A critical role for TORC1 in cellular senescence

Comment on: Kolesnichenko M, et al. Cell Cycle 2012; 11:2391-401 and Pospelova TV, et al. Cell Cycle 2012; 11:2402-407.Cellular senescence is a process initiated either when cells proliferate past their potential (replicative senescence) or by activation of an oncogenic stress (oncogene-induced senescence). Both of these events are characterized by the activation of a DNA damage response, which is initiated by eroded telomeres in the case of replicative senescence, and aberrant products of DNA replication in the case of oncogene induced senescence.¹ Senescence plays a critical tumor-suppression role in vivo, and alterations in the senescence program are a hallmark of cancer cells. Bypass of senescence is critical for tumor progression and involves the p53 and pRB tumor-suppressor pathways.² Indeed, expression of DNA tumor virus oncoproteins that target p53 and pRB can bypass senescence in cultured cells,³ and concomitant loss of pRB and p53 bypasses senescence in human diploid fibroblasts.⁴ In addition to being an obligatory step for tumor progression, bypass of senescence creates a favorable environment in which additional tumor-promoting mutations can be acquired. For example, inactivation of p53 in the context of telomere erosion promotes rampant genomic instability mediated by cycles of aberrant DNA damage/DNA repair events.⁵In a new study, Kolesnichenko et al. describe a critical role for the mTOR pathway in senescence induction.⁶ This work demonstrates that inhibition of mTOR is sufficient to delay RAS-induced senescence as well as replicative senescence. Using a combination of inhibitory molecules, shRNA-mediated knockdown and expression of inhibitory proteins, the authors demonstrate that inhibition of the TORC1 complex is sufficient to delay senescence induction. These findings are further corroborated by the independent work of Pospelova and colleagues showing that rapamycin treatment delays senescence induction in murine fibroblasts.⁷ These intriguing findings raise the question of why mTOR inhibition inhibits senescence induction. The work of Kolesnchenko and colleagues provides two clues to explain this phenotype. First, mTOR inhibition results in the activation of the pro-survival factor AKT, a factor that could explain how cells can proliferate in the face of an ongoing senescence-inducing signal. In addition, the authors find reduced levels of p53 and its target gene p21 upon mTOR inhibition. These findings are particularly significant considering the critical role for both p53 activation and p21 induction in senescence induction.In conclusion, the finding that inhibition of the TORC1 complex has a profound effect on the onset of senescence might explain why rapamycin treatment had limited success in the treatment of cancer.⁸ On the other hand, rapamycin slows aging and thus delays cancer in mice.⁹     

TOR Complex 2 Controls Gene Silencing,Telomere Length Maintenance,and Survival under DNA-Damaging Conditions

The Target Of Rapamycin (TOR) kinase belongs to the highly conserved eukaryotic family of phosphatidylinositol-3-kinase-related kinases (PIKKs). TOR proteins are found at the core of two distinct evolutionarily conserved complexes, TORC1 and TORC2. Disruption of TORC1 or TORC2 results in characteristically dissimilar phenotypes. TORC1 is a major cell growth regulator, while the cellular roles of TORC2 are not well understood. In the fission yeast Schizosaccharomyces pombe, Tor1 is a component of the TORC2 complex, which is particularly required during starvation and various stress conditions. Our genome-wide gene expression analysis of Δtor1 mutants indicates an extensive similarity with chromatin structure mutants. Consistently, TORC2 regulates several chromatin-mediated functions, including gene silencing, telomere length maintenance, and tolerance to DNA damage. These novel cellular roles of TORC2 are rapamycin insensitive. Cells lacking Tor1 are highly sensitive to the DNA-damaging drugs hydroxyurea (HU) and methyl methanesulfonate, similar to mutants of the checkpoint kinase Rad3 (ATR). Unlike Rad3, Tor1 is not required for the cell cycle arrest in