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Morea V, Angelucci F, Bellelli A. Is allostery a fuzzy concept? FEBS Open Bio 2024; 14:1040-1056. [PMID: 38783588 PMCID: PMC11216940 DOI: 10.1002/2211-5463.13794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/30/2024] [Accepted: 03/11/2024] [Indexed: 05/25/2024] Open
Abstract
Allostery is an important property of biological macromolecules which regulates diverse biological functions such as catalysis, signal transduction, transport, and molecular recognition. However, the concept was expressed using two different definitions by J. Monod and, over time, more have been added by different authors, making it fuzzy. Here, we reviewed the different meanings of allostery in the current literature and found that it has been used to indicate that the function of a protein is regulated by heterotropic ligands, and/or that the binding of ligands and substrates presents homotropic positive or negative cooperativity, whatever the hypothesized or demonstrated reaction mechanism might be. Thus, proteins defined to be allosteric include not only those that obey the two-state concerted model, but also those that obey different reaction mechanisms such as ligand-induced fit, possibly coupled to sequential structure changes, and ligand-linked dissociation-association. Since each reaction mechanism requires its own mathematical description and is defined by it, there are many possible 'allosteries'. This lack of clarity is made even fuzzier by the fact that the reaction mechanism is often assigned imprecisely and/or implicitly in the absence of the necessary experimental evidence. In this review, we examine a list of proteins that have been defined to be allosteric and attempt to assign a reaction mechanism to as many as possible.
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Affiliation(s)
- Veronica Morea
- Institute of Molecular Biology and Pathology, CNRRomeItaly
| | - Francesco Angelucci
- Department of Life, Health, and Environmental SciencesUniversity of L'AquilaItaly
| | - Andrea Bellelli
- Department of Biochemical Sciences “A. Rossi Fanelli”Sapienza University of RomeItaly
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2
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Chen N, Wang X, Guo Y, Zhao M, Cao B, Zhan B, Li Y, Zhou T, Zhu F, Guo C, Shi Y, Wang Q, Zhang L, Li Y. IL-37d suppresses Rheb-mTORC1 axis independently of TCS2 to alleviate alcoholic liver disease. Commun Biol 2024; 7:756. [PMID: 38907105 PMCID: PMC11192940 DOI: 10.1038/s42003-024-06427-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 06/07/2024] [Indexed: 06/23/2024] Open
Abstract
Tuberous sclerosis complex 2 (TSC2) crucially suppresses Rheb activity to prevent mTORC1 activation. However, mutations in TSC genes lead to mTORC1 overactivation, thereby causing various developmental disorders and cancer. Therefore, the discovery of novel Rheb inhibitors is vital to prevent mTOR overactivation. Here, we reveals that the anti-inflammatory cytokine IL-37d can bind to lysosomal Rheb and suppress its activity independent of TSC2, thereby preventing mTORC1 activation. The binding of IL-37d to Rheb switch-II subregion destabilizes the Rheb-mTOR and mTOR-S6K interactions, further halting mTORC1 signaling. Unlike TSC2, IL-37d is reduced under ethanol stimulation, which results in mitigating the suppression of lysosomal Rheb-mTORC1 activity. Consequently, the recombinant human IL-37d protein (rh-IL-37d) with a TAT peptide greatly improves alcohol-induced liver disorders by hindering Rheb-mTORC1 axis overactivation in a TSC2- independent manner. Together, IL-37d emerges as a novel Rheb suppressor independent of TSC2 to terminate mTORC1 activation and improve abnormal lipid metabolism in the liver.
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Affiliation(s)
- Nuo Chen
- Department of Immunology, School of Basic Medical Science, Shandong University, Jinan, China
| | - Xiaoyu Wang
- Department of Immunology, School of Basic Medical Science, Shandong University, Jinan, China
| | - Yaxin Guo
- Department of Immunology, School of Basic Medical Science, Shandong University, Jinan, China
| | - Ming Zhao
- Department of Immunology, School of Basic Medical Science, Shandong University, Jinan, China
| | - Baihui Cao
- Department of Immunology, School of Basic Medical Science, Shandong University, Jinan, China
| | - Bing Zhan
- Department of Immunology, School of Basic Medical Science, Shandong University, Jinan, China
| | - Yubin Li
- Department of Immunology, School of Basic Medical Science, Shandong University, Jinan, China
| | - Tian Zhou
- Department of Immunology, School of Basic Medical Science, Shandong University, Jinan, China
| | - Faliang Zhu
- Department of Immunology, School of Basic Medical Science, Shandong University, Jinan, China
| | - Chun Guo
- Department of Immunology, School of Basic Medical Science, Shandong University, Jinan, China
| | - Yongyu Shi
- Department of Immunology, School of Basic Medical Science, Shandong University, Jinan, China
| | - Qun Wang
- Department of Immunology, School of Basic Medical Science, Shandong University, Jinan, China
| | - Lining Zhang
- Department of Immunology, School of Basic Medical Science, Shandong University, Jinan, China.
| | - Yan Li
- Department of Pathogen Biology, School of Basic Medical Science, Shandong University, Jinan, China.
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3
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Rahman M, Nguyen TM, Lee GJ, Kim B, Park MK, Lee CH. Unraveling the Role of Ras Homolog Enriched in Brain (Rheb1 and Rheb2): Bridging Neuronal Dynamics and Cancer Pathogenesis through Mechanistic Target of Rapamycin Signaling. Int J Mol Sci 2024; 25:1489. [PMID: 38338768 PMCID: PMC10855792 DOI: 10.3390/ijms25031489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/14/2024] [Accepted: 01/17/2024] [Indexed: 02/12/2024] Open
Abstract
Ras homolog enriched in brain (Rheb1 and Rheb2), small GTPases, play a crucial role in regulating neuronal activity and have gained attention for their implications in cancer development, particularly in breast cancer. This study delves into the intricate connection between the multifaceted functions of Rheb1 in neurons and cancer, with a specific focus on the mTOR pathway. It aims to elucidate Rheb1's involvement in pivotal cellular processes such as proliferation, apoptosis resistance, migration, invasion, metastasis, and inflammatory responses while acknowledging that Rheb2 has not been extensively studied. Despite the recognized associations, a comprehensive understanding of the intricate interplay between Rheb1 and Rheb2 and their roles in both nerve and cancer remains elusive. This review consolidates current knowledge regarding the impact of Rheb1 on cancer hallmarks and explores the potential of Rheb1 as a therapeutic target in cancer treatment. It emphasizes the necessity for a deeper comprehension of the molecular mechanisms underlying Rheb1-mediated oncogenic processes, underscoring the existing gaps in our understanding. Additionally, the review highlights the exploration of Rheb1 inhibitors as a promising avenue for cancer therapy. By shedding light on the complicated roles between Rheb1/Rheb2 and cancer, this study provides valuable insights to the scientific community. These insights are instrumental in guiding the identification of novel targets and advancing the development of effective therapeutic strategies for treating cancer.
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Affiliation(s)
- Mostafizur Rahman
- College of Pharmacy, Dongguk University, Seoul 04620, Republic of Korea; (M.R.); (G.J.L.)
| | - Tuan Minh Nguyen
- College of Pharmacy, Dongguk University, Seoul 04620, Republic of Korea; (M.R.); (G.J.L.)
| | - Gi Jeong Lee
- College of Pharmacy, Dongguk University, Seoul 04620, Republic of Korea; (M.R.); (G.J.L.)
| | - Boram Kim
- College of Pharmacy, Dongguk University, Seoul 04620, Republic of Korea; (M.R.); (G.J.L.)
| | - Mi Kyung Park
- Department of BioHealthcare, Hwasung Medi-Science University, Hwaseong-si 18274, Republic of Korea
| | - Chang Hoon Lee
- College of Pharmacy, Dongguk University, Seoul 04620, Republic of Korea; (M.R.); (G.J.L.)
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Koukos PI, Dehghani-Ghahnaviyeh S, Velez-Vega C, Manchester J, Tieleman DP, Duca JS, Souza PCT, Cournia Z. Martini 3 Force Field Parameters for Protein Lipidation Post-Translational Modifications. J Chem Theory Comput 2023; 19:8901-8918. [PMID: 38019969 DOI: 10.1021/acs.jctc.3c00604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Protein lipidations are vital co/post-translational modifications that tether lipid tails to specific protein amino acids, allowing them to anchor to biological membranes, switch their subcellular localization, and modulate association with other proteins. Such lipidations are thus crucial for multiple biological processes including signal transduction, protein trafficking, and membrane localization and are implicated in various diseases as well. Examples of lipid-anchored proteins include the Ras family of proteins that undergo farnesylation; actin and gelsolin that are myristoylated; phospholipase D that is palmitoylated; glycosylphosphatidylinositol-anchored proteins; and others. Here, we develop parameters for cysteine-targeting farnesylation, geranylgeranylation, and palmitoylation, as well as glycine-targeting myristoylation for the latest version of the Martini 3 coarse-grained force field. The parameters are developed using the CHARMM36m all-atom force field parameters as reference. The behavior of the coarse-grained models is consistent with that of the all-atom force field for all lipidations and reproduces key dynamical and structural features of lipid-anchored peptides, such as the solvent-accessible surface area, bilayer penetration depth, and representative conformations of the anchors. The parameters are also validated in simulations of the lipid-anchored peripheral membrane proteins Rheb and Arf1, after comparison with independent all-atom simulations. The parameters, along with mapping schemes for the popular martinize2 tool, are available for download at 10.5281/zenodo.7849262 and also as supporting information.
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Affiliation(s)
- Panagiotis I Koukos
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
| | - Sepehr Dehghani-Ghahnaviyeh
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Camilo Velez-Vega
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - John Manchester
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - D Peter Tieleman
- Department of Biological Sciences, University of Calgary, Calgary T2N 1N4 Alberta, Canada
- Centre for Molecular Simulation, University of Calgary, Calgary T2N 1N4 Alberta, Canada
| | - José S Duca
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, (MMSB, UMR 5086), CNRS & University of Lyon, 69367 Lyon, France
- Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239 and Inserm U1293, 46 Allée d'Italie, 69364 Lyon, France
| | - Zoe Cournia
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
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Franz M, Mörchen B, Degenhart C, Gülden D, Shkura O, Wolters D, Koch U, Klebl B, Stoll R, Helfrich I, Scherkenbeck J. Sequence-Selective Covalent CaaX-Box Receptors Prevent Farnesylation of Oncogenic Ras Proteins and Impact MAPK/PI3 K Signaling. ChemMedChem 2021; 16:2504-2514. [PMID: 33899342 PMCID: PMC8453727 DOI: 10.1002/cmdc.202100167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Indexed: 01/21/2023]
Abstract
Oncogenic Ras proteins are implicated in the most common life-threatening cancers. Despite intense research over the past two decades, the progress towards small-molecule inhibitors has been limited. One reason for this failure is that Ras proteins interact with their effectors only via protein-protein interactions, which are notoriously difficult to address with small organic molecules. Herein we describe an alternative strategy, which prevents farnesylation and subsequent membrane insertion, a prerequisite for the activation of Ras proteins. Our approach is based on sequence-selective supramolecular receptors which bind to the C-terminal farnesyl transferase recognition unit of Ras and Rheb proteins and covalently modify the essential cysteine in the so-called CaaX-box.
