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A Poly-ADP-Ribose Trigger Releases the Auto-Inhibition of a Chromatin Remodeling Oncogene. Mol Cell 2017; 68:860-871.e7. [PMID: 29220653 DOI: 10.1016/j.molcel.2017.11.019] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 10/05/2017] [Accepted: 11/15/2017] [Indexed: 11/24/2022]
Abstract
DNA damage triggers chromatin remodeling by mechanisms that are poorly understood. The oncogene and chromatin remodeler ALC1/CHD1L massively decompacts chromatin in vivo yet is inactive prior to DNA-damage-mediated PARP1 induction. We show that the interaction of the ALC1 macrodomain with the ATPase module mediates auto-inhibition. PARP1 activation suppresses this inhibitory interaction. Crucially, release from auto-inhibition requires a poly-ADP-ribose (PAR) binding macrodomain. We identify tri-ADP-ribose as a potent PAR-mimic and synthetic allosteric effector that abrogates ATPase-macrodomain interactions, promotes an ungated conformation, and activates the remodeler's ATPase. ALC1 fragments lacking the regulatory macrodomain relax chromatin in vivo without requiring PARP1 activation. Further, the ATPase restricts the macrodomain's interaction with PARP1 under non-DNA damage conditions. Somatic cancer mutants disrupt ALC1's auto-inhibition and activate chromatin remodeling. Our data show that the NAD+-metabolite and nucleic acid PAR triggers ALC1 to drive chromatin relaxation. Modular allostery in this oncogene tightly controls its robust, DNA-damage-dependent activation.
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252
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Guidelines on experimental methods to assess mitochondrial dysfunction in cellular models of neurodegenerative diseases. Cell Death Differ 2017; 25:542-572. [PMID: 29229998 PMCID: PMC5864235 DOI: 10.1038/s41418-017-0020-4] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 10/06/2017] [Accepted: 10/12/2017] [Indexed: 01/22/2023] Open
Abstract
Neurodegenerative diseases are a spectrum of chronic, debilitating disorders characterised by the progressive degeneration and death of neurons. Mitochondrial dysfunction has been implicated in most neurodegenerative diseases, but in many instances it is unclear whether such dysfunction is a cause or an effect of the underlying pathology, and whether it represents a viable therapeutic target. It is therefore imperative to utilise and optimise cellular models and experimental techniques appropriate to determine the contribution of mitochondrial dysfunction to neurodegenerative disease phenotypes. In this consensus article, we collate details on and discuss pitfalls of existing experimental approaches to assess mitochondrial function in in vitro cellular models of neurodegenerative diseases, including specific protocols for the measurement of oxygen consumption rate in primary neuron cultures, and single-neuron, time-lapse fluorescence imaging of the mitochondrial membrane potential and mitochondrial NAD(P)H. As part of the Cellular Bioenergetics of Neurodegenerative Diseases (CeBioND) consortium (www.cebiond.org), we are performing cross-disease analyses to identify common and distinct molecular mechanisms involved in mitochondrial bioenergetic dysfunction in cellular models of Alzheimer’s, Parkinson’s, and Huntington’s diseases. Here we provide detailed guidelines and protocols as standardised across the five collaborating laboratories of the CeBioND consortium, with additional contributions from other experts in the field.
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253
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Searcy DG. Elemental sulfur reduction to H 2S by Tetrahymena thermophila. Eur J Protistol 2017; 62:56-68. [PMID: 29248819 DOI: 10.1016/j.ejop.2017.11.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 11/22/2017] [Accepted: 11/24/2017] [Indexed: 11/19/2022]
Abstract
Eukaryotic nucleocytoplasm is believed to be descended from ancient Archaea that respired on elemental sulfur. If so, a vestige of sulfur reduction might persist in modern eukaryotic cells. That was tested in Tetrahymena thermophila, chosen as a model organism. When oxygenated, the cells consumed H2S rapidly, but when made anoxic they produced H2S mostly by amino acid catabolism. That could be inhibited by adding aminooxyacetic acid, and then H2S production from elemental sulfur became more evident. Anoxic cell lysates produced H2S when provided with sulfur and NADH, but not with either substrate alone. When lysates were fractionated by centrifugation, NADH-dependent H2S production was 83% in the soluble fraction. When intact cells that had just previously oxidized H2S were shifted to anoxia, the cells produced H2S evidently by re-using the oxidized sulfur. After aerobic H2S oxidation was stopped, the oxidation product remained available for H2S production for about 10 min. The observed H2S production is consistent with an evolutionary relationship of nucleocytoplasm to sulfur-reducing Archaea. Mitochondria often are the cellular site of H2S oxidation, suggesting that eukaryotic cells might have evolved from an ancient symbiosis that was based upon sulfur exchange.
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Affiliation(s)
- Dennis G Searcy
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA.
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255
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Khaidizar FD, Nakahata Y, Kume A, Sumizawa K, Kohno K, Matsui T, Bessho Y. Nicotinamide phosphoribosyltransferase delays cellular senescence by upregulating SIRT1 activity and antioxidant gene expression in mouse cells. Genes Cells 2017; 22:982-992. [PMID: 29178516 DOI: 10.1111/gtc.12542] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 10/11/2017] [Indexed: 12/21/2022]
Abstract
Senescent cells accumulate in tissues of aged animals and deteriorate tissue functions. The elimination of senescent cells from aged mice not only attenuates progression of already established age-related disorders, but also extends median lifespan. Nicotinamide phosphoribosyltransferase (NAMPT), the rate-limiting enzyme in mammalian NAD+ salvage pathway, has shown a protective effect on cellular senescence of human primary cells. However, it still remains unclear how NAMPT has a protective impact on aging in vitro and in vivo. In this study, we found that primary mouse embryonic fibroblast (MEF) cells undergo progressive decline of NAMPT and NAD+ contents during serial passaging before becoming senescent. Furthermore, we showed that constitutive Nampt over-expression increases cellular NAD+ content and delays cellular senescence of MEF cells in vitro. We further found that constitutive Nampt over-expression increases SIRT1 activity, increases the expression of antioxidant genes, superoxide dismutase 2 and catalase and promotes resistance against oxidative stress. These findings suggest that Nampt over-expression in MEF cells delays cellular senescence by the mitigation of oxidative stress via the upregulation of superoxide dismutase 2 and catalase gene expressions by SIRT1 activation.
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Affiliation(s)
- Fiqri D Khaidizar
- Laboratory of Gene Regulation Research, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), Ikoma, Nara, Japan
| | - Yasukazu Nakahata
- Laboratory of Gene Regulation Research, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), Ikoma, Nara, Japan
| | - Akira Kume
- Laboratory of Gene Regulation Research, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), Ikoma, Nara, Japan
| | - Kyosuke Sumizawa
- Laboratory of Gene Regulation Research, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), Ikoma, Nara, Japan
| | - Kenji Kohno
- Laboratory of Molecular and Cell Genetics, Graduate School of Biological Sciences and Institute for Research Initiatives, Nara Institute of Science and Technology (NAIST), Ikoma, Nara, Japan
| | - Takaaki Matsui
- Laboratory of Gene Regulation Research, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), Ikoma, Nara, Japan
| | - Yasumasa Bessho
- Laboratory of Gene Regulation Research, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), Ikoma, Nara, Japan
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256
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Chini CCS, Tarragó MG, Chini EN. NAD and the aging process: Role in life, death and everything in between. Mol Cell Endocrinol 2017; 455:62-74. [PMID: 27825999 PMCID: PMC5419884 DOI: 10.1016/j.mce.2016.11.003] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 09/22/2016] [Accepted: 11/03/2016] [Indexed: 12/11/2022]
Abstract
Life as we know it cannot exist without the nucleotide nicotinamide adenine dinucleotide (NAD). From the simplest organism, such as bacteria, to the most complex multicellular organisms, NAD is a key cellular component. NAD is extremely abundant in most living cells and has traditionally been described to be a cofactor in electron transfer during oxidation-reduction reactions. In addition to participating in these reactions, NAD has also been shown to play a key role in cell signaling, regulating several pathways from intracellular calcium transients to the epigenetic status of chromatin. Thus, NAD is a molecule that provides an important link between signaling and metabolism, and serves as a key molecule in cellular metabolic sensoring pathways. Importantly, it has now been clearly demonstrated that cellular NAD levels decline during chronological aging. This decline appears to play a crucial role in the development of metabolic dysfunction and age-related diseases. In this review we will discuss the molecular mechanisms responsible for the decrease in NAD levels during aging. Since other reviews on this subject have been recently published, we will concentrate on presenting a critical appraisal of the current status of the literature and will highlight some controversial topics in the field. In particular, we will discuss the potential role of the NADase CD38 as a driver of age-related NAD decline.
