101
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Grudzien-Nogalska E, Wu Y, Jiao X, Cui H, Mateyak MK, Hart RP, Tong L, Kiledjian M. Structural and mechanistic basis of mammalian Nudt12 RNA deNADding. Nat Chem Biol 2019; 15:575-582. [PMID: 31101919 PMCID: PMC6527130 DOI: 10.1038/s41589-019-0293-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 03/18/2019] [Indexed: 11/21/2022]
Abstract
We recently demonstrated mammalian cells harbor NAD-capped mRNAs that are hydrolyzed by the DXO deNADding enzyme. Here we report the Nudix protein Nudt12 is a second mammalian deNADding enzyme structurally and mechanistically distinct from DXO and targeting different RNAs. Crystal structure of mouse Nudt12 in complex with the deNADding product AMP and three Mg2+ ions at 1.6 Å resolution provides exquisite insights into the molecular basis of the deNADding activity within the NAD pyrophosphate. Disruption of the Nudt12 gene stabilizes transfected NAD-capped RNA in cells and its endogenous NAD-capped mRNA targets are enriched in those encoding proteins involved in cellular energetics. Furthermore, exposure of cells to nutrient or environmental stress manifests changes in NAD-capped RNA levels that are selectively responsive to Nudt12 or DXO respectively, indicating an association of deNADding to cellular metabolism.
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Affiliation(s)
| | - Yixuan Wu
- Department Biological Sciences, Columbia University, New York, NY, USA
| | - Xinfu Jiao
- Department Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA
| | - Huijuan Cui
- Department Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA
| | - Maria K Mateyak
- Department Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA
| | - Ronald P Hart
- Department Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA
| | - Liang Tong
- Department Biological Sciences, Columbia University, New York, NY, USA.
| | - Megerditch Kiledjian
- Department Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA.
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105
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Visnes T, Cázares-Körner A, Hao W, Wallner O, Masuyer G, Loseva O, Mortusewicz O, Wiita E, Sarno A, Manoilov A, Astorga-Wells J, Jemth AS, Pan L, Sanjiv K, Karsten S, Gokturk C, Grube M, Homan EJ, Hanna BMF, Paulin CBJ, Pham T, Rasti A, Berglund UW, von Nicolai C, Benitez-Buelga C, Koolmeister T, Ivanic D, Iliev P, Scobie M, Krokan HE, Baranczewski P, Artursson P, Altun M, Jensen AJ, Kalderén C, Ba X, Zubarev RA, Stenmark P, Boldogh I, Helleday T. Small-molecule inhibitor of OGG1 suppresses proinflammatory gene expression and inflammation. Science 2019; 362:834-839. [PMID: 30442810 DOI: 10.1126/science.aar8048] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 04/30/2018] [Accepted: 09/24/2018] [Indexed: 12/11/2022]
Abstract
The onset of inflammation is associated with reactive oxygen species and oxidative damage to macromolecules like 7,8-dihydro-8-oxoguanine (8-oxoG) in DNA. Because 8-oxoguanine DNA glycosylase 1 (OGG1) binds 8-oxoG and because Ogg1-deficient mice are resistant to acute and systemic inflammation, we hypothesized that OGG1 inhibition may represent a strategy for the prevention and treatment of inflammation. We developed TH5487, a selective active-site inhibitor of OGG1, which hampers OGG1 binding to and repair of 8-oxoG and which is well tolerated by mice. TH5487 prevents tumor necrosis factor-α-induced OGG1-DNA interactions at guanine-rich promoters of proinflammatory genes. This, in turn, decreases DNA occupancy of nuclear factor κB and proinflammatory gene expression, resulting in decreased immune cell recruitment to mouse lungs. Thus, we present a proof of concept that targeting oxidative DNA repair can alleviate inflammatory conditions in vivo.
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Affiliation(s)
- Torkild Visnes
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden.,Department of Biotechnology and Nanomedicine, SINTEF Industry, N-7465 Trondheim, Norway
| | - Armando Cázares-Körner
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Wenjing Hao
- Department of Microbiology and Immunology, Sealy Center for Molecular Medicine, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Olov Wallner
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Geoffrey Masuyer
- Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden
| | - Olga Loseva
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Oliver Mortusewicz
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Elisée Wiita
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Antonio Sarno
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,The Liaison Committee for Education, Research, and Innovation in Central Norway, Trondheim, Norway
| | - Aleksandr Manoilov
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden.,SciLifeLab, SE-17121 Solna, Sweden
| | - Juan Astorga-Wells
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden.,SciLifeLab, SE-17121 Solna, Sweden
| | - Ann-Sofie Jemth
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Lang Pan
- Department of Microbiology and Immunology, Sealy Center for Molecular Medicine, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Kumar Sanjiv
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Stella Karsten
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Camilla Gokturk
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Maurice Grube
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Evert J Homan
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Bishoy M F Hanna
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Cynthia B J Paulin
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Therese Pham
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Azita Rasti
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Ulrika Warpman Berglund
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Catharina von Nicolai
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Carlos Benitez-Buelga
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Tobias Koolmeister
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Dag Ivanic
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Petar Iliev
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Martin Scobie
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Hans E Krokan
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,The Liaison Committee for Education, Research, and Innovation in Central Norway, Trondheim, Norway
| | - Pawel Baranczewski
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden.,Science for Life Laboratory Drug Discovery and Development Platform, ADME of Therapeutics Facility, Department of Pharmacy, Uppsala University, Uppsala, Sweden.,Uppsala Drug Optimisation and Pharmaceutical Profiling Platform (UDOPP), Department of Pharmacy, Uppsala University, Uppsala, Sweden
| | - Per Artursson
- Science for Life Laboratory Drug Discovery and Development Platform, ADME of Therapeutics Facility, Department of Pharmacy, Uppsala University, Uppsala, Sweden.,Uppsala Drug Optimisation and Pharmaceutical Profiling Platform (UDOPP), Department of Pharmacy, Uppsala University, Uppsala, Sweden
| | - Mikael Altun
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Annika Jenmalm Jensen
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
| | - Christina Kalderén
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Xueqing Ba
- Department of Microbiology and Immunology, Sealy Center for Molecular Medicine, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Roman A Zubarev
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden.,SciLifeLab, SE-17121 Solna, Sweden.,Department of Pharmacological and Technological Chemistry, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden.,Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Istvan Boldogh
- Department of Microbiology and Immunology, Sealy Center for Molecular Medicine, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA.