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Affiliation(s)
- Matthias Franz
- Faculty of Mathematics and Natural SciencesUniversity of Wuppertal42119WuppertalGermany
| | - Britta Mörchen
- Vascular Oncology & MetastasisUniversity Hospital Essen45147EssenGermany
| | | | - Daniel Gülden
- Faculty of Mathematics and Natural SciencesUniversity of Wuppertal42119WuppertalGermany
| | - Oleksandr Shkura
- Faculty of Chemistry and BiochemistryRuhr-University Bochum44780BochumGermany
| | - Dirk Wolters
- Faculty of Chemistry and BiochemistryRuhr-University Bochum44780BochumGermany
| | - Uwe Koch
- Lead Discovery Center GmbH44227DortmundGermany
| | - Bert Klebl
- Lead Discovery Center GmbH44227DortmundGermany
| | - Raphael Stoll
- Faculty of Chemistry and BiochemistryRuhr-University Bochum44780BochumGermany
| | - Iris Helfrich
- Vascular Oncology & MetastasisUniversity Hospital Essen45147EssenGermany
| | - Jürgen Scherkenbeck
- Faculty of Mathematics and Natural SciencesUniversity of Wuppertal42119WuppertalGermany
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6
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Feng X, Ding W, Ma J, Liu B, Yuan H. Targeted Therapies in Lung Cancers: Current Landscape and Future Prospects. Recent Pat Anticancer Drug Discov 2021; 16:540-551. [PMID: 34132185 DOI: 10.2174/1574892816666210615161501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/09/2021] [Accepted: 03/31/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Lung cancer is the most common and malignant cancer worldwide. Targeted therapies have emerged as a promising treatment strategy for lung cancers. OBJECTIVE The objective of this study is to evaluate the current landscape of targets and finding promising targets for future new drug discovery for lung cancers by identifying the science-technology-clinical development pattern and mapping the interaction network of targets. METHODS Targets for cancers were classified into 3 groups based on a paper published in Nature. We search for scientific literature, patent documents and clinical trials of targets in Group 1 and Group 2 for lung cancers. Then, a target-target interaction network of Group 1 was constructed, and the science-technology-clinical(S-T-C) development patterns of targets in Group 1 were identified. Finally, based on the cluster distribution and the development pattern of targets in Group 1, interactions between the targets were employed to predict potential targets in Group 2 on drug development. RESULTS The target-target interaction(TTI)network of group 1 resulted in 3 clusters with different developmental stages. The potential targets in Group 2 are divided into 3 ranks. Level-1 is the first priority and level-3 is the last. Level-1 includes 16 targets, such as STAT3, CRKL, and PTPN11, that are mostly involved in signaling transduction pathways. Level-2 and level-3 contain 8 and 6 targets related to various biological functions. CONCLUSION This study will provide references for drug development in lung cancers, emphasizing that priorities should be given to targets in Level-1, whose mechanisms are worth further exploration.
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Affiliation(s)
- Xin Feng
- School of Business Administration, Shenyang Pharmaceutical University, Shenyang, China
| | - Wenqing Ding
- School of Business Administration, Shenyang Pharmaceutical University, Shenyang, China
| | - Junhong Ma
- School of Business Administration, Shenyang Pharmaceutical University, Shenyang, China
| | - Baijun Liu
- School of Business Administration, Shenyang Pharmaceutical University, Shenyang, China
| | - Hongmei Yuan
- School of Business Administration, Shenyang Pharmaceutical University, Shenyang, China
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7
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TSC1 binding to lysosomal PIPs is required for TSC complex translocation and mTORC1 regulation. Mol Cell 2021; 81:2705-2721.e8. [PMID: 33974911 DOI: 10.1016/j.molcel.2021.04.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 03/13/2021] [Accepted: 04/19/2021] [Indexed: 11/21/2022]
Abstract
The TSC complex is a critical negative regulator of the small GTPase Rheb and mTORC1 in cellular stress signaling. The TSC2 subunit contains a catalytic GTPase activating protein domain and interacts with multiple regulators, while the precise function of TSC1 is unknown. Here we provide a structural characterization of TSC1 and define three domains: a C-terminal coiled-coil that interacts with TSC2, a central helical domain that mediates TSC1 oligomerization, and an N-terminal HEAT repeat domain that interacts with membrane phosphatidylinositol phosphates (PIPs). TSC1 architecture, oligomerization, and membrane binding are conserved in fungi and humans. We show that lysosomal recruitment of the TSC complex and subsequent inactivation of mTORC1 upon starvation depend on the marker lipid PI3,5P2, demonstrating a role for lysosomal PIPs in regulating TSC complex and mTORC1 activity via TSC1. Our study thus identifies a vital role of TSC1 in TSC complex function and mTORC1 signaling.
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8
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Nam Y, Moon GJ, Kim SR. Therapeutic Potential of AAV1-Rheb(S16H) Transduction against Neurodegenerative Diseases. Int J Mol Sci 2021; 22:ijms22063064. [PMID: 33802760 PMCID: PMC8002454 DOI: 10.3390/ijms22063064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/08/2021] [Accepted: 03/16/2021] [Indexed: 01/19/2023] Open
Abstract
Neurotrophic factors (NTFs) are essential for cell growth, survival, synaptic plasticity, and maintenance of specific neuronal population in the central nervous system. Multiple studies have demonstrated that alterations in the levels and activities of NTFs are related to the pathology and symptoms of neurodegenerative disorders, such as Parkinson’s disease (PD), Alzheimer’s disease (AD), and Huntington’s disease. Hence, the key molecule that can regulate the expression of NTFs is an important target for gene therapy coupling adeno-associated virus vector (AAV) gene. We have previously reported that the Ras homolog protein enriched in brain (Rheb)–mammalian target of rapamycin complex 1 (mTORC1) axis plays a vital role in preventing neuronal death in the brain of AD and PD patients. AAV transduction using a constitutively active form of Rheb exerts a neuroprotective effect through the upregulation of NTFs, thereby promoting the neurotrophic interaction between astrocytes and neurons in AD conditions. These findings suggest the role of Rheb as an important regulator of the regulatory system of NTFs to treat neurodegenerative diseases. In this review, we present an overview of the role of Rheb in neurodegenerative diseases and summarize the therapeutic potential of AAV serotype 1 (AAV1)-Rheb(S16H) transduction in the treatment of neurodegenerative disorders, focusing on diseases, such as AD and PD.
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Affiliation(s)
- Youngpyo Nam
- Brain Science and Engineering Institute, Kyungpook National University, Daegu 41944, Korea;
| | - Gyeong Joon Moon
- Center for Cell Therapy, Asan Institute for Life Science, Asan Medical Center, Seoul 05505, Korea;
- Department of Convergence Medicine, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Sang Ryong Kim
- Brain Science and Engineering Institute, Kyungpook National University, Daegu 41944, Korea;
- School of Life Sciences, Kyungpook National University, Daegu 41566, Korea
- BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Korea
- Correspondence: ; Tel.: +82-53-950-7362; Fax: +82-53-943-2762
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Nesterov SV, Yaguzhinsky LS, Podoprigora GI, Nartsissov YR. Amino Acids as Regulators of Cell Metabolism. BIOCHEMISTRY (MOSCOW) 2021; 85:393-408. [PMID: 32569548 DOI: 10.1134/s000629792004001x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In this review, we discuss the principles of regulation and synchronization of metabolic processes in mammalian cells using a two-component model of cell metabolism consisting of a controlling signaling system that regulates major enzymatic cascades and executive metabolic system that directly performs biosynthetic reactions. This approach has allowed us to distinguish two transitional metabolic states (from catabolism to anabolism and vice versa) accompanied by major rearrangements in the signaling system. The signaling system of natural amino acids was selected, because amino acids are involved in both signaling and executive metabolic subsystems of general cell metabolism. We have developed a graphical representation of metabolic events that allowed us to demonstrate the succession of processes occurring in both metabolic subsystems during complete metabolic cycle in a non-dividing cell. An important revealed feature of the amino acid signaling system is that the signaling properties of amino acid are determined not only by their molecular structure, but also by the location within the cell. Four major signaling groups of amino acids have been identified that localize to lysosomes, mitochondria, cytosol, and extracellular space adjacent to the plasma membrane. Although these amino acids groups are similar in the composition, they have different receptors. We also proposed a scheme for the metabolism regulation by amino acids signaling that can serve as a basis for developing more complete spatio-temporal picture of metabolic regulation involving a wide variety of intracellular signaling cascades.
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Affiliation(s)
- S V Nesterov
- Institute of Cytochemistry and Molecular Pharmacology, Moscow, 115404, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - L S Yaguzhinsky
- Institute of Cytochemistry and Molecular Pharmacology, Moscow, 115404, Russia. .,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - G I Podoprigora
- Institute of Cytochemistry and Molecular Pharmacology, Moscow, 115404, Russia
| | - Ya R Nartsissov
- Institute of Cytochemistry and Molecular Pharmacology, Moscow, 115404, Russia
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Yang H, Yu Z, Chen X, Li J, Li N, Cheng J, Gao N, Yuan HX, Ye D, Guan KL, Xu Y. Structural insights into TSC complex assembly and GAP activity on Rheb. Nat Commun 2021; 12:339. [PMID: 33436626 PMCID: PMC7804450 DOI: 10.1038/s41467-020-20522-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 12/04/2020] [Indexed: 12/13/2022] Open
Abstract
Tuberous sclerosis complex (TSC) integrates upstream stimuli and regulates cell growth by controlling the activity of mTORC1. TSC complex functions as a GTPase-activating protein (GAP) towards small GTPase Rheb and inhibits Rheb-mediated activation of mTORC1. Mutations in TSC genes cause tuberous sclerosis. In this study, the near-atomic resolution structure of human TSC complex reveals an arch-shaped architecture, with a 2:2:1 stoichiometry of TSC1, TSC2, and TBC1D7. This asymmetric complex consists of two interweaved TSC1 coiled-coil and one TBC1D7 that spans over the tail-to-tail TSC2 dimer. The two TSC2 GAP domains are symmetrically cradled within the core module formed by TSC2 dimerization domain and central coiled-coil of TSC1. Structural and biochemical analyses reveal TSC2 GAP-Rheb complimentary interactions and suggest a catalytic mechanism, by which an asparagine thumb (N1643) stabilizes γ-phosphate of GTP and accelerate GTP hydrolysis of Rheb. Our study reveals mechanisms of TSC complex assembly and GAP activity.
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Affiliation(s)
- Huirong Yang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
- The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
- Human Phenome Institute, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China.
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
| | - Zishuo Yu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Xizi Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Jiabei Li
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Ningning Li
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Jiaxuan Cheng
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Ning Gao
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Hai-Xin Yuan
- The Molecular and Cell Biology Research Lab, The Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Dan Ye
- The Molecular and Cell Biology Research Lab, The Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Kun-Liang Guan
- Department of Pharmacology and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
- The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
- Human Phenome Institute, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China.
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
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11
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Zhang C, Liu Y, Zhang Y, Wang X, Zhang T, Ding J. Molecular basis for the functions of dominantly active Y35N and inactive D60K Rheb mutants in mTORC1 signaling. J Mol Cell Biol 2020; 12:741-744. [PMID: 32470140 PMCID: PMC7749741 DOI: 10.1093/jmcb/mjaa025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/05/2020] [Accepted: 05/25/2020] [Indexed: 11/18/2022] Open
Affiliation(s)
- Chunxiao Zhang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yan Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yifang Zhang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiangxiang Wang
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Tianlong Zhang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jianping Ding
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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12
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Natarajan N, Thiruvenkatam V. An Insight of Scientific Developments in TSC for Better Therapeutic Strategy. Curr Top Med Chem 2020; 20:2080-2093. [PMID: 32842942 DOI: 10.2174/1568026620666200825170355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/15/2020] [Accepted: 07/20/2020] [Indexed: 11/22/2022]
Abstract
Tuberous sclerosis complex (TSC) is a rare genetic disease, which is characterized by noncancerous tumors in multi-organ systems in the body. Mutations in the TSC1 or TSC2 genes are known to cause the disease. The resultant mutant proteins TSC1 (hamartin) and TSC2 (tuberin) complex evade its normal tumor suppressor function, which leads to abnormal cell growth and proliferation. Both TSC1 and TSC2 are involved in several protein-protein interactions, which play a significant role in maintaining cellular homeostasis. The recent biochemical, genetic, structural biology, clinical and drug discovery advancements on TSC give a useful insight into the disease as well as the molecular aspects of TSC1 and TSC2. The complex nature of TSC disease, a wide range of manifestations, mosaicism and several other factors limits the treatment choices. This review is a compilation of the course of TSC, starting from its discovery to the current findings that would take us a step ahead in finding a cure for TSC.
