Employing Genome Mining to Unveil a Potential Contribution of Endophytic Bacteria to Antimicrobial Compounds in the Origanum vulgare L. Essential Oil

Abstract

Essential oils (EOs) from medicinal plants have long been used in traditional medicine for their widely known antimicrobial properties and represent a promising reservoir of bioactive compounds against multidrug-resistant pathogens. Endophytes may contribute to the yield and composition of EOs, representing a useful tool for biotechnological applications. In this work, we investigated the genomic basis of this potential contribution. The annotated genomes of four endophytic strains isolated from Origanum vulgare L. were used to obtain KEGG ortholog codes, which were used for the annotation of different pathways in KEGG, and to evaluate whether endophytes might harbor the (complete) gene sets for terpene and/or plant hormone biosynthesis. All strains possessed ortholog genes for the mevalonate-independent pathway (MEP/DOXP), allowing for the production of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) precursors. Ortholog genes for the next steps in terpenoid biosynthesis were scarce. All the strains possess potential plant growth promotion (PGP) ability, as shown by the presence of orthologous genes involved in the biosynthesis of indoleacetic acid. The main contribution of endophytes to the yield and composition of O. vulgare EO very likely resides in their PGP activities and in the biosynthesis of precursors of bioactive compounds.

Keywords: VOCs; biosynthesis pathways; endophyte; medicinal plants.

Figure 1

(a) Principal component analysis (PCA) of the main compounds in the VOCs of the four endophytic strains. (b) VENN diagram reporting the comparison of PubChem annotations of volatile compounds in the O. vulgare EO (violet) and in the volatile compounds synthesized by the four endophytic strains (yellow). Numbers represent the number of compounds in the endophytic VOC profiles and plant EO.

Figure 2

(a) Annotated pathway for the biosynthesis of the terpenoid backbone (KEGG map00900), precursor of the other pathways for the biosynthesis of specific terpenoid classes. (b) Annotated pathway for the biosynthesis of sesquiterpenoid and triterpenoid (KEGG map00909). In the pathway, genes (rectangular symbols) are annotated based on their presence in the O. vulgare genome (violet) or in the list of annotated orthologs from all endophytes (yellow); enzymes in gray are absent either in the O. vulgare genome and/or in the list of annotated orthologs of the four endophytes.

Scheme 1

General terpenoid compound biosynthesis scheme.

Figure 3

Venn diagrams reporting the number of KEGG orthologs included in the pathway for terpenoid backbone biosynthesis (a), tryptophan metabolism (b), and carotenoid biosynthesis (c) KEGG pathways in comparison between different endophytes.