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Broderick K, Moutaoufik MT, Aly KA, Babu M. Sanitation enzymes: Exquisite surveillance of the noncanonical nucleotide pool to safeguard the genetic blueprint. Semin Cancer Biol 2023; 94:11-20. [PMID: 37211293 DOI: 10.1016/j.semcancer.2023.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/14/2023] [Accepted: 05/17/2023] [Indexed: 05/23/2023]
Abstract
Reactive oxygen species (ROS) are common products of normal cellular metabolism, but their elevated levels can result in nucleotide modifications. These modified or noncanonical nucleotides often integrate into nascent DNA during replication, causing lesions that trigger DNA repair mechanisms such as the mismatch repair machinery and base excision repair. Four superfamilies of sanitization enzymes can effectively hydrolyze noncanonical nucleotides from the precursor pool and eliminate their unintended incorporation into DNA. Notably, we focus on the representative MTH1 NUDIX hydrolase, whose enzymatic activity is ostensibly nonessential under normal physiological conditions. Yet, the sanitization attributes of MTH1 are more prevalent when ROS levels are abnormally high in cancer cells, rendering MTH1 an interesting target for developing anticancer treatments. We discuss multiple MTH1 inhibitory strategies that have emerged in recent years, and the potential of NUDIX hydrolases as plausible targets for the development of anticancer therapeutics.
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Affiliation(s)
- Kirsten Broderick
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | | | - Khaled A Aly
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada.
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2
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Tong S, Xia M, Xu Y, Sun Q, Ye L, Yuan F, Wang Y, Cai J, Ye Z, Tian D. Identification and validation of a novel prognostic signature based on mitochondria and oxidative stress related genes for glioblastoma. J Transl Med 2023; 21:136. [PMID: 36814293 PMCID: PMC9948483 DOI: 10.1186/s12967-023-03970-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 02/05/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Mitochondria represent a major source of reactive oxygen species (ROS) in cells, and the direct increase in ROS content is the primary cause of oxidative stress, which plays an important role in tumor proliferation, invasion, angiogenesis, and treatment. However, the relationship between mitochondrial oxidative stress-related genes and glioblastoma (GBM) remains unclear. This study aimed to investigate the value of mitochondria and oxidative stress-related genes in the prognosis and therapeutic targets of GBM. METHODS We retrieved mitochondria and oxidative stress-related genes from several public databases. The LASSO regression and Cox analyses were utilized to build a risk model and the ROC curve was used to assess its performance. Then, we analyzed the correlation between the model and immunity and mutation. Furthermore, CCK8 and EdU assays were utilized to verify the proliferative capacity of GBM cells and flow cytometry was used to analyze apoptosis rates. Finally, the JC-1 assay and ATP levels were utilized to detect mitochondrial function, and the intracellular ROS levels were determined using MitoSOX and BODIPY 581/591 C11. RESULTS 5 mitochondrial oxidative stress-related genes (CTSL, TXNRD2, NUDT1, STOX1, CYP2E1) were screened by differential expression analysis and Cox analysis and incorporated in a risk model which yielded a strong prediction accuracy (AUC value = 0.967). Furthermore, this model was strongly related to immune cell infiltration and mutation status and could identify potential targeted therapeutic drugs for GBM. Finally, we selected NUDT1 for further validation in vitro. The results showed that NUDT1 was elevated in GBM, and knockdown of NUDT1 inhibited the proliferation and induced apoptosis of GBM cells, while knockdown of NUDT1 damaged mitochondrial homeostasis and induced oxidative stress in GBM cells. CONCLUSION Our study was the first to propose a prognostic model of mitochondria and oxidative stress-related genes, which provided potential therapeutic strategies for GBM patients.
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Affiliation(s)
- Shiao Tong
- grid.412632.00000 0004 1758 2270Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Minqi Xia
- grid.412632.00000 0004 1758 2270Department of Endocrinology & Metabolism, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yang Xu
- grid.412632.00000 0004 1758 2270Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Qian Sun
- grid.412632.00000 0004 1758 2270Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Liguo Ye
- grid.412632.00000 0004 1758 2270Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Fanen Yuan
- grid.412632.00000 0004 1758 2270Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yixuan Wang
- grid.412632.00000 0004 1758 2270Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jiayang Cai
- grid.412632.00000 0004 1758 2270Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zhang Ye
- grid.412632.00000 0004 1758 2270Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Daofeng Tian
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China.
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Kiyama T, Chen CK, Zhang A, Mao CA. Differential Susceptibility of Retinal Neurons to the Loss of Mitochondrial Biogenesis Factor Nrf1. Cells 2022; 11:cells11142203. [PMID: 35883647 PMCID: PMC9321222 DOI: 10.3390/cells11142203] [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: 04/27/2022] [Revised: 07/10/2022] [Accepted: 07/13/2022] [Indexed: 12/14/2022] Open
Abstract
The retina, the accessible part of the central nervous system, has served as a model system to study the relationship between energy utilization and metabolite supply. When the metabolite supply cannot match the energy demand, retinal neurons are at risk of death. As the powerhouse of eukaryotic cells, mitochondria play a pivotal role in generating ATP, produce precursors for macromolecules, maintain the redox homeostasis, and function as waste management centers for various types of metabolic intermediates. Mitochondrial dysfunction has been implicated in the pathologies of a number of degenerative retinal diseases. It is well known that photoreceptors are particularly vulnerable to mutations affecting mitochondrial function due to their high energy demand and susceptibility to oxidative stress. However, it is unclear how defective mitochondria affect other retinal neurons. Nuclear respiratory factor 1 (Nrf1) is the major transcriptional regulator of mitochondrial biogenesis, and loss of Nrf1 leads to defective mitochondria biogenesis and eventually cell death. Here, we investigated how different retinal neurons respond to the loss of Nrf1. We provide in vivo evidence that the disruption of Nrf1-mediated mitochondrial biogenesis results in a slow, progressive degeneration of all retinal cell types examined, although they present different sensitivity to the deletion of Nrf1, which implicates differential energy demand and utilization, as well as tolerance to mitochondria defects in different neuronal cells. Furthermore, transcriptome analysis on rod-specific Nrf1 deletion uncovered a previously unknown role of Nrf1 in maintaining genome stability.
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Affiliation(s)
- Takae Kiyama
- Ruiz Department of Ophthalmology and Visual Science, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth), 6431 Fannin St., MSB 7.024, Houston, TX 77030, USA; (T.K.); (A.Z.)
| | - Ching-Kang Chen
- Department of Ophthalmology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA;
| | - Annie Zhang
- Ruiz Department of Ophthalmology and Visual Science, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth), 6431 Fannin St., MSB 7.024, Houston, TX 77030, USA; (T.K.); (A.Z.)
| | - Chai-An Mao
- Ruiz Department of Ophthalmology and Visual Science, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth), 6431 Fannin St., MSB 7.024, Houston, TX 77030, USA; (T.K.); (A.Z.)
- The MD Anderson Cancer Center/UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- Correspondence:
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4
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Chen D, Zhang R, Xie A, Yuan J, Zhang J, Huang Y, Zhang H, Zhang F. Clinical correlations and prognostic value of Nudix hydroxylase 10 in patients with gastric cancer. Bioengineered 2021; 12:9779-9789. [PMID: 34696672 PMCID: PMC8809933 DOI: 10.1080/21655979.2021.1995104] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 02/05/2023] Open
Abstract
Gastric cancer (GC) is one of the most common and lethal cancers worldwide. The Nudix hydroxylase (NUDT) genes have been reported to play notable roles in tumor progression. However, the role of NUDT10 in GC has not been reported. In this study, we investigated the expression of NUDT10 in GC and its association with clinicopathological characteristics. Quantitative real-time polymerase chain reaction and analyses of The Cancer Genome Atlas and Human Protein Atlas databases were performed to determine NUDT10 mRNA and protein expression. Receiver operating characteristic curve analysis was used to assess the diagnostic value of NUDT10 in patients with GC. We used Cox regression and the Kaplan-Meier method to assess the correlations between clinicopathological factors and survival outcomes of patients with GC. Gene set enrichment analysis (GSEA) was performed to identify the underlying signaling pathways. NUDT10 mRNA and protein expression was significantly lower in GC tissues compared to normal tissues. Interestingly, higher NUDT10 expression was correlated with advanced tumor stage, deeper local invasion, and worse survival outcomes. Patients with higher NUDT10 expression had a significantly worse prognosis than those with lower NUDT10 expression. Multivariate analysis showed that high NUDT10 expression was an independent predictor of survival outcome. Several pathways, including mismatch repair, nucleotide excision repair, extracellular matrix receptor interaction, and cancer signaling, were identified as enriched pathways in GC through GSEA. To our knowledge, this study is the first to characterize NUDT10 expression in GC. Our study demonstrates that NUDT10 is a promising independent biomarker for GC prognosis.
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Affiliation(s)
- Diqun Chen
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Rouxin Zhang
- College of Science and Technology, China Three Gorges University, Yichang, China
| | - Aosi Xie
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Jinpeng Yuan
- Department of Abdominal Surgery, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Jinhai Zhang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Yongjian Huang
- Department of Gastrointestinal Surgery, Shantou Guorui Hospital, Shantou, China
| | - Hongxia Zhang
- Health Care Center, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
- CONTACT Hongxia Zhang Health Care Center, The First Affiliated Hospital of Shantou University Medical College, Shantou, China; Feiran Zhang Department of Gastrointestinal Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Feiran Zhang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
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5
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Zhang X, Li L. The Significance of 8-oxoGsn in Aging-Related Diseases. Aging Dis 2020; 11:1329-1338. [PMID: 33014540 PMCID: PMC7505272 DOI: 10.14336/ad.2019.1021] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/21/2019] [Indexed: 01/10/2023] Open
Abstract
Aging is a common risk factor for the occurrence and development of many diseases, such as Parkinson’s disease, Alzheimer’s disease, diabetes, hypertension, atherosclerosis and coronary heart disease, and cancer, among others, and is a key problem threatening the health and life expectancy of the elderly. Oxidative damage is an important mechanism involved in aging. The latest discovery pertaining to oxidative damage is that 8-oxoGsn (8-oxo-7,8-dihydroguanosine), an oxidative damage product of RNA, can represent the level of oxidative stress. The significance of RNA oxidative damage to aging has not been fully explained, but the relationship between the accumulation of 8-oxoGsn, a marker of RNA oxidative damage, and the occurrence of diseases has been confirmed in many aging-related diseases. Studying the aging mechanism, monitoring the aging level of the body and exploring the corresponding countermeasures are of great significance for achieving healthy aging and promoting public health and social development. This article reviews the progress of research on 8-oxoGsn in aging-related diseases.
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Affiliation(s)
- Xinmu Zhang
- Department of Medical Oncology, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Lin Li
- Department of Medical Oncology, Beijing Hospital, National Center of Gerontology, Beijing, China
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Boguszewska K, Szewczuk M, Kaźmierczak-Barańska J, Karwowski BT. The Similarities between Human Mitochondria and Bacteria in the Context of Structure, Genome, and Base Excision Repair System. Molecules 2020; 25:E2857. [PMID: 32575813 PMCID: PMC7356350 DOI: 10.3390/molecules25122857] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 02/06/2023] Open
Abstract
Mitochondria emerged from bacterial ancestors during endosymbiosis and are crucial for cellular processes such as energy production and homeostasis, stress responses, cell survival, and more. They are the site of aerobic respiration and adenosine triphosphate (ATP) production in eukaryotes. However, oxidative phosphorylation (OXPHOS) is also the source of reactive oxygen species (ROS), which are both important and dangerous for the cell. Human mitochondria contain mitochondrial DNA (mtDNA), and its integrity may be endangered by the action of ROS. Fortunately, human mitochondria have repair mechanisms that allow protecting mtDNA and repairing lesions that may contribute to the occurrence of mutations. Mutagenesis of the mitochondrial genome may manifest in the form of pathological states such as mitochondrial, neurodegenerative, and/or cardiovascular diseases, premature aging, and cancer. The review describes the mitochondrial structure, genome, and the main mitochondrial repair mechanism (base excision repair (BER)) of oxidative lesions in the context of common features between human mitochondria and bacteria. The authors present a holistic view of the similarities of mitochondria and bacteria to show that bacteria may be an interesting experimental model for studying mitochondrial diseases, especially those where the mechanism of DNA repair is impaired.