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Affiliation(s)
- Nalini Natarajan
- Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gujarat-382355, India
| | - Vijay Thiruvenkatam
- Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gujarat-382355, India
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13
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Hansmann P, Brückner A, Kiontke S, Berkenfeld B, Seebohm G, Brouillard P, Vikkula M, Jansen FE, Nellist M, Oeckinghaus A, Kümmel D. Structure of the TSC2 GAP Domain: Mechanistic Insight into Catalysis and Pathogenic Mutations. Structure 2020; 28:933-942.e4. [PMID: 32502382 DOI: 10.1016/j.str.2020.05.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 02/06/2020] [Accepted: 05/15/2020] [Indexed: 12/17/2022]
Abstract
The TSC complex is the cognate GTPase-activating protein (GAP) for the small GTPase Rheb and a crucial regulator of the mechanistic target of rapamycin complex 1 (mTORC1). Mutations in the TSC1 and TSC2 subunits of the complex cause tuberous sclerosis complex (TSC). We present the crystal structure of the catalytic asparagine-thumb GAP domain of TSC2. A model of the TSC2-Rheb complex and molecular dynamics simulations suggest that TSC2 Asn1643 and Rheb Tyr35 are key active site residues, while Rheb Arg15 and Asp65, previously proposed as catalytic residues, contribute to the TSC2-Rheb interface and indirectly aid catalysis. The TSC2 GAP domain is further stabilized by interactions with other TSC2 domains. We characterize TSC2 variants that partially affect TSC2 functionality and are associated with atypical symptoms in patients, suggesting that mutations in TSC1 and TSC2 might predispose to neurological and vascular disorders without fulfilling the clinical criteria for TSC.
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Affiliation(s)
- Patrick Hansmann
- Westfälische Wilhelms-Universität, Institute of Biochemistry, Wilhelm Klemm-Str. 2, 48149 Münster, Germany
| | - Anne Brückner
- Westfälische Wilhelms-Universität, Institute of Biochemistry, Wilhelm Klemm-Str. 2, 48149 Münster, Germany; Westfälische Wilhelms-Universität, Institute of Molecular Tumor Biology, Robert-Koch-Str. 43, 48149 Münster, Germany
| | - Stephan Kiontke
- Philipps-Universität Marburg, Faculty of Biology, Department of Plant Physiology and Photobiology, Karl-von-Frisch-Str. 8, 35032 Marburg, Germany
| | - Bianca Berkenfeld
- Westfälische Wilhelms-Universität, Institute of Biochemistry, Wilhelm Klemm-Str. 2, 48149 Münster, Germany
| | - Guiscard Seebohm
- University Hospital Münster, Institute for Genetics of Heart Diseases, Department of Cardiovascular Medicine, Robert-Koch-Str. 45, 48149 Münster, Germany
| | - Pascal Brouillard
- Université Catholique de Louvain, de Duve Institute, Human Molecular Genetics, Brussels, Belgium
| | - Miikka Vikkula
- Université Catholique de Louvain, de Duve Institute, Human Molecular Genetics, Brussels, Belgium; WELBIO (Walloon Excellence in Lifesciences and Biotechnology), de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Floor E Jansen
- Department of Child Neurology, Brain Center UMC Utrecht, Utrecht, the Netherlands
| | - Mark Nellist
- Department of Clinical Genetics, Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands
| | - Andrea Oeckinghaus
- Westfälische Wilhelms-Universität, Institute of Molecular Tumor Biology, Robert-Koch-Str. 43, 48149 Münster, Germany
| | - Daniel Kümmel
- Westfälische Wilhelms-Universität, Institute of Biochemistry, Wilhelm Klemm-Str. 2, 48149 Münster, Germany.
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14
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Zhu M, Wang XQ. Regulation of mTORC1 by Small GTPases in Response to Nutrients. J Nutr 2020; 150:1004-1011. [PMID: 31965176 DOI: 10.1093/jn/nxz301] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 10/07/2019] [Accepted: 11/18/2019] [Indexed: 12/15/2022] Open
Abstract
Mechanistic target of rapamycin complex 1 (mTORC1) is a highly evolutionarily conserved serine/threonine kinase that regulates cell growth and metabolism in response to multiple environmental cues, such as nutrients, hormones, energy, and stress. Deregulation of mTORC1 can lead to diseases such as diabetes, obesity, and cancer. A series of small GTPases, including Rag, Ras homolog enriched in brain (Rheb), adenosine diphosphate ribosylation factor 1 (Arf1), Ras-related protein Ral-A, Ras homolog (Rho), and Rab, are involved in regulating mTORC1 in response to nutrients, and mTORC1 is differentially regulated via these small GTPases according to specific conditions. Leucine and arginine sensing are considered to be well-confirmed amino acid-sensing signals, activating mTORC1 via a Rag GTPase-dependent mechanism as well as the Ragulator complex and vacuolar H+-adenosine triphosphatase (v-ATPase). Glutamine promotes mTORC1 activation via Arf1 independently of the Rag GTPase. In this review, we summarize current knowledge regarding the regulation of mTORC1 activity by small GTPases in response to nutrients, focusing on the function of small GTPases in mTORC1 activation and how small GTPases are regulated by nutrients.
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Affiliation(s)
- Min Zhu
- College of Animal Science, South China Agricultural University/Guangdong Provincial Key Laboratory of Animal Nutrition Control/National Engineering Research Center for Breeding Swine Industry, Guangzhou, Guangdong, China
| | - Xiu-Qi Wang
- College of Animal Science, South China Agricultural University/Guangdong Provincial Key Laboratory of Animal Nutrition Control/National Engineering Research Center for Breeding Swine Industry, Guangzhou, Guangdong, China
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15
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Moon GJ, Shin M, Kim SR. Upregulation of Neuronal Rheb(S16H) for Hippocampal Protection in the Adult Brain. Int J Mol Sci 2020; 21:E2023. [PMID: 32188096 PMCID: PMC7139780 DOI: 10.3390/ijms21062023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/14/2020] [Accepted: 03/16/2020] [Indexed: 12/20/2022] Open
Abstract
Ras homolog protein enriched in brain (Rheb) is a key activator of mammalian target of rapamycin complex 1 (mTORC1). The activation of mTORC1 by Rheb is associated with various processes such as protein synthesis, neuronal growth, differentiation, axonal regeneration, energy homeostasis, autophagy, and amino acid uptake. In addition, Rheb-mTORC1 signaling plays a crucial role in preventing the neurodegeneration of hippocampal neurons in the adult brain. Increasing evidence suggests that the constitutive activation of Rheb has beneficial effects against neurodegenerative diseases such as Alzheimer's disease (AD) and Parkinson's disease (PD). Our recent studies revealed that adeno-associated virus serotype 1 (AAV1) transduction with Rheb(S16H), a constitutively active form of Rheb, exhibits neuroprotective properties through the induction of various neurotrophic factors, promoting neurotrophic interactions between neurons and astrocytes in the hippocampus of the adult brain. This review provides compelling evidence for the therapeutic potential of AAV1-Rheb(S16H) transduction in the hippocampus of the adult brain by exploring its neuroprotective effects and mechanisms.
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Affiliation(s)
- Gyeong Joon Moon
- BK21 plus KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Korea;
| | - Minsang Shin
- Brain Science and Engineering Institute, Kyungpook National University, Daegu 41566, Korea;
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu 41944, Korea
| | - Sang Ryong Kim
- BK21 plus KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Korea;
- Brain Science and Engineering Institute, Kyungpook National University, Daegu 41566, Korea;
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16
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Zhao S, Li Z, Zhang M, Zhang L, Zheng H, Ning J, Wang Y, Wang F, Zhang X, Gan H, Wang Y, Zhang X, Luo H, Bu G, Xu H, Yao Y, Zhang YW. A brain somatic RHEB doublet mutation causes focal cortical dysplasia type II. Exp Mol Med 2019; 51:1-11. [PMID: 31337748 PMCID: PMC6802736 DOI: 10.1038/s12276-019-0277-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 03/27/2019] [Accepted: 04/10/2019] [Indexed: 01/16/2023] Open
Abstract
Focal cortical dysplasia type II (FCDII) is a cerebral cortex malformation characterized by local cortical structure disorganization, neuronal dysmorphology, and refractory epilepsy. Brain somatic mutations in several genes involved in the PI3K/AKT/mTOR pathway are associated with FCDII, but they are only found in a proportion of patients with FCDII. The genetic causes underlying the development FCDII in other patients remain unclear. Here, we carried out whole exome sequencing and targeted sequencing in paired brain–blood DNA from patients with FCDII and identified a brain somatic doublet mutation c.(A104T, C105A) in the Ras homolog, mTORC1 binding (RHEB) gene, which led to the RHEB p.Y35L mutation in one patient with FCDII. This RHEB mutation carrier had a dramatic increase of ribosomal protein S6 phosphorylation, indicating mTOR activation in the region of the brain lesion. The RHEB p.Y35L mutant protein had increased GTPλS-binding activity compared with wild-type RHEB. Overexpression of the RHEB p.Y35L variant in cultured cells also resulted in elevated S6 phosphorylation compared to wild-type RHEB. Importantly, in utero electroporation of the RHEB p.Y35L variant in mice induced S6 phosphorylation, cytomegalic neurons, dysregulated neuron migration, abnormal electroencephalogram, and seizures, all of which are found in patients with FCDII. Rapamycin treatment rescued abnormal electroencephalograms and alleviated seizures in these mice. These results demonstrate that brain somatic mutations in RHEB are also responsible for the pathogenesis of FCDII, indicating that aberrant activation of mTOR signaling is a primary driver and potential drug target for FCDII. Identifying a genetic mutation causing a congenital brain disorder that triggers difficult-to-treat epilepsy suggests a potential therapeutic target, according to Chinese scientists. Focal cortical dysplasia type II (FCDII) is one of a group of brain development abnormalities that cause intractable epilepsy. Scientists have identified gene mutations in some FCDII patients linked to a signaling pathway involved in cell proliferation and metabolism in the developing brain. Now, Yun-wu Zhang and Yi Yao at Xiamen University in Fujian, China, and co-workers have discovered a mutation on a gene which triggers abnormal activation of the same signaling pathway. The team found that the drug rapamycin, which inhibits this pathway, alleviated epileptic seizures in mice with the mutant gene. Their findings add weight to the theory that this pathway may be a viable target for future therapies.
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Affiliation(s)
- Shanshan Zhao
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, China
| | - Zhenghui Li
- Neuromedicine Center, the 174th Hospital of Chinese People's Liberation Army, Affiliated Chenggong Hospital, Xiamen University, Xiamen, 361003, Fujian, China.,Department of Neurosurgery, Kaifeng Central Hospital, Kaifeng, 475000, Henan, China
| | - Muxian Zhang
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, China
| | - Lingliang Zhang
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, China
| | - Honghua Zheng
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, China
| | - Jinhuan Ning
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, China
| | - Yanyan Wang
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, China
| | - Fengpeng Wang
- Neuromedicine Center, the 174th Hospital of Chinese People's Liberation Army, Affiliated Chenggong Hospital, Xiamen University, Xiamen, 361003, Fujian, China.,XiaMen Humanity Hospital, No.3777 XianYue Road, HuLi District, XiaMen, 361015, FuJian, China
| | - Xiaobin Zhang
- Neuromedicine Center, the 174th Hospital of Chinese People's Liberation Army, Affiliated Chenggong Hospital, Xiamen University, Xiamen, 361003, Fujian, China.,XiaMen Humanity Hospital, No.3777 XianYue Road, HuLi District, XiaMen, 361015, FuJian, China
| | - Hexia Gan
- Neuromedicine Center, the 174th Hospital of Chinese People's Liberation Army, Affiliated Chenggong Hospital, Xiamen University, Xiamen, 361003, Fujian, China
| | - Yuanqing Wang
- Neuromedicine Center, the 174th Hospital of Chinese People's Liberation Army, Affiliated Chenggong Hospital, Xiamen University, Xiamen, 361003, Fujian, China
| | - Xian Zhang
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, China
| | - Hong Luo
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, China
| | - Guojun Bu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Huaxi Xu
- Neuroscience Initiative, Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Yi Yao
- Neuromedicine Center, the 174th Hospital of Chinese People's Liberation Army, Affiliated Chenggong Hospital, Xiamen University, Xiamen, 361003, Fujian, China. .,XiaMen Humanity Hospital, No.3777 XianYue Road, HuLi District, XiaMen, 361015, FuJian, China. .,Department of Pediatric Neurology, Shenzhen Children's Hospital, Shenzhen, 518026, Guangdong Province, China.
| | - Yun-Wu Zhang
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, China.
