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Biomolecules
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TOR Signaling Pathway
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TOR Signaling Pathway

A special issue of Biomolecules (ISSN 2218-273X).

Deadline for manuscript submissions: closed (31 May 2017) | Viewed by 111044

Special Issue Editors

Prof. Kazuhiro Shiozaki

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Guest Editor
1. Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma 630-0192, Nara, Japan
2. Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA
Interests: cellular signal transduction pathways in yeast and humans
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Ted Powers

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Guest Editor
Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA
Interests: cellular responses to growth and stress signals in budding yeast
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Among the numerous protein kinases that play key roles in signal transduction pathways of eukaryotic cells, Target of Rapamycin (TOR) stands out because of its unique characteristics. TOR is a serine/threonine-specific protein kinase, but it is structurally related to lipid kinases, such as PI3K. It forms at least two distinct high-molecular weight complexes, known as TOR complex 1 (TORC1) and TOR complex 2 (TORC2), with multiple regulatory subunits that determine signal inputs, substrate specificities, and intracellular localization. Rapamycin and other inhibitors of TOR affect diverse aspects of cellular physiology, such as growth, proliferation, as well as catabolic and anabolic processes, suggesting TOR functions at pivotal nodes of cellular signaling networks.

We invite contributions from researchers who have been exploring distinct aspects of this unique protein kinase through studies in diverse model organisms. Both original research articles and reviews are welcome. Together, these studies will contribute to an integrated view of the emerging TOR network, implicated in cancers, metabolic diseases and aging in humans.

Prof. Kazuhiro Shiozaki
Prof. Ted Powers
Guest Editors

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Keywords

  • Target of Rapamycin
  • TOR
  • mTOR
  • rapamycin

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Related Special Issue

Published Papers (11 papers)

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19 pages, 11919 KiB  
Article
Redesigning TOR Kinase to Explore the Structural Basis for TORC1 and TORC2 Assembly
by Andrew Hill, Brad Niles, Andrew Cuyegkeng and Ted Powers
Biomolecules 2018, 8(2), 36; https://doi.org/10.3390/biom8020036 - 1 Jun 2018
Cited by 10 | Viewed by 5591
Abstract
TOR is a serine/threonine protein kinase that assembles into distinct TOR Complexes 1 and 2 (TORC1 or TORC2) to regulate cell growth. In mammalian cells, a single mTOR incorporates stably into mTORC1 and mTORC2. By contrast, in Saccharomyces cerevisiae, two highly similar [...] Read more.
TOR is a serine/threonine protein kinase that assembles into distinct TOR Complexes 1 and 2 (TORC1 or TORC2) to regulate cell growth. In mammalian cells, a single mTOR incorporates stably into mTORC1 and mTORC2. By contrast, in Saccharomyces cerevisiae, two highly similar Tor1 and Tor2 proteins exist, where Tor1 assembles exclusively into TORC1 and Tor2 assembles preferentially into TORC2. To gain insight into TOR complex assembly, we used this bifurcation in yeast to identify structural elements within Tor1 and Tor2 that govern their complex specificity. We have identified a concise region of ~500 amino acids within the N-terminus of Tor2, which we term the Major Assembly Specificity (MAS) domain, that is sufficient to confer significant TORC2 activity when placed into an otherwise Tor1 protein. Consistently, introduction of the corresponding MAS domain from Tor1 into an otherwise Tor2 is sufficient to confer stable association with TORC1-specific components. Remarkably, much like mTOR, this latter chimera also retains stable interactions with TORC2 components, indicating that determinants throughout Tor1/Tor2 contribute to complex specificity. Our findings are in excellent agreement with recent ultrastructural studies of TORC1 and TORC2, where the MAS domain is involved in quaternary interactions important for complex formation and/or stability. Full article
(This article belongs to the Special Issue TOR Signaling Pathway)
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Review

