignin, and anthocyanins, respectively. Three-dimensional structural modeling and molecular docking of the OePAR1 revealed that hydrogen bonds, hydrophobic interactions, and π–π stacking interactions collectively influence the affinity between PAR and its substrates. Residues at the active site form hydrogen bonds, with variations contributing to substrate specificity. The substrate with the strongest affinity for OePAR1 was identified as 3,4-dihydroxyphenylacetaldehyde (3, 4-DHPAA), with a binding energy of −4.98 kcal/mol, in agreement with previous enzymatic activity validation. Subcellular localization studies revealed that OePAR1 is localized to the chloroplast. This study provides essential insights into the biological functions of OePARs in olives and lays the groundwork for enhancing olive oil quality through genetic engineering.