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Yudkina AV, Kim DV, Zharkov TD, Zharkov DO, Endutkin AV. Probing the Conformational Restraints of DNA Damage Recognition with β-L-Nucleotides. Int J Mol Sci 2024; 25:6006. [PMID: 38892193 PMCID: PMC11172447 DOI: 10.3390/ijms25116006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
The DNA building blocks 2'-deoxynucleotides are enantiomeric, with their natural β-D-configuration dictated by the sugar moiety. Their synthetic β-L-enantiomers (βLdNs) can be used to obtain L-DNA, which, when fully substituted, is resistant to nucleases and is finding use in many biosensing and nanotechnology applications. However, much less is known about the enzymatic recognition and processing of individual βLdNs embedded in D-DNA. Here, we address the template properties of βLdNs for several DNA polymerases and the ability of base excision repair enzymes to remove these modifications from DNA. The Klenow fragment was fully blocked by βLdNs, whereas DNA polymerase κ bypassed them in an error-free manner. Phage RB69 DNA polymerase and DNA polymerase β treated βLdNs as non-instructive but the latter enzyme shifted towards error-free incorporation on a gapped DNA substrate. DNA glycosylases and AP endonucleases did not process βLdNs. DNA glycosylases sensitive to the base opposite their cognate lesions also did not recognize βLdNs as a correct pairing partner. Nevertheless, when placed in a reporter plasmid, pyrimidine βLdNs were resistant to repair in human cells, whereas purine βLdNs appear to be partly repaired. Overall, βLdNs are unique modifications that are mostly non-instructive but have dual non-instructive/instructive properties in special cases.
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Affiliation(s)
- Anna V. Yudkina
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.V.Y.); (D.V.K.); (T.D.Z.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
| | - Daria V. Kim
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.V.Y.); (D.V.K.); (T.D.Z.)
| | - Timofey D. Zharkov
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.V.Y.); (D.V.K.); (T.D.Z.)
| | - Dmitry O. Zharkov
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.V.Y.); (D.V.K.); (T.D.Z.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
| | - Anton V. Endutkin
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.V.Y.); (D.V.K.); (T.D.Z.)
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2
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Hua AB, Sweasy JB. Functional roles and cancer variants of the bifunctional glycosylase NEIL2. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2024; 65 Suppl 1:40-56. [PMID: 37310399 DOI: 10.1002/em.22555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/23/2023] [Accepted: 06/08/2023] [Indexed: 06/14/2023]
Abstract
Over 70,000 DNA lesions occur in the cell every day, and the inability to properly repair them can lead to mutations and destabilize the genome, resulting in carcinogenesis. The base excision repair (BER) pathway is critical for maintaining genomic integrity by repairing small base lesions, abasic sites and single-stranded breaks. Monofunctional and bifunctional glycosylases initiate the first step of BER by recognizing and excising specific base lesions, followed by DNA end processing, gap filling, and finally nick sealing. The Nei-like 2 (NEIL2) enzyme is a critical bifunctional DNA glycosylase in BER that preferentially excises cytosine oxidation products and abasic sites from single-stranded, double-stranded, and bubble-structured DNA. NEIL2 has been implicated to have important roles in several cellular functions, including genome maintenance, participation in active demethylation, and modulation of the immune response. Several germline and somatic variants of NEIL2 with altered expression and enzymatic activity have been reported in the literature linking them to cancers. In this review, we provide an overview of NEIL2 cellular functions and summarize current findings on NEIL2 variants and their relationship to cancer.
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Affiliation(s)
- Anh B Hua
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, Tucson, Arizona, USA
| | - Joann B Sweasy
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, Tucson, Arizona, USA
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3
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Sugiyama T, Sanyal MR. Biochemical analysis of H 2O 2-induced mutation spectra revealed that multiple damages were involved in the mutational process. DNA Repair (Amst) 2024; 134:103617. [PMID: 38154332 PMCID: PMC10842480 DOI: 10.1016/j.dnarep.2023.103617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 12/30/2023]
Abstract
Reactive oxygen species (ROS) are a major threat to genomic integrity and believed to be one of the etiologies of cancers. Here we developed a cell-free system to analyze ROS-induced mutagenesis, in which DNA was exposed to H2O2 and then subjected to translesion DNA synthesis by various DNA polymerases. Then, frequencies of mutations on the DNA products were determined by using next-generation sequencing technology. The majority of observed mutations were either C>A or G>A, caused by dAMP insertion at G and C residues, respectively. These mutations showed similar spectra to COSMIC cancer mutational signature 18 and 36, which are proposed to be caused by ROS. The in vitro mutations can be produced by replicative DNA polymerases (yeast DNA polymerase δ and ε), suggesting that ordinary DNA replication is sufficient to produce them. Very little G>A mutation was observed immediately after exposure to H2O2, but the frequency was increased during the 24 h after the ROS was removed, indicating that the initial oxidation product of cytosine needs to be maturated into a mutagenic lesion. Glycosylase-sensitivities of these mutations suggest that the C>A were made on 8-oxoguanine or Fapy-guanine, and that G>A were most likely made on 5-hydroxycytosine modification.
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Affiliation(s)
- Tomohiko Sugiyama
- Department of Biological Sciences, Ohio University, Athens, OH 45701, USA; Molecular and Cellular Biology Graduate Program, Ohio University, Athens, OH 45701, USA.
| | - Mahima R Sanyal
- Department of Biological Sciences, Ohio University, Athens, OH 45701, USA; Molecular and Cellular Biology Graduate Program, Ohio University, Athens, OH 45701, USA
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4
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Kruchinin AA, Kamzeeva PN, Zharkov DO, Aralov AV, Makarova AV. 8-Oxoadenine: A «New» Player of the Oxidative Stress in Mammals? Int J Mol Sci 2024; 25:1342. [PMID: 38279342 PMCID: PMC10816367 DOI: 10.3390/ijms25021342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/13/2024] [Accepted: 01/15/2024] [Indexed: 01/28/2024] Open
Abstract
Numerous studies have shown that oxidative modifications of guanine (7,8-dihydro-8-oxoguanine, 8-oxoG) can affect cellular functions. 7,8-Dihydro-8-oxoadenine (8-oxoA) is another abundant paradigmatic ambiguous nucleobase but findings reported on the mutagenicity of 8-oxoA in bacterial and eukaryotic cells are incomplete and contradictory. Although several genotoxic studies have demonstrated the mutagenic potential of 8-oxoA in eukaryotic cells, very little biochemical and bioinformatics data about the mechanism of 8-oxoA-induced mutagenesis are available. In this review, we discuss dual coding properties of 8-oxoA, summarize historical and recent genotoxicity and biochemical studies, and address the main protective cellular mechanisms of response to 8-oxoA. We also discuss the available structural data for 8-oxoA bypass by different DNA polymerases as well as the mechanisms of 8-oxoA recognition by DNA repair enzymes.
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Affiliation(s)
- Alexander A. Kruchinin
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova St., 119334 Moscow, Russia; (A.A.K.); (P.N.K.)
- National Research Center, Kurchatov Institute, Kurchatov sq. 2, 123182 Moscow, Russia
| | - Polina N. Kamzeeva
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova St., 119334 Moscow, Russia; (A.A.K.); (P.N.K.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia;
| | - Dmitry O. Zharkov
- Department of Natural Sciences, Novosibirsk State University, 1 Pirogova St., 630090 Novosibirsk, Russia;
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Andrey V. Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia;
| | - Alena V. Makarova
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova St., 119334 Moscow, Russia; (A.A.K.); (P.N.K.)
- National Research Center, Kurchatov Institute, Kurchatov sq. 2, 123182 Moscow, Russia
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5
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Eroshenko DA, Diatlova EA, Golyshev VM, Endutkin AV, Zharkov DO. Aberrant Repair of 8-Oxoguanine in Short DNA Bulges. DOKL BIOCHEM BIOPHYS 2023; 513:S82-S86. [PMID: 38337103 DOI: 10.1134/s1607672923600355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 11/25/2023] [Accepted: 11/25/2023] [Indexed: 02/12/2024]
Abstract
The presence of DNA damage can increase the likelihood of DNA replication errors and promote mutations. In particular, pauses of DNA polymerase at the site of damage can lead to polymerase slippage and the formation of 1-2-nucleotide bulges. Repair of such structures using an undamaged DNA template leads to small deletions. One of the most abundant oxidative DNA lesions, 8-oxoguanine (oxoG), was shown to induce small deletions, but the mechanism of this phenomenon is currently unknown. We studied the aberrant repair of oxoG located in one- and two-nucleotide bulges by the Escherichia coli and human base excision repair systems. Our results indicate that the repair in such substrates can serve as a mechanism for fixing small deletions in bacteria but not in humans.
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Affiliation(s)
- D A Eroshenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - E A Diatlova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - V M Golyshev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - A V Endutkin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - D O Zharkov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia.
- Novosibirsk State University, Novosibirsk, Russia.
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6
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Draxler A, Blaschke A, Binar J, Weber M, Haslacher M, Bartak V, Bragagna L, Mare G, Maqboul L, Klapp R, Herzog T, Széll M, Petrera A, Laky B, Wagner KH, Thell R. Age-related influence on DNA damage, proteomic inflammatory markers and oxidative stress in hospitalized COVID-19 patients compared to healthy controls. Redox Biol 2023; 67:102914. [PMID: 37832397 PMCID: PMC10585323 DOI: 10.1016/j.redox.2023.102914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/29/2023] [Accepted: 10/01/2023] [Indexed: 10/15/2023] Open
Abstract
COVID-19 infections are accompanied by adverse changes in inflammatory pathways that are also partly influenced by increased oxidative stress and might result in elevated DNA damage. The aim of this case-control study was to examine whether COVID-19 patients show differences in oxidative stress-related markers, unconjugated bilirubin (UCB), an inflammation panel and DNA damage compared to healthy, age-and sex-matched controls. The Comet assay with and without the treatment of formamidopyrimidine DNA glycosylase (FPG) and H2O2 challenge was used to detect DNA damage in whole blood. qPCR was applied for gene expression, UCB was analyzed via HPLC, targeted proteomics were applied using Olink® inflammation panel and various oxidative stress as well as clinical biochemistry markers were analyzed in plasma. Hospitalized COVID-19 patients (n = 48) demonstrated higher serum levels of 55 inflammatory proteins (p < 0.001), including hs-C-reactive protein levels (p < 0.05), compared to healthy controls (n = 48). Interestingly, significantly increased age-related DNA damage (%-DNA in tail) after formamidopyrimidine DNA glycosylase (FPG) treatment was measured in younger (n = 24, average age 55.7 years; p < 0.05) but not in older COVID-19 patients (n = 24, average age 83.5 years; p > 0.05). Although various oxidative stress markers were not altered (e.g., FRAP, malondialdehyde, p > 0.05), a significant increased ratio of oxidized to reduced glutathione was detected in COVID-19 patients compared to healthy controls (p < 0.05). UCB levels were significantly lower in individuals with COVID-19, especially in younger COVID-19 patients (p < 0.05). These results suggest that COVID-19 infections exert effects on DNA damage related to age in hospitalized COVID-19 patients that might be driven by changes in inflammatory pathways but are not altered by oxidative stress parameters.
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Affiliation(s)
- Agnes Draxler
- Department of Nutritional Sciences, University of Vienna, Austria; Vienna Doctoral School for Pharmaceutical, Nutritional and Sport Sciences (PhaNuSpo), University of Vienna, Josef Holaubek-Platz 2, 1090, Vienna, Austria.
| | | | - Jessica Binar
- Department of Nutritional Sciences, University of Vienna, Austria.
| | - Maria Weber
- Department of Nutritional Sciences, University of Vienna, Austria; Research Platform Active Ageing, University of Vienna, Austria.
| | | | - Viktoria Bartak
- Department of Nutritional Sciences, University of Vienna, Austria.
| | - Laura Bragagna
- Department of Nutritional Sciences, University of Vienna, Austria; Vienna Doctoral School for Pharmaceutical, Nutritional and Sport Sciences (PhaNuSpo), University of Vienna, Josef Holaubek-Platz 2, 1090, Vienna, Austria.
| | - George Mare
- Department of Nutritional Sciences, University of Vienna, Austria.
| | - Lina Maqboul
- Department of Nutritional Sciences, University of Vienna, Austria; Research Platform Active Ageing, University of Vienna, Austria.
| | - Rebecca Klapp
- Department of Nutritional Sciences, University of Vienna, Austria.
| | - Theresa Herzog
- Klinik Donaustadt, Emergency Department, Langobardenstraße 122, 1220, Vienna, Austria.
| | - Marton Széll
- Klinik Donaustadt, Emergency Department, Langobardenstraße 122, 1220, Vienna, Austria.
| | - Agnese Petrera
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Brenda Laky
- Medical University of Vienna, Austria; Austrian Society of Regenerative Medicine, Vienna, Austria.
| | - Karl-Heinz Wagner
- Department of Nutritional Sciences, University of Vienna, Austria; Research Platform Active Ageing, University of Vienna, Austria.
| | - Rainer Thell
- Medical University of Vienna, Austria; Klinik Donaustadt, Emergency Department, Langobardenstraße 122, 1220, Vienna, Austria.
