How Lysosomes Sense, Integrate, and Cope with Stress

Abstract

Lysosomes are in the center of the cellular control of catabolic and anabolic processes. These membrane-surrounded acidic organelles contain around 70 hydrolases, 200 membrane proteins, and numerous accessory proteins associated with the cytosolic surface of lysosomes. Accessory and transmembrane proteins assemble in signaling complexes that sense and integrate multiple signals and transmit the information to the nucleus. This communication allows cells to respond to changes in multiple environmental conditions, including nutrient levels, pathogens, energy availability, and lysosomal damage, with the goal of restoring cellular homeostasis. This review summarizes our current understanding of the major molecular players and known pathways that are involved in control of metabolic and stress responses that either originate from lysosomes or regulate lysosomal functions.

Keywords: TFEB; autophagy; lysosomes; mTOR; nutrient sensing; transcription factors.

Figure 1.. Metabolic regulation in lysosomes.

Scheme of the different signaling pathways assembled on the lysosome surface in response to variations in the levels of amino acids, glucose, growth factors and cholesterol. Multiple nutrient signals, including glucose, amino acids and cholesterol converge to regulate the activity of Rag GTPases. When the levels of these nutrients are elevated (left panel), Rag GTPases activate, promoting the recruitment of the mTORC1 complex to the lysosome surface. At the same time, high levels of growth factors cause displacement of the TSC complex from the lysosomal surface, preventing its GAP activity towards Rheb. GTP-bound Rheb then promotes mTORC1 activation. A number of sensors, including Castor, Sestrin2 and Samtor, detect variations in the cytosolic pool of amino acids, whereas the lysosomal amino acid permease SLC38A9 recognizes amino acid concentration, in particular arginine, inside the lysosome lumen. Cholesterol transfer from the endoplasmic reticulum (ER) to the lysosomal membrane via OSBP1 also favors mTORC1 activation. Active mTORC1 phosphorylates members of the MiT/TFE family of transcription factors, such as TFEB and TFE3, promoting their binding to 14-3-3 and consequent cytosolic sequestration. At the same time, active AKT promotes autophagy inhibition through phosphorylation and inactivation of beclin and FoxO transcription factors. When the nutrients are scarce (right panel), GATOR1 is recruited to lysosomes inducing GDP-loading of RagA/B and inactivation of mTORC1. This allows translocation of TFEB and TFE3 to the nucleus to induce expression of multiple genes implicated in lysosomal biogenesis, autophagy, and metabolic regulation. The autophagic/lysosomal axis is also modulated by activation of FoxO and STAT3. Low glucose levels, results in recruitment of Axin-LKB1 to lysosomes and activation of AMPK, which balance energy homeostasis by promoting catabolic processed to restore ATP levels. Dashed lines indicate inactivation; P inside a red circle represents inhibitory phosphorylation, P inside a green circle represents activating phosphorylation.

Figure 2.. Activation of the immune response in lysosomes.

Multiple cellular stress responses are initiated on lysosome membranes. Sensing of nucleic acids in the lysosome is critical for detection of microbial infections and activation of immune responses. Binding of double-stranded RNA (dsRNA) to TLR3, single-stranded RNA (ssRNA) to TLR7 and TLR8, and single-stranded unmethylated DNA containing the cytosine-phosphate-guanine (CpG) to TLR9 in the lumen of endolysosomes induces TLR dimerization and oligomerization of their cytoplasmic motifs, resulting in recruitment of signaling adaptor proteins and activation of signaling cascades that trigger transcription of interferons and inflammatory cytokines. TLR9 also senses mitochondrial DNA (mtDNA) as a readout of the autophagy-mediated delivery of mitochondria to lysosomes.

Figure 3.. Detection and elimination of damaged lysosomes

Cell must be able to detect, repair and eliminate damaged lysosomes. Minor damage of the lysosomal membrane results in the calcium-dependent recruitment of ALIX and ESCRT-I, followed by the recruitment of ESCRT-III and VPS4. This results in the sealing or repair of the membrane by a mechanism yet to be characterized, although it has been suggested that may implicate the formation of luminal vesicles. Lysosomal damage that cannot be repaired by the ESCRT complex triggers the recruitment of galectins, which recruit adaptors to promote lysosome degradation via autophagy (lysophagy). In addition, galectin 8 and galectin 9 inactivate mTORC1 and activate AMPK, respectively, to further activate autophagy and modulate metabolism and removal of damaged lysosomes.