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14 pages, 1877 KiB  
Review
Regulation of Cellular Metabolism through Phase Separation of Enzymes
by Manoël Prouteau and Robbie Loewith
Biomolecules 2018, 8(4), 160; https://doi.org/10.3390/biom8040160 - 3 Dec 2018
Cited by 61 | Viewed by 8577
Abstract
Metabolism is the sum of the life-giving chemical processes that occur within a cell. Proper regulation of these processes is essential for all organisms to thrive and prosper. When external factors are too extreme, or if internal regulation is corrupted through genetic or [...] Read more.
Metabolism is the sum of the life-giving chemical processes that occur within a cell. Proper regulation of these processes is essential for all organisms to thrive and prosper. When external factors are too extreme, or if internal regulation is corrupted through genetic or epigenetic changes, metabolic homeostasis is no longer achievable and diseases such as metabolic syndrome or cancer, aging, and, ultimately, death ensue. Metabolic reactions are catalyzed by proteins, and the in vitro kinetic properties of these enzymes have been studied by biochemists for many decades. These efforts led to the appreciation that enzyme activities can be acutely regulated and that this regulation is critical to metabolic homeostasis. Regulation can be mediated through allosteric interactions with metabolites themselves or via post-translational modifications triggered by intracellular signal transduction pathways. More recently, enzyme regulation has attracted the attention of cell biologists who noticed that change in growth conditions often triggers the condensation of diffusely localized enzymes into one or more discrete foci, easily visible by light microscopy. This reorganization from a soluble to a condensed state is best described as a phase separation. As summarized in this review, stimulus-induced phase separation has now been observed for dozens of enzymes suggesting that this could represent a widespread mode of activity regulation, rather than, or in addition to, a storage form of temporarily superfluous enzymes. Building on our recent structure determination of TOROIDs (TORc1 Organized in Inhibited Domain), the condensate formed by the protein kinase Target Of Rapamycin Complex 1 (TORC1), we will highlight that the molecular organization of enzyme condensates can vary dramatically and that future work aimed at the structural characterization of enzyme condensates will be critical to understand how phase separation regulates enzyme activity and consequently metabolic homeostasis. This information may ultimately facilitate the design of strategies to target the assembly or disassembly of specific enzymes condensates as a therapeutic approach to restore metabolic homeostasis in certain diseases. Full article
(This article belongs to the Special Issue TOR Signaling Pathway)
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14 pages, 1055 KiB  
Review
PIM Kinases and Their Relevance to the PI3K/AKT/mTOR Pathway in the Regulation of Ovarian Cancer
by Aziz Ur Rehman Aziz, Sumbal Farid, Kairong Qin, Hanqin Wang and Bo Liu
Biomolecules 2018, 8(1), 7; https://doi.org/10.3390/biom8010007 - 4 Feb 2018
Cited by 66 | Viewed by 14130
Abstract
Ovarian cancer is a medical term that includes a number of tumors with different molecular biology, phenotypes, tumor progression, etiology, and even different diagnosis. Some specific treatments are required to address this heterogeneity of ovarian cancer, thus molecular characterization may provide an important [...] Read more.
Ovarian cancer is a medical term that includes a number of tumors with different molecular biology, phenotypes, tumor progression, etiology, and even different diagnosis. Some specific treatments are required to address this heterogeneity of ovarian cancer, thus molecular characterization may provide an important tool for this purpose. On a molecular level, proviral-integration site for Moloney-murine leukemia virus (PIM) kinases are over expressed in ovarian cancer and play a vital role in the regulation of different proteins responsible for this tumorigenesis. Likewise, the phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT)/mammalian target of rapamycin (mTOR) pathway is also a central regulator of the ovarian cancer. Interestingly, recent research has linked the PIM kinases to the PI3K/AKT/mTOR pathway in several types of cancers, but their connection in ovarian cancer has not been studied yet. Once the exact relationship of PIM kinases with the PI3K/AKT/mTOR pathway is acquired in ovarian cancer, it will hopefully provide effective treatments on a molecular level. This review mainly focuses on the role of PIM kinases in ovarian cancer and their interactions with proteins involved in its progression. In addition, this review suggests a connection between the PIM kinases and the PI3K/AKT/mTOR pathway and their parallel mechanism in the regulation of ovarian cancer. Full article
(This article belongs to the Special Issue TOR Signaling Pathway)
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1255 KiB  
