It was initially proposed that plasma membrane amino acid transporters be potential candidates for amino acid sensors because of their roles in controlling the influx of amino acids into the cell Christie et al. However, treatment with cycloheximide, a protein synthesis blocker that increases the concentration of free amino acids in the cytoplasm, is sufficient to restore mTORC1 signaling in cells that have been deprived of extracellular amino acids.
This evidence strongly suggests that amino acid sensing should originate intracellularly Price et al. The presence of the molecular machinery for amino acid—regulated mTORC1 activation at the lysosome membrane also implies that amino acids may be sensed somewhere in close proximity to the lysosome.
Similar to the vacuole in yeast, the lysosome appears to accumulate significant amounts of amino acids within its lumen Harms et al. Conversely, both in vitro and in cells, preventing lysosomal amino acid accumulation blocked mTORC1 binding to the lysosomal surface Zoncu et al. These results are compatible with a model for amino acid sensing by mTORC1 in which accumulation of amino acids in the lysosomal lumen is relayed to the Rag GTPases at the lysosomal surface in an inside-out manner.
SLC38A9, a putative sodium-coupled amino acid transporter in the lysosome membrane, recently has been proposed as a sensor that signals arginine sufficiency to mTORC1 Jung et al. In amino acid transport assays using reconstituted liposomes, SLC38A9 transports arginine, but not leucine, into the lysosome, albeit with relatively low affinity compared with other amino acid transporters.
How arginine binding mechanistically regulates SLC38A9 remains to be determined. Glutamine, the most abundant free amino acid in the human body, provides a carbon and nitrogen source for cell growth.
On one hand, several studies indicated that glutamine and glutamine-derived metabolites appear to function upstream of the Rag GTPase orthologues, Gtr1 and 2 Binda et al. On the other hand, it was shown that glutamine can stimulate lysosomal translocation and activation of mTORC1 via a Rag GTPase-independent mechanism, as revealed in recent studies using yeast Stracka et al.
Further investigations are necessary to determine the location of the mTORC1-activating glutamine pool and to establish the glutamine sensor upstream of Arf1. Recent evidence indicates that cytosolic free amino acids also play a major role in mTORC1 activation. Sestrin-2, a member of the Sestrin family of stress-responsive proteins Budanov and Karin, , has been shown to be a specific sensor for leucine in mammalian cells Saxton et al.
The crystal structure of Sestrin-2 revealed that Sestrin-2 contains a leucine-binding pocket localized to its C-terminal domain Kim et al. The presence of both cytoplasmic and lysosomal amino acid sensing systems raises intriguing questions about their relative importance and the mechanisms that coordinate their activities upstream of mTORC1.
Further work is needed to determine the specific role of each protein and how their regulatory inputs are coordinated upstream of mTORC1. In summary, the aforementioned discoveries are illuminating the pivotal roles of the lysosome in regulating the switch between catabolic and anabolic metabolism and foster a unifying model of nutrient sensing by which all the signals from intracellular nutrients and exogenous growth factors are integrated at the lysosomal surface Fig.
This model likely undergoes variations between species or even among different organs and tissues of multicellular organisms. Interestingly, S. Also, any proteins or small molecules able to interact with and regulate the mTORC1-activating supercomplex may provide additional regulatory mechanisms. Thus, it is conceivable that additional nutrient inputs upstream of mTORC1 wait to be discovered.
In addition to regulating mTORC1, the lysosome plays an important role in other major signaling pathways by mediating either the breakdown of activated receptors for signal termination or the proteolytic activation of signaling ligands. Two notable examples are discussed here:.
The degradation of activated EGFR in the lysosome is a key step for termination of this highly mitogenic signal. Phosphorylated EGFR triggers its own ubiquitination by the E3 ligase Cbl; endocytic adaptors containing ubiquitin-interacting motif, such as epsin and Eps15, recognize ubiquitinated EGFR and promote its internalization into endocytic vesicles Tomas et al.
Internalized EGFR is then trafficked via Rab5-positive early endosomes to Rab7-positive late endosomes and progressively removed from the endosomal-limiting membrane via ESCRT-mediated budding of intraluminal vesicles. Through further rounds of fusion, these EGFR-loaded late endosomes then convert into mature lysosomes, wherein cathepsin proteases and lipases degrade the EGFR-loaded intraluminal vesicles Tomas et al. The key role of this lysosome-based degradative pathway in signal down-regulation is highlighted by the presence of inactivating mutations of Cbl in various malignancies Makishima et al.