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Affiliation(s)
| | | | | | - Bolesław T. Karwowski
- DNA Damage Laboratory of Food Science Department, Faculty of Pharmacy, Medical University of Lodz, ul. Muszynskiego 1, 90-151 Lodz, Poland; (K.B.); (M.S.); (J.K.-B.)
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7
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Gurunathan S, Jeyaraj M, La H, Yoo H, Choi Y, Do JT, Park C, Kim JH, Hong K. Anisotropic Platinum Nanoparticle-Induced Cytotoxicity, Apoptosis, Inflammatory Response, and Transcriptomic and Molecular Pathways in Human Acute Monocytic Leukemia Cells. Int J Mol Sci 2020; 21:ijms21020440. [PMID: 31936679 PMCID: PMC7014054 DOI: 10.3390/ijms21020440] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/06/2020] [Accepted: 01/07/2020] [Indexed: 12/18/2022] Open
Abstract
The thermoplasmonic properties of platinum nanoparticles (PtNPs) render them desirable for use in diagnosis, detection, therapy, and surgery. However, their toxicological effects and impact at the molecular level remain obscure. Nanotoxicology is mainly focused on the interactions of nanostructures with biological systems, particularly with an emphasis on elucidating the relationship between the physical and chemical properties such as size and shape. Therefore, we hypothesized whether these unique anisotropic nanoparticles could induce cytotoxicity similar to that of spherical nanoparticles and the mechanism involved. Thus, we synthesized unique and distinct anisotropic PtNPs using lycopene as a biological template and investigated their biological activities in model human acute monocytic leukemia (THP-1) macrophages. Exposure to PtNPs for 24 h dose-dependently decreased cell viability and proliferation. Levels of the cytotoxic markers lactate dehydrogenase and intracellular protease significantly and dose-dependently increased with PtNP concentration. Furthermore, cells incubated with PtNPs dose-dependently produced oxidative stress markers including reactive oxygen species (ROS), malondialdehyde, nitric oxide, and carbonylated protein. An imbalance in pro-oxidants and antioxidants was confirmed by significant decreases in reduced glutathione, thioredoxin, superoxide dismutase, and catalase levels against oxidative stress. The cell death mechanism was confirmed by mitochondrial dysfunction and decreased ATP levels, mitochondrial copy numbers, and PGC-1α expression. To further substantiate the mechanism of cell death mediated by endoplasmic reticulum stress (ERS), we determined the expression of the inositol-requiring enzyme (IRE1), (PKR-like ER kinase) PERK, activating transcription factor 6 (ATF6), and activating transcription factor 4 ATF4, the apoptotic markers p53, Bax, and caspase 3, and the anti-apoptotic marker Bcl-2. PtNPs could activate ERS and apoptosis mediated by mitochondria. A proinflammatory response to PtNPs was confirmed by significant upregulation of interleukin-1-beta (IL-1β), interferon γ (IFNγ), tumor necrosis factor alpha (TNFα), and interleukin (IL-6). Transcriptomic and molecular pathway analyses of THP-1 cells incubated with the half maximal inhibitory concentration (IC50) of PtNPs revealed the altered expression of genes involved in protein misfolding, mitochondrial function, protein synthesis, inflammatory responses, and transcription regulation. We applied transcriptomic analyses to investigate anisotropic PtNP-induced toxicity for further mechanistic studies. Isotropic nanoparticles are specifically used to inhibit non-specific cellular uptake, leading to enhanced in vivo bio-distribution and increased targeting capabilities due to the higher radius of curvature. These characteristics of anisotropic nanoparticles could enable the technology as an attractive platform for nanomedicine in biomedical applications.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Kwonho Hong
- Correspondence: ; Tel.: +82-2-450-0560; Fax: +82-2-444-3490
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8
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Shen Y, Zhang L, Piao S, Li L, Li J, Xia Y, Li J, Saiyin W. NUDT1: A potential independent predictor for the prognosis of patients with oral squamous cell carcinoma. J Oral Pathol Med 2019; 49:210-218. [PMID: 31732994 DOI: 10.1111/jop.12974] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/24/2019] [Accepted: 10/28/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Yuchen Shen
- Department of Oral and Maxillofacial Surgery The First Affiliated Hospital of Harbin Medical University Harbin China
| | - Lei Zhang
- Department of Oral and Maxillofacial Surgery The First Affiliated Hospital of Harbin Medical University Harbin China
| | - Songlin Piao
- Department of Oral and Maxillofacial Surgery The First Affiliated Hospital of Harbin Medical University Harbin China
| | - Lili Li
- Department of Implant Dentistry The First Affiliated Hospital of Harbin Medical University Harbin China
| | - Jianhao Li
- Department of Oral and Maxillofacial Surgery The First Affiliated Hospital of Harbin Medical University Harbin China
| | - Yanyun Xia
- Department of Oral and Maxillofacial Surgery The First Affiliated Hospital of Harbin Medical University Harbin China
| | - Jichen Li
- Department of Oral and Maxillofacial Surgery The First Affiliated Hospital of Harbin Medical University Harbin China
| | - Wuliji Saiyin
- Department of Oral and Maxillofacial Surgery The First Affiliated Hospital of Harbin Medical University Harbin China
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9
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Czarny P, Bialek K, Ziolkowska S, Strycharz J, Sliwinski T. DNA damage and repair in neuropsychiatric disorders. What do we know and what are the future perspectives? Mutagenesis 2019; 35:79-106. [DOI: 10.1093/mutage/gez035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 09/27/2019] [Indexed: 12/11/2022] Open
Abstract
AbstractOver the past two decades, extensive research has been done to elucidate the molecular etiology and pathophysiology of neuropsychiatric disorders. In majority of them, including Alzheimer’s disease (AD), Parkinson’s disease (PD), amyotrophic lateral sclerosis (ALS), bipolar disorder (BD), schizophrenia and major depressive disorder, increased oxidative and nitrosative stress was found. This stress is known to induce oxidative damage to biomolecules, including DNA. Accordingly, increased mitochondrial and nuclear DNA, as well as RNA damage, were observed in patients suffering from these diseases. However, recent findings indicate that the patients are characterised by impaired DNA repair pathways, which may suggest that these DNA lesions could be also a result of their insufficient repair. In the current systematic, critical review, we aim to sum up, using available literature, the knowledge about the involvement of nuclear and mitochondrial DNA damage and repair, as well as about damage to RNA in pathoetiology of neuropsychiatric disorders, i.e., AD, PD, ALS, BD, schizophrenia and major depressive disorder, as well as the usefulness of the discussed factors as being diagnostic markers and targets for new therapies. Moreover, we also underline the new directions to which future studies should head to elucidate these phenomena.
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Affiliation(s)
- Piotr Czarny
- Department of Medical Biochemistry, Medical University of Lodz, Lodz, Poland
| | - Katarzyna Bialek
- Laboratory of Medical Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Sylwia Ziolkowska
- Department of Medical Biochemistry, Medical University of Lodz, Lodz, Poland
| | - Justyna Strycharz
- Department of Medical Biochemistry, Medical University of Lodz, Lodz, Poland
| | - Tomasz Sliwinski
- Laboratory of Medical Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
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Çağlayan M. Interplay between DNA Polymerases and DNA Ligases: Influence on Substrate Channeling and the Fidelity of DNA Ligation. J Mol Biol 2019; 431:2068-2081. [PMID: 31034893 DOI: 10.1016/j.jmb.2019.04.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 04/18/2019] [Accepted: 04/18/2019] [Indexed: 02/06/2023]
Abstract
DNA ligases are a highly conserved group of nucleic acid enzymes that play an essential role in DNA repair, replication, and recombination. This review focuses on functional interaction between DNA polymerases and DNA ligases in the repair of single- and double-strand DNA breaks, and discusses the notion that the substrate channeling during DNA polymerase-mediated nucleotide insertion coupled to DNA ligation could be a mechanism to minimize the release of potentially mutagenic repair intermediates. Evidence suggesting that DNA ligases are essential for cell viability includes the fact that defects or insufficiency in DNA ligase are casually linked to genome instability. In the future, it may be possible to develop small molecule inhibitors of mammalian DNA ligases and/or their functional protein partners that potentiate the effects of chemotherapeutic compounds and improve cancer treatment outcomes.
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Affiliation(s)
- Melike Çağlayan
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA.
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11
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Niu RJ, Zheng QC, Zhang HX. The influence of residue in the position of 116 on the inhibitory potency of TH588 for MTH1. J Mol Graph Model 2018; 85:75-83. [PMID: 30103119 DOI: 10.1016/j.jmgm.2018.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/23/2018] [Accepted: 08/03/2018] [Indexed: 11/29/2022]
Abstract
As one of the first-in-class inhibitor, TH588 was found to be efficient in the suppression of MutT homolog1 (MTH1). A recent work shows that the inhibitory potency of TH588 against human MTH1 (hsMTH1) is approximately 20-fold over that of mouse MTH1 (mmMTH1) and identifies residue in position 116 in MTH1 has an important contribution to TH588 affinity. But the effect of residue Leu or Met in position 116 on the binding affinity remains unclear. In this study, molecular dynamics (MD) simulations and free energy calculations were used to elucidate the mechanism about the effect of residue 116 to the different inhibitory potency of TH588 against MTH1. The binding free energy of TH588 in M116 complexes predicated by the Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) is much lower than that in L116 complexes, which is consistent with the experiment results. The analysis of the individual energy terms suggests that the non-polar interactions are important for distinguishing the binding of TH588. The MD results show that the Leu116 disrupts the interactions between Asn33 and TH588, thus induces the conformational changes of Asn33 as well as TH588. The altered interactions between TH588 and mmMTH1 change the flexibility of TH588, which could induce the remarkable conformational fluctuation of mmMTH1. The conformations of the two loops covering the binding pocket have obvious influence on the opening or closure of the active site. The more open binding site may explain the lower inhibitor potency of TH588 against mmMTH1 than hsMTH1. Our results provide mechanistic insight into the effect of different residue Leu or Met in position 116 on the binding affinity of TH588 for MTH1, which is expected to contribute to the further rational design of more potent inhibitors.
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Affiliation(s)
- Rui-Juan Niu
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, 130023, PR China
| | - Qing-Chuan Zheng
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, 130023, PR China; Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun, 130023, PR China.
| | - Hong-Xing Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, 130023, PR China.