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Affiliation(s)
- Claudia C S Chini
- Signal Transduction Laboratory, Kogod Aging Center, Department of Anesthesiology, Oncology Research, GI Signaling Center, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Mariana G Tarragó
- Signal Transduction Laboratory, Kogod Aging Center, Department of Anesthesiology, Oncology Research, GI Signaling Center, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Eduardo N Chini
- Signal Transduction Laboratory, Kogod Aging Center, Department of Anesthesiology, Oncology Research, GI Signaling Center, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
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257
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Posavec Marjanović M, Hurtado-Bagès S, Lassi M, Valero V, Malinverni R, Delage H, Navarro M, Corujo D, Guberovic I, Douet J, Gama-Perez P, Garcia-Roves PM, Ahel I, Ladurner AG, Yanes O, Bouvet P, Suelves M, Teperino R, Pospisilik JA, Buschbeck M. MacroH2A1.1 regulates mitochondrial respiration by limiting nuclear NAD + consumption. Nat Struct Mol Biol 2017; 24:902-910. [PMID: 28991266 PMCID: PMC5791885 DOI: 10.1038/nsmb.3481] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 09/13/2017] [Indexed: 02/06/2023]
Abstract
Histone variants are structural components of eukaryotic chromatin that can replace replication-coupled histones in the nucleosome. The histone variant macroH2A1.1 contains a macrodomain capable of binding NAD+-derived metabolites. Here we report that macroH2A1.1 is rapidly induced during myogenic differentiation through a switch in alternative splicing, and that myotubes that lack macroH2A1.1 have a defect in mitochondrial respiratory capacity. We found that the metabolite-binding macrodomain was essential for sustained optimal mitochondrial function but dispensable for gene regulation. Through direct binding, macroH2A1.1 inhibits basal poly-ADP ribose polymerase 1 (PARP-1) activity and thus reduces nuclear NAD+ consumption. The resultant accumulation of the NAD+ precursor NMN allows for maintenance of mitochondrial NAD+ pools that are critical for respiration. Our data indicate that macroH2A1.1-containing chromatin regulates mitochondrial respiration by limiting nuclear NAD+ consumption and establishing a buffer of NAD+ precursors in differentiated cells.
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Affiliation(s)
- Melanija Posavec Marjanović
- Programme of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Spain
- PhD Program in Biomedicine, Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Sarah Hurtado-Bagès
- Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Germans Trias I Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
- PhD Program in Biomedicine, Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Maximilian Lassi
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Vanesa Valero
- Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Germans Trias I Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Roberto Malinverni
- Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Germans Trias I Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Hélène Delage
- Université de Lyon, Centre de Recherche en Cancérologie de Lyon, Cancer Cell Plasticity Department, UMR INSERM 1052 CNRS 5286, Centre Léon Bérard, Lyon, France
| | - Miriam Navarro
- Metabolomics Platform, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili, Tarragona, Spain
- Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
| | - David Corujo
- Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Germans Trias I Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Iva Guberovic
- Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Germans Trias I Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Julien Douet
- Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Germans Trias I Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Pau Gama-Perez
- Department of Physiological Sciences II, Faculty of Medicine - University of Barcelona, Spain
| | - Pablo M. Garcia-Roves
- Department of Physiological Sciences II, Faculty of Medicine - University of Barcelona, Spain
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Andreas G. Ladurner
- Biomedical Center Munich (BMC) - Physiological Chemistry, Center for Integrated Protein Science Munich, Munich Cluster for Systems Neurology, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
| | - Oscar Yanes
- Metabolomics Platform, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili, Tarragona, Spain
- Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
| | - Philippe Bouvet
- Université de Lyon, Centre de Recherche en Cancérologie de Lyon, Cancer Cell Plasticity Department, UMR INSERM 1052 CNRS 5286, Centre Léon Bérard, Lyon, France
- Université de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Mònica Suelves
- Programme of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Spain
| | - Raffaele Teperino
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Marcus Buschbeck
- Programme of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Spain
- Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Germans Trias I Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
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258
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Ryu KW, Kraus WL. Who Put the "A" in ATP? Generation of ATP from ADP-Ribose in the Nucleus for Hormone-Dependent Gene Regulation. Mol Cell 2017; 63:349-51. [PMID: 27494555 DOI: 10.1016/j.molcel.2016.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In a recent issue of Science, Wright et al. (2016) describe a pathway for the synthesis of nuclear ATP, leading from NAD(+) to poly(ADP-ribose) to ADP-ribose to ATP, which supports the activity of ATP-dependent chromatin remodeling enzymes during hormone-dependent transcription.
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Affiliation(s)
- Keun Woo Ryu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - W Lee Kraus
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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259
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Fang EF, Lautrup S, Hou Y, Demarest TG, Croteau DL, Mattson MP, Bohr VA. NAD + in Aging: Molecular Mechanisms and Translational Implications. Trends Mol Med 2017; 23:899-916. [PMID: 28899755 PMCID: PMC7494058 DOI: 10.1016/j.molmed.2017.08.001] [Citation(s) in RCA: 306] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 07/31/2017] [Accepted: 08/07/2017] [Indexed: 12/19/2022]
Abstract
The coenzyme NAD+ is critical in cellular bioenergetics and adaptive stress responses. Its depletion has emerged as a fundamental feature of aging that may predispose to a wide range of chronic diseases. Maintenance of NAD+ levels is important for cells with high energy demands and for proficient neuronal function. NAD+ depletion is detected in major neurodegenerative diseases, such as Alzheimer's and Parkinson's diseases, cardiovascular disease and muscle atrophy. Emerging evidence suggests that NAD+ decrements occur in various tissues during aging, and that physiological and pharmacological interventions bolstering cellular NAD+ levels might retard aspects of aging and forestall some age-related diseases. Here, we discuss aspects of NAD+ biosynthesis, together with putative mechanisms of NAD+ action against aging, including recent preclinical and clinical trials.
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Affiliation(s)
- Evandro F Fang
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA; Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, 1478 Lørenskog, Norway; Co-first authors
| | - Sofie Lautrup
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA; Danish Aging Research Center, Department of Molecular Biology and Genetics, University of Aarhus, 8000 Aarhus C, Denmark; Co-first authors
| | - Yujun Hou
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Tyler G Demarest
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA; Laboratory of Neurosciences, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Deborah L Croteau
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Mark P Mattson
- Laboratory of Neurosciences, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA; Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Vilhelm A Bohr
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA; Danish Center for Healthy Aging, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
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260
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Galindo R, Banks Greenberg M, Araki T, Sasaki Y, Mehta N, Milbrandt J, Holtzman DM. NMNAT3 is protective against the effects of neonatal cerebral hypoxia-ischemia. Ann Clin Transl Neurol 2017; 4:722-738. [PMID: 29046881 PMCID: PMC5634348 DOI: 10.1002/acn3.450] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 07/11/2017] [Accepted: 07/14/2017] [Indexed: 01/10/2023] Open
Abstract
OBJECTIVE To determine whether the NAD+ biosynthetic protein, nicotinamide mononucleotide adenylyltransferase-3 (NMNAT3), is a neuroprotective inducible enzyme capable of decreasing cerebral injury after neonatal hypoxia-ischemia (H-I) and reducing glutamate receptor-mediated excitotoxic neurodegeneration of immature neurons. METHODS Using NMNAT3-overexpressing mice we investigated whether increases in brain NMNAT3 reduced cerebral tissue loss following H-I. We then employed biochemical methods from injured neonatal brains to examine the inducibility of NMNAT3 and the mechanism of NMNAT3-dependent neuroprotection. Using AAV8-mediated vectors for in vitro neuronal NMNAT3 knockdown, we then examine the endogenous role of this protein on immature neuronal survival prior and following NMDA receptor-mediated excitotoxicity. RESULTS NMNAT3 mRNA and protein levels increased after neonatal H-I. In addition, NMNAT3 overexpression decreased cortical and hippocampal tissue loss 7 days following injury. We further show that the NMNAT3 neuroprotective mechanism involves a decrease in calpastatin degradation, and a decrease in caspase-3 activity and calpain-mediated cleavage. Conversely, NMNAT3 knockdown of cortical and hippocampal neurons in vitro caused neuronal degeneration and increased excitotoxic cell death. The neurodegenerative effects of NMNAT3 knockdown were counteracted by exogenous upregulation of NMNAT3. CONCLUSIONS Our observations provide new insights into the neuroprotective mechanisms of NMNATs in the injured developing brain, adding NMNAT3 as an important neuroprotective enzyme in neonatal H-I via inhibition of apoptotic and necrotic neurodegeneration. Interestingly, we find that endogenous NMNAT3 is an inducible protein important for maintaining the survival of immature neurons. Future studies aimed at uncovering the mechanisms of NMNAT3 upregulation and neuroprotection may offer new therapies against the effects of hypoxic-ischemic encephalopathy.
