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nucleotide excision repair

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https://www.readbyqxmd.com/read/29785501/improving-the-acetic-acid-tolerance-and-fermentation-of-acetobacter-pasteurianus-by-nucleotide-excision-repair-protein-uvra
#1
Yu Zheng, Jing Wang, Xiaolei Bai, Yangang Chang, Jun Mou, Jia Song, Min Wang
Acetic acid bacteria (AAB) are widely used in acetic acid fermentation due to their remarkable ability to oxidize ethanol and high tolerance against acetic acid. In Acetobacter pasteurianus, nucleotide excision repair protein UvrA was up-regulated 2.1 times by acetic acid when compared with that without acetic acid. To study the effects of UvrA on A. pasteurianus acetic acid tolerance, uvrA knockout strain AC2005-ΔuvrA, uvrA overexpression strain AC2005 (pMV24-uvrA), and the control strain AC2005 (pMV24), were constructed...
May 21, 2018: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29779017/-xpg-rs17655-g-c-polymorphism-associated-with-cancer-risk-evidence-from-60-studies
#2
Jie Zhao, Shanshan Chen, Haixia Zhou, Ting Zhang, Yang Liu, Jing He, Jinhong Zhu, Jichen Ruan
Xeroderma pigmentosum group G (XPG), a key component in nucleotide excision repair pathway, functions to cut DNA lesions during DNA repair. Genetic variations that alter DNA repair gene expression or function may decrease DNA repair ability and impair genome integrity, thereby predisposing to cancer. The association between XPG rs17655 G>C polymorphism and cancer risk has been investigated extensively, but the results remain contradictory. To get a more accurate conclusion, we performed a comprehensive meta-analysis of 60 case-control studies, involving 27,098 cancer cases and 30,535 healthy controls...
May 20, 2018: Aging
https://www.readbyqxmd.com/read/29768183/ndrg1-disruption-alleviates-cisplatin-sodium-glycididazole-induced-dna-damage-response-and-apoptosis-in-ercc1-defective-lung-cancer-cells
#3
Lang He, Kang Liu, Xiaoshan Wang, Hong Chen, Jin Zhou, Xun Wu, Tao Liu, Yongxue Yang, Xuemei Yang, Dandan Cui, Guiqin Song, Jianguo Lei, Jun Wang
BACKGROUND: Resistance to platinum-based chemotherapy becomes a major obstacle in lung cancer treatment. Compensatory activation of nucleotide excision repair (NER) pathway is the major mechanism accounting for cisplatin-resistance. We aimed at identifying additional regulators in NER-mediated chemoresistance in a hypoxic setting induced by sodium glycididazole (CMNa)-sensitized cisplatin chemotherapy of non-small cell lung cancer (NSCLC). METHODS: We performed an RNA-sequencing (RNA-Seq) analysis to identify the genes whose expression had been differentially regulated in NER-deficient cells that had been treated by cisplatin/CMNa...
May 13, 2018: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/29762710/base-flipping-dynamics-from-an-intrahelical-to-an-extrahelical-state-exerted-by-thymine-dna-glycosylase-during-dna-repair-process
#4
Lin-Tai Da, Jin Yu
Thymine DNA glycosylase (TDG) is a DNA repair enzyme that excises a variety of mismatched or damaged nucleotides (nts), e.g. dU, dT, 5fC and 5caC. TDG is shown to play essential roles in maintaining genome integrity and correctly programming epigenetic modifications through DNA demethylation. After locating the lesions, TDG employs a base-flipping strategy to recognize the damaged nucleobases, whereby the interrogated nt is extruded from the DNA helical stack and binds into the TDG active site. The dynamic mechanism of the base-flipping process at an atomistic resolution, however, remains elusive...
May 14, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29756644/metabolic-and-gene-expression-hallmarks-of-seed-germination-uncovered-by-sodium-butyrate-in-medicago-truncatula
#5
Andrea Pagano, Susana de Sousa Araújo, Anca Macovei, Daniele Dondi, Simone Lazzaroni, Alma Balestrazzi
Since high-quality seeds are essential for successful crop production in challenging environments, understanding the molecular bases of seed vigor will lead to advances in seed technology. Histone deacetylase (HDAC) inhibitors, promoting histone hyperacetylation, are used as tools to explore aspects still uncovered of the abiotic stress response in plants. The aim of this work was to investigate novel signatures of seed germination in Medicago truncatula, using the HDAC inhibitor sodium butyrate (NaB) as stress agent...