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17
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Locke MN, Thorner J. Regulation of TORC2 function and localization by Rab5 GTPases in Saccharomyces cerevisiae. Cell Cycle 2019; 18:1084-1094. [PMID: 31068077 DOI: 10.1080/15384101.2019.1616999] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The evolutionarily conserved Target of Rapamycin (TOR) complex-2 (TORC2) is an essential regulator of plasma membrane homeostasis in budding yeast (Saccharomyces cerevisiae). In this yeast, TORC2 phosphorylates and activates the effector protein kinase Ypk1 and its paralog Ypk2. These protein kinases, in turn, carry out all the crucial functions of TORC2 by phosphorylating and thereby controlling the activity of at least a dozen downstream substrates. A previously uncharacterized interplay between the Rab5 GTPases and TORC2 signaling was uncovered through analysis of a newly suspected Ypk1 target. Muk1, one of two guanine nucleotide exchange factors for the Rab5 GTPases, was found to be a physiologically relevant Ypk1 substrate; and, genetic analysis indicates that Ypk1-mediated phosphorylation activates the guanine nucleotide exchange activity of Muk1. Second, it was demonstrated both in vivo and in vitro that the GTP-bound state of the Rab5 GTPase Vps21/Ypt51 physically associates with TORC2 and acts as a direct positive effector required for full TORC2 activity. These interrelationships provide a self-reinforcing control circuit for sustained up-regulation of TORC2-Ypk1 signaling. In this overview, we summarize the experimental basis of these findings, their implications, and speculate as to the molecular basis for Rab5-mediated TORC2 activation.
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Affiliation(s)
- Melissa N Locke
- a Division of Biochemistry, Biophysics & Structural Biology, and Division of Cell & Developmental Biology, Department of Molecular and Cell Biology , University of California at Berkeley , Berkeley , CA , USA
| | - Jeremy Thorner
- a Division of Biochemistry, Biophysics & Structural Biology, and Division of Cell & Developmental Biology, Department of Molecular and Cell Biology , University of California at Berkeley , Berkeley , CA , USA
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18
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Killoran RC, Smith MJ. Conformational resolution of nucleotide cycling and effector interactions for multiple small GTPases determined in parallel. J Biol Chem 2019; 294:9937-9948. [PMID: 31088913 DOI: 10.1074/jbc.ra119.008653] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/09/2019] [Indexed: 12/31/2022] Open
Abstract
Small GTPases alternatively bind GDP/GTP guanine nucleotides to gate signaling pathways that direct most cellular processes. Numerous GTPases are implicated in oncogenesis, particularly the three RAS isoforms HRAS, KRAS, and NRAS and the RHO family GTPase RAC1. Signaling networks comprising small GTPases are highly connected, and there is some evidence of direct biochemical cross-talk between their functional G-domains. The activation potential of a given GTPase is contingent on a codependent interaction with the nucleotide and a Mg2+ ion, which bind to individual variants with distinct affinities coordinated by residues in the GTPase nucleotide-binding pocket. Here, we utilized a selective-labeling strategy coupled with real-time NMR spectroscopy to monitor nucleotide exchange, GTP hydrolysis, and effector interactions of multiple small GTPases in a single complex system. We provide insight into nucleotide preference and the role of Mg2+ in activating both WT and oncogenic mutant enzymes. Multiplexing revealed guanine nucleotide exchange factor (GEF), GTPase-activating protein (GAP), and effector-binding specificities in mixtures of GTPases and resolved that the three related RAS isoforms are biochemically equivalent. This work establishes that direct quantitation of the nucleotide-bound conformation is required to accurately determine an activation potential for any given GTPase, as small GTPases such as RAS-like proto-oncogene A (RALA) or the G12C mutant of KRAS display fast exchange kinetics but have a high affinity for GDP. Furthermore, we propose that the G-domains of small GTPases behave autonomously in solution and that nucleotide cycling proceeds independently of protein concentration but is highly impacted by Mg2+ abundance.
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Affiliation(s)
- Ryan C Killoran
- From the Institute for Research in Immunology and Cancer and
| | - Matthew J Smith
- From the Institute for Research in Immunology and Cancer and .,Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
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19
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Shen Y, Zhao Y, Wang L, Zhang W, Liu C, Yin A. MicroRNA-194 overexpression protects against hypoxia/reperfusion-induced HK-2 cell injury through direct targeting Rheb. J Cell Biochem 2019; 120:8311-8318. [PMID: 30485514 DOI: 10.1002/jcb.28114] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 10/29/2018] [Indexed: 01/24/2023]
Abstract
Renal ischemia-reperfusion injury, a major cause of renal failure, always leads to acute kidney injury and kidney fibrosis. MicroRNAs (miRs) have been reported to be associated with renal ischemia-reperfusion injury. miR-194 was downregulated following renal ischemia-reperfusion injury; however, the function and mechanism of miR-194 in renal ischemia-reperfusion injury have not yet been fully understood. In the present study, we constructed renal ischemia-reperfusion injury model in vitro through treatment of human kidney proximal tubular epithelial cells HK-2 by hypoxia/reperfusion (H/R). We observed that miR-194 was decreased in H/R-induced HK-2 cells. miR-194 mimic increased H/R-induced HK-2 cell survival, whereas miR-194 inhibitor further strengthened H/R- inhibited HK-2 cell survival. Also, we observed that miR-194 overexpression suppressed oxidative stress markers, including malondialdehyde, glutathione, and secretion of pro-inflammatory cytokines, including IL-6, IL-1β, and TNF-α; however, miR-194 inhibitor showed the reverse effects. Results from dual-luciferase analysis confirmed that Ras homology enriched in brain (Rheb) was a direct target of miR-194. Finally, we corroborated that miR-194 affected cell growth, oxidative stress, and inflammation through targeting Rheb in H/R-induced HK-2 cells. In conclusion, our results suggested that miR-194 protect against H/R-induced injury in HK-2 cells through direct targeting Rheb.
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Affiliation(s)
- Yan Shen
- Department of Nephrology, First Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, China
| | - Yan Zhao
- Department of Cardiovascular Medicine, First Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, China
| | - Lijun Wang
- Department of Cardiovascular Medicine, First Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, China
| | - Wenjing Zhang
- Department of Nephrology, First Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, China
| | - Chao Liu
- Department of Nephrology, First Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, China
| | - Aiping Yin
- Department of Nephrology, First Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, China
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20
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Chao LH, Avruch J. Cryo-EM insight into the structure of MTOR complex 1 and its interactions with Rheb and substrates. F1000Res 2019; 8. [PMID: 30647914 PMCID: PMC6325617 DOI: 10.12688/f1000research.16109.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/18/2018] [Indexed: 12/31/2022] Open
Abstract
The mechanistic target of rapamycin (MTOR) is a giant protein kinase that, together with the accessory proteins Raptor and mLst8, forms a complex of over 1 MDa known as MTOR complex 1 (MTORC1). MTORC1, through its protein kinase activity, controls the accretion of cell mass through the regulation of gene transcription, mRNA translation, and protein turnover. MTORC1 is activated in an interdependent manner by insulin/growth factors and nutrients, especially amino acids, and is inhibited by stressors such as hypoxia and by the drug rapamycin. The action of insulin/growth factors converges on the small GTPase Rheb, which binds directly to the MTOR polypeptide in MTORC1 and, in its GTP-bound state, initiates kinase activation. Biochemical studies established that MTORC1 exists as a dimer of the MTOR/Raptor/mLst8 trimer, and progressive refinements in cryo-electron microscopy (cryo-EM) have enabled an increasingly clear picture of the architecture of MTORC1, culminating in a deep understanding of how MTORC1 interacts with and phosphorylates its best-known substrates-the eIF-4E binding protein/4E-BP, the p70 S6 kinase/S6K1B, and PRAS40/AKT1S1-and how this is inhibited by rapamycin. Most recently, Rheb-GTP has been shown to bind to MTORC1 in a cooperative manner at an allosteric site remote from the kinase domain that twists the latter into a catalytically competent configuration. Herein, we review the recent cryo-EM and associated biochemical studies of MTORC1 and seek to integrate these new results with the known physiology of MTORC1 regulation and signaling.
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Affiliation(s)
- Luke H Chao
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Joseph Avruch
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
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21
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Abstract
Background The protein kinase Target Of Rapamycin (TOR) is a nexus for the regulation of eukaryotic cell growth. TOR assembles into one of two distinct signalling complexes, TOR complex 1 (TORC1) and TORC2 (mTORC1/2 in mammals), with a set of largely non-overlapping protein partners. (m)TORC1 activation occurs in response to a series of stimuli relevant to cell growth, including nutrient availability, growth factor signals and stress, and regulates much of the cell's biosynthetic activity, from proteins to lipids, and recycling through autophagy. mTORC1 regulation is of great therapeutic significance, since in humans many of these signalling complexes, alongside subunits of mTORC1 itself, are implicated in a wide variety of pathophysiologies, including multiple types of cancer, neurological disorders, neurodegenerative diseases and metabolic disorders including diabetes. Methodology Recent years have seen numerous structures determined of (m)TOR, which have provided mechanistic insight into (m)TORC1 activation in particular, however the integration of cellular signals occurs upstream of the kinase and remains incompletely understood. Here we have collected and analysed in detail as many as possible of the molecular and structural studies which have shed light on (m)TORC1 repression, activation and signal integration. Conclusions A molecular understanding of this signal integration pathway is required to understand how (m)TORC1 activation is reconciled with the many diverse and contradictory stimuli affecting cell growth. We discuss the current level of molecular understanding of the upstream components of the (m)TORC1 signalling pathway, recent progress on this key biochemical frontier, and the future studies necessary to establish a mechanistic understanding of this master-switch for eukaryotic cell growth.
