The protein kinase complex mechanistic target of rapamycin complex 1 (mTORC1) serves as a key conduit between growth signals and the metabolic processes underlying cell growth. The activation state of mTORC1 is controlled by intracellular nutrients and energy, as well as exogenous hormones and growth factors, thereby integrating local and systemic growth signals. Here we discuss the molecular logic of the mTORC1 signalling network and its importance in coupling growth signals to the control of cellular metabolism. After activation, mTORC1 promotes the conversion of available nutrients and energy into the major macromolecular species contributing to cellular mass, including proteins, nucleic acids and lipids, while suppressing the autophagic recycling of these macromolecules back into their nutrient constituents. Given that uncoupling of mTORC1 from its normal regulatory inputs contributes to many diseases—including cancer, genetic tumour syndromes, metabolic diseases, autoimmune diseases and neurological disorders—understanding the molecular logic of the mTORC1 network and how to modulate it may present therapeutic opportunities for treatment of a broad range of diseases and potentially even for the extension of lifespan.
Cellular metabolism—broadly divided into catabolism, in which macromolecules and nutrients are consumed to produce ATP, and anabolism, in which ATP is consumed to convert nutrients into macromolecules—is inherently self-regulated by the intracellular concentrations of the substrates and products of individual metabolic pathways. However, the ability of external cues to coordinately influence metabolic pathways in an interconnected manner is key to cellular adaptability and fitness in typical niches in which the availability of specific nutrients can fluctuate. The cellular lines of communication, in the form of signal-transduction networks, have evolved the ability to sense changes in nutrients and metabolites to direct adaptive changes in the activity of metabolic networks. This critical control of the cellular metabolic program by signalling pathways also links changes in cellular metabolism to other aspects of cell physiology, such as growth, survival, division, migration and differentiation. The need for such coordinated regulation is particularly evident during cell growth and proliferation.
Cell growth (that is, an increase in cell mass) and cell proliferation (that is, an increase in cell number through cell division) are fundamental for the propagation of unicellular organisms and the development, maturation and maintenance of multicellular organisms. Both growth and proliferation involve an increase in biomass requiring extracellular nutrients to supply the major elemental components (for example, carbon, nitrogen and oxygen) that compose the macromolecular constituents of cells (proteins, lipids, nucleic acids and complex carbohydrates). The underlying metabolic program must balance biosynthetic processes with resource availability (for example, nutrients and energy). The need for nutrient-sensing mechanisms to constantly monitor nutrient and energy status and link their abundance to the control of metabolic pathways and larger metabolic networks is evident in that specific nutrients are often limiting for cell growth and proliferation. Without the ability to sense nutrients and globally adapt metabolism accordingly, depletion of a single nutrient that might affect the synthesis of one macromolecular species (such as leucine for protein synthesis) might go undetected by the cell, thereby leading to a futile and deleterious imbalance in the synthesis of other macromolecules. The inability to sense that nutrient could also lead to its complete exhaustion, potentially resulting in catastrophic consequences. Thus, sensing nutrient status to appropriately adapt cellular metabolism provides an important survival advantage under typical conditions under which the availability of nutrients fluctuates.
In eukaryotic cells, mechanistic target of rapamycin (mTOR) complex 1 (mTORC1) is a central signalling node that receives and integrates signals from many upstream inputs and exerts widespread control over cellular metabolism. In this manner, mTORC1 acts as a metabolic ‘rheostat’ linking nutrient levels and other growth signals to the coordinated tuning of anabolic and catabolic metabolism (Fig. 1). Amino acids, glucose, oxygen, ATP, nucleotides and other nutrients, metabolic intermediates and building blocks are sensed by signalling pathways that converge on mTORC1 regulation, along with canonical growth-factor and hormone signalling pathways (for example, insulin/IGF1). The sufficient presence of these growth signals activates mTORC1, thereby promoting anabolic metabolism and attenuating catabolic activities, leading to net macromolecular synthesis that allows biomass production to support, among other processes, cell growth and proliferation. Here we will discuss the molecular logic of the expansive network upstream and downstream of mTORC1 that connects cell signalling to metabolic control.
Regulation of cellular metabolism through the mTORC1 signalling network
To understand why mTORC1 senses specific nutrients and other cues, it is helpful to first consider the downstream consequences of mTORC1 activation and inhibition. Through a variety of downstream effectors, mTORC1 induces an anabolic program that converts available nutrients and energy into the major macromolecules required for cell growth and proliferation. mTORC1 activation leads to specific transcriptional, translational and post-translational effects on key regulatory factors and metabolic enzymes, thus resulting in a coordinated series of events that both directly stimulate and indirectly support macromolecular synthesis. Notably, mTORC1 is generally not required for the basal activity of the processes and metabolic pathways that it regulates, as a specific enzyme in a given pathway might be. Instead, mTORC1 regulation links upstream signals to controlled increases or decreases in multiple downstream metabolic processes1,2, as described briefly below.
Stimulation of anabolic processes
Proteins compose approximately half the cellular dry mass, and their synthesis is the most nutrient- and energy-demanding cellular process. mTORC1 activation leads to an increased cellular capacity for protein synthesis through at least two connected mechanisms: acute induction of translation of specific messenger RNAs and promotion of ribosome biogenesis (Fig. 2). mTORC1 acutely stimulates mRNA translation through direct phosphorylation of eukaryotic translation initiation factor 4E (eIF4E)-binding proteins 1 and 2 (4E-BP). 4E-BP binds eIF4E at the 7-methyl-GTP cap at the 5′ ends of mRNAs and attenuates translation initiation3 (Fig. 2a). mTORC1 phosphorylation of 4E-BP disrupts its interaction with eIF4E, thus enabling recruitment of eIF4G and assembly of a larger translation initiation complex on the mRNA, including recruitment of the small (40S) subunit of the ribosome (Fig. 2b). mTORC1 also phosphorylates and activates ribosomal protein S6 kinases 1 and 2 (S6K1/2), which contribute to acute stimulation of mRNA translation by phosphorylating multiple translation factors4. The S6K-mediated phosphorylation of eIF4B stimulates the unwinding of mRNA secondary structure via the eIF4A helicase, thereby promoting the translation of mRNAs with complex 5′ untranslated regions (UTRs), such as c-Myc5,6,7. Of note, the molecular effect of S6K-mediated phosphorylation of its namesake substrate, the S6 protein component of the 40S ribosome, remains unknown. Importantly, mTORC1 signalling preferentially but not exclusively stimulates the translation of mRNAs containing a 5′ terminal oligopyrimidine tract (TOP) or 5′-TOP-like sequence at the start of its 5′ UTR, which are enriched in mRNAs encoding ribosomal proteins and translation initiation and elongation factors8,9,10. Although the molecular mechanisms underlying this selectivity are still being established, current evidence indicates a role of 4E-BP and another substrate of mTORC1, the RNA-binding protein La-related protein 1 (LARP1). LARP1 appears to directly bind 5′-TOP sequences and repress mRNA translation. The mTORC1-mediated phosphorylation of LARP1 causes it to dissociate from the 5′ UTR, thus allowing for eIF4G recruitment11,12,13. mTORC1 and S6K1 also regulate other aspects of mRNA translation and maturation, including splicing4,14,15,16.
