scholarly journals Base Excision Repair in Sugarcane – A New Outlook

2021 ◽  
Author(s):  
Nathalia Maíra Cabral de Medeiros ◽  
Katia Castanho Scortecci
Keyword(s):  
Dna Repair ◽  
Base Excision Repair ◽  
Excision Repair ◽  
Complete Sequence ◽  
Protein Protein Interaction ◽  
Poaceae Family ◽  
Domains Of Life ◽  
Base Excision ◽  
Protein Models ◽  
Sugarcane Genome

The base excision repair (BER) pathway has been associated with genome integrity maintenance. Owing to its central role, BER is present in all three domains of life. The studies in plants, considering BER, have been conducted using Arabidopsis and rice models. Therefore, future studies regarding BER are required in other organisms, particularly in crops such as sugarcane, to understand its mechanism, which may reflect the uniqueness of DNA repair in monocots. Our previous results have revealed that sugarcane is an interesting plant for studying this pathway considering the polyploidy genome and genome evolution. This chapter aimed to characterize the BER pathway in sugarcane by using different bioinformatics tools, for example, screening for BER homologs in the sugarcane genome to identify its members. Each sequence obtained was subjected to structural analysis, and certain differences were identified when Arabidopsis was compared to other monocots, including sugarcane. Moreover, ROS1, DEM, and DML3 were not identified as a complete sequence in the sugarcane EST database. Furthermore, FEN1 is present as two sequences, namely FEN1A and FEN1B, both featuring different amino acid sequence and motif presence. Furthermore, FEN1 sequence was selected for further characterization considering its evolutionary history, as sequence duplication was observed only in the Poaceae family. Considering the importance of this protein for BER pathway, this sequence was evaluated using protein models (3D), and a possible conservation was observed during protein–protein interaction. Thus, these results help us understand the roles of certain BER components in sugarcane, and may reveal the aspects and functions of this pathway beyond those already established in the literature.

Incorporation of 5’,8-cyclo-2’deoxyadenosines by DNA repair polymerases via base excision repair

DNA Repair ◽  
2021 ◽  
pp. 103258
Author(s):  
Pawlos S. Tsegay ◽  
Daniela Hernandez ◽  
Christopher Brache ◽  
Chryssostomos Chatgilialoglu ◽  
Marios G. Krokidis ◽  
...  
Keyword(s):  
Dna Repair ◽  
Base Excision Repair ◽  
Excision Repair ◽  
Base Excision

scholarly journals Expansion of base excision repair compensates for a lack of DNA repair by oxidative dealkylation in budding yeast

2019 ◽  
Vol 294 (37) ◽  
pp. 13629-13637 ◽  
Author(s):  
Suzanne J. Admiraal ◽  
Daniel E. Eyler ◽  
Michael R. Baldwin ◽  
Emily M. Brines ◽  
Christopher T. Lohans ◽  
...  
Keyword(s):  
Dna Repair ◽  
Base Excision Repair ◽  
Excision Repair ◽  
Budding Yeast ◽  
Base Excision

scholarly journals Impact of hypoxia on DNA repair and genome integrity

Mutagenesis ◽  
2019 ◽  
Vol 35 (1) ◽  
pp. 61-68 ◽  
Author(s):  
Alanna R Kaplan ◽  
Peter M Glazer
Keyword(s):  
Dna Repair ◽  
Cancer Progression ◽  
Base Excision Repair ◽  
Mutation Frequency ◽  
Excision Repair ◽  
Tumour Microenvironment ◽  
Genome Integrity ◽  
Future Directions ◽  
Homology Directed Repair ◽  
Base Excision

Abstract Hypoxia is a hallmark of the tumour microenvironment with profound effects on tumour biology, influencing cancer progression, the development of metastasis and patient outcome. Hypoxia also contributes to genomic instability and mutation frequency by inhibiting DNA repair pathways. This review summarises the diverse mechanisms by which hypoxia affects DNA repair, including suppression of homology-directed repair, mismatch repair and base excision repair. We also discuss the effects of hypoxia mimetics and agents that induce hypoxia on DNA repair, and we highlight areas of potential clinical relevance as well as future directions.

