How does mtor regulate autophagy

The autophagic machinery is evolutionarily conserved from yeast to mammals where a set of autophagy-related Atg proteins orchestrates distinct stages of the pathway, such as initiation, elongation, maturation and fusion.

Autophagy occurs in the cell at a basal level in order to maintain energy homoeostasis and cellular functions. However, it can be further activated above basal levels in response to many cellular stressors such as oxygen, energy and nutrient e. AMPK is crucial to the cellular response to low energy levels and, once active, drives processes which will replenish cellular energy stores, such as autophagy while inhibiting biogenic synthesis [ ].

Opposite to AMPK, activated mTORC1 shifts the metabolic programme of the cell from catabolic to anabolic metabolism by up-regulating the synthesis of building blocks for cell proliferation, including proteins, lipids and nucleotides [ ]. As both mTORC1 and AMPK are essential for the cell to maintain energy and nutrient homoeostasis, it has been appreciated that their signalling pathways must be coordinated. Several mechanisms of cross-talk have been identified. Recent research has also revealed that the lysosome may function as a crucial hub for integration of signalling in response to both nutrients and energy by reporting the lysosomal v-ATPase—Ragulator complex as a common activator for AMPK and mTORC1 [ ].

Whereas the role of amino acids as key signal factors in the activation of mTORC1 has been accepted, to date, the inhibitory effect of amino acids on AMPK has been a debatable issue. Some studies have observed the inhibition of AMPK by amino acids [ — ], though this has not always been the case [ , ].

A recent work suggests amino acids as novel metabolic activators of AMPK. It should be noted that all previous studies observed AMPK phosphorylation at the earliest at 15 min post amino acid addition. This study explains that, at this time point, AMPK is repressed and postulates this as the reason why earlier studies may have missed the early AMPK induction by amino acids.

They propose that this sustained autophagy under amino acid sufficiency might be required to maintain protein homoeostasis and deliver metabolite intermediates for biosynthetic processes [ ]. Autophagy pathway is mostly orchestrated by Atg proteins that nucleate distinct complexes, amongst which ULK1 and Vps34 complexes act as important gatekeepers for autophagy induction [ — ].

ULK1 is essential for autophagy induced by amino acid starvation and is directly regulated by mTORC1 through phosphorylation at Ser [ , ]. The reversible phosphorylation of ULK1 is a central mechanism by which starvation-induced autophagy is regulated.

This coordinated phosphorylation shows a finely balanced regulatory signalling network [ ]. It has been proposed that amino acid deprivation triggers more rapid autophagy than chemical inhibition of mTORC1. Indeed, in addition to the inhibition of mTORC1, amino acid starvation causes an increase in the phosphatase activity of PP2A towards ULK1 which triggers the rapid dephosphorylation of ULK1 and consequently, accelerates the autophagic response [ ].

Another autophagic complex required for autophagy induction, the Vps34 complex which includes Atg14, Vps15 and Beclin-1, can be regulated by amino acid sufficiency. Conversely, depletion of amino acids causes mTORC1 inhibition, thereby relieving this pro-autophagy complex to stimulate autophagy [ ].

Vps34 contributes to a variety of cellular functions and, as discussed above, this lipid kinase also participates in amino acid-dependent activation of mTORC1 [ , ]. Vps34 may exist as in yeast in two different populations, with and without Beclin-1 association [ ].

In addition to autophagic complexes, amino acids also control autophagy through the family of transcriptional factors regulating autophagic and lysosomal gene expression Figure 3. TFEB controls lysosomal biogenesis and autophagy by positively regulating genes belonging to the CLEAR coordinated lysosomal expression and regulation network [ — ].

Thus, TFEB activation leads to an increased number of autophagosomes and autophagic flux, biogenesis of new lysosomes, and clearance of storage material [ , , , ]. TFEB activity and its nuclear translocation correlate with its phosphorylation status [ , ].

Recent studies have reported that Rag GTPases and lysosomal mTORC1 regulate TFEB localization by phosphorylating the transcription factor on several serine and threonine residues, including Ser, under nutrient-rich conditions [ , ]. TFEB phosphorylation on Ser facilitates its interaction with the cytosolic chaperone protein which retains and therefore inactivates TFEB in the cytoplasm [ ]. Under amino acid deprivation, mTORC1 inactivation leads to dephosphorylation and relocalization of TFEB to the nucleus where it promotes the expression of lysosomal and autophagy-related genes [ ].