Nucleotide and nucleic acid synthesis
Ribosomes are large protein–RNA complexes in which ribosomal RNA makes up more than 50% of the ribosome mass. The importance of mTORC1 signalling in promoting the synthesis of ribosomes, which constitute approximately 15% of total cellular dry mass17, is underscored by the existence of downstream molecular mechanisms that enhance rRNA synthesis (Fig. 2b). Through molecular mechanisms that are incompletely understood, mTORC1 induces the transcription of all four rRNA species through RNA polymerase (Pol) I (5.8S, 18S and 28S rRNAs) and RNA Pol III (5S rRNA)18. Evidence suggests that mTORC1 regulates Pol I through the transcription factors upstream binding factor (UBF) and transcription initiation factor-1A (TIF-1A)19,20. mTORC1 activation has also been suggested to influence chromatin architecture, thereby promoting Pol I recruitment to rDNA promoters21,22. mTORC1 induces RNA Pol III–dependent transcription by phosphorylating MAFI and consequently relieving its inhibition of RNA Pol III23,24. Finally, mTORC1 inhibition has been found to cause accumulation of pre-rRNA species, thus suggesting that mTORC1 activation might also promote rRNA processing25. These mechanisms enhancing the production of rRNA act in concert with the increased translation of ribosomal proteins, thereby promoting ribosome biogenesis in cells with activated mTORC1.
Given that at least 80% of all cellular RNA is ribosomal26, the mTORC1-stimulated production of rRNA would be predicted to create a high demand for nucleotides to support the synthesis of these nucleic acids. To meet this demand, mTORC1 stimulates the de novo synthesis of both pyrimidine and purine nucleotides27,28,29 (Fig. 3). Activation of mTORC1 acutely stimulates an increased flux through the de novo pyrimidine-synthesis pathway through S6K1-mediated phosphorylation of the multi-functional enzyme carbamoyl-phosphate synthase 2, aspartate transcarbamylase, dihydroorotase (CAD). CAD catalyses the first three steps in de novo pyrimidine synthesis, and CAD phosphorylation by S6K1 is required to link growth signals upstream of mTORC1 to the stimulated flux through this biosynthetic pathway to synthesize UTP, CTP, dTTP and dCTP27,29. mTORC1 signalling enhances de novo purine synthesis in a more delayed manner, through regulation of the transcription factors Myc, sterol regulatory element binding protein (SREBP) and activating transcription factor 4 (ATF4), which induce the expression of specific metabolic enzymes required for this process28. For instance, through its activation of ATF4, mTORC1 signalling induces the expression of enzymes of the serine/glycine-biosynthesis pathway and mitochondrial tetrahydrofolate cycle, which produces one-carbon formyl units required for assembly of the purine ring in the cytosol. Through unknown mechanisms, mTORC1 has also been proposed to promote formation and clustering on the surface of mitochondria of so-called ‘purinosomes’ (large complexes of the enzymes in the de novo purine-synthesis pathway), which are believed to facilitate flux through this metabolic pathway30. Finally, the synthesis of both pyrimidines and purines might be further enhanced by increased eIF4E-driven translation of phosphoribosyl-pyrophosphate synthetase 2, which directs ribose to the nucleotide-synthesis pathways31.
mTORC1 also stimulates de novo lipid synthesis through activation of the SREBP family of transcription factors2,32,33. The SREBPs (SREBP1a, SREBP1c and SREBP2) are master regulators of de novo lipid synthesis that induce the expression of enzymes involved in both fatty acid and sterol synthesis34 (Fig. 3). SREBPs are produced as transmembrane proteins residing in the endoplasmic reticulum (ER) membrane in an inactive state. The canonical signal that activates the SREBPs is sterol depletion, which triggers SREBP translocation to the Golgi apparatus, where it undergoes proteolytic processing, and an active amino-terminal fragment is released. The mature active form of SREBP then enters the nucleus and binds sterol regulatory elements within the promoters of its target genes, thus inducing their expression. mTORC1 activates SREBP by promoting its processing and nuclear localization through an unresolved mechanism involving S6K1, Lipin1 and perhaps other downstream targets of mTORC1 (refs. 2,32,35,36). mTORC1 and S6K1 have also been found to promote the splicing and maturation of SREBP-dependent transcripts encoding lipogenic enzymes through phosphorylation and activation of SR protein kinase 2 (SRPK2), which regulates RNA-binding splicing factors16. Whether mTORC1 signalling influences which lipid species are produced is less well understood, but a recent study has suggested a role in synthesis of the abundant membrane phospholipid phosphatidylcholine, at least in the liver37.
