1
|
de Abreu RMF, Brockmann T, Villinger A, Ehlers P, Langer P. Synthesis and properties of 6-alkynyl-5-aryluracils. Beilstein J Org Chem 2024; 20:898-911. [PMID: 38711590 PMCID: PMC11070962 DOI: 10.3762/bjoc.20.80] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/09/2024] [Indexed: 05/08/2024] Open
Abstract
The development of a new and straightforward chemoselective method for the synthesis of uracil-based structures by combining Suzuki-Miyaura and Sonogashira-Hagihara cross-coupling is reported. The methodology was applied to synthesize a series of novel compounds. The tolerance of the combination of different functional groups was tested. The influence of different functional groups on the physical properties was studied by ultraviolet-visible (UV-vis) and fluorescence spectroscopy, providing new insights into the potential applications of uracil-based structures.
Collapse
Affiliation(s)
| | - Till Brockmann
- Universität Rostock, Institut für Chemie, A.-Einstein-Str.3a, 18059 Rostock, Germany
| | - Alexander Villinger
- Universität Rostock, Institut für Chemie, A.-Einstein-Str.3a, 18059 Rostock, Germany
| | - Peter Ehlers
- Universität Rostock, Institut für Chemie, A.-Einstein-Str.3a, 18059 Rostock, Germany
| | - Peter Langer
- Universität Rostock, Institut für Chemie, A.-Einstein-Str.3a, 18059 Rostock, Germany
- Leibniz Institut für Katalyse an der Universität Rostock, A.-Einstein-Str.29a, 18059 Rostock, Germany
| |
Collapse
|
2
|
Odstrcil RE, Dutta P, Liu J. Enhanced Sampling for Conformational Changes and Molecular Mechanisms of Human NTHL1. J Phys Chem Lett 2024; 15:3206-3213. [PMID: 38483510 PMCID: PMC11059236 DOI: 10.1021/acs.jpclett.4c00161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
The functionalities of proteins rely on protein conformational changes during many processes. Identification of the protein conformations and capturing transitions among different conformations are important but extremely challenging in both experiments and simulations. In this work, we develop a machine learning based approach to identify a reaction coordinate that accelerates the exploration of protein conformational changes in molecular simulations. We implement our approach to study the conformational changes of human NTHL1 during DNA repair. Our results identified three distinct conformations: open (stable), closed (unstable), and bundle (stable). The existence of the bundle conformation can rationalize recent experimental observations. Comparison with an NTHL1 mutant demonstrates that a closely packed cluster of positively charged residues in the linker could be a factor to search when screening for genetic abnormalities. Results will lead to a better modulation of the DNA repair pathway to protect against carcinogenesis.
Collapse
Affiliation(s)
- Ryan E. Odstrcil
- School of Mechanical and Materials Engineering, Washington State University, Pullman, Washington 99164, USA
| | - Prashanta Dutta
- School of Mechanical and Materials Engineering, Washington State University, Pullman, Washington 99164, USA
| | - Jin Liu
- School of Mechanical and Materials Engineering, Washington State University, Pullman, Washington 99164, USA
| |
Collapse
|
3
|
Neurauter CG, Pannone M, Sousa MMLD, Wang W, Kuśnierczyk A, Luna L, Sætrom P, Scheffler K, Bjørås M. Enhanced glutathione levels confer resistance to apoptotic and ferroptotic programmed cell death in NEIL DNA glycosylase deficient HAP1 cells. Free Radic Biol Med 2024; 213:470-487. [PMID: 38301978 DOI: 10.1016/j.freeradbiomed.2024.01.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/12/2024] [Accepted: 01/21/2024] [Indexed: 02/03/2024]
Abstract
The NTHL1 and NEIL1-3 DNA glycosylases are major enzymes in the removal of oxidative DNA base lesions, via the base excision repair (BER) pathway. It is expected that lack of these DNA glycosylases activities would render cells vulnerable to oxidative stress, promoting cell death. Intriguingly, we found that single, double, triple, and quadruple DNA glycosylase knockout HAP1 cells are, however, more resistant to oxidative stress caused by genotoxic agents than wild type cells. Furthermore, glutathione depletion in NEIL deficient cells further enhances resistance to cell death induced via apoptosis and ferroptosis. Finally, we observed higher basal level of glutathione and differential expression of NRF2-regulated genes associated with glutathione homeostasis in the NEIL triple KO cells. We propose that lack of NEIL DNA glycosylases causes aberrant transcription and subsequent errors in protein synthesis. This leads to increased endoplasmic reticulum stress and proteotoxic stress. To counteract the elevated intracellular stress, an adaptive response mediated by increased glutathione basal levels, rises in these cells. This study reveals an unforeseen role of NEIL glycosylases in regulation of resistance to oxidative stress, suggesting that modulation of NEIL glycosylase activities is a potential approach to improve the efficacy of e.g. anti-inflammatory therapies.
Collapse
Affiliation(s)
- Christine Gran Neurauter
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, 0424, Norway; Centre for Embryology and Healthy Development, University of Oslo, Oslo, 0373, Norway.
| | - Marco Pannone
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, 0424, Norway; Centre for Embryology and Healthy Development, University of Oslo, Oslo, 0373, Norway; Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), Trondheim, 7491, Norway.
| | - Mirta Mittelstedt Leal de Sousa
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, 0424, Norway; Centre for Embryology and Healthy Development, University of Oslo, Oslo, 0373, Norway; Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), Trondheim, 7491, Norway.
| | - Wei Wang
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), Trondheim, 7491, Norway.
| | - Anna Kuśnierczyk
- Proteomics and Modomics Experimental Core Facility (PROMEC), Norwegian University of Science and Technology (NTNU), Trondheim, 7491, Norway.
| | - Luisa Luna
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, 0424, Norway; Centre for Embryology and Healthy Development, University of Oslo, Oslo, 0373, Norway.
| | - Pål Sætrom
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), Trondheim, 7491, Norway.
| | - Katja Scheffler
- Department of Neurology, St.Olavs University Hospital, Trondheim, 7006, Norway; Department of Neuromedicine and Movement Science (INB), Norwegian University of Science and Technology (NTNU), Trondheim, 7491, Norway.
| | - Magnar Bjørås
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, 0424, Norway; Centre for Embryology and Healthy Development, University of Oslo, Oslo, 0373, Norway; Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), Trondheim, 7491, Norway.
| |
Collapse
|
4
|
Kogay R, Zhaxybayeva O. Co-evolution of gene transfer agents and their alphaproteobacterial hosts. J Bacteriol 2024; 206:e0039823. [PMID: 38240570 PMCID: PMC10883770 DOI: 10.1128/jb.00398-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 12/19/2023] [Indexed: 02/23/2024] Open
Abstract
Gene transfer agents (GTAs) are enigmatic elements that resemble small viruses and are known to be produced during nutritional stress by some bacteria and archaea. The production of GTAs is regulated by quorum sensing, under which a small fraction of the population acts as GTA producers, while the rest becomes GTA recipients. In contrast to canonical viruses, GTAs cannot propagate themselves because they package pieces of the producing cell's genome. In alphaproteobacteria, GTAs are mostly vertically inherited and reside in their hosts' genomes for hundreds of millions of years. While GTAs' ability to transfer genetic material within a population and their long-term preservation suggest an increased fitness of GTA-producing microbes, the associated benefits and type of selection that maintains GTAs are poorly understood. By comparing rates of evolutionary change in GTA genes to the rates in gene families abundantly present across 293 alphaproteobacterial genomes, we detected 59 gene families that likely co-evolve with GTA genes. These gene families are predominantly involved in stress response, DNA repair, and biofilm formation. We hypothesize that biofilm formation enables the physical proximity of GTA-producing cells, limiting GTA-derived benefits only to a group of closely related cells. We further conjecture that the population structure of biofilm-forming sub-populations ensures that the trait of GTA production is maintained despite the inevitable rise of "cheating" genotypes. Because release of GTA particles kills the producing cell, maintenance of GTAs is an exciting example of social evolution in a microbial population.IMPORTANCEGene transfer agents (GTAs) are viruses domesticated by some archaea and bacteria as vehicles for carrying pieces of the host genome. Produced under certain environmental conditions, GTA particles can deliver DNA to neighboring, closely related cells. The function of GTAs remains uncertain. While making GTAs is suicidal for a cell, GTA-encoding genes are widespread in genomes of alphaproteobacteria. Such GTA persistence implies functional benefits but raises questions about how selection maintains this lethal trait. By showing that GTA genes co-evolve with genes involved in stress response, DNA repair, and biofilm formation, we provide support for the hypothesis that GTAs facilitate DNA exchange during the stress conditions and present a model for how GTAs persist in biofilm-forming bacterial populations despite being lethal.
Collapse
Affiliation(s)
- Roman Kogay
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
| | - Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
- Department of Computer Science, Dartmouth College, Hanover, New Hampshire, USA
| |
Collapse
|
5
|
Berfelde J, Hildebrand LS, Kuhlmann L, Fietkau R, Distel LV. FEN1 Inhibition as a Potential Novel Targeted Therapy against Breast Cancer and the Prognostic Relevance of FEN1. Int J Mol Sci 2024; 25:2110. [PMID: 38396787 PMCID: PMC10889347 DOI: 10.3390/ijms25042110] [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: 01/23/2024] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
To improve breast cancer treatment and to enable new strategies for therapeutic resistance, therapeutic targets are constantly being studied. Potential targets are proteins of DNA repair and replication and genomic integrity, such as Flap Endonuclease 1 (FEN1). This study investigated the effects of FEN1 inhibitor FEN1-IN-4 in combination with ionizing radiation on cell death, clonogenic survival, the cell cycle, senescence, doubling time, DNA double-strand breaks and micronuclei in breast cancer cells, breast cells and healthy skin fibroblasts. Furthermore, the variation in the baseline FEN1 level and its influence on treatment prognosis was investigated. The cell lines show specific response patterns in the aspects studied and have heterogeneous baseline FEN1 levels. FEN1-IN-4 has cytotoxic, cytostatic and radiosensitizing effects, expressed through increasing cell death by apoptosis and necrosis, G2M share, senescence, double-strand breaks and a reduced survival fraction. Nevertheless, some cells are less affected by the cytotoxicity and fibroblasts show a rather limited response. In vivo, high FEN1 mRNA expression worsens the prognosis of breast cancer patients. Due to the increased expression in breast cancer tissue, FEN1 could represent a new tumor and prognosis marker and FEN1-IN-4 may serve as a new potent agent in personalized medicine and targeted breast cancer therapy.
Collapse
Affiliation(s)
- Johanna Berfelde
- Department of Radiation Oncology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Laura S. Hildebrand
- Department of Radiation Oncology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-Europäische Metropolregion Nürnberg (CCC ER-EMN), 91054 Erlangen, Germany
| | - Lukas Kuhlmann
- Department of Radiation Oncology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-Europäische Metropolregion Nürnberg (CCC ER-EMN), 91054 Erlangen, Germany
| | - Rainer Fietkau
- Department of Radiation Oncology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-Europäische Metropolregion Nürnberg (CCC ER-EMN), 91054 Erlangen, Germany
| | - Luitpold V. Distel
- Department of Radiation Oncology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-Europäische Metropolregion Nürnberg (CCC ER-EMN), 91054 Erlangen, Germany
| |
Collapse
|
6
|
Caffrey PJ, Eckenroth BE, Burkhart BW, Zatopek KM, McClung CM, Santangelo TJ, Doublié S, Gardner AF. Thermococcus kodakarensis TK0353 is a novel AP lyase with a new fold. J Biol Chem 2024; 300:105503. [PMID: 38013090 PMCID: PMC10731606 DOI: 10.1016/j.jbc.2023.105503] [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: 04/12/2023] [Revised: 11/02/2023] [Accepted: 11/12/2023] [Indexed: 11/29/2023] Open
Abstract
Hyperthermophilic organisms thrive in extreme environments prone to high levels of DNA damage. Growth at high temperature stimulates DNA base hydrolysis resulting in apurinic/apyrimidinic (AP) sites that destabilize the genome. Organisms across all domains have evolved enzymes to recognize and repair AP sites to maintain genome stability. The hyperthermophilic archaeon Thermococcus kodakarensis encodes several enzymes to repair AP site damage including the essential AP endonuclease TK endonuclease IV. Recently, using functional genomic screening, we discovered a new family of AP lyases typified by TK0353. Here, using biochemistry, structural analysis, and genetic deletion, we have characterized the TK0353 structure and function. TK0353 lacks glycosylase activity on a variety of damaged bases and is therefore either a monofunctional AP lyase or may be a glycosylase-lyase on a yet unidentified substrate. The crystal structure of TK0353 revealed a novel fold, which does not resemble other known DNA repair enzymes. The TK0353 gene is not essential for T. kodakarensis viability presumably because of redundant base excision repair enzymes involved in AP site processing. In summary, TK0353 is a novel AP lyase unique to hyperthermophiles that provides redundant repair activity necessary for genome maintenance.