May 14, 2018: Plant, Cell & Environment
https://www.readbyqxmd.com/read/29752965/recq-helicase-disease-and-related-progeroid-syndromes-recq2018-meeting
#6
REVIEW
Junko Oshima, Hisaya Kato, Yoshiro Maezawa, Koutaro Yokote
Progeroid syndrome is a group of disorders characterized by the early onset of diseases that are associated with aging. Best known examples are Werner syndrome, which is adult onset and results from disease-causing DNA sequence variants in the RecQ helicase gene WRN, and Hutchison-Gilford progeria syndrome, which is childhood-onset and results from unique, recurrent disease-causing DNA sequence variants of the gene LMNA that encodes nuclear intermediate filaments. Related single gene RecQ disorders are Bloom syndrome and Rothmund-Thomson syndrome...
May 9, 2018: Mechanisms of Ageing and Development
https://www.readbyqxmd.com/read/29741625/dna-repair-in-the-archaea-an-emerging-picture
#7
Malcolm F White, Thorsten Allers
There has long been a fascination in the DNA Repair pathways of archaea, for two main reasons. Firstly, many archaea inhabit extreme environments where the rate of physical damage to DNA is accelerated. These archaea might reasonably be expected to have particularly robust or novel DNA repair pathways to cope with this. Secondly, the archaea have long been understood to be a lineage distinct from the bacteria, and to share a close relationship with the eukarya, particularly in their information processing systems...
May 5, 2018: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/29738624/saccharomyces-cerevisiae-mus81-mms4-and-rad52-can-cooperate-in-the-resolution-of-recombination-intermediates
#8
Huong Thi Thu Phung, Hoa Luong Hieu Nguyen, Sang Thanh Vo, Dung Hoang Nguyen, Minh Van Le
Mus81 is a well conserved DNA structure-specific endonuclease which belongs to the XPF/Rad1 family of proteins that are involved in DNA nucleotide excision repair. Mus81 forms a heterodimer with a non-catalytic subunit, Mms4 in Saccharomyces cerevisiae (Eme1/EME1 in Schizosaccharomyces pombe and mammals). Recent evidence shows that Mus81 functions redundantly with Sgs1, a member of the ubiquitous RecQ family of DNA helicases, to process toxic recombinant intermediates. In budding yeast, homologous recombination is regulated by the Rad52 epistasis group of proteins, including Rad52, which stimulates the main steps of DNA sequence-homology searching...
May 8, 2018: Yeast
https://www.readbyqxmd.com/read/29735688/cisplatin-dna-adduct-repair-of-transcribed-genes-is-controlled-by-two-circadian-programs-in-mouse-tissues
#9
Yanyan Yang, Ogun Adebali, Gang Wu, Christopher P Selby, Yi-Ying Chiou, Naim Rashid, Jinchuan Hu, John B Hogenesch, Aziz Sancar
Cisplatin is a major cancer chemotherapeutic drug. It kills cancer cells by damaging their DNA, mainly in the form of Pt-d(GpG) diadducts. However, it also has serious side effects, including nephrotoxicity and hepatotoxicity that limit its usefulness. Chronotherapy is taking circadian time into account during therapy to improve the therapeutic index, by improving efficacy and/or limiting toxicity. To this end, we tested the impact of clock time on excision repair of cisplatin-induced DNA damage at single-nucleotide resolution across the genome in mouse kidney and liver...
May 7, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29733857/transcription-coupled-repair-and-complex-biology
#10
REVIEW
James R Portman, Terence R Strick
All active living organisms mitigate DNA damage via DNA repair, and the so-called nucleotide excision repair pathway (NER) represents a functionally major part of the cell's DNA repair repertoire [1]. In this pathway, the damaged strand of DNA is incised and removed before being resynthesized. This form of DNA repair requires a multitude of proteins working in a complex choreography. Repair thus typically involves detection of a DNA lesion; validation of that detection event; search for an appropriate incision site and subsequent DNA incision; DNA unwinding/removal; and DNA resynthesis and religation...
