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Surányi ÉV, Perey-Simon V, Hirmondó R, Trombitás T, Kazzazy L, Varga M, Vértessy BG, Tóth J. Using Selective Enzymes to Measure Noncanonical DNA Building Blocks: dUTP, 5-Methyl-dCTP, and 5-Hydroxymethyl-dCTP. Biomolecules 2023; 13:1801. [PMID: 38136671 PMCID: PMC10742078 DOI: 10.3390/biom13121801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Cells maintain a fine-tuned balance of deoxyribonucleoside 5'-triphosphates (dNTPs), a crucial factor in preserving genomic integrity. Any alterations in the nucleotide pool's composition or chemical modifications to nucleotides before their incorporation into DNA can lead to increased mutation frequency and DNA damage. In addition to the chemical modification of canonical dNTPs, the cellular de novo dNTP metabolism pathways also produce noncanonical dNTPs. To keep their levels low and prevent them from incorporating into the DNA, these noncanonical dNTPs are removed from the dNTP pool by sanitizing enzymes. In this study, we introduce innovative protocols for the high-throughput fluorescence-based quantification of dUTP, 5-methyl-dCTP, and 5-hydroxymethyl-dCTP. To distinguish between noncanonical dNTPs and their canonical counterparts, specific enzymes capable of hydrolyzing either the canonical or noncanonical dNTP analogs are employed. This approach provides a more precise understanding of the composition and noncanonical constituents of dNTP pools, facilitating a deeper comprehension of DNA metabolism and repair. It is also crucial for accurately interpreting mutational patterns generated through the next-generation sequencing of biological samples.
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Affiliation(s)
- Éva Viola Surányi
- Institute of Enzymology, Research Centre for Natural Sciences, H-1117 Budapest, Hungary; (V.P.-S.); (R.H.)
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, H-1111 Budapest, Hungary
| | - Viktória Perey-Simon
- Institute of Enzymology, Research Centre for Natural Sciences, H-1117 Budapest, Hungary; (V.P.-S.); (R.H.)
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, H-1111 Budapest, Hungary
| | - Rita Hirmondó
- Institute of Enzymology, Research Centre for Natural Sciences, H-1117 Budapest, Hungary; (V.P.-S.); (R.H.)
| | - Tamás Trombitás
- Institute of Enzymology, Research Centre for Natural Sciences, H-1117 Budapest, Hungary; (V.P.-S.); (R.H.)
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, H-1111 Budapest, Hungary
| | - Latifa Kazzazy
- Department of Genetics, ELTE Eötvös Loránd University, H-1117 Budapest, Hungary (M.V.)
| | - Máté Varga
- Department of Genetics, ELTE Eötvös Loránd University, H-1117 Budapest, Hungary (M.V.)
| | - Beáta G. Vértessy
- Institute of Enzymology, Research Centre for Natural Sciences, H-1117 Budapest, Hungary; (V.P.-S.); (R.H.)
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, H-1111 Budapest, Hungary
| | - Judit Tóth
- Institute of Enzymology, Research Centre for Natural Sciences, H-1117 Budapest, Hungary; (V.P.-S.); (R.H.)
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, H-1111 Budapest, Hungary
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2
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Rácz GA, Nagy N, Várady G, Tóvári J, Apáti Á, Vértessy BG. Discovery of two new isoforms of the human DUT gene. Sci Rep 2023; 13:7760. [PMID: 37173337 PMCID: PMC10181998 DOI: 10.1038/s41598-023-32970-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 04/05/2023] [Indexed: 05/15/2023] Open
Abstract
In human cells two dUTPase isoforms have been described: one nuclear (DUT-N) and one mitochondrial (DUT-M), with cognate localization signals. In contrast, here we identified two additional isoforms; DUT-3 without any localization signal and DUT-4 with the same nuclear localization signal as DUT-N. Based on an RT-qPCR method for simultaneous isoform-specific quantification we analysed the relative expression patterns in 20 human cell lines of highly different origins. We found that the DUT-N isoform is expressed by far at the highest level, followed by the DUT-M and the DUT-3 isoform. A strong correlation between expression levels of DUT-M and DUT-3 suggests that these two isoforms may share the same promoter. We analysed the effect of serum starvation on the expression of dUTPase isoforms compared to non-treated cells and found that the mRNA levels of DUT-N decreased in A-549 and MDA-MB-231 cells, but not in HeLa cells. Surprisingly, upon serum starvation DUT-M and DUT-3 showed a significant increase in the expression, while the expression level of the DUT-4 isoform did not show any changes. Taken together our results indicate that the cellular dUTPase supply may also be provided in the cytoplasm and starvation stress induced expression changes are cell line dependent.