the presence of damaged DNA. Instead, Tor1 becomes essential for dephosphorylation and reactivation of the cyclin-dependent kinase Cdc2, thus allowing reentry into mitosis following recovery from DNA replication arrest. Taken together, our data highlight critical roles for TORC2 in chromatin metabolism and in promoting mitotic entry, most notably after recovery from DNA-damaging conditions. These data place TOR proteins in line with other PIKK members, such as ATM and ATR, as guardians of genome stability.The TOR protein kinase is a major cell growth regulator that links cellular growth with cell divisions (18, 42, 64, 65). TOR is an atypical protein kinase conserved from yeast to humans that was isolated as the target of the immunosuppressive and anticancer drug rapamycin (28). TOR proteins can be found in two distinct complexes, known as TORC1 and TORC2 (27, 64). These complexes mediate their distinct cellular functions via phosphorylation and activation of different sets of AGC-like kinases, including mammalian p70S6K, downstream of TORC1, and AKT/protein kinase B (PKB) downstream of TORC2 (18). TORC1 in mammals contains mTOR (Tor1 or Tor2 in Saccharomyces cerevisiae; Tor2 in Schizosaccharomyces pombe) and the Raptor protein (Kog1 in S. cerevisiae; Mip1 in S. pombe). TORC1 in many different eukaryotes plays a central role in the control of growth (mass accumulation) in response to external stimuli, particularly nutrient availability. Disruption of TORC1, either by mutating its components or by rapamycin treatment, can lead to a starvation-like phenotype (64). The cellular roles of TORC2, on the other hand, are less well defined. TORC2 in mammals contains mTOR (Tor2 in S. cerevisiae; Tor1 in S. pombe) together with Rictor (Avo3 in S. cerevisiae; Ste20 in S. pombe) and mSin1 (Avo1 in S. cerevisiae; Sin1 in S. pombe). TORC2 plays a role in regulating the actin cytoskeleton and cell wall integrity pathway in S. cerevisiae (3, 15, 27), a function that is at least partially conserved in human cells (17, 47).Fission yeast contains two TOR homologues, Tor1 and Tor2 (59), which form the TORC2 and TORC1 complexes, respectively (14, 32). Disruption tor2⁺ (TORC1) mimics nitrogen starvation responses (1, 14, 32, 56, 57, 62), while disruption of tor1⁺ (TORC2) results in pleiotropic defects, including elongated cells, sensitivity to osmotic and oxidative stress, inability to execute developmental processes in response to nutrient depletion, and a decrease in amino acid uptake (16, 22, 59). Tor1 regulates cell survival under stress conditions and starvation responses via the AGC protein kinase Gad8, a putative homologue of mammalian AKT/PKB (16).In budding yeast and mammalian cells, TORC1 mediates the rapamycin-sensitive signaling branch while TORC2 is far less sensitive to inhibition by this drug (27, 48). Curiously, rapamycin does not inhibit growth of S. pombe cells but partially inhibits sexual development and amino acid uptake (60-62). Inhibition of amino acid uptake is likely a result of inhibiting Tor1 (61, 62). Accordingly, a tor1 rapamycin-defective allele (tor1^S1834E) confers rapamycin resistance to strains that are dependent on amino acid uptake for their growth (61). Yet rapamycin also induces a response similar to that for a shift from rich to poor nitrogen conditions, an effect that may involve inhibition of both Tor1 and Tor2 (41).While other members of the phosphatidylinositol-3-kinase-related kinase (PIKK) family of proteins, such as ATM and ATR, have been shown to play central roles in the DNA damage response, little is known about roles that TOR proteins might play in such processes. Recently it was shown that the rapamycin-sensitive TORC1 complex participates in regulating cell survival under DNA-damaging conditions (24, 42, 49). Currently, no such role has been attributed to TORC2.Here we show that Tor1 (TORC2) is critical for cell survival under DNA-damaging conditions, gene silencing at heterochromatic regions, and telomere length maintenance and for regulation of cell cycle progression. Since the TOR complexes are highly conserved in evolution, this novel TORC2 function may also be conserved in other organisms.     

