The isopentenyl diphosphate synthase gene family in Cinnamomum burmanni: Genome-wide identification and functional analysis

Cinnamomum burmanni(Nees and T. Nees) Blume, as a prominent tree of essential oil, contains various terpenoids in its leaves, which are valued in the cosmetic and pharmaceutical industries. Isopentenyl diphosphate synthase (IDS), serving as the central enzymatic core for the terpenoid biosynthetic pathway, generates the fundamental precursors for diverse terpenoid skeletons. However, currently research of the IDS genes in C. burmanni has been restricted to some genes which were putatively synthesized as the monoterpene and sesquiterpene precursor, with their catalytic roles remain unverified. This study identified 13 candidate CbIDS genes (CbIDS1-13) from the genome of borneol-type C. burmanni, which were categorized as five phylogenetic subfamilies (IDS-a to IDS-e) and distributed across six chromosomes. Evolutionary and collinearity analyses demonstrated that CbIDS family has likely expanded via segmental duplication. The molecular docking simulations were employed to obtain the potentially binding mechanisms of substrate and each CbIDS protein and the prospectively catalytic functions for each subfamily. The vitro enzymatic assays validated that CbIDS1 and CbIDS4 respectively function as geranylgeranyl diphosphate synthase (GGPPS) and geranyl diphosphate synthase (GPPS) activities, while both CbIDS8 and CbIDS12 possess farnesyl diphosphate synthase (FPPS) activity. Other CbIDS enzymes were inactive alone, but the combination of the small subunit of GPPS (GPPS.SSU), including CbIDS6 or CbIDS11, with the large subunit (GPPS.LSU) CbIDS13 restored GPPS activity. This functional elucidation of the CbIDS genes established the basis for future genetic improvement of chemical phenotypes in C. burmanni and enhancement of its borneol essential oil quality.