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DNA glycosylases

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https://www.readbyqxmd.com/read/28107710/in-vivo-assesment-of-the-genotoxic-and-oxidative-stress-effects-of-particulate-matter-on-echinogammarus-veneris
#1
Melissa Marcoccia, Lucilla Ronci, Elvira De Matthaeis, Andrea Setini, Cinzia Perrino, Silvia Canepari
Seven types of atmospheric dusts (road dust, soil dust, brake dust, desert dust, pellet ash and coke and certified material NIST1648a - urban dust) have been tested for their genotoxicity on specimens of Echinogammarus veneris, a small aquatic amphipod. Experiments were carried out in vivo, by exposing the animals for 24 h to water containing 25 mg/L of dust. Each dust has been chemically analyzed for ions, elemental carbon, organic carbon and for the soluble and insoluble fractions of elements. Non-specific damages to DNA have been evaluated by the comet test, while oxidative damages have been estimated by coupling the comet test with formamido pyrimidine DNA glycosylase reaction...
January 6, 2017: Chemosphere
https://www.readbyqxmd.com/read/28106786/sulfolobus-acidocaldarius-udg-can-remove-du-from-the-rna-backbone-insight-into-the-specific-recognition-of-uracil-linked-with-deoxyribose
#2
Gang-Shun Yi, Wei-Wei Wang, Wei-Guo Cao, Feng-Ping Wang, Xi-Peng Liu
Sulfolobus acidocaldarius encodes family 4 and 5 uracil-DNA glycosylase (UDG). Two recombinant S. acidocaldarius UDGs (SacUDG) were prepared and biochemically characterized using oligonucleotides carrying a deaminated base. Both SacUDGs can remove deoxyuracil (dU) base from both double-stranded DNA and single-stranded DNA. Interestingly, they can remove U linked with deoxyribose from single-stranded RNA backbone, suggesting that the riboses on the backbone have less effect on the recognition of dU and hydrolysis of the C-N glycosidic bond...
January 18, 2017: Genes
https://www.readbyqxmd.com/read/28098999/dna-deformation-coupled-recognition-of-8-oxoguanine-conformational-kinetic-gating-in-human-dna-glycosylase
#3
Haoquan Li, Anton V Endutkin, Christina Bergonzo, Fu Lin, Arthur P Grollman, Dmitry O Zharkov, Carlos Simmerling
8-Oxoguanine (8-oxoG), a mutagenic DNA lesion generated under oxidative stress, differs from its precursor guanine by only two substitutions (O8 and H7). Human 8-oxoguanine glycosylase 1 (OGG1) can locate and remove 8-oxoG through extrusion and excision. To date, it remains unclear how OGG1 efficiently distinguishes 8-oxoG from a large excess of undamaged DNA bases. We recently showed that formamidopyrimidine-DNA glycosylase (Fpg), a bacterial functional analog of OGG1, can selectively facilitate eversion of oxoG by stabilizing several intermediate states, and it is intriguing whether OGG1 also employs a similar mechanism in lesion recognition...
January 18, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28098985/hmgb1-stimulates-activity-of-polymerase-%C3%AE-on-nucleosome-substrates
#4
Angela Balliano, Fanfan Hao, Catherine Njeri, Lata Balakrishnan, Jeffrey J Hayes
The process of base excision repair (BER) recognizes and repairs small lesions or inappropriate bases on DNA through either a short-patch or long-patch pathway. The enzymes involved in BER have been well-characterized on DNA substrates, and, somewhat surprisingly, many of these enzymes, including several DNA glycosylases, AP endonuclease (APE), FEN1 endonuclease, and DNA ligases, have been shown to have activity on DNA substrates within nucleosomes. DNA polymerase β (Pol β), however, exhibits drastically reduced or no activity on nucleosomal DNA...
January 18, 2017: Biochemistry
https://www.readbyqxmd.com/read/28098352/dna-repair-and-erasure-of-5-methylcytosine-in-vertebrates
#5
Lars Schomacher, Christof Niehrs
DNA methylation plays important roles in development and disease. Yet, only recently has the dynamic nature of this epigenetic mark via oxidation and DNA repair-mediated demethylation been recognized. A major conceptual challenge to the model that DNA methylation is reversible is the risk of genomic instability, which may come with widespread DNA repair activity. Here, we focus on recent advances in mechanisms of TET-TDG mediated demethylation and cellular strategies that avoid genomic instability. We highlight the recently discovered involvement of NEIL DNA glycosylases, which cooperate with TDG in oxidative demethylation to accelerate substrate turnover and promote the organized handover of harmful repair intermediates to maintain genome stability...