Collapse
Affiliation(s)
| | - Brian E Eckenroth
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, USA
| | - Brett W Burkhart
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | | | | | - Thomas J Santangelo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, USA
| | | |
Collapse
|
7
|
Huang Q, Zhang Y, Hu W, Chen K, Zhang J, Luo Z, Lu C. Characterization of Heat-labile Uracil-DNA Glycosylase from Oncorhynchus mykiss and its Application for Carry-over Contamination Control in RT-qPCR. Protein Pept Lett 2024; 31:169-177. [PMID: 38343045 DOI: 10.2174/0109298665283737240122105923] [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: 10/23/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 06/14/2024]
Abstract
BACKGROUND Heat-labile uracil-DNA glycosylase (HL-UDG) is commonly employed to eliminate carry-over contamination in DNA amplifications. However, the prevailing HL-UDG is markedly inactivated at 50°C, rendering it unsuitable for specific one-step RT-qPCR protocols utilizing reverse transcriptase at an optimal temperature of 42°C. OBJECTIVE This study aimed to explore novel HL-UDG with lower inactivation temperature and for recombinant expression. METHODS The gene encoding an HL-UDG was cloned from the cold-water fish rainbow trout (Oncorhynchus mykiss) and expressed in Escherichia coli with high yield. The thermostability of this enzyme and other enzymatic characteristics were thoroughly examined. The novel HL-UDG was then applied for controlling carry-over contamination in one-step RT-qPCR. RESULTS This recombinantly expressed truncated HL-UDG of rainbow trout (OmUDG) exhibited high amino acids similarity (84.1% identity) to recombinant Atlantic cod UDG (rcUDG) and was easily denatured at 40°C. The optimal pH of OmUDG was 8.0, and the optimal concentrations of both Na+ and K+ were 10 mM. Since its inactivation temperature was lower than that of rcUDG, the OmUDG could be used to eliminate carry-over contamination in one-step RT-qPCR with moderate reverse transcription temperature. CONCLUSION We successfully identified and recombinantly expressed a novel HL-UDG with an inactivation temperature of 40°C. It is suitable for eliminating carry-over contamination in one-step RT-qPCR.
Collapse
Affiliation(s)
- Qingyuan Huang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, 222005, China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Yaqi Zhang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, 222005, China
- Jiangsu Food & Pharmaceutical Science College, Huai'an 223023, China
| | - Wenhao Hu
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, 222005, China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Keqi Chen
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China
- Jiangsu Best Enzymes Biotech Co., Ltd., Lianyungang, 222005, China
| | - Jian Zhang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, 222005, China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Zhidan Luo
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, 222005, China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Chen Lu
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, 222005, China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China
- Jiangsu Best Enzymes Biotech Co., Ltd., Lianyungang, 222005, China
| |
Collapse
|
8
|
Jung KW, Kwon S, Jung JH, Lim S, Bahn YS. Functional Characterization of DNA N-Glycosylase Ogg1 and Ntg1 in DNA Damage Stress of Cryptococcus neoformans. J Microbiol 2023; 61:981-992. [PMID: 38055144 DOI: 10.1007/s12275-023-00092-y] [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: 10/05/2023] [Accepted: 10/31/2023] [Indexed: 12/07/2023]
Abstract
Reactive oxygen species induce DNA strand breaks and DNA oxidation. DNA oxidation leads to DNA mismatches, resulting in mutations in the genome if not properly repaired. Homologous recombination (HR) and non-homologous end-joining (NHEJ) are required for DNA strand breaks, whereas the base excision repair system mainly repairs oxidized DNAs, such as 8-oxoguanine and thymine glycol, by cleaving the glycosidic bond, inserting correct nucleotides, and sealing the gap. Our previous studies revealed that the Rad53-Bdr1 pathway mainly controls DNA strand breaks through the regulation of HR- and NHEJ-related genes. However, the functional roles of genes involved in the base excision repair system remain elusive in Cryptococcus neoformans. In the present study, we identified OGG1 and NTG1 genes in the base excision repair system of C. neoformans, which are involved in DNA oxidation repair. The expression of OGG1 was induced in a Hog1-dependent manner under oxidative stress. On the other hand, the expression of NTG1 was strongly induced by DNA damage stress in a Rad53-independent manner. We demonstrated that the deletion of NTG1, but not OGG1, resulted in elevated susceptibility to DNA damage agents and oxidative stress inducers. Notably, the ntg1Δ mutant showed growth defects upon antifungal drug treatment. Although deletion of OGG1 or NTG1 did not increase mutation rates, the mutation profile of each ogg1Δ and ntg1Δ mutant was different from that of the wild-type strain. Taken together, we found that DNA N-glycosylase Ntg1 is required for oxidative DNA damage stress and antifungal drug resistance in C. neoformans.
Collapse
Affiliation(s)
- Kwang-Woo Jung
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea.
| | - Sunhak Kwon
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Jong-Hyun Jung
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Sangyong Lim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
- Department of Radiation Science, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Yong-Sun Bahn
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| |
Collapse
|
9
|
Sahakian L, Robinson AM, Sahakian L, Stavely R, Kelley MR, Nurgali K. APE1/Ref-1 as a Therapeutic Target for Inflammatory Bowel Disease. Biomolecules 2023; 13:1569. [PMID: 38002251 PMCID: PMC10669584 DOI: 10.3390/biom13111569] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/18/2023] [Accepted: 10/22/2023] [Indexed: 11/26/2023] Open
Abstract
Inflammatory bowel disease (IBD) is characterized by chronic relapsing inflammation of the gastrointestinal tract. The prevalence of IBD is increasing with approximately 4.9 million cases reported worldwide. Current therapies are limited due to the severity of side effects and long-term toxicity, therefore, the development of novel IBD treatments is necessitated. Recent findings support apurinic/apyrimidinic endonuclease 1/reduction-oxidation factor 1 (APE1/Ref-1) as a target in many pathological conditions, including inflammatory diseases, where APE1/Ref-1 regulation of crucial transcription factors impacts significant pathways. Thus, a potential target for a novel IBD therapy is the redox activity of the multifunctional protein APE1/Ref-1. This review elaborates on the status of conventional IBD treatments, the role of an APE1/Ref-1 in intestinal inflammation, and the potential of a small molecule inhibitor of APE1/Ref-1 redox activity to modulate inflammation, oxidative stress response, and enteric neuronal damage in IBD.
Collapse
Affiliation(s)
- Lauren Sahakian
- Institute for Health & Sport, Victoria University, Melbourne, VIC 3021, Australia; (L.S.); (A.M.R.)
| | - Ainsley M. Robinson
- Institute for Health & Sport, Victoria University, Melbourne, VIC 3021, Australia; (L.S.); (A.M.R.)
| | - Linda Sahakian
- Department of Medicine Western Health, The University of Melbourne, Melbourne, VIC 3010, Australia; (L.S.); (R.S.)
| | - Rhian Stavely
- Department of Medicine Western Health, The University of Melbourne, Melbourne, VIC 3010, Australia; (L.S.); (R.S.)
- Department of Pediatric Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Mark R. Kelley
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Kulmira Nurgali
- Institute for Health & Sport, Victoria University, Melbourne, VIC 3021, Australia; (L.S.); (A.M.R.)
- Department of Medicine Western Health, The University of Melbourne, Melbourne, VIC 3010, Australia; (L.S.); (R.S.)
- Regenerative Medicine and Stem Cells Program, Australian Institute for Musculoskeletal Science (AIMSS), Melbourne, VIC 3021, Australia
| |
Collapse
|
10
|
Kim M, Jang HJ, Baek SY, Choi KJ, Han DH, Sung JS. Regulation of base excision repair during adipogenesis and osteogenesis of bone marrow-derived mesenchymal stem cells. Sci Rep 2023; 13:16384. [PMID: 37773206 PMCID: PMC10542337 DOI: 10.1038/s41598-023-43737-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 09/27/2023] [Indexed: 10/01/2023] Open
Abstract
Bone marrow-derived human mesenchymal stem cells (hMSCs) can differentiate into various lineages, such as chondrocytes, adipocytes, osteoblasts, and neuronal lineages. It has been shown that the high-efficiency DNA-repair capacity of hMSCs is decreased during their differentiation. However, the underlying its mechanism during adipogenesis and osteogenesis is unknown. Herein, we investigated how alkyl-damage repair is modulated during adipogenic and osteogenic differentiation, especially focusing on the base excision repair (BER) pathway. Response to an alkylation agent was assessed via quantification of the double-strand break (DSB) foci and activities of BER-related enzymes during differentiation in hMSCs. Adipocytes showed high resistance against methyl methanesulfonate (MMS)-induced alkyl damage, whereas osteoblasts were more sensitive than hMSCs. During the differentiation, activities, and protein levels of uracil-DNA glycosylase were found to be regulated. In addition, ligation-related proteins, such as X-ray repair cross-complementing protein 1 (XRCC1) and DNA polymerase β, were upregulated in adipocytes, whereas their levels and recruitment declined during osteogenesis. These modulations of BER enzyme activity during differentiation influenced DNA repair efficiency and the accumulation of DSBs as repair intermediates in the nucleus. Taken together, we suggest that BER enzymatic activity is regulated in adipogenic and osteogenic differentiation and these alterations in the BER pathway led to different responses to alkyl damage from those in hMSCs.
Collapse
Affiliation(s)
- Min Kim
- Department of Life Science, Dongguk University-Seoul, Biomedi Campus, 32 Dongguk-ro, Ilsandong-gu, Goyang, Gyeonggi-do, 10326, Republic of Korea
| | - Hyun-Jin Jang
- Department of Life Science, Dongguk University-Seoul, Biomedi Campus, 32 Dongguk-ro, Ilsandong-gu, Goyang, Gyeonggi-do, 10326, Republic of Korea
| | - Song-Yi Baek
- Department of Life Science, Dongguk University-Seoul, Biomedi Campus, 32 Dongguk-ro, Ilsandong-gu, Goyang, Gyeonggi-do, 10326, Republic of Korea
| | - Kyung-Jin Choi
- Department of Life Science, Dongguk University-Seoul, Biomedi Campus, 32 Dongguk-ro, Ilsandong-gu, Goyang, Gyeonggi-do, 10326, Republic of Korea
| | - Dong-Hee Han
- Department of Life Science, Dongguk University-Seoul, Biomedi Campus, 32 Dongguk-ro, Ilsandong-gu, Goyang, Gyeonggi-do, 10326, Republic of Korea
| | - Jung-Suk Sung
- Department of Life Science, Dongguk University-Seoul, Biomedi Campus, 32 Dongguk-ro, Ilsandong-gu, Goyang, Gyeonggi-do, 10326, Republic of Korea.
| |
Collapse
|
11
|
Kladova OA, Tyugashev TE, Mikushina ES, Kuznetsov NA, Novopashina DS, Kuznetsova AA. The Activity of Natural Polymorphic Variants of Human DNA Polymerase β Having an Amino Acid Substitution in the Transferase Domain. Cells 2023; 12:cells12091300. [PMID: 37174699 PMCID: PMC10177036 DOI: 10.3390/cells12091300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/26/2023] [Accepted: 04/29/2023] [Indexed: 05/15/2023] Open
Abstract
To maintain the integrity of the genome, there is a set of enzymatic systems, one of which is base excision repair (BER), which includes sequential action of DNA glycosylases, apurinic/apyrimidinic endonucleases, DNA polymerases, and DNA ligases. Normally, BER works efficiently, but the enzymes themselves (whose primary function is the recognition and removal of damaged bases) are subject to amino acid substitutions owing to natural single-nucleotide polymorphisms (SNPs). One of the enzymes in BER is DNA polymerase β (Polβ), whose function is to fill gaps in DNA with complementary dNMPs. It is known that many SNPs can cause an amino acid substitution in this enzyme and a significant decrease in the enzymatic activity. In this study, the activity of four natural variants of Polβ, containing substitution E154A, G189D, M236T, or R254I in the transferase domain, was analyzed using molecular dynamics simulations and pre-steady-state kinetic analyses. It was shown that all tested substitutions lead to a significant reduction in the ability to form a complex with DNA and with incoming dNTP. The G189D substitution also diminished Polβ catalytic activity. Thus, a decrease in the activity of studied mutant forms may be associated with an increased risk of damage to the genome.