Review
Evolutionary Conservation of the Components in the TOR Signaling Pathways
by Hisashi Tatebe and Kazuhiro Shiozaki
Biomolecules 2017, 7(4), 77; https://doi.org/10.3390/biom7040077 - 1 Nov 2017
Cited by 84 | Viewed by 9302
Abstract
Target of rapamycin (TOR) is an evolutionarily conserved protein kinase that controls multiple cellular processes upon various intracellular and extracellular stimuli. Since its first discovery, extensive studies have been conducted both in yeast and animal species including humans. Those studies have revealed that [...] Read more.
Target of rapamycin (TOR) is an evolutionarily conserved protein kinase that controls multiple cellular processes upon various intracellular and extracellular stimuli. Since its first discovery, extensive studies have been conducted both in yeast and animal species including humans. Those studies have revealed that TOR forms two structurally and physiologically distinct protein complexes; TOR complex 1 (TORC1) is ubiquitous among eukaryotes including animals, yeast, protozoa, and plants, while TOR complex 2 (TORC2) is conserved in diverse eukaryotic species other than plants. The studies have also identified two crucial regulators of mammalian TORC1 (mTORC1), Ras homolog enriched in brain (RHEB) and RAG GTPases. Of these, RAG regulates TORC1 in yeast as well and is conserved among eukaryotes with the green algae and land plants as apparent exceptions. RHEB is present in various eukaryotes but sporadically missing in multiple taxa. RHEB, in the budding yeast Saccharomyces cerevisiae, appears to be extremely divergent with concomitant loss of its function as a TORC1 regulator. In this review, we summarize the evolutionarily conserved functions of the key regulatory subunits of TORC1 and TORC2, namely RAPTOR, RICTOR, and SIN1. We also delve into the evolutionary conservation of RHEB and RAG and discuss the conserved roles of these GTPases in regulating TORC1. Full article
(This article belongs to the Special Issue TOR Signaling Pathway)
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5755 KiB  
Review
The TORC2‐Dependent Signaling Network in the Yeast Saccharomyces cerevisiae
by Françoise M. Roelants, Kristin L. Leskoske, Maria Nieves Martinez Marshall, Melissa N. Locke and Jeremy Thorner
Biomolecules 2017, 7(3), 66; https://doi.org/10.3390/biom7030066 - 5 Sep 2017
Cited by 59 | Viewed by 10042
Abstract
To grow, eukaryotic cells must expand by inserting glycerolipids, sphingolipids, sterols, and proteins into their plasma membrane, and maintain the proper levels and bilayer distribution. A fungal cell must coordinate growth with enlargement of its cell wall. In Saccharomyces cerevisiae, a plasma [...] Read more.
To grow, eukaryotic cells must expand by inserting glycerolipids, sphingolipids, sterols, and proteins into their plasma membrane, and maintain the proper levels and bilayer distribution. A fungal cell must coordinate growth with enlargement of its cell wall. In Saccharomyces cerevisiae, a plasma membrane‐localized protein kinase complex, Target of Rapamicin (TOR) complex‐2 (TORC2) (mammalian ortholog is mTORC2), serves as a sensor and masterregulator of these plasma membrane‐ and cell wall‐associated events by directly phosphorylating and thereby stimulating the activity of two types of effector protein kinases: Ypk1 (mammalian ortholog is SGK1), along with a paralog (Ypk2); and, Pkc1 (mammalian ortholog is PKN2/PRK2). Ypk1 is a central regulator of pathways and processes required for plasma membrane lipid and protein homeostasis, and requires phosphorylation on its T‐loop by eisosome‐associated protein kinase Pkh1 (mammalian ortholog is PDK1) and a paralog (Pkh2). For cell survival under various stresses, Ypk1 function requires TORC2‐mediated phosphorylation at multiple sites near its C terminus. Pkc1 controls diverse processes, especially cell wall synthesis and integrity. Pkc1 is also regulated by Pkh1‐ and TORC2‐dependent phosphorylation, but, in addition, by interaction with Rho1‐GTP and lipids phosphatidylserine (PtdSer) and diacylglycerol (DAG). We also describe here what is currently known about the downstream substrates modulated by Ypk1‐mediated and Pkc1‐mediated phosphorylation. Full article
(This article belongs to the Special Issue TOR Signaling Pathway)
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804 KiB  
Review
Coupling TOR to the Cell Cycle by the Greatwall–Endosulfine–PP2A-B55 Pathway
by Livia Pérez-Hidalgo and Sergio Moreno
Biomolecules 2017, 7(3), 59; https://doi.org/10.3390/biom7030059 - 4 Aug 2017
Cited by 22 | Viewed by 7438
Abstract
Cell growth and division are two processes tightly coupled in proliferating cells. While Target of Rapamycin (TOR) is the master regulator of growth, the cell cycle is dictated by the activity of the cyclin-dependent kinases (CDKs). A long-standing question in cell biology is [...] Read more.