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden. .,Sheffield Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK
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109
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Grzela R, Nasilowska K, Lukaszewicz M, Tyras M, Stepinski J, Jankowska-Anyszka M, Bojarska E, Darzynkiewicz E. Hydrolytic activity of human Nudt16 enzyme on dinucleotide cap analogs and short capped oligonucleotides. RNA (NEW YORK, N.Y.) 2018; 24:633-642. [PMID: 29483298 PMCID: PMC5900562 DOI: 10.1261/rna.065698.118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 02/20/2018] [Indexed: 05/30/2023]
Abstract
Human Nudt16 (hNudt16) is a member of the Nudix family of hydrolases, comprising enzymes catabolizing various substrates including canonical (d)NTPs, oxidized (d)NTPs, nonnucleoside polyphosphates, and capped mRNAs. Decapping activity of the Xenopus laevis (X29) Nudt16 homolog was observed in the nucleolus, with a high specificity toward U8 snoRNA. Subsequent studies have reported cytoplasmic localization of mammalian Nudt16 with cap hydrolysis activity initiating RNA turnover, similar to Dcp2. The present study focuses on hNudt16 and its hydrolytic activity toward dinucleotide cap analogs and short capped oligonucleotides. We performed a screening assay for potential dinucleotide and oligonucleotide substrates for hNudt16. Our data indicate that dinucleotide cap analogs and capped oligonucleotides containing guanine base in the first transcribed nucleotide are more susceptible to enzymatic digestion by hNudt16 than their counterparts containing adenine. Furthermore, unmethylated dinucleotides (GpppG and ApppG) and respective oligonucleotides (GpppG-16nt and GpppA-16nt) were hydrolyzed by hNudt16 with greater efficiency than were m7GpppG and m7GpppG-16nt. In conclusion, we found that hNudt16 hydrolysis of dinucleotide cap analogs and short capped oligonucleotides displayed a broader spectrum specificity than is currently known.
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Affiliation(s)
- Renata Grzela
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Karolina Nasilowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-097 Warsaw, Poland
| | - Maciej Lukaszewicz
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-097 Warsaw, Poland
| | - Michal Tyras
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Janusz Stepinski
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | | | - Elzbieta Bojarska
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Edward Darzynkiewicz
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-097 Warsaw, Poland
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110
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Ji D, Kietrys AM, Lee Y, Kool ET. ATP-Linked Chimeric Nucleotide as a Specific Luminescence Reporter of Deoxyuridine Triphosphatase. Bioconjug Chem 2018; 29:1614-1621. [PMID: 29578692 DOI: 10.1021/acs.bioconjchem.8b00124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nucleotide surveillance enzymes play important roles in human health, by monitoring damaged monomers in the nucleotide pool and deactivating them before they are incorporated into chromosomal DNA or disrupt nucleotide metabolism. In particular, deamination of cytosine, leading to uracil in DNA and in the nucleotide pool, can be deleterious, causing DNA damage. The enzyme deoxyuridine triphosphatase (dUTPase) is currently under study as a therapeutic and prognostic target for cancer. Measuring the activity of this enzyme is important both in basic research and in clinical applications involving this pathway, but current methods are nonselective, detecting pyrophosphate, which is produced by many enzymes. Here we describe the design and synthesis of a dUTPase enzyme-specific chimeric dinucleotide (DUAL) that replaces the pyrophosphate leaving group of the native substrate with ATP, enabling sensitive detection via luciferase luminescence signaling. The DUAL probe functions sensitively and selectively to quantify enzyme activities in vitro and in cell lysates. We further report the first measurements of dUTPase activities in eight different cell lines, which are found to vary by a factor of 7-fold. We expect that the new probe can be of considerable utility in research involving this clinically significant enzyme.
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Affiliation(s)
- Debin Ji
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Anna M Kietrys
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Yujeong Lee
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Eric T Kool
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
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