Collapse
Affiliation(s)
- Olga A Kladova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Timofey E Tyugashev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Elena S Mikushina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Nikita A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Daria S Novopashina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Aleksandra A Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| |
Collapse
|
12
|
Bowhead NEIL1: molecular cloning, characterization, and enzymatic properties. Biochimie 2023; 206:136-149. [PMID: 36334646 DOI: 10.1016/j.biochi.2022.10.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/19/2022] [Accepted: 10/25/2022] [Indexed: 11/08/2022]
Abstract
Nei Like DNA Glycosylase 1 (NEIL1) is a DNA glycosylase, which specifically processes oxidative DNA damage by initiating base excision repair. NEIL1 recognizes and removes bases, primarily oxidized pyrimidines, which have been damaged by endogenous oxidation or exogenous mutagenic agents. NEIL1 functions through a combined glycosylase/AP (apurinic/apyrimidinic)-lyase activity, whereby it cleaves the N-glycosylic bond between the DNA backbone and the damaged base via its glycosylase activity and hydrolysis of the DNA backbone through beta-delta elimination due to its AP-lyase activity. In our study we investigated our hypothesis proposing that the cancer resistance of the bowhead whale can be associated with a better DNA repair with NEIL1 being upregulated or more active. Here, we report the molecular cloning and characterization of three transcript variants of bowhead whale NEIL1 of which two were homologous to human transcripts. In addition, a novel NEIL1 transcript variant was found. A differential expression of NEIL mRNA was detected in bowhead eye, liver, kidney, and muscle. The A-to-I editing of NEIL1 mRNA was shown to be conserved in the bowhead and two adenosines in the 242Lys codon were subjected to editing. A mass spectroscopy analysis of liver and eye tissue failed to demonstrate the existence of a NEIL1 isoform originating from RNA editing. Recombinant bowhead and human NEIL1 were expressed in E. coli and assayed for enzymatic activity. Both bowhead and human recombinant NEIL1 catalyzed, with similar efficiency, the removal of a 5-hydroxyuracil lesion in a DNA bubble structure. Hence, these results do not support our hypothesis but do not refute the hypothesis either.
Collapse
|
13
|
Ahmad S, Tan M, Hamid S. DNA repair mechanisms: Exploring potentials of nutraceutical. J Funct Foods 2023. [DOI: 10.1016/j.jff.2023.105415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
|
14
|
Du J, Liu Y, Lu L, Shi J, Xu L, Li Q, Cheng X, Chen J, Zhang X. Accumulation of DNA damage alters microRNA gene transcription in Arabidopsis thaliana. BMC PLANT BIOLOGY 2022; 22:576. [PMID: 36503409 PMCID: PMC9743578 DOI: 10.1186/s12870-022-03951-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) and other epigenetic modifications play fundamental roles in all eukaryotic biological processes. DNA damage repair is a key process for maintaining the genomic integrity of different organisms exposed to diverse stresses. However, the reaction of miRNAs in the DNA damage repair process is unclear. RESULTS In this study, we found that the simultaneous mutation of zinc finger DNA 3'-phosphoesterase (ZDP) and AP endonuclease 2 (APE2), two genes that play overlapping roles in active DNA demethylation and base excision repair (BER), led to genome-wide alteration of miRNAs. The transcripts of newly transcribed miRNA-encoding genes (MIRs) decreased significantly in zdp/ape2, indicating that the mutation of ZDP and APE2 affected the accumulation of miRNAs at the transcriptional level. In addition, the introduction of base damage with the DNA-alkylating reagent methyl methanesulfonate (MMS) accelerated the reduction of miRNAs in zdp/ape2. Further mutation of FORMAMIDOPYRIMIDINE DNA GLYCOSYLASE (FPG), a bifunctional DNA glycosylase/lyase, rescued the accumulation of miRNAs in zdp/ape2, suggesting that the accumulation of DNA damage repair intermediates induced the transcriptional repression of miRNAs. CONCLUSIONS Our investigation indicates that the accumulation of DNA damage repair intermediates inhibit miRNAs accumulation by inhibiting MIR transcriptions.
Collapse
Affiliation(s)
- Juan Du
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lu Lu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jianfei Shi
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Longqian Xu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Department of Life Sciences, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Qi Li
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaofei Cheng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region of Chinese Education Ministry, College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China
| | - Jinfeng Chen
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xiaoming Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
15
|
Ulhusna A, Murata A, Nakatani K. Inhibitory Effects of Mismatch Binding Molecules on the Repair Reaction of Uracil-Containing DNA. Biochemistry 2022; 61:2522-2530. [PMID: 36250600 DOI: 10.1021/acs.biochem.2c00344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The stable R-loop formed during transcription induces enzyme-mediated deamination of cytosine, and the uracil in the DNA produced activates the base excision repair (BER) pathway. DNA cleavage involved in the BER pathway is thought to be one of the possible causes of trinucleotide repeat instability. Here, we performed an in vitro assay to investigate the effect of a DNA-binding small molecule, naphthyridine carbamate dimer (NCD), on BER enzyme reactions. The gel electrophoretic mobility shift assay (EMSA) and thermal melting analysis revealed the binding of NCD to a 5'-XGG-3'/5'-XGG-3' triad (X = C or U or apurinic/apyrimidinic site), which is a mimic of a BER enzyme substrate. Polyacrylamide gel electrophoresis (PAGE) of the reaction products of these substrates with hSMUG1 and APE1 enzymes in the presence of NCD showed that NCD interfered with the repair reaction in the 5'-XGG-3'/5'-XGG-3' triad. These findings would broaden the potential of small molecules in modulating trinucleotide repeat instability.
Collapse
Affiliation(s)
- Anisa Ulhusna
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Asako Murata
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| |
Collapse
|
16
|
Bellamri M, Walmsley SJ, Brown C, Brandt K, Konorev D, Day A, Wu CF, Wu MT, Turesky RJ. DNA Damage and Oxidative Stress of Tobacco Smoke Condensate in Human Bladder Epithelial Cells. Chem Res Toxicol 2022; 35:1863-1880. [PMID: 35877975 PMCID: PMC9665352 DOI: 10.1021/acs.chemrestox.2c00153] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Smoking is a major risk factor for bladder cancer (BC), with up to 50% of BC cases being attributed to smoking. There are 70 known carcinogens in tobacco smoke; however, the principal chemicals responsible for BC remain uncertain. The aromatic amines 4-aminobiphenyl (4-ABP) and 2-naphthylamine (2-NA) are implicated in BC pathogenesis of smokers on the basis of the elevated BC risk in factory workers exposed to these chemicals. However, 4-ABP and 2-NA only occur at several nanograms per cigarette and may be insufficient to induce BC. In contrast, other genotoxicants, including acrolein, occur at 1000-fold or higher levels in tobacco smoke. There is limited data on the toxicological effects of tobacco smoke in human bladder cells. We have assessed the cytotoxicity, oxidative stress, and DNA damage of tobacco smoke condensate (TSC) in human RT4 bladder cells. TSC was fractionated by liquid-liquid extraction into an acid-neutral fraction (NF), containing polycyclic aromatic hydrocarbons (PAHs), nitro-PAHs, phenols, and aldehydes, and a basic fraction (BF) containing aromatic amines, heterocyclic aromatic amines, and N-nitroso compounds. The TSC and NF induced a time- and concentration-dependent cytotoxicity associated with oxidative stress, lipid peroxide formation, glutathione (GSH) depletion, and apurinic/apyrimidinic (AP) site formation, while the BF showed weak effects. LC/MS-based metabolomic approaches showed that TSC and NF altered GSH biosynthesis pathways and induced more than 40 GSH conjugates. GSH conjugates of several hydroquinones were among the most abundant conjugates. RT4 cell treatment with synthetic hydroquinones and cresol mixtures at levels present in tobacco smoke accounted for most of the TSC-induced cytotoxicity and the AP sites formed. GSH conjugates of acrolein, methyl vinyl ketone, and crotonaldehyde levels also increased owing to TSC-induced oxidative stress. Thus, TSC is a potent toxicant and DNA-damaging agent, inducing deleterious effects in human bladder cells at concentrations of <1% of a cigarette in cell culture media.
Collapse
Affiliation(s)
- Madjda Bellamri
- Masonic Cancer Center, University of Minnesota, MN 55455
- Department of Medicinal Chemistry, University of Minnesota, MN 55455
| | - Scott J. Walmsley
- Masonic Cancer Center, University of Minnesota, MN 55455
- Division of Biostatistics, Institute of Health Informatics, University of Minnesota, MN 55455
| | - Christina Brown
- Masonic Cancer Center, University of Minnesota, MN 55455
- Department of Medicinal Chemistry, University of Minnesota, MN 55455
| | - Kyle Brandt
- Masonic Cancer Center, University of Minnesota, MN 55455
- Department of Medicinal Chemistry, University of Minnesota, MN 55455
| | - Dmitri Konorev
- Masonic Cancer Center, University of Minnesota, MN 55455
- Department of Medicinal Chemistry, University of Minnesota, MN 55455
| | - Abderrahman Day
- Masonic Cancer Center, University of Minnesota, MN 55455
- Department of Medicinal Chemistry, University of Minnesota, MN 55455
| | - Chia-Fang Wu
- Department of Environmental and Occupational Medicine, Kaohsiung Medical University, CS Building, 100 Shih-Chuan 1st Road, Kaohsiung, Taiwan
| | - Ming Tsang Wu
- Department of Environmental and Occupational Medicine, Kaohsiung Medical University, CS Building, 100 Shih-Chuan 1st Road, Kaohsiung, Taiwan
| | - Robert J. Turesky
- Masonic Cancer Center, University of Minnesota, MN 55455
- Department of Medicinal Chemistry, University of Minnesota, MN 55455
| |
Collapse
|
17
|
Malinowska K, Bukowska B, Piwoński I, Foksiński M, Kisielewska A, Zarakowska E, Gackowski D, Sicińska P. Polystyrene nanoparticles: the mechanism of their genotoxicity in human peripheral blood mononuclear cells. Nanotoxicology 2022; 16:791-811. [PMID: 36427221 DOI: 10.1080/17435390.2022.2149360] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Plastic nanoparticles are widely spread in the biosphere, but health risk associated with their effect on the human organism has not yet been assessed. The purpose of this study was to determine the genotoxic potential of non-functionalized polystyrene nanoparticles (PS-NPs) of different diameters of 29, 44, and 72 nm in human peripheral blood mononuclear cells (PBMCs) (in vitro). To select non-cytotoxic concentrations of tested PS-NPs, we analyzed metabolic activity of PBMCs incubated with these particles in concentrations ranging from 0.001 to 1000 µg/mL. Then, PS-NPs were used in concentrations from 0.0001 to 100 μg/mL and incubated with tested cells for 24 h. Physico-chemical properties of PS-NPs in media and suspension were analyzed using dynamic light scattering (DLS), atomic force microscopy (AFM), scanning electron microscopy (SEM) and zeta potential. For the first time, we investigated the mechanism of genotoxic action of PS-NPs based on detection of single/double DNA strand-breaks and 8-oxo-2'-deoxyguanosine (8-oxodG) formation, as well as determination of oxidative modification of purines and pyrimidines and repair efficiency of DNA damage. Obtained results have shown that PS-NPs caused a decrease in PBMCs metabolic activity, increased single/double-strand break formation, oxidized purines and pyrimidines and increased 8oxodG levels. The resulting damage was completely repaired in the case of the largest PS-NPs. It was also found that extent of genotoxic changes in PBMCs depended on the size of tested particles and their ζ-potential value.