May 4, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29719287/downregulation-of-rif1-enhances-sensitivity-to-platinum-based-chemotherapy-in-epithelial-ovarian-cancer-eoc-by-regulating-nucleotide-excision-repair-ner-pathway
#11
Yong-Bin Liu, Ying Mei, Zheng-Wen Tian, Jing Long, Chen-Hui Luo, Hong-Hao Zhou
BACKGROUND/AIMS: Rap1 interacting factor 1 (RIF1) was deemed to be involved in replication timing regulation and DNA damage response. However, little is known about the role of RIF1 in malignancies. Thus, this study aimed to investigate whether the expression of RIF1 is relevant to the response of epithelial ovarian cancer (EOC) patients to cisplatin chemotherapy and its underlying mechanism. METHODS: Immunohistochemistry was used for detecting the expression of RIF1 in 72 human ovarian cancer tissues followed by association analysis of RIF1 expression with patients' responses to platinum-based chemotherapy...
April 26, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29717169/ung-1-and-apn-1-are-the-major-enzymes-to-efficiently-repair-5-hydroxymethyluracil-dna-lesions-in-c-elegans
#12
Arturo Papaluca, J Richard Wagner, H Uri Saragovi, Dindial Ramotar
In Caenorhabditis elegans, two DNA glycosylases, UNG-1 and NTH-1, and two AP endonucleases, APN-1 and EXO-3, have been characterized from the base-excision repair (BER) pathway that repairs oxidatively modified DNA bases. UNG-1 removes uracil, while NTH-1 can remove 5-hydroxymethyluracil (5-hmU), an oxidation product of thymine, as well as other lesions. Both APN-1 and EXO-3 can incise AP sites and remove 3'-blocking lesions at DNA single strand breaks, and only APN-1 possesses 3'- to 5'-exonulease and nucleotide incision repair activities...
May 1, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29710850/computational-characterization-of-small-molecules-binding-to-the-human-xpf-active-site-and-virtual-screening-to-identify-potential-new-dna-repair-inhibitors-targeting-the-ercc1-xpf-endonuclease
#13
Francesco Gentile, Khaled H Barakat, Jack A Tuszynski
The DNA excision repair protein ERCC-1-DNA repair endonuclease XPF (ERCC1-XPF) is a heterodimeric endonuclease essential for the nucleotide excision repair (NER) DNA repair pathway. Although its activity is required to maintain genome integrity in healthy cells, ERCC1-XPF can counteract the effect of DNA-damaging therapies such as platinum-based chemotherapy in cancer cells. Therefore, a promising approach to enhance the effect of these therapies is to combine their use with small molecules, which can inhibit the repair mechanisms in cancer cells...
April 30, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29700578/specialised-dna-polymerases-in-escherichia-coli-roles-within-multiple-pathways
#14
REVIEW
Sarah S Henrikus, Antoine M van Oijen, Andrew Robinson
In many bacterial species, DNA damage triggers the SOS response; a pathway that regulates the production of DNA repair and damage tolerance proteins, including error-prone DNA polymerases. These specialised polymerases are capable of bypassing lesions in the template DNA, a process known as translesion synthesis (TLS). Specificity for lesion types varies considerably between the different types of TLS polymerases. TLS polymerases are mainly described as working in the context of replisomes that are stalled at lesions or in lesion-containing gaps left behind the replisome...