scholarly journals Dynamic Compartmentalization of Base Excision Repair Proteins in Response to Nuclear and Mitochondrial Oxidative Stress

2008 ◽  
Vol 29 (3) ◽  
pp. 794-807 ◽  
Author(s):  
Lyra M. Griffiths ◽  
Dan Swartzlander ◽  
Kellen L. Meadows ◽  
Keith D. Wilkinson ◽  
Anita H. Corbett ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Dna Damage ◽  
Dna Repair ◽  
Base Excision Repair ◽  
Oxidative Dna Damage ◽  
Excision Repair ◽  
Intracellular Localization ◽  
Genotoxic Stress ◽  
Mitochondrial Oxidative Stress ◽  
Base Excision

ABSTRACT DNAs harbored in both nuclei and mitochondria of eukaryotic cells are subject to continuous oxidative damage resulting from normal metabolic activities or environmental insults. Oxidative DNA damage is primarily reversed by the base excision repair (BER) pathway, initiated by N-glycosylase apurinic/apyrimidinic (AP) lyase proteins. To execute an appropriate repair response, BER components must be distributed to accommodate levels of genotoxic stress that may vary considerably between nuclei and mitochondria, depending on the growth state and stress environment of the cell. Numerous examples exist where cells respond to signals, resulting in relocalization of proteins involved in key biological transactions. To address whether such dynamic localization contributes to efficient organelle-specific DNA repair, we determined the intracellular localization of the Saccharomyces cerevisiae N-glycosylase/AP lyases, Ntg1 and Ntg2, in response to nuclear and mitochondrial oxidative stress. Fluorescence microscopy revealed that Ntg1 is differentially localized to nuclei and mitochondria, likely in response to the oxidative DNA damage status of the organelle. Sumoylation is associated with targeting of Ntg1 to nuclei containing oxidative DNA damage. These studies demonstrate that trafficking of DNA repair proteins to organelles containing high levels of oxidative DNA damage may be a central point for regulating BER in response to oxidative stress.

The Polymorphism Of Base Excision Repair Gene, XRCC1 Arg399Gln Is Associated With The Therapy-Related Myelodysplastic Syndromes (MDS)

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 4085-4085
Author(s):  
Batchimeg Norjmaa ◽  
Takayuki Saitoh ◽  
Atsushi Iwasaki ◽  
Yasuhiro Nitta ◽  
Yuta Masuda ◽  
...  
Keyword(s):  
Dna Repair ◽  
Clinical Features ◽  
Base Excision Repair ◽  
Myelodysplastic Syndromes ◽  
Excision Repair ◽  
Control Group ◽  
Xrcc1 Arg399gln ◽  
History Of ◽  
Base Excision ◽  
Ape1 Asp148glu

