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

Abstract

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.

Lysosome Associated Protein Transmembrane 4B-24 Is the Predominant Protein Isoform in Human Tissues and Undergoes Rapid, Nutrient-Regulated Turnover

“…1 The LAPTM4B-35especific N-terminus has been reported to contain two functional amino acid motifs, an SH3-domain binding motif (amino acids 12 to 15) interacting with the p85a subunit of phosphatidylinositol 3-kinase (PI3K) to promote efflux of chemotherapeutic drugs, 4 and an arginine-rich polybasic stretch (amino acids 52 to 67) interacting with phosphoinositides to regulate autophagy. 5 Both LAPTM4B isoforms have in common the following motifs: a conserved sphingolipid interaction motif in the third transmembrane span (amino acids 208 to 216) important for mammalian target of rapamycin complex 1 (mTORC1) signaling, 6 C-terminal lysosomal targeting signals, 1,7 and PY motifs (amino acids 295 to 298, 311 to 314) required for binding the ubiquitin ligase Nedd4. 7 LAPTM4B- 35 represents the longest open reading frame (ORF) of the LAPTM4B transcript, and is commonly considered to be the major isoform.…”

Identification of Lysosome‐Associated Protein Transmembrane‐4 as a Novel Therapeutic Target for Osteosarcoma Treatment

“…In addition to its regulatory function in a variety of tumors, LAPTM4B also has several important physiological functions in non-tumor cells. LAPTM4B mediates amino acid transporter interaction and late endosomal ceramide export, and hence regulates cell death pathways 14,31 . In addition, LAPTM4B could lead to uptake of Leu into lysosomes and activate the mTORC1 through recruiting LAT1-4F2hc to lysosomes 15 .…”

Inconspicuous Little Allies: How Membrane Lipids Help Modulate Protein Function

“…As yet another example, Zhou et al now provide compelling evidence for the role of a cell membrane lipid, ceramide, in controlling the function of a membrane protein involved in a signaling pathway that is responsible for cell metabolism, proliferation, and survival. 1 …”

“… 8 Indeed, in analogy to the lipid-facilitated dimerization of the transmembrane trafficking protein, 8 the absence of the lipid-binding feature in LAPTM4B attenuated dimerization with the amino acid transporter. 1 Contradictory at first glance, exchange of the central aspartate residue in the TM3 domain, which contributes to ceramide binding, led to a stronger rather than a weaker interaction of LAPTM4B and the amino acid transporter. However, the absence of this aspartate residue compromised downstream signaling.…”