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12
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Mur P, Jemth AS, Bevc L, Amaral N, Navarro M, Valdés-Mas R, Pons T, Aiza G, Urioste M, Valencia A, Lázaro C, Moreno V, Puente XS, Stenmark P, Warpman-Berglund U, Capellá G, Helleday T, Valle L. Germline variation in the oxidative DNA repair genes NUDT1 and OGG1 is not associated with hereditary colorectal cancer or polyposis. Hum Mutat 2018; 39:1214-1225. [PMID: 29900613 DOI: 10.1002/humu.23564] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 06/05/2018] [Accepted: 06/05/2018] [Indexed: 01/03/2023]
Abstract
The causal association of NUDT1 (=MTH1) and OGG1 with hereditary colorectal cancer (CRC) remains unclear. Here, we sought to provide additional evidence for or against the causal contribution of NUDT1 and OGG1 mutations to hereditary CRC and/or polyposis. Mutational screening was performed using pooled DNA amplification and targeted next-generation sequencing in 529 families (441 uncharacterized MMR-proficient familial nonpolyposis CRC and 88 polyposis cases). Cosegregation, in silico analyses, in vitro functional assays, and case-control associations were carried out to characterize the identified variants. Five heterozygous carriers of novel (n = 1) or rare (n = 4) NUDT1 variants were identified. In vitro deleterious effects were demonstrated for c.143G>A p.G48E (catalytic activity and protein stability) and c.403G>T p.G135W (protein stability), although cosegregation data in the carrier families were inconclusive or nonsupportive. The frequency of missense, loss-of-function, and splice-site NUDT1 variants in our familial CRC cohort was similar to the one observed in cancer-free individuals, suggesting lack of association with CRC predisposition. No OGG1 pathogenic mutations were identified. Our results suggest that the contribution of NUDT1 and OGG1 germline mutations to hereditary CRC and to polyposis is inexistent or, at most, negligible. The inclusion of these genes in routine genetic testing is not recommended.
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Affiliation(s)
- Pilar Mur
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Ann-Sofie Jemth
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Luka Bevc
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Nuno Amaral
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Matilde Navarro
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Rafael Valdés-Mas
- Department of Biochemistry and Molecular Biology, Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain
| | - Tirso Pons
- Structural Biology and Biocomputing Program, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Gemma Aiza
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Miguel Urioste
- Familial Cancer Clinical Unit, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO) and Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Alfonso Valencia
- Life Science Department, Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Victor Moreno
- Unit of Biomarkers and Susceptibility, Catalan Institute of Oncology, IDIBELL and CIBERESP, Hospitalet de Llobregat, Barcelona, Spain.,Department of Clinical Sciences, School of Medicine, University of Barcelona, Hospitalet de Llobregat, Barcelona, Spain
| | - Xose S Puente
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Department of Biochemistry and Molecular Biology, Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Ulrika Warpman-Berglund
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
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13
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Rahm F, Viklund J, Trésaugues L, Ellermann M, Giese A, Ericsson U, Forsblom R, Ginman T, Günther J, Hallberg K, Lindström J, Persson LB, Silvander C, Talagas A, Díaz-Sáez L, Fedorov O, Huber KVM, Panagakou I, Siejka P, Gorjánácz M, Bauser M, Andersson M. Creation of a Novel Class of Potent and Selective MutT Homologue 1 (MTH1) Inhibitors Using Fragment-Based Screening and Structure-Based Drug Design. J Med Chem 2018; 61:2533-2551. [DOI: 10.1021/acs.jmedchem.7b01884] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Fredrik Rahm
- Sprint Bioscience AB, Novum, 14157 Huddinge, Sweden
| | | | | | | | - Anja Giese
- Bayer AG, Muellerstrasse 178, 13353 Berlin, Germany
| | | | | | | | | | | | | | | | | | | | - Laura Díaz-Sáez
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom
| | - Oleg Fedorov
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom
| | - Kilian V. M. Huber
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom
| | - Ioanna Panagakou
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom
| | - Paulina Siejka
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom
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14
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Narwal M, Jemth AS, Gustafsson R, Almlöf I, Warpman Berglund U, Helleday T, Stenmark P. Crystal Structures and Inhibitor Interactions of Mouse and Dog MTH1 Reveal Species-Specific Differences in Affinity. Biochemistry 2018; 57:593-603. [PMID: 29281266 DOI: 10.1021/acs.biochem.7b01163] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
MTH1 hydrolyzes oxidized nucleoside triphosphates, thereby sanitizing the nucleotide pool from oxidative damage. This prevents incorporation of damaged nucleotides into DNA, which otherwise would lead to mutations and cell death. The high level of reactive oxygen species in cancer cells leads to a higher level of oxidized nucleotides in cancer cells compared to that in nonmalignant cells, making cancer cells more dependent on MTH1 for survival. The possibility of specifically targeting cancer cells by inhibiting MTH1 has highlighted MTH1 as a promising cancer target. The progression of MTH1 inhibitors into the clinic requires animal studies, and knowledge of species differences in the potency of inhibitors is vitally important. We here show that the human MTH1 inhibitor TH588 is approximately 20-fold less potent with respect to inhibition of mouse MTH1 than the human, rat, pig, and dog MTH1 proteins are. We present the crystal structures of mouse MTH1 in complex with TH588 and dog MTH1 and elucidate the structural and sequence basis for the observed difference in affinity for TH588. We identify amino acid residue 116 in MTH1 as an important determinant of TH588 affinity. Furthermore, we present the structure of mouse MTH1 in complex with the substrate 8-oxo-dGTP. The crystal structures provide insight into the high degree of structural conservation between MTH1 proteins from different organisms and provide a detailed view of interactions between MTH1 and the inhibitor, revealing that minute structural differences can have a large impact on affinity and specificity.
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Affiliation(s)
- Mohit Narwal
- Department of Biochemistry and Biophysics, Stockholm University , S-106 91 Stockholm, Sweden
| | - Ann-Sofie Jemth
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet , S-171 21 Stockholm, Sweden
| | - Robert Gustafsson
- Department of Biochemistry and Biophysics, Stockholm University , S-106 91 Stockholm, Sweden
| | - Ingrid Almlöf
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet , S-171 21 Stockholm, Sweden
| | - Ulrika Warpman Berglund
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet , S-171 21 Stockholm, Sweden
| | - Thomas Helleday
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet , S-171 21 Stockholm, Sweden
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University , S-106 91 Stockholm, Sweden
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15
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Duan J, Zhang H, Li S, Wang X, Yang H, Jiao S, Ba Y. The role of miR-485-5p/NUDT1 axis in gastric cancer. Cancer Cell Int 2017; 17:92. [PMID: 29075149 PMCID: PMC5645910 DOI: 10.1186/s12935-017-0462-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 10/08/2017] [Indexed: 11/25/2022] Open
Abstract
Background Cancers can survive the oxidative conditions by upregulating nucleoside diphosphate linked moiety X-type motif 1 (NUDT1). However, the mechanisms underlying gastric carcinogenesis and the dys-regulation of NUDT1 in gastric cancer (GC) remain unknown. Our study aimed to explore the role of NUDT1 and its regulatory pathway by miR-485-5p in GC. Methods Gastric cancer tissues and paired noncancerous tissue samples were collected, and the expression level of NUDT1 and miR-485-5p were detected. Two cohorts from The Cancer Genome Atlas (TCGA) database and another cohort from the Tianjin Medical University Cancer Institute and Hospital were further analyzed. Luciferase assays were performed, and the effects of the miR-485-5p/NUDT1 axis on GC cells and normal gastric cells were determined by subsequent experiments. Results We found that the expression of miR-485-5p was clearly repressed in GC tissues, while NUDT1 expression level was dramatically increased. The overexpression of NUDT1 correlated closely with an increase in invasive depth and a decrease in survival in GC patients. MiR-485-5p could directly bind to the 3′UTR of NUDT1 mRNA and induce its degradation, thus down-regulate its expression. The miR-485-5p/NUDT1 axis could lead to the changes of 8-oxo-dG in GC cells. And the increased expression of NUDT1 resulting from the downregulation of miR-485-5p could accelerate cell proliferation and metastasis in GC. However, the growth and migration of normal gastric cells did not depend on the protection of NUDT1, while the overexpression of NUDT1 could promote malignant transition in normal gastric cells. Conclusions MiR-485-5p acts as a tumor suppressor by targeting NUDT1 in GC. The miR-485-5p/NUDT1 axis is involved in the processes of cell growth and cell motility and plays a key role in the tumorigenesis of GC. Electronic supplementary material The online version of this article (doi:10.1186/s12935-017-0462-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jingjing Duan
- Medical College, Nankai University, Weijin Road 94, Tianjin, 300071 China.,Department of Oncology, Chinese PLA General Hospital, Fuxing Road 28, Beijing, 100853 China
| | - Haiyang Zhang
- Department of Gastrointestinal Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Huan hu xi Road 18, Tianjin, 300060 China
| | - Shuang Li
- Department of Gastrointestinal Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Huan hu xi Road 18, Tianjin, 300060 China
| | - Xinyi Wang
- Department of Gastrointestinal Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Huan hu xi Road 18, Tianjin, 300060 China
| | - Haiou Yang
- Department of Gastrointestinal Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Huan hu xi Road 18, Tianjin, 300060 China
| | - Shunchang Jiao
- Medical College, Nankai University, Weijin Road 94, Tianjin, 300071 China.,Department of Oncology, Chinese PLA General Hospital, Fuxing Road 28, Beijing, 100853 China
| | - Yi Ba
- Department of Gastrointestinal Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Huan hu xi Road 18, Tianjin, 300060 China
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16
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Consequences of RNA oxidation on protein synthesis rate and fidelity: implications for the pathophysiology of neuropsychiatric disorders. Biochem Soc Trans 2017; 45:1053-1066. [DOI: 10.1042/bst20160433] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 07/03/2017] [Accepted: 07/05/2017] [Indexed: 12/17/2022]
Abstract
Unlike DNA, oxidative damage to RNA has received little attention presumably due to the assumed transient nature of RNA. However, RNAs including mRNA can persist for several hours to days in certain tissues and are demonstrated to sustain greater oxidative damage than DNA. Because neuronal cells in the brain are continuously exposed to reactive oxygen species due to a high oxygen consumption rate, it is not surprising that neuronal RNA oxidation is observed as a common feature at an early stage in a series of neurodegenerative disorders. A recent study on a well-defined bacterial translation system has revealed that mRNA containing 8-oxo-guanosine (8-oxoGuo) has little effect on fidelity despite the anticipated miscoding. Indeed, 8-oxoGuo-containing mRNA leads to ribosomal stalling with a reduced rate of peptide-bond formation by 3–4 orders of magnitude and is subject to no-go decay, a ribosome-based mRNA surveillance mechanism. Another study demonstrates that transfer RNA oxidation catalyzed by cytochrome c (cyt c) leads to its depurination and cross-linking, which may facilitate cyt c release from mitochondria and subsequently induce apoptosis. Even more importantly, a discovery of oxidized microRNA has been recently reported. The oxidized microRNA causes misrecognizing the target mRNAs and subsequent down-regulation in the protein synthesis. It is noteworthy that oxidative modification to RNA not only interferes with the translational machinery but also with regulatory mechanisms of noncoding RNAs that contribute toward the biological complexity of the mammalian brain. Oxidative RNA damage might be a promising therapeutic target potentially useful for an early intervention of diverse neuropsychiatric disorders.
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17
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Abstract
Trypanosoma cruzi is exposed to oxidative stresses during its life cycle, and amongst the strategies employed by this parasite to deal with these situations sits a peculiar trypanothione-dependent antioxidant system. Remarkably, T. cruzi's antioxidant repertoire does not include catalase. In an attempt to shed light on what are the reasons by which this parasite lacks this enzyme, a T. cruzi cell line stably expressing catalase showed an increased resistance to hydrogen peroxide (H2O2) when compared with wild-type cells. Interestingly, preconditioning carried out with low concentrations of H2O2 led untransfected parasites to be as much resistant to this oxidant as cells expressing catalase, but did not induce the same level of increased resistance in the latter ones. Also, presence of catalase decreased trypanothione reductase and increased superoxide dismutase levels in T. cruzi, resulting in higher levels of residual H2O2 after challenge with this oxidant. Although expression of catalase contributed to elevated proliferation rates of T. cruzi in Rhodnius prolixus, it failed to induce a significant increase of parasite virulence in mice. Altogether, these results indicate that the absence of a gene encoding catalase in T. cruzi has played an important role in allowing this parasite to develop a shrill capacity to sense and overcome oxidative stress.