This cellular response allows the adaptation to diminished amino acid levels by increasing lysosomal and autophagic compartments in order to maintain the levels of energy and metabolites required to survive starvation condition. Schematic representation of the cellular signalling pathways governed by amino acids in the regulation of autophagy via mTORC1.

Amino acid sufficiency activates the mTORC1 pathway which inhibits autophagy at multiple steps. This allows the cell to maintain a critical level of energy and metabolites for surviving the starvation condition. Similarly, the transcription factor TFE3, which belongs to the same family that TFEB, is recruited to lysosomes through direct interaction with active Rags and this recruitment is critical to inactivate TFE3 under nutrient-rich conditions.

Specifically, mTORC1 phosphorylates TFE3 at several residues but Ser is particularly relevant as this phosphorylation creates a binding site for the cytosolic chaperone which sequestrates this transcription factor in the cytosol [ , — ]. TFEB and TFE3 are partially redundant in their ability to induce lysosomal biogenesis in response to nutrient starvation, but both must be present for a maximal response [ ].

The fine modulation of this circuit is essential for metabolic adaptation to nutrient availability. Overall, the emerging picture reveals the close collaboration between mTORC1 and several other master regulators of autophagy and lysosomal biogenesis in order to facilitate an efficient response to the varying nutrient demands of the cell [ ].

However, it has been recently shown that amino acid withdrawal, besides increased turnover of autophagic cargo, causes selective remodelling of the plasma membrane in yeast [ , ]. In this model system, endocytic trafficking of membrane proteins to the vacuole the yeast equivalent of the lysosome allows their hydrolysis into amino acids which provide material to fuel biosynthesis of more lysosomal proteins.

These newly synthesized lysosomal proteins enhance hydrolysis of a later wave of autophagic cargo [ ]. This starvation-induced protein turnover has been proposed to be regulated by TORC1. On one hand, TORC1 signalling promotes the endocytosis of certain plasma membrane proteins [ ]. On the other hand, TORC1 inactivation triggers endocytosis of other plasma membrane proteins that are degraded in an endosomal sorting complex required for transport ESCRT -dependent manner via the multivesicular body MVB pathway [ , — ].

Although it has been proposed that TORC1 signalling controls the major ubiquitin ligase required for endocytosis in yeast, Rsp5, how TORC1 signalling controls Rsp5-dependent cargo specificity and the selective ubiquitination of many different cargoes at the same time is currently not clear [ ].

Furthermore, how the subsequent ubiquitin-dependent degradation of membrane proteins via the MVB pathway helps to meet the specific metabolic and energetic demands of the cell during nutrient limitation is not fully understood. The result of starvation-induced up-regulation of endocytosis and vacuolar degradation is a pool of amino acids that is essential for the adaptation to the lack of nutrients. Thus, the MVB pathway helps to maintain translation during acute starvation until autophagy, the long-term starvation—response pathway, is fully active.

However, is not clear how selective MVB and non-selective autophagy lysosomal proteolysis pathways cooperate to mediate cell survival during nutrient limitation. Autophagy is an important avenue for nutrient supply, particularly during amino acid starvation, which contributes amino acids to restore mTORC1 activity [ , ].

In turn, autophagy-mediated restoration of mTORC1 induces autophagy termination and reformation to lysosomes which complete the feedback loop [ ]. Although it would be tempting to envisage that autophagy restores the amino acid pool to reactivate mTORC1, some studies have detected only a partial restoration of amino acid abundance by autophagy [ , ], which suggests the existence of a more precise mechanism.

Specifically, an increase in the synthesis and release of glutamine during starvation has been reported. A recent work shows that glutamine is required for autophagy-induced mTORC1 reactivation during amino acid starvation and suggests that extracellular glutamine may function as specific starvation-induced nutrient signal to regulate mTORC1 [ ].

In addition, this study demonstrates that the restorative effect of glutamine on mTORC1 signalling requires the conversion of glutamine to glutamate, which in turn sustains the non-essential amino acid pool via transamination [ ].

Since amino acids are essential building blocks in the cell, the ability to regulate their levels is fundamental for cell survival, growth and development. The control of intake, utilization and recycling of amino acids is subjected to a fine regulation which involves a number of mechanisms that ensure amino acid availability in order to support cellular function. All these mechanisms integrate amino acid sufficiency with anabolic processes and autophagy.

Given the massive impact of amino acids on autophagy and the importance of autophagy for cell function, the research in the field of amino acid sensing has expanded exponentially over the last years [ — ].

