The Lysosome as a Regulatory Hub

Abstract

The lysosome has long been viewed as the recycling center of the cell. However, recent discoveries have challenged this simple view and have established a central role of the lysosome in nutrient-dependent signal transduction. The degradative role of the lysosome and its newly discovered signaling functions are not in conflict but rather cooperate extensively to mediate fundamental cellular activities such as nutrient sensing, metabolic adaptation, and quality control of proteins and organelles. Moreover, lysosome-based signaling and degradation are subject to reciprocal regulation. Transcriptional programs of increasing complexity control the biogenesis, composition, and abundance of lysosomes and fine-tune their activity to match the evolving needs of the cell. Alterations in these essential activities are, not surprisingly, central to the pathophysiology of an ever-expanding spectrum of conditions, including storage disorders, neurodegenerative diseases, and cancer. Thus, unraveling the functions of this fascinating organelle will contribute to our understanding of the fundamental logic of metabolic organization and will point to novel therapeutic avenues in several human diseases.

Keywords: TFEB; autophagy; cancer metabolism; lysosomal adaptation; mTORC1; neurodegeneration; nutrient sensing.

Figure 1.

A) The endolysosomal system. The lysosome is the terminal degradative station of multiple trafficking routes including endocytic and scavenging pathways. Extracellular material or pathogens are endocytosed through macropinocytosis or phagocytosis while plasma membrane localized proteins such as signaling receptors are internalized via clathrin mediated endocytosis (CME). Endocytosed material is trafficked to intracellular sorting stations – early endosomes – where cargo can be re-routed back to the plasma membrane or retained for degradation. Through progressive maturation, early endosomes convert to late endosomes that contain intraluminal vesicles. Intracellular constituents (protein aggregates, worn out organelles) are targeted for degradation via the process of autophagy. Autophagosomes containing cargo material fuse with lysosomes to mediate degradation. Autophagosomes can also fuse with late endosomes to form amphisomes – an intermediary station between classical endocytic routes and autophagic degradation. Additional mechanisms of degradation include chaperone-mediated autophagy (CMA), which involves direct translocation of cytosolic protein across the lysosome membrane in order to be degraded. During autophagic lysosome reformation (ALR), sorting of lysosome-specific components from the hybrid autolysosome regenerates a full complement of primary lysosomes. B) Snare mediated fusion of autophagosomes and lysosomes in mammalian cells. During starvation-induced autophagy, the Qa-SNARE, syntaxin 17 (Stx17) present on autophagosomes interacts with the cytosolic Qbc-SNARE SNAP-29 and the R-SNARE VAMP8 present on the lysosomal membane. In nutrient replete conditions, SNAP-29 is O-GlcNAcylated (red symbols) by O-GlcNAc transferase (OGT), which inhibits the formation of the SNARE complex and subsequent fusion between the autophagosome and lysosome.

Figure 2.

(Left) mTORC1 activation requires the simultaneous presence of amino acids and growth factors. Under low amino acid conditions, the GATOR1 complex stimulates GTP hydrolysis by RagA/B. Moreover the Ragulator complex, which functions in concert with SLC38A9 and the v-ATPase, is unable to promote GTP loading of RagA/B. As a consequence, the Rag GTPases are locked in an A/B^GDP-C/D^GTP nucleotide state and cannot bind to mTORC1, which remains inactive in the cytoplasm. Absence of insulin or growth factors increases the GAP activity of the Tuberous Sclerosis Complex (TSC) toward Rheb, blocking its ability to stimulate the kinase activity of mTORC1. (Right) In the presence of amino acids, the Rag GTPase heterodimer becomes competent to physically bind to mTORC1. Amino acids within the lysosome signal through SLC38A9 and the v-ATPase and enable Ragulator to promote loading of RagA/B with GTP. Amino acids in the cytoplasm (specifically leucine) cause the dissociation of Sestrin2 from GATOR2, and enable GATOR2-mediated inhibition of GATOR1. Moreover, amino acids activate the FLCN/FNIP complex, which stimulates GTP hydrolysis by RagC/D. In the resulting A/B^GTP-C/D^GDP nucleotide state, the Rag heterodimer recruits mTORC1 to the lysosomal surface. Growth factor signals originating at the plasma membrane lead to the inhibition of TSC, switching Rheb toward the GTP bound state and enabling it to turn on the kinase activity of mTORC1.

Figure 3.

Transcriptional regulation of autophagy and lysosome biogenesis. Under nutrient replete conditions, TFEB is phosphorylated by mTORC1 on conserved serine residues, which inhibits its nuclear translocation and activation. Negative transcriptional regulators of autophagosome and lysosome biogenesis are also activated including ZKSCAN3, and Farnesoid X Receptor (FXR). ZKSCAN3 binds to the promoters of lysosomal and autophagic genes and blocks their expression. FXR binds and displaces positive transcriptional regulators such as cAMP response element-binding protein (CREB) by disrupting formation of a complex between CREB and its co-activator CRTC2. FXR also displaces peroxisome proliferator activator receptor-a (PPARα) from binding to promoter regions upstream of autophagy and lysosome genes. Hence the cumulative effect is suppression of autophagy and lysosome gene induction under nutrient replete conditions. In contrast, starvation results in de-phosphorylation of TFEB via the combined action of calcineurin and inactivation of mTORC1. This allows for nuclear translocation of TFEB and binding to CLEAR elements present within the promoters of target genes. Starvation also inactivates FXR, enabling formation of the CREB-CRTC2 complex, which in turn activates TFEB transcription. Similarly suppression of FXR allows PPARα to activate autophagy and lysosme gene expression.