Moreover, this mode of regulation is shared by other RTKs, including platelet-derived growth factor receptor and insulin-like growth factor receptor. Thus, in the context of RTK signaling, the lysosomal lumen functions primarily as an endpoint for signal down-regulation, thereby playing an important role in limiting the mitogenic effect of EGFR. This is an ancient pathogen-defense system in which specialized pattern recognition receptors PRRs recognize and bind to molecular signatures known as pathogen-associated molecular patterns shared by several classes of pathogens.
TLRs consist of leucine-rich repeat motifs in an antigen-binding ectodomain, a single pass transmembrane portion, and an intracellular Toll—IL-1 receptor TIR domain. Upon binding of the ectodomain to microbial ligands such as viral or bacterial proteins and nucleic acids, the ectodomain undergoes a conformational change that leads to the recruitment of specific adaptor proteins to the TIR.
This binding event initiates a signaling cascade that mounts several anti-pathogen responses, including secretion of inflammatory cytokines and anti-microbial peptides, as well as activation of dendritic cells. These TLRs specialize in recognizing nucleic acids, which are released from invading pathogens that were taken up in intracellular compartments. Moreover, full activation of these TLRs requires proteolytic processing of their ectodomain by proteases such as asparagine endopeptidases and cathepsins in the acidic lumen of the lysosome Lee and Barton, After ligand binding and activation, TLR3 and TLR9 recruit adaptor proteins, such as TRIF and MyD88, respectively, to their TIR, triggering parallel signaling cascades that culminate with the activation of transcription factors and the release of inflammatory cytokines and interferons.
Thus, in the context of innate immunity, the lysosomal lumen provides an ideal environment in which TLRs become fully activated and where they bind to their respective ligands, whereas the cytoplasmic face provides a platform for the recruitment of secondary effectors that propagate the pathogen-initiated signal all the way to the nucleus.
The nutrient status of the cell, along with other environmental cues, tightly controls the expression of the CLEAR network through the cytoplasmic-nuclear shuttling of TFEB. Upon nutrient withdrawal or lysosomal stress, TFEB undergoes dephosphorylation and rapidly translocates to the nucleus to activate the transcription of CLEAR genes, including lysosomal hydrolases, pumps, and permeases, along with autophagic regulatory proteins. Thus, the net effect of TFEB activation is an increase in autophagic flux matched by an expansion of the lysosomal compartment, thereby boosting the ability of the cell to adapt to nutrient-poor and stressful conditions.
Interestingly, it is thought that the lysosomal calcium pool controls calcineurin activation and TFEB dephosphorylation. A recent study Wang et al. Phosphoproteomic studies revealed that TFEB possesses multiple sites of phosphorylation Dephoure et al.
Consistently, the ERK2 kinase phosphorylates TFEB at serine in response to growth factor stimulation and restricts its nuclear localization Settembre et al. All these findings indicate that the phosphorylation-dependent regulation of TFEB represents a universal mechanism of lysosomal adaptation to combat cellular stresses.
TFEB regulation and function are evolutionarily conserved from nematodes to humans, and at the organism level TFEB-driven transcriptional responses mediate important physiological processes such as lipid catabolism, longevity, and organismal survival. Experimental evidence indicates that TFEB expression is up-regulated in mice after food deprivation or energy expenditure Settembre et al.
Overexpression of TFEB in mouse liver attenuated diet-induced obesity by promoting lipid catabolism. In contrast, lipid degradation pathways were impaired in hepatocytes from liver-specific TFEB knockout mice Settembre et al. Thus, TFEB-mediated programs allow the organism to derive energy from the stored lipids, linking lysosomal function to the maintenance of cellular energy balance Rabinowitz and White, ; Singh and Cuervo, A TFEB-mediated adaptive response could also contribute to the extended lifespan seen in the nematode Caenorhabditis elegans , in which the TFEB homologue, known as HLH, acts similarly to its human counterpart to promote lipid mobilization and autophagy in fasting worms Kaeberlein et al.
Further investigation is required to determine whether modulating the expression and activity of TFEB would impact the lifespan of higher organisms. Of note, the capability of TFEB to promote cellular clearance could also be exploited to develop novel therapeutics for diseases associated with lysosomal and autophagic dysfunction such as lysosomal storage diseases Settembre et al.
It was observed that TFEB activation by overexpression or pharmacological stimulation can attenuate protein aggregation in cellular and mouse models of neurodegenerative disease, likely through increased autophagic clearance of protein aggregates Polito et al. Prosurvival effects of autophagy elicited by TFEB may also induce metabolic reprogramming that favors cancer growth, for example, by deliberately accumulating nutrients such as amino acids in lysosomes.