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Affiliation(s)
- Rafael Galindo
- Department of NeurologyHope Center for Neurological DisordersWashington UniversitySt. LouisMissouri63110
| | - Marianne Banks Greenberg
- Department of NeurologyHope Center for Neurological DisordersWashington UniversitySt. LouisMissouri63110
| | - Toshiyuki Araki
- Department of Peripheral Nervous System ResearchNational Institute of NeuroscienceKodairaTokyoJapan
| | - Yo Sasaki
- Department of GeneticsWashington UniversitySt. LouisMissouri63110
| | - Nehali Mehta
- Department of NeurologyHope Center for Neurological DisordersWashington UniversitySt. LouisMissouri63110
| | | | - David M. Holtzman
- Department of NeurologyHope Center for Neurological DisordersWashington UniversitySt. LouisMissouri63110
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261
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Sultani G, Samsudeen AF, Osborne B, Turner N. NAD + : A key metabolic regulator with great therapeutic potential. J Neuroendocrinol 2017; 29. [PMID: 28718934 DOI: 10.1111/jne.12508] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 06/27/2017] [Accepted: 07/13/2017] [Indexed: 12/14/2022]
Abstract
Nicotinamide adenine dinucleotide (NAD+ ) is a ubiquitous metabolite that serves an essential role in the catabolism of nutrients. Recently, there has been a surge of interest in NAD+ biology, with the recognition that NAD+ influences many biological processes beyond metabolism, including transcription, signalling and cell survival. There are a multitude of pathways involved in the synthesis and breakdown of NAD+ , and alterations in NAD+ homeostasis have emerged as a common feature of a range of disease states. Here, we provide an overview of NAD+ metabolism and summarise progress on the development of NAD+ -related therapeutics.
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Affiliation(s)
- G Sultani
- Department of Pharmacology, School of Medical Sciences, UNSW Australia, Kensington, NSW, Australia
| | - A F Samsudeen
- Department of Pharmacology, School of Medical Sciences, UNSW Australia, Kensington, NSW, Australia
| | - B Osborne
- Department of Pharmacology, School of Medical Sciences, UNSW Australia, Kensington, NSW, Australia
| | - N Turner
- Department of Pharmacology, School of Medical Sciences, UNSW Australia, Kensington, NSW, Australia
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262
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Long A, Klimova N, Kristian T. Mitochondrial NUDIX hydrolases: A metabolic link between NAD catabolism, GTP and mitochondrial dynamics. Neurochem Int 2017; 109:193-201. [PMID: 28302504 DOI: 10.1016/j.neuint.2017.03.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 02/28/2017] [Accepted: 03/09/2017] [Indexed: 12/19/2022]
Abstract
NAD+ catabolism and mitochondrial dynamics are important parts of normal mitochondrial function and are both reported to be disrupted in aging, neurodegenerative diseases, and acute brain injury. While both processes have been extensively studied there has been little reported on how the mechanisms of these two processes are linked. This review focuses on how downstream NAD+ catabolism via NUDIX hydrolases affects mitochondrial dynamics under pathologic conditions. Additionally, several potential targets in mitochondrial dysfunction and fragmentation are discussed, including the roles of mitochondrial poly(ADP-ribose) polymerase 1(mtPARP1), AMPK, AMP, and intra-mitochondrial GTP metabolism. Mitochondrial and cytosolic NUDIX hydrolases (NUDT9α and NUDT9β) can affect mitochondrial and cellular AMP levels by hydrolyzing ADP- ribose (ADPr) and subsequently altering the levels of GTP and ATP. Poly (ADP-ribose) polymerase 1 (PARP1) is activated after DNA damage, which depletes NAD+ pools and results in the PARylation of nuclear and mitochondrial proteins. In the mitochondria, ADP-ribosyl hydrolase-3 (ARH3) hydrolyzes PAR to ADPr, while NUDT9α metabolizes ADPr to AMP. Elevated AMP levels have been reported to reduce mitochondrial ATP production by inhibiting the adenine nucleotide translocase (ANT), allosterically activating AMPK by altering the cellular AMP: ATP ratio, and by depleting mitochondrial GTP pools by being phosphorylated by adenylate kinase 3 (AK3), which uses GTP as a phosphate donor. Recently, activated AMPK was reported to phosphorylate mitochondria fission factor (MFF), which increases Drp1 localization to the mitochondria and promotes mitochondrial fission. Moreover, the increased AK3 activity could deplete mitochondrial GTP pools and possibly inhibit normal activity of GTP-dependent fusion enzymes, thus altering mitochondrial dynamics.
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Affiliation(s)
- Aaron Long
- Veterans Affairs Maryland Health Center System, 10 North Greene Street, Baltimore, MD 21201, United States
| | - Nina Klimova
- Veterans Affairs Maryland Health Center System, 10 North Greene Street, Baltimore, MD 21201, United States; Department of Anesthesiology and the Center for Shock, Trauma, and Anesthesiology Research (S.T.A.R.), United States; Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD 21201, United States
| | - Tibor Kristian
- Veterans Affairs Maryland Health Center System, 10 North Greene Street, Baltimore, MD 21201, United States; Department of Anesthesiology and the Center for Shock, Trauma, and Anesthesiology Research (S.T.A.R.), United States.
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263
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Anderson KA, Madsen AS, Olsen CA, Hirschey MD. Metabolic control by sirtuins and other enzymes that sense NAD +, NADH, or their ratio. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:991-998. [PMID: 28947253 DOI: 10.1016/j.bbabio.2017.09.005] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/15/2017] [Accepted: 09/20/2017] [Indexed: 01/12/2023]
Abstract
NAD+ is a dinucleotide cofactor with the potential to accept electrons in a variety of cellular reduction-oxidation (redox) reactions. In its reduced form, NADH is a ubiquitous cellular electron donor. NAD+, NADH, and the NAD+/NADH ratio have long been known to control the activity of several oxidoreductase enzymes. More recently, enzymes outside those participating directly in redox control have been identified that sense these dinucleotides, including the sirtuin family of NAD+-dependent protein deacylases. In this review, we highlight examples of non-redox enzymes that are controlled by NAD+, NADH, or NAD+/NADH. In particular, we focus on the sirtuin family and assess the current evidence that the sirtuin enzymes sense these dinucleotides and discuss the biological conditions under which this might occur; we conclude that sirtuins sense NAD+, but neither NADH nor the ratio. Finally, we identify future studies that might be informative to further interrogate physiological and pathophysiological changes in NAD+ and NADH, as well as enzymes like sirtuins that sense and respond to redox changes in the cell.
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Affiliation(s)
- Kristin A Anderson
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, United States; Department of Pharmacology & Cancer Biology, Duke University Medical Center, Durham, NC 27710, United States
| | - Andreas S Madsen
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Matthew D Hirschey
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, United States; Department of Pharmacology & Cancer Biology, Duke University Medical Center, Durham, NC 27710, United States; Department of Medicine, Duke University Medical Center, Durham, NC 27710, United States.