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18
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Dai D, Zhou L, Zhu X, You R, Zhong L. Combined multi-pharmacophore, molecular docking and molecular dynamic study for discovery of promising MTH1 inhibitors. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.02.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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19
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Arif SM, Patil AG, Varshney U, Vijayan M. Biochemical and structural studies of Mycobacterium smegmatis MutT1, a sanitization enzyme with unusual modes of association. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2017; 73:349-364. [PMID: 28375146 DOI: 10.1107/s2059798317002534] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 02/14/2017] [Indexed: 01/12/2023]
Abstract
Mycobacterium smegmatis MutT1, which is made up of a Nudix domain (domain 1) and a histidine phosphatase domain (domain 2), efficiently hydrolyses 8-oxo-GTP and 8-oxo-dGTP to the corresponding nucleoside diphosphates and phosphate in the presence of magnesium ions. Domain 1 alone hydrolyses nucleoside triphosphates less efficiently. Under high concentrations and over long periods, the full-length enzyme as well as domain 1 catalyses the hydrolysis of the nucleoside triphosphates to the respective nucleoside monophosphates and pyrophosphate. The role of domain 2 appears to be limited to speeding up the reaction. Crystal structures of the apoenzyme and those of ligand-bound enzyme prepared in the presence of 8-oxo-GTP or 8-oxo-dGTP and different concentrations of magnesium were determined. In all of the structures except one, the molecules arrange themselves in a head-to-tail fashion in which domain 1 is brought into contact with domain 2 (trans domain 2) of a neighbouring molecule. The binding site for NTP (site A) is almost exclusively made up of residues from domain 1, while those for NDP (site B) and NMP (site C) are at the interface between domain 1 and trans domain 2 in an unusual instance of intermolecular interactions leading to binding sites. Protein-ligand interactions at site A lead to a proposal for the mechanism of hydrolysis of NTP to NDP and phosphate. A small modification in site A in the crystal which does not exhibit the head-to-tail arrangement appears to facilitate the production of NMP and pyrophosphate from NTP. The two arrangements could be in dynamic equilibrium in the cellular milieu.
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Affiliation(s)
- S M Arif
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - A G Patil
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
| | - U Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
| | - M Vijayan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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20
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Prakash A, Doublié S. Base Excision Repair in the Mitochondria. J Cell Biochem 2016; 116:1490-9. [PMID: 25754732 DOI: 10.1002/jcb.25103] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 01/23/2015] [Indexed: 01/01/2023]
Abstract
The 16.5 kb human mitochondrial genome encodes for 13 polypeptides, 22 tRNAs and 2 rRNAs involved in oxidative phosphorylation. Mitochondrial DNA (mtDNA), unlike its nuclear counterpart, is not packaged into nucleosomes and is more prone to the adverse effects of reactive oxygen species (ROS) generated during oxidative phosphorylation. The past few decades have witnessed an increase in the number of proteins observed to translocate to the mitochondria for the purposes of mitochondrial genome maintenance. The mtDNA damage produced by ROS, if not properly repaired, leads to instability and can ultimately manifest in mitochondrial dysfunction and disease. The base excision repair (BER) pathway is employed for the removal and consequently the repair of deaminated, oxidized, and alkylated DNA bases. Specialized enzymes called DNA glycosylases, which locate and cleave the damaged base, catalyze the first step of this highly coordinated repair pathway. This review focuses on members of the four human BER DNA glycosylase superfamilies and their subcellular localization in the mitochondria and/or the nucleus, as well as summarizes their structural features, biochemical properties, and functional role in the excision of damaged bases.
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Affiliation(s)
- Aishwarya Prakash
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, Vermont
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, Vermont
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21
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Bjørge M, Hildrestrand G, Scheffler K, Suganthan R, Rolseth V, Kuśnierczyk A, Rowe A, Vågbø C, Vetlesen S, Eide L, Slupphaug G, Nakabeppu Y, Bredy T, Klungland A, Bjørås M. Synergistic Actions of Ogg1 and Mutyh DNA Glycosylases Modulate Anxiety-like Behavior in Mice. Cell Rep 2015; 13:2671-8. [DOI: 10.1016/j.celrep.2015.12.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 10/23/2015] [Accepted: 11/19/2015] [Indexed: 12/21/2022] Open
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22
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Rampazzo C, Tozzi MG, Dumontet C, Jordheim LP. The druggability of intracellular nucleotide-degrading enzymes. Cancer Chemother Pharmacol 2015; 77:883-93. [PMID: 26614508 DOI: 10.1007/s00280-015-2921-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/13/2015] [Indexed: 01/24/2023]
Abstract
Nucleotide metabolism is the target of a large number of anticancer drugs including antimetabolites and specific enzyme inhibitors. We review scientific findings that over the last 10-15 years have allowed the identification of several intracellular nucleotide-degrading enzymes as cancer drug targets, and discuss further potential therapeutic applications for Rcl, SAMHD1, MTH1 and cN-II. We believe that enzymes involved in nucleotide metabolism represent potent alternatives to conventional cancer chemotherapy targets.
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Affiliation(s)
- Chiara Rampazzo
- Department of Biology, University of Padova, 35131, Padua, Italy
| | - Maria Grazia Tozzi
- Department of Biology, Biochemistry Unit, University of Pisa, Pisa, Italy
| | - Charles Dumontet
- Université de Lyon, 69000, Lyon, France.,Université de Lyon 1, 69622, Lyon, France.,Université de Lyon 1, 69000, Lyon, France.,INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69000, Lyon, France.,CNRS UMR 5286, Centre de Recherche en Cancérologie de Lyon, 69000, Lyon, France.,Centre Léon Bérard, 69008, Lyon, France.,Hospices Civils de Lyon, 69000, Lyon, France
| | - Lars Petter Jordheim
- Université de Lyon, 69000, Lyon, France. .,Université de Lyon 1, 69622, Lyon, France. .,Université de Lyon 1, 69000, Lyon, France. .,INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69000, Lyon, France. .,CNRS UMR 5286, Centre de Recherche en Cancérologie de Lyon, 69000, Lyon, France. .,Centre Léon Bérard, 69008, Lyon, France. .,Equipe Anticorps-Anticancer, INSERM U1052 - CNRS UMR 5286, Faculté Rockefeller, Centre de Recherche en Cancérologie de Lyon, 8 avenue Rockefeller, 69008, Lyon, France.
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23
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Abstract
Cancer was recognized as a genetic disease at least four decades ago, with the realization that the spontaneous mutation rate must increase early in tumorigenesis to account for the many mutations in tumour cells compared with their progenitor pre-malignant cells. Abnormalities in the deoxyribonucleotide pool have long been recognized as determinants of DNA replication fidelity, and hence may contribute to mutagenic processes that are involved in carcinogenesis. In addition, many anticancer agents antagonize deoxyribonucleotide metabolism. Here, we consider the extent to which aspects of deoxyribonucleotide metabolism contribute to our understanding of both carcinogenesis and to the effective use of anticancer agents.
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Affiliation(s)
- Christopher K Mathews
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-7305, USA
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24
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Vyas R, Reed AJ, Tokarsky EJ, Suo Z. Viewing Human DNA Polymerase β Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography. J Am Chem Soc 2015; 137:5225-30. [PMID: 25825995 DOI: 10.1021/jacs.5b02109] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One common oxidative DNA lesion, 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxoG), is highly mutagenic in vivo due to its anti-conformation forming a Watson-Crick base pair with correct deoxycytidine 5'-triphosphate (dCTP) and its syn-conformation forming a Hoogsteen base pair with incorrect deoxyadenosine 5'-triphosphate (dATP). Here, we utilized time-resolved X-ray crystallography to follow 8-oxoG bypass by human DNA polymerase β (hPolβ). In the 12 solved structures, both Watson-Crick (anti-8-oxoG:anti-dCTP) and Hoogsteen (syn-8-oxoG:anti-dATP) base pairing were clearly visible and were maintained throughout the chemical reaction. Additionally, a third Mg(2+) appeared during the process of phosphodiester bond formation and was located between the reacting α- and β-phosphates of the dNTP, suggesting its role in stabilizing reaction intermediates. After phosphodiester bond formation, hPolβ reopened its conformation, pyrophosphate was released, and the newly incorporated primer 3'-terminal nucleotide stacked, rather than base paired, with 8-oxoG. These structures provide the first real-time pictures, to our knowledge, of how a polymerase correctly and incorrectly bypasses a DNA lesion.
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Affiliation(s)
- Rajan Vyas
- †Department of Chemistry and Biochemistry, ‡The Ohio State Biochemistry and §Biophysics Programs, The Ohio State University, Columbus, Ohio 43210, United States
| | - Andrew J Reed
- †Department of Chemistry and Biochemistry, ‡The Ohio State Biochemistry and §Biophysics Programs, The Ohio State University, Columbus, Ohio 43210, United States
| | - E John Tokarsky
- †Department of Chemistry and Biochemistry, ‡The Ohio State Biochemistry and §Biophysics Programs, The Ohio State University, Columbus, Ohio 43210, United States
| | - Zucai Suo
- †Department of Chemistry and Biochemistry, ‡The Ohio State Biochemistry and §Biophysics Programs, The Ohio State University, Columbus, Ohio 43210, United States
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25
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Oka S, Leon J, Tsuchimoto D, Sakumi K, Nakabeppu Y. MUTYH, an adenine DNA glycosylase, mediates p53 tumor suppression via PARP-dependent cell death. Oncogenesis 2014; 3:e121. [PMID: 25310643 PMCID: PMC4216901 DOI: 10.1038/oncsis.2014.35] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 07/15/2014] [Accepted: 08/25/2014] [Indexed: 12/12/2022] Open
Abstract
p53-regulated caspase-independent cell death has been implicated in suppression of tumorigenesis, however, the regulating mechanisms are poorly understood. We previously reported that 8-oxoguanine (8-oxoG) accumulation in nuclear DNA (nDNA) and mitochondrial DNA triggers two distinct caspase-independent cell death through buildup of single-strand DNA breaks by MutY homolog (MUTYH), an adenine DNA glycosylase. One pathway depends on poly-ADP-ribose polymerase (PARP) and the other depends on calpains. Deficiency of MUTYH causes MUTYH-associated familial adenomatous polyposis. MUTYH thereby suppresses tumorigenesis not only by avoiding mutagenesis, but also by inducing cell death. Here, we identified the functional p53-binding site in the human MUTYH gene and demonstrated that MUTYH is transcriptionally regulated by p53, especially in the p53/DNA mismatch repair enzyme, MLH1-proficient colorectal cancer-derived HCT116+Chr3 cells. MUTYH-small interfering RNA, an inhibitor for p53 or PARP suppressed cell death without an additive effect, thus revealing that MUTYH is a potential mediator of p53 tumor suppression, which is known to be upregulated by MLH1. Moreover, we found that the p53-proficient, mismatch repair protein, MLH1-proficient colorectal cancer cell line express substantial levels of MUTYH in nuclei but not in mitochondria, suggesting that 8-oxoG accumulation in nDNA triggers MLH1/PARP-dependent cell death. These results provide new insights on the molecular mechanism of tumorigenesis and potential new strategies for cancer therapies.