Molecular functions of the PP2A regulatory subunit Tap46 in plants

Tap42/α4 is a regulatory subunit of the protein phosphatase 2A (PP2A) family of phosphatases and plays a role in the target of rapamycin (TOR) pathway that regulates cell growth, ribosome biogenesis, translation and cell cycle progression in both yeast and mammals. We determined the cellular functions of Tap46, the plant homolog of Tap42/α4, in both Arabidopsis thaliana and Nicotiana benthamiana. Tap46 associated with the catalytic subunits of PP2A and the PP2A-like phosphatases PP4 and PP6 in vivo. Tap46 was phosphorylated by TOR in vitro, indicating that Tap46 is a direct substrate of TOR kinase. Tap46 deficiency caused cellular phenotypes that are similar to TOR-depletion phenotypes, including repression of global translation and activation of both autophagy and nitrogen recycling. Furthermore, Tap46 depletion regulated total PP2A activity in a time-dependent manner similar to TOR deficiency. These results suggest that Tap46 acts as a positive effector of the TOR signaling pathway in controlling diverse metabolic processes in plants. However, Tap46 silencing caused acute cell death, while TOR silencing only hastened senescence. Furthermore, mitotic cells with reduced Tap46 levels exhibited chromatin bridges at anaphase, while TOR depletion did not cause a similar defect. These findings suggest that Tap46 may have TOR-independent functions as well as functions related to TOR signaling in plants.Key words: acute cell death, autophagy, chromatin bridge, nitrogen mobilization, protein phosphatases, target of rapamycin (TOR)Yeast type 2A phosphatase-associated protein 42 kDa (Tap42) is a regulatory subunit that directly associates with catalytic subunits of the protein phosphatase 2A (PP2A) family of protein phosphatases to make a heterodimer and regulates the activity and substrate specificity of the intact enzyme complex.¹ Functions of Tap42 as a component of the target of rapamycin (TOR) signaling pathway have been well characterized in yeast.^1–3 Tap42-regulated phosphatase activities play a major role in signal transduction mediated by TOR. Accumulating evidence suggest that TOR regulates phosphorylation of target proteins by restraining PP2A activity through Tap42 phosphorylation.^1–3 Rapamycin inhibits TOR activity and also influences Tap42-mediated phosphatase regulation in yeast.^3–5α4, the mammalian homolog of Tap42, also associates with the catalytic subunits of PP2A, PP4 and PP6 to make a heterodimer.⁶ Rapamycin inhibits mammalian TOR (mTOR) activity, but it is not clear whether rapamycin prevents the formation of the α4/PP2Ac complex or whether α4 stimulates or represses PP2Ac activity.^7–9 Interestingly, loss of Tap42 function in Drosophila does not affect TOR-regulated activities, including cell growth, metabolism and S6 kinase activity, but results in mitotic arrest caused by spindle anomalies and subsequent activation of c-Jun N-terminal kinase signaling and apoptosis.¹⁰ Similarly, α4 deletion in mice leads to the rapid onset of apoptosis in both proliferating and differentiated cells, while rapamycin itself does not severely affect adult cells.¹¹ Furthermore, while TOR depletion causes developmental arrest and organ degeneration at the L3 stage in Caenorhabditis elegans, loss of α4 does not reproduce TOR deficiency phenotypes, but mainly leads to a fertility defect.¹² Taken together, these results suggest that the yeast Tap42/TOR paradigm is not completely conserved in higher eukaryotes and that Tap42/α4 functions may not be exclusively dependent on the Tor signaling pathway.In this study, we investigated the in vivo functions and phosphatase regulation of Tap46, the plant Tap42/α4 homolog, in relation to TOR in Nicotiana benthamiana, Arabidopsis and tobacco BY2 cells. Tap46 was shown to interact with the catalytic subunits of PP2A, PP4 and PP6 in vivo. Recombinant Tap46 protein was phosphorylated by immunoprecipitated TOR kinase and its deletion forms in vitro. Dexamethasone-induced RNAi of Tap46 caused dramatic repression of global translation and activation of both autophagy and nitrogen mobilization in the early stages of gene silencing. These phenotypes mimic those of TOR inactivation or TOR deficiency in Arabidopsis, yeast and mammals, indicating that Tap46 is a critical mediator of the Tor pathway in the regulation of these metabolic processes in plants. However, these early phenotypes of Tap46-deficient plants were soon followed by an acute and rapid programmed cell-death (PCD), while TOR silencing only led to growth retardation and premature senescence in Arabidopsis and N. benthamiana, confirming results from a previous study.¹³ The PCD caused by Tap46 deficiency is consistent with the apoptosis induced by loss of Tap42/α4 function in both Drosophila and mice.^10,11 Thus Tap42/α4/Tap46 appears to have a strong anti-apoptotic activity in higher eukaryotes. The underlying mechanisms of PCD activation caused by Tap46 depletion remain to be revealed, but it is possible that the inappropriate modulation of phosphatase activity and aberrant protein phosphorylation led to stress signaling and PCD activation.Another interesting phenotype of Tap46 deficiency is the formation of chromatin bridges in anaphase during mitosis, suggesting a role for Tap46 in plant cell mitotic progression. However, there have been no reports of anaphase bridge formation in tor mutants of any organisms. In Drosophila, loss of Tap42 function causes spindle disorganization and pre-anaphase arrest prior to the onset of apoptosis.¹⁰ In addition, Drosophila mutants with a defective regulatory subunit of PP2A exhibit an increased number of lagging chromosomes and chromatin bridges in anaphase.^14,15 Tap46 likely regulates the functions of PP2A family phosphatases during mitosis by direct association with their catalytic subunits, thereby modulating both the activity and specificity of the enzyme. Accumulating evidence reveals dynamic functions of PP2A during mitosis in both yeast and mammals: PP2A regulates kinetochore function, sister chromatid cohesion, spindle bipolarity and progression to anaphase.^15–17 Counteracting the activity of protein kinases, PP4 has also been implicated in both centrosome maturation and function during mitosis.¹⁸ Based on immunolabeling results, Tap46 was visualized as distinct spots around chromatin and mitotic spindles during mitosis in tobacco BY2 cells (Lee HS and Pai HS, unpublished results). Further studies will address the interacting partners and dynamic relocation of Tap46 during the cell cycle.Our results in this study demonstrated that Tap46 plays an important regulatory role in plant growth and metabolism; a major part of its function appears related to TOR signaling. However, we consistently observed certain phenotypic differences between Tap46-silenced and TOR-silenced Arabidopsis and N. benthamiana plants: an acute and rapid PCD occurred upon Tap46 silencing but not upon TOR silencing, despite a similar degree of gene silencing. Furthermore, we did not observe anaphase bridge formation in mitotic root-tip cells of ethanol-induced TOR RNAi Arabidopsis plants, while chromatin bridges were repeatedly observed in Tap46-silenced tobacco BY2 and Arabidopsis root-tip cells. Although an ancient Tap42/TOR paradigm observed in yeast appears to be conserved in plants, new TOR-independent functions of Tap46 might have evolved, the abrogation of which can cause massive PCD activation and anaphase bridge formation. Tap46 is a major regulator of cellular PP2A activity in plant cells by interacting with multiple phosphatase partners. Unraveling the molecular networks of Tap46 activity and interactions is essential for understanding its TOR-dependent and -independent functions in plants.     