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264
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Mauvoisin D, Atger F, Dayon L, Núñez Galindo A, Wang J, Martin E, Da Silva L, Montoliu I, Collino S, Martin FP, Ratajczak J, Cantó C, Kussmann M, Naef F, Gachon F. Circadian and Feeding Rhythms Orchestrate the Diurnal Liver Acetylome. Cell Rep 2017; 20:1729-1743. [PMID: 28813682 PMCID: PMC5568034 DOI: 10.1016/j.celrep.2017.07.065] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 06/12/2017] [Accepted: 07/24/2017] [Indexed: 12/24/2022] Open
Abstract
Lysine acetylation is involved in various biological processes and is considered a key reversible post-translational modification in the regulation of gene expression, enzyme activity, and subcellular localization. This post-translational modification is therefore highly relevant in the context of circadian biology, but its characterization on the proteome-wide scale and its circadian clock dependence are still poorly described. Here, we provide a comprehensive and rhythmic acetylome map of the mouse liver. Rhythmic acetylated proteins showed subcellular localization-specific phases that correlated with the related metabolites in the regulated pathways. Mitochondrial proteins were over-represented among the rhythmically acetylated proteins and were highly correlated with SIRT3-dependent deacetylation. SIRT3 activity being nicotinamide adenine dinucleotide (NAD)+ level-dependent, we show that NAD+ is orchestrated by both feeding rhythms and the circadian clock through the NAD+ salvage pathway but also via the nicotinamide riboside pathway. Hence, the diurnal acetylome relies on a functional circadian clock and affects important diurnal metabolic pathways in the mouse liver.
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Affiliation(s)
- Daniel Mauvoisin
- Diabetes and Circadian Rhythms Department, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland; Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Florian Atger
- Diabetes and Circadian Rhythms Department, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland; Department of Pharmacology and Toxicology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Loïc Dayon
- Systems Nutrition, Metabonomics & Proteomics, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Antonio Núñez Galindo
- Systems Nutrition, Metabonomics & Proteomics, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Jingkui Wang
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Eva Martin
- Diabetes and Circadian Rhythms Department, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Laetitia Da Silva
- Systems Nutrition, Metabonomics & Proteomics, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Ivan Montoliu
- Systems Nutrition, Metabonomics & Proteomics, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Sebastiano Collino
- Systems Nutrition, Metabonomics & Proteomics, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Francois-Pierre Martin
- Systems Nutrition, Metabonomics & Proteomics, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Joanna Ratajczak
- Diabetes and Circadian Rhythms Department, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland; School of Life Sciences, Ecole Polytechnique Fédérale Lausanne, 1015 Lausanne, Switzerland
| | - Carles Cantó
- Diabetes and Circadian Rhythms Department, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland; School of Life Sciences, Ecole Polytechnique Fédérale Lausanne, 1015 Lausanne, Switzerland
| | - Martin Kussmann
- Systems Nutrition, Metabonomics & Proteomics, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Felix Naef
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Frédéric Gachon
- Diabetes and Circadian Rhythms Department, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland; School of Life Sciences, Ecole Polytechnique Fédérale Lausanne, 1015 Lausanne, Switzerland.
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265
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Katsyuba E, Auwerx J. Modulating NAD + metabolism, from bench to bedside. EMBO J 2017; 36:2670-2683. [PMID: 28784597 DOI: 10.15252/embj.201797135] [Citation(s) in RCA: 157] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 05/15/2017] [Accepted: 05/16/2017] [Indexed: 12/11/2022] Open
Abstract
Discovered in the beginning of the 20th century, nicotinamide adenine dinucleotide (NAD+) has evolved from a simple oxidoreductase cofactor to being an essential cosubstrate for a wide range of regulatory proteins that include the sirtuin family of NAD+-dependent protein deacylases, widely recognized regulators of metabolic function and longevity. Altered NAD+ metabolism is associated with aging and many pathological conditions, such as metabolic diseases and disorders of the muscular and neuronal systems. Conversely, increased NAD+ levels have shown to be beneficial in a broad spectrum of diseases. Here, we review the fundamental aspects of NAD+ biochemistry and metabolism and discuss how boosting NAD+ content can help ameliorate mitochondrial homeostasis and as such improve healthspan and lifespan.
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Affiliation(s)
- Elena Katsyuba
- Laboratory of Integrative and Systems Physiology, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Johan Auwerx
- Laboratory of Integrative and Systems Physiology, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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266
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Neukomm LJ, Burdett TC, Seeds AM, Hampel S, Coutinho-Budd JC, Farley JE, Wong J, Karadeniz YB, Osterloh JM, Sheehan AE, Freeman MR. Axon Death Pathways Converge on Axundead to Promote Functional and Structural Axon Disassembly. Neuron 2017; 95:78-91.e5. [PMID: 28683272 DOI: 10.1016/j.neuron.2017.06.031] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 05/25/2017] [Accepted: 06/19/2017] [Indexed: 01/04/2023]
Abstract
Axon degeneration is a hallmark of neurodegenerative disease and neural injury. Axotomy activates an intrinsic pro-degenerative axon death signaling cascade involving loss of the NAD+ biosynthetic enzyme Nmnat/Nmnat2 in axons, activation of dSarm/Sarm1, and subsequent Sarm-dependent depletion of NAD+. Here we identify Axundead (Axed) as a mediator of axon death. axed mutants suppress axon death in several types of axons for the lifespan of the fly and block the pro-degenerative effects of activated dSarm in vivo. Neurodegeneration induced by loss of the sole fly Nmnat ortholog is also fully blocked by axed, but not dsarm, mutants. Thus, pro-degenerative pathways activated by dSarm signaling or Nmnat elimination ultimately converge on Axed. Remarkably, severed axons morphologically preserved by axon death pathway mutations remain integrated in circuits and able to elicit complex behaviors after stimulation, indicating that blockade of axon death signaling results in long-term functional preservation of axons.
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Affiliation(s)
- Lukas J Neukomm
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA, USA.
| | - Thomas C Burdett
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Andrew M Seeds
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Stefanie Hampel
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Jaeda C Coutinho-Budd
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jonathan E Farley
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jack Wong
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Yonca B Karadeniz
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jeannette M Osterloh
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Amy E Sheehan
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Marc R Freeman
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA, USA.
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267
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Bilan DS, Belousov VV. New tools for redox biology: From imaging to manipulation. Free Radic Biol Med 2017; 109:167-188. [PMID: 27939954 DOI: 10.1016/j.freeradbiomed.2016.12.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 12/02/2016] [Accepted: 12/03/2016] [Indexed: 12/12/2022]
Abstract
Redox reactions play a key role in maintaining essential biological processes. Deviations in redox pathways result in the development of various pathologies at cellular and organismal levels. Until recently, studies on transformations in the intracellular redox state have been significantly hampered in living systems. The genetically encoded indicators, based on fluorescent proteins, have provided new opportunities in biomedical research. The existing indicators already enable monitoring of cellular redox parameters in different processes including embryogenesis, aging, inflammation, tissue regeneration, and pathogenesis of various diseases. In this review, we summarize information about all genetically encoded redox indicators developed to date. We provide the description of each indicator and discuss its advantages and limitations, as well as points that need to be considered when choosing an indicator for a particular experiment. One chapter is devoted to the important discoveries that have been made by using genetically encoded redox indicators.
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Affiliation(s)
- Dmitry S Bilan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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268
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Gupte R, Liu Z, Kraus WL. PARPs and ADP-ribosylation: recent advances linking molecular functions to biological outcomes. Genes Dev 2017; 31:101-126. [PMID: 28202539 PMCID: PMC5322727 DOI: 10.1101/gad.291518.116] [Citation(s) in RCA: 484] [Impact Index Per Article: 69.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In this review, Gupte et al. discuss new findings on the diverse roles of PARPs in chromatin regulation, transcription, RNA biology, and DNA repair as well as recent advances that link ADP-ribosylation to stress responses, metabolism, viral infections, and cancer. The discovery of poly(ADP-ribose) >50 years ago opened a new field, leading the way for the discovery of the poly(ADP-ribose) polymerase (PARP) family of enzymes and the ADP-ribosylation reactions that they catalyze. Although the field was initially focused primarily on the biochemistry and molecular biology of PARP-1 in DNA damage detection and repair, the mechanistic and functional understanding of the role of PARPs in different biological processes has grown considerably of late. This has been accompanied by a shift of focus from enzymology to a search for substrates as well as the first attempts to determine the functional consequences of site-specific ADP-ribosylation on those substrates. Supporting these advances is a host of methodological approaches from chemical biology, proteomics, genomics, cell biology, and genetics that have propelled new discoveries in the field. New findings on the diverse roles of PARPs in chromatin regulation, transcription, RNA biology, and DNA repair have been complemented by recent advances that link ADP-ribosylation to stress responses, metabolism, viral infections, and cancer. These studies have begun to reveal the promising ways in which PARPs may be targeted therapeutically for the treatment of disease. In this review, we discuss these topics and relate them to the future directions of the field.