Metabolic processes supporting anabolism
mTORC1 signalling stimulates other metabolic pathways that are likely to support its primary function in promoting biosynthetic processes (Fig. 3). mTORC1 signalling increases aerobic glycolysis (a process also known as the Warburg effect) by increasing expression of the glucose transporter Glut1 and key glycolytic enzymes encoded by gene targets of hypoxia-inducible factor 1α (HIF1α)2. The HIF1α protein is rapidly degraded under normal oxygen concentrations (normoxia) but is stabilized and greatly increased under oxygen depletion (hypoxia), a regulation independent of mTORC1 activity38. However, mTORC1 activation leads to an increase in HIF1α levels even under normoxic conditions, albeit substantially less than under hypoxia, owing to a selective increase in translation of its mRNA; this induction is sufficient to increase glucose uptake and glycolysis2. mTORC1 also activates the transcription factor forkhead box k1 (Foxk1), which increases mRNA expression of HIF1α and its gene targets39. Elevated glycolysis under aerobic growth conditions is recognized to support anabolic metabolism by facilitating the use of glycolytic intermediates for key side branches, such as the pentose-phosphate and serine/glycine-synthesis pathways40. These pathways provide essential precursors, such as ribose, glycerol, non-essential amino acids and one-carbon units for the synthesis of proteins, nucleotides and lipids (Fig. 3). mTORC1 activation also selectively stimulates glucose flux through the oxidative branch of the pentose-phosphate pathway via transcriptional induction of enzymes in the pathway, including glucose-6-phosphate dehydrogenase (G6PD)2. In most cells, the oxidative pentose-phosphate pathway serves as a primary source of reducing equivalents41, generating two molecules of reduced nicotinamide adenine dinucleotide phosphate (NADPH) while oxidizing glucose-6 phosphate, thus yielding ribose-5-phosphate. mTORC1 increases metabolic flux through this pathway through its activation of SREBP, which in turn regulates G6PD expression and thus couples the major NADPH-consuming anabolic process of de novo lipid synthesis to increased production of NADPH2. Similarly to aerobic glycolysis, the tricarboxylic acid (TCA) cycle also provides a source of biosynthetic precursors. Although there is little evidence that mTORC1 signalling promotes the catabolic, oxidative functions of the mitochondria, it has been found to promote glutamine carbon flux into the TCA cycle (glutaminolysis) and consequently replenish TCA-cycle intermediates consumed for biosynthesis (that is, anaplerosis) through c-Myc-induced expression of glutaminase (GLS)7. A recent study has also found that mTORC1 activation results in increased synthesis of polyamines42, positively charged metabolites with suggested roles in nucleic acid and protein synthesis43,44. Finally, insulin has been found to stimulate uptake of long-chain fatty acids into adipocytes through S6K1-mediated phosphorylation of the glutamyl-prolyl-tRNA synthetase EPRS, which subsequently interacts with and promotes the plasma-membrane translocation of the adipocyte fatty acid transporter FATP1 (ref. 45). This finding highlights the existence of tissue-specific effects of mTORC1 signalling on specific metabolic parameters, an important area of current and future studies.
Suppression of catabolic processes: autophagy and lysosomal function
When nutrients or energy is limiting, existing macromolecules can be degraded into their nutrient components and further catabolized to produce ATP. Parallel to its role in promoting macromolecular synthesis, mTORC1 suppresses the turnover of macromolecules by inhibiting autophagy and perhaps other lysosomal functions. Inhibition of mTORC1 by nutrient deprivation or pharmacological inhibition leads to rapid activation of autophagy as an adaptive mechanism to replenish depleted nutrients. mTORC1 inhibits autophagy through a number of mechanisms, the best characterized of which is the direct, rapid phosphorylation and inhibition of the autophagy-initiating kinase UNC-51-like kinase 1 (ULK1)46,47,48,49. The transcription factor EB (TFEB) and related members of this transcription factor family induce the global expression of genes encoding both the autophagy machinery and components of the lysosome50,51. mTORC1 signalling suppresses this transcriptional program through the direct phosphorylation of TFEB, thus leading to its cytosolic sequestration, which probably contributes to the long-term inhibitory effect of mTORC1 signalling on autophagy and perhaps lysosome biogenesis and function52,53,54,55. Protein degradation by autophagy can replenish amino acids during starvation, and a role for autophagy in restoring intracellular nucleotides has also been suggested56. Lysosomal degradation of the protein- and nucleic acid–rich ribosomes may be a particularly important means of restoring amino acids and nucleotides in response to nutrient deprivation57, a process that would also conserve nutrients by decreasing protein synthesis. To this end, mTORC1 inhibition has been found to induce degradation of ribosomes through autophagy, coincident with autophagic degradation of other cytosolic components58. The selective targeting of ribosomes for autophagy, termed ‘ribophagy’, has also been found to be induced by mTORC1 inhibition59. In agreement with this control of ribosome turnover, the mTOR inhibitor Torin1 greatly increases intra-lysosomal nucleoside levels in a manner dependent on autophagy59,60. Through an unknown mechanism independent of autophagy, mTORC1 also suppresses lysosome-mediated degradation of extracellular proteins that are taken up through macropinocytosis, and thus mTORC1 inhibition can promote scavenging of extracellular proteins as a source of amino acids61,62. This effect may be mediated in part by mTORC1 suppression of lysosome biogenesis through phosphorylation and inhibition of TFEB52,53,54,55.
Logic of the integrated regulation of mTORC1 signalling
Although it is evident that mTORC1 is a master regulator of the major metabolic processes underlying cell growth, the importance of co-regulating these processes may be less obvious. The coordinated anabolic program downstream of mTORC1 requires a substantial input of nutrients and energy to properly execute. For this reason, the activation state of mTORC1 is strongly influenced by the availability of building blocks for the macromolecules whose production it stimulates (Fig. 4a). For instance, mTORC1 activation is highly sensitive to depletion of specific amino acids, which are required for protein synthesis; nucleotides, which are required for nucleic acid synthesis; and glucose, which is the major carbon source for lipid synthesis and an essential substrate for glycolysis and its biosynthetic side branches63,64,65,66. mTORC1 signalling is also strongly inhibited by depletion of ATP, which is required for all biosynthetic processes and consumed at particularly high rates during protein synthesis67,68. A critical feature of the regulatory network upstream of mTORC1 is that all these factors are required for mTORC1 activation, and depletion of any one of them inhibits the ability of mTORC1 to stimulate the entire downstream anabolic program, thereby coordinately and globally decreasing macromolecular synthesis63,64,65,66,67,68 (Fig. 4b). The resulting repression of mTORC1 signalling induces concurrent autophagic turnover of macromolecules back into their nutrient components.