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Affiliation(s)
- S Oka
- 1] Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan [2] Research Center for Nucleotide Pool, Kyushu University, Fukuoka, Japan
| | - J Leon
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - D Tsuchimoto
- 1] Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan [2] Research Center for Nucleotide Pool, Kyushu University, Fukuoka, Japan
| | - K Sakumi
- 1] Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan [2] Research Center for Nucleotide Pool, Kyushu University, Fukuoka, Japan
| | - Y Nakabeppu
- 1] Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan [2] Research Center for Nucleotide Pool, Kyushu University, Fukuoka, Japan
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Ke Y, Lv Z, Yang X, Zhang J, Huang J, Wu S, Li YR. Compensatory effects of hOGG1 for hMTH1 in oxidative DNA damage caused by hydrogen peroxide. Toxicol Lett 2014; 230:62-8. [PMID: 25127756 DOI: 10.1016/j.toxlet.2014.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 08/01/2014] [Accepted: 08/10/2014] [Indexed: 11/15/2022]
Abstract
OBJECTIVE To investigate the potential compensatory effects of hOGG1 and hMTH1 in the repair of oxidative DNA damage. METHODS The hOGG1 and hMTH1 gene knockdown human embryonic pulmonary fibroblast cell lines were established by lentivirus-mediated RNA interference. The messenger RNA (mRNA) levels of hOGG1 and hM1TH1 were analyzed by the real-time polymerase chain reaction, and 8-hydroxy-2'-deoxyguanosine (8-oxo-dG) formation was analyzed in a high-performance liquid chromatography-electrochemical detection system. RESULTS The hOGG1 and hMTH1 knockdown cells were obtained through blasticidin selection. After transfection of hOGG1 and hMTH1 small interfering RNA, the expression levels of the mRNA of hOGG1 and hMTH1 genes were decreased by 97.2% and 96.2%, respectively. The cells then were exposed to 100 μmol/L of hydrogen peroxide (H2O2) for 12 h to induce oxidative DNA damage. After H2O2 exposure, hMTH1 mRNA levels were increased by 25% in hOGG1 gene knockdown cells, whereas hOGG1 mRNA levels were increased by 52% in hMTH1 gene knockdown cells. Following the treatment with H2O2, the 8-oxo-dG levels in the DNA of hOGG1 gene knockdown cells were 3.1-fold higher than those in untreated HFL cells, and 1.67-fold higher than those in H2O2-treated wild-type cells. The 8-oxo-dG levels in hMTH1 gene knockdown cells were 2.3-fold higher than those in untreated human embryonic pulmonary fibroblast cells, but did not differ significantly from those in H2O2-treated wild-type cells. CONCLUSION Our data suggested that hOGG1 could compensate for hMTH1 during oxidative DNA damage caused by H2O2, whereas hMTH1 could not compensate sufficiently for hOGG1 during the process.
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Affiliation(s)
- Yuebin Ke
- Key Laboratory of Genetics & Molecular Medicine of Shenzhen, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China.
| | - Ziquan Lv
- Key Laboratory of Genetics & Molecular Medicine of Shenzhen, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Xifei Yang
- Key Laboratory of Genetics & Molecular Medicine of Shenzhen, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Jianqing Zhang
- Key Laboratory of Genetics & Molecular Medicine of Shenzhen, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Juan Huang
- Key Laboratory of Genetics & Molecular Medicine of Shenzhen, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Shuang Wu
- Key Laboratory of Genetics & Molecular Medicine of Shenzhen, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Y Robert Li
- Department of Pharmacology, Campbell University School of Medicine, Buies Creek, NC 27546, USA; Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, and Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Blacksburg, VA 24061, USA
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Fujiwara SI, Sawada K, Amisaki T. Molecular dynamics study on conformational differences between dGMP and 8-oxo-dGMP: Effects of metal ions. J Mol Graph Model 2014; 51:158-67. [PMID: 24929814 DOI: 10.1016/j.jmgm.2014.05.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 05/09/2014] [Accepted: 05/22/2014] [Indexed: 01/05/2023]
Abstract
The modified nucleotide base 7,8-dihydro-8-oxo-guanine (8-oxo-G) is one of the major sources of spontaneous mutagenesis. Nucleotide-sanitizing enzymes, such as the MutT homolog-1 (MTH1) and nudix-type motif 5 (NUDT5), selectively remove 8-oxo-G from the cellular pool of nucleotides. Previous studies showed that, although the syn conformation generally predominates in purine nucleotides with a bulky substituent at the 8-position, 8-oxo-dGMP binds to both MTH1 and NUDT5 in the anti conformation. This study was initiated to investigate the possibility that 8-oxo-dGMP itself may adopt the anti conformation. Molecular dynamics simulations of mononucleotides (dGMP, 8-oxo-dGMP) in aqueous solution were performed. 8-oxo-dGMP adopted the anti conformation as well as the syn conformation, and the proportion of adopting the anti conformation increased in the presence of metal ions. When 8-oxo-dGMP was in the anti conformation, a metal ion was located between the oxygen atom of phosphate and the oxygen atom at the 8-position of 8-oxo-G. The types of stable anti conformations of 8-oxo-dGMP differed, depending on the ionic radii and charges of coexisting ions. These data suggested a role for metal ions, other than as cofactors for the hydrolysis of the di- and tri-phosphate forms of mononucleotides; that the metal ions help retain the anti conformation of the N-glycosidic torsion angle of 8-oxo-dGMP to promote the binding between the 8-oxo-G deoxynucleotide and the nucleotide-sanitizing enzymes.
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Affiliation(s)
- Shin-Ichi Fujiwara
- Department of Biological Regulation, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago 683-8503, Japan.
| | - Kenichiro Sawada
- Department of Biological Regulation, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago 683-8503, Japan
| | - Takashi Amisaki
- Department of Biological Regulation, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago 683-8503, Japan
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28
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Li Z, Malla S, Shin B, Li JM. Battle against RNA oxidation: molecular mechanisms for reducing oxidized RNA to protect cells. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 5:335-46. [PMID: 24375979 DOI: 10.1002/wrna.1214] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 09/17/2013] [Accepted: 09/18/2013] [Indexed: 01/08/2023]
Abstract
Oxidation is probably the most common type of damage that occurs in cellular RNA. Oxidized RNA may be dysfunctional and is implicated in the pathogenesis of age-related human diseases. Cellular mechanisms controlling oxidized RNA have begun to be revealed. Currently, a number of ribonucleases and RNA-binding proteins have been shown to reduce oxidized RNA and to protect cells under oxidative stress. Although information about how these factors work is still very limited, we suggest several mechanisms that can be used to minimize oxidized RNA in various organisms.
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Affiliation(s)
- Zhongwei Li
- Department of Biomedical Science, Florida Atlantic University, Boca Raton, FL, USA
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29
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Aguiar PHN, Furtado C, Repolês BM, Ribeiro GA, Mendes IC, Peloso EF, Gadelha FR, Macedo AM, Franco GR, Pena SDJ, Teixeira SMR, Vieira LQ, Guarneri AA, Andrade LO, Machado CR. Oxidative stress and DNA lesions: the role of 8-oxoguanine lesions in Trypanosoma cruzi cell viability. PLoS Negl Trop Dis 2013; 7:e2279. [PMID: 23785540 PMCID: PMC3681716 DOI: 10.1371/journal.pntd.0002279] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 04/29/2013] [Indexed: 01/09/2023] Open
Abstract
The main consequence of oxidative stress is the formation of DNA lesions, which can result in genomic instability and lead to cell death. Guanine is the base that is most susceptible to oxidation, due to its low redox potential, and 8-oxoguanine (8-oxoG) is the most common lesion. These characteristics make 8-oxoG a good cellular biomarker to indicate the extent of oxidative stress. If not repaired, 8-oxoG can pair with adenine and cause a G:C to T:A transversion. When 8-oxoG is inserted during DNA replication, it could generate double-strand breaks, which makes this lesion particularly deleterious. Trypanosoma cruzi needs to address various oxidative stress situations, such as the mammalian intracellular environment and the triatomine insect gut where it replicates. We focused on the MutT enzyme, which is responsible for removing 8-oxoG from the nucleotide pool. To investigate the importance of 8-oxoG during parasite infection of mammalian cells, we characterized the MutT gene in T. cruzi (TcMTH) and generated T. cruzi parasites heterologously expressing Escherichia coli MutT or overexpressing the TcMTH enzyme. In the epimastigote form, the recombinant and wild-type parasites displayed similar growth in normal conditions, but the MutT-expressing cells were more resistant to hydrogen peroxide treatment. The recombinant parasite also displayed significantly increased growth after 48 hours of infection in fibroblasts and macrophages when compared to wild-type cells, as well as increased parasitemia in Swiss mice. In addition, we demonstrated, using western blotting experiments, that MutT heterologous expression can influence the parasite antioxidant enzyme protein levels. These results indicate the importance of the 8-oxoG repair system for cell viability.
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Affiliation(s)
- Pedro H. N. Aguiar
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - UFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Carolina Furtado
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - UFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Bruno M. Repolês
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - UFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Grazielle A. Ribeiro
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - UFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Isabela C. Mendes
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - UFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Eduardo F. Peloso
- Departamento de Bioquímica, Instituto de Biologia - UNICAMP, Campinas, Sa˜o Paulo, Brazil
| | - Fernanda R. Gadelha
- Departamento de Bioquímica, Instituto de Biologia - UNICAMP, Campinas, Sa˜o Paulo, Brazil
| | - Andrea M. Macedo
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - UFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Glória R. Franco
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - UFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Sérgio D. J. Pena
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - UFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Santuza M. R. Teixeira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - UFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Leda Q. Vieira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - UFMG, Belo Horizonte, Minas Gerais, Brazil
| | | | - Luciana O. Andrade
- Departamento de Morfologia, Instituto de Ciências Biológicas - UFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Carlos R. Machado
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - UFMG, Belo Horizonte, Minas Gerais, Brazil
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Epidemiological, Clinical, and Molecular Study of a Cohort of Italian Parkinson Disease Patients: Association with Glutathione-S-Transferase and DNA Repair Gene Polymorphisms. Cell Mol Neurobiol 2013; 33:673-80. [DOI: 10.1007/s10571-013-9933-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 03/22/2013] [Indexed: 11/26/2022]
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31
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Cao L, Zhou W, Zhu Y, Guo W, Cai Z, He X, Xie Y, Li X, Zhu D, Wang Y. Combined analysis of polymorphism variants in hMTH1, hOGG1 and MUTYH genes on the risk of type 2 diabetes in the Chinese population. Gene 2013; 519:50-4. [PMID: 23396182 DOI: 10.1016/j.gene.2013.01.053] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 01/04/2013] [Accepted: 01/28/2013] [Indexed: 12/13/2022]
Abstract
Reactive oxygen species are considered to play a role in the development of type 2 diabetes mellitus (T2DM) and its complications. 8-Oxoguanine, which is one of the major oxidation base lesions produced by reactive oxygen species, may cause G:C to T:A transversion mutations because it can mispair with adenine. hMTH1 (human mutT homolog 1), hOGG1 (human 8-oxoguanine glycosylase 1) and MUTYH (human mutY homolog) genes constitute the 8-oxoG repair pathway. In this study, we screened for the polymorphism variants Val83Met (c.247G>A, rs4866) in hMTH1; c.-53G>C (rs56387615), c.-23A>G (rs1801129) and c.-18G>T (rs1801126) in the 5'-UTR of hOGG1; and AluYb8 insertion in MUTYH (AluYb8MUTYH, rs10527342) and investigated their synergistic effect on the risk of T2DM in the Chinese population. The genotypes were determined by electrophoresis, a high-resolution melting technique and sequencing of PCR products. Our results showed that the c.247G>A variant in the hMTH1 gene increased the risk of T2DM in >55 years of age groups (OR=1.579; 95%CI: 1.029-2.421). The set of c.-53G>C, c.-23A>G and c.-18G>T variants detected in the 5'-UTR of the hOGG1 gene and the AluYb8 insertion in the MUTYH gene were each associated with an increased risk of T2DM (OR=1.507, 95%CI: 1.122-2.024; OR=1.229, 95%CI: 1.030-1.466, respectively). Combined analysis of the variations among the three genes suggested that the c.247G>A variant in hMTH1 combined with AluYb8MUTYH variant had a synergistic effect on increasing the risk of T2DM (OR=1.635; 95%CI: 1.147-2.330). This synergy was also observed between the variants in the 5'-UTR of the hOGG1 and the AluYb8MUTYH variant (OR=1.804; 95%CI: 1.254-2.595). Our results suggest, for the first time, the combined effects of AluYb8MUTYH with either hMTH1 c.247G>A or variants in the 5'-UTR of the hOGG1 on the risk of T2DM.