Collapse
Affiliation(s)
- Kinga Malinowska
- Department of Biophysics of Environmental Pollution, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Bożena Bukowska
- Department of Biophysics of Environmental Pollution, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Ireneusz Piwoński
- Department of Materials Technology and Chemistry, Faculty of Chemistry, University of Lodz, Lodz, Poland
| | - Marek Foksiński
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Aneta Kisielewska
- Department of Materials Technology and Chemistry, Faculty of Chemistry, University of Lodz, Lodz, Poland
| | - Ewelina Zarakowska
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Daniel Gackowski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Paulina Sicińska
- Department of Biophysics of Environmental Pollution, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| |
Collapse
|
18
|
Oxidative Stress, Genomic Integrity, and Liver Diseases. Molecules 2022; 27:molecules27103159. [PMID: 35630636 PMCID: PMC9147071 DOI: 10.3390/molecules27103159] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 02/04/2023] Open
Abstract
Excess reactive oxygen species production and free radical formation can lead to oxidative stress that can damage cells, tissues, and organs. Cellular oxidative stress is defined as the imbalance between ROS production and antioxidants. This imbalance can lead to malfunction or structure modification of major cellular molecules such as lipids, proteins, and DNAs. During oxidative stress conditions, DNA and protein structure modifications can lead to various diseases. Various antioxidant-specific gene expression and signal transduction pathways are activated during oxidative stress to maintain homeostasis and to protect organs from oxidative injury and damage. The liver is more vulnerable to oxidative conditions than other organs. Antioxidants, antioxidant-specific enzymes, and the regulation of the antioxidant responsive element (ARE) genes can act against chronic oxidative stress in the liver. ARE-mediated genes can act as the target site for averting/preventing liver diseases caused by oxidative stress. Identification of these ARE genes as markers will enable the early detection of liver diseases caused by oxidative conditions and help develop new therapeutic interventions. This literature review is focused on antioxidant-specific gene expression upon oxidative stress, the factors responsible for hepatic oxidative stress, liver response to redox signaling, oxidative stress and redox signaling in various liver diseases, and future aspects.
Collapse
|
19
|
Xie B, Luo A. Nucleic Acid Sensing Pathways in DNA Repair Targeted Cancer Therapy. Front Cell Dev Biol 2022; 10:903781. [PMID: 35557952 PMCID: PMC9089908 DOI: 10.3389/fcell.2022.903781] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/08/2022] [Indexed: 12/24/2022] Open
Abstract
The repair of DNA damage is a complex process, which helps to maintain genome fidelity, and the ability of cancer cells to repair therapeutically DNA damage induced by clinical treatments will affect the therapeutic efficacy. In the past decade, great success has been achieved by targeting the DNA repair network in tumors. Recent studies suggest that DNA damage impacts cellular innate and adaptive immune responses through nucleic acid-sensing pathways, which play essential roles in the efficacy of DNA repair targeted therapy. In this review, we summarize the current understanding of the molecular mechanism of innate immune response triggered by DNA damage through nucleic acid-sensing pathways, including DNA sensing via the cyclic GMP-AMP synthase (cGAS), Toll-like receptor 9 (TLR9), absent in melanoma 2 (AIM2), DNA-dependent protein kinase (DNA-PK), and Mre11-Rad50-Nbs1 complex (MRN) complex, and RNA sensing via the TLR3/7/8 and retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs). Furthermore, we will focus on the recent developments in the impacts of nucleic acid-sensing pathways on the DNA damage response (DDR). Elucidating the DDR-immune response interplay will be critical to harness immunomodulatory effects to improve the efficacy of antitumor immunity therapeutic strategies and build future therapeutic approaches.
Collapse
Affiliation(s)
- Bingteng Xie
- School of Life Science, Beijing Institute of Technology, Beijing, China.,Key Laboratory of Molecular Medicine and Biological Diagnosis and Treatment, Beijing Institute of Technology, Ministry of Industry and Information Technology, Beijing, China
| | - Aiqin Luo
- School of Life Science, Beijing Institute of Technology, Beijing, China.,Key Laboratory of Molecular Medicine and Biological Diagnosis and Treatment, Beijing Institute of Technology, Ministry of Industry and Information Technology, Beijing, China
| |
Collapse
|
20
|
Kapoor I, Shaw A, Naha A, Emam EAF, Varshney U. Role of the nucleotide excision repair pathway proteins (UvrB and UvrD2) in recycling UdgB, a base excision repair enzyme in Mycobacterium smegmatis. DNA Repair (Amst) 2022; 113:103316. [PMID: 35306347 DOI: 10.1016/j.dnarep.2022.103316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/30/2022] [Accepted: 03/02/2022] [Indexed: 11/24/2022]
Abstract
Cross-talks between DNA repair pathways are emerging as a crucial strategy in the maintenance of the genomic integrity. A double-stranded (ds) DNA specific DNA glycosylase, UdgB is known to excise uracil, hypoxanthine and ethenocytosine. We earlier showed that Mycobacterium smegmatis (Msm) UdgB stays back on the AP-sites it generates in the DNA upon excision of the damaged bases. Here, we show that in an Msm strain deleted for a nucleotide excision repair (NER) protein, UvrB (uvrB-), UdgB expression is toxic, and its deletion from the genome (udgB-) rescues the strain from the genotoxic stress. However, UdgB bound AP-site is not a direct substrate for NER in vitro. We show that UvrD2 and UvrB, known helicases with single-stranded (ss) DNA translocase activity, facilitate recycling of UdgB from AP-DNA. Our studies reveal that the helicases play an important role in exposing the AP-sites in DNA and make them available for further repair.
Collapse
Affiliation(s)
- Indu Kapoor
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Abhirup Shaw
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Arindam Naha
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Elhassan Ali Fathi Emam
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India.
| |
Collapse
|
21
|
Chakraborty A, Tapryal N, Islam A, Mitra S, Hazra T. Transcription coupled base excision repair in mammalian cells: So little is known and so much to uncover. DNA Repair (Amst) 2021; 107:103204. [PMID: 34390916 DOI: 10.1016/j.dnarep.2021.103204] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/06/2021] [Accepted: 08/03/2021] [Indexed: 12/31/2022]
Abstract
Oxidized bases in the genome has been implicated in various human pathologies, including cancer, aging and neurological diseases. Their repair is initiated with excision by DNA glycosylases (DGs) in the base excision repair (BER) pathway. Among the five oxidized base-specific human DGs, OGG1 and NTH1 preferentially excise oxidized purines and pyrimidines, respectively, while NEILs remove both oxidized purines and pyrimidines. However, little is known about why cells possess multiple DGs with overlapping substrate specificities. Studies of the past decades revealed that some DGs are involved in repair of oxidized DNA base lesions in the actively transcribed regions. Preferential removal of lesions from the transcribed strands of active genes, called transcription-coupled repair (TCR), was discovered as a distinct sub-pathway of nucleotide excision repair; however, such repair of oxidized DNA bases had not been established until our recent demonstration of NEIL2's role in TC-BER of the nuclear genome. We have shown that NEIL2 forms a distinct transcriptionally active, repair proficient complex. More importantly, we for the first time reconstituted TC-BER using purified components. These studies are important for characterizing critical requirement for the process. However, because NEIL2 cannot remove all types of oxidized bases, it is unlikely to be the only DNA glycosylase involved in TC-BER. Hence, we postulate TC-BER process to be universally involved in maintaining the functional integrity of active genes, especially in post-mitotic, non-growing cells. We further postulate that abnormal bases (e.g., uracil), and alkylated and other small DNA base adducts are also repaired via TC-BER. In this review, we have provided an overview of the various aspects of TC-BER in mammalian cells with the hope of generating significant interest of many researchers in the field. Further studies aimed at better understanding the mechanistic aspects of TC-BER could help elucidate the linkage of TC-BER deficiency to various human pathologies.
Collapse
Affiliation(s)
- Anirban Chakraborty
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Nisha Tapryal
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Azharul Islam
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Sankar Mitra
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Tapas Hazra
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA.
| |
Collapse
|
22
|
Xie Y, Karki CB, Chen J, Liu D, Li L. Computational Study on DNA Repair: The Roles of Electrostatic Interactions Between Uracil-DNA Glycosylase (UDG) and DNA. Front Mol Biosci 2021; 8:718587. [PMID: 34422909 PMCID: PMC8377759 DOI: 10.3389/fmolb.2021.718587] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 06/30/2021] [Indexed: 11/28/2022] Open
Abstract
Uracil-DNA glycosylase (UDG) is one of the most important base excision repair (BER) enzymes involved in the repair of uracil-induced DNA lesion by removing uracil from the damaged DNA. Uracil in DNA may occur due to cytosine deamination or deoxy uridine monophosphate (dUMP) residue misincorporation during DNA synthesis. Medical evidences show that an abnormal expression of UDG is related to different types of cancer, including colorectal cancer, lung cancer, and liver cancer. Therefore, the research of UDG is crucial in cancer treatment and prevention as well as other clinical activities. Here we applied multiple computational methods to study UDG in several perspectives: Understanding the stability of the UDG enzyme in different pH conditions; studying the differences in charge distribution between the pocket side and non-pocket side of UDG; analyzing the field line distribution at the interfacial area between UDG and DNA; and performing electrostatic binding force analyses of the special region of UDG (pocket area) and the target DNA base (uracil) as well as investigating the charged residues on the UDG binding pocket and binding interface. Our results show that the whole UDG binding interface, and not the UDG binding pocket area alone, provides the binding attractive force to the damaged DNA at the uracil base.
Collapse
Affiliation(s)
- Yixin Xie
- Computational Science Program, University of Texas at El Paso, El Paso, TX, United States
| | - Chitra B Karki
- Computational Science Program, University of Texas at El Paso, El Paso, TX, United States
| | - Jiawei Chen
- Computer Science Program, Santa Monica College, Santa Monica, CA, United States
| | - Dongfang Liu
- Department of Computer Engineering, Rochester Institute of Technology, Rochester, NY, United States
| | - Lin Li
- Computational Science Program, University of Texas at El Paso, El Paso, TX, United States.,Department of Physics, University of Texas at El Paso, El Paso, TX, United States
| |
Collapse
|
23
|
Structural basis for recognition of distinct deaminated DNA lesions by endonuclease Q. Proc Natl Acad Sci U S A 2021; 118:2021120118. [PMID: 33658373 DOI: 10.1073/pnas.2021120118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Spontaneous deamination of DNA cytosine and adenine into uracil and hypoxanthine, respectively, causes C to T and A to G transition mutations if left unrepaired. Endonuclease Q (EndoQ) initiates the repair of these premutagenic DNA lesions in prokaryotes by cleaving the phosphodiester backbone 5' of either uracil or hypoxanthine bases or an apurinic/apyrimidinic (AP) lesion generated by the excision of these damaged bases. To understand how EndoQ achieves selectivity toward these structurally diverse substrates without cleaving undamaged DNA, we determined the crystal structures of Pyrococcus furiosus EndoQ bound to DNA substrates containing uracil, hypoxanthine, or an AP lesion. The structures show that substrate engagement by EndoQ depends both on a highly distorted conformation of the DNA backbone, in which the target nucleotide is extruded out of the helix, and direct hydrogen bonds with the deaminated bases. A concerted swing motion of the zinc-binding and C-terminal helical domains of EndoQ toward its catalytic domain allows the enzyme to clamp down on a sharply bent DNA substrate, shaping a deep active-site pocket that accommodates the extruded deaminated base. Within this pocket, uracil and hypoxanthine bases interact with distinct sets of amino acid residues, with positioning mediated by an essential magnesium ion. The EndoQ-DNA complex structures reveal a unique mode of damaged DNA recognition and provide mechanistic insights into the initial step of DNA damage repair by the alternative excision repair pathway. Furthermore, we demonstrate that the unique activity of EndoQ is useful for studying DNA deamination and repair in mammalian systems.
Collapse
|
24
|
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.
Collapse
|
25
|
Huang D, Jing G, Zhang L, Chen C, Zhu S. Interplay Among Hydrogen Sulfide, Nitric Oxide, Reactive Oxygen Species, and Mitochondrial DNA Oxidative Damage. FRONTIERS IN PLANT SCIENCE 2021; 12:701681. [PMID: 34421950 PMCID: PMC8377586 DOI: 10.3389/fpls.2021.701681] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 07/06/2021] [Indexed: 06/01/2023]
Abstract
Hydrogen sulfide (H2S), nitric oxide (NO), and reactive oxygen species (ROS) play essential signaling roles in cells by oxidative post-translational modification within suitable ranges of concentration. All of them contribute to the balance of redox and are involved in the DNA damage and repair pathways. However, the damage and repair pathways of mitochondrial DNA (mtDNA) are complicated, and the interactions among NO, H2S, ROS, and mtDNA damage are also intricate. This article summarized the current knowledge about the metabolism of H2S, NO, and ROS and their roles in maintaining redox balance and regulating the repair pathway of mtDNA damage in plants. The three reactive species may likely influence each other in their generation, elimination, and signaling actions, indicating a crosstalk relationship between them. In addition, NO and H2S are reported to be involved in epigenetic variations by participating in various cell metabolisms, including (nuclear and mitochondrial) DNA damage and repair. Nevertheless, the research on the details of NO and H2S in regulating DNA damage repair of plants is in its infancy, especially in mtDNA.