A Role for p38 Stress-Activated Protein Kinase in Regulation of Cell Growth via TORC1

The target of rapamycin (TOR) complex 1 (TORC1) signaling pathway is a critical regulator of translation and cell growth. To identify novel components of this pathway, we performed a kinome-wide RNA interference (RNAi) screen in Drosophila melanogaster S2 cells. RNAi targeting components of the p38 stress-activated kinase cascade prevented the cell size increase elicited by depletion of the TOR negative regulator TSC2. In mammalian and Drosophila tissue culture, as well as in Drosophila ovaries ex vivo, p38-activating stresses, such as H₂O₂ and anisomycin, were able to activate TORC1. This stress-induced TORC1 activation could be blocked by RNAi against mitogen-activated protein kinase kinase 3 and 6 (MKK3/6) or by the overexpression of dominant negative Rags. Interestingly, p38 was also required for the activation of TORC1 in response to amino acids and growth factors. Genetic ablation either of p38b or licorne, its upstream kinase, resulted in small flies consisting of small cells. Mutants with mutations in licorne or p38b are nutrition sensitive; low-nutrient food accentuates the small-organism phenotypes, as well as the partial lethality of the p38b null allele. These data suggest that p38 is an important positive regulator of TORC1 in both mammalian and Drosophila systems in response to certain stresses and growth factors.The target of rapamycin, TOR, is a highly conserved serine/threonine kinase that is a critical regulator of cell growth. It is a core component of two signaling complexes, TORC1 and TORC2 (60, 74). TORC1 is defined by the presence of Raptor in the complex, while TORC2 contains Rictor. Rictor and Raptor are mutually exclusive. Activation of the TORC1 pathway leads to increased protein translation, increased cell size, and increased proliferation, making this pathway an important target for emerging cancer therapies. Rapamycin is an inhibitor of TORC1 that is commonly used as an immunosuppressant following kidney transplantation (51). At least three analogs of rapamycin are currently being tested in solid and hematological tumors and have shown some promising results (21).The TORC1 pathway responds to numerous inputs, sensing both the desirability of and the capacity for growth. Many of these pathways control TORC1 signaling through phosphorylation of the tuberous sclerosis protein TSC2. TSC2 associates with TSC1 to form a heterodimeric GTPase-activating protein complex (GAP) that inactivates the small GTPase Rheb (24, 29, 67). While the exact molecular mechanism remains a topic of debate, activation of Rheb promotes the kinase activity of TORC1 (24, 29, 67). Rheb is required for the activation of TORC1 in response to both amino acids and growth factors (55, 62). In Drosophila melanogaster, mutation of either TOR or Rheb inhibits growth, leading to reduced body size and reduced cell size in mutant clones (42, 64). Mutation of either TSC1 or TSC2 has the predicted opposite effect, as tissue deficient for either of these proteins overgrows and contains large cells (49, 66).TORC1 is activated via the phosphatidylinositol 3′ kinase (PI3′K) pathway by growth-promoting mitogens, such as insulin and growth factors. Drosophila mutants with mutations of PI3′K pathway components have size phenotypes similar to those of the TOR and Rheb mutants (71). In mammalian cells, the PI3′K-mediated activation of TORC1 occurs at least in part through the phosphorylation of TSC2 by the PI3′K target AKT (30, 50). Interestingly, mutation of these residues in Drosophila has no impact on TSC2 function in vivo, suggesting that there may be other mechanisms through which PI3′K can activate Drosophila TOR (20). Recent work has suggested that the proline-rich AKT substrate PRAS40 may provide part of this link (23, 59, 69, 70). In addition, signaling through RAS activates extracellular signal-regulated kinase (ERK) and ribosomal S6 kinase (RSK), which can phosphorylate TSC2 and Raptor to activate TORC1 (13, 40, 56). There are also likely to be additional mechanisms through which growth factors activate Drosophila TOR that have not yet been identified.TORC1 activity is also controlled by the intracellular building blocks necessary to support cellular growth. The energy-sensing AMP-activated protein kinase (AMPK) pathway relays information about the energy status of the cell to TORC1 by phosphorylating TSC2. Unlike the inactivating phosphorylation of TSC2 by Akt, phosphorylation of TSC2 by AMPK promotes the GAP activity of the TSC complex (31). AMPK also phosphorylates Raptor, leading to decreased TORC1 activity (28). Thus, when energy levels are low, active AMPK inhibits TORC1.Amino acids also activate the TORC1 pathway, through a mechanism that requires Rheb, as well as the type III PI3′K VPS34 and the serine/threonine kinase mitogen-activated protein kinase kinase kinase kinase 3 (MAP4K3) (11, 22, 43). TORC1 thereby integrates information about the availability of amino acids and the amount of energy available for growth with growth factor signaling. Given its ancient function in adapting growth rates to environmental conditions, it is likely that TOR responds to a variety of stimuli, suggesting that many TOR control mechanisms remain to be uncovered. The Rag family of Ras-related small GTPases has recently been identified as a key component of the amino acid-sensing pathway, acting in parallel to Rheb (34, 58). Rag GTPases form heterodimers; RagA or RagB interacts with RagC or RagD. RagA and RagB are active when GTP bound, while RagC and RagD are active when bound to GDP (34, 58). Activation of the Rags by amino acids results in TOR relocalization to Rab7-containing vesicles (58). While the function of these vesicles in TORC1 signaling remains unclear, this relocalization is associated with increased TORC1 activity.TORC1 controls cell growth and translation through the phosphorylation and activation of components of the translational machinery, such as S6 kinase (S6K) and 4EBP1, an inhibitor of eukaryotic translation initiation factor 4E (eIF4E) activity (reviewed in reference 27). S6K phosphorylates the S6 ribosomal subunit, thereby increasing translation. Mice deficient for S6K1 are small and have small pancreatic beta cells and a correspondingly low level of circulating insulin (45). Mutation of the phosphorylation sites on S6 results in a similar phenotype, with small beta cells and fibroblasts (57). In Drosophila, mutation of S6K again reduces both cell and organism size (42), as does the overexpression of 4EBP (41).Interestingly, while mutation of the TORC1 pathway in mammalian cells reduces cell size by 10 to 15%, ablation of core TORC1 pathway components in Drosophila cells can affect cell size by up to 40% (73). In an attempt to identify novel components of the TORC1 pathway, we undertook an RNA interference (RNAi)-based screen of Drosophila S2 cells. We reasoned that the extreme size phenotypes observed in Drosophila cells upon TORC1 manipulations would facilitate the identification of modulators. In order to increase the likelihood of isolating novel regulators of TOR, we uncoupled TOR activity from many of its known nutritional controls by depleting TSC2 and screened for double-stranded RNAs (dsRNAs) that could reverse the cell size increase elicited by loss of TSC2. Depletion of multiple components of the p38 pathway was found to revert the TSC2 RNAi-induced cell size increase. Furthermore, activation of p38 is necessary and sufficient for the activation of TOR. Strikingly, mutation of components of the stress-activated p38 pathway in Drosophila has a similar phenotype to mutations in the TOR and insulin signaling pathway: a cell-autonomous cell size decrease, reduced body size, and a sensitization to the effects of nutritional stress.     