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Affiliation(s)
- Gergely Attila Rácz
- Department of Applied Biotechnology and Food Sciences, Faculty of Chemical Technology and Biotechnology, BME Budapest University of Technology and Economics, Műegyetem Rkp. 3., Budapest, 1111, Hungary.
- Institute of Enzymology, Research Centre for Natural Sciences, ELKH Eötvös Loránd Research Network, Budapest, Hungary.
| | - Nikolett Nagy
- Institute of Enzymology, Research Centre for Natural Sciences, ELKH Eötvös Loránd Research Network, Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest Pázmány Péter Sétány 1/C, Budapest, Hungary
| | - György Várady
- Institute of Enzymology, Research Centre for Natural Sciences, ELKH Eötvös Loránd Research Network, Budapest, Hungary
| | - József Tóvári
- Department of Experimental Pharmacology, National Institute of Oncology, Ráth Gy. U. 7-9, Budapest, 1122, Hungary
| | - Ágota Apáti
- Institute of Enzymology, Research Centre for Natural Sciences, ELKH Eötvös Loránd Research Network, Budapest, Hungary
| | - Beáta G Vértessy
- Department of Applied Biotechnology and Food Sciences, Faculty of Chemical Technology and Biotechnology, BME Budapest University of Technology and Economics, Műegyetem Rkp. 3., Budapest, 1111, Hungary.
- Institute of Enzymology, Research Centre for Natural Sciences, ELKH Eötvös Loránd Research Network, Budapest, Hungary.
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3
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Szabó JE, Nyíri K, Andrási D, Matejka J, Ozohanics O, Vértessy B. Redox status of cysteines does not alter functional properties of human dUTPase but the Y54C mutation involved in monogenic diabetes decreases protein stability. Sci Rep 2021; 11:19197. [PMID: 34584184 PMCID: PMC8478915 DOI: 10.1038/s41598-021-98790-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/13/2021] [Indexed: 02/08/2023] Open
Abstract
Recently it was proposed that the redox status of cysteines acts as a redox switch to regulate both the oligomeric status and the activity of human dUTPase. In a separate report, a human dUTPase point mutation, resulting in a tyrosine to cysteine substitution (Y54C) was identified as the monogenic cause of a rare syndrome associated with diabetes and bone marrow failure. These issues prompt a critical investigation about the potential regulatory role of cysteines in the enzyme. Here we show on the one hand that independently of the redox status of wild-type cysteines, human dUTPase retains its characteristic trimeric assembly and its catalytic activity. On the other hand, the Y54C mutation did not compromise the substrate binding and the catalytic properties of the enzyme at room temperature. The thermal stability of the mutant protein was found to be decreased, which resulted in the loss of 67% of its activity after 90 min incubation at the physiological temperature in contrast to the wild-type enzyme. In addition, the presence or absence of reducing agents had no effect on hDUTY54C activity and stability, although it was confirmed that the introduced cysteine contains a solvent accessible thiol group.
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Affiliation(s)
- Judit Eszter Szabó
- Institute of Enzymology, RCNS, Eötvös Loránd Research Network, Budapest, Hungary.
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary.
| | - Kinga Nyíri
- Institute of Enzymology, RCNS, Eötvös Loránd Research Network, Budapest, Hungary
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Dániel Andrási
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Judit Matejka
- Institute of Enzymology, RCNS, Eötvös Loránd Research Network, Budapest, Hungary
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Olivér Ozohanics
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Beáta Vértessy
- Institute of Enzymology, RCNS, Eötvös Loránd Research Network, Budapest, Hungary.
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary.