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Affiliation(s)
- Lili Cao
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing, Jiangsu, China
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32
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McLennan AG. Substrate ambiguity among the nudix hydrolases: biologically significant, evolutionary remnant, or both? Cell Mol Life Sci 2013; 70:373-85. [PMID: 23184251 PMCID: PMC11113851 DOI: 10.1007/s00018-012-1210-3] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 11/01/2012] [Accepted: 11/05/2012] [Indexed: 12/20/2022]
Abstract
Many members of the nudix hydrolase family exhibit considerable substrate multispecificity and ambiguity, which raises significant issues when assessing their functions in vivo and gives rise to errors in database annotation. Several display low antimutator activity when expressed in bacterial tester strains as well as some degree of activity in vitro towards mutagenic, oxidized nucleotides such as 8-oxo-dGTP. However, many of these show greater activity towards other nucleotides such as ADP-ribose or diadenosine tetraphosphate (Ap(4)A). The antimutator activities have tended to gain prominence in the literature, whereas they may in fact represent the residual activity of an ancestral antimutator enzyme that has become secondary to the more recently evolved major activity after gene duplication. Whether any meaningful antimutagenic function has also been retained in vivo requires very careful assessment. Then again, other examples of substrate ambiguity may indicate as yet unexplored regulatory systems. For example, bacterial Ap(4)A hydrolases also efficiently remove pyrophosphate from the 5' termini of mRNAs, suggesting a potential role for Ap(4)A in the control of bacterial mRNA turnover, while the ability of some eukaryotic mRNA decapping enzymes to degrade IDP and dIDP or diphosphoinositol polyphosphates (DIPs) may also be indicative of new regulatory networks in RNA metabolism. DIP phosphohydrolases also degrade diadenosine polyphosphates and inorganic polyphosphates, suggesting further avenues for investigation. This article uses these and other examples to highlight the need for a greater awareness of the possible significance of substrate ambiguity among the nudix hydrolases as well as the need to exert caution when interpreting incomplete analyses.
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Affiliation(s)
- Alexander G McLennan
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown St., Liverpool, L69 7ZB, UK.
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Mesaros C, Arora JS, Wholer A, Vachani A, Blair IA. 8-Oxo-2'-deoxyguanosine as a biomarker of tobacco-smoking-induced oxidative stress. Free Radic Biol Med 2012; 53:610-7. [PMID: 22613262 PMCID: PMC4283839 DOI: 10.1016/j.freeradbiomed.2012.04.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2011] [Revised: 04/02/2012] [Accepted: 04/06/2012] [Indexed: 11/19/2022]
Abstract
7,8-Dihydro-8-oxo-2'-deoxyguanosine (8-oxo-dGuo) is a useful biomarker of oxidative stress. However, its analysis can be challenging because 8-oxo-dGuo must be quantified in the presence of dGuo, without artifactual conversion to 8-oxo-dGuo. Urine is the ideal biological fluid for population studies, because it can be obtained noninvasively and it is less likely that artifactual oxidation of dGuo can occur because of the relatively low amounts that are present compared with hydrolyzed DNA. Stable isotope dilution liquid chromatography-selected reaction monitoring/mass spectrometry (LC-SRM/MS) with 8-oxo-[(15)N(5)]dGuo as internal standard provided the highest possible specificity for 8-oxo-dGuo analysis. Furthermore, artifact formation was determined by addition of [(13)C(10)(15)N(5)]dGuo and monitoring of its conversion to 8-oxo-[(13)C(10)(15)N(5)]dGuo during the analytical procedure. 8-Oxo-dGuo concentrations were normalized for interindividual differences in urine flow by analysis of creatinine using stable isotope dilution LC-SRM/MS. A significant increase in urinary 8-oxo-dGuo was observed in tobacco smokers compared with nonsmokers either using simple urinary concentrations or after normalization for creatinine excretion. The mean levels of 8-oxo-dGuo were 1.65ng/ml and the levels normalized to creatinine were 1.72μg/g creatinine. Therefore, stable isotope dilution LC-SRM/MS analysis of urinary 8-oxo-dGuo complements urinary isoprostane (isoP) analysis for assessing tobacco-smoking-induced oxidative stress. This method will be particularly useful for studies that employ polyunsaturated fatty acids, in which a reduction in arachidonic acid precursor could confound isoP measurements.
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Affiliation(s)
- Clementina Mesaros
- Centers for Cancer Pharmacology and Excellence in Environmental Toxicology, Department of Pharmacology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160, USA
| | - Jasbir S. Arora
- Centers for Cancer Pharmacology and Excellence in Environmental Toxicology, Department of Pharmacology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160, USA
| | - Ashley Wholer
- Centers for Cancer Pharmacology and Excellence in Environmental Toxicology, Department of Pharmacology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160, USA
| | - Anil Vachani
- Division of Pulmonary Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160, USA
| | - Ian A. Blair
- Centers for Cancer Pharmacology and Excellence in Environmental Toxicology, Department of Pharmacology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160, USA
- Corresponding author: Ian A. Blair, Center for Cancer Pharmacology, University of Pennsylvania School of Medicine, 856 BRB II/III, 421 Curie Boulevard, Philadelphia, PA 19104-6160. Tel: 215-573-9885. Fax: 215-573-9889.
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34
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Oxidative Damage to RNA in Aging and Neurodegenerative Disorders. Neurotox Res 2012; 22:231-48. [DOI: 10.1007/s12640-012-9331-x] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Revised: 05/13/2012] [Accepted: 05/17/2012] [Indexed: 12/14/2022]
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Ogasawara Y, Umezu N, Ishii K. [DNA damage in human pleural mesothelial cells induced by exposure to carbon nanotubes]. Nihon Eiseigaku Zasshi 2012; 67:76-83. [PMID: 22449827 DOI: 10.1265/jjh.67.76] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
OBJECTIVES Nanomaterials are currently used in electronics, industrial materials, cosmetics, and medicine because they have useful physicochemical properties, such as strength, conductivity, durability, and chemical stability. As these materials have become widespread, many questions have arisen regarding their effects on health and the environment. In particular, recent studies have demonstrated that carbon nanotubes (CNTs) cause significant inflammation and mesothelioma in vivo. In this study, we investigated the potential risk posed by singlewalled carbon nanotube (SWCNT) and multiwalled carbon nanotube (MWCNT) exposure in human pleural mesothelial cells. METHODS CNT cytotoxicity was determined by a trypan blue exclusion assay, and DNA damage was detected by an alkaline comet assay. The concentration of 8-oxodeoxyguanosine (8-OHdG) in DNA was measured by high perhormance liquid chromatography with electrochemical detection. The expression of base excision repair enzymes in the cell was estimated by immunoblot analysis. RESULTS We observed inhibitory effects on cell proliferation and the induction of DNA damage following exposure of cells to purified CNTs that were suspended in dispersion medium. However, accumulation of 8-OHdG in DNA was not found. In addition, the expression levels of base excision enzymes that are involved in hOGG1, hMTH1, and MYH in MeT-5A cells remained unchanged for 24 h after carbon nanotube exposure. CONCLUSIONS CNTs significantly inhibit cell proliferation and decrease DNA damage in human pleural mesothelial cells. Our results indicate that the mechanism of CNT-induced genotoxicity is different from that following exposure to reactive oxygen species, which causes oxidative DNA modifications and 8-OHdG production. Further investigation is required to characterize the specific DNA mutations that occur following CNT exposure.
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Affiliation(s)
- Yuki Ogasawara
- Department of Hygienic Chemistry, Meiji Pharmaceutical University, Kiyose-shi, Tokyo, Japan.
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36
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Svensson LM, Jemth AS, Desroses M, Loseva O, Helleday T, Högbom M, Stenmark P. Crystal structure of human MTH1 and the 8-oxo-dGMP product complex. FEBS Lett 2011; 585:2617-21. [PMID: 21787772 DOI: 10.1016/j.febslet.2011.07.017] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Revised: 07/04/2011] [Accepted: 07/13/2011] [Indexed: 11/24/2022]
Abstract
MTH1 hydrolyzes oxidized nucleotide triphosphates, thereby preventing them from being incorporated into DNA. We here present the structures of human MTH1 (1.9Å) and its complex with the product 8-oxo-dGMP (1.8Å). Unexpectedly MTH1 binds the nucleotide in the anti conformation with no direct interaction between the 8-oxo group and the protein. We suggest that the specificity depends on the stabilization of an enol tautomer of the 8-oxo form of dGTP. The binding of the product induces no major structural changes. The structures reveal the mode of nucleotide binding in MTH1 and provide the structural basis for inhibitor design.
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Affiliation(s)
- Linda M Svensson
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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37
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Svilar D, Goellner EM, Almeida KH, Sobol RW. Base excision repair and lesion-dependent subpathways for repair of oxidative DNA damage. Antioxid Redox Signal 2011; 14:2491-507. [PMID: 20649466 PMCID: PMC3096496 DOI: 10.1089/ars.2010.3466] [Citation(s) in RCA: 194] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Nuclear and mitochondrial genomes are under continuous assault by a combination of environmentally and endogenously derived reactive oxygen species, inducing the formation and accumulation of mutagenic, toxic, and/or genome-destabilizing DNA lesions. Failure to resolve these lesions through one or more DNA-repair processes is associated with genome instability, mitochondrial dysfunction, neurodegeneration, inflammation, aging, and cancer, emphasizing the importance of characterizing the pathways and proteins involved in the repair of oxidative DNA damage. This review focuses on the repair of oxidative damage-induced lesions in nuclear and mitochondrial DNA mediated by the base excision repair (BER) pathway in mammalian cells. We discuss the multiple BER subpathways that are initiated by one of 11 different DNA glycosylases of three subtypes: (a) bifunctional with an associated β-lyase activity; (b) monofunctional; and (c) bifunctional with an associated β,δ-lyase activity. These three subtypes of DNA glycosylases all initiate BER but yield different chemical intermediates and hence different BER complexes to complete repair. Additionally, we briefly summarize alternate repair events mediated by BER proteins and the role of BER in the repair of mitochondrial DNA damage induced by ROS. Finally, we discuss the relation of BER and oxidative DNA damage in the onset of human disease.