Collapse
Affiliation(s)
- Dandan Huang
- Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, College of Chemistry and Material Science, Shandong Agricultural University, Tai’an, China
| | - Guangqin Jing
- Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, College of Chemistry and Material Science, Shandong Agricultural University, Tai’an, China
- College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Lili Zhang
- Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, College of Chemistry and Material Science, Shandong Agricultural University, Tai’an, China
| | - Changbao Chen
- Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, College of Chemistry and Material Science, Shandong Agricultural University, Tai’an, China
| | - Shuhua Zhu
- Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, College of Chemistry and Material Science, Shandong Agricultural University, Tai’an, China
| |
Collapse
|
26
|
Jung KW, Jung JH, Park HY. Functional Roles of Homologous Recombination and Non-Homologous End Joining in DNA Damage Response and Microevolution in Cryptococcus neoformans. J Fungi (Basel) 2021; 7:jof7070566. [PMID: 34356945 PMCID: PMC8307084 DOI: 10.3390/jof7070566] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 11/16/2022] Open
Abstract
DNA double-strand breaks (DSBs) are the most deleterious type of DNA lesions because they cause loss of genetic information if not properly repaired. In eukaryotes, homologous recombination (HR) and non-homologous end joining (NHEJ) are required for DSB repair. However, the relationship of HR and NHEJ in DNA damage stress is unknown in the radiation-resistant fungus Cryptococcus neoformans. In this study, we found that the expression levels of HR- and NHEJ-related genes were highly induced in a Rad53-Bdr1 pathway-dependent manner under genotoxic stress. Deletion of RAD51, which is one of the main components in the HR, resulted in growth under diverse types of DNA damage stress, whereas perturbations of KU70 and KU80, which belong to the NHEJ system, did not affect the genotoxic stresses except when bleomycin was used for treatment. Furthermore, deletion of both RAD51 and KU70/80 renders cells susceptible to oxidative stress. Notably, we found that deletion of RAD51 induced a hypermutator phenotype in the fluctuation assay. In contrast to the fluctuation assay, perturbation of KU70 or KU80 induced rapid microevolution similar to that induced by the deletion of RAD51. Collectively, Rad51-mediated HR and Ku70/Ku80-mediated NHEJ regulate the DNA damage response and maintain genome stability.
Collapse
Affiliation(s)
- Kwang-Woo Jung
- Radiation Research Division, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-Si 56212, Jeollabuk-Do, Korea; (J.-H.J.); (H.-Y.P.)
- Correspondence: ; Tel.: +82-63-570-3337
| | - Jong-Hyun Jung
- Radiation Research Division, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-Si 56212, Jeollabuk-Do, Korea; (J.-H.J.); (H.-Y.P.)
- Department of Radiation Science and Technology, University of Science and Technology, Daejeon 34113, Korea
| | - Ha-Young Park
- Radiation Research Division, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-Si 56212, Jeollabuk-Do, Korea; (J.-H.J.); (H.-Y.P.)
| |
Collapse
|
27
|
The influence of oxoG on the electronic properties of ds-DNA. Damage versus mismatch: A theoretical approach. Comput Biol Chem 2021; 92:107485. [PMID: 33872920 DOI: 10.1016/j.compbiolchem.2021.107485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/04/2021] [Indexed: 11/20/2022]
Abstract
The seed of life is concealed in the base sequence in DNA. This macromolecule is continuously exposed to harmful factors which can cause it damage. The stability of genetic information depends on the protein efficiency of repair systems. Glycosylases are the scouts which recognize and remove damaged bases. Their efficiency depends on how rapidly they recognize DNA lesions. One theory states that charge transfer is involved in protein cross talking through ds-DNA. For these reasons a comparative analysis of ds-oligo containing a mismatched base pair dA:::dG and a damaged dA::dGOXO is proposed. Additionally, the electronic properties of the short ds-oligo in the context of non-equilibrated and equilibrated solvent modes were taken into theoretical consideration. All energetic calculations were performed at the M062x/6-31++G** level of theory, while for geometry optimized ONIOM methodology was used. The lowest adiabatic ionization potential was assigned for DNA containing a dA:dGOXO pair. Moreover, the adiabatic electron affinity was assigned at the same level for the mismatched and lesioned ds-oligo. Surprisingly, in the non-equilibrated mode, a significantly higher vertical electro affinity was found for lesioned DNA. The higher VEA in a non-equilibrated solvent state supported faster recognition in the A:GOXO base pair than A:G by MutY glycosylases under electron transfer mechanism.
Collapse
|
28
|
Wang B, Chen Y, Zhang X, Jiang Z, Wang Y, Chen K, Wang F, Weng X, Zhou X. A far-red emissive two-photon fluorescent probe for quantification of uracil in genomic DNA. Chem Commun (Camb) 2021; 57:2784-2787. [PMID: 33599665 DOI: 10.1039/d1cc00016k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a new method for dU detection in genomic DNA combined with UNG excision and fluorescent probe labeling. UNG can remove uracil bases to introduce abasic sites, which can react with NRNO to produce intense fluorescence because of the inhibition of the PET effect. It can also cause the polymerase extension to stop to provide details of dU site information.
Collapse
Affiliation(s)
- Bingyao Wang
- The Institute of Advanced Studies, College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China.
| | - Yi Chen
- The Institute of Advanced Studies, College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China.
| | - Xiong Zhang
- The Institute of Advanced Studies, College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China.
| | - Zhuoran Jiang
- The Institute of Advanced Studies, College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China.
| | - Yafen Wang
- The Institute of Advanced Studies, College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China.
| | - Kun Chen
- The Institute of Advanced Studies, College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China.
| | - Fang Wang
- Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China
| | - Xiaocheng Weng
- The Institute of Advanced Studies, College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China.
| | - Xiang Zhou
- The Institute of Advanced Studies, College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China.
| |
Collapse
|
29
|
Nguyen MT, Moiani D, Ahmed Z, Arvai AS, Namjoshi S, Shin DS, Fedorov Y, Selvik EJ, Jones DE, Pink J, Yan Y, Laverty DJ, Nagel ZD, Tainer JA, Gerson SL. An effective human uracil-DNA glycosylase inhibitor targets the open pre-catalytic active site conformation. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 163:143-159. [PMID: 33675849 PMCID: PMC8722130 DOI: 10.1016/j.pbiomolbio.2021.02.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/13/2021] [Accepted: 02/22/2021] [Indexed: 02/07/2023]
Abstract
Human uracil DNA-glycosylase (UDG) is the prototypic and first identified DNA glycosylase with a vital role in removing deaminated cytosine and incorporated uracil and 5-fluorouracil (5-FU) from DNA. UDG depletion sensitizes cells to high APOBEC3B deaminase and to pemetrexed (PEM) and floxuridine (5-FdU), which are toxic to tumor cells through incorporation of uracil and 5-FU into DNA. To identify small-molecule UDG inhibitors for pre-clinical evaluation, we optimized biochemical screening of a selected diversity collection of >3,000 small-molecules. We found aurintricarboxylic acid (ATA) as an inhibitor of purified UDG at an initial calculated IC50 < 100 nM. Subsequent enzymatic assays confirmed effective ATA inhibition but with an IC50 of 700 nM and showed direct binding to the human UDG with a KD of <700 nM. ATA displays preferential, dose-dependent binding to purified human UDG compared to human 8-oxoguanine DNA glycosylase. ATA did not bind uracil-containing DNA at these concentrations. Yet, combined crystal structure and in silico docking results unveil ATA interactions with the DNA binding channel and uracil-binding pocket in an open, destabilized UDG conformation. Biologically relevant ATA inhibition of UDG was measured in cell lysates from human DLD1 colon cancer cells and in MCF-7 breast cancer cells using a host cell reactivation assay. Collective findings provide proof-of-principle for development of an ATA-based chemotype and “door stopper” strategy targeting inhibitor binding to a destabilized, open pre-catalytic glycosylase conformation that prevents active site closing for functional DNA binding and nucleotide flipping needed to excise altered bases in DNA.
Collapse
Affiliation(s)
- My T Nguyen
- Case Western Reserve University, Department of Biochemistry, Cleveland, OH, 44106, USA
| | - Davide Moiani
- Departments of Cancer Biology and of Molecular & Cellular Oncology, University of Texas MD Anderson Cancer Center, 1515 Holcomb Blvd, Houston, TX, 77030, USA
| | - Zamal Ahmed
- Departments of Cancer Biology and of Molecular & Cellular Oncology, University of Texas MD Anderson Cancer Center, 1515 Holcomb Blvd, Houston, TX, 77030, USA
| | - Andrew S Arvai
- Integrative Structural & Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Sarita Namjoshi
- Departments of Cancer Biology and of Molecular & Cellular Oncology, University of Texas MD Anderson Cancer Center, 1515 Holcomb Blvd, Houston, TX, 77030, USA
| | - Dave S Shin
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yuriy Fedorov
- Case Small-Molecule Screening Core, School of Medicine, Case Western Reserve University, Cleveland, OH, 44016, USA
| | - Edward J Selvik
- Department of Pharmaceutical Sciences, The University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, AR, 72205, USA
| | - Darin E Jones
- Department of Pharmaceutical Sciences, The University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, AR, 72205, USA
| | - John Pink
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Yan Yan
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Daniel J Laverty
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, 02115, USA
| | - Zachary D Nagel
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, 02115, USA
| | - John A Tainer
- Departments of Cancer Biology and of Molecular & Cellular Oncology, University of Texas MD Anderson Cancer Center, 1515 Holcomb Blvd, Houston, TX, 77030, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Stanton L Gerson
- Case Western Reserve University, Department of Biochemistry, Cleveland, OH, 44106, USA; Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA.
| |
Collapse
|
30
|
D'Amico AM, Vasquez KM. The multifaceted roles of DNA repair and replication proteins in aging and obesity. DNA Repair (Amst) 2021; 99:103049. [PMID: 33529944 DOI: 10.1016/j.dnarep.2021.103049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/12/2021] [Accepted: 01/14/2021] [Indexed: 12/14/2022]
Abstract
Efficient mechanisms for genomic maintenance (i.e., DNA repair and DNA replication) are crucial for cell survival. Aging and obesity can lead to the dysregulation of genomic maintenance proteins/pathways and are significant risk factors for the development of cancer, metabolic disorders, and other genetic diseases. Mutations in genes that code for proteins involved in DNA repair and DNA replication can also exacerbate aging- and obesity-related disorders and lead to the development of progeroid diseases. In this review, we will discuss the roles of various DNA repair and replication proteins in aging and obesity as well as investigate the possible mechanisms by which aging and obesity can lead to the dysregulation of these proteins and pathways.
Collapse
Affiliation(s)
- Alexandra M D'Amico
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Boulevard, Austin, TX, 78723, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Boulevard, Austin, TX, 78723, USA.
| |
Collapse
|
31
|
Jiang Y, Kong X, Jiang Y, Zhao W, Zhou H, Zhang S. DNA Nanodevices for Base Excision Repair Regulates ATP In Situ Imaging and Tumor Therapy. ACS APPLIED BIO MATERIALS 2020; 3:8507-8514. [PMID: 35019620 DOI: 10.1021/acsabm.0c00884] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The design of DNA nanodevices has attracted broad attention in detecting specific targets and targeted drug delivery capacities of tumor cells. Here, we report the facile fluorometric method of dual-targeting DNA nanodevices for base excision repair (BER) regulates adenosine triphosphate (ATP) in situ imaging and tumor therapy that can counteract the mutagenic effects of uracil (U) on ATP aptamer based on the binding of U-containing damaged ATP aptamer. We prove that the DNA nanodevices not only effectively deliver the aptamer probe and tumor therapy but also able to analyze the overexpression of APE1 and uracil-DNA glycosylases (UDG) in the BER pathway via ATP in situ imaging in tumor cells. Therefore, the DNA nanodevices of the BER pathway provide the potential for tumor theranostics.