January 18, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28093361/neil1-is-a-candidate-gene-associated-with-common-variable-immunodeficiency-in-a-patient-with-a-chromosome-15q24-deletion
#6
Rosa Romano, Apostolos Zaravinos, Kyriaki Liadaki, Rozina Caridha, Johanna Lundin, Göran Carlsson, Jacek Winiarski, Qiang Pan-Hammarström, Lennart Hammarström
We report the first patient with an interstitial deletion of chromosome 15q24.1-q24.3 associated with common variable immunodeficiency (CVID). The 18-year old female patient's clinical and immunological phenotype was compared with 8 additional previously published patients with chr15q24 deletions. A CGH analysis estimated the deletion to be 3.767Mb in size (chr15: 74,410,916-78,178,418) and the result was confirmed using qRT-PCR. We defined an immune-related commonly deleted region (ICDR) within the chromosomal band 15q24...
January 13, 2017: Clinical Immunology: the Official Journal of the Clinical Immunology Society
https://www.readbyqxmd.com/read/28087410/repair-of-8-oxog-a-mismatches-by-the-mutyh-glycosylase-mechanism-metals-medicine
#7
REVIEW
Douglas M Banda, Nicole N Nuñez, Michael A Burnside, Katie M Bradshaw, Sheila S David
Reactive oxygen and nitrogen species (RONS) may infringe on the passing of pristine genetic information by inducing DNA inter- and intra-strand crosslinks, protein-DNA crosslinks, and chemical alterations to the sugar or base moieties of DNA. 8-Oxo-7,8-dihydroguanine (8-oxoG) is one of the most prevalent DNA lesions formed by RONS and is repaired through the base excision repair (BER) pathway involving the DNA repair glycosylases OGG1 and MUTYH in eukaryotes. MUTYH removes adenine (A) from 8-oxoG:A mispairs, thus mitigating the potential of G:C to T:A transversion mutations from occurring in the genome...
January 10, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/28059467/muty-dna-glycosylase-protects-cells-from-tumor-necrosis-factor-alpha-induced-necroptosis
#8
An Hue Vy Tran, Se Hee Han, Joon Kim, Francesca Grasso, Ye Sun Han
Numerous studies have implied that mutY DNA glycosylase (MYH) is involved in the repair of post-replicative mispairs and plays a critical role in the base excision repair pathway. Recent in vitro studies have shown that MYH interacts with tumor necrosis factor receptor type 1-associated death domain (TRADD), a key effector protein of tumor necrosis factor receptor-1 (TNFR1) signaling. The association between MYH and TRADD is reversed during tumor necrosis factor alpha (TNF-α)- and camptothecin (CPT)-induced apoptosis, and enhanced during TNF-α-induced survival...
January 6, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28049757/smug2-dna-glycosylase-from-pedobacter-heparinus-as-a-new-subfamily-in-udg-superfamily
#9
Panjiao Pang, Ye Yang, Jing Li, Zhong Wang, Weiguo Cao, Wei Xie
Base deamination is a common type of DNA damage that occurs in all organisms. DNA repair mechanisms are essential to maintain genome integrity, in which the base excision repair (BER) pathway plays a major role in the removal of base damage. In the BER pathway, the uracil DNA glycosylase superfamily is responsible for excising the deaminated bases from DNA and generates apurinic/apyrimidinic (AP) sites. Using bioinformatics tools, we identified a family 3 SMUG1-like DNA glycoyslase from Pedobacter heparinus (named as Phe SMUG2), which display catalytic activities towards DNA containing uracil or hypoxanthine/xanthine...
January 3, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28039450/aberrant-promoter-methylation-of-hogg1-may-be-associated-with-increased-risk-of-non-small-cell-lung-cancer
#10
Hualong Qin, Jianjie Zhu, Yuanyuan Zeng, Wenwen Du, Dan Shen, Zhe Lei, Qian Qian, Jian-An Huang, Zeyi Liu
DNA methylation may epigenetically inactivate tumor suppressor genes in NSCLC. As the human 8-oxoguanine DNA glycosylase (hOGG1) gene promoter is frequently methylated in NSCLC, we evaluated whether genetic or epigenetic alterations of hOGG1 are associated with increased risk of non-small cell lung cancer. Three hOGG1 haplotype-tagging SNPs (htSNP) were genotyped in PCR-restriction fragment length polymorphism assays, and one htSNP was genotyped in a PCR-single-strand conformation polymorphism assay in case-control studies of 217 NSCLC patients and 226 healthy controls...