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Serafin P, Kowalczyk P, Mollica A, Stefanucci A, Laskowska AK, Zawadzka M, Kramkowski K, Kleczkowska P. Evaluation of Antimicrobial Activities against Various E. coli Strains of a Novel Hybrid Peptide-LENART01. Molecules 2023; 28:4955. [PMID: 37446618 DOI: 10.3390/molecules28134955] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
Finding the ideal antimicrobial drug with improved efficacy and a safety profile that eliminates antibiotic resistance caused by pathogens remains a difficult task. Indeed, there is an urgent need for innovation in the design and development of a microbial inhibitor. Given that many promising antimicrobial peptides with excellent broad-spectrum antibacterial properties are secreted by some frog species (e.g., bombesins, opioids, temporins, etc.), our goal was to identify the antimicrobial properties of amphibian-derived dermorphin and ranatensin peptides, which were combined to produce a hybrid compound. This new chimera (named LENART01) was tested for its antimicrobial activity against E. coli strains K12 and R1-R4, which are characterized by differences in lipopolysaccharide (LPS) core oligosaccharide structure. The results showed that LENART01 had superior activity against the R2 and R4 strains compared with the effects of the clinically available antibiotics ciprofloxacin or bleomycin (MIC values). Importantly, the inhibitory effect was not concentration dependent; however, LENART01 showed a time- and dose-dependent hemolytic effect in hemolytic assays.
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Affiliation(s)
- Pawel Serafin
- Military Institute of Hygiene and Epidemiology, 01-163 Warsaw, Poland
| | - Paweł Kowalczyk
- Department of Animal Nutrition, The Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Sciences, 05-110 Jabłonna, Poland
| | - Adriano Mollica
- Department of Pharmacy, University "G. d'Annunzio" of Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | - Azzurra Stefanucci
- Department of Pharmacy, University "G. d'Annunzio" of Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | - Anna K Laskowska
- Centre for Preclinical Research and Technology (CePT), Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Magdalena Zawadzka
- Military Institute of Hygiene and Epidemiology, 01-163 Warsaw, Poland
- Department of Epidemiology and Public Health Lodz, Medical University of Lodz, 90-419 Lodz, Poland
| | - Karol Kramkowski
- Department of Physical Chemistry, Medical University of Bialystok, 15-089 Białystok, Poland
| | - Patrycja Kleczkowska
- Military Institute of Hygiene and Epidemiology, 01-163 Warsaw, Poland
- Maria Sklodowska-Curie Medical Academy in Warsaw, 03-411 Warsaw, Poland
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8
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Nguyen DD, Kim E, Le NT, Ding X, Jaiswal RK, Kostlan RJ, Nguyen TNT, Shiva O, Le MT, Chai W. Deficiency in mammalian STN1 promotes colon cancer development via inhibiting DNA repair. SCIENCE ADVANCES 2023; 9:eadd8023. [PMID: 37163605 PMCID: PMC10171824 DOI: 10.1126/sciadv.add8023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 04/05/2023] [Indexed: 05/12/2023]
Abstract
Despite the high lethality of colorectal cancers (CRCs), only a limited number of genetic risk factors are identified. The mammalian ssDNA-binding protein complex CTC1-STN1-TEN1 protects genome stability, yet its role in tumorigenesis is unknown. Here, we show that attenuated CTC1/STN1 expression is common in CRCs. We generated an inducible STN1 knockout mouse model and found that STN1 deficiency in young adult mice increased CRC incidence, tumor size, and tumor load. CRC tumors exhibited enhanced proliferation, reduced apoptosis, and elevated DNA damage and replication stress. We found that STN1 deficiency down-regulated multiple DNA glycosylases, resulting in defective base excision repair (BER) and accumulation of oxidative damage. Collectively, this study identifies STN1 deficiency as a risk factor for CRC and implicates the previously unknown STN1-BER axis in protecting colon tissues from oxidative damage, therefore providing insights into the CRC tumor-suppressing mechanism.
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Affiliation(s)
- Dinh Duc Nguyen
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Eugene Kim
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Nhat Thong Le
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
| | - Xianzhong Ding
- Department of Pathology, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Rishi Kumar Jaiswal
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Raymond Joseph Kostlan
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Thi Ngoc Thanh Nguyen
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Olga Shiva
- Office of Research, Washington State University-Spokane, Spokane, WA, USA
| | - Minh Thong Le
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
| | - Weihang Chai
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
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9
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Cooper CR, Jones DJL, Jones GDD, Petersson K. Comet Assay Profiling of FLASH-Induced Damage: Mechanistic Insights into the Effects of FLASH Irradiation. Int J Mol Sci 2023; 24:7195. [PMID: 37108360 PMCID: PMC10138874 DOI: 10.3390/ijms24087195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/06/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Numerous studies have demonstrated the normal tissue-sparing effects of ultra-high dose rate 'FLASH' irradiation in vivo, with an associated reduction in damage burden being reported in vitro. Towards this, two key radiochemical mechanisms have been proposed: radical-radical recombination (RRR) and transient oxygen depletion (TOD), with both being proposed to lead to reduced levels of induced damage. Previously, we reported that FLASH induces lower levels of DNA strand break damage in whole-blood peripheral blood lymphocytes (WB-PBL) ex vivo, but our study failed to distinguish the mechanism(s) involved. A potential outcome of RRR is the formation of crosslink damage (particularly, if any organic radicals recombine), whilst a possible outcome of TOD is a more anoxic profile of induced damage resulting from FLASH. Therefore, the aim of the current study was to profile FLASH-induced damage via the Comet assay, assessing any DNA crosslink formation as a putative marker of RRR and/or anoxic DNA damage formation as an indicative marker of TOD, to determine the extent to which either mechanism contributes to the "FLASH effect". Following FLASH irradiation, we see no evidence of any crosslink formation; however, FLASH irradiation induces a more anoxic profile of induced damage, supporting the TOD mechanism. Furthermore, treatment of WB-PBLs pre-irradiation with BSO abrogates the reduced strand break damage burden mediated by FLASH exposures. In summary, we do not see any experimental evidence to support the RRR mechanism contributing to the reduced damage burden induced by FLASH. However, the observation of a greater anoxic profile of damage following FLASH irradiation, together with the BSO abrogation of the reduced strand break damage burden mediated by FLASH, lends further support to TOD being a driver of the reduced damage burden plus a change in the damage profile mediated by FLASH.
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Affiliation(s)
- Christian R. Cooper
- Leicester Cancer Research Centre, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester LE2 7LX, UK; (D.J.L.J.); (G.D.D.J.)
- MRC Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Donald J. L. Jones
- Leicester Cancer Research Centre, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester LE2 7LX, UK; (D.J.L.J.); (G.D.D.J.)
| | - George D. D. Jones
- Leicester Cancer Research Centre, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester LE2 7LX, UK; (D.J.L.J.); (G.D.D.J.)
| | - Kristoffer Petersson
- MRC Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
- Department of Haematology, Oncology and Radiation Physics, Skåne University Hospital Lund University, 221 85 Lund, Sweden
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10
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Franck C, Stéphane G, Julien C, Virginie G, Martine G, Norbert G, Fabrice C, Didier F, Josef SM, Bertrand C. Structural and functional determinants of the archaeal 8-oxoguanine-DNA glycosylase AGOG for DNA damage recognition and processing. Nucleic Acids Res 2022; 50:11072-11092. [PMID: 36300625 PMCID: PMC9638937 DOI: 10.1093/nar/gkac932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/31/2022] [Accepted: 10/25/2022] [Indexed: 11/29/2022] Open
Abstract
8-Oxoguanine (GO) is a major purine oxidation product in DNA. Because of its highly mutagenic properties, GO absolutely must be eliminated from DNA. To do this, aerobic and anaerobic organisms from the three kingdoms of life have evolved repair mechanisms to prevent its deleterious effect on genetic integrity. The major way to remove GO is the base excision repair pathway, usually initiated by a GO-DNA glycosylase. First identified in bacteria (Fpg) and eukaryotes (OGG1), GO-DNA glycosylases were more recently identified in archaea (OGG2 and AGOG). AGOG is the less documented enzyme and its mode of damage recognition and removing remains to be clarified at the molecular and atomic levels. This study presents a complete structural characterisation of apo AGOGs from Pyrococcus abyssi (Pab) and Thermococcus gammatolerans (Tga) and the first structure of Pab-AGOG bound to lesion-containing single- or double-stranded DNA. By combining X-ray structure analysis, site directed mutagenesis and biochemistry experiments, we identified key amino acid residues of AGOGs responsible for the specific recognition of the lesion and the base opposite the lesion and for catalysis. Moreover, a unique binding mode of GO, involving double base flipping, never observed for any other DNA glycosylases, is revealed. In addition to unravelling the properties of AGOGs, our study, through comparative biochemical and structural analysis, offers new insights into the evolutionary plasticity of DNA glycosylases across all three kingdoms of life.
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Affiliation(s)
- Coste Franck
- Centre de Biophysique Moléculaire (CBM), UPR4301 CNRS, Université d’Orléans , CS 80054, rue Charles Sadron , F-45071 Orléans cedex 02 , France
| | - Goffinont Stéphane
- Centre de Biophysique Moléculaire (CBM), UPR4301 CNRS, Université d’Orléans , CS 80054, rue Charles Sadron , F-45071 Orléans cedex 02 , France
| | - Cros Julien
- Centre de Biophysique Moléculaire (CBM), UPR4301 CNRS, Université d’Orléans , CS 80054, rue Charles Sadron , F-45071 Orléans cedex 02 , France
| | - Gaudon Virginie
- Centre de Biophysique Moléculaire (CBM), UPR4301 CNRS, Université d’Orléans , CS 80054, rue Charles Sadron , F-45071 Orléans cedex 02 , France
| | - Guérin Martine
- Centre de Biophysique Moléculaire (CBM), UPR4301 CNRS, Université d’Orléans , CS 80054, rue Charles Sadron , F-45071 Orléans cedex 02 , France
| | - Garnier Norbert
- Centre de Biophysique Moléculaire (CBM), UPR4301 CNRS, Université d’Orléans , CS 80054, rue Charles Sadron , F-45071 Orléans cedex 02 , France
| | - Confalonieri Fabrice
- Institut de Biologie Intégrative de la cellule (I2BC), UMR 9198 Université Paris-Saclay-CNRS-CEA , Bâtiment 21, Avenue de la Terrasse , F-91190 Gif-sur-Yvette , France
| | - Flament Didier
- Université de Brest, Ifremer, CNRS, Unité Biologie et Ecologie des Ecosystèmes marins Profonds (BEEP) , F-29280 Plouzané , France
| | - Suskiewicz Marcin Josef
- Centre de Biophysique Moléculaire (CBM), UPR4301 CNRS, Université d’Orléans , CS 80054, rue Charles Sadron , F-45071 Orléans cedex 02 , France
| | - Castaing Bertrand
- Centre de Biophysique Moléculaire (CBM), UPR4301 CNRS, Université d’Orléans , CS 80054, rue Charles Sadron , F-45071 Orléans cedex 02 , France
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11
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Arbo MD, Garcia SC, Sarpa M, Da Silva Junior FM, Nascimento SN, Garcia ALH, Da Silva J. Brazilian workers occupationally exposed to different toxic agents: A systematic review on DNA damage. MUTATION RESEARCH/GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2022; 879-880:503519. [PMID: 35914865 DOI: 10.1016/j.mrgentox.2022.503519] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 04/23/2022] [Accepted: 06/21/2022] [Indexed: 10/17/2022]
Abstract
The evaluation of genotoxicity in workers exposed to different toxic agents is very important, especially considering the association between these exposures in a chronic context and DNA damage. Assessing biomarkers of exposure and, when possible, early biomarkers of effect, contributes to elucidating the potential toxic mechanisms involved in genotoxicity and its contribution to chronic non-communicable diseases. In Brazil, the biggest country in South America, workers are exposed to hazardous physical and chemical agents. Considering that these exposures occur, in most cases, throughout the worker's whole life, this is an important public health concern in Brazil. Therefore, this systematic review aims to analyze occupational exposure to chemical and physical agents and the association with DNA damage in studies carried out in Brazil from 1980 to 2021. A systematic and comprehensive literature search was performed in different databases based on occupational exposure to chemical and physical agents and DNA damage. Only full articles on studies that investigated experimental evidence on occupational exposure in Brazil and assessed DNA damage were included, amounting to 89 articles. Five main occupational exposure groups were identified: pesticides (36%), organic solvents (20%), dust and particles (16%), metals (11%), and ionizing radiation (6%). Another group called "others" included studies (11%) that did not fall into these main groups. It was found that comet assay and micronucleus tests are the most adopted methods to detect DNA damage. Occupational exposures were most associated with DNA damage. However, further improvements in study design would be needed to better characterize the association between biomonitoring and DNA damage, particularly to account for confounding factors.