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4
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Wang YP, Sharda A, Xu SN, van Gastel N, Man CH, Choi U, Leong WZ, Li X, Scadden DT. Malic enzyme 2 connects the Krebs cycle intermediate fumarate to mitochondrial biogenesis. Cell Metab 2021; 33:1027-1041.e8. [PMID: 33770508 PMCID: PMC10472834 DOI: 10.1016/j.cmet.2021.03.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/21/2020] [Accepted: 03/03/2021] [Indexed: 12/13/2022]
Abstract
Mitochondria have an independent genome (mtDNA) and protein synthesis machinery that coordinately activate for mitochondrial generation. Here, we report that the Krebs cycle intermediate fumarate links metabolism to mitobiogenesis through binding to malic enzyme 2 (ME2). Mechanistically, fumarate binds ME2 with two complementary consequences. First, promoting the formation of ME2 dimers, which activate deoxyuridine 5'-triphosphate nucleotidohydrolase (DUT). DUT fosters thymidine generation and an increase of mtDNA. Second, fumarate-induced ME2 dimers abrogate ME2 monomer binding to mitochondrial ribosome protein L45, freeing it for mitoribosome assembly and mtDNA-encoded protein production. Methylation of the ME2-fumarate binding site by protein arginine methyltransferase-1 inhibits fumarate signaling to constrain mitobiogenesis. Notably, acute myeloid leukemia is highly dependent on mitochondrial function and is sensitive to targeting of the fumarate-ME2 axis. Therefore, mitobiogenesis can be manipulated in normal and malignant cells through ME2, an unanticipated governor of mitochondrial biomass production that senses nutrient availability through fumarate.
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Affiliation(s)
- Yi-Ping Wang
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Key Laboratory of Breast Cancer in Shanghai, Cancer Institute, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College, Fudan University, Shanghai 20032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 20032, China
| | - Azeem Sharda
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Shuang-Nian Xu
- Department of Hematology, Southwest Hospital, Army Medical University, Chongqing 400038, China
| | - Nick van Gastel
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Cheuk Him Man
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Una Choi
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Wei Zhong Leong
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Xi Li
- Department of Hematology, Southwest Hospital, Army Medical University, Chongqing 400038, China
| | - David T Scadden
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.
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5
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Hewitt G, Borel V, Segura-Bayona S, Takaki T, Ruis P, Bellelli R, Lehmann LC, Sommerova L, Vancevska A, Tomas-Loba A, Zhu K, Cooper C, Fugger K, Patel H, Goldstone R, Schneider-Luftman D, Herbert E, Stamp G, Brough R, Pettitt S, Lord CJ, West SC, Ahel I, Ahel D, Chapman JR, Deindl S, Boulton SJ. Defective ALC1 nucleosome remodeling confers PARPi sensitization and synthetic lethality with HRD. Mol Cell 2021; 81:767-783.e11. [PMID: 33333017 PMCID: PMC7895907 DOI: 10.1016/j.molcel.2020.12.006] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 11/09/2020] [Accepted: 12/03/2020] [Indexed: 12/19/2022]
Abstract
Chromatin is a barrier to efficient DNA repair, as it hinders access and processing of certain DNA lesions. ALC1/CHD1L is a nucleosome-remodeling enzyme that responds to DNA damage, but its precise function in DNA repair remains unknown. Here we report that loss of ALC1 confers sensitivity to PARP inhibitors, methyl-methanesulfonate, and uracil misincorporation, which reflects the need to remodel nucleosomes following base excision by DNA glycosylases but prior to handover to APEX1. Using CRISPR screens, we establish that ALC1 loss is synthetic lethal with homologous recombination deficiency (HRD), which we attribute to chromosome instability caused by unrepaired DNA gaps at replication forks. In the absence of ALC1 or APEX1, incomplete processing of BER intermediates results in post-replicative DNA gaps and a critical dependence on HR for repair. Hence, targeting ALC1 alone or as a PARP inhibitor sensitizer could be employed to augment existing therapeutic strategies for HRD cancers.
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Affiliation(s)
- Graeme Hewitt
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Valerie Borel
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | - Tohru Takaki
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Phil Ruis
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | - Laura C Lehmann
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden
| | - Lucia Sommerova
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | | | - Antonia Tomas-Loba
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Kang Zhu
- Sir William Dunn School of Pathology, South Parks Road, University of Oxford, Oxford OX1 3RE, UK
| | - Christopher Cooper
- Sir William Dunn School of Pathology, South Parks Road, University of Oxford, Oxford OX1 3RE, UK
| | - Kasper Fugger
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Harshil Patel
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | | | - Ellie Herbert
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Gordon Stamp
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Rachel Brough
- The CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Stephen Pettitt
- The CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Christopher J Lord
- The CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Stephen C West
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ivan Ahel
- Sir William Dunn School of Pathology, South Parks Road, University of Oxford, Oxford OX1 3RE, UK
| | - Dragana Ahel
- Sir William Dunn School of Pathology, South Parks Road, University of Oxford, Oxford OX1 3RE, UK
| | - J Ross Chapman
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Sebastian Deindl
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden
| | - Simon J Boulton
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Artios Pharma Ltd., Meditrina, Babraham Research Campus, Cambridge CB22 3AT, UK.