At the epicentre of amino acid sensing is the kinase mTORC1 that governs a rapid cellular response to fluctuations in amino acid levels. Thus, the study of the mechanisms via which mTORC1 senses amino acid levels has become fundamental to the understanding of amino acid signalling. The discovery of the lysosomal Rag GTPases as important regulators of amino acid-dependent mTORC1 activation has focused most of the studies on the identification of molecules that could be involved in amino acid sensing by modulating the nucleotide state of the Rag GTPases.

To date, one of the most relevant has been the characterization of the v-ATPase, which has led to the prediction that amino acids are sensed within the lysosome [ 69 ]. Nonetheless, besides the well-known role of lysosomes in amino acid sensing, it is now accepted that mTORC1 senses both intralysosomal and cytosolic amino acids through different mechanisms.

From the plasma membrane to the cytosol, novel molecules directly involved in the sensing of amino acids have recently been revealed. Some examples are IPMK, MAPK43 or Vps34, which have been proposed as important intracellular proteins in amino acid signalling, although the mechanisms via which these molecules sense amino acids and activate mTORC1 still remain elusive.

An exciting advance in the field represents the identification of specific cytoplasmic amino acid sensors for some of the most potent activators of mTORC1, leucine and arginine [ 90 , 92 , ]. These findings leave open the question of the existence of additional amino acid sensors in the cytosol with specificity for other amino acids. Furthermore, intracellular amino acids exist as free forms or bound to proteins, lipids or other molecules.

Future work will be needed to clarify whether the equilibrium between these different pools determine which amino acids are available to the sensors [ ]. One particular aspect that will be of interest is the relative contribution of these different pools of amino acids in the activation of mTORC1.

An interesting avenue that is expanding in this field is the importance of extracellular amino acids in determining intracellular amino acid concentrations. This has led to the study of cell surface amino acid transporters since they are in an ideal location to relay nutritional information, as well as amino acids themselves, to the cell interior. Although these transporters were initially classified by their ability to translocate specific amino acids across the lipid bilayer, they have lately emerged as important amino acid sensors controlling mTOR recruitment and activation [ 73 , ].

Indeed, increasing evidence exists suggesting that they can activate amino acid-dependent signalling either in the presence or absence of transport, by acting as transceptors [ ].

This concept of dual-function suggests that part of the sophisticated control governing the trafficking of amino acids has to do with their signalling function rather than with the control of transport. Thus, for those amino acid transporters that act as sensors for mTORC1 future work is likely to unveil whether they directly interact with the amino acids they are believed to sense [ ].

As shown by recent studies, amino acid transporters do not function exclusively at the plasma membrane; they can also be found intracellularly where they may increase local concentrations of amino acids. These findings, in addition to reinforce the role of lysosome as amino acid storage sites with high concentrations of amino acids at their surface, open an exciting field of research that predicts that amino acids could be sensed in other subcellular compartments.

Thus, the concentration of amino acids may exist in gradients across the intracellular space, specifically within various organelles, and could differ significantly compared with those found in the cytosol since they contain a distinct set of amino acid transporters [ ].

Despite the explosion of knowledge in amino acid sensing in the last years, one major unsolved question in this field revolves around how these novel mechanisms fit with the model of Rag GTPases-dependent amino acid regulation. The C. Cell 28, 43— Manzoni, C. Martin, D. Autophagy in Huntington disease and huntingtin in autophagy.

Trends Neurosci. Martina, J. Autophagy 8, — Martinez-Vicente, M. Matecic, M. A microarray-based genetic screen for yeast chronological aging factors. Matsunaga, K. Two Beclin 1-binding proteins, Atg14L and Rubicon, reciprocally regulate autophagy at different stages. Mauvezin, C. Assays to monitor autophagy in Drosophila. Methods 68, — Max, X. Melendez, A. Autophagy genes are essential for dauer development and life-span extension in C.

Merenlender-Wagner, A. Autophagy has a key role in the pathophysiology of schizophrenia. Psychiatry 20, — Michel, P. Understanding dopaminergic cell death pathways in parkinson disease. Neuron 90, — Miyamoto, S. Autophagy and cardiac aging. Mizushima, N. Autophagy: renovation of cells and tissues.

Montagne, J. Drosophila S6 kinase: a regulator of cell size. Moorad, J. Age-dependent mutational effects curtail the evolution of senescence by antagonistic pleiotropy.