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12
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Nwokwu CD, Xiao AY, Harrison L, Nestorova GG. Identification of microRNA-mRNA regulatory network associated with oxidative DNA damage in human astrocytes. ASN Neuro 2022; 14:17590914221101704. [PMID: 35570825 PMCID: PMC9118907 DOI: 10.1177/17590914221101704] [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: 01/27/2022] [Revised: 03/23/2022] [Accepted: 04/21/2022] [Indexed: 11/23/2022] Open
Abstract
The high lipid content of the brain, coupled with its heavy oxygen dependence and relatively weak antioxidant system, makes it highly susceptible to oxidative DNA damage that contributes to neurodegeneration. This study is aimed at identifying specific ROS-responsive miRNAs that modulate the expression and activity of the DNA repair proteins in human astrocytes, which could serve as potential biomarkers and lead to the development of targeted therapeutic strategies for neurological diseases. Oxidative DNA damage was established after treatment of human astrocytes with 10μM sodium dichromate for 16 h. Comet assay analysis indicated a significant increase in oxidized guanine lesions. RT-qPCR and ELISA assays confirmed that sodium dichromate reduced the mRNA and protein expression levels of the human base-excision repair enzyme, 8-deoxyguanosine DNA glycosylase 1 (hOGG1). Small RNAseq data were generated on an Ion Torrent™ system and the differentially expressed miRNAs were identified using Partek Flow® software. The biologically significant miRNAs were selected using miRNet 2.0. Oxidative-stress-induced DNA damage was associated with a significant decrease in miRNA expression: 231 downregulated miRNAs and 2 upregulated miRNAs (p < 0.05; >2-fold). In addition to identifying multiple miRNA-mRNA pairs involved in DNA repair processes, this study uncovered a novel miRNA-mRNA pair interaction: miR-1248:OGG1. Inhibition of miR-1248 via the transfection of its inhibitor restored the expression levels of hOGG1. Therefore, targeting the identified microRNA candidates could ameliorate the nuclear DNA damage caused by the brain's exposure to mutagens, reduce the incidence and improve the treatment of cancer and neurodegenerative disorders.
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Affiliation(s)
| | - Adam Y. Xiao
- Department of Molecular and Cellular Physiology, Louisiana State University Health Sciences Center, Shreveport, LA, USA
| | - Lynn Harrison
- Department of Molecular and Cellular Physiology, Louisiana State University Health Sciences Center, Shreveport, LA, USA
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13
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Wang HT, Lee HW, Weng MW, Liu Y, Huang WC, Lepor H, Wu XR, Tang MS. The role of TAp63γ and P53 point mutations in regulating DNA repair, mutational susceptibility and invasion of bladder cancer cells. eLife 2021; 10:71184. [PMID: 34747697 PMCID: PMC8575459 DOI: 10.7554/elife.71184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 10/21/2021] [Indexed: 11/13/2022] Open
Abstract
It has long been recognized that non-muscle-invasive bladder cancer (NMIBC) has a low propensity (20%) of becoming muscle-invasive (MIBC), and that MIBC carry many more p53 point mutations (p53m) than NMIBC (50% vs 10%). MIBC also has a higher mutation burden than NMIBC. These results suggest that DNA repair capacities, mutational susceptibility and p53m are crucial for MIBC development. We found MIBC cells are hypermutable, deficient in DNA repair and have markedly downregulated DNA repair genes, XPC, hOGG1/2 and Ref1, and the tumor suppressor, TAp63γ. In contrast, NMIBC cells are hyperactive in DNA repair and exhibit upregulated DNA repair genes and TAp63γ. A parallel exists in human tumors, as MIBC tissues have markedly lower DNA repair activity, and lower expression of DNA repair genes and TAp63γ compared to NMIBC tissues. Forced TAp63γ expression in MIBC significantly mitigates DNA repair deficiencies and reduces mutational susceptibility. Knockdown of TAp63γ in NMIBC greatly reduces DNA repair capacity and enhances mutational susceptibility. Manipulated TAp63γ expression or knockdown of p53m reduce the invasion of MIBC by 40–60%. However, the combination of p53m knockdown with forced TAp63γ expression reduce the invasion ability to nil suggesting that p53m contributes to invasion phenotype independent from TAp63γ. These results indicate that in BC, TAp63γ regulates DNA repair capacities, mutational susceptibility and invasion, and that p53m contribute to the invasion phenotype. We conclude that concurrent TAp63γ suppression and acquisition of p53m are a major cause for MIBC development.
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Affiliation(s)
- Hsiang-Tsui Wang
- Department of Environmental Medicine, New York University Grossman School of Medicine, New York, United States
| | - Hyun-Wook Lee
- Department of Environmental Medicine, New York University Grossman School of Medicine, New York, United States
| | - Mao-Wen Weng
- Department of Environmental Medicine, New York University Grossman School of Medicine, New York, United States
| | - Yan Liu
- Department of Urology, New York University Grossman School of Medicine, New York, United States
| | - William C Huang
- Department of Urology, New York University Grossman School of Medicine, New York, United States
| | - Herbert Lepor
- Department of Urology, New York University Grossman School of Medicine, New York, United States
| | - Xue-Ru Wu
- Department of Urology, New York University Grossman School of Medicine, New York, United States
| | - Moon-Shong Tang
- Department of Environmental Medicine, New York University Grossman School of Medicine, New York, United States
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14
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Balasubramaniyam T, Oh KI, Jin HS, Ahn HB, Kim BS, Lee JH. Non-Canonical Helical Structure of Nucleic Acids Containing Base-Modified Nucleotides. Int J Mol Sci 2021; 22:9552. [PMID: 34502459 PMCID: PMC8430589 DOI: 10.3390/ijms22179552] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/27/2021] [Accepted: 08/29/2021] [Indexed: 12/12/2022] Open
Abstract
Chemically modified nucleobases are thought to be important for therapeutic purposes as well as diagnosing genetic diseases and have been widely involved in research fields such as molecular biology and biochemical studies. Many artificially modified nucleobases, such as methyl, halogen, and aryl modifications of purines at the C8 position and pyrimidines at the C5 position, are widely studied for their biological functions. DNA containing these modified nucleobases can form non-canonical helical structures such as Z-DNA, G-quadruplex, i-motif, and triplex. This review summarizes the synthesis of chemically modified nucleotides: (i) methylation, bromination, and arylation of purine at the C8 position and (ii) methylation, bromination, and arylation of pyrimidine at the C5 position. Additionally, we introduce the non-canonical structures of nucleic acids containing these modifications.
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Affiliation(s)
- Thananjeyan Balasubramaniyam
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
| | - Kwnag-Im Oh
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
| | - Ho-Seong Jin
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
| | - Hye-Bin Ahn
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
| | - Byeong-Seon Kim
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
- Department of Chemistry Education, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
| | - Joon-Hwa Lee
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
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15
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Complementary Functions of Plant AP Endonucleases and AP Lyases during DNA Repair of Abasic Sites Arising from C:G Base Pairs. Int J Mol Sci 2021; 22:ijms22168763. [PMID: 34445469 PMCID: PMC8395712 DOI: 10.3390/ijms22168763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 11/23/2022] Open
Abstract
Abasic (apurinic/apyrimidinic, AP) sites are ubiquitous DNA lesions arising from spontaneous base loss and excision of damaged bases. They may be processed either by AP endonucleases or AP lyases, but the relative roles of these two classes of enzymes are not well understood. We hypothesized that endonucleases and lyases may be differentially influenced by the sequence surrounding the AP site and/or the identity of the orphan base. To test this idea, we analysed the activity of plant and human AP endonucleases and AP lyases on DNA substrates containing an abasic site opposite either G or C in different sequence contexts. AP sites opposite G are common intermediates during the repair of deaminated cytosines, whereas AP sites opposite C frequently arise from oxidized guanines. We found that the major Arabidopsis AP endonuclease (ARP) exhibited a higher efficiency on AP sites opposite G. In contrast, the main plant AP lyase (FPG) showed a greater preference for AP sites opposite C. The major human AP endonuclease (APE1) preferred G as the orphan base, but only in some sequence contexts. We propose that plant AP endonucleases and AP lyases play complementary DNA repair functions on abasic sites arising at C:G pairs, neutralizing the potential mutagenic consequences of C deamination and G oxidation, respectively.
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16
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Ray U, Sharma S, Kapoor I, Kumari S, Gopalakrishnan V, Vartak SV, Kumari N, Varshney U, Raghavan SC. G4 DNA present at human telomeric DNA contributes toward reduced sensitivity to γ-radiation induced oxidative damage, but not bulky adduct formation. Int J Radiat Biol 2021; 97:1166-1180. [PMID: 34259614 DOI: 10.1080/09553002.2021.1955997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/11/2021] [Accepted: 06/23/2021] [Indexed: 12/15/2022]
Abstract
PURPOSE DNA, the hereditary material of a human cell generally exists as Watson-Crick base paired double-stranded B-DNA. Studies suggest that DNA can also exist in non-B forms, such as four stranded G-quadruplexes (G4 DNA). Recently, our studies revealed that the regions of DNA that can fold into G-quadruplex structures are less sensitive to ionizing radiation (IR) compared to B-DNA. Importantly, we reported that the planar G-quartet of a G4 structure is shielded from radiation induced DNA breaks, while the single- and double-stranded DNA regions remained susceptible. Thus, in the present study, we investigate whether telomeric repeat DNA present at the end of telomere, known to fold into G4 DNA can protect from radiation induced damages including strand breaks, oxidation of purines and bulky adduct formation on DNA. MATERIALS AND METHODS For plasmid irradiation assay, plasmids containing human telomeric repeat DNA sequence TTAGGG (0.8 kb or 1.8 kb) were irradiated with increasing doses of IR along with appropriate control plasmids and products were resolved on 1% agarose gel. Radioprotection was evaluated based on extent of conversion of supercoiled to nicked or linear forms of the DNA following irradiation. Formation of G-quadruplex structure on supercoiled DNA was evaluated based on circular dichroism (CD) spectroscopy studies. Cleavage of radiation induced oxidative damage and extent of formation of nicks was further evaluated using base and nucleotide excision repair proteins. RESULTS Results from CD studies showed that the plasmid DNA harboring human telomeric repeats (TTAGGG) can fold into G-quadruplex DNA structures. Further, results showed that human telomeric repeat sequence when present on a plasmid can protect the plasmid DNA against IR induced DNA strand breaks, unlike control plasmids bearing random DNA sequence. CONCLUSIONS Human telomeric repeat sequence when present on plasmids can fold into G-quadruplex DNA structures, and can protect the DNA against IR induced DNA strand breaks and oxidative damage. These results in conjunction with our previous studies suggest that telomeric repeat sequence imparts less sensitivity to IR and thus telomeres of chromosomes are protected from radiation.
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Affiliation(s)
- Ujjayinee Ray
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Shivangi Sharma
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Indu Kapoor
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Susmita Kumari
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Vidya Gopalakrishnan
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
- Department of Zoology, St. Joseph's College, Irinjalakuda, India
| | - Supriya V Vartak
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Nitu Kumari
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
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17
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Shieh P, Hill MR, Zhang W, Kristufek SL, Johnson JA. Clip Chemistry: Diverse (Bio)(macro)molecular and Material Function through Breaking Covalent Bonds. Chem Rev 2021; 121:7059-7121. [PMID: 33823111 DOI: 10.1021/acs.chemrev.0c01282] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In the two decades since the introduction of the "click chemistry" concept, the toolbox of "click reactions" has continually expanded, enabling chemists, materials scientists, and biologists to rapidly and selectively build complexity for their applications of interest. Similarly, selective and efficient covalent bond breaking reactions have provided and will continue to provide transformative advances. Here, we review key examples and applications of efficient, selective covalent bond cleavage reactions, which we refer to herein as "clip reactions." The strategic application of clip reactions offers opportunities to tailor the compositions and structures of complex (bio)(macro)molecular systems with exquisite control. Working in concert, click chemistry and clip chemistry offer scientists and engineers powerful methods to address next-generation challenges across the chemical sciences.
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Affiliation(s)
- Peyton Shieh
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Megan R Hill
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Wenxu Zhang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Samantha L Kristufek
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jeremiah A Johnson
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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18
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DNA glycosylases for 8-oxoguanine repair in Staphylococcus aureus. DNA Repair (Amst) 2021; 105:103160. [PMID: 34192601 DOI: 10.1016/j.dnarep.2021.103160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 11/20/2022]
Abstract
GO system is part of base excision DNA repair and is required for the correct repair of 8-oxoguanine (8-oxoG), one of the most abundant oxidative lesions. Due to the ability of 8-oxoG to mispair with A, this base is highly mutagenic, and its repair requires two enzymes: Fpg that removes 8-oxoG from 8-oxoG:C pairs, and MutY that excises the normal A from 8-oxoG:A mispairs. Here we characterize the properties of putative GO system DNA glycosylases from Staphylococcus aureus, an important human opportunistic pathogen that causes hospital infections and presents a serious health concern due to quick spread of antibiotic-resistant strains. In addition to Fpg and MutY from the reference NCTC 8325 strain (SauFpg1 and SauMutY), we have also studied an Fpg homolog from a multidrug-resistant C0673 isolate (SauFpg2), which is different from SauFpg1 in its sequence. Both SauFpg enzymes showed the highest activity at pH 7.0-9.0 and NaCl concentrations 25-75 mM (SauFpg1) or 50-100 mM (SauFpg2), whereas SauMutY was active at a broad pH range and had a salt optimum at ∼75 mM NaCl. Both SauFpg1 and SauFpg2 bound and cleaved duplexes containing 8-oxoG, 5-hydroxyuracil, 5,6-dihydrouracil or apurinic/apyrimidinic site paired with C, T, or G, but not with A. For SauFpg1 and SauFpg2, 8-oxoG was the best substrate tested, and 5,6-dihydrouracil was the worst one. SauMutY efficiently excised adenine from duplex substrates containing A:8-oxoG or A:G pairs. SauFpg enzymes were readily trapped on DNA by NaBH4 treatment, indicating formation of a Schiff base reaction intermediate. Surprisingly, SauMutY was also trapped significantly better than its E. coli homolog. All three S. aureus GO glycosylases drastically reduced spontaneous mutagenesis when expressed in an fpg mutY E. coli double mutant. Overall, we conclude that S. aureus possesses an active GO system, which could possibly be targeted for sensitization of this pathogen to oxidative stress.