In multicellular organisms, anabolic metabolism and cell growth are coupled not only to the availability of intracellular nutrients and energy but also to the presence of signals from other cells and organ systems, in the form of extracellular hormones, growth factors and cytokines. Although nutrients are required for basal mTORC1 signalling, these exogenous signals are required for full activation of mTORC1. Importantly, however, growth-factor signals do not activate mTORC1 if any individual nutrient that is sensed by mTORC1 is depleted. Thus, the nutrient signals are not sufficient for full activation of mTORC1, but they are absolutely required. In this manner, the logic of mTORC1 regulation operates as an ‘AND gate’, such that both nutrient and growth-factor signals are required for full mTORC1 activation (Fig. 4c). The signal integration that underlies this AND gate is controlled at least in part through molecular mechanisms influencing the spatial localization of mTORC1 and key regulators to the lysosomal surface69,70.
Small G proteins integrate signals upstream of mTORC1 at the lysosome
mTORC1 is activated by the coordinated regulation of two sets of small G proteins, the Rag and Rheb GTPases, which directly engage mTORC1 (refs. 69,71,72,73,74,75,76). mTORC1 comprises three core essential components: the protein kinase mTOR, the mTORC1-specific binding partner Raptor and mammalian lethal with SEC13 protein 8 (mLST8), which associates with the mTOR kinase domain in both mTORC1 and mTORC2 (ref. 77). Rheb appears to be required for mTORC1 activation by all signals78. Recent structural data indicate that GTP-loaded Rheb directly binds mTOR within mTORC1 and induces a conformational change that activates the kinase76. A subpopulation of Rheb resides on the cytosolic surface of the lysosomal membrane where it encounters mTORC1, and this localization is mediated at least in part through its carboxy-terminal farnesylation70,79. The role of the Rag GTPases is to recruit mTORC1 to lysosomal Rheb69,79,80. The Rag proteins are unusual in that there are four family members, which function as obligate heterodimers. RagA and B share high sequence similarity, and Rag C and D are more similar to each other81. A RagA or RagB subunit forms heterodimers with a RagC or RagD subunit, and these heterodimers localize to the lysosomal surface through interactions with a protein complex called the Ragulator (also known as LAMTOR) and a lysosomal amino acid transporter, SLC38A9 (refs. 79,82,83). The Rag heterodimers directly bind the Raptor subunit of mTORC1 when the RagA/B subunit is GTP loaded and RagC/D is GDP loaded, but, in contrast to Rheb-GTP binding, mTORC1 activity is not directly influenced by its association with the Rag heterodimer79,84. Instead, this binding recruits mTORC1 to the lysosomal surface, where it can be activated by Rheb, when Rheb is GTP bound. Thus, the Rag GTPases can recruit mTORC1 to the lysosome but not activate it, and Rheb can activate mTORC1 but is not sufficient for its lysosomal recruitment. These properties are key to the signal-integrating ability of the mTORC1 network.
The predominant activation of mTORC1 at the lysosome raises the question of how active mTORC1 subsequently comes in contact with its direct downstream targets. Substrates of mTORC1 may be present at the lysosome, although outside of TFEB53,55,85, mTORC1 substrates are not known for such localization. Alternatively, after Rheb–GTP engages mTORC1 at the lysosome, the active Rheb–mTORC1 complex may dissociate and traffic to various locations, where it encounters a multitude of substrates. A third possibility is that there may be additional subcellular pools of Rheb and mTORC1 that can be activated elsewhere. Importantly, Rag mutants that stabilize mTORC1 lysosomal localization also increase phosphorylation of mTORC1 substrates, and artificially targeting both mTORC1 and Rheb to alternative organelles can likewise increase phosphorylation of those same downstream targets86. These data suggest that at least some mTORC1 substrates are able to find mTORC1 at its site of activation by Rheb, but they do not exclude the possibility that active mTORC1 might be released from the lysosome and subsequently find other substrates.
Growth factors and nutrients control mTORC1 through upstream regulators of the Rheb and Rag GTPases
The extensive network of signals that influence the activation state of mTORC1 do so predominantly by converging on upstream regulators of the GDP/GTP-bound state of the Rheb and Rag GTPases (Fig. 5a). The only well-established regulator of Rheb identified to date is the TSC protein complex, comprising TSC1 and TSC2, which are mutated in the pleiotropic genetic disorder tuberous sclerosis complex (TSC), and the protein TBC1D7; the TSC2 subunit possesses highly specific GTPase-activating protein (GAP) activity towards Rheb70,72,73,87,88,89. Thus, by promoting the conversion to GDP-bound Rheb, the TSC complex acts as a key molecular brake on the Rheb-dependent activation of mTORC1. TSC2 is a heavily phosphorylated protein, and several known upstream protein kinases regulate mTORC1 activity through site-specific phosphorylation and regulation of TSC2 within the TSC complex78. These kinases include growth-factor-stimulated kinases, such as Akt, extracellular signal-regulated kinase (ERK) and p90 ribosomal S6 kinase (RSK), which stimulate mTORC1 signalling by functionally inhibiting the TSC complex, thereby allowing the accumulation of Rheb–GTP90,91,92,93. Reciprocally, the AMP-activated protein kinase (AMPK) phosphorylates distinct sites on TSC2, thus promoting its ability to turn Rheb–mTORC1 signalling off under conditions of cellular energy depletion68,94,95, an effect that inhibits mTORC1 in the liver in response to the anti-diabetes drug metformin96. The TSC complex is also required to properly inhibit mTORC1 signalling in response to the depletion of specific nutrients, including oxygen and purine nucleotides64,65,78,97, and under fasting conditions in the liver98,99. Thus, loss of TSC complex components or constitutive activation of upstream pathways that inhibit the TSC complex (for example, activating mutations in the phosphoinositide 3-kinase (PI3K)–Akt or Ras pathways, which are common in cancer) results in aberrantly high Rheb–GTP loading and uncontrolled mTORC1 activation, even after the withdrawal of growth factors or specific nutrients.
