Comparative bioinformatics analysis of the biosynthetic pathways and key candidate genes of three species, Vitis vinifera, Fragaria vesca and Olea europaea, furnish enzyme sets for the production of pharmaceutically valuable terpenes in heterologous hosts

Abstract

Plants represent a rich repository of taxonomically restricted, yet chemically diverse, secondary metabolites that are synthesised via specific metabolic pathways. Enzyme specificity and biosynthetic gene clustering are the bottleneck of secondary metabolite evolution. As economically important food crops, grape, strawberry, and olive produce many pharmaceutically important molecules; however, their specific biosynthetic pathways remain inaccessible. Our genomic-based analysis of these three species reveal the biosynthetic diversity of their specialised secondary metabolites. We found over 20 BGCs predicted, most of which were characterised in two species, grape and strawberry. Gene annotation of the biosynthetic candidate genes predicted the production of many medically and industrially important compounds including cycloartenol, nerolidol, farnesene and valencene. Although most of the predicted clusters are concentrated in specific genomic positions, some have shown gene duplications in their clusters, which is suggestive of pseudogenes or misassembled genomes. Our genome mining and putative functional analysis of the biosynthetic genes annotated in the three species indicated the evolutionary processes that have shaped their current genetic structure and the structural diversity of their chemical compositions. Revealing the biogenetic background of these natural molecules is a step forward towards the expansion of their chemical diversification via engineering their biosynthetic genes heterologously, as well as the identification of their role in the interaction between those plants and their biotic and abiotic conditions.