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19
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Zhao J, Schank M, Wang L, Li Z, Nguyen LN, Dang X, Cao D, Khanal S, Nguyen LNT, Thakuri BKC, Ogbu SC, Lu Z, Wu XY, Morrison ZD, Gazzar ME, Liu Y, Zhang J, Ning S, Moorman JP, Yao ZQ. Mitochondrial Functions Are Compromised in CD4 T Cells From ART-Controlled PLHIV. Front Immunol 2021; 12:658420. [PMID: 34017335 PMCID: PMC8129510 DOI: 10.3389/fimmu.2021.658420] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/15/2021] [Indexed: 01/05/2023] Open
Abstract
The hallmark of HIV/AIDS is a gradual depletion of CD4 T cells. Despite effective control by antiretroviral therapy (ART), a significant subgroup of people living with HIV (PLHIV) fails to achieve complete immune reconstitution, deemed as immune non-responders (INRs). The mechanisms underlying incomplete CD4 T cell recovery in PLHIV remain unclear. In this study, CD4 T cells from PLHIV were phenotyped and functionally characterized, focusing on their mitochondrial functions. The results show that while total CD4 T cells are diminished, cycling cells are expanded in PLHIV, especially in INRs. HIV-INR CD4 T cells are more activated, displaying exhausted and senescent phenotypes with compromised mitochondrial functions. Transcriptional profiling and flow cytometry analysis showed remarkable repression of mitochondrial transcription factor A (mtTFA) in CD4 T cells from PLHIV, leading to abnormal mitochondrial and T cell homeostasis. These results demonstrate a sequential cellular paradigm of T cell over-activation, proliferation, exhaustion, senescence, apoptosis, and depletion, which correlates with compromised mitochondrial functions. Therefore, reconstituting the mtTFA pathway may provide an adjunctive immunological approach to revitalizing CD4 T cells in ART-treated PLHIV, especially in INRs.
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Affiliation(s)
- Juan Zhao
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States.,Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States
| | - Madison Schank
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States.,Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States
| | - Ling Wang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States.,Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States
| | - Zhengke Li
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States.,Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States
| | - Lam Nhat Nguyen
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States.,Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States
| | - Xindi Dang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States.,Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States
| | - Dechao Cao
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States.,Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States
| | - Sushant Khanal
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States.,Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States
| | - Lam Ngoc Thao Nguyen
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States.,Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States
| | - Bal Krishna Chand Thakuri
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States.,Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States
| | - Stella C Ogbu
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States.,Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States
| | - Zeyuan Lu
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States.,Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States
| | - Xiao Y Wu
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States.,Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States
| | - Zheng D Morrison
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States.,Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States
| | - Mohamed El Gazzar
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States.,Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States
| | - Ying Liu
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States.,Department of Biostatistics and Epidemiology, College of Public Health, East Tennessee State University, Johnson City, TN, United States
| | - Jinyu Zhang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States.,Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States
| | - Shunbin Ning
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States.,Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States
| | - Jonathan P Moorman
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States.,Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States.,Hepatitis (HCV/HBV/HIV) Program, James H. Quillen VA Medical Center, Department of Veterans Affairs, Johnson City, TN, United States
| | - Zhi Q Yao
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States.,Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States.,Hepatitis (HCV/HBV/HIV) Program, James H. Quillen VA Medical Center, Department of Veterans Affairs, Johnson City, TN, United States
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21
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Selbach MT, Scotti AS, Feistel CC, Nicolau CC, Dalberto D, Dos Santos NG, Borsoi G, Ferraz ABF, Grivicich I, de Souza GMS, Chytry P, Dias JF, Corrêa DS, da Silva J. Evaluation of the cytotoxic and genotoxic effects of Sida planicaulis Cav extract using human neuroblastoma cell line SH-SY5Y. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2021; 84:345-355. [PMID: 33435828 DOI: 10.1080/15287394.2020.1871144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Sida planicaulis is a weed thought to have originated in Brazil, where it is present in abundant quantities, but also this plant is also found in south-central Florida, Indian Ocean Islands, and the Pacific Islands. Sida planicaulis produces neurotoxicity that adversely affects livestock breeding with heavy animal losses and consequent negative impact on Brazil's economy. The aim of this study was to determine the chemical profile, cytotoxic and genotoxic effects of ethanolic extracts of S. planicaulis collected in winter (leaf extract) and summer (leaf extract and leaf + flower extract) using an in vitro model of human neuroblastoma cell line SH-SY5Y. Phytochemical screening demonstrated the presence of alkaloids, flavonoids, and apolar compounds. Rutin, quercetin, and swainsonine were detected by HPLC and GC/MS, respectively. Phosphorus, potassium, iron, and zinc were the inorganic elements found. Extracts produced cytotoxicity at all concentrations tested (7-4,000 μg/ml) as evidenced by the colorimetric assay [3-(4,5-dimethyl-thiazol-2-yl) -2,5-diphenyl-tetrazolium bromide (MTT)]. Based upon the alkaline comet assay extracts were found to induce genotoxicity at concentrations ranging from 0.437 to 7 μg/ml. DNA damage produced by extracts was affirmed using a modified comet assay with the enzymes Endo III and FPG in a concentration dependent manner. Further, enzyme-modified comet assay showed both oxidized purines and pyrimidines, and consequently oxidative stress was related to genomic instability and cell death. Data suggest that low concentrations of ethanolic extracts of S. planicaulis (different seasons) induced increased DNA damage related to oxidative stress and chemical composition.
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Affiliation(s)
- Mariana Terezinha Selbach
- Laboratory of Genetic Toxicology, PPGBioSaúde (Postgraduate Program in Cellular and Molecular Biology Applied to Health), Lutheran University of Brazil (ULBRA), Canoas, RS, Brazil
| | - Amanda Souza Scotti
- Laboratory of Genetic Toxicology, PPGBioSaúde (Postgraduate Program in Cellular and Molecular Biology Applied to Health), Lutheran University of Brazil (ULBRA), Canoas, RS, Brazil
| | - Cleverson Costa Feistel
- Pharmacognosy and Phytochemistry Laboratory, PPGBioSaúde (Postgraduate Program in Cellular and Molecular Biology Applied to Health), Lutheran University of Brazil (ULBRA), Canoas, RS, Brazil
| | - Caroline C Nicolau
- Laboratory of Genetic Toxicology, PPGBioSaúde (Postgraduate Program in Cellular and Molecular Biology Applied to Health), Lutheran University of Brazil (ULBRA), Canoas, RS, Brazil
| | - Daiana Dalberto
- Laboratory of Genetic Toxicology, PPGBioSaúde (Postgraduate Program in Cellular and Molecular Biology Applied to Health), Lutheran University of Brazil (ULBRA), Canoas, RS, Brazil
| | - Natália Garcia Dos Santos
- Pharmacognosy and Phytochemistry Laboratory, PPGBioSaúde (Postgraduate Program in Cellular and Molecular Biology Applied to Health), Lutheran University of Brazil (ULBRA), Canoas, RS, Brazil
| | - Guilherme Borsoi
- Pharmacognosy and Phytochemistry Laboratory, PPGBioSaúde (Postgraduate Program in Cellular and Molecular Biology Applied to Health), Lutheran University of Brazil (ULBRA), Canoas, RS, Brazil
| | - Alexandre Barros Falcão Ferraz
- Pharmacognosy and Phytochemistry Laboratory, PPGBioSaúde (Postgraduate Program in Cellular and Molecular Biology Applied to Health), Lutheran University of Brazil (ULBRA), Canoas, RS, Brazil
| | - Ivana Grivicich
- Laboratory of Cancer Biology, PPGBioSaúde (Postgraduate Program in Cellular and Molecular Biology Applied to Health), Lutheran University of Brazil (ULBRA), Canoas, RS, Brazil
| | | | - Paola Chytry
- Ion Implantation Laboratory, Institute of Physics, Federal University of Rio Grande Do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Johnny Ferraz Dias
- Ion Implantation Laboratory, Institute of Physics, Federal University of Rio Grande Do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Dione Silva Corrêa
- Center for Research in Product and Development (CEPPED), Lutheran University of Brazil (ULBRA), Canoas, RS, Brazil
| | - Juliana da Silva
- Laboratory of Genetic Toxicology, PPGBioSaúde (Postgraduate Program in Cellular and Molecular Biology Applied to Health), Lutheran University of Brazil (ULBRA), Canoas, RS, Brazil
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22
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Makasheva KA, Endutkin AV, Zharkov DO. Requirements for DNA bubble structure for efficient cleavage by helix-two-turn-helix DNA glycosylases. Mutagenesis 2021; 35:119-128. [PMID: 31784740 DOI: 10.1093/mutage/gez047] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 11/18/2019] [Indexed: 12/12/2022] Open
Abstract
Oxidative DNA lesions, constantly generated by both endogenous and environmentally induced reactive oxygen species, are removed via the base excision repair pathway. In bacteria, Fpg and Nei DNA glycosylases, belonging to the helix-two-turn-helix (H2TH) structural superfamily, remove oxidised purines and pyrimidines, respectively. Interestingly, the human H2TH family glycosylases, NEIL1, NEIL2 and NEIL3, have been reported to prefer oxidative lesions in DNA bubbles or single-stranded DNA. It had been hypothesised that NEIL2 might be involved in the repair of lesions in transcription bubbles; however, bubble-like structures may appear in other cellular contexts such as displacement loops (D-loops) associated with transcription, recombination or telomere maintenance. The activities of bacterial Fpg and Nei on bubble substrates were not addressed. Also, it is not known whether H2TH enzymes process bubbles containing the third DNA or RNA strand, and how the bubble length and position of the lesion within a bubble affect the excision. We have investigated the removal of 8-oxoguanine (8-oxoG) and 5,6-dihydrouracil (DHU) by Escherichia coli Fpg and Nei and human NEIL1 and NEIL2 from single-strand oligonucleotides, perfect duplexes, bubbles with different numbers of unpaired bases (6-30), bubbles containing the lesion in different positions and D-loops with the third strand made of DNA or RNA. Fpg, NEIL1 and NEIL2 efficiently excised lesions located within bubbles, with NEIL1 and NEIL2 being specific for DHU, and Fpg removing both 8-oxoG and DHU. Nei, in contrast, was significantly active only on DHU located in double-stranded DNA. Fpg and NEIL1 also tolerated the presence of the third strand of either DNA or RNA in D-loops if the lesion was in the single-stranded part, and Fpg, Nei and NEIL1 excised lesions from the double-stranded DNA part of D-loops. The presence of an additional unpaired 5'-tail of DNA or RNA did not affect the activity. No significant position preference for lesions in a 12-mer bubble was found. Overall, the activities of Fpg, NEIL1 and NEIL2 on these non-canonical substrates are consistent with the possibility that these enzymes may participate in the repair in structures arising during transcription or homologous recombination.