Elegant work over the past decade has revealed an entire new pathway upstream of mTORC1 dedicated to its sensing of amino acids100. The guanine-nucleotide-binding state of the Rag GTPases, and thus their ability to recruit mTORC1 to the lysosome for activation by Rheb, is predominantly regulated by specific intracellular amino acids, which are sensed by upstream regulators of the Rag heterodimer (Fig. 5a–c). Underscoring the critical role of mTORC1 in controlling the protein synthesis capacity of the cell, mammalian cells have evolved an elaborate system to sense changes in specific amino acids and ensure that mTORC1 enhances protein synthesis only when sufficient amino acid building blocks are available. These mechanisms converge on GAP and guanine nucleotide exchange factor (GEF) complexes to control the nucleotide-binding state of Rag heterodimers. The ‘GAP activity toward Rags 1’ (GATOR1) complex is an evolutionarily conserved GAP for RagA/B that associates with the lysosome and Rag heterodimers through a lysosome-resident protein complex termed KICSTOR (comprising KPTN, ITFG2, C12orf66 and SZT2)101,102,103,104. GATOR1 is active in the absence of amino acids, and it promotes the accumulation of Rag heterodimers containing GDP-bound RagA/B, thereby blocking recruitment of mTORC1 to the lysosome101,102. The action of GATOR1 is somehow antagonized by the GATOR2 complex, a positive regulator of mTORC1 with unknown molecular function. GATOR2 in turn is inhibited by its interaction with cellular arginine sensor for mTORC1 (CASTOR1) and Sestrin2 (Fig. 5b). When arginine and leucine are present, they bind defined pockets on CASTOR1 and Sestrin2, respectively; this binding triggers conformational changes that cause them to dissociate from their inhibitory interactions with GATOR2, thus allowing GATOR2 to inhibit GATOR1 and promote RagA/B-GTP loading and mTORC1 recruitment105,106,107,108 (Fig. 5c). Methionine levels are sensed by mTORC1 through an intermediate in the methionine cycle, S-adenosylmethionine (SAM), which binds a protein called SAMTOR that interacts with and inhibits GATOR1 (ref. 109). Why this upstream network has evolved to specifically sense these three amino acids is not entirely clear but is likely to be related to the primary role of mTORC1 in inducing protein synthesis. Leucine and arginine, together with serine, are the only amino acids encoded by six different codons and are therefore among the most abundant amino acids in the mammalian proteome. Furthermore, ribosomal proteins are highly enriched in arginine59, thus suggesting that an abundant supply of this amino acid would be particularly important for mTORC1-stimulated translation of ribosomal proteins from 5′-TOP mRNAs59. Methionine, in contrast, is one of the least abundant amino acids in proteins but is required to initiate the translation of all proteins, and SAM is essential for polyamine synthesis, a process also induced by mTORC1 signalling42.
In addition to overriding the inhibitory effects of the GATOR1 complex, amino acid–replete conditions promote the conversion of RagA/B to the GTP-bound, active state through GEF activity at the lysosomal surface79,110. The lysosomal transmembrane protein SLC38A9 is a multifunctional direct sensor of intra-lumenal arginine that serves both as a transporter for efflux of leucine and other neutral amino acids out of the lysosome and as a GEF for RagA/B that functions in concert with the Ragulator80,82,83,110,111,112. Thus, in response to lysosomal arginine, SLC38A9 promotes RagA/B-GTP loading indirectly, through its cytosolic release of leucine, as well as directly, through its GEF activity83,111 (Fig. 5c). SLC38A9 has also been proposed to directly sense cholesterol within the lysosomal membrane and consequently link exogenous cholesterol availability to the activation of mTORC1 (ref. 113). The RagC/D subunit of the heterodimer is also regulated to influence recruitment of mTORC1 to the lysosome. Although a RagC/D GEF has yet to be identified, the folliculin–FNIP complex has been found to act as a GAP for RagC/D at the lysosomal surface, thereby promoting the RagA/BGTP–RagC/DGDP state capable of recruiting mTORC1 (refs. 114,115). How the folliculin–FNIP complex is regulated is currently unknown. Interestingly, the guanine-nucleotide-binding status of the individual Rag subunits within a Rag heterodimer rapidly influence the guanine-nucleotide-binding state of the other subunit. Therefore, RagA/B-GDP binding favours RagC/D-GTP within the same heterodimer (that is, the ‘off’ state), and RagA/B-GTP binding favours RagC/D-GDP (that is, the ‘on’ state), thus indicating that the GAPs and GEFs for one subunit influence the dynamic switch between the inhibited or activated state of the entire heterodimer, which in turn influences binding cycles with the Ragulator and mTORC1 (refs. 86,116).
mTORC1 signalling is highly sensitive to glucose depletion, but how glucose is sensed upstream of mTORC1 is currently unknown. However, genetic evidence suggests potential roles of both the TSC–Rheb and GATOR–Rag circuits. Loss of any single TSC complex component renders mTORC1 signalling more resistant to glucose starvation, thus suggesting that its GAP activity is required to suppress Rheb and mTORC1 under such conditions68,89,117. Likewise, mTORC1 signalling remains active in glucose-deprived cells lacking GATOR1 or KICSTOR components, thereby suggesting a role of the Rag heterodimers in glucose sensing by mTORC1 (refs. 103,118). Furthermore, cells expressing a constitutively GTP-bound mutant of RagA (RagAGTP) display sustained mTORC1 signalling after depletion of either amino acids or glucose, in agreement with a need to suppress Rag-heterodimer recruitment of mTORC1 to appropriately inhibit its activity under diverse conditions of nutrient deprivation118. Homozygous RagAGTP knock-in mice die from severe hypoglycaemia shortly after birth, thus demonstrating the importance of controlling mTORC1 activity in response to nutrient availability118.
The spatial AND-gate model of signal integration by mTORC1
After mTORC1 is recruited to the lysosome through the Rag GTPases, its activation requires engagement with Rheb–GTP, a process believed to occur at this location. In the absence of growth factors, the TSC complex co-localizes with a fraction of Rheb that overlaps with lysosomal markers, and the TSC complex maintains this subpopulation of Rheb in a GDP-bound, inactive state70 (Fig. 5d). Insulin-stimulated PI3K signalling induces Akt-mediated phosphorylation of TSC2, which in turn causes the TSC complex to acutely dissociate from Rheb and the lysosome, thereby allowing Rheb to become GTP loaded and activate mTORC1 (Fig. 5e)70. Although the TSC complex is known to be required to suppress mTORC1 signalling in the absence of growth factors, it is currently unknown whether other growth-factor signalling pathways similarly induce mTORC1 activation through spatial regulation of the TSC complex. Collectively, these studies suggest a model of signal integration by mTORC1 that involves independent signals from amino acids and growth factors that respectively control mTORC1 and TSC complex colocalization with a pool of lysosomal Rheb. Through this spatial AND gate, amino acids recruit mTORC1 to lysosomal Rheb, which is GTP loaded in response to the stimulated release of the TSC complex downstream of growth-factor signalling.