December 26, 2016: Oncotarget
https://www.readbyqxmd.com/read/28032397/dna-base-excision-repair-and-nucleotide-excision-repair-synergistically-contribute-to-survival-of-stationary-phase-cells-of-the-fission-yeast-schizosaccharomyces-pombe
#11
Takanori Senoo, Shinji Kawano, Shogo Ikeda
Defects of genome maintenance may causally contribute to aging. In general, base excision repair (BER) is involved in the repair of subtle base lesions and AP sites, and bulky helix-distorting lesions are restored by nucleotide excision repair (NER). Here, we measured the chronological lifespan (CLS) of BER- and NER-deficient mutants of the fission yeast Schizosaccharomyces pombe, and observed the aging process of cells. The CLS of the nth1 (gene for DNA glycosylase/AP lyase) mutant and the rad16 (a homolog of human XPF) mutant were slightly shorter than that of the wild-type (WT) strain...
December 29, 2016: Cell Biology International
https://www.readbyqxmd.com/read/28028224/ape2-zf-grf-facilitates-3-5-resection-of-dna-damage-following-oxidative-stress
#12
Bret D Wallace, Zachary Berman, Geoffrey A Mueller, Yunfeng Lin, Timothy Chang, Sara N Andres, Jessica L Wojtaszek, Eugene F DeRose, C Denise Appel, Robert E London, Shan Yan, R Scott Williams
The Xenopus laevis APE2 (apurinic/apyrimidinic endonuclease 2) nuclease participates in 3'-5' nucleolytic resection of oxidative DNA damage and activation of the ATR-Chk1 DNA damage response (DDR) pathway via ill-defined mechanisms. Here we report that APE2 resection activity is regulated by DNA interactions in its Zf-GRF domain, a region sharing high homology with DDR proteins Topoisomerase 3α (TOP3α) and NEIL3 (Nei-like DNA glycosylase 3), as well as transcription and RNA regulatory proteins, such as TTF2 (transcription termination factor 2), TFIIS, and RPB9...
December 27, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27995963/histone-deacetylase-inhibitors-mediate-dna-damage-repair-in-ameliorating-hemorrhagic-cystitis
#13
Subhash Haldar, Christopher Dru, Rajeev Mishra, Manisha Tripathi, Frank Duong, Bryan Angara, Ana Fernandez, Moshe Arditi, Neil A Bhowmick
Hemorrhagic cystitis is an inflammatory and ulcerative bladder condition associated with systemic chemotherapeutics, like cyclophosphomide. Earlier, we reported reactive oxygen species resulting from cyclophosphamide metabolite, acrolein, causes global methylation followed by silencing of DNA damage repair genes. Ogg1 (8-oxoguanine DNA glycosylase) is one such silenced base excision repair enzyme that can restore DNA integrity. The accumulation of DNA damage results in subsequent inflammation associated with pyroptotic death of bladder smooth muscle cells...
December 20, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27994910/resveratrol-protects-sepsis-induced-oxidative-dna-damage-in-liver-and-kidney-of-rats
#14
Sevtap Aydın, Tevfik Tolga Şahin, Merve Bacanlı, Gökçe Taner, Arif Ahmet Başaran, Mehtap Aydın, Nurşen Başaran
BACKGROUND: The increases of free radicals have been proposed to be involved in the pathogenesis of sepsis, which leads to multiple-organ dysfunction syndromes. The uses of antioxidants as a complementary tool in the medical care of oxidative stress-related diseases have attracted attention of researchers. Resveratrol (RV) has suggested being antioxidant, anti-proliferative, and anti-inflammatory effects in various experimental models and clinical settings. AIMS: This study was undertaken to evaluate the protective effects of RV on oxidative DNA damage induced by sepsis in the liver and kidney tissues of Wistar albino rats...
November 2016: Balkan Medical Journal
https://www.readbyqxmd.com/read/27994037/destabilization-of-the-pcna-trimer-mediated-by-its-interaction-with-the-neil1-dna-glycosylase
#15
Aishwarya Prakash, Kedar Moharana, Susan S Wallace, Sylvie Doublié
The base excision repair (BER) pathway repairs oxidized lesions in the DNA that result from reactive oxygen species generated in cells. If left unrepaired, these damaged DNA bases can disrupt cellular processes such as replication. NEIL1 is one of the 11 human DNA glycosylases that catalyze the first step of the BER pathway, i.e. recognition and excision of DNA lesions. NEIL1 interacts with essential replication proteins such as the ring-shaped homotrimeric proliferating cellular nuclear antigen (PCNA). We isolated a complex formed between NEIL1 and PCNA (±DNA) using size exclusion chromatography (SEC)...