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Affiliation(s)
| | - Anton V Endutkin
- Novosibirsk State University, Novosibirsk, Russia.,SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Dmitry O Zharkov
- Novosibirsk State University, Novosibirsk, Russia.,SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
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23
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Schank M, Zhao J, Wang L, Li Z, Cao D, Nguyen LN, Dang X, Khanal S, Nguyen LNT, Thakuri BKC, Ogbu SC, Lu Z, Zhang J, Wu XY, Morrison ZD, El Gazzar M, Ning S, Moorman JP, Yao ZQ. Telomeric injury by KML001 in human T cells induces mitochondrial dysfunction through the p53-PGC-1α pathway. Cell Death Dis 2020; 11:1030. [PMID: 33268822 PMCID: PMC7710715 DOI: 10.1038/s41419-020-03238-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 12/31/2022]
Abstract
Telomere erosion and mitochondrial dysfunction are prominent features of aging cells with progressive declines of cellular functions. Whether telomere injury induces mitochondrial dysfunction in human T lymphocytes, the major component of adaptive host immunity against infection and malignancy, remains unclear. We have recently shown that disruption of telomere integrity by KML001, a telomere-targeting drug, induces T cell senescence and apoptosis via the telomeric DNA damage response (DDR). In this study, we used KML001 to further investigate the role and mechanism of telomere injury in mitochondrial dysregulation in aging T cells. We demonstrate that targeting telomeres by KML001 induces mitochondrial dysfunction, as evidenced by increased mitochondrial swelling and decreased mitochondrial membrane potential, oxidative phosphorylation, mitochondrial DNA content, mitochondrial respiration, oxygen consumption, glycolysis, and ATP energy production. Mechanistically, we found that the KML001-induced telomeric DDR activated p53 signaling, which in turn repressed the expression of peroxisome proliferator-activated receptor-gamma coactivator 1 alpha (PGC-1α) and nuclear respiratory factor 1 (NRF-1), leading to T cell mitochondrial dysfunction. These results, forging a direct link between telomeric and mitochondrial biology, shed new light on the human T cell aging network, and demonstrate that the p53-PGC-1α-NRF-1 axis contributes to mitochondrial dysfunction in the setting of telomeric DDR. This study suggests that targeting this axis may offer an alternative, novel approach to prevent telomere damage-mediated mitochondrial and T cell dysfunctions to combat a wide range of immune aging-associated human diseases.
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Affiliation(s)
- Madison Schank
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, TN, 37614, USA
| | - Juan Zhao
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, TN, 37614, USA
| | - Ling Wang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, TN, 37614, USA
| | - Zhengke Li
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, TN, 37614, USA
| | - Dechao Cao
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, TN, 37614, USA
| | - Lam Nhat Nguyen
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, TN, 37614, USA
| | - Xindi Dang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, TN, 37614, USA
| | - Sushant Khanal
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, TN, 37614, USA
| | - Lam Ngoc Thao Nguyen
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, TN, 37614, USA
| | - Bal Krishna Chand Thakuri
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, TN, 37614, USA
| | - Stella C Ogbu
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, TN, 37614, USA
| | - Zeyuan Lu
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, TN, 37614, USA
| | - Jinyu Zhang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, TN, 37614, USA
| | - Xiao Y Wu
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, TN, 37614, USA
| | - Zheng D Morrison
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, TN, 37614, USA
| | - Mohamed El Gazzar
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
| | - Shunbin Ning
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, TN, 37614, USA
| | - Jonathan P Moorman
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, TN, 37614, USA
- Hepatitis (HCV/HBV/HIV) Program, James H. Quillen VA Medical Center, Department of Veterans Affairs, Johnson City, TN, 37614, USA
| | - Zhi Q Yao
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA.
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, TN, 37614, USA.
- Hepatitis (HCV/HBV/HIV) Program, James H. Quillen VA Medical Center, Department of Veterans Affairs, Johnson City, TN, 37614, USA.
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24
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Kuznetsova AA, Fedorova OS, Kuznetsov NA. Lesion Recognition and Cleavage of Damage-Containing Quadruplexes and Bulged Structures by DNA Glycosylases. Front Cell Dev Biol 2020; 8:595687. [PMID: 33330484 PMCID: PMC7734321 DOI: 10.3389/fcell.2020.595687] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 11/10/2020] [Indexed: 12/22/2022] Open
Abstract
Human telomeres as well as more than 40% of human genes near the promoter regions have been found to contain the sequence that may form a G-quadruplex structure. Other non-canonical DNA structures comprising bulges, hairpins, or bubbles may have a functionally important role during transcription, replication, or recombination. The guanine-rich regions of DNA are hotspots of oxidation that forms 7,8-dihydro-8-oxoguanine, thymine glycol, and abasic sites: the lesions that are handled by the base excision repair pathway. Nonetheless, the features of DNA repair processes in non-canonical DNA structures are still poorly understood. Therefore, in this work, a comparative analysis of the efficiency of the removal of a damaged nucleotide from various G-quadruplexes and bulged structures was performed using endonuclease VIII-like 1 (NEIL1), human 8-oxoguanine-DNA glycosylase (OGG1), endonuclease III (NTH1), and prokaryotic formamidopyrimidine-DNA glycosylase (Fpg), and endonuclease VIII (Nei). All the tested enzymes were able to cleave damage-containing bulged DNA structures, indicating their important role in the repair process when single-stranded DNA and intermediate non–B-form structures such as bubbles and bulges are formed. Nevertheless, our results suggest that the ability to cleave damaged quadruplexes is an intrinsic feature of members of the H2tH structural family, suggesting that these enzymes can participate in the modulation of processes controlled by the formation of quadruplex structures in genomic DNA.
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Affiliation(s)
| | - Olga S Fedorova
- Institute of Chemical Biology and Fundamental Medicine of SB RAS, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Nikita A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine of SB RAS, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
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25
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Kowalczyk P, Madej A, Szymczak M, Ostaszewski R. α-Amidoamids as New Replacements of Antibiotics-Research on the Chosen K12, R2-R4 E. coli Strains. MATERIALS (BASEL, SWITZERLAND) 2020; 13:E5169. [PMID: 33207799 PMCID: PMC7697494 DOI: 10.3390/ma13225169] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/03/2020] [Accepted: 11/12/2020] [Indexed: 01/04/2023]
Abstract
A preliminary study of α-amidoamids as new potential antimicrobial drugs was performed. Special emphasis was placed on selection of structure of α-amidoamids with the highest biological activity against different types of Gram-stained bacteria by lipopolysaccharide (LPS). Herein, Escherichia coli model strains K12 (without LPS in its structure) and R1-R4 (with different length LPS in its structure) were used. The presented work showed that the antibacterial activity of α-amidoamids depends on their structure and affects the LPS of bacteria. Moreover, the influence of various newly synthesized α-amidoamids on bacteria possessing smooth and rought LPS and oxidative damage of plasmid DNA caused by all newly obtained compounds was indicated. The presented studies clearly explain that α-amidoamids can be used as substitutes for antibiotics. The chemical and biological activity of the analysed α-amidoamids was associated with short alkyl chain and different isocyanides molecules in their structure such as: tetr-butyl isocyanide or 2,5-dimethoxybenzyl isocyanide. The observed results are especially important in the case of the increasing resistance of bacteria to various drugs and antibiotics.
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Affiliation(s)
- Paweł Kowalczyk
- Department of Animal Nutrition, The Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Sciences, Instytucka 3, 05-110 Jabłonna, Poland
| | - Arleta Madej
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland;
| | - Mateusz Szymczak
- Department of Molecular Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland;
| | - Ryszard Ostaszewski
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland;
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26
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Caliri AW, Tommasi S, Bates SE, Besaratinia A. Spontaneous and photosensitization-induced mutations in primary mouse cells transitioning through senescence and immortalization. J Biol Chem 2020; 295:9974-9985. [PMID: 32487750 DOI: 10.1074/jbc.ra120.014465] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/02/2020] [Indexed: 01/15/2023] Open
Abstract
To investigate the role of oxidative stress-induced DNA damage and mutagenesis in cellular senescence and immortalization, here we profiled spontaneous and methylene blue plus light-induced mutations in the cII gene from λ phage in transgenic mouse embryonic fibroblasts during the transition from primary culture through senescence and immortalization. Consistent with detection of characteristic oxidized guanine lesions (8-oxodG) in the treated cells, we observed significantly increased relative cII mutant frequency in the treated pre-senescent cells which was augmented in their immortalized counterparts. The predominant mutation type in the treated pre-senescent cells was G:C→T:A transversion, whose frequency was intensified in the treated immortalized cells. Conversely, the prevailing mutation type in the treated immortalized cells was A:T→C:G transversion, with a unique sequence-context specificity, i.e. flanking purines at the 5' end of the mutated nucleotide. This mutation type was also enriched in the treated pre-senescent cells, although to a lower extent. The signature mutation of G:C→T:A transversions in the treated cells accorded with the well-established translesion synthesis bypass caused by 8-oxodG, and the hallmark A:T→C:G transversions conformed to the known replication errors because of oxidized guanine nucleosides (8-OHdGTPs). The distinctive features of photosensitization-induced mutagenesis in the immortalized cells, which were present at attenuated levels, in spontaneously immortalized cells provide insights into the role of oxidative stress in senescence bypass and immortalization. Our results have important implications for cancer biology because oxidized purines in the nucleoside pool can significantly contribute to genetic instability in DNA mismatch repair-defective human tumors.
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Affiliation(s)
- Andrew W Caliri
- Department of Preventive Medicine, USC Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Stella Tommasi
- Department of Preventive Medicine, USC Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Steven E Bates
- Department of Cancer Biology, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | - Ahmad Besaratinia
- Department of Preventive Medicine, USC Keck School of Medicine, University of Southern California, Los Angeles, California, USA
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27
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Dalberto D, Nicolau CC, Garcia ALH, Nordin AP, Grivicich I, Silva JD. Cytotoxic and genotoxic evaluation of cotinine using human neuroblastoma cells (SH-SY5Y). Genet Mol Biol 2020; 43:e20190123. [PMID: 32478795 PMCID: PMC7271658 DOI: 10.1590/1678-4685-gmb-2019-0123] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/11/2019] [Indexed: 02/06/2023] Open
Abstract
Cotinine is the main metabolite of nicotine, which is metabolized in the liver
through a cytochrome P450 enzyme. Different studies point to genetic instability
caused by nicotine, such as single and double DNA strand breaks and micronuclei
formation, but little is known about the effect of cotinine. Therefore, the
present in vitro study assessed the effects of cotinine on cell
viability and DNA damage in SH-SY5Y neuroblastoma cells, as well as genotoxicity
related to oxidative stress mechanisms. Comparisons with nicotine were also
performed. An alkaline comet assay modified by repair endonucleases (FPG, OGG1,
and Endo III) was used to detect oxidized nucleobases. SH-SY5Y neuronal cells
were cultured under standard conditions and exposed for 3 h to different
concentrations of cotinine and nicotine. Cytotoxicity was observed at higher
doses of cotinine and nicotine in the MTT assay. In the trypan blue assay, cells
showed viability above 80% for both compounds. Alkaline comet assay results
demonstrated a significant increase in damage index and frequency for cells
treated with cotinine and nicotine, presenting genotoxicity. The results of the
enzyme-modified comet assay suggest a DNA oxidative damage induced by nicotine.
Unlike other studies, our results demonstrated genotoxicity induced by both
cotinine and nicotine. The similar effects observed for these two pyridine
alkaloids may be due to the similarity of their structures.
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Affiliation(s)
- Daiana Dalberto
- Universidade Luterana do Brasil (ULBRA), Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde - PPGBioSaúde, Laboratório de Toxicologia Genética, Canoas, RS, Brazil
| | - Caroline Cardoso Nicolau
- Universidade Luterana do Brasil (ULBRA), Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde - PPGBioSaúde, Laboratório de Toxicologia Genética, Canoas, RS, Brazil
| | - Ana Leticia Hilario Garcia
- Universidade Luterana do Brasil (ULBRA), Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde - PPGBioSaúde, Laboratório de Toxicologia Genética, Canoas, RS, Brazil.,Universidade Feevale, Programa de Pós-Graduação em Qualidade Ambiental, Laboratório de Ecotoxicologia, Novo Hamburgo, RS, Brazil
| | - Adriane Perachi Nordin
- Universidade Luterana do Brasil (ULBRA), Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde - PPGBioSaúde, Laboratório de Toxicologia Genética, Canoas, RS, Brazil
| | - Ivana Grivicich
- Universidade Luterana do Brasil (ULBRA), Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde - PPGBioSaúde, , Laboratório de Biologia de Cancer, Canoas, RS, Brazil
| | - Juliana da Silva
- Universidade Luterana do Brasil (ULBRA), Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde - PPGBioSaúde, Laboratório de Toxicologia Genética, Canoas, RS, Brazil.,Universidade La Salle, Programa de Pós-Graduação em Saúde e Desenvolvimento Humano, Canoas, RS, Brazil
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28
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Barreto A, Dias A, Duarte B, Pinto E, Almeida A, Trindade T, Soares AMVM, Hylland K, Loureiro S, Oliveira M. Biological effects and bioaccumulation of gold in gilthead seabream (Sparus aurata) - Nano versus ionic form. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 716:137026. [PMID: 32036137 DOI: 10.1016/j.scitotenv.2020.137026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 06/10/2023]
Abstract
The question of whether gold (Au) is more toxic as nanoparticles or in its ionic form remains unclear and controversial. The present work aimed to clarify the effects of 96 h exposure to 4, 80 and 1600 μg·L-1 of 7 nm gold nanoparticles (AuNPs) - (citrate coated (cAuNPs) or polyvinylpyrrolidone coated (PVP-AuNPs)) - and ionic Au (iAu) on gilthead seabream (Sparus aurata). Effects at different levels of biological organization (behaviour, neurotransmission, biotransformation, oxidative stress/damage and genotoxicity) were assessed. cAuNPs induced oxidative stress and damage (lipid peroxidation increase), even at 4 μg·L-1, and reduced the ability of S. aurata to swim against a water flow at 1600 μg·L-1. Exposure to cAuNPs induced more adverse effects than exposure to PVP-AuNPs. All tested concentrations of Au (nano or ionic form) induced DNA breaks and cytogenetic damage in erythrocytes of S. aurata. Generally, iAu induced significantly more effects in fish than the nano form, probably associated with the significantly higher accumulation in the fish tissues. No fish mortality was observed following exposure to AuNPs, but mortality was observed in the group exposed to 1600 μg·L-1 of iAu.
