The C-terminal regulatory domain of IPMS enzyme maintains leucine homeostasis by bypassing a hidden negative feedback loop in plants

Abstract

In the leucine biosynthesis pathway, homeostasis is achieved through a feedback regulatory mechanism facilitated by binding of the end-product Leu at the C-terminal regulatory domain of the first committed enzyme, isopropylmalate synthase (IPMS). In-vitro studies showed that removal of the regulatory domain abolishes the feedback regulation on plant IPMS while retaining its catalytic activity. However, the physiological consequences and underlying molecular regulation upon removal of the IPMS C-terminal domain on the Leu flux have not been previously explored in plants. Here, we show that in the absence of its regulatory domain, an unexpected alternative regulatory loop acts to control plant IPMS catalysis. Removal of IPMS regulatory domain using CRISPR/Cas9 significantly reduced the formation of end-product Leu in-planta, but increased the levels of Leu pathway intermediates. Additionally, delayed growth was observed when IPMS devoid of regulatory domain was introduced into IPMS-null mutants of E. coli and Arabidopsis. Combining the metabolomic and biochemical analysis, we found that the Leu pathway intermediate, -ketoisocaproate, was a competitive inhibitor of IPMS with a truncated regulatory domain. Thus, we demonstrate that the C-terminal regulatory domain of IPMS is biologically favored since it maintains Leu homeostasis while bypassing the possibility of competitive inhibition by a pathway intermediate. SignificanceTill date it was known that the limited profile of essential amino acid-leucine in plants, is majorly due to the feedback inhibition of its pathway enzyme, IPMS, by the binding of accumulating leucine at its regulatory domain. So, can we increase the leucine pool in plants by removing the IPMS regulatory domain? Herein we show that, the targeted removal of this domain under native condition had led to low leucine pool and compromised growth phenotype but observed an accumulation in the leucine pathway intermediates. We uncover a hidden function of the IPMS regulatory domain to avoid an intermediate inhibition on IPMS activity, which could limit the end-product. The study brings an unknown regulatory checkpoint in maintaining leucine homeostasis in plants.