Cell growth and division are two processes tightly coupled in proliferating cells. While Target of Rapamycin (TOR) is the master regulator of growth, the cell cycle is dictated by the activity of the cyclin-dependent kinases (CDKs). A long-standing question in cell biology is how these processes may be connected. Recent work has highlighted that regulating the phosphatases that revert CDK phosphorylations is as important as regulating the CDKs for cell cycle progression. At mitosis, maintaining a low level of protein phosphatase 2A (PP2A)-B55 activity is essential for CDK substrates to achieve the correct level of phosphorylation. The conserved Greatwall–Endosulfine pathway has been shown to be required for PP2A-B55 inhibition at mitosis in yeasts and multicellular organisms. Interestingly, in yeasts, the Greatwall–Endosulfine pathway is negatively regulated by TOR Complex 1 (TORC1). Moreover, Greatwall–Endosulfine activation upon TORC1 inhibition has been shown to regulate the progression of the cell cycle at different points: the G1 phase in budding yeast, the G2/M transition and the differentiation response in fission yeast, and the entry into quiescence in both budding and fission yeasts. In this review, we discuss the recent findings on how the Greatwall–Endosulfine pathway may provide a connection between cell growth and the cell cycle machinery. Full article
(This article belongs to the Special Issue TOR Signaling Pathway)
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508 KiB  
Review
The TOR Signaling Network in the Model Unicellular Green Alga Chlamydomonas reinhardtii
by María Esther Pérez-Pérez, Inmaculada Couso and José L. Crespo
Biomolecules 2017, 7(3), 54; https://doi.org/10.3390/biom7030054 - 12 Jul 2017
Cited by 52 | Viewed by 10010
Abstract
Cell growth is tightly coupled to nutrient availability. The target of rapamycin (TOR) kinase transmits nutritional and environmental cues to the cellular growth machinery. TOR functions in two distinct multiprotein complexes, termed TOR complex 1 (TORC1) and TOR complex 2 (TORC2). While the [...] Read more.
Cell growth is tightly coupled to nutrient availability. The target of rapamycin (TOR) kinase transmits nutritional and environmental cues to the cellular growth machinery. TOR functions in two distinct multiprotein complexes, termed TOR complex 1 (TORC1) and TOR complex 2 (TORC2). While the structure and functions of TORC1 are highly conserved in all eukaryotes, including algae and plants, TORC2 core proteins seem to be missing in photosynthetic organisms. TORC1 controls cell growth by promoting anabolic processes, including protein synthesis and ribosome biogenesis, and inhibiting catabolic processes such as autophagy. Recent studies identified rapamycin-sensitive TORC1 signaling regulating cell growth, autophagy, lipid metabolism, and central metabolic pathways in the model unicellular green alga Chlamydomonas reinhardtii. The central role that microalgae play in global biomass production, together with the high biotechnological potential of these organisms in biofuel production, has drawn attention to the study of proteins that regulate cell growth such as the TOR kinase. In this review we discuss the recent progress on TOR signaling in algae. Full article
(This article belongs to the Special Issue TOR Signaling Pathway)
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878 KiB  
Review
Regulation of Autophagy through TORC1 and mTORC1
by Takeshi Noda
Biomolecules 2017, 7(3), 52; https://doi.org/10.3390/biom7030052 - 7 Jul 2017
Cited by 112 | Viewed by 11092
Abstract
Autophagy is an intracellular protein-degradation process that is conserved across eukaryotes including yeast and humans. Under nutrient starvation conditions, intracellular proteins are transported to lysosomes and vacuoles via membranous structures known as autophagosomes, and are degraded. The various steps of autophagy are regulated [...] Read more.
Autophagy is an intracellular protein-degradation process that is conserved across eukaryotes including yeast and humans. Under nutrient starvation conditions, intracellular proteins are transported to lysosomes and vacuoles via membranous structures known as autophagosomes, and are degraded. The various steps of autophagy are regulated by the target of rapamycin complex 1 (TORC1/mTORC1). In this review, a history of this regulation and recent advances in such regulation both in yeast and mammals will be discussed. Recently, the mechanism of autophagy initiation in yeast has been deduced. The autophagy-related gene 13 (Atg13) and the unc-51 like autophagy activating kinase 1 (Ulk1) are the most crucial substrates of TORC1 in autophagy, and by its dephosphorylation, autophagosome formation is initiated. Phosphorylation/dephosphorylation of Atg13 is regulated spatially inside the cell. Another TORC1-dependent regulation lies in the expression of autophagy genes and vacuolar/lysosomal hydrolases. Several transcriptional and post-transcriptional regulations are controlled by TORC1, which affects autophagy activity in yeast and mammals. Full article
(This article belongs to the Special Issue TOR Signaling Pathway)
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581 KiB  
Review
Lysosomal Regulation of mTORC1 by Amino Acids in Mammalian Cells
by Yao Yao, Edith Jones and Ken Inoki