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Affiliation(s)
- David Svilar
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
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Iwama E, Tsuchimoto D, Iyama T, Sakumi K, Nakagawara A, Takayama K, Nakanishi Y, Nakabeppu Y. Cancer-related PRUNE2 protein is associated with nucleotides and is highly expressed in mature nerve tissues. J Mol Neurosci 2011; 44:103-14. [PMID: 21234814 DOI: 10.1007/s12031-010-9490-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 12/28/2010] [Indexed: 10/18/2022]
Abstract
Human PRUNE is thought to enhance the metastasis of tumor cells. We found that a hypothetical paralog of PRUNE, PRUNE2, binds to 8-oxo-GTP, an oxidized form of GTP. Hypothetical PRUNE2 gene consists of C9orf65 and BMCC1/BNIPXL, both of which are malignant tumor-associated genes. We isolated PRUNE2 complementary DNA and revealed that the protein is composed of 3,062 residues. C9orf65 and BMCC1/BNIPXL encode the N-terminal part (259 residues) and C-terminal part (2,729 residues) of PRUNE2, respectively. We demonstrated the endogenous full-length PRUNE2 protein (338 kDa) by Western blot and mass spectrometry. PRUNE2 bound to 8-oxo-GTP as well as GTP. The expression levels of human PRUNE2 and mouse Prune2 messenger RNA (mRNA) were highest in the dorsal root ganglia (DRG) and, to a lesser extent, in other nerve tissues. DRG neurons express higher levels of PRUNE2 in their soma compared with adjacent cells. In addition, their expression levels in the adult nerve tissues were higher than those in fetal or neonatal nerve tissues. The present study indicates that C9orf65 and BMCC1/BNIPXL are transcribed as PRUNE2 mRNA, which is translated to a large PRUNE2 protein. The nerve tissue-specific and post-development expression of PRUNE2/Prune2 suggests that PRUNE2 may contribute to the maintenance of mature nervous systems.
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Affiliation(s)
- Eiji Iwama
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Japan
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Tsuchimoto D, Iyama T, Nonaka M, Abolhassani N, Ohta E, Sakumi K, Nakabeppu Y. A comprehensive screening system for damaged nucleotide-binding proteins. Mutat Res 2010; 703:37-42. [PMID: 20542141 DOI: 10.1016/j.mrgentox.2010.06.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Accepted: 06/04/2010] [Indexed: 11/20/2022]
Abstract
To identify novel nucleotide pool sanitizing enzymes, we have established a comprehensive screening system for damaged nucleotide-binding proteins based on proteomics technology. In the screening system, affinity chromatography with resins carrying various damaged nucleotides is used for the purification of binding proteins, and the purified proteins are identified by mass-spectrometry. Inosine triphosphate (ITP) is a deleterious damaged nucleotide, and can be generated by nitrosative deamination of ATP or phosphorylation of inosine monophosphate (IMP). Using the above system, we performed screens for ITP-binding proteins from mouse and human cell extracts, and identified several ITP-binding enzymes. We identified both mouse inosine triphosphatase (ITPA) and human ITPA, well-known ITP hydrolyzing enzymes, as ITP-binding proteins. These results support the validity of this screening system. In addition to ITPA, we identified human nucleoside diphosphate linked moiety X-type motif 16 (NUDT16) protein as an ITP-binding protein. Biochemical analysis revealed that NUDT16 selectively hydrolyzes deoxyinosine diphosphate (dIDP) and IDP to deoxyinosine monophosphate (dIMP) and IMP, respectively. dITP and ITP are also hydrolyzed by NUDT16 to a lesser extent. The knockdown of NUDT16 in HeLa MR cells suppressed cell proliferation, and was accompanied by a significantly increased accumulation of strand breaks in nuclear DNA, suggesting that NUDT16 has an essential role in the maintenance of genome stability. RS21-C6, another ITP-binding protein identified in our screen, binds not only to ITP, but also to ATP. RS21-C6 hydrolyzes dCTP and 5-halo-dCTP, but does not hydrolyze ITP or ATP. It is likely that RS21-C6 may control dCTP levels or eliminate 5-halo-dCTP in the nucleotide pools. In conclusion, the results of these studies show that our screening system is applicable in studying the health effects of damaged nucleotides and cellular sanitizing systems for nucleotide pools.
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Affiliation(s)
- Daisuke Tsuchimoto
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan.
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van Loon B, Markkanen E, Hübscher U. Oxygen as a friend and enemy: How to combat the mutational potential of 8-oxo-guanine. DNA Repair (Amst) 2010; 9:604-16. [PMID: 20399712 DOI: 10.1016/j.dnarep.2010.03.004] [Citation(s) in RCA: 237] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Accepted: 03/17/2010] [Indexed: 12/20/2022]
Abstract
The maintenance of genetic stability is of crucial importance for any form of life. Prior to cell division in each mammalian cell, the process of DNA replication must faithfully duplicate the three billion bases with an absolute minimum of mistakes. Various environmental and endogenous agents, such as reactive oxygen species (ROS), can modify the structural properties of DNA bases and thus damage the DNA. Upon exposure of cells to oxidative stress, an often generated and highly mutagenic DNA damage is 7,8-dihydro-8-oxo-guanine (8-oxo-G). The estimated steady-state level of 8-oxo-G lesions is about 10(3) per cell/per day in normal tissues and up to 10(5) lesions per cell/per day in cancer tissues. The presence of 8-oxo-G on the replicating strand leads to frequent (10-75%) misincorporations of adenine opposite the lesion (formation of A:8-oxo-G mispairs), subsequently resulting in C:G to A:T transversion mutations. These mutations are among the most predominant somatic mutations in lung, breast, ovarian, gastric and colorectal cancers. Thus, in order to reduce the mutational burden of ROS, human cells have evolved base excision repair (BER) pathways ensuring (i) the correct and efficient repair of A:8-oxo-G mispairs and (ii) the removal of 8-oxo-G lesions from the genome. Very recently it was shown that MutY glycosylase homologue (MUTYH) and DNA polymerase lambda play a crucial role in the accurate repair of A:8-oxo-G mispairs. Here we review the importance of accurate BER of 8-oxo-G damage and its regulation in prevention of cancer.
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Affiliation(s)
- Barbara van Loon
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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41
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Nakabeppu Y, Oka S, Sheng Z, Tsuchimoto D, Sakumi K. Programmed cell death triggered by nucleotide pool damage and its prevention by MutT homolog-1 (MTH1) with oxidized purine nucleoside triphosphatase. Mutat Res 2010; 703:51-8. [PMID: 20542142 DOI: 10.1016/j.mrgentox.2010.06.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Accepted: 06/04/2010] [Indexed: 01/10/2023]
Abstract
Accumulation of oxidized bases such as 8-oxoguanine in either nuclear or mitochondrial DNA triggers various cellular dysfunctions including mutagenesis, and programmed cell death or senescence. Recent studies have revealed that oxidized nucleoside triphosphates such as 8-oxo-dGTP in the nucleotide pool are the main source of oxidized bases accumulating in the DNA of cells under oxidative stress. To counteract such deleterious effects of nucleotide pool damage, mammalian cells possess MutT homolog-1 (MTH1) with oxidized purine nucleoside triphosphatase and related enzymes, thus minimizing the accumulation of oxidized bases in cellular DNA. Depletion or increased expression of the MTH1 protein have revealed its significant roles in avoiding programmed cell death or senescence as well as mutagenesis, and accumulating evidences indicate that MTH1 is involved in suppression of degenerative disorders such as neurodegeneration.
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Affiliation(s)
- Yusaku Nakabeppu
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
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42
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Abolhassani N, Iyama T, Tsuchimoto D, Sakumi K, Ohno M, Behmanesh M, Nakabeppu Y. NUDT16 and ITPA play a dual protective role in maintaining chromosome stability and cell growth by eliminating dIDP/IDP and dITP/ITP from nucleotide pools in mammals. Nucleic Acids Res 2010; 38:2891-903. [PMID: 20081199 PMCID: PMC2875033 DOI: 10.1093/nar/gkp1250] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2009] [Revised: 12/20/2009] [Accepted: 12/26/2009] [Indexed: 11/14/2022] Open
Abstract
Mammalian inosine triphosphatase encoded by ITPA gene hydrolyzes ITP and dITP to monophosphates, avoiding their deleterious effects. Itpa(-) mice exhibited perinatal lethality, and significantly higher levels of inosine in cellular RNA and deoxyinosine in nuclear DNA were detected in Itpa(-) embryos than in wild-type embryos. Therefore, we examined the effects of ITPA deficiency on mouse embryonic fibroblasts (MEFs). Itpa(-) primary MEFs lacking ITP-hydrolyzing activity exhibited a prolonged doubling time, increased chromosome abnormalities and accumulation of single-strand breaks in nuclear DNA, compared with primary MEFs prepared from wild-type embryos. However, immortalized Itpa(-) MEFs had neither of these phenotypes and had a significantly higher ITP/IDP-hydrolyzing activity than Itpa(-) embryos or primary MEFs. Mammalian NUDT16 proteins exhibit strong dIDP/IDP-hydrolyzing activity and similarly low levels of Nudt16 mRNA and protein were detected in primary MEFs derived from both wild-type and Itpa(-) embryos. However, immortalized Itpa(-) MEFs expressed significantly higher levels of Nudt16 than the wild type. Moreover, introduction of silencing RNAs against Nudt16 into immortalized Itpa(-) MEFs reproduced ITPA-deficient phenotypes. We thus conclude that NUDT16 and ITPA play a dual protective role for eliminating dIDP/IDP and dITP/ITP from nucleotide pools in mammals.
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Affiliation(s)
| | | | | | | | | | | | - Yusaku Nakabeppu
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
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Iyama T, Abolhassani N, Tsuchimoto D, Nonaka M, Nakabeppu Y. NUDT16 is a (deoxy)inosine diphosphatase, and its deficiency induces accumulation of single-strand breaks in nuclear DNA and growth arrest. Nucleic Acids Res 2010; 38:4834-43. [PMID: 20385596 PMCID: PMC2919730 DOI: 10.1093/nar/gkq249] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Nucleotides function in a variety of biological reactions; however, they can undergo various chemical modifications. Such modified nucleotides may be toxic to cells if not eliminated from the nucleotide pools. We performed a screen for modified-nucleotide binding proteins and identified human nucleoside diphosphate linked moiety X-type motif 16 (NUDT16) protein as an inosine triphosphate (ITP)/xanthosine triphosphate (XTP)/GTP-binding protein. Recombinant NUDT16 hydrolyzes purine nucleoside diphosphates to the corresponding nucleoside monophosphates. Among 29 nucleotides examined, the highest kcat/Km values were for inosine diphosphate (IDP) and deoxyinosine diphosphate (dIDP). Moreover, NUDT16 moderately hydrolyzes (deoxy)inosine triphosphate ([d]ITP). NUDT16 is mostly localized in the nucleus, and especially in the nucleolus. Knockdown of NUDT16 in HeLa MR cells caused cell cycle arrest in S-phase, reduced cell proliferation, increased accumulation of single-strand breaks in nuclear DNA as well as increased levels of inosine in RNA. We thus concluded that NUDT16 is a (deoxy)inosine diphosphatase that may function mainly in the nucleus to protect cells from deleterious effects of (d)ITP.
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Affiliation(s)
- Teruaki Iyama
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Japan
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Wu M, Audet A, Cusic J, Seeger D, Cochran R, Ghribi O. Broad DNA repair responses in neural injury are associated with activation of the IL-6 pathway in cholesterol-fed rabbits. J Neurochem 2009; 111:1011-21. [PMID: 19765189 DOI: 10.1111/j.1471-4159.2009.06390.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The importance of DNA repair in the pathogenic mechanism of Alzheimer's Disease (AD) is still poorly understood. Here, we report that a broad range of responses by DNA repair proteins plays a critical role in the regulation of inflammatory response in rabbits fed with cholesterol-rich diet, a model system for AD. We found accumulation of oxodG DNA adduct in the brain of rabbits fed with cholesterol-enriched diets compared to control diets, which subsequently induced a broad range of DNA repair protein activities. Also, the hippocampus was identified as the primary site of oxidative DNA damage and elevated OGG1 activity. In addition, a physical interaction between XPB and OGG1 may account for a potential mechanism involving these DNA repair responses. DNA repair proteins also impact activation of various signaling cascades, including Src in response to cholesterol oxidation. Furthermore, OGG1 deficient mice showed no IL-6 activation as seen in wt mice but a drastic increase of TNF-alpha, a pro-inflammatory cytokine. Thus, OGG1 may be associated with cytokine production induced by high cholesterol levels, impacting neurodegeneration. Together, our studies suggest that critical DNA repair proteins are associated with development of AD, and may serve as potential targets for the treatment of AD.
