Modeling the effect of daytime duration on the biosynthesis of terpenoid precursors

Abstract

Terpenoids are valued chemicals in the pharmaceutical, biotechnological, cosmetic, and biomedical industries. Biosynthesis of these chemicals relies on polymerization of Isopentenyl di-phosphate (IPP) and/or dimethylallyl diphosphate (DMAPP) monomers, which plants synthesize using a cytosolic mevalonic acid (MVA) pathway and a plastidic methyleritritol-4-phosphate (MEP) pathway. Circadian regulation affects MVA and MEP pathway activity at three levels: substrate availability, gene expression of pathway enzymes, and utilization of IPP and DMAPP for synthesizing complex terpenoids. There is a gap in understanding the interplay between the circadian rhythm and the dynamics and regulation of the two pathways. In this paper we create a mathematical model of the MVA and MEP pathways in plants that incorporates the effects of circadian rhythms. We then used the model to investigate how annual and latitudinal variations in circadian rhythm affect IPP and DMAPP biosynthesis. We found that, despite significant fluctuations in daylight hours, the amplitude of oscillations in IPP and DMAPP concentrations remains stable, highlighting the robustness of the system. We also examined the impact of removing circadian regulation from different parts of the model on its dynamic behavior. We found that regulation of pathway substrate availability alone results in higher sensitivity to daylight changes, while gene expression regulation alone leads to less robust IPP/DMAPP concentration oscillations. Our results suggest that the combined circadian regulation of substrate availability, gene expression, and product utilization, along with MVA- and MEP-specific regulatory loops, create an optimal operating regime. This regime maintains pathway flux closely coupled to demand and stable across a wide range of daylight hours, balancing the dynamic behavior of the pathways and ensuring robustness in response to cellular demand for IPP/DMAPP.

Keywords: biological design principles; circadian regulation; mathematical modeling; synthetic biology; systems biology; terpenoid biosynthesis.

Figure 1

Representation of the two terpenoid biosynthesis pathways plus the ectopic pathway, the MVA pathway (left, cytosol and peroxisome) and the MEP pathway (right, plastid). DXR, DXP reductoisomerase; MCT, 2-C-methyl-D-erythrtle 4-phosphate cytidylyl transferase; CDP-ME, 4-(Citidine 5’-difosfo)-2-C-methyl-D-eritritol; CMK, 4-difosfocitidil-2-C-methyl-D-erythrtol kinase; CDP-MEP, 2-Fosfo-4-(cytidine 5’- diphospho)-2-C-methyl-D-eritritol; MDS, 2-C-methyl-D-eritritol 2,4-cyclodifosphate synthase; MEcPP, 2-C-methyl-D-eritritol 2,4-cycdiphosphate; HDS, 4-hydroxy-3-methylbut-2-en-1-il diphosphate synthase; HMBPP, 4-hydroxy-3-methylbut-2-in-1-il diphosphate; HDR, 4-hydroxy-3-methylbut-2-en-1-il diphosphate reductase; IDI, isopentenyl diphosphate Delta-isomerase; PhyPP, phytyl diphosphate.

Figure 2

Time course simulation of IPP and DMAPP concentrations throughout 48h at different latitudes and times of the year: equator/spring and fall equinoxes (dusk = 12h), middle latitudes (winter, dusk = 9h; summer, dusk = 15h) and near polar circle latitudes (winter, dusk = 3h; summer, dusk = 21h). T = 1h. Green lines – MEP pathway. Magenta lines – MVA pathway.

Figure 3

Relative amplitude of the circadian IPP concentration and flux oscillations as a function of the number of daylight hours (h). X-axis – number of daylight hours. Y-axis – minimum value/maximum value of a variable during a day. (A, B) Relative amplitude of IPP_cyt concentration, (C) Relative amplitude of the flux going through the MVA pathway to produce IPP, (D) Relative amplitude of the flux going through the MEP pathway to produce IPP and (E) Relative amplitude of the flux going through both pathways to produce IPP.

Figure 4

Model B Time course simulation of IPP and DMAPP concentrations throughout 48h at different latitudes and times of the year: equator/spring and fall equinoxes (dusk = 12h), middle latitudes (winter, dusk = 9h; summer, dusk = 15h) and near polar circle latitudes (winter, dusk = 3h; summer, dusk = 21h). T = 1h Green lines – MEP pathway. Magenta lines – MVA pathway.

Figure 5

Model C. Time course simulation of IPP and DMAPP concentrations throughout 48h at different latitudes and times of the year: equator/spring and fall equinoxes (dusk = 12h), middle latitudes (winter, dusk = 9h; summer, dusk = 15h) and near polar circle latitudes (winter, dusk = 3h; summer, dusk = 21h). T = 1h. Green lines – MEP pathway. Magenta lines – MVA pathway.

Figure 6

Model D. Time course simulation of IPP and DMAPP concentrations throughout 48h at different latitudes and times of the year: equator/spring and fall equinoxes (dusk = 12h), middle latitudes (winter, dusk = 9h; summer, dusk = 15h) and near polar circle latitudes (winter, dusk = 3h; summer, dusk = 21h). T = 1h. Green lines – MEP pathway. Magenta lines – MVA pathway.