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Affiliation(s)
- Rebecca Gupte
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Ziying Liu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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269
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Chang M, Li L, Hu H, Hu Q, Wang A, Cao X, Yu X, Zhang S, Zhao Y, Chen J, Yang Y, Xu J. Using Fractional Intensities of Time-resolved Fluorescence to Sensitively Quantify NADH/NAD + with Genetically Encoded Fluorescent Biosensors. Sci Rep 2017. [PMID: 28646144 PMCID: PMC5482812 DOI: 10.1038/s41598-017-04051-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In this paper, we propose a novel and sensitive ratiometric analysis method that uses the fractional intensities of time-resolved fluorescence of genetically encoded fluorescent NADH/NAD+ biosensors, Peredox, SoNar, and Frex. When the conformations of the biosensors change upon NADH/NAD+ binding, the fractional intensities (αiτi) have opposite changing trends. Their ratios could be exploited to quantify NADH/NAD+ levels with a larger dynamic range and higher resolution versus commonly used fluorescence intensity and lifetime methods. Moreover, only one excitation and one emission wavelength are required for this ratiometric measurement. This eliminates problems of traditional excitation-ratiometric and emission-ratiometric methods. This method could be used to simplify the design and achieve highly sensitive analyte quantification of genetically encoded fluorescent biosensors. Wide potential applications could be developed for imaging live cell metabolism based on this new method.
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Affiliation(s)
- Mengfang Chang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Lei Li
- State Key Laboratory of Precision Spectroscopy, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Hanyang Hu
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Mei Long Road, Shanghai, 200237, China.,Optogenetics & Synthetic Biology Interdisciplinary Research Center, CAS Center for Excellence in Brain Science, 130 Mei Long Road, Shanghai, 200237, China.,Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Qingxun Hu
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Mei Long Road, Shanghai, 200237, China.,Optogenetics & Synthetic Biology Interdisciplinary Research Center, CAS Center for Excellence in Brain Science, 130 Mei Long Road, Shanghai, 200237, China.,Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Aoxue Wang
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Mei Long Road, Shanghai, 200237, China.,Optogenetics & Synthetic Biology Interdisciplinary Research Center, CAS Center for Excellence in Brain Science, 130 Mei Long Road, Shanghai, 200237, China.,Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Xiaodan Cao
- State Key Laboratory of Precision Spectroscopy, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Xiantong Yu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Sanjun Zhang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China.
| | - Yuzheng Zhao
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Mei Long Road, Shanghai, 200237, China. .,Optogenetics & Synthetic Biology Interdisciplinary Research Center, CAS Center for Excellence in Brain Science, 130 Mei Long Road, Shanghai, 200237, China. .,Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China.
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Yi Yang
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Mei Long Road, Shanghai, 200237, China.,Optogenetics & Synthetic Biology Interdisciplinary Research Center, CAS Center for Excellence in Brain Science, 130 Mei Long Road, Shanghai, 200237, China.,Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Jianhua Xu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
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270
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Tateishi K, Higuchi F, Miller JJ, Koerner MVA, Lelic N, Shankar GM, Tanaka S, Fisher DE, Batchelor TT, Iafrate AJ, Wakimoto H, Chi AS, Cahill DP. The Alkylating Chemotherapeutic Temozolomide Induces Metabolic Stress in IDH1-Mutant Cancers and Potentiates NAD + Depletion-Mediated Cytotoxicity. Cancer Res 2017. [PMID: 28625978 DOI: 10.1158/0008-5472.can-16-2263] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
IDH1-mutant gliomas are dependent upon the canonical coenzyme NAD+ for survival. It is known that PARP activation consumes NAD+ during base excision repair (BER) of chemotherapy-induced DNA damage. We therefore hypothesized that a strategy combining NAD+ biosynthesis inhibitors with the alkylating chemotherapeutic agent temozolomide could potentiate NAD+ depletion-mediated cytotoxicity in mutant IDH1 cancer cells. To investigate the impact of temozolomide on NAD+ metabolism, patient-derived xenografts and engineered mutant IDH1-expressing cell lines were exposed to temozolomide, in vitro and in vivo, both alone and in combination with nicotinamide phosphoribosyltransferase (NAMPT) inhibitors, which block NAD+ biosynthesis. The acute time period (<3 hours) after temozolomide treatment displayed a burst of NAD+ consumption driven by PARP activation. In IDH1-mutant-expressing cells, this consumption reduced further the abnormally lowered basal steady-state levels of NAD+, introducing a window of hypervulnerability to NAD+ biosynthesis inhibitors. This effect was selective for IDH1-mutant cells and independent of methylguanine methyltransferase or mismatch repair status, which are known rate-limiting mediators of adjuvant temozolomide genotoxic sensitivity. Combined temozolomide and NAMPT inhibition in an in vivo IDH1-mutant cancer model exhibited enhanced efficacy compared with each agent alone. Thus, we find IDH1-mutant cancers have distinct metabolic stress responses to chemotherapy-induced DNA damage and that combination regimens targeting nonredundant NAD+ pathways yield potent anticancer efficacy in vivo Such targeting of convergent metabolic pathways in genetically selected cancers could minimize treatment toxicity and improve durability of response to therapy. Cancer Res; 77(15); 4102-15. ©2017 AACR.
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Affiliation(s)
- Kensuke Tateishi
- Department of Neurosurgery, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.,Department of Neurosurgery, Yokohama City University, Yokohama, Kanagawa, Japan.,Translational Neuro-Oncology Laboratory, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Fumi Higuchi
- Department of Neurosurgery, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.,Translational Neuro-Oncology Laboratory, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Julie J Miller
- Translational Neuro-Oncology Laboratory, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.,Division of Hematology/Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.,Stephen E. and Catherine Pappas Center for Neuro-Oncology, Department of Neurology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Mara V A Koerner
- Department of Neurosurgery, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.,Translational Neuro-Oncology Laboratory, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Nina Lelic
- Department of Neurosurgery, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.,Translational Neuro-Oncology Laboratory, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Ganesh M Shankar
- Department of Neurosurgery, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.,Translational Neuro-Oncology Laboratory, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Shota Tanaka
- Translational Neuro-Oncology Laboratory, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.,Division of Hematology/Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.,Stephen E. and Catherine Pappas Center for Neuro-Oncology, Department of Neurology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - David E Fisher
- Department of Dermatology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Tracy T Batchelor
- Division of Hematology/Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.,Stephen E. and Catherine Pappas Center for Neuro-Oncology, Department of Neurology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - A John Iafrate
- Translational Neuro-Oncology Laboratory, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.,Department of Pathology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Hiroaki Wakimoto
- Department of Neurosurgery, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts. .,Translational Neuro-Oncology Laboratory, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Andrew S Chi
- Translational Neuro-Oncology Laboratory, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts. .,Laura and Isaac Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
| | - Daniel P Cahill
- Department of Neurosurgery, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts. .,Translational Neuro-Oncology Laboratory, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
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271
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Abstract
In this review, van der Knapp and Verrijzer discuss the current understanding of the molecular mechanisms connecting metabolism to gene expression and their implications for development and disease. To make the appropriate developmental decisions or maintain homeostasis, cells and organisms must coordinate the expression of their genome and metabolic state. However, the molecular mechanisms that relay environmental cues such as nutrient availability to the appropriate gene expression response remain poorly understood. There is a growing awareness that central components of intermediary metabolism are cofactors or cosubstrates of chromatin-modifying enzymes. As such, their concentrations constitute a potential regulatory interface between the metabolic and chromatin states. In addition, there is increasing evidence for a direct involvement of classic metabolic enzymes in gene expression control. These dual-function proteins may provide a direct link between metabolic programing and the control of gene expression. Here, we discuss our current understanding of the molecular mechanisms connecting metabolism to gene expression and their implications for development and disease.