Distinct requirements of Autophagy-related genes in programmed cell death

Although most programmed cell death (PCD) during animal development occurs by caspase-dependent apoptosis, autophagy-dependent cell death is also important in specific contexts. In previous studies, we established that PCD of the obsolete Drosophila larval midgut tissue is dependent on autophagy and can occur in the absence of the main components of the apoptotic pathway. As autophagy is primarily a survival mechanism in response to stress such as starvation, it is currently unclear if the regulation and mechanism of autophagy as a pro-death pathway is distinct to that as pro-survival. To establish the requirement of the components of the autophagy pathway during cell death, we examined the effect of systematically knocking down components of the autophagy machinery on autophagy induction and timing of midgut PCD. We found that there is a distinct requirement of the individual components of the autophagy pathway in a pro-death context. Furthermore, we show that TORC1 is upstream of autophagy induction in the midgut indicating that while the machinery may be distinct the activation may occur similarly in PCD and during starvation-induced autophagy signalling. Our data reveal that while autophagy initiation occurs similarly in different cellular contexts, there is a tissue/function-specific requirement for the components of the autophagic machinery.There is a fundamental requirement for multicellular organisms to remove excess, detrimental, obsolete and damaged cells by programmed cell death (PCD).^{1, 2} In the majority of cases caspase-dependent apoptosis is the principle pathway of PCD; however, there are other modes of cell death with important context-specific roles, such as autophagy.^{3, 4} Defects in autophagy have significant adverse consequences to normal cellular functions and contribute to the pathogenesis of numerous human diseases. This is particularly evident in cancer where depending on the context autophagy can have tumour-suppressing or -promoting roles. Given the number of clinical trials targeting autophagy in cancer therapy, it will be critically important to understand the context-specific regulation and functions of autophagy.⁵Autophagy is a highly conserved multi-step catabolic process characterised by the encapsulation of part of the cytoplasm inside a double-membrane vesicle called the autophagosome. Autophagosomes then fuse with lysosomes and the components are subsequently degraded by acidic lysosomal hydrolases.⁶ The process of autophagy can be functionally divided into four groups: (1) serine/threonine kinase Atg1 (ULK1 in mammals) complex and its regulators responsible for the induction of autophagy; (2) the class III phosphatidylinositol 3-kinase (PI3K) complex, which involves Atg6 and functions in the nucleation of the autophagosome; (3) the Atg8 and Atg12 conjugation systems, which involves several Autophagy-related (Atg) proteins essential for the expansion of autophagosome; and (4) Atg9 and its associated proteins including Atg2 and Atg18, which aids the recycling of lipid and proteins.⁷ In addition, several of the Atg proteins can function in multiple steps. For example, Atg1 interacts with proteins with different functions (e.g. Atg8, Atg18 and others), suggesting that it is not only required for initiation but also participates in the formation of autophagosomes.⁸ It is yet to be fully established if the context-specific functions of autophagy have distinct requirements for select components of the autophagy pathway.High levels of autophagy are induced in response to stress, such as nutrient deprivation, intracellular stress, high temperature, high culture density, hormones and growth factor deprivation.^{9, 10} The target of rapamycin (TOR) pathway is a central mediator in regulating the response to nutrients and growth signalling. TOR functions in two distinct complexes, with regulatory associated protein of TOR (Raptor) in TOR complex 1 (TORC1) or with rapamycin insensitive companion of TOR (Rictor) in TOR complex 2 (TORC2).^{11, 12, 13, 14, 15} Of these, TORC1 regulates autophagy; in nutrient-rich conditions, TORC1 activity inhibits the Atg1 complex preventing autophagy and cellular stress such as starvation leads to inactivation of TORC1 promoting a dramatic increase in autophagy. TORC2 can also negatively regulate autophagy via the FoxO3 complex in specific context.¹⁶Most direct in vivo evidence for a role of autophagy in cell death has emerged from studies in Drosophila.⁵ Developmentally regulated removal of the Drosophila larval midgut can occur in the absence of canonical apoptosis pathway, whereas inhibiting autophagy delays the process.^{17, 18} Also, inhibition of autophagy leads to delayed degradation of larval salivary glands in Drosophila.¹⁹ Genetic studies have shown that many of the Atg genes known to be involved in starvation-induced autophagy in the Drosophila fat body are also involved in autophagy-dependent degradation of salivary glands and midgut.^{5, 20, 21} However, systematic studies to test whether starvation-induced autophagy and autophagy required for PCD require identical components have not been carried out, and there are some observations suggesting that there may be distinctions. For example, in Atg7-null mutants autophagy is perturbed but the larval–adult midgut transition proceeds normally.²² In addition, a novel Atg7- and Atg3-independent autophagy pathway is required for cell size reduction during midgut removal.²³ Here we show that downregulation of TORC1 activity is required for induction of autophagy during midgut removal. Surprisingly, however, the requirement of part of the autophagy machinery during midgut degradation was found to be distinct to that which is required during autophagy induced by starvation. We report that Atg genes required for autophagy initiation, Atg8a and recycling are all essential for autophagy-dependent midgut removal, whereas other components of the elongation and nucleation steps are not essential.     