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6
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Szabó JE, Surányi ÉV, Mébold BS, Trombitás T, Cserepes M, Tóth J. A user-friendly, high-throughput tool for the precise fluorescent quantification of deoxyribonucleoside triphosphates from biological samples. Nucleic Acids Res 2020; 48:e45. [PMID: 32103262 PMCID: PMC7192609 DOI: 10.1093/nar/gkaa116] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 02/05/2020] [Accepted: 02/17/2020] [Indexed: 12/24/2022] Open
Abstract
Cells maintain a fine-tuned, dynamic concentration balance in the pool of deoxyribonucleoside 5′-triphosphates (dNTPs). This balance is essential for physiological processes including cell cycle control or antiviral defense. Its perturbation results in increased mutation frequencies, replication arrest and may promote cancer development. An easily accessible and relatively high-throughput method would greatly accelerate the exploration of the diversified consequences of dNTP imbalances. The dNTP incorporation based, fluorescent TaqMan-like assay published by Wilson et al. has the aforementioned advantages over mass spectrometry, radioactive or chromatography based dNTP quantification methods. Nevertheless, the assay failed to produce reliable data in several biological samples. Therefore, we applied enzyme kinetics analysis on the fluorescent dNTP incorporation curves and found that the Taq polymerase exhibits a dNTP independent exonuclease activity that decouples signal generation from dNTP incorporation. Furthermore, we found that both polymerization and exonuclease activities are unpredictably inhibited by the sample matrix. To resolve these issues, we established a kinetics based data analysis method which identifies the signal generated by dNTP incorporation. We automated the analysis process in the nucleoTIDY software which enables even the inexperienced user to calculate the final and accurate dNTP amounts in a 96-well-plate setup within minutes.
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Affiliation(s)
- Judit Eszter Szabó
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest 1117, Hungary.,Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest 1111, Hungary
| | - Éva Viola Surányi
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest 1117, Hungary.,Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest 1111, Hungary
| | - Bence Sándor Mébold
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest 1117, Hungary
| | - Tamás Trombitás
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest 1117, Hungary.,Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest 1111, Hungary
| | - Mihály Cserepes
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest 1117, Hungary.,Department of Experimental Pharmacology, National Institute of Oncology, Budapest, Hungary
| | - Judit Tóth
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest 1117, Hungary
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7
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Chakraborty J, Stover PJ. Deoxyuracil in DNA in health and disease. Curr Opin Clin Nutr Metab Care 2020; 23:247-252. [PMID: 32398439 PMCID: PMC7347158 DOI: 10.1097/mco.0000000000000660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW Genome instability has long been implicated as a primary causal factor in cancer and diseases of aging. The genome is constantly under attack from extrinsic and intrinsic damaging agents. Uracil misincorporation in DNA and its repair is an intrinsic factor resulting in genomic instability and DNA mutations. Additionally, the presence of uracil in DNA can modify gene expression by interfering with promoter binding and transcription inhibition or upregulation of apoptotic proteins. In immune cells, uracil in DNA drives beneficial genomic diversity for antigen-driven immunity. This review addresses diseases that are linked to uracil accumulation in DNA, its causes, consequences, and the associated biomarkers of risk factors. RECENT FINDINGS Elevated genomic uracil is associated with megaloblastic anemia, neural tube defects, and retroviral immunity. Current evidence supporting causal mechanisms and nutritional interventions that rescue impaired pathways associated with uracil accumulation in DNA are summarized in this review. SUMMARY Nutritional deficiencies in B vitamins can cause uracil misincorporation into DNA leading to genome instability and associated diseases. Nutritional approaches to preventing uracil accumulation in DNA show some promise to address its associated diseases, but additional randomized controlled trials are needed.