April 26, 2018: Current Genetics
https://www.readbyqxmd.com/read/29696001/the-pivotal-role-of-dna-repair-in-infection-mediated-inflammation-and-cancer
#15
REVIEW
Ayse Z Sahan, Tapas K Hazra, Soumita Das
Pathogenic and commensal microbes induce various levels of inflammation and metabolic disease in the host. Inflammation caused by infection leads to increased production of reactive oxygen species (ROS) and subsequent oxidative DNA damage. These in turn cause further inflammation and exacerbation of DNA damage, and pose a risk for cancer development. Helicobacter pylori -mediated inflammation has been implicated in gastric cancer in many previously established studies, and Fusobacterium nucleatum presence has been observed with greater intensity in colorectal cancer patients...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29695933/genetic-variants-in-the-nucleotide-excision-repair-pathway-genes-and-gastric-cancer-susceptibility-in-a-southern-chinese-population
#16
Jing He, Zhen-Jian Zhuo, Anqi Zhang, Jinhong Zhu, Rui-Xi Hua, Wen-Qiong Xue, Shao-Dan Zhang, Jiang-Bo Zhang, Xi-Zhao Li, Wei-Hua Jia
Background: Potentially functional polymorphisms can modulate protein activities and host's DNA repair capacity, thereby influencing cancer susceptibility. The association of the polymorphisms in the nucleotide excision repair core pathway genes and gastric cancer susceptibility remains largely unknown. Methods: Here, we systematically analyzed the associations between nine polymorphisms in four key genes ( XPA , ERCC1 , ERCC2 , and ERCC4 ) in the nucleotide excision repair pathway and gastric cancer risk in a Chinese population including 1142 patients and 1173 controls...
2018: Cancer Management and Research
https://www.readbyqxmd.com/read/29695696/-dna-bearing-bulky-fluorescent-and-photoreactive-damage-in-both-strands-as-substrates-of-the-nucleotide-excision-repair-system
#17
N V Lukyanchikova, I O Petruseva, A N Evdokimov, L S Koroleva, O I Lavrik
Model DNA molecules that contain bulky lesions in both strands have been created, and their properties as substrates of the nucleotide excision repair (NER) system have been analyzed. The modified nucleoside, 5-[3-(4-azido-2,3,5,6-tetrafluorobenzamido)-1-propoxypropyl]-2'-deoxycytidine (dC^(FAB)), or the nonnucleoside fragment, N-[6-(9-anthracenylcarbamoyl)hexanoyl]-3-amino-1,2-propanediol (nAnt), have been inserted as damage in certain positions of the first DNA strand ("0"). The position of N-[6-5(6)-fluoresceinylcarbamoyl]hexanoyl] -3-amino-1,2-propanediol (nFlu) has been varied within the second DNA strand...
March 2018: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/29683386/coupling-between-nucleotide-excision-repair-and-gene-expression
#18
Adrián E Cambindo Botto, Juan C Muñoz, Manuel J Muñoz
Gene expression and DNA repair are fundamental processes for life. During the last decade, accumulating experimental evidence point towards different modes of coupling between these processes. Here we discuss the molecular mechanisms by which RNAPII-dependent transcription affects repair by the Nucleotide Excision Repair system (NER) and how NER activity, through the generation of single stranded DNA intermediates and activation of the DNA damage response kinase ATR, drives gene expression in a genotoxic scenario...
April 23, 2018: RNA Biology
https://www.readbyqxmd.com/read/29676391/author-correction-phosphorylated-hbo1-at-uv-irradiated-sites-is-essential-for-nucleotide-excision-repair
#19
Hiroyuki Niida, Ryoichi Matsunuma, Ryo Horiguchi, Chiharu Uchida, Yuka Nakazawa, Akira Motegi, Koji Nishimoto, Satoshi Sakai, Tatsuya Ohhata, Kyoko Kitagawa, Shinichi Moriwaki, Hideo Nishitani, Ayako Ui, Tomoo Ogi, Masatoshi Kitagawa
This corrects the article DOI: 10.1038/ncomms16102.
April 20, 2018: Nature Communications
https://www.readbyqxmd.com/read/29675892/dna-repair-protein-xpa-is-differentially-expressed-in-colorectal-cancer-and-predicts-better-prognosis
#20
Xue Feng, Jingwei Liu, Yuehua Gong, Kaihua Gou, Huaiwei Yang, Yuan Yuan, Chengzhong Xing
As an indispensable factor in DNA damage recognition step of nucleotide excision repair, XPA interacts with a series of proteins to initiate repair process. The expression characteristics of XPA in colorectal cancer (CRC) and its influence on CRC prognosis remain elusive. Tissue specimens of CRC and nontumor adjacent tissues from 283 patients were collected. XPA protein expressions were detected by immunohistochemistry staining. Nonparametric test was used to investigate the difference of XPA expression between CRC and nontumor adjacent tissues, as well as the correlation between XPA expression and clinicopathological parameters of CRC...
April 19, 2018: Cancer Medicine
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