Collapse
Affiliation(s)
- Yao Jiang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, P. R. China.,Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Xiangjuan Kong
- Jiangxi Key Laboratory of Organic Chemistry, Jiangxi Science and Technology Normal University, Nanchang 330013, P. R. China
| | - Yanxialei Jiang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Wenjing Zhao
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Huimin Zhou
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Shusheng Zhang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| |
Collapse
|
32
|
Aspholm EE, Matečko-Burmann I, Burmann BM. Keeping α-Synuclein at Bay: A More Active Role of Molecular Chaperones in Preventing Mitochondrial Interactions and Transition to Pathological States? Life (Basel) 2020; 10:E289. [PMID: 33227899 PMCID: PMC7699229 DOI: 10.3390/life10110289] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/10/2020] [Accepted: 11/16/2020] [Indexed: 01/04/2023] Open
Abstract
The property of molecular chaperones to dissolve protein aggregates of Parkinson-related α-synuclein has been known for some time. Recent findings point to an even more active role of molecular chaperones preventing the transformation of α-synuclein into pathological states subsequently leading to the formation of Lewy bodies, intracellular inclusions containing protein aggregates as well as broken organelles found in the brains of Parkinson's patients. In parallel, a short motif around Tyr39 was identified as being crucial for the aggregation of α-synuclein. Interestingly, this region is also one of the main segments in contact with a diverse pool of molecular chaperones. Further, it could be shown that the inhibition of the chaperone:α-synuclein interaction leads to a binding of α-synuclein to mitochondria, which could also be shown to lead to mitochondrial membrane disruption as well as the possible proteolytic processing of α-synuclein by mitochondrial proteases. Here, we will review the current knowledge on the role of molecular chaperones in the regulation of physiological functions as well as the direct consequences of impairing these interactions-i.e., leading to enhanced mitochondrial interaction and consequential mitochondrial breakage, which might mark the initial stages of the structural transition of α-synuclein towards its pathological states.
Collapse
Affiliation(s)
- Emelie E. Aspholm
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Göteborg, Sweden;
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 40530 Göteborg, Sweden;
| | - Irena Matečko-Burmann
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 40530 Göteborg, Sweden;
- Department of Psychiatry and Neurochemistry, University of Gothenburg, 40530 Göteborg, Sweden
| | - Björn M. Burmann
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Göteborg, Sweden;
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 40530 Göteborg, Sweden;
| |
Collapse
|
33
|
Peralta-Castro A, García-Medel PL, Baruch-Torres N, Trasviña-Arenas CH, Juarez-Quintero V, Morales-Vazquez CM, Brieba LG. Plant Organellar DNA Polymerases Evolved Multifunctionality through the Acquisition of Novel Amino Acid Insertions. Genes (Basel) 2020; 11:genes11111370. [PMID: 33228188 PMCID: PMC7699545 DOI: 10.3390/genes11111370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/15/2020] [Accepted: 11/17/2020] [Indexed: 12/20/2022] Open
Abstract
The majority of DNA polymerases (DNAPs) are specialized enzymes with specific roles in DNA replication, translesion DNA synthesis (TLS), or DNA repair. The enzymatic characteristics to perform accurate DNA replication are in apparent contradiction with TLS or DNA repair abilities. For instance, replicative DNAPs incorporate nucleotides with high fidelity and processivity, whereas TLS DNAPs are low-fidelity polymerases with distributive nucleotide incorporation. Plant organelles (mitochondria and chloroplast) are replicated by family-A DNA polymerases that are both replicative and TLS DNAPs. Furthermore, plant organellar DNA polymerases from the plant model Arabidopsis thaliana (AtPOLIs) execute repair of double-stranded breaks by microhomology-mediated end-joining and perform Base Excision Repair (BER) using lyase and strand-displacement activities. AtPOLIs harbor three unique insertions in their polymerization domain that are associated with TLS, microhomology-mediated end-joining (MMEJ), strand-displacement, and lyase activities. We postulate that AtPOLIs are able to execute those different functions through the acquisition of these novel amino acid insertions, making them multifunctional enzymes able to participate in DNA replication and DNA repair.
Collapse
Affiliation(s)
- Antolín Peralta-Castro
- Laboratorio Nacional de Genomica para la Biodiversidad, Centro de Investigacion y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato CP 36821, Mexico; (A.P.-C.); (P.L.G.-M.); (N.B.-T.); (C.H.T.-A.); (V.J.-Q.); (C.M.M.-V.)
| | - Paola L. García-Medel
- Laboratorio Nacional de Genomica para la Biodiversidad, Centro de Investigacion y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato CP 36821, Mexico; (A.P.-C.); (P.L.G.-M.); (N.B.-T.); (C.H.T.-A.); (V.J.-Q.); (C.M.M.-V.)
| | - Noe Baruch-Torres
- Laboratorio Nacional de Genomica para la Biodiversidad, Centro de Investigacion y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato CP 36821, Mexico; (A.P.-C.); (P.L.G.-M.); (N.B.-T.); (C.H.T.-A.); (V.J.-Q.); (C.M.M.-V.)
| | - Carlos H. Trasviña-Arenas
- Laboratorio Nacional de Genomica para la Biodiversidad, Centro de Investigacion y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato CP 36821, Mexico; (A.P.-C.); (P.L.G.-M.); (N.B.-T.); (C.H.T.-A.); (V.J.-Q.); (C.M.M.-V.)
- Department of Chemistry, University of California, Davis, One Shields Ave, Davis, CA 95616, USA
| | - Víctor Juarez-Quintero
- Laboratorio Nacional de Genomica para la Biodiversidad, Centro de Investigacion y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato CP 36821, Mexico; (A.P.-C.); (P.L.G.-M.); (N.B.-T.); (C.H.T.-A.); (V.J.-Q.); (C.M.M.-V.)
| | - Carlos M. Morales-Vazquez
- Laboratorio Nacional de Genomica para la Biodiversidad, Centro de Investigacion y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato CP 36821, Mexico; (A.P.-C.); (P.L.G.-M.); (N.B.-T.); (C.H.T.-A.); (V.J.-Q.); (C.M.M.-V.)
| | - Luis G. Brieba
- Laboratorio Nacional de Genomica para la Biodiversidad, Centro de Investigacion y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato CP 36821, Mexico; (A.P.-C.); (P.L.G.-M.); (N.B.-T.); (C.H.T.-A.); (V.J.-Q.); (C.M.M.-V.)
- Correspondence: ; Tel.: +52-462-1663007
| |
Collapse
|
34
|
Muruzabal D, Collins A, Azqueta A. The enzyme-modified comet assay: Past, present and future. Food Chem Toxicol 2020; 147:111865. [PMID: 33217526 DOI: 10.1016/j.fct.2020.111865] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 11/08/2020] [Accepted: 11/13/2020] [Indexed: 12/17/2022]
Abstract
The enzyme-modified comet assay was developed in order to detect DNA lesions other than those detected by the standard version (single and double strand breaks and alkali-labile sites). Various lesion-specific enzymes, from the DNA repair machinery of bacteria and humans, have been combined with the comet assay, allowing detection of different oxidized and alkylated bases as well as cyclobutane pyrimidine dimers, mis-incorporated uracil and apurinic/apyrimidinic sites. The enzyme-modified comet assay has been applied in different fields - human biomonitoring, environmental toxicology, and genotoxicity testing (both in vitro and in vivo) - as well as in basic research. Up to now, twelve enzymes have been employed; here we describe the enzymes and give examples of studies in which they have been applied. The bacterial formamidopyrimidine DNA glycosylase (Fpg) and endonuclease III (EndoIII) have been extensively used while others have been used only rarely. Adding further enzymes to the comet assay toolbox could potentially increase the variety of DNA lesions that can be detected. The enzyme-modified comet assay can play a crucial role in the elucidation of the mechanism of action of both direct and indirect genotoxins, thus increasing the value of the assay in the regulatory context.
Collapse
Affiliation(s)
- Damián Muruzabal
- Universidad de Navarra, Department of Pharmacology and Toxicology, Faculty of Pharmacy and Nutrition, Irunlarrea 1, 310008, Pamplona, Spain
| | - Andrew Collins
- Department of Nutrition, Institute for Basic Medical Sciences, University of Oslo, Sognsvannsveien 9, 0372, Oslo, Norway
| | - Amaya Azqueta
- Universidad de Navarra, Department of Pharmacology and Toxicology, Faculty of Pharmacy and Nutrition, Irunlarrea 1, 310008, Pamplona, Spain; IdiSNA, Navarra Institute for Health Research, Pamplona, Spain.
| |
Collapse
|
35
|
Cheng K, Xu Y, Chen X, Lu H, He Y, Wang L, Hua Y. Participation of RecJ in the base excision repair pathway of Deinococcus radiodurans. Nucleic Acids Res 2020; 48:9859-9871. [PMID: 32870272 PMCID: PMC7515722 DOI: 10.1093/nar/gkaa714] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 08/07/2020] [Accepted: 08/20/2020] [Indexed: 12/03/2022] Open
Abstract
RecJ reportedly participates in the base excision repair (BER) pathway, but structural and functional data are scarce. Herein, the Deinococcus radiodurans RecJ (drRecJ) deletion strain exhibited extreme sensitivity to hydrogen peroxide and methyl-methanesulphonate, as well as a high spontaneous mutation rate and an accumulation of unrepaired abasic sites in vivo, indicating the involvement of drRecJ in the BER pathway. The binding affinity and nuclease activity preference of drRecJ toward DNA substrates containing a 5'-P-dSpacer group, a 5'-deoxyribose-phosphate (dRP) mimic, were established. A 1.9 Å structure of drRecJ in complex with 5'-P-dSpacer-modified single-stranded DNA (ssDNA) revealed a 5'-monophosphate binding pocket and occupancy of 5'-dRP in the drRecJ nuclease core. The mechanism for RecJ 5'-dRP catalysis was explored using structural and biochemical data, and the results implied that drRecJ is not a canonical 5'-dRP lyase. Furthermore, in vitro reconstitution assays indicated that drRecJ tends to participate in the long-patch BER pathway rather than the short-patch BER pathway.
Collapse
Affiliation(s)
- Kaiying Cheng
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, China
| | - Ying Xu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, China
| | - Xuanyi Chen
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, China
| | - Huizhi Lu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, China
| | - Yuan He
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, China
| | - Liangyan Wang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, China
| | - Yuejin Hua
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, China
| |
Collapse
|
36
|
Kara H, Chazal N, Bouaziz S. Is Uracil-DNA Glycosylase UNG2 a New Cellular Weapon Against HIV-1? Curr HIV Res 2020; 17:148-160. [PMID: 31433761 DOI: 10.2174/1570162x17666190821154331] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 08/01/2019] [Accepted: 08/09/2019] [Indexed: 01/12/2023]
Abstract
Uracil-DNA glycosylase-2 (UNG2) is a DNA repair protein that removes uracil from single and double-stranded DNA through a basic excision repair process. UNG2 is packaged into new virions by interaction with integrase (IN) and is needed during the early stages of the replication cycle. UNG2 appears to play both a positive and negative role during HIV-1 replication; UNG2 improves the fidelity of reverse transcription but the nuclear isoform of UNG2 participates in the degradation of cDNA and the persistence of the cellular genome by repairing its uracil mismatches. In addition, UNG2 is neutralized by Vpr, which redirects it to the proteasome for degradation, suggesting that UNG2 may be a new cellular restriction factor. So far, we have not understood why HIV-1 imports UNG2 via its IN and why it causes degradation of endogenous UNG2 by redirecting it to the proteasome via Vpr. In this review, we propose to discuss the ambiguous role of UNG2 during the HIV-1 replication cycle.
Collapse
Affiliation(s)
- Hesna Kara
- Cibles Therapeutiques et Conception de Medicaments (CiTCoM), CNRS UMR8038, Faculte des Sciences Pharmaceutiques et Biologiques, Universite Paris Descartes, Paris, France
| | - Nathalie Chazal
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS UMR9004, Universite de Montpellier, Montpellier, France
| | - Serge Bouaziz
- Cibles Therapeutiques et Conception de Medicaments (CiTCoM), CNRS UMR8038, Faculte des Sciences Pharmaceutiques et Biologiques, Universite Paris Descartes, Paris, France
| |
Collapse
|
37
|
Structural biology of DNA abasic site protection by SRAP proteins. DNA Repair (Amst) 2020; 94:102903. [PMID: 32663791 DOI: 10.1016/j.dnarep.2020.102903] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/24/2020] [Accepted: 06/25/2020] [Indexed: 11/24/2022]
Abstract
Abasic (AP) sites are one of the most frequently occurring types of DNA damage. They lead to DNA strand breaks, interstrand DNA crosslinks, and block transcription and replication. Mutagenicity of AP sites arises from translesion synthesis (TLS) by error-prone bypass polymerases. Recently, a new cellular response to AP sites was discovered, in which the protein HMCES (5-hydroxymethlycytosine (5hmC) binding, embryonic stem cell-specific) forms a stable, covalent DNA-protein crosslink (DPC) to AP sites at stalled replication forks. The stability of the HMCES-DPC prevents strand cleavage by endonucleases and mutagenic bypass by TLS polymerases. Crosslinking is carried out by a unique SRAP (SOS Response Associated Peptidase) domain conserved across all domains of life. Here, we review the collection of recently reported SRAP crystal structures from human HMCES and E. coli YedK, which provide a unified basis for SRAP specificity and a putative chemical mechanism of AP site crosslinking. We discuss the structural and chemical basis for the stability of the SRAP DPC and how it differs from covalent protein-DNA intermediates in DNA lyase catalysis of strand scission.
