Lysosomal Ion Channels as Decoders of Cellular Signals

Abstract

Lysosomes, the degradation center of the cell, are filled with acidic hydrolases. Lysosomes generate nutrient-sensitive signals to regulate the import of H⁺, hydrolases, and endocytic and autophagic cargos, as well as the export of their degradation products (catabolites). In response to environmental and cellular signals, lysosomes change their positioning, number, morphology, size, composition, and activity within minutes to hours to meet the changing cellular needs. Ion channels in the lysosome are essential transducers that mediate signal-initiated Ca²⁺/Fe²⁺/Zn²⁺ release and H⁺/Na⁺/K⁺-dependent changes of membrane potential across the perimeter membrane. Dysregulation of lysosomal ion flux impairs lysosome movement, membrane trafficking, nutrient sensing, membrane repair, organelle membrane contact, and lysosome biogenesis and adaptation. Hence, activation and inhibition of lysosomal channels by synthetic modulators may tune lysosome function to maintain cellular health and promote cellular clearance in lysosome storage disorders.

Keywords: TFEB; TPC2; TRPML1; lysosomal exocytosis; lysosomal storage disease; mTOR.

Fig 1.. Function and regulation of lysosomes.

Receiving inputs from both endocytic and autophagic pathways, lysosomes are the degradation center in the cell under both normal and starvation conditions. The degradation products, i.e., catabolites, are released through exporters, vesicular trafficking, lysosomal exocytosis, or interorganelle material exchange at membrane contact sites. Lysosomes are formed de novo through endosome maturation, or reformed from autolysosomes or endolysosome hybrids. Lysosomes form membrane contact sites with ER and other organelles, at which export of lipids and ions takes place. Lysosomal membrane proteins bridge the information of cytoplasmic signaling and luminal degradation. Lysosomal ion channels, by mediating signal-dependent lysosomal ion flux, participate in various lysosomal functions, including lysosomal membrane trafficking, catabolite export, nutrient sensing, and mTOR signaling. Triggered by various cellular cues, lysosomal Ca²⁺ release regulates lysosomal trafficking, lysosomal exocytosis, autophagic clearance of damaged mitochondria, plasma membrane repair, lysosomal membrane repair, TFEB nuclear translocation, and lysosome biogenesis.

Fig 2.. Lysosomal ion channels and transporters.

Compared with cytoplasm, the lysosome lumen contains high H⁺, Ca²⁺, and Na⁺, but low K⁺. At resting conditions, lysosomal Δψ is close to 0 mV. Lysosomal channels that have been characterized using lysosomal patch-clamp include Na⁺/Ca²⁺-permeable TRPMLs, P2X4, and TPCs, and K⁺-selective channels BK/LysoK_vca and TMEM175. V-ATPase is the proton pump that acidifies lysosomes. The molecular identities of lysosomal Cl⁻ and H⁺ conductances are not yet known. SLC38A9 is the lysosomal arginine sensor and transporter; NPC1 is the lysosomal cholesterol transporter.

Fig 3.. Regulation of lysosomal membrane potential.

A. Lysosomal membrane potential (Δψ) is determined by the relative permeability of the lysosomal membranes to H⁺, Na⁺, and K⁺, through an unidentified H⁺-leak conductance (LysoH), LysoNa channels (e.g., TPCs), and LysoK channels (e.g., BK/LsyoK_vca and TMEM175). TPCs are Na⁺ channels activated by PI(3,5)P₂; TMEM175 is a K⁺ leak channel; BK channels are activated by both voltage and Ca²⁺. Lysosomal Δψ is depolarized when LysoH and LysoNa channels are open (left panels), and hyperpolarized when LysoK channels are open (right panels). In the resting conditions, lysosome Δψ fluctuates around 0 mV (±20 mV), due to minimal activation of lysosomal ion channels by ambient levels of cellular signals. Large Δψ changes (± 50 mV) occur when the levels of lysosomal ion channel-activating signals are high. Activation of LysoK reduces or reverses lysosomal Δψ, providing a larger driving force for LysoCa-mediated lysosomal Ca²⁺ release. B. Lysosome size may influence the duration and amplitude of lysosome Δψ changes. Luminal ion composition changes more dramatically in small-sized lysosomes. Hence, larger lysosomes exhibit bigger and longer lasting Δψ changes upon identical (in strength and duration) stimulation.

Fig 4.. Structural mechanisms of ligand-dependent activation of lysosomal TRPML and TPC channels.

A. High-resolution structures of TRPML1. a) The upper panel shows the top view of TRPML1 in the tetrameric assembly. Red and green boxes indicate the ML-SA1 and PI(3,5)P₂ binding sites, respectively. The lower panels illustrate the ML-SA1 and PI(3,5)P₂ binding sites in one single TRPML1 subunit, b) Carton illustrations of ligand-induced channel opening. B. High-resolution structures of TPC2. a) The upper panel shows the top view of TPC2 in the dimeric assembly. The PI(3,5)P₂ binding sites are enclosed in the red box. The lower panel illustrates the PI(3,5)P₂ binding sites in one single TPC2 subunit, b) Carton illustrations of PI(3,5)P₂-induced channel opening.