Nakamura, S. Suppression of autophagic activity by Rubicon is a signature of aging. Nazio, F. Neufeld, T. TOR-dependent control of autophagy: biting the hand that feeds. Nixon, R. The role of autophagy in neurodegenerative disease. Noda, T. Tor, a phosphatidylinositol kinase homologue, controls autophagy in yeast. Nojima, H. Ott, C. Macroautophagy is impaired in old murine brain tissue as well as in senescent human fibroblasts.

Redox Biol. Pattingre, S. Bcl-2 antiapoptotic proteins inhibit Beclin 1-dependent autophagy. Pearce, L. Peterson, T. Piras, A. Autophagic and lysosomal defects in human tauopathies: analysis of post-mortem brain from patients with familial Alzheimer disease, corticobasal degeneration and progressive supranuclear palsy.

Porstmann, T. Rabinowitz, J. Autophagy and metabolism. Ravikumar, B. Inhibition of mTOR induces autophagy, and reduces toxicity of polyglutamine expansions in fly, and mouse models of Huntington disease. Ristow, M.

Dose Response 12, — Roczniak-Ferguson, A. Rodriguez, J. Antagonistic pleiotropy and mutation accumulation influence human senescence and disease. Saha, S. Autophagy in health and disease: a comprehensive review. Saito, T. Autophagy regulates lipid metabolism through selective turnover of NCoR1. Sarbassov, D. Rictor, a novel binding partner of mTOR, defines a rapamycin-insensitive and raptor-independent pathway that regulates the cytoskeleton.

Cell 22, — Sarkar, S. Trehalose, a novel mTOR-independent autophagy enhancer, accelerates the clearance of mutant huntingtin and alpha-synuclein. Lithium induces autophagy by inhibiting inositol monophosphatase. Rapamycin and mTOR-independent autophagy inducers ameliorate toxicity of polyglutamine-expanded huntingtin and related proteinopathies.

Saxton, R. Schmeisser, K. Nicotinamide-N-methyltransferase controls behavior, neurodegeneration and lifespan by regulating neuronal autophagy. Scott, R. Role and regulation of starvation-induced autophagy in the Drosophila fat body. Cell 7, — Settembre, C. EMBO J. Shi, J. Shin, H. Shiota, C. Multiallelic disruption of the rictor gene in mice reveals that mTOR complex 2 is essential for fetal growth and viability.

Shokeir, M. Fecundity and fitness. Singh, A. Rapamycin confers neuroprotection against aging-induced oxidative stress, mitochondrial dysfunction, and neurodegeneration in old rats through activation of autophagy. Rejuvenation Res. Son, J. Neuronal autophagy and neurodegenerative diseases. Sonenberg, N. Regulation of translation initiation in eukaryotes: mechanisms and biological targets. Sorensen, S. Significantly lower incidence of cancer among patients with Huntington disease: an apoptotic effect of an expanded polyglutamine tract?

Cancer 86, — Sutter, B. Tashiro, K. Age-related disruption of autophagy in dermal fibroblasts modulates extracellular matrix components. Tissenbaum, H. An insulin-like signaling pathway affects both longevity and reproduction in Caenorhabditis elegans. Genetics , — Toth, M. Cell, —e12 CrossRef Google Scholar. Ying Wang 1 2 Hongbing Zhang 1 Email author 1. Personalised recommendations.

Cite chapter How to cite? ENW EndNote. Buy options. Stipanuk, M. Macroautophagy and its role in nutrient homeostasis. Article PubMed Google Scholar. Huang, J. Autophagy and human disease. Cell Cycle 6 , — Liang, C. Autophagy genes as tumor suppressors. Sarkar, S. Huntington's disease: degradation of mutant huntingtin by autophagy. FEBS J. Cadwell, K. Role of autophagy and autophagy genes in inflammatory bowel disease.

Lerena, M. Bacterial pathogens and the autophagic response. Cell Microbiol. Tal, M. Autophagy and innate recognition systems. Nakatogawa, H. Dynamics and diversity in autophagy mechanisms: lessons from yeast. Xie, Z. Autophagosome formation: core machinery and adaptations. Inoue, Y. Regulation of macroautophagy in Saccharomyces cerevisiae. Cell Dev. Mizushima, N. Chan, E. Evolution of Atg1 function and regulation. Autophagy 5 , — Kamada, Y. Tor-mediated induction of autophagy via an Apg1 protein kinase complex.

Kabeya, Y. Atg17 functions in cooperation with Atg1 and Atg13 in yeast autophagy. Cell 16 , — Chang, Y. Cell 20 , — Young, A.