Allosteric feedback inhibition of deoxy-D-xylulose-5-phosphate synthase involves monomerization of the active dimer

Abstract

AbstractIsoprenoids are a very large and diverse family of metabolites required by all living organisms. All isoprenoids derive from the double-bond isomers isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), which are produced by the methylerythritol 4-phosphate (MEP) pathway in bacteria and plant plastids. Understanding the regulation of the MEP pathway, probably the main metabolic pathway elucidated in this century, is a must for the rational design of biotechnological endeavors aimed at increasing isoprenoid contents in microbial and plant systems. It has been reported that IPP and DMAPP feedback regulate the activity of deoxyxylulose 5-phosphate (DXS), a dimeric enzyme catalyzing the main flux-controlling step of the MEP pathway. Here we provide experimental insights on the underlying mechanism. Our data show that direct allosteric binding of IPP and DMAPP to bacterial and plant DXS promotes monomerization of the enzyme. This allows a fast response to a sudden increase or decrease in IPP/DMAPP supply by rapidly shifting the dimer-monomer equilibrium accordingly. DXS monomers expose hydrophobic domains that are hidden in the dimer, resulting in aggregation and eventual degradation. Removal of monomers that would otherwise be available for dimerization and enzyme reactivation appears as a more drastic response in case of persistent IPP/DMAPP overabundance (e.g., by a blockage in their conversion to downstream isoprenoids). Our model provides a mechanistic explanation of how IPP and DMAPP supply can be adapted to changes in their demand and it also explains the changes in DXS protein levels observed after long-term interference of the MEP pathway flux.Significance StatementIsoprenoids are a vast family of organic compounds with essential roles in respiration, photosynthesis, photoprotection, membrane structure, and signaling. Many of them have great economic and nutritional relevance as pigments, aromas, drugs or phytonutrients. Despite their functional and structural diversity, they all derive from the same five-carbon precursors. We show that these precursors feedback-regulate their own synthesis in bacteria and plant plastids by allosterically shifting the dimer:monomer equilibrium of the enzyme that catalyzes the first step of their biosynthetic pathway towards the inactive monomeric form. This evolutionary conserved mechanism allows for both short-term (immediate) and long-term (sustained) control of the pathway flux, and its manipulation could be critical for the rational engineering of high-value isoprenoid products in bacterial and plant systems.