As with all upstream signals, Rheb is required for amino acids to activate mTORC1 signalling, and cells with elevated Rheb–GTP levels due to loss of TSC complex components or overexpression of Rheb tend to be more resistant to the inhibitory effects of amino acid deprivation on mTORC1 signalling119,120. Depending on how cells were deprived of amino acids in culture, most studies have found that mTORC1 signalling is ultimately suppressed after amino acid starvation in a manner independent of the TSC complex and Rheb regulation69,120,121. However, Demetriades et al. have concluded that amino acids signal through spatial regulation of TSC2, which they have found to be recruited to the lysosome after amino acid starvation. The authors have proposed that TSC2 directly binds the inactive RagA/BGDP–RagC/DGTP heterodimer122. In contrast to these findings, Menon et al. have found that amino acid starvation and acute refeeding, conditions that cause rapid Rag-dependent recruitment of mTORC1 to the lysosome, do not affect TSC complex localization in the same cells70. Carroll et al. have found that arginine deprivation promotes further recruitment of the TSC complex to the lysosome in cells also deprived of growth factors, albeit through an unknown mechanism123. As established for growth-factor withdrawal alone70, sustained lysosomal localization of the TSC complex in cells deprived of both amino acids and growth factors has been reported by Carroll et al. to be dependent on Rheb but not the Rag GTPases123. Thus, further studies are needed to clarify the degree and mechanisms of cross-talk between the amino acid and growth-factor-sensing pathways upstream of the Rag and Rheb GTPases. However, the independence of these two signals from each other is further supported by previous findings that artificially targeting mTORC1 to the lysosome is sufficient to render mTORC1 signalling independent of amino acids while maintaining dependence on growth-factor signalling through the TSC complex and Rheb for full mTORC1 activation79. Finally, data suggest that a wide range of cellular stresses promote localization of the TSC complex to the lysosome, a process that coincides with suppression of mTORC1 signalling124. However, the molecular mechanisms underlying these responses remain undefined.
Although nearly all established signals that regulate mTORC1 do so by acting through the Rag or Rheb GTPases, some have also been found to directly affect mTORC1, predominantly through phosphorylation of Raptor. In addition to phosphorylating TSC2, AMPK directly phosphorylates Raptor at sites that contribute to mTORC1 inhibition by energy stress125. ERK and RSK also directly phosphorylate Raptor at distinct sites that are believed to contribute to mTORC1 activation126,127,128. Akt phosphorylates proline-rich Akt substrate of 40 kDa (PRAS40), a non-essential component of mTORC1 that has inhibitory activity, but the functional role of PRAS40 within mTORC1 is unclear74,129,130. Other mechanisms of amino acid sensing affecting mTORC1 signalling have also been proposed but lack connections to defined amino acid sensors. For instance, glutamine has been reported to promote mTORC1 lysosomal localization and activation independently of Rag heterodimers, in a manner involving the ADP ribosylation factor 1 (ARF1) GTPase, which is best known for its role in controlling trafficking to and from the Golgi apparatus131.
Tuning the mTORC1 dial
As with the study of any signalling pathway, defining the molecular nature of mTORC1 regulation and function has required the use of reductionist systems and approaches. Such systems often involve complete removal and acute re-addition of nutrients and growth factors, thereby creating binary OFF and ON states that facilitate the characterization of underlying mechanisms. As understanding of the core inputs and outputs of the network evolves, researchers can begin to consider how the network functions under more physiological and homeostatic fluctuations in upstream signals such as insulin, amino acids and glucose. Although the hierarchy and integration of signals established through cell culture studies provides a good framework (Figs. 4 and 5), the nature of the dominant or limiting signals for full mTORC1 activation in various cell types and tissues remains largely unknown. For instance, mTORC1 signalling in the liver is highly responsive to fasting, which suppresses mTORC1, and feeding, which robustly stimulates its activity. Although the signals determining this regulation have not been established, genetic mouse models with activation of either the Rag or Rheb pathway display chronic activation of mTORC1 signalling in the liver that is no longer sensitive to fasting98,118.
Diverse parameters, such as concentrations of free amino acids, levels of specific amino acid sensors and the degree of basal signalling through insulin and growth-factor-responsive pathways such as the PI3K–Akt pathway, all influence the threshold at which specific signals must be received to activate mTORC1 and the degree to which mTORC1 is activated. Free amino acid concentrations alone are determined by numerous factors that vary across tissues, including rates of amino acid influx and efflux and of protein synthesis and turnover. Furthermore, the Sestrins and perhaps other amino acid sensors upstream of the Rag GTPases vary in expression between tissues and are also transcriptionally regulated by nutrient-and stress-responsive pathways132,133. Sestrin2 levels strongly influence the amount of intracellular leucine needed to activate mTORC1 (refs. 108,134,135). Prolonged amino acid deprivation leads to an increase in Sestrin2 expression, which contributes to the sustained inhibition of mTORC1 (ref. 132). Such a mechanism should also increase the threshold concentration of leucine needed for mTORC1 reactivation under these conditions, thus perhaps ensuring that mTORC1 is not activated by small or transient influxes of leucine when the bulk of amino acids are limiting. Likewise, there are many cellular conditions and upstream signals that influence the function of the TSC complex to affect the basal state of Rheb–GTP loading78. The PI3K–Akt pathway alone is stimulated by most growth-factor, cytokine and chemokine receptors136. Under conditions with basally elevated Rheb–GTP at the lysosome, mTORC1 might be predicted to be activated by a lower threshold of amino acids. Thus, although the Rag- and Rheb-GTPase circuits appear to function in a manner largely independent of each other, cellular conditions that affect their regulation will clearly affect the ability of the other circuit to control the activation state of mTORC1.
