Lysosome biogenesis: Regulation and functions

Abstract

Lysosomes are degradation centers and signaling hubs in cells and play important roles in cellular homeostasis, development, and aging. Changes in lysosome function are essential to support cellular adaptation to multiple signals and stimuli. Therefore, lysosome biogenesis and activity are regulated by a wide variety of intra- and extracellular cues. Here, we summarize current knowledge of the regulatory mechanisms of lysosome biogenesis, including synthesis of lysosomal proteins and their delivery via the endosome-lysosome pathway, reformation of lysosomes from degradative vesicles, and transcriptional regulation of lysosomal genes. We survey the regulation of lysosome biogenesis in response to nutrient and nonnutrient signals, the cell cycle, stem cell quiescence, and cell fate determination. Finally, we discuss lysosome biogenesis and functions in the context of organismal development and aging.

Figure 1.

Lysosomes receive proteins and cargos from multiple pathways. Lysosomal hydrolases are synthesized and modified by linkage with oligosaccharides in the ER and transported to the Golgi apparatus. Following recognition of the mannose residues in the oligosaccharide chain by MPR, the hydrolase–MPR complexes are delivered to early endosomes. Newly synthesized lysosomal membrane proteins are either sorted at the TGN and delivered to endosomes (direct pathway) or first delivered to the plasma membrane and then endocytosed to reach early endosomes (indirect pathway). Receptors not destined for lysosomes are recycled back to the plasma membrane or Golgi. Early endosomes undergo a conversion to late endosomes, which then fuse with lysosomes. Phagocytosed cargos are enclosed in phagosomes, which undergo a maturation process and fuse with lysosomes. Autophagic cargos are delivered to lysosomes by fusion of autophagosomes with lysosomes. Lysosomes reform from digestive lysosomes (endo-, phago-, and autolysosomes) by tubulation and scission to form protolysosomes, which mature into functional lysosomes.

Figure 2.

Graphic summary of lysosome reformation. (A) ELR is regulated by PIKfyve, TRPML1, and Ca²⁺. PIKfyve converts PtdIns3P to PtdIns(3,5)P₂, which activates TRPML1 to regulate lysosomal Ca²⁺ efflux required for lysosomal tubulation. (B) ALR is achieved by PtdIns(4,5)P₂-, clathrin-, and AP2-mediated membrane budding on autolysosomes; KIF5B-driven elongation of membrane tubules along microtubules; dynamin 2–dependent protolysosome scission; and finally protolysosome maturation. AP4 enriches lysosomal membrane proteins for tubulation. WHAMM promotes lysosome tubulation by binding to PtdIns(4,5)P₂. The sugar transporter Spinster is also involved in ALR. The generation of PtdIns(4,5)P₂ from PtdIns4P is controlled by PtdIns4P 5-kinase 1B on autolysosome membranes and PtdIns4P 5-kinase 1A on protolysosomal tubules. The balance between PtdIns4P and PtdIns(4,5)P₂ is also regulated by inositol polyphosphate-5-phosphatase K. Spastizin and spatacsin form a complex to promote tubule initiation on the autolysosome. (C) PLR is regulated by PIKfyve, TRPML1, and amino acid transporters (e.g., SLC-36.1/SLC36A1-4 and LAAT-1/PQLC2). PIKfyve probably regulates the activity of these lysosomal transporters through PtdIns(3,5)P₂ to promote lysosome tubulation from phagolysosomes.

Figure 3.

TFEB/TFE3-dependent lysosome biogenesis. (A) Regulatory modifications of TFEB/TFE3. TFEB/TFE3 are phosphorylated (orange arrows), acetylated (green arrow), and ubiquitinated (gray arrow) by the indicated enzymes. Direct oxidation by reactive oxygen species can also occur (red arrow). (B) mTOR-dependent and PKC-dependent lysosome biogenesis pathways. Under nutrient-rich conditions, TFEB/TFE3 is phosphorylated by lysosome-localized mTOR. Phosphorylated TFEB/TFE3 bind to 14-3-3 proteins and are sequestered in the cytoplasm. With starvation, mTOR is inactivated and unable to phosphorylate TFEB/TFE3, leading to their nuclear translocation and activation. Activation of PKC leads to phosphorylation and inactivation of GSK3β, which then fails to phosphorylate TFEB, thereby inducing nuclear translocation of TFEB. Activated PKC induces JNK2/p38 activation, which phosphorylates ZKSCAN3 and leads to its cytoplasmic translocation and de-repression of lysosomal genes. Nuclear TFEB/TFE3 are rephosphorylated by CDK4/6 (and probably also by mTOR and GSK3β) and relocate back to the cytoplasm in a CRM1-dependent manner.

Figure 4.

Role of lysosome biogenesis and function in development and aging. (A) The correlation between lysosomes and the different states of NSCs or HSCs. qNSCs and qHSCs have larger and more abundant lysosomes with lower degradation activity (indicated in pink). qNSCs exhibit an age-dependent decrease in lysosome levels (indicated in blue). (B) The correlation between lysosomes and the asymmetric division and differentiation of HSCs. Lysosomes are asymmetrically distributed to daughter cells, and the daughter cells with low levels of lysosomes are metabolically active and induced to differentiate. (C) STA-2– and ELT-3–dependent lysosome biogenesis in ECM remodeling during C. elegans molt. During molt, the cuticle-epidermis attachments are damaged and detected by STA-2. STA-2 translocates to the nucleus and functions together with ELT-3 to activate the expression of lysosomal V-ATPase genes. This accelerates lysosome maturation at molt and facilitates the ECM remodeling required for larval development. (D) The correlation between lysosome biogenesis and lifespan in C. elegans. In aging C. elegans, lysosomes show reduced vesicular morphology; increased tubular morphology; increased mean and total volume; and decreased acidity, motility, and degradation activity. In long-lived mutants from three different longevity pathways, lysosomal gene expression is up-regulated, which requires DAF-16/FOXO and SKN-1/NRF2. Lysosome morphology and activity are well maintained during aging.