Thrombospondin-1 signaling through CD47 inhibits cell cycle progression and induces senescence in endothelial cells

CD47 signaling in endothelial cells has been shown to suppress angiogenesis, but little is known about the link between CD47 and endothelial senescence. Herein, we demonstrate that the thrombospondin-1 (TSP1)-CD47 signaling pathway is a major mechanism for driving endothelial cell senescence. CD47 deficiency in endothelial cells significantly improved their angiogenic function and attenuated their replicative senescence. Lack of CD47 also suppresses activation of cell cycle inhibitors and upregulates the expression of cell cycle promoters, leading to increased cell cycle progression. Furthermore, TSP1 significantly accelerates replicative senescence and associated cell cycle arrest in a CD47-dependent manner. These findings demonstrate that TSP1-CD47 signaling is an important mechanism driving endothelial cell senescence. Thus, TSP1 and CD47 provide attractive molecular targets for treatment of aging-associated cardiovascular dysfunction and diseases involving endothelial dysregulation.Endothelial cell (EC) senescence is accompanied with vascular dysfunction, including arterial stiffening and remodeling,¹ impaired angiogenesis,^{2, 3} reduced endothelial repair capability and increased incidence of cardiovascular disease.^{4, 5, 6} Cellular senescence can occur in vivo or in vitro in response to various stressors,^{7, 8, 9, 10} leading to suppression of cell proliferation. EC senescence has been reported to contribute to the pathogenesis of age-associated vascular diseases, such as atherosclerosis.¹¹ Thus, further understanding the mechanisms of EC senescence may help to identify effective targets for antisenescence therapy and treatment aging-associated cardiovascular disorders.Previous studies have shown that the secreted matricellular protein thrombospondin-1 (TSP1) is as potent inhibitor of angiogenesis¹² and its antiangiogenic activity is mediated by its receptors, CD36^{13, 14} and CD47.^{15, 16} CD47 is a ubiquitously expressed transmembrane protein that serves as a ligand for signal regulatory protein-α and is a signaling receptor of TSP1. The TSP1-CD47 pathway has an important role in several fundamental cellular functions, including proliferation, apoptosis, inflammation and atherosclerotic response.¹⁷ Ligation of CD47 by TSP1 has been shown to inhibit nitric oxide (NO)/cGMP signaling in vascular cells, leading to suppression of angiogenic responses.¹⁶ Recently, it was reported that lack of CD47 expression in ECs may enable these cells to spontaneously gain characteristics of embryonic stem cells.¹⁸ However, the potential role of CD47 in regulation of EC senescence has not been well explored. The present study was initiated to determine the role and mechanisms of TSP1-CD47 signaling pathway in regulating cell cycle progression and replicative senescence of ECs.     

The TORC1 inhibitors Nprl2 and Nprl3 mediate an adaptive response to amino-acid starvation in Drosophila