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Affiliation(s)
- A Barreto
- Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal.
| | - A Dias
- Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - B Duarte
- Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - E Pinto
- LAQV/REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal; Department of Environmental Health, School of Health, P.Porto. CISA/Research Center in Environment and Health, 4200-072 Porto, Portugal
| | - A Almeida
- LAQV/REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal
| | - T Trindade
- Departamento de Química & CICECO, Aveiro Instituto de Materiais, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - A M V M Soares
- Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - K Hylland
- Department of Biosciences, University of Oslo, PO Box 1066, N-0316 Oslo, Norway
| | - S Loureiro
- Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - M Oliveira
- Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal
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Pellegri V, Gorbi G, Buschini A. DNA damage detection by Comet Assay on Daphnia magna: Application in freshwater biomonitoring. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 705:135780. [PMID: 31972938 DOI: 10.1016/j.scitotenv.2019.135780] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/04/2019] [Accepted: 11/24/2019] [Indexed: 06/10/2023]
Abstract
Monitoring of water genotoxicity still remains underexploited in risk assessment. The present study aimed at standardizing and evaluating the sensitivity and applicability of the Comet Assay adapted for Daphnia magna in genotoxicological investigations in freshwater environments. Two sampling campaigns (2014-2015) were performed in the watercourses of a pilot basin located in the Parma district (Italy). Fourteen sampling stations with different Ecological Status and/or EBI values were selected, all with a good Chemical Status according to the EU-Water Framework Directive 2000/60. The Alkaline Comet Assay was performed on 48 h-aged daphnids exposed (24 h) to 23 water samples. In parallel, the acute toxicity test was carried out. Daphnids exposed to samples, collected upstream the main watercourses in non-impacted areas, showed low DNA migration (Tail Intensity percentage - TI% - in the range 2.97-13.21), similar to laboratory controls. An increase in genotoxicity (TI% in the range 20-40) proceeding from the mountain towards the plain area was observed, in agreement with the land uses and the ES/EBI values of the stations. The highest genotoxic damage was observed after exposure to samples from watercourses of the minor hydrographic network in the plain area and waterbodies receiving wastewater treatment plant outflows. A modified version of the Comet Assay able to identify the presence of genotoxins inducing DNA oxidative damage, after standardization, was applied to daphnids treated with waters from 4 selected monitoring stations. The presence of oxidative contaminants was detected downstream a wastewater treatment plant outflow. The Comet Assay on D. magna has proven to be sensitive and able to discriminate among differently impacted areas and might be applied routinely. The FPG-Comet proved to be able to highlight the presence of contaminants causing oxidative stress. In our knowledge, this is the first time that Comet Assay on Daphnia magna is successfully applied for freshwater monitoring.
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Affiliation(s)
- Valerio Pellegri
- Department of Chemistry, Life Sciences and Environmental Sustainability, Parco Area delle Scienze 11/a, 43124 Parma, Italy.
| | - Gessica Gorbi
- Department of Chemistry, Life Sciences and Environmental Sustainability, Parco Area delle Scienze 11/a, 43124 Parma, Italy.
| | - Annamaria Buschini
- Department of Chemistry, Life Sciences and Environmental Sustainability, Parco Area delle Scienze 11/a, 43124 Parma, Italy; Centre for Molecular and Translational Oncology-COMT, University of Parma, Parco Area delle Scienze 11/a, 43124 Parma, Italy.
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30
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Gehring AM, Zatopek KM, Burkhart BW, Potapov V, Santangelo TJ, Gardner AF. Biochemical reconstitution and genetic characterization of the major oxidative damage base excision DNA repair pathway in Thermococcus kodakarensis. DNA Repair (Amst) 2020; 86:102767. [PMID: 31841800 PMCID: PMC8061334 DOI: 10.1016/j.dnarep.2019.102767] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/22/2019] [Accepted: 12/04/2019] [Indexed: 11/16/2022]
Abstract
Reactive oxygen species drive the oxidation of guanine to 8-oxoguanine (8oxoG), which threatens genome integrity. The repair of 8oxoG is carried out by base excision repair enzymes in Bacteria and Eukarya, however, little is known about archaeal 8oxoG repair. This study identifies a member of the Ogg-subfamily archaeal GO glycosylase (AGOG) in Thermococcus kodakarensis, an anaerobic, hyperthermophilic archaeon, and delineates its mechanism, kinetics, and substrate specificity. TkoAGOG is the major 8oxoG glycosylase in T. kodakarensis, but is non-essential. In addition to TkoAGOG, the major apurinic/apyrimidinic (AP) endonuclease (TkoEndoIV) required for archaeal base excision repair and cell viability was identified and characterized. Enzymes required for the archaeal oxidative damage base excision repair pathway were identified and the complete pathway was reconstituted. This study illustrates the conservation of oxidative damage repair across all Domains of life.
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Affiliation(s)
| | | | - Brett W Burkhart
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, United States
| | | | - Thomas J Santangelo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, United States
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31
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Kuznetsova AA, Kladova OA, Barthes NPF, Michel BY, Burger A, Fedorova OS, Kuznetsov NA. Comparative Analysis of Nucleotide Fluorescent Analogs for Registration of DNA Conformational Changes Induced by Interaction with Formamidopyrimidine-DNA Glycosylase Fpg. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162019060256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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32
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Safaeipour M, Jauregui J, Castillo S, Bekarian M, Esparza D, Sanchez M, Stemp EDA. Glutathione Directly Intercepts DNA Radicals To Inhibit Oxidative DNA–Protein Cross-Linking Induced by the One-Electron Oxidation of Guanine. Biochemistry 2019; 58:4621-4631. [DOI: 10.1021/acs.biochem.9b00697] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Mary Safaeipour
- Department of Physical Sciences and Mathematics, Mount St. Mary’s University, Los Angeles, California 90049, United States
| | - Juliette Jauregui
- Department of Physical Sciences and Mathematics, Mount St. Mary’s University, Los Angeles, California 90049, United States
| | - Sarah Castillo
- Department of Physical Sciences and Mathematics, Mount St. Mary’s University, Los Angeles, California 90049, United States
| | - Mary Bekarian
- Department of Physical Sciences and Mathematics, Mount St. Mary’s University, Los Angeles, California 90049, United States
| | - Diana Esparza
- Department of Physical Sciences and Mathematics, Mount St. Mary’s University, Los Angeles, California 90049, United States
| | - Maritza Sanchez
- Department of Physical Sciences and Mathematics, Mount St. Mary’s University, Los Angeles, California 90049, United States
| | - Eric D. A. Stemp
- Department of Physical Sciences and Mathematics, Mount St. Mary’s University, Los Angeles, California 90049, United States
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33
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Fang Y, Zou P. Genome-Wide Mapping of Oxidative DNA Damage via Engineering of 8-Oxoguanine DNA Glycosylase. Biochemistry 2019; 59:85-89. [PMID: 31618020 DOI: 10.1021/acs.biochem.9b00782] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The occurrence of 8-oxo-7,8-dihydroguanine (OG) in the genome, as one of the major DNA oxidative damages, has been implicated in an array of biological processes, ranging from mutagenesis to transcriptional regulation. Genome-wide mapping of oxidative damages could shed light on the underlying cellular mechanism. In the present study, we engineered the hOGG1 enzyme, a primary 8-oxoguanine DNA glycosylase, into a guanine oxidation-profiling tool. Our method, called enTRAP-seq, successfully identified more than 1400 guanine oxidation sites in the mouse embryonic fibroblast genome. These OG peaks were enriched in open chromatin regions and regulatory elements, including promoters, 5' untranslated regions, and CpG islands. Collectively, we present a simple and generalizable approach for the genome-wide profiling of DNA damages with high sensitivity and specificity.
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Affiliation(s)
- Yuxin Fang
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education , Peking University , Beijing 100871 , China
| | - Peng Zou
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education , Peking University , Beijing 100871 , China.,Peking-Tsinghua Center for Life Sciences , Peking University , Beijing 100871 , China.,PKU-IDG/McGovern Institute for Brain Research , Peking University , Beijing 100871 , China
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34
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Tsou HH, Ko HT, Chen CT, Wang TW, Lee CH, Liu TY, Wang HT. Betel quid containing safrole enhances metabolic activation of tobacco specific 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 251:13-21. [PMID: 31071628 DOI: 10.1016/j.envpol.2019.04.080] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/03/2019] [Accepted: 04/15/2019] [Indexed: 06/09/2023]
Abstract
Cigarette smoking (CS) and betel quid (BQ) chewing are two known risk factors that have synergistic potential for the enhancing the development of oral squamous cell carcinoma (OSCC) in Taiwan. Most mutagens and carcinogens are metabolically activated by cytochrome P450 (CYP450) to exert their mutagenicity or carcinogenicity. Previous studies have shown that metabolic activation of the tobacco-specific nitrosamine, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), by CYP2A6 activity determines NNK-induced carcinogenesis. In addition, safrole affects cytochrome P450 activity in rodents. However, the effect of BQ safrole on the metabolism of tobacco-specific NNK and its carcinogenicity remains elusive. This study demonstrates that safrole (1 mg/kg/d) induced CYP2A6 activity, reduced urinary 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL) levels, and increased NNK-induced DNA damage, including N7-methylguanine, 8-OH-deoxyguanosine and DNA strand breaks in a Syrian golden hamster model. Furthermore, altered NNK metabolism and increased NNK-induced DNA damage were also observed in healthy subjects with CS and BQ chewing histories compared to healthy subjects with CS histories. In conclusion, BQ containing safrole induced tobacco-specific NNK metabolic activation, resulting in higher NNK-induced genotoxicity. This study provides valuable insight into the synergistic mechanisms of CS- and BQ-induced OSCC.
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Affiliation(s)
- Han-Hsing Tsou
- Institute of Environmental and Occupational Health Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Hsiao-Tung Ko
- Institute of Food Safety and Health Risk Assessment, National Yang-Ming University, Taipei, Taiwan
| | - Chia-Tzu Chen
- Institute of Environmental and Occupational Health Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Tse-Wen Wang
- Institute of Food Safety and Health Risk Assessment, National Yang-Ming University, Taipei, Taiwan
| | - Chien-Hung Lee
- Department of Public Health, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan; Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Tsung-Yun Liu
- Institute of Environmental and Occupational Health Sciences, National Yang-Ming University, Taipei, Taiwan; Institute of Food Safety and Health Risk Assessment, National Yang-Ming University, Taipei, Taiwan
| | - Hsiang-Tsui Wang
- Department of Pharmacology, National Yang-Ming University, Taipei, Taiwan.
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35
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Liang XX, Qian L, Huang RF. Label-free and ultrasensitive electrochemiluminescence detection of oxidative DNA damage using DNA repair enzyme. Electrochim Acta 2019. [DOI: 10.1016/j.electacta.2019.05.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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36
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Endutkin AV, Zharkov DO. Critical Sites of DNA Backbone Integrity for Damaged Base Removal by Formamidopyrimidine-DNA Glycosylase. Biochemistry 2019; 58:2740-2749. [PMID: 31120733 DOI: 10.1021/acs.biochem.9b00134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA glycosylases, the enzymes that initiate base excision DNA repair, recognize damaged bases through a series of precisely orchestrated movements. Most glycosylases sharply kink the DNA axis at the lesion site and extrude the target base from the DNA double helix into the enzyme's active site. Little attention has been paid so far to the role of the physical continuity of the DNA backbone in allowing the required conformational distortion. Here, we analyze base excision by formamidopyrimidine-DNA glycosylase (Fpg) from substrates keeping all phosphates but containing a nick within three nucleotides of the lesion in either DNA strand. Four phosphoester linkages at the damaged nucleotide and two nucleotides 3' to it were essential for Fpg activity, while the breakage of the others, even at the same critical phosphates, had no effect or even stimulated the reaction. Reduction of the likelihood of hydrogen bonding at the nicks by using dideoxynucleotides as their 3'-terminal groups was more detrimental for the activity. All phosphoester bonds in the complementary strand were dispensable for base excision, but nicks close to the orphaned nucleotide caused early termination of damaged strand cleavage. Elastic network analysis of Fpg-DNA structures showed that the vibrational motions of the critical phosphates are strongly correlated, in part due to the presence of the protein. Overall, our results suggest that mechanical forces propagating along the DNA backbone play a critical role in the correct conformational distortion of DNA by Fpg and possibly by other target base-everting DNA glycosylases.