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Affiliation(s)
| | - Patrick J. Stover
- All correspondence must be addressed to: Patrick J. Stover: Agriculture and Life Sciences Building, 600 John Kimbrough Blvd, Suite 510, 2142 TAMU, College Station, TX 77843; 979-862-4384
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8
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Miggiano R, Morrone C, Rossi F, Rizzi M. Targeting Genome Integrity in Mycobacterium Tuberculosis: From Nucleotide Synthesis to DNA Replication and Repair. Molecules 2020; 25:E1205. [PMID: 32156001 PMCID: PMC7179400 DOI: 10.3390/molecules25051205] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/04/2020] [Accepted: 03/05/2020] [Indexed: 12/12/2022] Open
Abstract
Mycobacterium tuberculosis (MTB) is the causative agent of tuberculosis (TB), an ancient disease which still today causes 1.4 million deaths worldwide per year. Long-term, multi-agent anti-tubercular regimens can lead to the anticipated non-compliance of the patient and increased drug toxicity, which in turn can contribute to the emergence of drug-resistant MTB strains that are not susceptible to first- and second-line available drugs. Hence, there is an urgent need for innovative antitubercular drugs and vaccines. A number of biochemical processes are required to maintain the correct homeostasis of DNA metabolism in all organisms. Here we focused on reviewing our current knowledge and understanding of biochemical and structural aspects of relevance for drug discovery, for some such processes in MTB, and particularly DNA synthesis, synthesis of its nucleotide precursors, and processes that guarantee DNA integrity and genome stability. Overall, the area of drug discovery in DNA metabolism appears very much alive, rich of investigations and promising with respect to new antitubercular drug candidates. However, the complexity of molecular events that occur in DNA metabolic processes requires an accurate characterization of mechanistic details in order to avoid major flaws, and therefore the failure, of drug discovery approaches targeting genome integrity.
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Affiliation(s)
- Riccardo Miggiano
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy; (C.M.); (F.R.)
| | | | | | - Menico Rizzi
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy; (C.M.); (F.R.)
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9
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Lopata A, Jójárt B, Surányi ÉV, Takács E, Bezúr L, Leveles I, Bendes ÁÁ, Viskolcz B, Vértessy BG, Tóth J. Beyond Chelation: EDTA Tightly Binds Taq DNA Polymerase, MutT and dUTPase and Directly Inhibits dNTPase Activity. Biomolecules 2019; 9:biom9100621. [PMID: 31627475 PMCID: PMC6843921 DOI: 10.3390/biom9100621] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/15/2019] [Accepted: 10/15/2019] [Indexed: 11/25/2022] Open
Abstract
EDTA is commonly used as an efficient chelator of metal ion enzyme cofactors. It is highly soluble, optically inactive and does not interfere with most chemicals used in standard buffers making EDTA a common choice to generate metal-free conditions for biochemical and biophysical investigations. However, the controversy in the literature on metal-free enzyme activities achieved using EDTA or by other means called our attention to a putative effect of EDTA beyond chelation. Here, we show that EDTA competes for the nucleotide binding site of the nucleotide hydrolase dUTPase by developing an interaction network within the active site similar to that of the substrate. To achieve these findings, we applied kinetics and molecular docking techniques using two different dUTPases. Furthermore, we directly measured the binding of EDTA to dUTPases and to two other dNTPases, the Taq polymerase and MutT using isothermal titration calorimetry. EDTA binding proved to be exothermic and mainly enthalpy driven with a submicromolar dissociation constant considerably lower than that of the enzyme:substrate or the Mg:EDTA complexes. Control proteins, including an ATPase, did not interact with EDTA. Our findings indicate that EDTA may act as a selective inhibitor against dNTP hydrolyzing enzymes and urge the rethinking of the utilization of EDTA in enzymatic experiments.
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Affiliation(s)
- Anna Lopata
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1113 Budapest, Hungary.
- Department of Applied Biotechnology, Budapest University of Technology and Economics, 1111 Budapest, Hungary.
- Institute of Biophysical Chemistry, Goethe University, Frankfurt am Main, 60438 Frankfurt, Germany.
| | - Balázs Jójárt
- Institute of Food Engineering, Faculty of Engineering, University of Szeged, 6724 Szeged, Hungary.
| | - Éva V Surányi
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1113 Budapest, Hungary.