Target of rapamycin complex 1 (TORC1) is a master regulator of metabolism in eukaryotes that integrates information from multiple upstream signaling pathways. In yeast, the Nitrogen permease regulators 2 and 3 (Npr2 and Npr3) mediate an essential response to amino-acid limitation upstream of TORC1. In mammals, the Npr2 ortholog, Nprl2, is a putative tumor suppressor gene that inhibits cell growth and enhances sensitivity to numerous anticancer drugs including cisplatin. However, the precise role of Nprl2 and Nprl3 in the regulation of metabolism in metazoans remains poorly defined. Here we demonstrate that the central importance of Nprl2 and Nprl3 in the response to amino-acid starvation has been conserved from single celled to multicellular animals. We find that in Drosophila Nprl2 and Nprl3 physically interact and are targeted to lysosomes and autolysosomes. Using oogenesis as a model system, we show that Nprl2 and Nprl3 inhibit TORC1 signaling in the female germline in response to amino-acid starvation. Moreover, the inhibition TORC1 by Nprl2/3 is critical to the preservation of female fertility during times of protein scarcity. In young egg chambers the failure to downregulate TORC1 in response to amino-acid limitation triggers apoptosis. Thus, our data suggest the presence of a metabolic checkpoint that initiates a cell death program when TORC1 activity remains inappropriately high during periods of amino-acid and/or nutrient scarcity in oogenesis. Finally, we demonstrate that Nprl2/3 work in concert with the TORC1 inhibitors Tsc1/2 to fine tune TORC1 activity during oogenesis and that Tsc1 is a critical downstream effector of Akt1 in the female germline.In Drosophila, egg production is an energy intensive process that occurs continuously throughout the lifetime of the female. Thus, to ensure that energy reserves remain sufficient to support the viability of the female and her progeny during times of food scarcity, Drosophila oogenesis is highly sensitive to nutritional inputs.^{1, 2, 3} The Drosophila ovary is comprised of approximately 15 ovarioles that contain strings of egg chambers in successively older stages of development.⁴ Each egg chamber contains a 16-cell interconnected germline syncytium comprised of 15 polyploid nurse cells and a single oocyte. Each ovarian cyst is surrounded by a somatically derived monolayer of cells called follicle cells. At the tip of the ovariole lies the germarium that contains both germline and somatic stem cells, allowing for the continuous production of new egg chambers throughout the life of the female. In mid-oogenesis, egg chambers begin the energy intensive process of yolk uptake, known as vitellogenesis, which is followed by a short period of rapid growth in late oogenesis prior to the eggs being laid.Faced with insufficient protein, the Drosophila ovary initiates a complex series of adaptive responses.^{2, 3, 5, 6, 7, 8} Egg chambers in mid-oogenesis (stages 8–9), which have begun vitellogenesis, undergo apoptosis as do a fraction of early ovarian cysts before their packing by follicle cells in the germarium.² In contrast, young egg chambers (stages 2–7) remain intact, but sharply reduce their growth rates and rearrange their cytoskeletal network.^{2, 5} After shutting down oogenesis during a period of starvation, these young dormant egg chambers can be used to rapidly restart egg production when nutrients are reintroduced.^{2, 5} Thus, protecting young egg chambers from the ravages of starvation is important for maximizing fecundity in an environment with uneven food availability.Recent evidence implicates the Target of Rapamycin Complex 1 (TORC1) in the regulation of growth and nutritional response during Drosophila oogenesis.^{6, 9, 10, 11} TORC1 contains the nutrient sensitive kinase Target of Rapamycin (TOR) and regulates cell growth and metabolism in response to multiple inputs including amino-acid availability and intracellular energy status.^{12, 13, 14, 15, 16} In the presence of sufficient nutrients and appropriate growth signals, the Ragulator and the Rag GTPases target TORC1 to lysosomal membranes where it comes in contact with its activator, the small GTPase Rheb.^{17, 18, 19} The downregulation of TORC1 activity under conditions of nutrient stress triggers catabolic metabolism and autophagy.²⁰ Autophagy involves the lysosomal degradation of cellular components to ensure adequate nutrients to support cellular survival during times of nutrient stress. Thus, the ability to downregulate TORC1 activity in response to environmental conditions is critical to cell survival.In both budding and fission yeast, Npr2 and Npr3 inhibit TORC1 activity in response to amino-acid scarcity.^{21, 22} The downregulation of TORC1 by Npr2 and Npr3 is essential to the adaptive response that allows these single-cell eukaryotes to grow on a poor nitrogen source. Recent evidence indicates that Npr2 and Npr3, and their respective mammalian orthologs Nitrogen permease regulator like 2 (Nprl2) and Nitrogen permease regulator like 3 (Nprl3), function as GTPase-activating proteins (GAP) that inhibit TORC1 activity by inactivating the Rag GTPases.^{23, 24} As is observed with other genes that inhibit TORC1 kinase activity, Npr2/Nprl2 is a putative tumor suppressor gene that is deleted in multiple cancers and cancer cell lines.^{24, 25} Yet, while Nprl2/3 have been shown to downregulate TORC1 activity in response to amino-acid starvation in tissue culture cells,²⁴ the precise physiological requirement for Nprl2 and Nprl3 in the response to nutrient stress remains undefined in metazoans.Here we demonstrate that in Drosophila Nprl2 and Nprl3 mediate an adaptive response to amino-acid scarcity that is essential to the maintenance of female fertility. We find that in nprl2 and nprl3 germline knockdowns, young egg chambers fail to adapt to amino-acid scarcity and undergo apoptosis. Feeding females the TORC1 inhibitor rapamycin prevents this apoptotic response. Thus, in Drosophila the failure to downregulate TORC1 activity during periods of nutrient stress triggers programmed cell death in early oogenesis. Finally, we demonstrate that the two TORC1 inhibitory complexes Nprl2/3 and Tsc1/2 both contribute to the regulation of TORC1 activity in the female germline.     

HdmX overexpression inhibits oncogene induced cellular senescence

Cellular senescence is an irreversible state of terminal growth arrest that requires functional p53. Acting to block tumor formation, induction of senescence has also been demonstrated to contribute to tumor clearance via the immune system following p53 reactivation.^1,2 the Hdm2-antagonist, Nutlin-3a, has been shown to reactivate p53 and induce a quiescent state in various cancer cell lines,^3,4 similar to the G₁ arrest observed upon RNAi targeting of Hdm2 in MCF7 breast cancer.⁵ In the present study we show that HdmX, a negative regulator of p53, impacts the senescence pathway. Specifically, overexpression of HdmX blocks Ras mediated senescence in primary human fibroblasts. the interaction of HdmX with p53 and the re-localization of HdmX to the nucleus through Hdm2 association appear to be required for this activity. Furthermore, inhibiting HdmX in prostate adenocarcinoma cells expressing wild-type p53, mutant Ras and high levels of HdmX-induced cellular senescence as measured by an increase in irreversible β-galactosidase staining. Together these results suggest that HdmX overexpression may contribute to tumor formation by blocking senescence and that targeting HdmX may represent an attractive anti-cancer therapeutic approach.Key words: HdmX, p53, Ras, senescence, LNCaP     