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Affiliation(s)
- Kailash Ramlaul
- Section of Structural Biology, Department of Medicine, Imperial College London, SW7 2AZ, UK
| | - Christopher H S Aylett
- Section of Structural Biology, Department of Medicine, Imperial College London, SW7 2AZ, UK
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22
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Nakhaei-Rad S, Haghighi F, Nouri P, Rezaei Adariani S, Lissy J, Kazemein Jasemi NS, Dvorsky R, Ahmadian MR. Structural fingerprints, interactions, and signaling networks of RAS family proteins beyond RAS isoforms. Crit Rev Biochem Mol Biol 2018; 53:130-156. [PMID: 29457927 DOI: 10.1080/10409238.2018.1431605] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Saeideh Nakhaei-Rad
- a Institute of Biochemistry and Molecular Biology II, Medical Faculty , Heinrich-Heine University , Düsseldorf , Germany
| | - Fereshteh Haghighi
- a Institute of Biochemistry and Molecular Biology II, Medical Faculty , Heinrich-Heine University , Düsseldorf , Germany
| | - Parivash Nouri
- a Institute of Biochemistry and Molecular Biology II, Medical Faculty , Heinrich-Heine University , Düsseldorf , Germany
| | - Soheila Rezaei Adariani
- a Institute of Biochemistry and Molecular Biology II, Medical Faculty , Heinrich-Heine University , Düsseldorf , Germany
| | - Jana Lissy
- a Institute of Biochemistry and Molecular Biology II, Medical Faculty , Heinrich-Heine University , Düsseldorf , Germany
| | - Neda S Kazemein Jasemi
- a Institute of Biochemistry and Molecular Biology II, Medical Faculty , Heinrich-Heine University , Düsseldorf , Germany
| | - Radovan Dvorsky
- a Institute of Biochemistry and Molecular Biology II, Medical Faculty , Heinrich-Heine University , Düsseldorf , Germany
| | - Mohammad Reza Ahmadian
- a Institute of Biochemistry and Molecular Biology II, Medical Faculty , Heinrich-Heine University , Düsseldorf , Germany
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23
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Mahoney SJ, Narayan S, Molz L, Berstler LA, Kang SA, Vlasuk GP, Saiah E. A small molecule inhibitor of Rheb selectively targets mTORC1 signaling. Nat Commun 2018; 9:548. [PMID: 29416044 PMCID: PMC5803267 DOI: 10.1038/s41467-018-03035-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 01/12/2018] [Indexed: 12/19/2022] Open
Abstract
The small G-protein Rheb activates the mechanistic target of rapamycin complex 1 (mTORC1) in response to growth factor signals. mTORC1 is a master regulator of cellular growth and metabolism; aberrant mTORC1 signaling is associated with fibrotic, metabolic, and neurodegenerative diseases, cancers, and rare disorders. Point mutations in the Rheb switch II domain impair its ability to activate mTORC1. Here, we report the discovery of a small molecule (NR1) that binds Rheb in the switch II domain and selectively blocks mTORC1 signaling. NR1 potently inhibits mTORC1 driven phosphorylation of ribosomal protein S6 kinase beta-1 (S6K1) but does not inhibit phosphorylation of AKT or ERK. In contrast to rapamycin, NR1 does not cause inhibition of mTORC2 upon prolonged treatment. Furthermore, NR1 potently and selectively inhibits mTORC1 in mouse kidney and muscle in vivo. The data presented herein suggest that pharmacological inhibition of Rheb is an effective approach for selective inhibition of mTORC1 with therapeutic potential.
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Affiliation(s)
- Sarah J Mahoney
- Navitor Pharmaceuticals, Inc., 1030 Massachusetts Ave. #410, Cambridge, MA, 02138, USA.
| | - Sridhar Narayan
- Navitor Pharmaceuticals, Inc., 1030 Massachusetts Ave. #410, Cambridge, MA, 02138, USA
| | - Lisa Molz
- Navitor Pharmaceuticals, Inc., 1030 Massachusetts Ave. #410, Cambridge, MA, 02138, USA
| | - Lauren A Berstler
- Navitor Pharmaceuticals, Inc., 1030 Massachusetts Ave. #410, Cambridge, MA, 02138, USA
| | - Seong A Kang
- Navitor Pharmaceuticals, Inc., 1030 Massachusetts Ave. #410, Cambridge, MA, 02138, USA
| | - George P Vlasuk
- Navitor Pharmaceuticals, Inc., 1030 Massachusetts Ave. #410, Cambridge, MA, 02138, USA
| | - Eddine Saiah
- Navitor Pharmaceuticals, Inc., 1030 Massachusetts Ave. #410, Cambridge, MA, 02138, USA
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24
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Heard JJ, Phung I, Potes MI, Tamanoi F. An oncogenic mutant of RHEB, RHEB Y35N, exhibits an altered interaction with BRAF resulting in cancer transformation. BMC Cancer 2018; 18:69. [PMID: 29320991 PMCID: PMC5763582 DOI: 10.1186/s12885-017-3938-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 12/19/2017] [Indexed: 12/31/2022] Open
Abstract
Background RHEB is a unique member of the RAS superfamily of small GTPases expressed in all tissues and conserved from yeast to humans. Early studies on RHEB indicated a possible RHEB-RAF interaction, but this has not been fully explored. Recent work on cancer genome databases has revealed a reoccurring mutation in RHEB at the Tyr35 position, and a recent study points to the oncogenic potential of this mutant that involves activation of RAF/MEK/ERK signaling. These developments prompted us to reassess the significance of RHEB effect on RAF, and to compare mutant and wild type RHEB. Methods To study RHEB-RAF interaction, and the effect of the Y35N mutation on this interaction, we used transfection, immunoprecipitation, and Western blotting techniques. We generated cell lines stably expressing RHEB WT, RHEB Y35N, and KRAS G12V, and monitored cellular transforming properties through cell proliferation, anchorage independent growth, cell cycle analysis, and foci formation assays. Results We observe a strong interaction between RHEB and BRAF, but not with CRAF. This interaction is dependent on an intact RHEB effector domain and RHEB-GTP loading status. RHEB overexpression decreases RAF activation of the RAF/MEK/ERK pathway and RHEB knockdown results in an increase in RAF/MEK/ERK activation. RHEB Y35N mutation has decreased interaction with BRAF, and RHEB Y35N cells exhibit greater BRAF/CRAF heterodimerization resulting in increased RAF/MEK/ERK signaling. This leads to cancer transformation of RHEB Y35N stably expressing cell lines, similar to KRAS G12 V expressing cell lines. Conclusions RHEB interaction with BRAF is crucial for inhibiting RAF/MEK/ERK signaling. The RHEB Y35N mutant sustains RAF/MEK/ERK signaling due to a decreased interaction with BRAF, leading to increased BRAF/CRAF heterodimerization. RHEB Y35N expressing cells undergo cancer transformation due to decreased interaction between RHEB and BRAF resulting in overactive RAF/MEK/ERK signaling. Taken together with the previously established function of RHEB to activate mTORC1 signaling, it appears that RHEB performs a dual function; one is to suppress the RAF/MEK/ERK signaling and the other is to activate mTORC1 signaling. Electronic supplementary material The online version of this article (10.1186/s12885-017-3938-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jeffrey J Heard
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, 1602 Molecular Sciences Bldg, 609 Charles E. Young Dr. East, Los Angeles, CA, 90095-1489, USA
| | - Ivy Phung
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, 1602 Molecular Sciences Bldg, 609 Charles E. Young Dr. East, Los Angeles, CA, 90095-1489, USA
| | - Mark I Potes
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, 1602 Molecular Sciences Bldg, 609 Charles E. Young Dr. East, Los Angeles, CA, 90095-1489, USA
| | - Fuyuhiko Tamanoi
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, 1602 Molecular Sciences Bldg, 609 Charles E. Young Dr. East, Los Angeles, CA, 90095-1489, USA. .,Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, Japan.
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25
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Sponder G, Abdulhanan N, Fröhlich N, Mastrototaro L, Aschenbach JR, Röntgen M, Pilchova I, Cibulka M, Racay P, Kolisek M. Overexpression of Na +/Mg 2+ exchanger SLC41A1 attenuates pro-survival signaling. Oncotarget 2017; 9:5084-5104. [PMID: 29435164 PMCID: PMC5797035 DOI: 10.18632/oncotarget.23598] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 11/13/2017] [Indexed: 01/07/2023] Open
Abstract
The Na+/Mg2+ exchanger SLC41A1 (A1), a key component of intracellular Mg homeostasis (IMH), is the major cellular Mg2+ efflux system, and its overexpression decreases [Mg2+]intracellular. IMH plays an important role in the regulation of many cellular processes, including cellular signaling. However, whether the overexpression of A1 and the consequent drop of [Mg2+]i impact on intracellular signaling is unknown. To examine the latter, we utilized dynamic mass redistribution (DMR) assay, PathScan® RTK signaling antibody (PRSA) array, confirmatory Western blot (WB) analyses of phosphorylation of kinases selected by PRSA, and mag-fura 2-assisted fast filter spectrometry (FFS). We demonstrate here that the overexpression of A1 quantitatively and qualitatively changes the DMR signal evoked by the application of PAR-1-selective activating peptide and/or by changing [Mg2+]extracellular in HEK293 cells. PRSA profiling of the phosphorylation of important signaling nodes followed by confirmatory WB has revealed that, in HEK293 cells, A1 overexpression significantly attenuates the phosphorylation of Akt/PKB on Thr308 and/or Ser473 and of Erk1/2 on Thr202/Tyr204 in the presence of 0 or 1 mM (physiological) Mg2+ in the bath solution. The latter is also true for SH-SY5Y and HeLa cells. Overexpression of A1 in HEK293 cells significantly lowers [Mg2+]i in the presence of [Mg2+]e = 0 or 1 mM. This correlates with the observed attenuation of prosurvival Akt/PKB - Erk1/2 signaling in these cells. Thus, A1 expression status and [Mg2+]e (and consequently also [Mg2+]i) modulate the complex physiological fingerprint of the cell and influence the activity of kinases involved in anti-apoptotic and, hence, pro-survival events in cells.
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Affiliation(s)
- Gerhard Sponder
- Institute of Veterinary-Physiology, Free University of Berlin, Berlin, Germany
| | - Nasrin Abdulhanan
- Institute of Veterinary-Physiology, Free University of Berlin, Berlin, Germany
| | - Nadine Fröhlich
- PerkinElmer Life and Analytical Sciences GmbH, Rodgau, Germany
| | - Lucia Mastrototaro
- Institute of Veterinary-Physiology, Free University of Berlin, Berlin, Germany
| | - Jörg R Aschenbach
- Institute of Veterinary-Physiology, Free University of Berlin, Berlin, Germany
| | - Monika Röntgen
- Leibnitz Institute for Farm Animal Biology, Department of Muscle and Growth Physiology, Dummerstorf, Germany
| | - Ivana Pilchova
- Biomedical Center Martin, Division of Neurosciences, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Michal Cibulka
- Institute of Medical Biochemistry, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Peter Racay
- Biomedical Center Martin, Division of Neurosciences, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia.,Institute of Medical Biochemistry, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Martin Kolisek
- Institute of Veterinary-Physiology, Free University of Berlin, Berlin, Germany.,Biomedical Center Martin, Division of Neurosciences, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
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26
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De Cicco M, Kiss L, Dames SA. NMR analysis of the backbone dynamics of the small GTPase Rheb and its interaction with the regulatory protein FKBP38. FEBS Lett 2017; 592:130-146. [PMID: 29194576 DOI: 10.1002/1873-3468.12925] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 10/06/2017] [Accepted: 11/17/2017] [Indexed: 12/19/2022]
Abstract
Ras homolog enriched in brain (Rheb) is a small GTPase that regulates mammalian/mechanistic target of rapamycin complex 1 (mTORC1) and, thereby, cell growth and metabolism. Here we show that cycling between the inactive GDP- and the active GTP-bound state modulates the backbone dynamics of a C-terminal truncated form, RhebΔCT, which is suggested to influence its interactions. We further investigated the interactions between RhebΔCT and the proposed Rheb-binding domain of the regulatory protein FKBP38. The observed weak interactions with the GTP-analogue- (GppNHp-) but not the GDP-bound state, appear to accelerate the GDP to GTP exchange, but only very weakly compared to a genuine GEF. Thus, FKBP38 is most likely not a GEF but a Rheb effector that may function in membrane targeting of Rheb.