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Affiliation(s)
- Jan A van der Knaap
- Department of Biochemistry, Erasmus University Medical Center, 3000 DR Rotterdam, the Netherlands
| | - C Peter Verrijzer
- Department of Biochemistry, Erasmus University Medical Center, 3000 DR Rotterdam, the Netherlands
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272
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Genetically encoded fluorescent sensors reveal dynamic regulation of NADPH metabolism. Nat Methods 2017; 14:720-728. [PMID: 28581494 DOI: 10.1038/nmeth.4306] [Citation(s) in RCA: 214] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 04/23/2017] [Indexed: 12/24/2022]
Abstract
Reduced nicotinamide adenine dinucleotide phosphate (NADPH) is essential for biosynthetic reactions and antioxidant functions; however, detection of NADPH metabolism in living cells remains technically challenging. We develop and characterize ratiometric, pH-resistant, genetically encoded fluorescent indicators for NADPH (iNap sensors) with various affinities and wide dynamic range. iNap sensors enabled quantification of cytosolic and mitochondrial NADPH pools that are controlled by cytosolic NAD+ kinase levels and revealed cellular NADPH dynamics under oxidative stress depending on glucose availability. We found that mammalian cells have a strong tendency to maintain physiological NADPH homeostasis, which is regulated by glucose-6-phosphate dehydrogenase and AMP kinase. Moreover, using the iNap sensors we monitor NADPH fluctuations during the activation of macrophage cells or wound response in vivo. These data demonstrate that the iNap sensors will be valuable tools for monitoring NADPH dynamics in live cells and gaining new insights into cell metabolism.
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273
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Shidore T, Broeckling CD, Kirkwood JS, Long JJ, Miao J, Zhao B, Leach JE, Triplett LR. The effector AvrRxo1 phosphorylates NAD in planta. PLoS Pathog 2017; 13:e1006442. [PMID: 28628666 PMCID: PMC5491322 DOI: 10.1371/journal.ppat.1006442] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 06/29/2017] [Accepted: 06/02/2017] [Indexed: 12/14/2022] Open
Abstract
Gram-negative bacterial pathogens of plants and animals employ type III secreted effectors to suppress innate immunity. Most characterized effectors work through modification of host proteins or transcriptional regulators, although a few are known to modify small molecule targets. The Xanthomonas type III secreted avirulence factor AvrRxo1 is a structural homolog of the zeta toxin family of sugar-nucleotide kinases that suppresses bacterial growth. AvrRxo1 was recently reported to phosphorylate the central metabolite and signaling molecule NAD in vitro, suggesting that the effector might enhance bacterial virulence on plants through manipulation of primary metabolic pathways. In this study, we determine that AvrRxo1 phosphorylates NAD in planta, and that its kinase catalytic sites are necessary for its toxic and resistance-triggering phenotypes. A global metabolomics approach was used to independently identify 3'-NADP as the sole detectable product of AvrRxo1 expression in yeast and bacteria, and NAD kinase activity was confirmed in vitro. 3'-NADP accumulated upon transient expression of AvrRxo1 in Nicotiana benthamiana and in rice leaves infected with avrRxo1-expressing strains of X. oryzae. Mutation of the catalytic aspartic acid residue D193 abolished AvrRxo1 kinase activity and several phenotypes of AvrRxo1, including toxicity in yeast, bacteria, and plants, suppression of the flg22-triggered ROS burst, and ability to trigger an R gene-mediated hypersensitive response. A mutation in the Walker A ATP-binding motif abolished the toxicity of AvrRxo1, but did not abolish the 3'-NADP production, virulence enhancement, ROS suppression, or HR-triggering phenotypes of AvrRxo1. These results demonstrate that a type III effector targets the central metabolite and redox carrier NAD in planta, and that this catalytic activity is required for toxicity and suppression of the ROS burst.
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Affiliation(s)
- Teja Shidore
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT, United States of America
| | - Corey D. Broeckling
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO, United States of America
| | - Jay S. Kirkwood
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO, United States of America
| | - John J. Long
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States of America
| | - Jiamin Miao
- Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States of America
| | - Bingyu Zhao
- Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States of America
| | - Jan E. Leach
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States of America
| | - Lindsay R. Triplett
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT, United States of America
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274
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Yu M, Jia HM, Zhou C, Yang Y, Sun LL, Zou ZM. Urinary and Fecal Metabonomics Study of the Protective Effect of Chaihu-Shu-Gan-San on Antibiotic-Induced Gut Microbiota Dysbiosis in Rats. Sci Rep 2017; 7:46551. [PMID: 28425490 PMCID: PMC5397834 DOI: 10.1038/srep46551] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 03/22/2017] [Indexed: 12/31/2022] Open
Abstract
Accumulating evidence suggests that the gut microbiota dysbiosis and their host metabolic phenotype alteration is an important factor in human disease development. A traditional Chinese herbal formula, Chaihu-Shu-Gan-San (CSGS), has been effectively used in the treatment of various gastrointestinal (GI) disorders. The present study was carried out to investigate whether CSGS modulates the host metabolic phenotype under the condition of gut microbiota dysbiosis. The metabonomics studies of biochemical changes in urine and feces of antibiotic-induced gut microbiota dysbiosis rats after treatment with CSGS were performed using UPLC-Q-TOF/MS. Partial least squares-discriminate analysis (PLS-DA) indicated that the CSGS treatment reduced the metabolic phenotype perturbation induced by antibiotic. In addition, there was a strong correlation between gut microbiota genera and urinary and fecal metabolites. Moreover, the correlation analysis and the metabolic pathway analysis (MetPA) identified that three key metabolic pathways including glycine, serine and threonine metabolism, nicotinate and nicotinamide metabolism, and bile acid metabolism were the most relevant pathways involved in antibiotic-induced gut microbiota dysbiosis. These findings provided a comprehensive understanding of the protective effects of CSGS on the host metabolic phenotype of the gut microbiota dysbiosis rats, and further as a new source for drug leads in gut microbiota-targeted disease management.
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Affiliation(s)
- Meng Yu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, P. R. China
| | - Hong-Mei Jia
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, P. R. China
| | - Chao Zhou
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, P. R. China
| | - Yong Yang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, P. R. China
| | - Li-Li Sun
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, P. R. China
| | - Zhong-Mei Zou
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, P. R. China
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275
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Krautkramer KA, Rey FE, Denu JM. Chemical signaling between gut microbiota and host chromatin: What is your gut really saying? J Biol Chem 2017; 292:8582-8593. [PMID: 28389558 DOI: 10.1074/jbc.r116.761577] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Mammals and their gut microbial communities share extensive and tightly coordinated co-metabolism of dietary substrates. A large number of microbial metabolites have been detected in host circulation and tissues and, in many cases, are linked to host metabolic, developmental, and immunological states. The presence of these metabolites in host tissues intersects with regulation of the host's epigenetic machinery. Although it is established that the host's epigenetic machinery is sensitive to levels of endogenous metabolites, the roles for microbial metabolites in epigenetic regulation are just beginning to be elucidated. This review focuses on eukaryotic chromatin regulation by endogenous and gut microbial metabolites and how these regulatory events may impact host developmental and metabolic phenotypes.
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Affiliation(s)
- Kimberly A Krautkramer
- From the Wisconsin Institute for Discovery, Morgridge Institute for Research, and the Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53715 and
| | - Federico E Rey
- the Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706
| | - John M Denu
- From the Wisconsin Institute for Discovery, Morgridge Institute for Research, and the Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53715 and
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276
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Lu Y, Kwintkiewicz J, Liu Y, Tech K, Frady LN, Su YT, Bautista W, Moon SI, MacDonald J, Ewend MG, Gilbert MR, Yang C, Wu J. Chemosensitivity of IDH1-Mutated Gliomas Due to an Impairment in PARP1-Mediated DNA Repair. Cancer Res 2017; 77:1709-1718. [PMID: 28202508 DOI: 10.1158/0008-5472.can-16-2773] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 12/07/2016] [Accepted: 12/22/2016] [Indexed: 12/20/2022]
Abstract
Mutations in isocitrate dehydrogenase (IDH) are the most prevalent genetic abnormalities in lower grade gliomas. The presence of these mutations in glioma is prognostic for better clinical outcomes with longer patient survival. In the present study, we found that defects in oxidative metabolism and 2-HG production confer chemosensitization in IDH1-mutated glioma cells. In addition, temozolomide (TMZ) treatment induced greater DNA damage and apoptotic changes in mutant glioma cells. The PARP1-associated DNA repair pathway was extensively compromised in mutant cells due to decreased NAD+ availability. Targeting the PARP DNA repair pathway extensively sensitized IDH1-mutated glioma cells to TMZ. Our findings demonstrate a novel molecular mechanism that defines chemosensitivity in IDH-mutated gliomas. Targeting PARP-associated DNA repair may represent a novel therapeutic strategy for gliomas. Cancer Res; 77(7); 1709-18. ©2017 AACR.