- Department of Applied Biotechnology, Budapest University of Technology and Economics, 1111 Budapest, Hungary.
| | - Enikő Takács
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1113 Budapest, Hungary.
| | - László Bezúr
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, 1111 Budapest, Hungary.
| | - Ibolya Leveles
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1113 Budapest, Hungary.
- Department of Applied Biotechnology, Budapest University of Technology and Economics, 1111 Budapest, Hungary.
| | - Ábris Á Bendes
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1113 Budapest, Hungary.
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90220 Oulu, Finland.
| | - Béla Viskolcz
- Institute of Chemistry, University of Miskolc, 3515 Miskolc, Hungary.
| | - Beáta G Vértessy
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1113 Budapest, Hungary.
- Department of Applied Biotechnology, Budapest University of Technology and Economics, 1111 Budapest, Hungary.
| | - Judit Tóth
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1113 Budapest, Hungary.
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10
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HDX and Native Mass Spectrometry Reveals the Different Structural Basis for Interaction of the Staphylococcal Pathogenicity Island Repressor Stl with Dimeric and Trimeric Phage dUTPases. Biomolecules 2019; 9:biom9090488. [PMID: 31540005 PMCID: PMC6770826 DOI: 10.3390/biom9090488] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 08/16/2019] [Accepted: 09/11/2019] [Indexed: 01/04/2023] Open
Abstract
The dUTPase enzyme family plays an essential role in maintaining the genome integrity and are represented by two distinct classes of proteins; the β-pleated homotrimeric and the all-α homodimeric dUTPases. Representatives of both trimeric and dimeric dUTPases are encoded by Staphylococcus aureus phage genomes and have been shown to interact with the Stl repressor protein of S. aureus pathogenicity island SaPIbov1. In the present work we set out to characterize the interactions between these proteins based on a range of biochemical and biophysical methods and shed light on the binding mechanism of the dimeric φNM1 phage dUTPase and Stl. Using hydrogen deuterium exchange mass spectrometry, we also characterize the protein regions involved in the dUTPase:Stl interactions. Based on these results we provide reasonable explanation for the enzyme inhibitory effect of Stl observed in both types of complexes. Our experiments reveal that Stl employs different peptide segments and stoichiometry for the two different phage dUTPases which allows us to propose a functional plasticity of Stl. The malleable character of Stl serves as a basis for the inhibition of both dimeric and trimeric dUTPases.
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The Role of a Key Amino Acid Position in Species-Specific Proteinaceous dUTPase Inhibition. Biomolecules 2019; 9:biom9060221. [PMID: 31174420 PMCID: PMC6627510 DOI: 10.3390/biom9060221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 05/27/2019] [Indexed: 02/06/2023] Open
Abstract
Protein inhibitors of key DNA repair enzymes play an important role in deciphering physiological pathways responsible for genome integrity, and may also be exploited in biomedical research. The staphylococcal repressor StlSaPIbov1 protein was described to be an efficient inhibitor of dUTPase homologues showing a certain degree of species-specificity. In order to provide insight into the inhibition mechanism, in the present study we investigated the interaction of StlSaPIbov1 and Escherichia coli dUTPase. Although we observed a strong interaction of these proteins, unexpectedly the E. coli dUTPase was not inhibited. Seeking a structural explanation for this phenomenon, we identified a key amino acid position where specific mutations sensitized E. coli dUTPase to StlSaPIbov1 inhibition. We solved the three-dimensional (3D) crystal structure of such a mutant in complex with the substrate analogue dUPNPP and surprisingly found that the C-terminal arm of the enzyme, containing the P-loop-like motif was ordered in the structure. This segment was never localized before in any other E. coli dUTPase crystal structures. The 3D structure in agreement with solution phase experiments suggested that ordering of the flexible C-terminal segment upon substrate binding is a major factor in defining the sensitivity of E. coli dUTPase for StlSaPIbov1 inhibition.