Molecular Architecture and Function of the SEA Complex,a Modulator of the TORC1 Pathway

The TORC1 signaling pathway plays a major role in the control of cell growth and response to stress. Here we demonstrate that the SEA complex physically interacts with TORC1 and is an important regulator of its activity. During nitrogen starvation, deletions of SEA complex components lead to Tor1 kinase delocalization, defects in autophagy, and vacuolar fragmentation. TORC1 inactivation, via nitrogen deprivation or rapamycin treatment, changes cellular levels of SEA complex members. We used affinity purification and chemical cross-linking to generate the data for an integrative structure modeling approach, which produced a well-defined molecular architecture of the SEA complex and showed that the SEA complex comprises two regions that are structurally and functionally distinct. The SEA complex emerges as a platform that can coordinate both structural and enzymatic activities necessary for the effective functioning of the TORC1 pathway.The highly conserved Target of Rapamycin Complex 1 (TORC1)¹ controls eukaryotic cell growth and cellular responses to a variety of signals, including nutrients, hormones, and stresses (1, 2). In a nutrient-rich environment, TORC1 promotes anabolic processes including ribosome biogenesis and translation. Nutrient limitation or treatment with rapamycin inhibits the Tor1 kinase and initiates autophagy, a catabolic process that mediates the degradation and recycling of cytoplasmic components. However, the nutrient-sensing function of TORC1 is not fully understood, and the mechanisms of TORC1 modulation by amino acid and nitrogen availability are not yet clear.In the yeast Saccharomyces cerevisiae, the TOR1 complex is composed of four subunits (Tor1, Kog1, Tco89, and Lst8) and is localized to the vacuole membrane. Amino acid levels are signaled to TORC1 (at least partially) via the EGO complex (Ragulator-Rag in mammals), which consists of Ego1, Ego3, Gtr1 (RagA/RagB), and Gtr2 (RagC/RagD) (3–6). The small GTPases Gtr1 and Gtr2 function as heterodimers and in their active form exist as the Gtr1-GTP/Gtr2-GDP complex. Amino acid sensing via the EGO complex involves the conserved vacuolar membrane protein Vam6, a member of the HOPS tethering complex. Vam6 is a GDP exchange factor that regulates the nucleotide-binding status of Gtr1 (6). At the same time, the GTP-bound state of Gtr1 is controlled by a leucyl t-RNA synthetase (7). In mammals, amino acids promote interaction of Ragulator-Rag with mTORC1 and its translocation to the lysosomal membrane (3, 4). Ragulator interacts with the v-ATPase complex at the lysosomal membrane (8), and leucyl t-RNA synthetase binds to RagD to activate mTORC1 (9).A genome-wide screen for TORC1 regulators in yeast identified two proteins, Npr2 and Npr3, as proteins that mediate amino acid starvation signal to TORC1 (10). Npr2 and Npr3 are both members of the SEA complex that we discovered recently (11–13). Besides Npr2 and Npr3, the SEA complex also contains four previously uncharacterized proteins (Sea1–Sea4) and two proteins also found in the nuclear pore complex, Seh1 and Sec13, the latter of which is additionally a component of the endoplasmic-reticulum-associated COPII coated vesicle. However, the SEA complex localizes to the vacuole membrane, and not to the nuclear pore complex or endoplasmic reticulum.The Sea proteins contain numerous structural elements present in intracellular structural trafficking complexes (11). For example, proteins Sea2–Sea4 are predicted to possess β-propeller/α-solenoid folds and contain RING domains, architectural combinations characteristic to protein complexes that form coats around membranes (e.g. coated vesicles, nuclear pore complexes) or participate in membrane tethering (e.g. HOPS, CORVET complexes). Npr2 and Npr3 possess a longin domain, found in many guanine nucleotide exchange factors (GEFs) (14–16), and Sea1/Iml1 is a GTPase activating protein (GAP) for Gtr1 (17). These structural characteristics, taken together with functional data, indicate a role for the SEA complex in intracellular trafficking, amino acid biogenesis, regulation of the TORC1 pathway, and autophagy (11–13, 17–20). A mammalian analog of the SEA complex, termed GATOR1/GATOR2, has recently been identified (21). GATORS are localized at the lysosome membrane and serve as upstream regulators of mammalian TORC1 via GATOR1 GAP activity toward RagA and RagB (21).In this study, we characterized the structural and functional organization of the yeast SEA complex. We present here a well-defined molecular architecture of the SEA complex obtained via an integrative modeling approach based on a variety of biochemical data. The structure reveals the relative positions and orientations of two SEA subcomplexes, Sea1/Npr2/Npr3 (or SEACIT (19)) and Sea2/Sea3/Sea4/Sec13/Seh1 (or SEACAT (19)), and identifies the Sea3/Sec13 dimer as a major interacting hub within the complex. We describe how the SEA complex interacts physically with TORC1 and the vacuole and is required for the relocalization of Tor1, and how every member of the Sea1/Npr2/Npr3 subcomplex is required for general autophagy.