The degree of mTORC1 activation has been found to have differential effects on its phosphorylation of downstream substrates137, but whether the route of mTORC1 activation or the magnitude of its activity differentially influence its downstream functions is poorly understood and will be an important area of future study. The control of autophagy is one function that appears to be particularly sensitive to the strength of the mTORC1 signal. In most described settings, the low basal activity of mTORC1 sustained during growth-factor withdrawal under nutrient-replete conditions (Fig. 4c) is sufficient to inhibit autophagy, whereas stronger inhibition of mTORC1 accompanying nutrient deprivation induces autophagy. The dependence of this difference on the degree of mTORC1 activity is supported by studies comparing the effects of the allosteric and partial mTORC1 inhibitor rapamycin, which modestly induces autophagy, to kinase-domain inhibitors of mTOR, which more strongly inhibit mTOR and induce autophagy138,139.
Maintaining anabolic balance downstream of mTORC1
As discussed above, a key feature of the mTORC1 signalling network is that loss of any individual nutrient signal or lack of a signal from exogenous growth factors decreases mTORC1 signalling and its full downstream anabolic program (Fig. 4b). For example, amino acid deprivation attenuates the mTORC1-stimulated flux through de novo pyrimidine synthesis27, and purine depletion blocks mTORC1-stimulated protein synthesis65. Two major factors are likely to underlie this molecular logic: first, the metabolic pathways and processes that mTORC1 regulate are connected and partially interdependent (Fig. 3), and second, cells must maintain anabolic balance by coordinately controlling multiple metabolic processes in parallel. Metabolic pathways induced by mTORC1 signalling function in concert to synthesize metabolites, cofactors and macromolecules in a manner that promotes healthy, sustainable growth while preventing stress. It would be futile and potentially stress inducing to force the synthesis of specific macromolecules when nutrients are limiting for the synthesis of other key macromolecules. The importance of balancing anabolic processes is underscored by the discovery of metabolic vulnerabilities that accompany genetic events leading to uncontrolled mTORC1 signalling117,140,141.
Temporal coordination of processes downstream of mTORC1 is also likely to be important for maintaining anabolic balance and mitigating stress142. mTORC1 acutely stimulates the synthesis of translation factors and ribosomes, thus resulting in a global increase in cellular protein synthetic capacity. Concomitantly, mTORC1 acutely suppresses autophagy and ubiquitin-mediated proteasomal degradation49,143,144, thereby preventing turnover of the newly synthesized translation machinery as well as longer-lived proteins. To meet the increased demand for nucleotides that accompanies the induction of rRNA synthesis for ribosome biogenesis, mTORC1 stimulates de novo nucleotide-synthesis pathways. Interestingly, mTORC1 acutely stimulates de novo pyrimidine synthesis through phosphorylation and activation of CAD27,29, but increased purine synthesis occurs through transcriptional mechanisms induced with delayed kinetics28. Why pyrimidine and purine synthesis are temporally separated downstream of mTORC1 remain unclear, but this phenomenon probably reflects the ability of cells to initially mobilize purines (ATP and GTP) from other cellular pools, because purines are more abundant than pyrimidines and have many other cellular functions beyond nucleic acid synthesis. In proliferating cells, mTORC1 activation confers dependence on de novo nucleotide-synthesis pathways to sustain sufficient nucleotide pools for both rRNA and DNA synthesis140. In cells and tumours lacking the TSC complex, inhibition of de novo guanylate-nucleotide synthesis results in DNA-replication stress and apoptosis driven by uncontrolled mTORC1 signalling and the excessive consumption of guanylate nucleotides for rRNA synthesis140. The parallel ability of mTORC1 to activate SREBP and induce de novo lipid synthesis is another important component of its balanced cell-growth program, thus facilitating the expansion of organellar and plasma membranes. This function might be particularly important to expand the membranous ER network as ribosome-rich rough ER becomes more abundant, and the protein load in the ER increases with mTORC1 activation. Indeed, the viability of cells with activated mTORC1 has been found to be dependent on lipid acquisition through either de novo synthesis or uptake, which is required to prevent ER stress and cell death141,145.
Prolonged mTORC1 activation has been found to induce the expression of proteasome subunits and to increase the cellular content of proteasomes and immunoproteasomes in several distinct settings146,147,148,149,150. The stimulation of proteasome synthesis downstream of mTORC1 involves the activation of SREBP and its subsequent transcriptional induction of the NFE2L1 (also known as NRF1) transcription factor146, which induces the expression of all proteasome-subunit genes151,152. Although this function of mTORC1 may seem paradoxical with regard to its role in stimulating protein synthesis, it serves to increase the degradation capacity of the cell under conditions of increased rates of protein synthesis, thus making the turnover of misfolded proteins or proteins targeted independently by ubiquitination more efficient. Enhanced protein turnover in settings with sustained mTORC1 signalling might also help to maintain the intracellular amino acid pools needed to endure a prolonged elevation in protein synthesis146. Thus, both lipid synthesis and proteasome synthesis, which temporally follow the acute stimulation of protein synthesis by mTORC1, may mitigate potential stresses associated with an increased protein load on the cell142.
Interestingly, as part of its control over anabolic metabolism, mTORC1 activates specific transcription factors that are also under mTORC1-independent control by specific nutrients, such as HIF1α, which is induced by oxygen depletion; SREBP, which is induced by sterol depletion; and ATF4, which is induced by amino acid deprivation2,28,32. mTORC1 activates these transcription factors together, but only in the presence of sufficient resources to drive anabolic metabolism. This scenario is in contrast to nutrient deprivation, in which these transcription factors are robustly activated individually after depletion of specific nutrients as part of adaptive response mechanisms to conserve or replenish the given nutrient, or otherwise survive its decreased abundance. These latter signals stemming from nutrient depletion are dominant over that from mTORC1 in the control of these transcription factors, because a decrease in these nutrients concomitantly inhibits mTORC1 and further facilitates a shift from anabolic metabolism to adaptive metabolism153.