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Pálinkás HL, Rácz GA, Gál Z, Hoffmann OI, Tihanyi G, Róna G, Gócza E, Hiripi L, Vértessy BG. CRISPR/Cas9-Mediated Knock-Out of dUTPase in Mice Leads to Early Embryonic Lethality. Biomolecules 2019; 9:biom9040136. [PMID: 30987342 PMCID: PMC6523736 DOI: 10.3390/biom9040136] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/01/2019] [Accepted: 04/02/2019] [Indexed: 01/05/2023] Open
Abstract
Sanitization of nucleotide pools is essential for genome maintenance. Deoxyuridine 5′-triphosphate nucleotidohydrolase (dUTPase) is a key enzyme in this pathway since it catalyzes the cleavage of 2′-deoxyuridine 5′-triphosphate (dUTP) into 2′-deoxyuridine 5′-monophosphate (dUMP) and inorganic pyrophosphate. Through its action dUTPase efficiently prevents uracil misincorporation into DNA and at the same time provides dUMP, the substrate for de novo thymidylate biosynthesis. Despite its physiological significance, knock-out models of dUTPase have not yet been investigated in mammals, but only in unicellular organisms, such as bacteria and yeast. Here we generate CRISPR/Cas9-mediated dUTPase knock-out in mice. We find that heterozygous dut +/– animals are viable while having decreased dUTPase levels. Importantly, we show that dUTPase is essential for embryonic development since early dut −/− embryos reach the blastocyst stage, however, they die shortly after implantation. Analysis of pre-implantation embryos indicates perturbed growth of both inner cell mass (ICM) and trophectoderm (TE). We conclude that dUTPase is indispensable for post-implantation development in mice.
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Affiliation(s)
- Hajnalka Laura Pálinkás
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, H-1117 Budapest, Hungary.
- Doctoral School of Multidisciplinary Medical Science, University of Szeged, H-6720 Szeged, Hungary.
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, H-1111 Budapest, Hungary.
| | - Gergely Attila Rácz
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, H-1117 Budapest, Hungary.
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, H-1111 Budapest, Hungary.
| | - Zoltán Gál
- Department of Animal Biotechnology, Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre, H-2100 Gödöllő, Hungary.
| | - Orsolya Ivett Hoffmann
- Department of Animal Biotechnology, Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre, H-2100 Gödöllő, Hungary.
| | - Gergely Tihanyi
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, H-1117 Budapest, Hungary.
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, H-1111 Budapest, Hungary.
| | - Gergely Róna
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, H-1111 Budapest, Hungary.
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA.
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA.
| | - Elen Gócza
- Department of Animal Biotechnology, Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre, H-2100 Gödöllő, Hungary.
| | - László Hiripi
- Department of Animal Biotechnology, Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre, H-2100 Gödöllő, Hungary.
| | - Beáta G Vértessy
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, H-1117 Budapest, Hungary.
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, H-1111 Budapest, Hungary.
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Alam MS, Moriyama H, Matsumoto M. Enzyme kinetics of dUTPase from the planarian Dugesia ryukyuensis. BMC Res Notes 2019; 12:163. [PMID: 30902068 PMCID: PMC6431053 DOI: 10.1186/s13104-019-4191-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 03/13/2019] [Indexed: 01/21/2023] Open
Abstract
Objective Planarians including Dugesia ryukyuensis (Dr) have strong regenerative abilities that require enhanced DNA replication. Knockdown of the DUT gene in Dr, which encodes deoxyuridine 5′-triphosphate pyrophosphatase (dUTPase), promotes DNA fragmentation, inhibits regeneration, and eventually leads to death. dUTPase catalyzes the hydrolysis of dUTP to dUMP and pyrophosphate. dUTPase is known to prevent uracil misincorporation in DNA by balancing the intracellular ratio between dUTP and dTTP, and contributes to genome stability. Nevertheless, the catalytic performance of Dr-dUTPase has not been reported. Results To confirm the catalytic activity of Dr-dUTPase, we cloned and expressed Dr-DUT in E. coli. Then, we purified Dr-dUTPase using His-tag and removed the tag with thrombin. The resulting Dr-dUTPase had the leading peptide Gly–Ser–His– originating from the vector at the amino terminus, and a mutation, Arg66Lys, to remove the internal thrombin site. We observed the hydrolysis of dUTP by Dr-dUTPase using Cresol Red as a proton sensor. The Km for dUTP was determined to be 4.0 µM, which is similar to that for human dUTPase. Dr-dUTPase exhibited a preference for dUTP over the other nucleotides. We conclude the Dr-dUTPase has catalytic activity. Electronic supplementary material The online version of this article (10.1186/s13104-019-4191-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Md Shahanoor Alam
- Department of Bioscience and Informatics, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama, 223-8522, Japan
| | - Hideaki Moriyama
- School of Biological Sciences, University of Nebraska-Lincoln, 243 Manter Hall, Lincoln, NE, 68588, USA
| | - Midori Matsumoto
- Department of Bioscience and Informatics, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama, 223-8522, Japan.