December 19, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27993944/effects-of-airborne-toxicants-on-pulmonary-function-and-mitochondrial-dna-damage-in-rodent-lungs
#16
William L Rumsey, Brian Bolognese, Alicia B Davis, Pearl L Flamberg, Joseph P Foley, Steven R Katchur, Charles J Kotzer, Ruth R Osborn, Patricia L Podolin
Inhalation of airborne toxicants such as cigarette smoke and ozone is a shared health risk among the world's populations. The use of toxic herbicides like paraquat (PQ) is restricted by many countries, yet in the developing world PQ has demonstrable ill effects. The present study examined changes in pulmonary function, mitochondrial DNA (mtDNA) integrity and markers of DNA repair induced by acute or repeated exposure of PQ to rats. Similar to cigarette smoke and ozone, PQ promotes oxidative stress, and the impact of PQ on mtDNA was compared with that obtained with these agents...
December 18, 2016: Mutagenesis
https://www.readbyqxmd.com/read/27980098/restriction-glycosylases-involvement-of-endonuclease-activities-in-the-restriction-process
#17
Yingbiao Zhang, Tomoyuki Matsuzaka, Hirokazu Yano, Yoshikazu Furuta, Toshiaki Nakano, Ken Ishikawa, Masaki Fukuyo, Noriko Takahashi, Yutaka Suzuki, Sumio Sugano, Hiroshi Ide, Ichizo Kobayashi
All restriction enzymes examined are phosphodiesterases generating 3'-OH and 5'-P ends, but one restriction enzyme (restriction glycosylase) excises unmethylated bases from its recognition sequence. Whether its restriction activity involves endonucleolytic cleavage remains unclear. One report on this enzyme, R.PabI from a hyperthermophile, ascribed the breakage to high temperature while another showed its weak AP lyase activity generates atypical ends. Here, we addressed this issue in mesophiles. We purified R...
December 14, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27974818/cadmium-ii-inhibition-of-human-uracil-dna-glycosylase-by-catalytic-water-supplantation
#18
Trevor Gokey, Bo Hang, Anton B Guliaev
Toxic metals are known to inhibit DNA repair but the underlying mechanisms of inhibition are still not fully understood. DNA repair enzymes such as human uracil-DNA glycosylase (hUNG) perform the initial step in the base excision repair (BER) pathway. In this work, we showed that cadmium [Cd(II)], a known human carcinogen, inhibited all activity of hUNG at 100 μM. Computational analyses based on 2 μs equilibrium, 1.6 μs steered molecular dynamics (SMD), and QM/MM MD determined that Cd(II) ions entered the enzyme active site and formed close contacts with both D145 and H148, effectively replacing the catalytic water normally found in this position...
December 15, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27951654/interaction-with-the-dna-repair-protein-thymine-dna-glycosylase-regulates-histone-acetylation-by-p300
#19
Ryan A Henry, Pietro Mancuso, Yin-Ming Kuo, Rossella Tricarico, Marc Tini, Philip A Cole, Alfonso Bellacosa, Andrew J Andrews
How protein-protein interactions regulate and alter histone modifications is a major unanswered question in epigenetics. The histone acetyltransferase p300 binds thymine DNA glycosylase (TDG); utilizing mass spectrometry to measure site-specific changes in histone acetylation, we found that the absence of TDG in mouse embryonic fibroblasts leads to a reduction in the rate of histone acetylation. We demonstrate that TDG interacts with the CH3 domain of p300 to allosterically promote p300 activity to specific lysines on histone H3 (K18 and K23)...
December 13, 2016: Biochemistry
https://www.readbyqxmd.com/read/27939754/increasing-no-level-regulates-apoptosis-and-inflammation-in-macrophages-after-2-chloroethyl-ethyl-sulphide-challenge
#20
Satish Sagar, Soumya Ranjan Parida, Silpa Sabnam, Huma Rizwan, Sweta Pal, Mitali Madhusmita Swain, Arttatrana Pal
Generation of nitric oxide (NO) in cellular compartments acts in a redox-dependent manner to counteract oxidative stress either by directly acting as an antioxidant through scavenging superoxide anions (O2(-)), to form peroxynitrite (ONOO-) or acting as a signaling molecule, altering gene expression that triggers various physiological processes. However, the molecular mechanisms of macrophage activation and NO production leads to apoptosis and inflammation after 2-chloroethyl ethyl sulphide (CEES) exposure remains unclear...
December 9, 2016: International Journal of Biochemistry & Cell Biology
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