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Affiliation(s)
- Yanxin Lu
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Jakub Kwintkiewicz
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Neurosurgery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Yang Liu
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Katherine Tech
- Department of Biomedical Engineering, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Lauren N Frady
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Neurosurgery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Yu-Ting Su
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Wendy Bautista
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Seog In Moon
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Jeffrey MacDonald
- Department of Biomedical Engineering, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Matthew G Ewend
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Neurosurgery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Mark R Gilbert
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Chunzhang Yang
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland.
| | - Jing Wu
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Neurosurgery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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277
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Zhang Y, Avalos JL. Traditional and novel tools to probe the mitochondrial metabolism in health and disease. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2017; 9. [PMID: 28067471 DOI: 10.1002/wsbm.1373] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/07/2016] [Accepted: 11/09/2016] [Indexed: 02/06/2023]
Abstract
Mitochondrial metabolism links energy production to other essential cellular processes such as signaling, cellular differentiation, and apoptosis. In addition to producing adenosine triphosphate (ATP) as an energy source, mitochondria are responsible for the synthesis of a myriad of important metabolites and cofactors such as tetrahydrofolate, α-ketoacids, steroids, aminolevulinic acid, biotin, lipoic acid, acetyl-CoA, iron-sulfur clusters, heme, and ubiquinone. Furthermore, mitochondria and their metabolism have been implicated in aging and several human diseases, including inherited mitochondrial disorders, cardiac dysfunction, heart failure, neurodegenerative diseases, diabetes, and cancer. Therefore, there is great interest in understanding mitochondrial metabolism and the complex relationship it has with other cellular processes. A large number of studies on mitochondrial metabolism have been conducted in the last 50 years, taking a broad range of approaches. In this review, we summarize and discuss the most commonly used tools that have been used to study different aspects of the metabolism of mitochondria: ranging from dyes that monitor changes in the mitochondrial membrane potential and pharmacological tools to study respiration or ATP synthesis, to more modern tools such as genetically encoded biosensors and trans-omic approaches enabled by recent advances in mass spectrometry, computation, and other technologies. These tools have allowed the large number of studies that have shaped our current understanding of mitochondrial metabolism. WIREs Syst Biol Med 2017, 9:e1373. doi: 10.1002/wsbm.1373 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Yanfei Zhang
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - José L Avalos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA.,Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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278
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Golia B, Moeller GK, Jankevicius G, Schmidt A, Hegele A, Preißer J, Tran ML, Imhof A, Timinszky G. ATM induces MacroD2 nuclear export upon DNA damage. Nucleic Acids Res 2017; 45:244-254. [PMID: 28069995 PMCID: PMC5224513 DOI: 10.1093/nar/gkw904] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 09/08/2016] [Accepted: 10/04/2016] [Indexed: 12/14/2022] Open
Abstract
ADP-ribosylation is a dynamic post-translation modification that regulates the early phase of various DNA repair pathways by recruiting repair factors to chromatin. ADP-ribosylation levels are defined by the activities of specific transferases and hydrolases. However, except for the transferase PARP1/ARDT1 little is known about regulation of these enzymes. We found that MacroD2, a mono-ADP-ribosylhydrolase, is exported from the nucleus upon DNA damage, and that this nuclear export is induced by ATM activity. We show that the export is dependent on the phosphorylation of two SQ/TQ motifs, suggesting a novel direct interaction between ATM and ADP-ribosylation. Lastly, we show that MacroD2 nuclear export temporally restricts its recruitment to DNA lesions, which may decrease the net ADP-ribosylhydrolase activity at the site of DNA damage. Together, our results identify a novel feedback regulation between two crucial DNA damage-induced signaling pathways: ADP-ribosylation and ATM activation.
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Affiliation(s)
- Barbara Golia
- Department of Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried 82152, Germany
| | - Giuliana Katharina Moeller
- Department of Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried 82152, Germany
| | - Gytis Jankevicius
- Department of Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried 82152, Germany
| | - Andreas Schmidt
- Zentrallabor für Proteinanalytik (Protein Analysis Unit), Ludwig-Maximilians-Universität München, Planegg-Martinsried 82152, Germany
| | - Anna Hegele
- Department of Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried 82152, Germany
| | - Julia Preißer
- Department of Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried 82152, Germany
| | - Mai Ly Tran
- Department of Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried 82152, Germany
| | - Axel Imhof
- Zentrallabor für Proteinanalytik (Protein Analysis Unit), Ludwig-Maximilians-Universität München, Planegg-Martinsried 82152, Germany
| | - Gyula Timinszky
- Department of Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried 82152, Germany
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279
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Yuan Z, Chen J, Li W, Li D, Chen C, Gao C, Jiang Y. PARP inhibitors as antitumor agents: a patent update (2013-2015). Expert Opin Ther Pat 2016; 27:363-382. [PMID: 27841036 DOI: 10.1080/13543776.2017.1259413] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
INTRODUCTION PARP inhibitors have been extensively explored as antitumor agents and have shown potent efficacy both in vitro and in vivo. They can be used in monotherapy under the synthetic lethality concept or in combination with radiotherapy or chemotherapy, inducing a synergistic effect. Areas covered: This review covers relevant efforts in the development of PARP inhibitors with a particular focus on recently patented PARP inhibitors, combination therapy involving PARP inhibitors, tumor responsiveness to PARP inhibitors as detailed in reports made from 2013 - 2015, and PARP drugs in clinical trials and other novel inhibitors that emerged in 2013 - 2015. Expert opinion: Clinical studies and applications of PARP inhibitors as antitumor agents have gained considerable recognition in the last few years. In addition to FDA-approved olaparib, an increasing number of new inhibitors have been designed and synthesized, some of which are under preclinical or clinical evaluation. Novel inhibitors are still required, especially new scaffold compounds or drugs with improved properties, such as higher selectivity, higher potency and lower toxicity. The development of combination therapies involving PARP inhibitors and the exploration of biomarkers to predict outcomes with PARP inhibitors would expand the applications of these inhibitors, allowing more patients to benefit from this promising class of drugs in the future.