Biomolecules 2017, 7(3), 51; https://doi.org/10.3390/biom7030051 - 7 Jul 2017
Cited by 52 | Viewed by 13549
Abstract
The mechanistic target of rapamycin complex 1 (mTORC1) is a master regulator of cell growth in eukaryotic cells. The active mTORC1 promotes cellular anabolic processes including protein, pyrimidine, and lipid biosynthesis, and inhibits catabolic processes such as autophagy. Consistent with its growth-promoting functions, [...] Read more.
The mechanistic target of rapamycin complex 1 (mTORC1) is a master regulator of cell growth in eukaryotic cells. The active mTORC1 promotes cellular anabolic processes including protein, pyrimidine, and lipid biosynthesis, and inhibits catabolic processes such as autophagy. Consistent with its growth-promoting functions, hyper-activation of mTORC1 signaling is one of the important pathomechanisms underlying major human health problems including diabetes, neurodegenerative disorders, and cancer. The mTORC1 receives multiple upstream signals such as an abundance of amino acids and growth factors, thus it regulates a wide range of downstream events relevant to cell growth and proliferation control. The regulation of mTORC1 by amino acids is a fast-evolving field with its detailed mechanisms currently being revealed as the precise picture emerges. In this review, we summarize recent progress with respect to biochemical and biological findings in the regulation of mTORC1 signaling on the lysosomal membrane by amino acids. Full article
(This article belongs to the Special Issue TOR Signaling Pathway)
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1362 KiB  
Review
TORC1-Dependent Phosphorylation Targets in Fission Yeast
by Yoko Otsubo, Akio Nakashima, Masayuki Yamamoto and Akira Yamashita
Biomolecules 2017, 7(3), 50; https://doi.org/10.3390/biom7030050 - 3 Jul 2017
Cited by 43 | Viewed by 9736
Abstract
Target of rapamycin (TOR) kinase controls cell metabolism and growth in response to environmental cues such as nutrients, growth factors, and stress. TOR kinase is widely conserved across eukaryotes. As in other organisms, the fission yeast Schizosaccharomyces pombe has two types of TOR [...] Read more.
Target of rapamycin (TOR) kinase controls cell metabolism and growth in response to environmental cues such as nutrients, growth factors, and stress. TOR kinase is widely conserved across eukaryotes. As in other organisms, the fission yeast Schizosaccharomyces pombe has two types of TOR complex, namely TOR complex 1 (TORC1) and TORC2. It is interesting that the two TOR complexes in S. pombe have opposite roles in sexual differentiation, which is induced by nutrient starvation. TORC1, which contains Tor2 as a catalytic subunit, promotes vegetative growth and represses sexual differentiation in nutrient-rich conditions, while TORC2 is required for the initiation of sexual differentiation. Multiple targets of TORC1 have been identified. Some of these, such as S6 kinase and an autophagy regulator Atg13, are known targets in other organisms. In addition, there is a novel group of TORC1 targets involved in the regulation of sexual differentiation. Here, we review recent findings on phosphorylation targets of TORC1 in S. pombe. Furthermore, we briefly report a novel S. pombe target of TORC1. Full article
(This article belongs to the Special Issue TOR Signaling Pathway)
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2689 KiB  
Review
The Architecture of the Rag GTPase Signaling Network
by Raffaele Nicastro, Alessandro Sardu, Nicolas Panchaud and Claudio De Virgilio
Biomolecules 2017, 7(3), 48; https://doi.org/10.3390/biom7030048 - 30 Jun 2017
Cited by 54 | Viewed by 9892
Abstract
The evolutionarily conserved target of rapamycin complex 1 (TORC1) couples an array of intra- and extracellular stimuli to cell growth, proliferation and metabolism, and its deregulation is associated with various human pathologies such as immunodeficiency, epilepsy, and cancer. Among the diverse stimuli impinging [...] Read more.
The evolutionarily conserved target of rapamycin complex 1 (TORC1) couples an array of intra- and extracellular stimuli to cell growth, proliferation and metabolism, and its deregulation is associated with various human pathologies such as immunodeficiency, epilepsy, and cancer. Among the diverse stimuli impinging on TORC1, amino acids represent essential input signals, but how they control TORC1 has long remained a mystery. The recent discovery of the Rag GTPases, which assemble as heterodimeric complexes on vacuolar/lysosomal membranes, as central elements of an amino acid signaling network upstream of TORC1 in yeast, flies, and mammalian cells represented a breakthrough in this field. Here, we review the architecture of the Rag GTPase signaling network with a special focus on structural aspects of the Rag GTPases and their regulators in yeast and highlight both the evolutionary conservation and divergence of the mechanisms that control Rag GTPases. Full article
(This article belongs to the Special Issue TOR Signaling Pathway)
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