Ca²⁺-activated sphingomyelin scrambling and turnover mediate ESCRT-independent lysosomal repair

Abstract

Lysosomes are vital organelles vulnerable to injuries from diverse materials. Failure to repair or sequester damaged lysosomes poses a threat to cell viability. Here we report that cells exploit a sphingomyelin-based lysosomal repair pathway that operates independently of ESCRT to reverse potentially lethal membrane damage. Various conditions perturbing organelle integrity trigger a rapid calcium-activated scrambling and cytosolic exposure of sphingomyelin. Subsequent metabolic conversion of sphingomyelin by neutral sphingomyelinases on the cytosolic surface of injured lysosomes promotes their repair, also when ESCRT function is compromised. Conversely, blocking turnover of cytosolic sphingomyelin renders cells more sensitive to lysosome-damaging drugs. Our data indicate that calcium-activated scramblases, sphingomyelin, and neutral sphingomyelinases are core components of a previously unrecognized membrane restoration pathway by which cells preserve the functional integrity of lysosomes.

Pathogenic variants of sphingomyelin synthase SMS2 disrupt lipid landscapes in the secretory pathway

“…SM adopts an asymmetric distribution across the bilayers of late secretory and endolysosomal organelles, with the bulk of SM residing in the luminal/exoplasmic leaflet. However, using GFP-tagged EqtSM as cytosolic SM reporter (EqtSM cyto ), we found that perturbation of lysosome or PM integrity by pore-forming chemicals or toxins disrupts transbilayer SM asymmetry by triggering a rapid transbilayer movement of SM catalyzed by Ca 2+ -activated scramblases (Niekamp et al, 2022). To perform its central task in membrane biogenesis, the ER harbors constitutively active scramblases that enable a rapid equilibration of newly synthesized phospholipids across its bilayer (Pomorski and Menon, 2016).…”

“…Subsequent conversion of SM to ceramides by neutral SMases on the cytosolic surface of injured lysosomes promotes their repair, presumably by driving an inverse budding of the damaged membrane area in a process akin to ESCRT-mediated formation of intraluminal vesicles. This SM-based membrane restoration pathway functions independently of ESCRT and may also operate at the PM (Niekamp et al, 2022).…”

“…Moreover, an asymmetric distribution of SM across late secretory and endolysosomal bilayers is relevant for an optimal repair of damaged organelles. Lysosome wounding by chemicals or bacterial toxins triggers a rapid Ca 2+ -activated scrambling and cytosolic exposure of SM (Ellison et al, 2020; Niekamp et al, 2022). Subsequent conversion of SM to ceramides by neutral SMases on the cytosolic surface of injured lysosomes promotes their repair, presumably by driving an inverse budding of the damaged membrane area in a process akin to ESCRT-mediated formation of intraluminal vesicles.…”

Maintenance and loss of endocytic organelle integrity: mechanisms and implications for antigen cross-presentation

“…The depletion of ESCRT components prevent this shedding and results in death of the cell [ 53 , 58 ]. Intriguingly, an ESCRT-independent repair pathway involving trans-bilayer motion of sphingomyelin on damaged lysosomes has also, recently, been reported [ 63 ].…”

Multiplicity of Glycosphingolipid-Enriched Microdomain-Driven Immune Signaling

“…More recently, SM was reported to be exposed on the cytosolic side of damaged phagosomal membranes around Salmonella or Listeria, with galectin-8 localizing to the phagosomal membranes [176,177]. The cytosolic exposure of SM by Ca 2+activated scramblase was recently reported to mediate lysosomal repair independently of the endosomal sorting complex required for the transport complex (ESCRT) [178]. Although the mechanisms by which pathogenic mycobacteria survive inside host cells remain unclear [179], an exploration of the involvement of cross-talk between GSL-enriched microdomains and other sphingolipids in intracellular events, such as phagosome maturation, may be key to the development of new treatments for mycobacterial infections.…”