Abstract Background Base excision repair (BER) is critical for genome maintenance, and is mainly responsible for the correction of small base changes of DNA damage. BER pathway involved many enzymes including OGG1, XRCC1, APE1 and MUTYH. Single nucleotide polymorphisms (SNPs) in DNA repair genes result reduced DNA repair capacity, have been reported to be associated with an increased risk of various cancers including hematologic malignancies. However, it is unclear that these polymorphisms alter the susceptibility and clinical outcome of myelodysplastic syndromes (MDS) patients. The aim of this study is to evaluate the association of polymorphisms in gene encoding four key proteins of DNA BER: OGG1 Ser326Cys, XRCC1 Arg399Gln, APE1 Asp148Glu, and MUTYHGln324His with the susceptibility and clinical features of MDS. Methods Our study included 113 MDS patients [median 68.3 years, range 17.1-86.5 years; male/female 76/37; RCUD (n=37), RARS (n=6), RCMD (n=21), MDS-u (n=11), RAEB-1(n=14), RAEB-2 (n=11), others (n=13)] and 192-health control group. Twenty four patients with MDS had the history of cancer. Genetic polymorphisms in BER pathway genes were examined using PCR and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique. Genotype and allele frequencies were compared between patients group and control group by using χ2-test. All patients and healthy controls received written information about the study. This study was approved by the International Research Board of Gunma University Hospital. Results There was no statistically significant difference in the allele and genotype frequencies of the OGG1 Ser326Cys, XRCC1 Arg399Gln, APE1 Asp148Glu, and MUTYH Gln324His polymorphisms between the MDS patients and the control group. In the analysis of clinical characteristics, XRCC1 non Arg/Arg genotype (low DNA repair type) was significantly associated with lower Hb level (8.64±2.29g/dL vs. 9.96±2.08 g/dL, p<0.005) and higher frequency of the complex karyotype (14.9% vs. 2.8%, p=0.05). Furthermore, XRCC1 non Arg/Arg genotype was associated with therapy- related MDS (OR 3.15, 95% CI 1.24-7.98, p=0.02) and especially the past history of radiotherapy (14.3% vs. 0%, p<0.005). In contrast, the polymorphisms in OGG1 Ser326Cys, APE1 Asp148Glu, and MUTYH Gln324His were not involved in the clinical features of MDS. Conclusion The low DNA repair polymorphism, XRCC1 Arg399Gln is associated with the clinical features of MDS, including therapy- related MDS. Further investigation of BER polymorphisms will provide the understanding of pathogenesis of therapy- related MDS in a larger sample size analysis. Disclosures: No relevant conflicts of interest to declare.

Incomplete complementation of the DNA repair defect in cockayne syndrome cells by the denV gene from bacteriophage T4 suggests a deficiency in base excision repair

1997 ◽  
Vol 385 (1) ◽  
pp. 59-74 ◽  
Author(s):  
Murray A Francis ◽  
Paramjeet S Bagga ◽  
Raghbir S Athwal ◽  
Andrew J Rainbow
Keyword(s):  
Dna Repair ◽  
Base Excision Repair ◽  
Excision Repair ◽  
Bacteriophage T4 ◽  
Cockayne Syndrome ◽  
Base Excision ◽  
Repair Defect ◽  
Denv Gene

Base excision repair in Archaea: Back to the future in DNA repair

DNA Repair ◽  
2014 ◽  
Vol 21 ◽  
pp. 148-157 ◽  
Author(s):  
Stefano Grasso ◽  
Gianluca Tell
Keyword(s):  
Dna Repair ◽  
Base Excision Repair ◽  
Excision Repair ◽  
The Future ◽  
Base Excision

scholarly journals siRNA Screening of a Targeted Library of DNA Repair Factors in HIV Infection Reveals a Role for Base Excision Repair in HIV Integration

PLoS ONE ◽  
2011 ◽  
Vol 6 (3) ◽  
pp. e17612 ◽  
Author(s):  
Amy S. Espeseth ◽  
Rick Fishel ◽  
Daria Hazuda ◽  
Qian Huang ◽  
Min Xu ◽  
...  
Keyword(s):  
Dna Repair ◽  
Hiv Infection ◽  
Base Excision Repair ◽  
Excision Repair ◽  
Base Excision ◽  
Hiv Integration ◽  
Targeted Library ◽  
Sirna Screening

scholarly journals The DNA repair protein NBS1 influences the base excision repair pathway

2009 ◽  
Vol 30 (3) ◽  
pp. 408-415 ◽  
Author(s):  
D. Sagan ◽  
R. Muller ◽  
C. Kroger ◽  
A. Hematulin ◽  
S. Mortl ◽  
...  
Keyword(s):  
Dna Repair ◽  
Base Excision Repair ◽  
Excision Repair ◽  
Repair Pathway ◽  
Base Excision Repair Pathway ◽  
Repair Protein ◽  
Dna Repair Protein ◽  
Base Excision
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