Ceramide sensing by human SPT-ORMDL complex for establishing sphingolipid homeostasis

The SPT-ORMDL complex is tightly regulated by cellular sphingolipid levels, but the sphingolipid sensing mechanism is unknown. Here, the authors elucidate the molecular basis of ceramide sensing by the human SPTORMDL complex for establishing sphingolipid homeostasis. The ORM/ORMDL family proteins function as regulatory subunits of the serine palmitoyltransferase (SPT) complex, which is the initiating and rate-limiting enzyme in sphingolipid biosynthesis. This complex is tightly regulated by cellular sphingolipid levels, but the sphingolipid sensing mechanism is unknown. Here we show that purified human SPT-ORMDL complexes are inhibited by the central sphingolipid metabolite ceramide. We have solved the cryo-EM structure of the SPT-ORMDL3 complex in a ceramide-bound state. Structure-guided mutational analyses reveal the essential function of this ceramide binding site for the suppression of SPT activity. Structural studies indicate that ceramide can induce and lock the N-terminus of ORMDL3 into an inhibitory conformation. Furthermore, we demonstrate that childhood amyotrophic lateral sclerosis (ALS) variants in the SPTLC1 subunit cause impaired ceramide sensing in the SPT-ORMDL3 mutants. Our work elucidates the molecular basis of ceramide sensing by the SPT-ORMDL complex for establishing sphingolipid homeostasis and indicates an important role of impaired ceramide sensing in disease development.

Automated summary

The researchers elucidated the molecular mechanism of ceramide sensing by the SPT-ORMDL complex, which is tightly regulated by cellular sphingolipid levels. They found that the ORM/ORMDL family proteins can bind to specific sites of the serine palmitoyltransferase (SPT) complex after modifying cellular sphingolipids, leading to the inhibition of its activity. Furthermore, they discovered that mutations in the SPTLC1 subunit in childhood amyotrophic lateral sclerosis (ALS) patients impair ceramide sensing.