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Affiliation(s)
- Anton V Endutkin
- SB RAS Institute of Chemical Biology and Fundamental Medicine , 8 Lavrentieva Avenue , Novosibirsk 630090 , Russia.,Novosibirsk State University , 2 Pirogova Street , Novosibirsk 630090 , Russia
| | - Dmitry O Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine , 8 Lavrentieva Avenue , Novosibirsk 630090 , Russia.,Novosibirsk State University , 2 Pirogova Street , Novosibirsk 630090 , Russia
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37
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Abstract
7,8-Dihydro-8-oxoguanine (oxoG) is the most abundant oxidative DNA lesion with dual coding properties. It forms both Watson–Crick (anti)oxoG:(anti)C and Hoogsteen (syn)oxoG:(anti)A base pairs without a significant distortion of a B-DNA helix. DNA polymerases bypass oxoG but the accuracy of nucleotide incorporation opposite the lesion varies depending on the polymerase-specific interactions with the templating oxoG and incoming nucleotides. High-fidelity replicative DNA polymerases read oxoG as a cognate base for A while treating oxoG:C as a mismatch. The mutagenic effects of oxoG in the cell are alleviated by specific systems for DNA repair and nucleotide pool sanitization, preventing mutagenesis from both direct DNA oxidation and oxodGMP incorporation. DNA translesion synthesis could provide an additional protective mechanism against oxoG mutagenesis in cells. Several human DNA polymerases of the X- and Y-families efficiently and accurately incorporate nucleotides opposite oxoG. In this review, we address the mutagenic potential of oxoG in cells and discuss the structural basis for oxoG bypass by different DNA polymerases and the mechanisms of the recognition of oxoG by DNA glycosylases and dNTP hydrolases.
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38
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Minko IG, Vartanian VL, Tozaki NN, Linde OK, Jaruga P, Coskun SH, Coskun E, Qu C, He H, Xu C, Chen T, Song Q, Jiao Y, Stone MP, Egli M, Dizdaroglu M, McCullough AK, Lloyd RS. Characterization of rare NEIL1 variants found in East Asian populations. DNA Repair (Amst) 2019; 79:32-39. [PMID: 31100703 DOI: 10.1016/j.dnarep.2019.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 04/30/2019] [Accepted: 05/01/2019] [Indexed: 10/26/2022]
Abstract
The combination of chronic dietary exposure to the fungal toxin, aflatoxin B1 (AFB1), and hepatitis B viral (HBV) infection is associated with an increased risk for early onset hepatocellular carcinomas (HCCs). An in-depth knowledge of the mechanisms driving carcinogenesis is critical for the identification of genetic risk factors affecting the susceptibility of individuals who are HBV infected and AFB1 exposed. AFB1-induced mutagenesis is characterized by G to T transversions. Hence, the DNA repair pathways that function on AFB1-induced DNA adducts or base damage from HBV-induced inflammation are anticipated to have a strong role in limiting carcinogenesis. These pathways define the mutagenic burden in the target tissues and ultimately limit cellular progression to cancer. Murine data have demonstrated that NEIL1 in the DNA base excision repair pathway was significantly more important than nucleotide excision repair relative to elevated risk for induction of HCCs. These data suggest that deficiencies in NEIL1 could contribute to the initiation of HCCs in humans. To investigate this hypothesis, publicly-available data on variant alleles of NEIL1 were analyzed and compared with genome sequencing data from HCC tissues derived from individuals residing in Qidong County (China). Three variant alleles were identified and the corresponding A51V, P68H, and G245R enzymes were characterized for glycosylase activity on genomic DNA containing a spectrum of oxidatively-induced base damage and an oligodeoxynucleotide containing a site-specific AFB1-formamidopyrimidine guanine adduct. Although the efficiency of the P68H variant was modestly decreased, the A51V and G245R variants showed nearly wild-type activities. Consistent with biochemical findings, molecular modeling of these variants demonstrated only slight local structural alterations. However, A51V was highly temperature sensitive suggesting that its biological activity would be greatly reduced. Overall, these studies have direct human health relevance pertaining to genetic risk factors and biochemical pathways previously not recognized as germane to induction of HCCs.
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Affiliation(s)
- Irina G Minko
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, 97239, United States
| | - Vladimir L Vartanian
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, 97239, United States
| | - Naoto N Tozaki
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, 97239, United States
| | - Oskar K Linde
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, 97239, United States
| | - Pawel Jaruga
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, United States
| | - Sanem Hosbas Coskun
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, United States
| | - Erdem Coskun
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, United States
| | - Chunfeng Qu
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Huan He
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Chungui Xu
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Taoyang Chen
- Qidong Liver Cancer Institute & Qidong People's Hospital, Qidong, 226200, Jiangsu Province, China
| | - Qianqian Song
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Yuchen Jiao
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Michael P Stone
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, United States
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, United States
| | - Miral Dizdaroglu
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, United States
| | - Amanda K McCullough
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, 97239, United States; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, 97239, United States
| | - R Stephen Lloyd
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, 97239, United States; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, 97239, United States; Department of Physiology and Pharmacology, Oregon Health & Science University, Portland, OR, 97239, United States.
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39
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Acute and Chronic Exposure of Toluene Induces Genotoxicity in Different Regions of the Brain in Normal and Allergic Mouse Models. Neurotox Res 2019; 36:669-678. [PMID: 30888611 DOI: 10.1007/s12640-019-00024-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/05/2019] [Accepted: 03/07/2019] [Indexed: 10/27/2022]
Abstract
Toluene is a widely used industrial organic solvent and is ubiquitous in our environment. The neurobehavioral and neurotoxic effects of toluene are well recognized; however, its genotoxicity is still under discussion. Toluene biotransformation leads to the generation of reactive oxygen species that cause oxidative stress and DNA damages. Individuals with different immunogenetic backgrounds have different sensitivities to toxic chemical exposure. Previous studies have suggested that allergic stimulation may influence the threshold for toluene sensitivity due to the modulation of neurotrophin-related genes. Therefore, we aimed to investigate toluene-induced genotoxicity in different brain regions following acute and chronic exposure in vivo and to further examine whether allergic stimulation may influence the sensitivity to toluene-induced genotoxicity. In this present study, we found that exposure of toluene induced oxidative DNA damages resulting in genotoxicity in different brain regions including cortex, cerebellum, and hippocampus using comet assay. Higher genotoxicity induced by toluene was observed in the hippocampus of control mice compared to OVA-immunized mice. These results provide evidence that toluene-induced genotoxicity may contribute to its neurotoxicity in different immunogenetic individuals.
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40
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Tang F, Liu S, Li QY, Yuan J, Li L, Wang Y, Yuan BF, Feng YQ. Location analysis of 8-oxo-7,8-dihydroguanine in DNA by polymerase-mediated differential coding. Chem Sci 2019; 10:4272-4281. [PMID: 31015952 PMCID: PMC6460952 DOI: 10.1039/c8sc04946g] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 03/11/2019] [Indexed: 12/17/2022] Open
Abstract
Bsu and Tth DNA polymerases-mediated DNA replication in conjugation with sequencing enables quantitative and location analysis of 8-oxo-7,8-dihydroguanine in DNA.
Accumulating lines of evidence indicate that reactive oxygen species (ROS) are important signalling molecules for various cellular processes. 8-Oxo-7,8-dihydroguanine (OG) is a prominent oxidative modification formed in DNA by ROS. Recently, it has been proposed that OG may have regulatory and possibly epigenetic-like properties in modulating gene expression by interfering with transcription components or affecting the formation of G-quadruplex structures. Deciphering the molecular mechanisms of OG on regulation of gene expression requires uncovering the location of OG on genome. In the current study, we characterized two commercially available DNA polymerases, Bsu DNA polymerase (Bsu Pol) and Tth DNA polymerase (Tth Pol), which can selectively incorporate adenine (A) and cytosine (C) opposite OG, respectively. By virtue of the differential coding properties of Bsu Pol and Tth Pol that can faithfully or error-prone copy a DNA strand carrying OG, we achieved quantitative and single-base resolution analysis of OG in synthesized DNA that carries OG as well as in the G-rich telomeric DNA from HeLa cells. In addition, the parallel analysis of the primer extension products with Bsu Pol and Tth Pol followed by sequencing provided distinct detection of OG in synthesized DNA. Future application of this approach will greatly increase our knowledge of the chemical biology of OG with respect to its epigenetic-like regulatory roles.
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Affiliation(s)
- Feng Tang
- Key Laboratory of Analytical Chemistry for Biology and Medicine , Ministry of Education , Department of Chemistry , Wuhan University , Wuhan 430072 , P. R. China . ; ; Tel: +86-27-68755595
| | - Shan Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine , Ministry of Education , Department of Chemistry , Wuhan University , Wuhan 430072 , P. R. China . ; ; Tel: +86-27-68755595
| | - Qiao-Ying Li
- Key Laboratory of Analytical Chemistry for Biology and Medicine , Ministry of Education , Department of Chemistry , Wuhan University , Wuhan 430072 , P. R. China . ; ; Tel: +86-27-68755595
| | - Jun Yuan
- Department of Chemistry and Environmental Toxicology Graduate Program , University of California , Riverside , CA 92521-0403 , USA
| | - Lin Li
- Department of Chemistry and Environmental Toxicology Graduate Program , University of California , Riverside , CA 92521-0403 , USA
| | - Yinsheng Wang
- Department of Chemistry and Environmental Toxicology Graduate Program , University of California , Riverside , CA 92521-0403 , USA
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine , Ministry of Education , Department of Chemistry , Wuhan University , Wuhan 430072 , P. R. China . ; ; Tel: +86-27-68755595
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine , Ministry of Education , Department of Chemistry , Wuhan University , Wuhan 430072 , P. R. China . ; ; Tel: +86-27-68755595
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41
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Kuchařová M, Hronek M, Rybáková K, Zadák Z, Štětina R, Josková V, Patková A. Comet assay and its use for evaluating oxidative DNA damage in some pathological states. Physiol Res 2019; 68:1-15. [DOI: 10.33549/physiolres.933901] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The comet assay, or single-cell gel electrophoresis (SCGE), is a sensitive, rapid, relatively simple and inexpensive method for detecting DNA strand breaks in individual cells. It is used in a broad variety of applications and as a tool to investigate DNA damage and repair. The sensitivity and specificity of the assay are greatly enhanced if the DNA incubated with an enzyme, whichrecognizes a specific kind of DNA damage. This damage induced by oxidative stress plays a pivotal role in many diseases and in aging. This article is a critical review of the possible application of the comet assay in some pathological states in clinical practice. Most of the studies relate to evaluating the response of an organism to chemotherapy or radiotherapy with statistically significant evidence of DNA damage in patients. Other useful applications have been demonstrated for patients with heart or neurodegenerative diseases. Only a few studies have been published on the use of this method in critically ill patients, although its use would be appropriate. There are also other scenarios where the comet assay could prove to be very useful in the future, such as in predicting the likelihood of certain pathological conditions.
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Affiliation(s)
- M. Kuchařová
- Department of Biophysics and Physical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Czech Republic
| | - M. Hronek
- Department of Biological and Medical Sciences, Faculty of Pharmacy in Hradec Králové, Charles University, Czech Republic
| | - K. Rybáková
- Department of Biological and Medical Sciences, Faculty of Pharmacy in Hradec Králové, Charles University, Czech Republic
| | - Z. Zadák
- Department of Research and Development, University Hospital Hradec Králové, Czech Republic
| | - R. Štětina
- Department of Research and Development, University Hospital Hradec Králové, Czech Republic
| | - V. Josková
- Department of Biological and Medical Sciences, Faculty of Pharmacy in Hradec Králové, Charles University, Czech Republic
| | - A. Patková
- Department of Biological and Medical Sciences, Faculty of Pharmacy in Hradec Králové, Charles University, Czech Republic
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Chondrou V, Trochoutsou K, Panayides A, Efthimiou M, Stephanou G, Demopoulos NA. Combined study on clastogenic, aneugenic and apoptotic properties of doxorubicin in human cells in vitro. JOURNAL OF BIOLOGICAL RESEARCH (THESSALONIKE, GREECE) 2018; 25:17. [PMID: 30338246 PMCID: PMC6180587 DOI: 10.1186/s40709-018-0089-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 09/25/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND Doxorubicin is a widely used anticancer drug due to its broad spectrum of antitumor activity. Various mechanisms have been proposed for its cytostatic activity, including DNA intercalation, topoisomerase II inhibition, generation of free radicals and apoptosis. The present study aims to further clarify the cytostatic activity of doxorubicin by its specific effect on (a) DNA damage, (b) micronucleation and (c) apoptosis, using a combination of different methods and cell systems such as human lymphocytes and HL-60 human leukemic cells. DNA lesions were analyzed by the alkaline comet assay in combination with formamidopyrimidine (Fpg) and human 8-oxoguanine (hOGG1) repair enzymes. Micronucleation was investigated by the Cytokinesis-Block Micronucleus assay (CBMN) in combination with Fluorescence In Situ Hybridization analysis. Impairment on mitotic apparatus was investigated by double immunofluorescence of β- and γ-tubulin. Apoptotic cell frequency was determined by the CBMN cytome assay. Complementary to the above, caspase-3 level was investigated by Western blot. RESULTS It was found that doxorubicin generates DNA breakage induced by oxidative damage in DNA bases, which can be repaired by the Fpg and hOGG1 enzymes. Increased micronucleus frequency was identified mainly through chromosome breakage and, at a lesser extent, through chromosome delay. Analysis of mitotic spindle showed disturbance of chromosome orientation and centrosome duplication and/or separation, leading to aneuploidy. Enhanced frequency of apoptotic leukemic cells was also observed. Caspase-3 seems to be involved in the generation of apoptosis. CONCLUSIONS The aforementioned findings derived from different treatment schedules, doses and time of exposure on primary versus transformed cells extend our knowledge about doxorubicin genotoxicity and contribute to the better understanding of the mechanisms by which doxorubicin induces genotoxic effects on human cells.