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Affiliation(s)
- Maristella De Cicco
- Technische Universität München, Department of Chemistry, Biomolecular NMR Spectroscopy, Garching, Germany
| | - Leo Kiss
- Technische Universität München, Department of Chemistry, Biomolecular NMR Spectroscopy, Garching, Germany
| | - Sonja A Dames
- Technische Universität München, Department of Chemistry, Biomolecular NMR Spectroscopy, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
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27
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Yang H, Jiang X, Li B, Yang HJ, Miller M, Yang A, Dhar A, Pavletich NP. Mechanisms of mTORC1 activation by RHEB and inhibition by PRAS40. Nature 2017; 552:368-373. [PMID: 29236692 PMCID: PMC5750076 DOI: 10.1038/nature25023] [Citation(s) in RCA: 333] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 11/08/2017] [Indexed: 12/13/2022]
Abstract
The mechanistic target of rapamycin complex 1 (mTORC1) controls cell growth and metabolism in response to nutrients, energy levels, and growth factors. It contains the atypical kinase mTOR and the RAPTOR subunit that binds to the Tor signalling sequence (TOS) motif of substrates and regulators. mTORC1 is activated by the small GTPase RHEB (Ras homologue enriched in brain) and inhibited by PRAS40. Here we present the 3.0 ångström cryo-electron microscopy structure of mTORC1 and the 3.4 ångström structure of activated RHEB-mTORC1. RHEB binds to mTOR distally from the kinase active site, yet causes a global conformational change that allosterically realigns active-site residues, accelerating catalysis. Cancer-associated hyperactivating mutations map to structural elements that maintain the inactive state, and we provide biochemical evidence that they mimic RHEB relieving auto-inhibition. We also present crystal structures of RAPTOR-TOS motif complexes that define the determinants of TOS recognition, of an mTOR FKBP12-rapamycin-binding (FRB) domain-substrate complex that establishes a second substrate-recruitment mechanism, and of a truncated mTOR-PRAS40 complex that reveals PRAS40 inhibits both substrate-recruitment sites. These findings help explain how mTORC1 selects its substrates, how its kinase activity is controlled, and how it is activated by cancer-associated mutations.
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Affiliation(s)
- Haijuan Yang
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Xiaolu Jiang
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Buren Li
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Hyo J Yang
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Meredith Miller
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Angela Yang
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Ankita Dhar
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Nikola P Pavletich
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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28
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Kotyada C, Maulik A, Srivastava A, Singh M. Mechanistic Insights into the Differential Catalysis by RheB and Its Mutants: Y35A and Y35A-D65A. ACS OMEGA 2017; 2:6691-6702. [PMID: 29750207 PMCID: PMC5937686 DOI: 10.1021/acsomega.7b01025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 09/28/2017] [Indexed: 06/08/2023]
Abstract
RheB GTPase is a Ras-related molecular switch, which regulates the mTOR signaling pathway by cycling between the active [guanosine triphosphate (GTP)] state and inactive [guanine diphosphate (GDP)] state. Impairment of GTPase activity because of mutations in several small GTPases is known to be associated with several cancers. The conventional GTPase mechanism such as in H-Ras requires a conserved glutamine (Q64) in the switch-II region of RheB to align the catalytic water molecule for efficient GTP hydrolysis. The conformation of this conserved glutamine is different in RheB, resulting in an altered conformation of the entire switch-II region. Studies on the atypical switch-II conformation in RheB revealed a distinct, noncanonical mode of GTP hydrolysis. An RheB mutant Y35A was previously shown to exclusively enhance the intrinsic GTPase activity of RheB, whereas the Y35A-D65A double mutant was shown to reduce the elevated GTPase activity. Here, we have used all-atom molecular dynamics (MD) simulations for comprehensive understanding of the conformational dynamics associated with the fast (Y35A) and slow (Y35A-D65A) hydrolyzing mutants of RheB. Using a combination of starting models from PDB structures and in-silico generated mutant structures, we discuss the observed conformational deviations in wild type (WT) versus mutants. Our results show that a number of interactions of RheB with phosphates of GTP as well as Mg2+ are destabilized in Y35A mutant in the switch-I region. We report distinct water dynamics at the active site of WT and mutants. Furthermore, principal component analysis showed significant differences in the conformational space sampled by the WT and mutants. Our observations provide improved understanding of the noncanonical GTP hydrolysis mechanism adopted by RheB and its modulation by Y35A and Y35A-D65A mutants.
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Affiliation(s)
- Chaithanya Kotyada
- Molecular
Biophysics Unit and NMR Research Centre, Indian Institute of
Science, Bengaluru 560012, India
| | - Aditi Maulik
- Molecular
Biophysics Unit and NMR Research Centre, Indian Institute of
Science, Bengaluru 560012, India
| | - Anand Srivastava
- Molecular
Biophysics Unit and NMR Research Centre, Indian Institute of
Science, Bengaluru 560012, India
| | - Mahavir Singh
- Molecular
Biophysics Unit and NMR Research Centre, Indian Institute of
Science, Bengaluru 560012, India
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29
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Nguyen TP, Frank AR, Jewell JL. Amino acid and small GTPase regulation of mTORC1. CELLULAR LOGISTICS 2017; 7:e1378794. [PMID: 29296509 PMCID: PMC5739091 DOI: 10.1080/21592799.2017.1378794] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 09/06/2017] [Accepted: 09/08/2017] [Indexed: 11/03/2022]
Abstract
The mammalian target of rapamycin (mTOR) is an evolutionarily conserved serine/threonine kinase that belongs to the phosphatidylinositol 3-kinase-related kinase (PIKK) family. mTOR is the catalytic subunit of mTOR complex 1 (mTORC1), which integrates multiple environmental signals to control cell growth and metabolism. Nutrients, specifically amino acids, are the most potent stimuli for mTORC1 activation. Multiple studies have focused on how leucine and arginine activate mTORC1 through the Rag GTPases, with mechanistic details slowly emerging. Recently, a Rag GTPase-independent glutamine signaling pathway to mTORC1 has been identified, suggesting that mTORC1 is differentially regulated through distinct pathways by specific amino acids. In this review, we summarize our current understanding of how amino acids modulate mTORC1, and the role of other small GTPases in the regulation of mTORC1 activity.
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Affiliation(s)
- Thu P Nguyen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Anderson R Frank
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Jenna L Jewell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX USA
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30
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Schöpel M, Potheraveedu VN, Al-Harthy T, Abdel-Jalil R, Heumann R, Stoll R. The small GTPases Ras and Rheb studied by multidimensional NMR spectroscopy: structure and function. Biol Chem 2017; 398:577-588. [DOI: 10.1515/hsz-2016-0276] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 01/23/2017] [Indexed: 12/15/2022]
Abstract
Abstract
Ras GTPases are key players in cellular signalling because they act as binary switches. These states manifest through toggling between an active (GTP-loaded) and an inactive (GDP-loaded) form. The hydrolysis and replenishing of GTP is controlled by two additional protein classes: GAP (GTPase-activating)- and GEF (Guanine nucleotide exchange factors)-proteins. The complex interplay of the proteins is known as the GTPase-cycle. Several point mutations of the Ras protein deregulate this cycle. Mutations in Ras are associated with up to one-third of human cancers. The three isoforms of Ras (H, N, K) exhibit high sequence similarity and mainly differ in a region called HVR (hypervariable region). The HVR governs the differential action and cellular distribution of the three isoforms. Rheb is a Ras-like GTPase that is conserved from yeast to mammals. Rheb is mainly involved in activation of cell growth through stimulation of mTORC1 activity. In this review, we summarise multidimensional NMR studies on Rheb and Ras carried out to characterise their structure-function relationship and explain how the activity of these small GTPases can be modulated by low molecular weight compounds. These might help to design GTPase-selective antagonists for treatment of cancer and brain disease.
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31
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Ghosh AP, Marshall CB, Coric T, Shim EH, Kirkman R, Ballestas ME, Ikura M, Bjornsti MA, Sudarshan S. Point mutations of the mTOR-RHEB pathway in renal cell carcinoma. Oncotarget 2016; 6:17895-910. [PMID: 26255626 PMCID: PMC4627224 DOI: 10.18632/oncotarget.4963] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 07/03/2015] [Indexed: 01/21/2023] Open
Abstract
Aberrations in the mTOR (mechanistic target of rapamycin) axis are frequently reported in cancer. Using publicly available tumor genome sequencing data, we identified several point mutations in MTOR and its upstream regulator RHEB (Ras homolog enriched in brain) in patients with clear cell renal cell carcinoma (ccRCC), the most common histology of kidney cancer. Interestingly, we found a prominent cluster of hyperactivating mutations in the FAT (FRAP-ATM-TTRAP) domain of mTOR in renal cell carcinoma that led to an increase in both mTORC1 and mTORC2 activities and led to an increased proliferation of cells. Several of the FAT domain mutants demonstrated a decreased binding of DEPTOR (DEP domain containing mTOR-interacting protein), while a subset of these mutations showed altered binding of the negative regulator PRAS40 (proline rich AKT substrate 40). We also identified a recurrent mutation in RHEB in ccRCC patients that leads to an increase in mTORC1 activity. In vitro characterization of this RHEB mutation revealed that this mutant showed considerable resistance to TSC2 (Tuberous Sclerosis 2) GAP (GTPase activating protein) activity, though its interaction with TSC2 remained unaltered. Mutations in the FAT domain of MTOR and in RHEB remained sensitive to rapamycin, though several of these mutations demonstrated residual mTOR kinase activity after treatment with rapamycin at clinically relevant doses. Overall, our data suggests that point mutations in the mTOR pathway may lead to downstream mTOR hyperactivation through multiple different mechanisms to confer a proliferative advantage to a tumor cell.
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Affiliation(s)
- Arindam P Ghosh
- Department of Urology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Christopher B Marshall
- Department of Medical Biophysics, Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, University of Toronto, Toronto, Canada
| | - Tatjana Coric
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Eun-Hee Shim
- Department of Urology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Richard Kirkman
- Department of Urology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Mary E Ballestas
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Mitsuhiko Ikura
- Department of Medical Biophysics, Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, University of Toronto, Toronto, Canada
| | - Mary-Ann Bjornsti
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Sunil Sudarshan
- Department of Urology, University of Alabama at Birmingham, Birmingham, Alabama, USA
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32
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Carroll B, Maetzel D, Maddocks ODK, Otten G, Ratcliff M, Smith GR, Dunlop EA, Passos JF, Davies OR, Jaenisch R, Tee AR, Sarkar S, Korolchuk VI. Control of TSC2-Rheb signaling axis by arginine regulates mTORC1 activity. eLife 2016; 5:e11058. [PMID: 26742086 PMCID: PMC4764560 DOI: 10.7554/elife.11058] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 12/30/2015] [Indexed: 01/07/2023] Open
Abstract
The mammalian target of rapamycin complex 1 (mTORC1) is the key signaling hub that regulates cellular protein homeostasis, growth, and proliferation in health and disease. As a prerequisite for activation of mTORC1 by hormones and mitogens, there first has to be an available pool of intracellular amino acids. Arginine, an amino acid essential during mammalian embryogenesis and early development is one of the key activators of mTORC1. Herein, we demonstrate that arginine acts independently of its metabolism to allow maximal activation of mTORC1 by growth factors via a mechanism that does not involve regulation of mTORC1 localization to lysosomes. Instead, arginine specifically suppresses lysosomal localization of the TSC complex and interaction with its target small GTPase protein, Rheb. By interfering with TSC-Rheb complex, arginine relieves allosteric inhibition of Rheb by TSC. Arginine cooperates with growth factor signaling which further promotes dissociation of TSC2 from lysosomes and activation of mTORC1. Arginine is the main amino acid sensed by the mTORC1 pathway in several cell types including human embryonic stem cells (hESCs). Dependence on arginine is maintained once hESCs are differentiated to fibroblasts, neurons, and hepatocytes, highlighting the fundamental importance of arginine-sensing to mTORC1 signaling. Together, our data provide evidence that different growth promoting cues cooperate to a greater extent than previously recognized to achieve tight spatial and temporal regulation of mTORC1 signaling.
