A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction

Membrane
proteins are functionally regulated by the composition
of the surrounding lipid bilayer. The late endosomal compartment is
a central site for the generation of ceramide, a bioactive sphingolipid,
which regulates responses to cell stress. The molecular interactions
between ceramide and late endosomal transmembrane proteins are unknown.
Here, we uncover in atomistic detail the ceramide interaction of Lysosome
Associated Protein Transmembrane 4B (LAPTM4B), implicated in ceramide-dependent
cell death and autophagy, and its functional relevance in lysosomal
nutrient signaling. The ceramide-mediated regulation of LAPTM4B depends
on a sphingolipid interaction motif and an adjacent aspartate residue
in the protein’s third transmembrane (TM3) helix. The interaction
motif provides the preferred contact points for ceramide while the
neighboring membrane-embedded acidic residue confers flexibility that
is subject to ceramide-induced conformational changes, reducing TM3
bending. This facilitates the interaction between LAPTM4B and the
amino acid transporter heavy chain 4F2hc, thereby controlling mTORC
signaling. These findings provide mechanistic insights into how transmembrane
proteins sense and respond to ceramide.