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Affiliation(s)
- Min Wu
- Department of Biochemistry and Molecular Biology, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58203, USA.
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Mangal D, Vudathala D, Park JH, Lee SH, Penning TM, Blair IA. Analysis of 7,8-dihydro-8-oxo-2'-deoxyguanosine in cellular DNA during oxidative stress. Chem Res Toxicol 2009; 22:788-97. [PMID: 19309085 PMCID: PMC2684441 DOI: 10.1021/tx800343c] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
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Analysis of cellular 7,8-dihydro-8-oxo-2′-deoxyguanosine (8-oxo-dGuo) as a biomarker of oxidative DNA damage has been fraught with numerous methodological problems. This is primarily due to artifactual oxidation of dGuo that occurs during DNA isolation and hydrolysis. Therefore, it has become necessary to rely on using the comet assay, which is not necessarily specific for 8-oxo-dGuo. A highly specific and sensitive method based on immunoaffinity purification and stable isotope dilution liquid chromatography (LC)-multiple reaction monitoring (MRM)/mass spectrometry (MS) that avoids artifact formation has now been developed. Cellular DNA was isolated using cold DNAzol (a proprietary product that contains guanidine thiocyanate) instead of chaotropic- or phenol-based methodology. Chelex-treated buffers were used to prevent Fenton chemistry-mediated generation of reactive oxygen species (ROS) and artifactual oxidation of DNA bases. Deferoxamine was also added to all buffers in order to complex any residual transition metal ions remaining after Chelex treatment. The LC-MRM/MS method was used to determine that the basal 8-oxo-dGuo level in DNA from human bronchoalveolar H358 cells was 2.2 ± 0.4 8-oxo-dGuo/107 dGuo (mean ± standard deviation) or 5.5 ± 1.0 8-oxo-dGuo/108 nucleotides. Similar levels were observed in human lung adenocarcinoma A549 cells, mouse hepatoma Hepa-1c1c7 cells, and human HeLa cervical epithelial adenocarcinoma cells. These values are an order of magnitude lower than is typically reported for basal 8-oxo-dGuo levels in DNA as determined by other MS- or chromatography-based assays. H358 cells were treated with increasing concentrations of potassium bromate (KBrO3) as a positive control or with the methylating agent methyl methanesulfonate (MMS) as a negative control. A linear dose−response for 8-oxo-dGuo formation (r2 = 0.962) was obtained with increasing concentrations of KBrO3 in the range of 0.05 mM to 2.50 mM. In contrast, no 8-oxo-dGuo was observed in H358 cell DNA after treatment with MMS. At low levels of oxidative DNA damage, there was an excellent correlation between a comet assay that measured DNA single strand breaks (SSBs) after treatment with human 8-oxo-guanine glycosylase-1 (hOGG1) when compared with 8-oxo-dGuo in the DNA as measured by the stable isotope dilution LC-MRM/MS method. Availability of the new LC-MRM/MS assay made it possible to show that the benzo[a]pyrene (B[a]P)-derived quinone, B[a]P-7,8-dione, could induce 8-oxo-dGuo formation in H358 cells. This most likely occurred through redox cycling between B[a]P-7,8-dione and B[a]P-7,8-catechol with concomitant generation of DNA damaging ROS. In keeping with this concept, inhibition of catechol-O-methyl transferase (COMT)-mediated detoxification of B[a]P-7,8-catechol with Ro 410961 caused increased 8-oxo-dGuo formation in the H358 cell DNA.
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Affiliation(s)
- Dipti Mangal
- Centers for Cancer Pharmacology and Excellence in Environmental Toxicology, University of Pennsylvania, 854 BRB II/III, 421 Curie Boulevard, Philadelphia, Pennsylvania 19104-6160, USA
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RNA oxidation in Alzheimer disease and related neurodegenerative disorders. Acta Neuropathol 2009; 118:151-66. [PMID: 19271225 DOI: 10.1007/s00401-009-0508-1] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2009] [Revised: 02/20/2009] [Accepted: 02/24/2009] [Indexed: 10/21/2022]
Abstract
RNA oxidation and its biological effects are less well studied compared to DNA oxidation. However, RNA may be more susceptible to oxidative insults than DNA, for RNA is largely single-stranded and its bases are not protected by hydrogen bonding and less protected by specific proteins. Also, cellular RNA locates in the vicinity of mitochondria, the primary source of reactive oxygen species. Oxidative modification can occur not only in protein-coding RNAs, but also in non-coding RNAs that have been recently revealed to contribute towards the complexity of the mammalian brain. Damage to coding and non-coding RNAs will cause errors in proteins and disturbances in the regulation of gene expression. While less lethal than mutations in the genome and not inheritable, such sublethal damage to cells might be associated with underlying mechanisms of degeneration, especially age-associated neurodegeneration that is commonly found in the elderly population. Indeed, oxidative RNA damage has been described recently in most of the common neurodegenerative disorders including Alzheimer disease, Parkinson disease, dementia with Lewy bodies and amyotrophic lateral sclerosis. Of particular interest, the accumulating evidence obtained from studies on either human samples or experimental models coincidentally suggests that oxidative RNA damage is a feature in vulnerable neurons at early-stage of these neurodegenerative disorders, indicating that RNA oxidation actively contributes to the onset or the development of the disorders. Further investigations aimed at understanding of the processing mechanisms related to oxidative RNA damage and its consequences may provide significant insights into the pathogenesis of neurodegenerative disorders and lead to better therapeutic strategies.
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Teichert F, Verschoyle RD, Greaves P, Thorpe JF, Mellon JK, Steward WP, Farmer PB, Gescher AJ, Singh R. Determination of 8-oxo-2'-deoxyguanosine and creatinine in murine and human urine by liquid chromatography/tandem mass spectrometry: application to chemoprevention studies. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2009; 23:258-266. [PMID: 19072863 DOI: 10.1002/rcm.3873] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Urinary 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) represents a non-invasive biomarker for oxidative stress and may be useful for monitoring chemotherapeutic and chemopreventive interventions associated with cancer-related alterations in oxidative stress. We describe the development and validation of two separate liquid chromatography/tandem mass spectrometry (LC/MS/MS) selected reaction monitoring (SRM) methods for the determination of 8-oxodG and creatinine in both murine and human urine using stable isotope labelled internal standards. Levels of 8-oxodG were normalised to creatinine. The LC/MS/MS methods were applied to two chemoprevention studies utilising tea polyphenols in humans and TRAMP (TRansgenic Adenocarcinoma of the Mouse Prostate) mice. Patients with benign prostatic hyperplasia received 1 g/day of green tea polyphenols (GTP), 1 g/day of black tea theaflavins (BTT) or no treatment for 4 weeks. TRAMP mice received GTP (0.05% in drinking water) for 4 or 25 weeks. Prostate pathology in TRAMP mice was not affected by GTP. Levels of 8-oxodG were not altered by tea polyphenols in either mice or humans. In TRAMP mice, urinary 8-oxodG levels were elevated with increasing age (p < 0.0001) but not changed by the presence of prostate tumours. In conclusion, the LC/MS/MS SRM methods described here are ideally suited for the accurate determination of 8-oxodG and creatinine in urine samples from both clinical and pre-clinical studies.
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Affiliation(s)
- Friederike Teichert
- Cancer Biomarkers and Prevention Group, Department of Cancer Studies and Molecular Medicine, University of Leicester, UK.
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48
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Youn CK, Jun JY, Hyun JW, Hwang G, Lee BR, Chung MH, Chang IY, You HJ. hMTH1 depletion promotes oxidative-stress-induced apoptosis through a Noxa- and caspase-3/7-mediated signaling pathway. DNA Repair (Amst) 2008; 7:1809-23. [DOI: 10.1016/j.dnarep.2008.07.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2008] [Revised: 07/09/2008] [Accepted: 07/10/2008] [Indexed: 12/30/2022]
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49
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Sublethal RNA oxidation as a mechanism for neurodegenerative disease. Int J Mol Sci 2008; 9:789-806. [PMID: 19325784 PMCID: PMC2635712 DOI: 10.3390/ijms9050789] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Revised: 05/15/2008] [Accepted: 05/16/2008] [Indexed: 12/27/2022] Open
Abstract
Although cellular RNA is subjected to the same oxidative insults as DNA and other cellular macromolecules, oxidative damage to RNA has not been a major focus in investigations of the biological consequences of free radical damage. In fact, because it is largely single-stranded and its bases lack the protection of hydrogen bonding and binding by specific proteins, RNA may be more susceptible to oxidative insults than is DNA. Oxidative damage to protein-coding RNA or non-coding RNA will, in turn, potentially cause errors in proteins and/or dysregulation of gene expression. While less lethal than mutations in the genome, such sublethal insults to cells might be associated with underlying mechanisms of several chronic diseases, including neurodegenerative disease. Recently, oxidative RNA damage has been described in several neurodegenerative diseases including Alzheimer disease, Parkinson disease, dementia with Lewy bodies, and prion diseases. Of particular interest, oxidative RNA damage can be demonstrated in vulnerable neurons early in disease, suggesting that RNA oxidation may actively contribute to the onset of the disease. An increasing body of evidence suggests that, mechanistically speaking, the detrimental effects of oxidative RNA damage to protein synthesis are attenuated, at least in part, by the existence of protective mechanisms that prevent the incorporation of the damaged ribonucleotides into the translational machinery. Further investigations aimed at understanding the processing mechanisms related to oxidative RNA damage and its consequences may provide significant insights into the pathogenesis of neurodegenerative and other degenerative diseases and lead to better therapeutic strategies.
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50
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Moreira PI, Nunomura A, Nakamura M, Takeda A, Shenk JC, Aliev G, Smith MA, Perry G. Nucleic acid oxidation in Alzheimer disease. Free Radic Biol Med 2008; 44:1493-505. [PMID: 18258207 DOI: 10.1016/j.freeradbiomed.2008.01.002] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2007] [Revised: 12/07/2007] [Accepted: 01/08/2008] [Indexed: 01/12/2023]
Abstract
Increasing evidence suggests that oxidative stress is intimately associated with Alzheimer disease pathophysiology. Nucleic acids (nuclear DNA, mitochondrial DNA, and RNA) are one of the several cellular macromolecules damaged by reactive oxygen species, particularly the hydroxyl radical. Because neurons are irreplaceable and survive as long as the organism does, they need elaborate defense mechanisms to ensure their longevity. In Alzheimer disease, however, an accumulation of nucleic acid oxidation is observed, indicating an increased level of oxidative stress and/or a decreased capacity to repair the nucleic acid damage. In this review, we present data supporting the notion that mitochondrial and metal abnormalities are key sources of oxidative stress in Alzheimer disease. Furthermore, we outline the mechanisms of nucleic acid oxidation and repair. Finally, evidence showing the occurrence of nucleic acid oxidation in Alzheimer disease will be discussed.
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Affiliation(s)
- Paula I Moreira
- Center for Neuroscience and Cell Biology, Institute of Physiology-Faculty of Medicine, University of Coimbra, Coimbra, Portugal
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