Importance of proper mTORC1 regulation in human health and disease
Given the central role of mTORC1 in linking signals from nutrient and energy status to induced changes in metabolism, it is unsurprising that proper control of mTORC1 is essential for human health and that the uncoupling of mTORC1 from its normal regulatory inputs contributes to many diseases. Dysregulated or chronic mTORC1 activation in cells and tissues can be achieved through either environmental (for example, dietary) or genetic factors and has been implicated in a broad set of seemingly unrelated diseases, including genetic tumour and overgrowth syndromes, obesity and type 2 diabetes, neurological disorders and autoimmune diseases77,154. Although mechanisms underlying its dysregulation with age are poorly defined, mTORC1 signalling has emerged as an important contributor to the inevitable decline of health with age. Attenuation of mTORC1 signalling through dietary restriction or pharmacological agents (for example, rapamycin or metformin) has been well established to extend lifespan in multiple model organisms, including yeast, worms, flies and mice155,156.
A multitude of disease-causing genetic events have been found to give rise to the shared feature of uncontrolled mTORC1 signalling. Mutations in tumour-suppressor genes and oncogenes encoding key regulators of mTORC1, including TSC1 and TSC2, and signalling proteins that function upstream of the TSC complex, such as PIK3CA, AKT, PTEN, RAS, BRAF, LKB1, APC and a variety of receptor tyrosine kinases, lead to activation of mTORC1 in a manner independent of its control by one or more upstream growth signals157. Thus, elevated mTORC1 signalling is observed in most human cancers and genetic tumour syndromes. Although mutations in the amino acid–sensing pathway upstream of the Rag proteins have been identified in tumour cells, they are much less common than those affecting the TSC–Rheb pathway, a finding possibly reflecting the continued need to sense and adapt to changes in nutrient availability within the tumour microenvironment, even in tumours that evade most other regulatory mechanisms. However, loss-of-function mutations in components of GATOR1, the RagA/B GAP, leading to amino acid–independent activation of mTORC1, have been identified in a small subset of ovarian cancers and glioblastomas101, and mutations in the Rag C/D GAP folliculin (encoded by FLCN) cause Birt–Hogg–Dubé syndrome, a rare inherited tumour syndrome158. Finally, rare activating mutations in the Rag proteins and mTOR itself have also been observed in human cancers159,160, and RagC mutations are enriched in follicular lymphoma161. Given the overall high frequency of its activation, there has been much interest in targeting mTORC1 in tumours. However, in more than 1,000 clinical trials to date, with few exceptions, rapamycin and its analogues (rapalogues) have generally been ineffective in inducing sustained tumour regression as single agents. mTOR inhibitors are generally cytostatic in nature and can attenuate the anabolic growth of cells but fail to induce cell death162. Further studies are needed to better understand the metabolic dependencies that accompany uncontrolled mTORC1 activation, a very common event in human cancers; such research could unveil new strategies to selectively induce the death of tumour cells.
A role of aberrant mTORC1 signalling in diverse neurological disorders has also emerged. In addition to having widespread tumours, up to 90% of patients with the TSC disease, caused by loss-of-function mutations in TSC1 or TSC2, have epilepsy, most often starting in infancy163, and clinical data indicate that mTOR inhibitors might decrease seizures in this population164. Further evidence that dysregulated mTORC1 signalling is a major driver of epilepsy stems from the discovery of activating mutations in mTOR and loss-of-function mutations in components of the GATOR1 and KICSTOR complexes underlying epilepsies associated with focal cortical dysplasia103,104,165. Patients with TSC also have a variety of other neuropychiatric disorders, including autism spectrum disorder166. The mechanisms through which aberrant mTORC1 signalling contributes to epilepsy and other neurological disorders are poorly understood, as is the role of mTORC1 in non-syndromic versions of these disorders. mTORC1 signalling has also been implicated in neurodegenerative diseases, such as Alzheimer’s disease, partly because of its regulation of autophagy, a degradative process that might contribute to the clearance of pathogenic protein aggregates and dysfunctional organelles167. Finally, interesting emerging evidence suggests that abnormally low mTORC1 signalling might contribute to clinical depression, and new therapeutics are aimed at stimulating mTORC1 signalling in the brain to enhance synaptic function168.
How dietary nutrients influence mTORC1 signalling in different tissues is an active area of research in fields related to metabolic diseases and longevity. Unlike cells grown in nutrient-rich, serum-fed culture conditions, mTORC1 signalling is generally low in mammalian tissues but is acutely responsive to feeding in the primary metabolic tissues of mammals (for example, liver, muscle and adipose), probably as a result of combined effects of nutrient signalling through the Rag proteins and insulin signalling through Rheb98,118. Under conditions of nutrient overload and obesity, mTORC1 signalling becomes more chronically activated in these tissues and, through inhibitory feedback mechanisms, might contribute to the development of insulin resistance, a hallmark of type 2 diabetes169.
The molecular wiring of the mTORC1 network allows it to monitor local nutrients and systemic growth signals and alter the metabolic states of cells, tissues and organisms accordingly. Despite remarkable progress in recent years, many questions remain regarding mTORC1’s upstream regulation, downstream functions and contributions to human health and disease. For instance, it will be important to determine the molecular mechanisms through which other growth-factor, nutrient and stress signals that influence the activation state of mTORC1 fit into the emerging model of signal integration by the Rag and Rheb GTPases at the surface of the lysosome and whether other major subcellular sites of mTORC1 regulation exist. It will also be important to determine how mTORC1, once active, finds its direct downstream substrates and whether additional factors give rise to differential substrate selectivity in various settings. How known and novel feedback mechanisms influence the temporal and spatial nature of mTORC1 activation in cells and tissues is also poorly defined. Whereas mTORC1 and its immediate upstream regulators and downstream effectors are ubiquitously expressed, the identity of the dominant regulatory signals and targets in any given tissue and whether these vary between states of physiological or pathological activation of mTORC1 are currently unknown. The answers to these questions hold the key to understanding the role of mTORC1 in a wide array of diseases and the ageing process and how best to inhibit or activate mTORC1 through pharmacological or dietary interventions, as appropriate, to improve human health77.
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Studies in the laboratory of B.D.M. related to this subject were supported by American Cancer Society postdoctoral fellowship 127106-PF-14-254-01-TBE to A.J.V., NIH grants R35-CA197459 and P01-CA120964 to B.D.M., and a Rothberg Courage Award from the Tuberous Sclerosis Alliance to B.D.M.
B.D.M. is a shareholder and scientific advisory board member of Navitor Pharmaceuticals and LAM Therapeutics.
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Human Genetics (2019)