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Affiliation(s)
- Zigao Yuan
- a Department of Chemistry , Tsinghua University , Beijing , P. R. China.,b The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology, the Graduate School at Shenzhen , Tsinghua University , Shenzhen , P. R. China
| | - Jiwei Chen
- a Department of Chemistry , Tsinghua University , Beijing , P. R. China.,b The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology, the Graduate School at Shenzhen , Tsinghua University , Shenzhen , P. R. China
| | - Wenlu Li
- a Department of Chemistry , Tsinghua University , Beijing , P. R. China.,b The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology, the Graduate School at Shenzhen , Tsinghua University , Shenzhen , P. R. China
| | - Dan Li
- a Department of Chemistry , Tsinghua University , Beijing , P. R. China.,b The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology, the Graduate School at Shenzhen , Tsinghua University , Shenzhen , P. R. China
| | - Changjun Chen
- a Department of Chemistry , Tsinghua University , Beijing , P. R. China.,b The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology, the Graduate School at Shenzhen , Tsinghua University , Shenzhen , P. R. China
| | - Chunmei Gao
- b The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology, the Graduate School at Shenzhen , Tsinghua University , Shenzhen , P. R. China.,c National & Local United Engineering Lab for Personalized anti-tumor drugs, the Graduate School at Shenzhen , Tsinghua University , Shenzhen , P. R. China
| | - Yuyang Jiang
- b The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology, the Graduate School at Shenzhen , Tsinghua University , Shenzhen , P. R. China.,c National & Local United Engineering Lab for Personalized anti-tumor drugs, the Graduate School at Shenzhen , Tsinghua University , Shenzhen , P. R. China.,d School of Medicine , Tsinghua University , Beijing , P. R. China
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280
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Kennedy BE, Sharif T, Martell E, Dai C, Kim Y, Lee PWK, Gujar SA. NAD + salvage pathway in cancer metabolism and therapy. Pharmacol Res 2016; 114:274-283. [PMID: 27816507 DOI: 10.1016/j.phrs.2016.10.027] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 10/30/2016] [Indexed: 12/22/2022]
Abstract
Nicotinamide adenine dinucleotide (NAD+) is an essential coenzyme for various physiological processes including energy metabolism, DNA repair, cell growth, and cell death. Many of these pathways are typically dysregulated in cancer cells, making NAD+ an intriguing target for cancer therapeutics. NAD+ is mainly synthesized by the NAD+ salvage pathway in cancer cells, and not surprisingly, the pharmacological targeting of the NAD+ salvage pathway causes cancer cell cytotoxicity in vitro and in vivo. Several studies have described the precise consequences of NAD+ depletion on cancer biology, and have demonstrated that NAD+ depletion results in depletion of energy levels through lowered rates of glycolysis, reduced citric acid cycle activity, and decreased oxidative phosphorylation. Additionally, depletion of NAD+ causes sensitization of cancer cells to oxidative damage by disruption of the anti-oxidant defense system, decreased cell proliferation, and initiation of cell death through manipulation of cell signaling pathways (e.g., SIRT1 and p53). Recently, studies have explored the effect of well-known cancer therapeutics in combination with pharmacological depletion of NAD+ levels, and found in many cases a synergistic effect on cancer cell cytotoxicity. In this context, we will discuss the effects of NAD+ salvage pathway inhibition on cancer cell biology and provide insight on this pathway as a novel anti-cancer therapeutic target.
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Affiliation(s)
- Barry E Kennedy
- Department of Microbiology & Immunology, Dalhousie University, Halifax, NS, Canada
| | - Tanveer Sharif
- Department of Microbiology & Immunology, Dalhousie University, Halifax, NS, Canada
| | - Emma Martell
- Department of Microbiology & Immunology, Dalhousie University, Halifax, NS, Canada
| | - Cathleen Dai
- Department of Microbiology & Immunology, Dalhousie University, Halifax, NS, Canada
| | - Youra Kim
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Patrick W K Lee
- Department of Microbiology & Immunology, Dalhousie University, Halifax, NS, Canada; Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Shashi A Gujar
- Department of Microbiology & Immunology, Dalhousie University, Halifax, NS, Canada; Department of Pathology, Dalhousie University, Halifax, NS, Canada; Centre for Innovative and Collaborative Health Systems Research, IWK Health Centre, Halifax, NS, Canada.
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281
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Bolbat A, Schultz C. Recent developments of genetically encoded optical sensors for cell biology. Biol Cell 2016; 109:1-23. [PMID: 27628952 DOI: 10.1111/boc.201600040] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/06/2016] [Accepted: 09/09/2016] [Indexed: 12/14/2022]
Abstract
Optical sensors are powerful tools for live cell research as they permit to follow the location, concentration changes or activities of key cellular players such as lipids, ions and enzymes. Most of the current sensor probes are based on fluorescence which provides great spatial and temporal precision provided that high-end microscopy is used and that the timescale of the event of interest fits the response time of the sensor. Many of the sensors developed in the past 20 years are genetically encoded. There is a diversity of designs leading to simple or sometimes complicated applications for the use in live cells. Genetically encoded sensors began to emerge after the discovery of fluorescent proteins, engineering of their improved optical properties and the manipulation of their structure through application of circular permutation. In this review, we will describe a variety of genetically encoded biosensor concepts, including those for intensiometric and ratiometric sensors based on single fluorescent proteins, Forster resonance energy transfer-based sensors, sensors utilising bioluminescence, sensors using self-labelling SNAP- and CLIP-tags, and finally tetracysteine-based sensors. We focus on the newer developments and discuss the current approaches and techniques for design and application. This will demonstrate the power of using optical sensors in cell biology and will help opening the field to more systematic applications in the future.
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Affiliation(s)
- Andrey Bolbat
- European Molecular Biology Laboratory (EMBL), Cell Biology & Biophysics Unit, Heidelberg, 69117, Germany
| | - Carsten Schultz
- European Molecular Biology Laboratory (EMBL), Cell Biology & Biophysics Unit, Heidelberg, 69117, Germany
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282
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Nardozza AP, Ladurner AG. Nick Your DNA, Mark Your Chromatin. Mol Cell 2016; 64:7-9. [PMID: 27716488 DOI: 10.1016/j.molcel.2016.09.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
DNA damage induces chemical and structural changes in our chromatin-embedded genome. In a recent issue of Nature Communications, Grundy et al. (2016) identify a role for PARP3 in the repair of single-strand breaks and reveal that PARP3 mono-ADP-ribosylates nucleosomal histone H2B.
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Affiliation(s)
- Aurelio P Nardozza
- Biomedical Center, Physiological Chemistry, Ludwig-Maximilians-University of Munich, Großhaderner Street 9, 82152 Planegg-Martinsried, Germany
| | - Andreas G Ladurner
- Biomedical Center, Physiological Chemistry, Ludwig-Maximilians-University of Munich, Großhaderner Street 9, 82152 Planegg-Martinsried, Germany; Center for Integrated Protein Science Munich (CIPSM), 81377 Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), 80336 Munich, Germany.
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283
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Huang G, Zhang Y, Shan Y, Yang S, Chelliah Y, Wang H, Takahashi JS. Circadian Oscillations of NADH Redox State Using a Heterologous Metabolic Sensor in Mammalian Cells. J Biol Chem 2016; 291:23906-23914. [PMID: 27645993 DOI: 10.1074/jbc.m116.728774] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 07/18/2016] [Indexed: 12/13/2022] Open
Abstract
It is known that there are mechanistic links between circadian clocks and metabolic cycles. Reduced nicotinamide adenine dinucleotide (NADH) is a key metabolic cofactor in all living cells; however, it is not known whether levels of NADH oscillate or not. Here we employed REX, a bacterial NADH-binding protein, fused to the VP16 activator to convert intracellular endogenous redox balance into transcriptional readouts by a reporter gene in mammalian cells. EMSA results show that the DNA binding activity of both T- and S-REX::VP16 fusions is decreased with a reduced-to-oxidized cofactor ratio increase. Transient and stabilized cell lines bearing the REX::VP16 and the REX binding operator (ROP) exhibit two circadian luminescence cycles. Consistent with these results, NADH oscillations are observed in host cells, indicating REX can act as a NADH sensor to report intracellular dynamic redox homeostasis in mammalian cells in real time. NADH oscillations provide another metabolic signal for coupling the circadian clock and cellular metabolic states.
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Affiliation(s)
- Guocun Huang
- From the Department of Neuroscience and .,Center for Circadian Clocks, Soochow University, Suzhou 215123, China
| | - Yunfeng Zhang
- Center for Circadian Clocks, Soochow University, Suzhou 215123, China
| | | | - Shuzhang Yang
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390 and
| | - Yogarany Chelliah
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390 and
| | - Han Wang
- Center for Circadian Clocks, Soochow University, Suzhou 215123, China
| | - Joseph S Takahashi
- From the Department of Neuroscience and .,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390 and
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284
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Making sense of NAD+ subcellular localization. Nat Methods 2016. [DOI: 10.1038/nmeth.3951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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285
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Affiliation(s)
- Leonard Guarente
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
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286
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Wang X, Ding S. Pre-B-cell colony-enhancing factor as a target for protecting against apoptotic neuronal death and mitochondrial damage in ischemia. Neural Regen Res 2016; 11:1914-1915. [PMID: 28197180 PMCID: PMC5270422 DOI: 10.4103/1673-5374.195275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Xiaowan Wang
- Department of Bioengineering, University of Missouri, Columbia, MO, USA
| | - Shinghua Ding
- Department of Bioengineering, University of Missouri, Columbia, MO, USA; Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, USA
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