A detailed investigation of the transcriptional programs that become constitutively activated will shed light on this important question Kauffman et al. Emerging evidence has also suggested a key role for forkhead box O FOXO transcription factor family in the regulation of autophagy Webb and Brunet, During starvation, when insulin and growth factors are absent, FOXO translocates into the nucleus and activates the expression of genes involved in stress response, metabolism, and cellular quality control Calnan and Brunet, Chromatin immunoprecipitation analysis in mouse muscle cells demonstrated that FOXO3 directly binds to the promoters of key autophagy genes including LC3b , Gabarapl1 , Atg12l , Bnip3 , and Bnip3l Mammucari et al.
Just as turning on autophagy and lysosomal biogenesis in response to nutrient scarcity is critical for cellular survival, turning off these processes is equally important, as it allows cells to readjust their metabolic requirements when nutrients are replete.
ZKSCAN3 directly represses the expression of a repertoire of genes involved in sequential steps of autophagic process ranging from lysosome biogenesis to trafficking and autophagosome-lysosome fusion. Hence, by switching on and off multiple components of the autophagy-lysosome system through reciprocal regulation of TFEB and ZKSCAN3, the lysosome exerts its adaptation to meet metabolic demands according to nutrient levels.
Farnesoid X receptor FXR , which is a bile acid—activated nuclear receptor involved in regulation of bile acid, lipid, and glucose homeostasis, has also been shown to negatively regulate autophagy in the liver through multiple mechanisms Lee et al. Increasing evidence also suggests that this organelle may constantly communicate with other cellular structures to carry out specific metabolic programs. For instance, a contact site between the yeast mitochondria and vacuole named vCLAMP vacuole and mitochondria patch provides an alternative route to phospholipid transfer to the conventional route via mitochondria—endoplasmic reticulum contacts, and thus participates in mitochondria biogenesis Elbaz-Alon et al.
From a cell biological standpoint, studying lysosomal organization and plasticity will answer longstanding questions regarding the functional diversity of lysosomes in different tissues and organs, which is mediated by tissue- and cell-type specific gene expression but is also likely influenced by local metabolic conditions and age. Deciphering the molecular basis that determines the differences in lysosomal composition and function will help us understand how the lysosome acquires specialized functions to carry out specific metabolic tasks.
A good example is provided by lysosome-related organelles known as melanosomes, which specialize in the synthesis and storage of melanin pigment Raposo and Marks, , The molecular composition of melanosomes changes through sequential and well-defined stages of maturation Raposo and Marks, , Moreover, melanosomes function differently according to cell type.
Importantly, loss of ability to synthesize pigments and disorganization of melanosomal structures are associated with development of malignant melanoma. Metabolic changes beyond autophagy were not investigated. Importantly, while physiological ROS levels likely play a key role in the coordinated regulation of mitochondria and lysosomes, increased ROS production is detrimental. This is evidenced by the observation that mitochondrial dysfunction impairs lysosomal structure in a ROS-dependent manner Demers-Lamarche et al.
Iron is a second highly regulated ion associated with mitochondria and the endosomal compartment. Within mitochondria, iron is assembled into Iron-Sulfur clusters, inorganic cofactors that participate in a large array of cellular processes including the electron transport chain, metabolic conversion and protein synthesis Braymer and Lill, To reach mitochondria, iron first enters the cell associated with transferrin and is subsequently released inside endosomes.
This mechanism would prevent the cytosolic accumulation of iron, which can catalyze the formation of damaging ROS. A second essential role of lysosomes is the degradation of macromolecules, generating free amino acids, sugars and lipids that can be used in biosynthetic pathways or for energy production. As mitochondria are a major metabolic hub, lysosome, and mitochondria could regulate the function of each other through the production, transfer, or degradation of metabolites.
In support of this hypothesis, mitochondria-lysosome contact sites participate in the transfer of phospholipids between the two organelles Elbaz-Alon et al.
Furthermore, respiratory growth on non-fermentable carbon sources in yeast increased ER-mitochondria contact sites at the expense of mitochondria-lysosome contacts sites Honscher et al. Their activation close to mitochondria could increase mitochondrial uptake of these ions, both of which stimulate mitochondrial activity Figure 1 , Box 2; Hackenbrock, ; Yamanaka et al. The close proximity of mitochondria and lysosomes could thus similarly provide an easy access to amino acids generated by lysosomal proteolysis, especially during starvation Figure 1 , Box 2.
However, the role of lysosomes in amino acid homeostasis extends well beyond protein degradation. In fact, lysosomes serve as a platform to sense amino acid contents both outside and inside of the organelle Bar-Peled and Sabatini, ; Lim and Zoncu, This nutrient-sensing machinery regulates the mammalian target of rapamycin mTOR , a crucial kinase that acts as a hub for the control of cell growth and metabolism.
In the presence of amino acids, mTOR activity stimulates protein translation and promotes cell growth, while inhibiting autophagy and suppressing TFEB activity. When amino acids become scarce, mTOR is inactivated. This relieves its inhibitory effect on autophagy and TFEB-dependent lysosomal biogenesis, thus promoting amino acid recycling Figure 1 ; Settembre et al.
