Mechanism of sphingolipid homeostasis revealed by structural analysis of Arabidopsis SPT-ORM1 complex

The serine palmitoyltransferase (SPT) complex catalyzes the first and rate-limiting step in sphingolipid biosyn-thesis in all eukaryotes. ORM/ORMDL proteins are negative regulators of SPT that respond to cellular sphingo-lipid levels. However, the molecular basis underlying ORM/ORMDL-dependent homeostatic regulation of SPT is not well understood. We determined the cryo-electron microscopy structure of Arabidopsis SPT-ORM1 complex, composed of LCB1, LCB2a, SPTssa, and ORM1, in an inhibited state. A ceramide molecule is sandwiched between ORM1 and LCB2a in the cytosolic membrane leaflet. Ceramide binding is critical for the ORM1-dependent SPT repression, and dihydroceramides and phytoceramides differentially affect this repression. A hybrid beta sheet, formed by the amino termini of ORM1 and LCB2a and induced by ceramide binding, stabilizes the amino ter -minus of ORM1 in an inhibitory conformation. Our findings provide mechanistic insights into sphingolipid ho-meostatic regulation via the binding of ceramide to the SPT-ORM/ORMDL complex that may have implications for plant-specific processes such as the hypersensitive response for microbial pathogen resistance.

Automated summary

This study reveals the structure of the serine palmitoyltransferase (SPT) complex and its interaction with ORM/ORMDL proteins. ORM1 acts as a negative regulator of SPT by binding to a small molecule derived from steroid degradation, thereby controlling lipid synthesis and homeostasis. This has implications for plant responses to microbial attacks.