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Affiliation(s)
- Bernadette Carroll
- Institute for Cell and Molecular BiosciencesNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Dorothea Maetzel
- Whitehead Institute for Biomedical ResearchMassachusetts Institute of TechnologyCambridgeUnited States
| | | | - Gisela Otten
- Institute for Cell and Molecular BiosciencesNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Matthew Ratcliff
- Institute for Cell and Molecular BiosciencesNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Graham R Smith
- Institute for Cell and Molecular BiosciencesNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Elaine A Dunlop
- Institute of Cancer and GeneticsCardiff UniversityCardiffUnited Kingdom
| | - João F Passos
- Institute for Cell and Molecular BiosciencesNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Owen R Davies
- Institute for Cell and Molecular BiosciencesNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical ResearchMassachusetts Institute of TechnologyCambridgeUnited States
| | - Andrew R Tee
- Institute of Cancer and GeneticsCardiff UniversityCardiffUnited Kingdom
| | - Sovan Sarkar
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental SciencesUniversity of BirminghamBirminghamUnited Kingdom
| | - Viktor I Korolchuk
- Institute for Cell and Molecular BiosciencesNewcastle UniversityNewcastle upon TyneUnited Kingdom
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33
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Chen YX, Koch S, Uhlenbrock K, Weise K, Das D, Gremer L, Brunsveld L, Wittinghofer A, Winter R, Triola G, Waldmann H. Synthesis of the Rheb and K-Ras4B GTPases. Angew Chem Int Ed Engl 2015; 49:6090-5. [PMID: 20652921 DOI: 10.1002/anie.201001884] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yong-Xiang Chen
- Abteilung Chemische Biologie, Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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34
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Dibble CC, Cantley LC. Regulation of mTORC1 by PI3K signaling. Trends Cell Biol 2015; 25:545-55. [PMID: 26159692 DOI: 10.1016/j.tcb.2015.06.002] [Citation(s) in RCA: 573] [Impact Index Per Article: 63.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 06/08/2015] [Accepted: 06/08/2015] [Indexed: 11/29/2022]
Abstract
The class I phosphoinositide 3-kinase (PI3K)-mechanistic target of rapamycin (mTOR) complex 1 (mTORC1) signaling network directs cellular metabolism and growth. Activation of mTORC1 [composed of mTOR, regulatory-associated protein of mTOR (Raptor), mammalian lethal with SEC13 protein 8(mLST8), 40-kDa proline-rich Akt substrate (PRAS40), and DEP domain-containing mTOR-interacting protein (DEPTOR)] depends on the Ras-related GTPases (Rags) and Ras homolog enriched in brain (Rheb) GTPase and requires signals from amino acids, glucose, oxygen, energy (ATP), and growth factors (including cytokines and hormones such as insulin). Here we discuss the signal transduction mechanisms through which growth factor-responsive PI3K signaling activates mTORC1. We focus on how PI3K-dependent activation of Akt and spatial regulation of the tuberous sclerosis complex (TSC) complex (TSC complex) [composed of TSC1, TSC2, and Tre2-Bub2-Cdc16-1 domain family member 7 (TBC1D7)] switches on Rheb at the lysosome, where mTORC1 is activated. Integration of PI3K- and amino acid-dependent signals upstream of mTORC1 at the lysosome is detailed in a working model. A coherent understanding of the PI3K-mTORC1 network is imperative as its dysregulation has been implicated in diverse pathologies including cancer, diabetes, autism, and aging.
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Affiliation(s)
- Christian C Dibble
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Lewis C Cantley
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA.
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Soltan Ghoraie L, Burkowski F, Zhu M. Using kernelized partial canonical correlation analysis to study directly coupled side chains and allostery in small G proteins. Bioinformatics 2015; 31:i124-32. [PMID: 26072474 PMCID: PMC4765857 DOI: 10.1093/bioinformatics/btv241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Motivation: Inferring structural dependencies among a protein’s side chains helps us understand their coupled motions. It is known that coupled fluctuations can reveal pathways of communication used for information propagation in a molecule. Side-chain conformations are commonly represented by multivariate angular variables, but existing partial correlation methods that can be applied to this inference task are not capable of handling multivariate angular data. We propose a novel method to infer direct couplings from this type of data, and show that this method is useful for identifying functional regions and their interactions in allosteric proteins. Results: We developed a novel extension of canonical correlation analysis (CCA), which we call ‘kernelized partial CCA’ (or simply KPCCA), and used it to infer direct couplings between side chains, while disentangling these couplings from indirect ones. Using the conformational information and fluctuations of the inactive structure alone for allosteric proteins in the Ras and other Ras-like families, our method identified allosterically important residues not only as strongly coupled ones but also in densely connected regions of the interaction graph formed by the inferred couplings. Our results were in good agreement with other empirical findings. By studying distinct members of the Ras, Rho and Rab sub-families, we show further that KPCCA was capable of inferring common allosteric characteristics in the small G protein super-family. Availability and implementation:https://github.com/lsgh/ismb15 Contact:lsoltang@uwaterloo.ca
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Affiliation(s)
- Laleh Soltan Ghoraie
- Department of Computer Science and Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, ON, Canada
| | - Forbes Burkowski
- Department of Computer Science and Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, ON, Canada
| | - Mu Zhu
- Department of Computer Science and Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, ON, Canada
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Düppe PM, Tran Thi Phuong T, Autzen J, Schöpel M, Yip KT, Stoll R, Scherkenbeck J. Sequence-selective molecular recognition of the C-terminal CaaX-boxes of Rheb and related Ras-proteins by synthetic receptors. ACS Chem Biol 2014; 9:1755-63. [PMID: 24856002 DOI: 10.1021/cb5002075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Constitutive activation of Ras-proteins plays an important role in the development of aggressive colorectal carcinomas and several other types of cancer. Despite some progress in recent years in the case of K-Ras4B, until now not a single small molecule inhibitor has been identified that binds efficiently to Rheb and interrupts the protein-protein interactions with mTOR. We describe here a complementary approach that aims at inhibiting membrane insertion of Rheb and related Ras proteins by masking the crucial C-terminal CaaX-box with peptidomimetic receptors identified in combinatorial solid-phase libraries.
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Affiliation(s)
- Peter M. Düppe
- University of Wuppertal, Gaußstraße
20, D-42119 Wuppertal, Germany
| | | | - Jasmin Autzen
- University of Wuppertal, Gaußstraße
20, D-42119 Wuppertal, Germany
| | - Miriam Schöpel
- Ruhr-University of Bochum, Universitätsstraße
150, D-44780 Bochum, Germany
| | - King Tuo Yip
- Ruhr-University of Bochum, Universitätsstraße
150, D-44780 Bochum, Germany
| | - Raphael Stoll
- Ruhr-University of Bochum, Universitätsstraße
150, D-44780 Bochum, Germany
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Recent progress in the study of the Rheb family GTPases. Cell Signal 2014; 26:1950-7. [PMID: 24863881 DOI: 10.1016/j.cellsig.2014.05.011] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 05/15/2014] [Indexed: 11/20/2022]
Abstract
In this review we highlight recent progress in the study of Rheb family GTPases. Structural studies using X-ray crystallography and NMR have given us insight into unique features of this GTPase. Combined with mutagenesis studies, these works have expanded our understanding of residues that affect Rheb GTP/GDP bound ratios, effector protein interactions, and stimulation of mTORC1 signaling. Analysis of cancer genome databases has revealed that several human carcinomas contain activating mutations of the protein. Rheb's role in activating mTORC1 signaling at the lysosome in response to stimuli has been further elucidated. Rheb has also been suggested to play roles in other cellular pathways including mitophagy and peroxisomal ROS response. A number of studies in mice have demonstrated the importance of Rheb in development, as well as in a variety of functions including cardiac protection and myelination. We conclude with a discussion of future prospects in the study of Rheb family GTPases.
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Mazhab-Jafari MT, Marshall CB, Ho J, Ishiyama N, Stambolic V, Ikura M. Structure-guided mutation of the conserved G3-box glycine in Rheb generates a constitutively activated regulator of mammalian target of rapamycin (mTOR). J Biol Chem 2014; 289:12195-201. [PMID: 24648513 DOI: 10.1074/jbc.c113.543736] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Constitutively activated variants of small GTPases, which provide valuable functional probes of their role in cellular signaling pathways, can often be generated by mutating the canonical catalytic residue (e.g. Ras Q61L) to impair GTP hydrolysis. However, this general approach is ineffective for a substantial fraction of the small GTPase family in which this residue is not conserved (e.g. Rap) or not catalytic (e.g. Rheb). Using a novel engineering approach, we have manipulated nucleotide binding through structure-guided substitutions of an ultraconserved glycine residue in the G3-box motif (DXXG). Substitution of Rheb Gly-63 with alanine impaired both intrinsic and TSC2 GTPase-activating protein (GAP)-mediated GTP hydrolysis by displacing the hydrolytic water molecule, whereas introduction of a bulkier valine side chain selectively blocked GTP binding by steric occlusion of the γ-phosphate. Rheb G63A stimulated phosphorylation of the mTORC1 substrate p70S6 kinase more strongly than wild-type, thus offering a new tool for mammalian target of rapamycin (mTOR) signaling.
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Affiliation(s)
- Mohammad T Mazhab-Jafari
- From the Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre and, Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 2M9, Canada
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Lee KM, Hwang SK, Lee JA. Neuronal autophagy and neurodevelopmental disorders. Exp Neurobiol 2013; 22:133-42. [PMID: 24167408 PMCID: PMC3807000 DOI: 10.5607/en.2013.22.3.133] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 09/12/2013] [Accepted: 09/12/2013] [Indexed: 12/15/2022] Open
Abstract
Neurodevelopmental disorders include a wide range of diseases such as autism spectrum disorders and mental retardation. Mutations in several genes that regulate neural development and synapse function have been identified in neurodevelopmental disorders. Interestingly, some affected genes and pathways in these diseases are associated with the autophagy pathway. Autophagy is a complex, bulky degradative process that involves the sequestration of cellular proteins, RNA, lipids, and cellular organelles into lysosomes. Despite recent progress in elucidating the genetics and molecular pathogenesis of these disorders, little is known about the pathogenic mechanisms and autophagy-related pathways involved in common neurodevelopmental disorders. Therefore, in this review, we focus on the current understanding of neuronal autophagy as well as recent findings on genetics and the roles of autophagy pathway in common neurodevelopmental disorders.
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Affiliation(s)
- Kyung-Min Lee
- Department of Anatomy, Graduate School of Medicine, Kyungpook National University, Daegu 700-422, Korea
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40
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Long D, Marshall CB, Bouvignies G, Mazhab-Jafari MT, Smith MJ, Ikura M, Kay LE. A Comparative CEST NMR Study of Slow Conformational Dynamics of Small GTPases Complexed with GTP and GTP Analogues. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201305434] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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41
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Long D, Marshall CB, Bouvignies G, Mazhab-Jafari MT, Smith MJ, Ikura M, Kay LE. A comparative CEST NMR study of slow conformational dynamics of small GTPases complexed with GTP and GTP analogues. Angew Chem Int Ed Engl 2013; 52:10771-4. [PMID: 24039022 DOI: 10.1002/anie.201305434] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Indexed: 01/14/2023]
Affiliation(s)
- Dong Long
- Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario M5S 1A8 (Canada)
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Abstract
The Ras superfamily G-proteins are monomeric proteins of approximately 21kDa that act as a molecular switch to regulate a variety of cellular processes. The structure of the Ras superfamily G-proteins, their regulators as well as posttranslational modification of these proteins leading to their membrane association have been elucidated. The Ras superfamily G-proteins interact at their effector domains with their downstream effectors via protein-protein interactions. Mutational activation or overexpression of the Ras superfamily G-proteins has been observed in a number of human cancer cases. Over the years, a variety of approaches to inhibit the Ras superfamily G-proteins have been developed. These different approaches are discussed in this volume.