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Combinatorial Loss of the Enzymatic Activities of Viral Uracil-DNA Glycosylase and Viral dUTPase Impairs Murine Gammaherpesvirus Pathogenesis and Leads to Increased Recombination-Based Deletion in the Viral Genome. mBio 2018; 9:mBio.01831-18. [PMID: 30377280 PMCID: PMC6212821 DOI: 10.1128/mbio.01831-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Unrepaired uracils in DNA can lead to mutations and compromise genomic stability. Herpesviruses have hijacked host processes of DNA repair and nucleotide metabolism by encoding a viral UNG that excises uracils and a viral dUTPase that initiates conversion of dUTP to dTTP. To better understand the impact of these processes on gammaherpesvirus pathogenesis, we examined the separate and collaborative roles of vUNG and vDUT upon MHV68 infection of mice. Simultaneous disruption of the enzymatic activities of both vUNG and vDUT led to a severe defect in acute replication and establishment of latency, while also revealing a novel, combinatorial function in promoting viral genomic stability. We propose that herpesviruses require these enzymatic processes to protect the viral genome from damage, possibly triggered by misincorporated uracil. This reveals a novel point of therapeutic intervention to potentially block viral replication and reduce the fitness of multiple herpesviruses. Misincorporation of uracil or spontaneous cytidine deamination is a common mutagenic insult to DNA. Herpesviruses encode a viral uracil-DNA glycosylase (vUNG) and a viral dUTPase (vDUT), each with enzymatic and nonenzymatic functions. However, the coordinated roles of these enzymatic activities in gammaherpesvirus pathogenesis and viral genomic stability have not been defined. In addition, potential compensation by the host UNG has not been examined in vivo. The genetic tractability of the murine gammaherpesvirus 68 (MHV68) system enabled us to delineate the contribution of host and viral factors that prevent uracilated DNA. Recombinant MHV68 lacking vUNG (ORF46.stop) was not further impaired for acute replication in the lungs of UNG−/− mice compared to wild-type (WT) mice, indicating host UNG does not compensate for the absence of vUNG. Next, we investigated the separate and combinatorial consequences of mutating the catalytic residues of the vUNG (ORF46.CM) and vDUT (ORF54.CM). ORF46.CM was not impaired for replication, while ORF54.CM had a slight transient defect in replication in the lungs. However, disabling both vUNG and vDUT led to a significant defect in acute expansion in the lungs, followed by impaired establishment of latency in the splenic reservoir. Upon serial passage of the ORF46.CM/ORF54.CM mutant in either fibroblasts or the lungs of mice, we noted rapid loss of the nonessential yellow fluorescent protein (YFP) reporter gene from the viral genome, due to recombination at repetitive elements. Taken together, our data indicate that the vUNG and vDUT coordinate to promote viral genomic stability and enable viral expansion prior to colonization of latent reservoirs.
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Abstract
Human deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase), essential for DNA integrity, acts as a survival factor for tumor cells and is a target for cancer chemotherapy. Here we report that the Staphylococcal repressor protein StlSaPIBov1 (Stl) forms strong complex with human dUTPase. Functional analysis reveals that this interaction results in significant reduction of both dUTPase enzymatic activity and DNA binding capability of Stl. We conducted structural studies to understand the mechanism of this mutual inhibition. Small-angle X-ray scattering (SAXS) complemented with hydrogen-deuterium exchange mass spectrometry (HDX-MS) data allowed us to obtain 3D structural models comprising a trimeric dUTPase complexed with separate Stl monomers. These models thus reveal that upon dUTPase-Stl complex formation the functional homodimer of Stl repressor dissociates, which abolishes the DNA binding ability of the protein. Active site forming dUTPase segments were directly identified to be involved in the dUTPase-Stl interaction by HDX-MS, explaining the loss of dUTPase activity upon complexation. Our results provide key novel structural insights that pave the way for further applications of the first potent proteinaceous inhibitor of human dUTPase.
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