Collapse
|
38
|
Rajapakse A, Suraweera A, Boucher D, Naqi A, O'Byrne K, Richard DJ, Croft LV. Redox Regulation in the Base Excision Repair Pathway: Old and New Players as Cancer Therapeutic Targets. Curr Med Chem 2020; 27:1901-1921. [PMID: 31258058 DOI: 10.2174/0929867326666190430092732] [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: 11/02/2018] [Revised: 02/09/2019] [Accepted: 04/05/2019] [Indexed: 01/03/2023]
Abstract
BACKGROUND Reactive Oxygen Species (ROS) are by-products of normal cellular metabolic processes, such as mitochondrial oxidative phosphorylation. While low levels of ROS are important signalling molecules, high levels of ROS can damage proteins, lipids and DNA. Indeed, oxidative DNA damage is the most frequent type of damage in the mammalian genome and is linked to human pathologies such as cancer and neurodegenerative disorders. Although oxidative DNA damage is cleared predominantly through the Base Excision Repair (BER) pathway, recent evidence suggests that additional pathways such as Nucleotide Excision Repair (NER) and Mismatch Repair (MMR) can also participate in clearance of these lesions. One of the most common forms of oxidative DNA damage is the base damage 8-oxoguanine (8-oxoG), which if left unrepaired may result in G:C to A:T transversions during replication, a common mutagenic feature that can lead to cellular transformation. OBJECTIVE Repair of oxidative DNA damage, including 8-oxoG base damage, involves the functional interplay between a number of proteins in a series of enzymatic reactions. This review describes the role and the redox regulation of key proteins involved in the initial stages of BER of 8-oxoG damage, namely Apurinic/Apyrimidinic Endonuclease 1 (APE1), human 8-oxoguanine DNA glycosylase-1 (hOGG1) and human single-stranded DNA binding protein 1 (hSSB1). Moreover, the therapeutic potential and modalities of targeting these key proteins in cancer are discussed. CONCLUSION It is becoming increasingly apparent that some DNA repair proteins function in multiple repair pathways. Inhibiting these factors would provide attractive strategies for the development of more effective cancer therapies.
Collapse
Affiliation(s)
- Aleksandra Rajapakse
- Queensland University of Technology, Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Cancer and Ageing Research Program, Translational Research Institute, Brisbane, QLD, Australia.,School of Natural Sciences, Griffith University, Nathan, QLD, Australia
| | - Amila Suraweera
- Queensland University of Technology, Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Cancer and Ageing Research Program, Translational Research Institute, Brisbane, QLD, Australia
| | - Didier Boucher
- Queensland University of Technology, Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Cancer and Ageing Research Program, Translational Research Institute, Brisbane, QLD, Australia
| | - Ali Naqi
- Department of Chemistry, Pennsylvania State University, United States
| | - Kenneth O'Byrne
- Queensland University of Technology, Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Cancer and Ageing Research Program, Translational Research Institute, Brisbane, QLD, Australia.,Cancer Services, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Derek J Richard
- Queensland University of Technology, Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Cancer and Ageing Research Program, Translational Research Institute, Brisbane, QLD, Australia
| | - Laura V Croft
- Queensland University of Technology, Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Cancer and Ageing Research Program, Translational Research Institute, Brisbane, QLD, Australia
| |
Collapse
|
39
|
Pathak D, Kwon E, Kim DY. Selective interactions between mimivirus uracil-DNA glycosylase and inhibitory proteins determined by a single amino acid. J Struct Biol 2020; 211:107552. [PMID: 32569642 DOI: 10.1016/j.jsb.2020.107552] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 06/06/2020] [Accepted: 06/16/2020] [Indexed: 11/27/2022]
Abstract
Uracil-N-glycosylase (UNG) is found in most organisms as well as in large DNA viruses. Its inhibitory proteins, including uracil glycosylase inhibitor (UGI) and p56, tightly bind to the active site of UNG by mimicking the DNA substrates. As the binding motifs are conserved in UNG family proteins, the inhibitory proteins bind to various UNG proteins across species. However, the intercalation residue that penetrates the DNA minor groove during uracil excision is not conserved among UNG proteins. To understand the role of the intercalation residue in their binding to the inhibitory proteins, we prepared mutants of mimivirus UNG, measured the binding affinity between the UNG mutants and inhibitory proteins, and analyzed the interactions based on the crystal structures of mimivirus UNG mutants complexed with UGI. The results show that mimivirus UNG, which harbors Tyr as an intercalation residue, did not interact with the inhibitory proteins intrinsically, whereas mutations of the intercalation residue to Phe or Leu resulted in tight interactions with UGI and p56; mutation to Met resulted in tight interactions only with p56. The crystal structures revealed that Phe and Leu stabilize the interactions by fitting into the hydrophobic pocket of UGI. These results show that differences in size and hydrophobicity of the intercalation residues determine the interactions between UNG family proteins and the inhibitory proteins, UGI and p56.
Collapse
Affiliation(s)
- Deepak Pathak
- College of Pharmacy, Yeungnam University, Gyeongsan, Gyeongbuk 38541, South Korea
| | - Eunju Kwon
- College of Pharmacy, Yeungnam University, Gyeongsan, Gyeongbuk 38541, South Korea.
| | - Dong Young Kim
- College of Pharmacy, Yeungnam University, Gyeongsan, Gyeongbuk 38541, South Korea.
| |
Collapse
|
40
|
Scheffler K, Jalland CMO, Benestad SL, Moldal T, Ersdal C, Gunnes G, Suganthan R, Bjørås M, Tranulis MA. DNA glycosylase Neil2 contributes to genomic responses in the spleen during clinical prion disease. Free Radic Biol Med 2020; 152:348-354. [PMID: 32259578 DOI: 10.1016/j.freeradbiomed.2020.03.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/19/2020] [Accepted: 03/29/2020] [Indexed: 02/02/2023]
Abstract
The DNA glycosylase Neil2 is a member of the base excision repair (BER) family of enzymes, which are important for repair of oxidative DNA damage. Specifically, Neil2 participates in repair of oxidized bases in single-stranded DNA of transcriptionally active genes. Mice with genetic ablation of Neil2 (Neil2-/-) display no overt phenotypes, but an age-dependent accumulation of oxidative DNA damage and increased inflammatory responsiveness. In young mice intra-cerebrally inoculated with prions, vigorous prion propagation starts rapidly in the germinal follicles of the spleen due to inoculum spillover. Here, we compare experimental prion disease in Neil2-/- mice with that in wild-type mice at disease onset and end-stage. Specifically, we investigated disease progression, accumulation of DNA damage, and mitochondrial respiratory complex activity in brain and spleen. We used genome-wide RNA sequencing of the spleen to compare the immune responses to prion propagation between the two groups of mice, at both onset and end-stage prion disease. The Neil2-/- mice deteriorated more rapidly than wild-type mice after onset of clinical signs. Levels of DNA damage in brain increased in both mouse groups, slightly more in the Neil2-/- mice. Transcriptome data from spleen at disease onset were similar between the mouse groups with moderate genomic responses. However, at end-stage a substantial response was evident in the wild-type mice but not in Neil2-/- mice. Our data show that Neil2 counteracts toxic signaling in clinical prion disease, and this is separate from gross pathological manifestations and PrPSc accumulation.
Collapse
Affiliation(s)
- Katja Scheffler
- Department of Neuromedicine and Movement Science, Norwegian University of Science and Technology, Trondheim, Norway; Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway; Department of Neurology, St. Olavs Hospital, Trondheim, Norway; Department of Laboratory Medicine, St. Olavs Hospital, Trondheim, Norway.
| | - Clara M O Jalland
- Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Campus Adamstuen, Oslo, Norway
| | | | | | - Cecilie Ersdal
- Department of Production Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Campus Sandnes, Norway
| | - Gjermund Gunnes
- Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Campus Adamstuen, Oslo, Norway
| | - Rajikala Suganthan
- Department of Microbiology, Oslo University Hospital and University of Oslo, Norway
| | - Magnar Bjørås
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway; Department of Laboratory Medicine, St. Olavs Hospital, Trondheim, Norway; Department of Microbiology, Oslo University Hospital and University of Oslo, Norway
| | - Michael A Tranulis
- Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Campus Adamstuen, Oslo, Norway
| |
Collapse
|
41
|
Oxidative Repair of Pyrimidine Cyclobutane Dimers by Nitrate Radicals (NO3•): A Kinetic and Computational Study. CHEMISTRY 2020. [DOI: 10.3390/chemistry2020027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Pyrimidine cyclobutane dimers are hazardous DNA lesions formed upon exposure of DNA to UV light, which can be repaired through oxidative electron transfer (ET). Laser flash photolysis and computational studies were performed to explore the role of configuration and constitution at the cyclobutane ring on the oxidative repair process, using the nitrate radical (NO3•) as oxidant. The rate coefficients of 8–280 × 107 M−1 s−1 in acetonitrile revealed a very high reactivity of the cyclobutane dimers of N,N’-dimethylated uracil (DMU), thymine (DMT), and 6-methyluracil (DMU6-Me) towards NO3•, which likely proceeds via ET at N(1) as a major pathway. The overall rate of NO3• consumption was determined by (i) the redox potential, which was lower for the syn- than for the anti-configured dimers, and (ii) the accessibility of the reaction site for NO3•. In the trans dimers, both N(1) atoms could be approached from above and below the molecular plane, whereas in the cis dimers, only the convex side was readily accessible for NO3•. The higher reactivity of the DMT dimers compared with isomeric DMU dimers was due to the electron-donating methyl groups on the cyclobutane ring, which increased their susceptibility to oxidation. On the other hand, the approach of NO3• to the dimers of DMU6-Me was hindered by the methyl substituents adjacent to N(1), making these dimers the least reactive in this series.
Collapse
|
42
|
Cervical carcinoma risk associate with genetic polymorphisms of NEIL2 gene in Chinese population and its significance as predictive biomarker. Sci Rep 2020; 10:5136. [PMID: 32198476 PMCID: PMC7083954 DOI: 10.1038/s41598-020-62040-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 03/06/2020] [Indexed: 12/17/2022] Open
Abstract
Genetic polymorphisms of NEIL1 and NEIL2 maybe change protein function, and increased carcinogenesis. In this study, seven NEIL1 SNPs and three NEIL2 SNPs were selected. 400 CSCCs, 400 CIN III, and 1200 normal healthy controls were genotyped by mismatch amplification PCR. mRNA and protein expression of NEIL2 was measured in 92 freshly-obtained CSCC tumor tissues. The association between homozygote CC genotype of NEIL2 rs804270 with susceptible risk was gradually increased in CIN III (OR = 1.44) and CSCC (OR = 2.22). Carriers of C-allele (GC + CC) at rs804270 had a high risk of CSCC (OR = 1.46). The heterozygote GT genotype of rs8191664 was also closely related to the higher risk of CINIII (OR = 1.59) and CSCC (OR = 2.54). Carriers of T-allele (GT + TT) at rs8191664 had a high risk for CIN III (OR = 1.55) and CSCC (OR = 2.34). The genotypes of NEIL2 rs804270 (G/C) and rs8191664 (G/T) that were related to the higher risk for CIN III were CC-GG (OR = 1.42) and CC-GT (OR = 2.07). More notably, there was a greater risk for CSCC with the GC-GT (OR = 1.91), CC-GG (OR = 1.67), and CC-GT (OR = 6.18) genotypes. NEIL2 mRNA expression in CSCCs with the rs804270-CC genotype was lower expression than those in CSCCs with the rs804270-GG and rs804270-GC genotypes. Similarly, NEIL2 protein expression was significantly decreased in CSCCs with the rs804270-CC genotype. In summary, the two genetic polymorphisms (rs804270 and rs8191664) of NEIL2 gene were significantly associated to the increased susceptibility of CIN III or CSCC. This increased susceptibility maybe due to altered NEIL2 repair activity through altered protein expression, or changed structure of the functional domain. The genotypes of GC-GT, CC-GG, and CC-GT of rs804270 and rs8191664 of NEIL2 gene could act as a genetic predictive biomarker of susceptibility to CIN III and CSCC.