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Affiliation(s)
- Vasiliki Chondrou
- Division of Genetics, Cell and Developmental Biology, Department of Biology, University of Patras, 26 504, Patras, Greece
| | - Katerina Trochoutsou
- Division of Genetics, Cell and Developmental Biology, Department of Biology, University of Patras, 26 504, Patras, Greece
| | - Andreas Panayides
- Division of Genetics, Cell and Developmental Biology, Department of Biology, University of Patras, 26 504, Patras, Greece
| | - Maria Efthimiou
- Division of Genetics, Cell and Developmental Biology, Department of Biology, University of Patras, 26 504, Patras, Greece
| | - Georgia Stephanou
- Division of Genetics, Cell and Developmental Biology, Department of Biology, University of Patras, 26 504, Patras, Greece
| | - Nikos A. Demopoulos
- Division of Genetics, Cell and Developmental Biology, Department of Biology, University of Patras, 26 504, Patras, Greece
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Zuin Fantoni N, Molphy Z, Slator C, Menounou G, Toniolo G, Mitrikas G, McKee V, Chatgilialoglu C, Kellett A. Polypyridyl‐Based Copper Phenanthrene Complexes: A New Type of Stabilized Artificial Chemical Nuclease. Chemistry 2018; 25:221-237. [DOI: 10.1002/chem.201804084] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Nicoló Zuin Fantoni
- School of Chemical Sciences and National Institute for Cellular, BiotechnologyDublin City University 9 Glasnevin, Dublin Ireland
| | - Zara Molphy
- School of Chemical Sciences and National Institute for Cellular, BiotechnologyDublin City University 9 Glasnevin, Dublin Ireland
| | - Creina Slator
- School of Chemical Sciences and National Institute for Cellular, BiotechnologyDublin City University 9 Glasnevin, Dublin Ireland
| | - Georgia Menounou
- ISOF-CNR Area della Ricerca di Bologna Via P. Gobetti 101 40129 Bologna Italy
| | - Gianluca Toniolo
- Institute of Nanoscience and Nanotechnology, N.C.S.R. Demokritos Agia Paraskevi Attikis P.O. Box 60037, 15341 Athens Greece
| | - George Mitrikas
- Institute of Nanoscience and Nanotechnology, N.C.S.R. Demokritos Agia Paraskevi Attikis P.O. Box 60037, 15341 Athens Greece
| | - Vickie McKee
- School of Chemical Sciences and National Institute for Cellular, BiotechnologyDublin City University 9 Glasnevin, Dublin Ireland
- Department of Physics, Chemistry and PharmacyUniversity of Southern Denmark Campusvej 55 5230 Odense M Denmark
| | - Chryssostomos Chatgilialoglu
- ISOF-CNR Area della Ricerca di Bologna Via P. Gobetti 101 40129 Bologna Italy
- Institute of Nanoscience and Nanotechnology, N.C.S.R. Demokritos Agia Paraskevi Attikis P.O. Box 60037, 15341 Athens Greece
| | - Andrew Kellett
- School of Chemical Sciences and National Institute for Cellular, BiotechnologyDublin City University 9 Glasnevin, Dublin Ireland
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Yukutake M, Hayashida M, Shioi Aoki N, Kuraoka I. Oligo swapping method for in vitro DNA repair substrate containing a single DNA lesion at a specific site. Genes Environ 2018; 40:23. [PMID: 30459925 PMCID: PMC6231255 DOI: 10.1186/s41021-018-0112-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/12/2018] [Indexed: 11/10/2022] Open
Abstract
Background A wide variety of DNA lesions interfere with replication and transcription, leading to mutations and cell death. DNA repair mechanisms act upon these DNA lesions present in the genomic DNA. To investigate a DNA repair mechanism elaborately, an in vitro DNA repair substrate containing DNA lesions at a specific site is required. Previously, to prepare the substrate, phagemid ssDNA and DNA lesion-harboring oligonucleotides were employed with considerable amounts of DNA polymerase and DNA ligase. However, preparing in vitro DNA repair substrate in general is difficult and labor intensive. Results Here, we modified the construction method of in vitro mismatch repair substrate using a nicking-endonuclease, which produces gap corresponding to the ssDNA in the plasmid DNA, and swaps DNA lesion-containing oligonucleotide upon addition of restriction enzyme and T5 exonuclease. This modified method is able to produce in vitro DNA repair substrates containing adenine:cytosine mismatch basepair, 8-oxoG, and uracil. The DNA repair enzyme, each Fpg, hOGG1 could cleave an 8-oxoG-containing DNA substrate, the mixture of UDG and APE1 could cleave a uracil-containing DNA substrate. Omitting a column purification step, DNA repair substrates were prepared by one-pot synthesis. Conclusions We were able to prepare in vitro DNA repair substrates using this simple method involving restriction enzymes and T5 exonuclease. It is anticipated that this method, termed as "Oligo Swapping Method", will be valuable for understanding the DNA repair machinery.
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Affiliation(s)
- Mika Yukutake
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka, 814-0180 Japan
| | - Mika Hayashida
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka, 814-0180 Japan
| | - Narumi Shioi Aoki
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka, 814-0180 Japan
| | - Isao Kuraoka
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka, 814-0180 Japan
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Hydrogen Peroxide-Induced DNA Damage and Repair through the Differentiation of Human Adipose-Derived Mesenchymal Stem Cells. Stem Cells Int 2018; 2018:1615497. [PMID: 30405718 PMCID: PMC6199883 DOI: 10.1155/2018/1615497] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 06/19/2018] [Accepted: 07/26/2018] [Indexed: 11/18/2022] Open
Abstract
Human adipose-derived mesenchymal stem cells (hADMSCs) are recognized as a potential tool in cell tissue therapy because of their capacity to proliferate and differentiate in vitro. Several studies have addressed their use in regenerative medicine; however, little is known regarding their response to DNA damage and in particular to the reactive oxygen species (ROS) that are present in the microenvironment of implantation. In this study, we used the ROS-inducing agent hydrogen peroxide to explore the responses of (1) hADMSCs and (2) derived terminally differentiated adipocytes to oxidatively generated DNA damage. Using single cell gel electrophoresis, a dose-related increase was found for both DNA breaks and oxidative lesions (formamidopyrimidine DNA glycosylase-sensitive sites) upon exposure of hADMSCs to hydrogen peroxide. DNA repair capacity of hADMSCs was affected in cells exposed to 150 and 200 μM of hydrogen peroxide. An increase in the basal levels of DNA breaks and oxidative DNA lesions was observed through adipocyte differentiation. In addition, hydrogen peroxide-induced DNA damage increased through adipocyte differentiation; DNA repair capacity also decreased. This study is the first follow-up report on DNA repair capacity during adipogenic differentiation. Remarkably, in terminally differentiated adipocytes, DNA breakage repair is abolished while the repair of DNA oxidative lesions remains efficient.
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Endutkin AV, Koptelov SS, Popov AV, Torgasheva NA, Lomzov AA, Tsygankova AR, Skiba TV, Afonnikov DA, Zharkov DO. Residue coevolution reveals functionally important intramolecular interactions in formamidopyrimidine-DNA glycosylase. DNA Repair (Amst) 2018; 69:24-33. [DOI: 10.1016/j.dnarep.2018.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 07/04/2018] [Accepted: 07/04/2018] [Indexed: 10/28/2022]
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Sowlati-Hashjin S, Wetmore SD. Structural Insight into the Discrimination between 8-Oxoguanine Glycosidic Conformers by DNA Repair Enzymes: A Molecular Dynamics Study of Human Oxoguanine Glycosylase 1 and Formamidopyrimidine-DNA Glycosylase. Biochemistry 2018; 57:1144-1154. [PMID: 29320630 DOI: 10.1021/acs.biochem.7b01292] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
hOgg1 and FPG are the primary DNA repair enzymes responsible for removing the major guanine (G) oxidative product, namely, 7,8-dihydro-8-oxoguanine (OG), in humans and bacteria, respectively. While natural G adopts the anti conformation and forms a Watson-Crick pair with cytosine (C), OG can also adopt the syn conformation and form a Hoogsteen pair with adenine (A). hOgg1 removes OG paired with C but is inactive toward the OG:A pair. In contrast, FPG removes OG from OG:C pairs and also exhibits appreciable (although diminished) activity toward OG:A pairs. As a first step toward understanding this difference in activity, we have employed molecular dynamics simulations to examine how the anti and syn conformers of OG are accommodated in the hOgg1 and FPG active sites. When anti-OG is bound, hOgg1 active site residues are properly aligned to initiate catalytic base departure, while geometrical parameters required for the catalytic reaction are not conserved for syn-OG. On the other hand, the FPG catalytic residues are suitably aligned for both OG conformers, with anti-OG being more favorably bound. Thus, our data suggests that the differential ability of hOgg1 and FPG to accommodate the anti- and syn-OG glycosidic conformations is an important factor that contributes to the relative experimental excision rates. Nevertheless, the positions of the nucleophiles with respect to the lesion in the active sites suggest that the reactant complex is poised to initiate catalysis through a similar mechanism for both repair enzymes and supports a recently proposed mechanism in which sugar-ring opening precedes nucleoside deglycosylation.
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Affiliation(s)
- Shahin Sowlati-Hashjin
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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Jayanth N, Puranik M. Mechanism of Discrimination of 8-Oxoguanosine versus Guanosine by Escherichia coli Fpg. J Phys Chem B 2017; 121:5679-5687. [DOI: 10.1021/acs.jpcb.7b00205] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Namrata Jayanth
- National Centre for Biological
Sciences, TIFR, GKVK Campus, Bellary Road, Bangalore 560065, India
| | - Mrinalini Puranik
- National Centre for Biological
Sciences, TIFR, GKVK Campus, Bellary Road, Bangalore 560065, India
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Popov AV, Endutkin AV, Vorobjev YN, Zharkov DO. Molecular dynamics simulation of the opposite-base preference and interactions in the active site of formamidopyrimidine-DNA glycosylase. BMC STRUCTURAL BIOLOGY 2017; 17:5. [PMID: 28482831 PMCID: PMC5422863 DOI: 10.1186/s12900-017-0075-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 04/20/2017] [Indexed: 01/20/2023]
Abstract
Background Formamidopyrimidine-DNA glycosylase (Fpg) removes abundant pre-mutagenic 8-oxoguanine (oxoG) bases from DNA through nucleophilic attack of its N-terminal proline at C1′ of the damaged nucleotide. Since oxoG efficiently pairs with both C and A, Fpg must excise oxoG from pairs with C but not with A, otherwise a mutation occurs. The crystal structures of several Fpg–DNA complexes have been solved, yet no structure with A opposite the lesion is available. Results Here we use molecular dynamic simulation to model interactions in the pre-catalytic complex of Lactococcus lactis Fpg with DNA containing oxoG opposite C or A, the latter in either syn or anti conformation. The catalytic dyad, Pro1–Glu2, was modeled in all four possible protonation states. Only one transition was observed in the experimental reaction rate pH dependence plots, and Glu2 kept the same set of interactions regardless of its protonation state, suggesting that it does not limit the reaction rate. The adenine base opposite oxoG was highly distorting for the adjacent nucleotides: in the more stable syn models it formed non-canonical bonds with out-of-register nucleotides in both the damaged and the complementary strand, whereas in the anti models the adenine either formed non-canonical bonds or was expelled into the major groove. The side chains of Arg109 and Phe111 that Fpg inserts into DNA to maintain its kinked conformation tended to withdraw from their positions if A was opposite to the lesion. The region showing the largest differences in the dynamics between oxoG:C and oxoG:A substrates was unexpectedly remote from the active site, located near the linker joining the two domains of Fpg. This region was also highly conserved among 124 analyzed Fpg sequences. Three sites trapping water molecules through multiple bonds were identified on the protein–DNA interface, apparently helping to maintain enzyme-induced DNA distortion and participating in oxoG recognition. Conclusion Overall, the discrimination against A opposite to the lesion seems to be due to incorrect DNA distortion around the lesion-containing base pair and, possibly, to gross movement of protein domains connected by the linker. Electronic supplementary material The online version of this article (doi:10.1186/s12900-017-0075-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexander V Popov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk, 630090, Russia
| | - Anton V Endutkin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk, 630090, Russia.,Novosibrsk State University, 2 Pirogova St., Novosibirsk, 630090, Russia
| | - Yuri N Vorobjev
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk, 630090, Russia. .,Novosibrsk State University, 2 Pirogova St., Novosibirsk, 630090, Russia.
| | - Dmitry O Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk, 630090, Russia. .,Novosibrsk State University, 2 Pirogova St., Novosibirsk, 630090, Russia.
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