Interestingly, mTOR also regulates the efflux of essential amino acids from lysosomes. During amino acid starvation, mTOR inhibition leads to the selective sequestration of essential amino acids within lysosomes as a preservation mechanism. On the other hand, non-essential amino acids such as glutamine and glutamate are not affected by mTOR and are thus still released under starvation conditions Abu-Remaileh et al.
As a result, they could potentially be imported into mitochondria and used as an energy source. In addition to this direct metabolic regulation, mTOR inhibition also relieves its inhibition of TFEB which, in turn, stimulates lysosomal biogenesis to help with the increased delivery of material to lysosomes caused by increased autophagy.
The metabolic changes caused by amino acid starvation also extend to mitochondria. Starvation promotes mitochondrial elongation and connectivity, and improves mitochondrial bioenergetics through ATP synthase assembly and changes in inner mitochondrial membrane cristae organization Gomes et al. While mitochondrial elongation is caused by the PKA-dependent inhibition of DRP1, a Dynamin related GTPase required for mitochondrial fission, other changes are likely controlled more directly by amino acids.
In addition to these direct changes, the fact that TFEB stimulates mitochondrial biogenesis in addition to lysosomal biogenesis suggests that there is a coordinated metabolic program that is activated by amino acid starvation to promote cellular adaptation to metabolic stress. Interestingly, a recent study indicated that mTOR also regulates mitochondrial structure through a TFEB-independent pathway that relies on MTFP1, a mitochondrial protein promoting mitochondrial fragmentation.
In nutrient-replete cells, a key role of mTOR is to repress 4eBP, an important translation inhibitor. However, during starvation, mTOR inactivation relieves this inhibition, thereby decreasing protein translation. Overall, these studies indicate that amino acid starvation co-ordinately regulates the function of mitochondria and lysosomes.
This metabolic control is driven by mTOR and TFEB, also at a more direct level by the flux of amino acids and fatty acids between the two organelles.
In the last decade, the realization that organelles interact in a close physical and functional manner has opened new research areas with important implications for our understanding of several diseases. Recent findings highlighting the physical and functional interaction between mitochondria and lysosomes suggest that this crosstalk plays a major role in metabolic regulation. However, several key questions remain unanswered Figure 1 , boxes 1—3. First, the nature of the physical interaction between the two organelles in mammalian cells remains unknown, making it difficult to assess to which extent their functional interaction requires direct physical contact.
Second, both mitochondria and lysosomes have independently been studied for their role in the regulation of amino acids and lipids, but how these processes are coordinated and integrated remains an open question. Given the intimate links between mitochondria and lysosomes in disease, especially neurodegenerative diseases, these are important areas that remain to be explored.
All authors listed have made a substantial, direct and intellectual contribution to the work, and approved it for publication. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Abu-Remaileh, M. Science , — Appelqvist, H. The lysosome: from waste bag to potential therapeutic target. Cell Biol. Aston, D. High resolution structural evidence suggests the sarcoplasmic reticulum forms microdomains with acidic stores lysosomes in the heart.
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Organelle biogenesis and interorganellar connections: better in contact than in isolation. Das, A. Endosome-mitochondria interactions are modulated by iron release from transferrin. DeBerardinis, R. This membrane protects the rest of the cell from the harsh digestive enzymes contained in the lysosomes, which would otherwise cause significant damage.
The cell is further safeguarded from exposure to the biochemical catalysts present in lysosomes by their dependency on an acidic environment. With an average pH of about 4.
The acidity of the lysosome is maintained with the help of hydrogen ion pumps, and the organelle avoids self-digestion by glucosylation of inner membrane proteins to prevent their degradation.
The discovery of lysosomes involved the use of a centrifuge to separate the various components of cells. To explain this phenomenon, de Duve suggested that the digestive enzyme was encased in some sort of membrane-bound organelle within the cell, which he dubbed the lysosome.
After estimating the probable size of the lysosome, he was able to identify the organelle in images produced with an electron microscope. Lysosomes are found in all animal cells, but are most numerous in disease-fighting cells, such as white blood cells. This is because white blood cells must digest more material than most other types of cells in their quest to battle bacteria, viruses, and other foreign intruders. Several human diseases are caused by lysosome enzyme disorders that interfere with cellular digestion.
Tay-Sachs disease, for example, is caused by a genetic defect that prevents the formation of an essential enzyme that breaks down complex lipids called gangliosides. An accumulation of these lipids damages the nervous system, causes mental retardation, and death in early childhood.
Also, arthritis inflammation and pain are related to the escape of lysosome enzymes. License Info.
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