Collapse
|
43
|
Wynn E, Purfeerst E, Christensen A. Mitochondrial DNA Repair in an Arabidopsis thaliana Uracil N-Glycosylase Mutant. PLANTS (BASEL, SWITZERLAND) 2020; 9:E261. [PMID: 32085412 PMCID: PMC7076443 DOI: 10.3390/plants9020261] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/14/2020] [Accepted: 02/16/2020] [Indexed: 02/07/2023]
Abstract
Substitution rates in plant mitochondrial genes are extremely low, indicating strong selective pressure as well as efficient repair. Plant mitochondria possess base excision repair pathways; however, many repair pathways such as nucleotide excision repair and mismatch repair appear to be absent. In the absence of these pathways, many DNA lesions must be repaired by a different mechanism. To test the hypothesis that double-strand break repair (DSBR) is that mechanism, we maintained independent self-crossing lineages of plants deficient in uracil-N-glycosylase (UNG) for 11 generations to determine the repair outcomes when that pathway is missing. Surprisingly, no single nucleotide polymorphisms (SNPs) were fixed in any line in generation 11. The pattern of heteroplasmic SNPs was also unaltered through 11 generations. When the rate of cytosine deamination was increased by mitochondrial expression of the cytosine deaminase APOBEC3G, there was an increase in heteroplasmic SNPs but only in mature leaves. Clearly, DNA maintenance in reproductive meristem mitochondria is very effective in the absence of UNG while mitochondrial genomes in differentiated tissue are maintained through a different mechanism or not at all. Several genes involved in DSBR are upregulated in the absence of UNG, indicating that double-strand break repair is a general system of repair in plant mitochondria. It is important to note that the developmental stage of tissues is critically important for these types of experiments.
Collapse
Affiliation(s)
- Emily Wynn
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; (E.W.); (E.P.)
- United States Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE 68933, USA
| | - Emma Purfeerst
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; (E.W.); (E.P.)
- Athletics Department, Bethany Lutheran College, Mankato, MN 56001, USA
| | - Alan Christensen
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; (E.W.); (E.P.)
| |
Collapse
|
44
|
Base excision repair pathways of bacteria: new promise for an old problem. Future Med Chem 2020; 12:339-355. [PMID: 32031026 DOI: 10.4155/fmc-2019-0267] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Infectious diseases continue to be a major cause of human mortality. With the emergence of drug resistance, diseases that were long thought to have been curable by antibiotics are resurging. There is an urgent clinical need for newer antibiotics that target novel cellular pathways to overcome resistance to currently used therapeutics. The base excision repair (BER) pathways of the pathogen restore altered bases and safeguard the genomic integrity of the pathogen from the host's immune response. Although the BER machinery is of paramount importance to the survival of the pathogens, its potential as a drug target is largely unexplored. In this review, we discuss the importance of BER in different pathogenic organisms and the potential of its inhibition with small molecules.
Collapse
|
45
|
Chevigny N, Schatz-Daas D, Lotfi F, Gualberto JM. DNA Repair and the Stability of the Plant Mitochondrial Genome. Int J Mol Sci 2020; 21:E328. [PMID: 31947741 PMCID: PMC6981420 DOI: 10.3390/ijms21010328] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 12/27/2019] [Accepted: 01/01/2020] [Indexed: 12/13/2022] Open
Abstract
The mitochondrion stands at the center of cell energy metabolism. It contains its own genome, the mtDNA, that is a relic of its prokaryotic symbiotic ancestor. In plants, the mitochondrial genetic information influences important agronomic traits including fertility, plant vigor, chloroplast function, and cross-compatibility. Plant mtDNA has remarkable characteristics: It is much larger than the mtDNA of other eukaryotes and evolves very rapidly in structure. This is because of recombination activities that generate alternative mtDNA configurations, an important reservoir of genetic diversity that promotes rapid mtDNA evolution. On the other hand, the high incidence of ectopic recombination leads to mtDNA instability and the expression of gene chimeras, with potential deleterious effects. In contrast to the structural plasticity of the genome, in most plant species the mtDNA coding sequences evolve very slowly, even if the organization of the genome is highly variable. Repair mechanisms are probably responsible for such low mutation rates, in particular repair by homologous recombination. Herein we review some of the characteristics of plant organellar genomes and of the repair pathways found in plant mitochondria. We further discuss how homologous recombination is involved in the evolution of the plant mtDNA.
Collapse
Affiliation(s)
| | | | | | - José Manuel Gualberto
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 67081 Strasbourg, France; (N.C.); (D.S.-D.); (F.L.)
| |
Collapse
|
46
|
Kuznetsov NA, Fedorova OS. Kinetic Milestones of Damage Recognition by DNA Glycosylases of the Helix-Hairpin-Helix Structural Superfamily. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1241:1-18. [DOI: 10.1007/978-3-030-41283-8_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
47
|
Stasińska AR, Putaj P, Chmielewski MK. Disulfide bridge as a linker in nucleic acids' bioconjugation. Part II: A summary of practical applications. Bioorg Chem 2019; 95:103518. [PMID: 31911308 DOI: 10.1016/j.bioorg.2019.103518] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/11/2019] [Accepted: 12/16/2019] [Indexed: 12/15/2022]
Abstract
Disulfide conjugation invariably remains a key tool in research on nucleic acids. This versatile and cost-effective method plays a crucial role in structural studies of DNA and RNA as well as their interactions with other macromolecules in a variety of biological systems. In this article we review applications of disulfide-bridged conjugates of oligonucleotides with other (bio)molecules such as peptides, proteins etc. and present key findings obtained with their help.
Collapse
Affiliation(s)
- Anna R Stasińska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Noskowskiego 12/14, 61-704 Poznań, Poland; FutureSynthesis sp. z o.o. ul. Rubież 46H, 61-612 Poznań, Poland
| | - Piotr Putaj
- FutureSynthesis sp. z o.o. ul. Rubież 46H, 61-612 Poznań, Poland
| | - Marcin K Chmielewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Noskowskiego 12/14, 61-704 Poznań, Poland; FutureSynthesis sp. z o.o. ul. Rubież 46H, 61-612 Poznań, Poland.
| |
Collapse
|
48
|
Krumkacheva OA, Shevelev GY, Lomzov AA, Dyrkheeva NS, Kuzhelev AA, Koval VV, Tormyshev VM, Polienko YF, Fedin MV, Pyshnyi DV, Lavrik OI, Bagryanskaya EG. DNA complexes with human apurinic/apyrimidinic endonuclease 1: structural insights revealed by pulsed dipolar EPR with orthogonal spin labeling. Nucleic Acids Res 2019; 47:7767-7780. [PMID: 31329919 PMCID: PMC6735896 DOI: 10.1093/nar/gkz620] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 07/04/2019] [Accepted: 07/11/2019] [Indexed: 12/19/2022] Open
Abstract
A DNA molecule is under continuous influence of endogenous and exogenous damaging factors, which produce a variety of DNA lesions. Apurinic/apyrimidinic sites (abasic or AP sites) are among the most common DNA lesions. In this work, we applied pulse dipolar electron paramagnetic resonance (EPR) spectroscopy in combination with molecular dynamics (MD) simulations to investigate in-depth conformational changes in DNA containing an AP site and in a complex of this DNA with AP endonuclease 1 (APE1). For this purpose, triarylmethyl (TAM)-based spin labels were attached to the 5' ends of an oligonucleotide duplex, and nitroxide spin labels were introduced into APE1. In this way, we created a system that enabled monitoring the conformational changes of the main APE1 substrate by EPR. In addition, we were able to trace substrate-to-product transformation in this system. The use of different (orthogonal) spin labels in the enzyme and in the DNA substrate has a crucial advantage allowing for detailed investigation of local damage and conformational changes in AP-DNA alone and in its complex with APE1.
Collapse
Affiliation(s)
- Olesya A Krumkacheva
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Lavrentiev ave, Novosibirsk 630090, Russia.,Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,International Tomography Center SB RAS, Institutskaya Str. 3a, Novosibirsk 630090, Russia
| | - Georgiy Yu Shevelev
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev ave, Novosibirsk 630090, Russia
| | - Alexander A Lomzov
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev ave, Novosibirsk 630090, Russia
| | - Nadezhda S Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev ave, Novosibirsk 630090, Russia
| | - Andrey A Kuzhelev
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Lavrentiev ave, Novosibirsk 630090, Russia.,Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,International Tomography Center SB RAS, Institutskaya Str. 3a, Novosibirsk 630090, Russia
| | - Vladimir V Koval
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev ave, Novosibirsk 630090, Russia
| | - Victor M Tormyshev
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Lavrentiev ave, Novosibirsk 630090, Russia.,Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
| | - Yuliya F Polienko
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Lavrentiev ave, Novosibirsk 630090, Russia.,Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
| | - Matvey V Fedin
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,International Tomography Center SB RAS, Institutskaya Str. 3a, Novosibirsk 630090, Russia
| | - Dmitrii V Pyshnyi
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev ave, Novosibirsk 630090, Russia
| | - Olga I Lavrik
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev ave, Novosibirsk 630090, Russia
| | - Elena G Bagryanskaya
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Lavrentiev ave, Novosibirsk 630090, Russia.,Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
| |
Collapse
|
49
|
Azman KF, Zakaria R. Honey as an antioxidant therapy to reduce cognitive ageing. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2019; 22:1368-1377. [PMID: 32133053 PMCID: PMC7043876 DOI: 10.22038/ijbms.2019.14027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
This paper reviews the potential role of honey as a therapeutic antioxidant to reduce oxidative stress and improve cognitive ageing. All articles indexed to PubMed Central (PMC) were searched using the following key words: honey, antioxidant, memory and ageing. Honey is a natural insect-derived product with therapeutic, medicinal and nutritional values. Antioxidant properties of honey quench biologically-circulating reactive oxygen species (ROS) and counter oxidative stress while restoring the cellular antioxidant defense system. Antioxidant properties of honey may complement its nootropic effects to reduce cognitive ageing.
Collapse
Affiliation(s)
- Khairunnuur Fairuz Azman
- Department of Physiology, School of Medical Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kota Bharu, Kelantan, Malaysia
| | - Rahimah Zakaria
- Department of Physiology, School of Medical Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kota Bharu, Kelantan, Malaysia ,Corresponding author: Rahimah Zakaria. Department of Physiology, School of Medical Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kota Bharu, Kelantan, Malaysia. Tel: +609-7676156;
| |
Collapse
|
50
|
Gajski G, Gerić M, Domijan AM, Golubović I, Garaj-Vrhovac V. Evaluation of oxidative stress responses in human circulating blood cells after imatinib mesylate treatment - Implications to its mechanism of action. Saudi Pharm J 2019; 27:1216-1221. [PMID: 31885482 PMCID: PMC6921178 DOI: 10.1016/j.jsps.2019.10.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 10/19/2019] [Indexed: 02/02/2023] Open
Abstract
Imatinib mesylate (IM) is the first developed protein kinase inhibitor and recently it has topped consumption rates among targeted and total anticancer drugs. Although there are indications that IM possesses cyto/genotoxic activities against normal non-target cells as well, there is a lack of information regarding the underlying mechanism involved in those actions. Therefore, we aimed to evaluate the response of human circulating blood cells towards oxidative stress after IM treatment (0.0001–10 µg/mL) in vitro. Based on the results, IM had an influence on all of the oxidative stress parameters tested. Lower concentrations of IM induced an increase of glutathione level, following its decrease at higher IM concentrations indicating impairment in oxidative stress defences. Concomitant to a glutathione decrease, an increase of malondialdehyde and protein carbonyls level was observed indicating oxidative damage of lipids and proteins. The observed effects overlapped with the observed formation of oxidative base damage detected by formamidopyrimidine-DNA glycosylase modified-comet assay indicating that IM managed to induce oxidative DNA damage. Our results provide novelty in their mechanistic approach to IM-induced toxicity in non-target cells and suggest that IM can affect blood cells and induce oxidative stress.
Collapse
Affiliation(s)
- Goran Gajski
- Institute for Medical Research and Occupational Health, Mutagenesis Unit, 10000 Zagreb, Croatia
- Corresponding author at: Institute for Medical Research and Occupational Health, Mutagenesis Unit, Ksaverska cesta 2, 10000 Zagreb, Croatia.
| | - Marko Gerić
- Institute for Medical Research and Occupational Health, Mutagenesis Unit, 10000 Zagreb, Croatia
| | - Ana-Marija Domijan
- University of Zagreb, Faculty of Pharmacy and Biochemistry, 10000 Zagreb, Croatia
| | - Ivana Golubović
- University of Zagreb, Faculty of Pharmacy and Biochemistry, 10000 Zagreb, Croatia
| | - Vera Garaj-Vrhovac
- Institute for Medical Research and Occupational Health, Mutagenesis Unit, 10000 Zagreb, Croatia
| |
Collapse
|