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Affiliation(s)
- Ashley L Tetlow
- Department of Microbiology, Immunology and Molecular Genetics, Molecular Biology Institute, Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California, USA
| | - Fuyuhiko Tamanoi
- Department of Microbiology, Immunology and Molecular Genetics, Molecular Biology Institute, Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California, USA.
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Mazhab-Jafari MT, Marshall CB, Stathopulos PB, Kobashigawa Y, Stambolic V, Kay LE, Inagaki F, Ikura M. Membrane-dependent modulation of the mTOR activator Rheb: NMR observations of a GTPase tethered to a lipid-bilayer nanodisc. J Am Chem Soc 2013; 135:3367-70. [PMID: 23409921 DOI: 10.1021/ja312508w] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Like most Ras superfamily proteins, the GTPase domain of Ras homologue enriched in brain (Rheb) is tethered to cellular membranes through a prenylated cysteine in a flexible C-terminal region; however, little is known about how Rheb or other GTPases interact with the membrane or how this environment may affect their GTPase functions. We used NMR methods to characterize Rheb tethered to nanodiscs, monodisperse protein-encapsulated lipid bilayers with a diameter of 10 nm. Membrane conjugation markedly reduced the rate of intrinsic nucleotide exchange, while GTP hydrolysis was unchanged. NMR measurements revealed that the GTPase domain interacts transiently with the surface of the bilayer in two distinct preferred orientations, which are determined by the bound nucleotide. We propose models of membrane-dependent signal regulation by Rheb that shed light on previously unexplained in vivo properties of this GTPase. The study presented provides a general approach for direct experimental investigation of membrane-dependent properties of other Ras-superfamily GTPases.
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Affiliation(s)
- Mohammad T Mazhab-Jafari
- Department of Medical Biophysics, Campbell Family Cancer Research Institute, Princess Margaret Cancer Center, University Health Network, University of Toronto, Toronto, Ontario M5G 2M9, Canada
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Mazhab-Jafari MT, Marshall CB, Ishiyama N, Ho J, Di Palma V, Stambolic V, Ikura M. An autoinhibited noncanonical mechanism of GTP hydrolysis by Rheb maintains mTORC1 homeostasis. Structure 2012; 20:1528-39. [PMID: 22819219 DOI: 10.1016/j.str.2012.06.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 06/18/2012] [Accepted: 06/20/2012] [Indexed: 01/28/2023]
Abstract
Rheb, an activator of mammalian target of rapamycin (mTOR), displays low intrinsic GTPase activity favoring the biologically activated, GTP-bound state. We identified a Rheb mutation (Y35A) that increases its intrinsic nucleotide hydrolysis activity ∼10-fold, and solved structures of both its active and inactive forms, revealing an unexpected mechanism of GTP hydrolysis involving Asp65 in switch II and Thr38 in switch I. In the wild-type protein this noncanonical mechanism is markedly inhibited by Tyr35, which constrains the active site conformation, restricting the access of the catalytic Asp65 to the nucleotide-binding pocket. Rheb Y35A mimics the enthalpic and entropic changes associated with GTP hydrolysis elicited by the GTPase-activating protein (GAP) TSC2, and is insensitive to further TSC2 stimulation. Overexpression of Rheb Y35A impaired the regulation of mTORC1 signaling by growth factor availability. We demonstrate that the opposing functions of Tyr35 in the intrinsic and GAP-stimulated GTP catalysis are critical for optimal mTORC1 regulation.
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45
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Ismail SA, Chen YX, Rusinova A, Chandra A, Bierbaum M, Gremer L, Triola G, Waldmann H, Bastiaens PIH, Wittinghofer A. Arl2-GTP and Arl3-GTP regulate a GDI-like transport system for farnesylated cargo. Nat Chem Biol 2011; 7:942-9. [PMID: 22002721 DOI: 10.1038/nchembio.686] [Citation(s) in RCA: 210] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 08/31/2011] [Indexed: 01/21/2023]
Abstract
Lipidated Rho and Rab GTP-binding proteins are transported between membranes in complex with solubilizing factors called 'guanine nucleotide dissociation inhibitors' (GDIs). Unloading from GDIs using GDI displacement factors (GDFs) has been proposed but remains mechanistically elusive. PDEδ is a putative solubilizing factor for several prenylated Ras-subfamily proteins. Here we report the structure of fully modified farnesylated Rheb-GDP in complex with PDEδ. The structure explains the nucleotide-independent binding of Rheb to PDEδ and the relaxed specificity of PDEδ. We demonstrate that the G proteins Arl2 and Arl3 act in a GTP-dependent manner as allosteric release factors for farnesylated cargo. We thus describe a new transport system for farnesylated G proteins involving a GDI-like molecule and an unequivocal GDF. Considering the importance of PDEδ for proper Ras and Rheb signaling, this study is instrumental in developing a new target for anticancer therapy.
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Affiliation(s)
- Shehab A Ismail
- Structural Biology Group, Max Planck Institute for Molecular Physiology, Dortmund, Germany
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46
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Inactivation of Rheb by PRAK-mediated phosphorylation is essential for energy-depletion-induced suppression of mTORC1. Nat Cell Biol 2011; 13:263-72. [PMID: 21336308 PMCID: PMC3070924 DOI: 10.1038/ncb2168] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 12/12/2010] [Indexed: 12/30/2022]
Abstract
Cell growth can be suppressed by stressful environments, but the role of stress pathways in this process is largely unknown. Here we show that a cascade of p38β mitogen activated protein kinase and p38 regulated/activated kinase (PRAK) plays a role in energy starvation-induced suppression of mammalian target of rapamycin (mTOR), that energy starvation activates the p38β-PRAK cascade, and that p38β- or PRAK-deletion diminishes energy depletion-induced suppression of mTORC1 and reduction of cell size. We show that p38β-PRAK operates independent from the known mTORC1 inactivation pathways – phosphorylation of tuberous sclerosis protein 2 (TSC2) and raptor by AMP activated protein kinase (AMPK), and surprisingly, PRAK directly regulates Ras homolog enriched in brain (Rheb), a key component of the mTORC1 pathway by phosphorylation. Phosphorylation of Rheb at serine 130 by PRAK impairs Rheb’s nucleotide-binding ability and inhibits Rheb-mediated mTORC1 activation. The direct regulation of Rheb by PRAK integrates a stress pathway with the mTORC1 pathway in response to energy depletion.
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Karassek S, Berghaus C, Schwarten M, Goemans CG, Ohse N, Kock G, Jockers K, Neumann S, Gottfried S, Herrmann C, Heumann R, Stoll R. Ras homolog enriched in brain (Rheb) enhances apoptotic signaling. J Biol Chem 2010; 285:33979-91. [PMID: 20685651 PMCID: PMC2962498 DOI: 10.1074/jbc.m109.095968] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2009] [Revised: 07/19/2010] [Indexed: 12/18/2022] Open
Abstract
Rheb is a homolog of Ras GTPase that regulates cell growth, proliferation, and regeneration via mammalian target of rapamycin (mTOR). Because of the well established potential of activated Ras to promote survival, we sought to investigate the ability of Rheb signaling to phenocopy Ras. We found that overexpression of lipid-anchored Rheb enhanced the apoptotic effects induced by UV light, TNFα, or tunicamycin in an mTOR complex 1 (mTORC1)-dependent manner. Knocking down endogenous Rheb or applying rapamycin led to partial protection, identifying Rheb as a mediator of cell death. Ras and c-Raf kinase opposed the apoptotic effects induced by UV light or TNFα but did not prevent Rheb-mediated apoptosis. To gain structural insight into the signaling mechanisms, we determined the structure of Rheb-GDP by NMR. The complex adopts the typical canonical fold of RasGTPases and displays the characteristic GDP-dependent picosecond to nanosecond backbone dynamics of the switch I and switch II regions. NMR revealed Ras effector-like binding of activated Rheb to the c-Raf-Ras-binding domain (RBD), but the affinity was 1000-fold lower than the Ras/RBD interaction, suggesting a lack of functional interaction. shRNA-mediated knockdown of apoptosis signal-regulating kinase 1 (ASK-1) strongly reduced UV or TNFα-induced apoptosis and suppressed enhancement by Rheb overexpression. In conclusion, Rheb-mTOR activation not only promotes normal cell growth but also enhances apoptosis in response to diverse toxic stimuli via an ASK-1-mediated mechanism. Pharmacological regulation of the Rheb/mTORC1 pathway using rapamycin should take the presence of cellular stress into consideration, as this may have clinical implications.
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Affiliation(s)
| | | | | | | | - Nadine Ohse
- Physical Chemistry I, Faculty of Chemistry and Biochemistry, Ruhr University of Bochum, 44780 Bochum, Germany
| | | | | | | | | | - Christian Herrmann
- Physical Chemistry I, Faculty of Chemistry and Biochemistry, Ruhr University of Bochum, 44780 Bochum, Germany
| | - Rolf Heumann
- From the Departments of Molecular Neurobiochemistry
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Chen YX, Koch S, Uhlenbrock K, Weise K, Das D, Gremer L, Brunsveld L, Wittinghofer A, Winter R, Triola G, Waldmann H. Synthesis of the Rheb and K-Ras4B GTPases. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201001884] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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49
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Weatherill DB, Dyer J, Sossin WS. Ribosomal protein S6 kinase is a critical downstream effector of the target of rapamycin complex 1 for long-term facilitation in Aplysia. J Biol Chem 2010; 285:12255-67. [PMID: 20177060 DOI: 10.1074/jbc.m109.071142] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Long-term facilitation (LTF) in Aplysia is a leading cellular model for elucidating the biochemical mechanisms of synaptic plasticity underlying learning. In Aplysia, LTF requires translational control downstream of the target of rapamycin (TOR) complex 1 (TORC1). The major known downstream targets of TORC1 are 4E binding protein (4E-BP) and S6 kinase (S6K). By removing the site within these regulators required for their interaction with TORC1, we have generated dominant negative proteins that disrupt specific pathways downstream of TORC1. Expression of dominant negative S6K, but not dominant negative 4E-BP, in Aplysia sensory neurons (SNs) blocked 24-h LTF. TORC1 is directly activated by the small GTP-binding protein, Ras homologue enriched in brain (Rheb). To determine the effects of TORC1 activation on translation in Aplysia neurons, we have examined the effects of expressing a constitutively active form of the Aplysia orthologue of Rheb, ApRheb (ApRheb(Q63L)). Expression of ApRheb(Q63L) increased 4E-BP phosphorylation and the level of general, cap-dependent translation within the SN cell soma in a rapamycin-sensitive manner. This increase in cap-dependent translation was blocked neither by dominant negative 4E-BP nor dominant negative S6K. Thus, we demonstrate that S6K is an important downstream target of TORC1 in Aplysia and that it is necessary for 24-h LTF, but not for TORC1-mediated increases in somatic cap-dependent translation.
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Affiliation(s)
- Daniel B Weatherill
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec H3A 2B4, Canada
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50
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Bai X, Jiang Y. Key factors in mTOR regulation. Cell Mol Life Sci 2010; 67:239-53. [PMID: 19823764 PMCID: PMC4780839 DOI: 10.1007/s00018-009-0163-7] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2009] [Revised: 09/22/2009] [Accepted: 09/23/2009] [Indexed: 12/12/2022]
Abstract
Mammalian target of rapamycin (mTOR) is a protein serine/threonine kinase that controls a wide range of growth-related cellular processes. In the past several years, many factors have been identified that are involved in controlling mTOR activity. Those factors in turn are regulated by diverse signaling cascades responsive to changes in intracellular and environmental conditions. The molecular connections between mTOR and its regulators form a complex signaling network that governs cellular metabolism, growth and proliferation. In this review, we discuss some key factors in mTOR regulation and mechanisms by which these factors control mTOR activity.
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Affiliation(s)
- Xiaochun Bai
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, 510515 Guangzhou, China
| | - Yu Jiang
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213 USA
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