scholarly journals Dissecting Highly Mutagenic Processing of Complex Clustered DNA Damage in Yeast Saccharomyces cerevisiae

Cells ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 2309
Author(s):  
Stanislav G. Kozmin ◽  
Gregory Eot-Houllier ◽  
Anne Reynaud-Angelin ◽  
Didier Gasparutto ◽  
Evelyne Sage
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Damage ◽  
Excision Repair ◽  
Cell Extract ◽  
Yeast Saccharomyces Cerevisiae ◽  
Strand Breaks ◽  
High Mutation Frequency ◽  
Base Excision ◽  
Ionizing Radiation Exposure

Clusters of DNA damage, also called multiply damaged sites (MDS), are a signature of ionizing radiation exposure. They are defined as two or more lesions within one or two helix turns, which are created by the passage of a single radiation track. It has been shown that the clustering of DNA damage compromises their repair. Unresolved repair may lead to the formation of double-strand breaks (DSB) or the induction of mutation. We engineered three complex MDS, comprised of oxidatively damaged bases and a one-nucleotide (1 nt) gap (or not), in order to investigate the processing and the outcome of these MDS in yeast Saccharomyces cerevisiae. Such MDS could be caused by high linear energy transfer (LET) radiation. Using a whole-cell extract, deficient (or not) in base excision repair (BER), and a plasmid-based assay, we investigated in vitro excision/incision at the damaged bases and the mutations generated at MDS in wild-type, BER, and translesion synthesis-deficient cells. The processing of the studied MDS did not give rise to DSB (previously published). Our major finding is the extremely high mutation frequency that occurs at the MDS. The proposed processing of MDS is rather complex, and it largely depends on the nature and the distribution of the damaged bases relative to the 1 nt gap. Our results emphasize the deleterious consequences of MDS in eukaryotic cells.

scholarly journals Astragalin from Cassia alata Induces DNA Adducts in Vitro and Repairable DNA Damage in the Yeast Saccharomyces cerevisiae

2012 ◽  
Vol 13 (3) ◽  
pp. 2846-2862 ◽  
Author(s):  
Samuel Saito ◽  
Givaldo Silva ◽  
Regineide Xavier Santos ◽  
Grace Gosmann ◽  
Cristina Pungartnik ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Damage ◽  
Dna Adducts ◽  
Yeast Saccharomyces Cerevisiae ◽  
Cassia Alata

scholarly journals DNA polymerase X from Deinococcus radiodurans implicated in bacterial tolerance to DNA damage is characterized as a short patch base excision repair polymerase

Microbiology ◽  
2009 ◽  
Vol 155 (9) ◽  
pp. 3005-3014 ◽  
Author(s):  
Nivedita P. Khairnar ◽  
Hari S. Misra
Keyword(s):  
Dna Damage ◽  
Dna Polymerase ◽  
Base Excision Repair ◽  
Deinococcus Radiodurans ◽  
Excision Repair ◽  
Strand Break ◽  
Klenow Fragment ◽  
E Coli ◽  
Base Excision

The Deinococcus radiodurans R1 genome encodes an X-family DNA repair polymerase homologous to eukaryotic DNA polymerase β. The recombinant deinococcal polymerase X (PolX) purified from transgenic Escherichia coli showed deoxynucleotidyltransferase activity. Unlike the Klenow fragment of E. coli, this enzyme showed short patch DNA synthesis activity on heteropolymeric DNA substrate. The recombinant enzyme showed 5′-deoxyribose phosphate (5′-dRP) lyase activity and base excision repair function in vitro, with the help of externally supplied glycosylase and AP endonuclease functions. A polX disruption mutant of D. radiodurans expressing 5′-dRP lyase and a truncated polymerase domain was comparatively less sensitive to γ-radiation than a polX deletion mutant. Both mutants showed higher sensitivity to hydrogen peroxide. Excision repair mutants of E. coli expressing this polymerase showed functional complementation of UV sensitivity. These results suggest the involvement of deinococcal polymerase X in DNA-damage tolerance of D. radiodurans, possibly by contributing to DNA double-strand break repair and base excision repair.

scholarly journals Repair of Endonuclease-Induced Double-Strand Breaks in Saccharomyces cerevisiae: Essential Role for Genes Associated with Nonhomologous End-Joining

Genetics ◽  
1999 ◽  
Vol 152 (4) ◽  
pp. 1513-1529 ◽  
Author(s):  
L Kevin Lewis ◽  
James W Westmoreland ◽  
Michael A Resnick
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cell Cycle ◽  
Excision Repair ◽  
Cell Killing ◽  
Double Strand Breaks ◽  
Nonhomologous End Joining ◽  
Chromosomal Dna ◽  
End Joining ◽  
Yeast Saccharomyces Cerevisiae ◽  
Strand Breaks

Abstract Repair of double-strand breaks (DSBs) in chromosomal DNA by nonhomologous end-joining (NHEJ) is not well characterized in the yeast Saccharomyces cerevisiae. Here we demonstrate that several genes associated with NHEJ perform essential functions in the repair of endonuclease-induced DSBs in vivo. Galactose-induced expression of EcoRI endonuclease in rad50, mre11, or xrs2 mutants, which are deficient in plasmid DSB end-joining and some forms of recombination, resulted in G2 arrest and rapid cell killing. Endonuclease synthesis also produced moderate cell killing in sir4 strains. In contrast, EcoRI caused prolonged cell-cycle arrest of recombination-defective rad51, rad52, rad54, rad55, and rad57 mutants, but cells remained viable. Cell-cycle progression was inhibited in excision repair-defective rad1 mutants, but not in rad2 cells, indicating a role for Rad1 processing of the DSB ends. Phenotypic responses of additional mutants, including exo1, srs2, rad5, and rdh54 strains, suggest roles in recombinational repair, but not in NHEJ. Interestingly, the rapid cell killing in haploid rad50 and mre11 strains was largely eliminated in diploids, suggesting that the cohesive-ended DSBs could be efficiently repaired by homologous recombination throughout the cell cycle in the diploid mutants. These results demonstrate essential but separable roles for NHEJ pathway genes in the repair of chromosomal DSBs that are structurally similar to those occurring during cellular development.

scholarly journals The Response to Oxidative DNA Damage in Neurons: Mechanisms and Disease

2016 ◽  
Vol 2016 ◽  
pp. 1-14 ◽  
Author(s):  
Laura Narciso ◽  
Eleonora Parlanti ◽  
Mauro Racaniello ◽  
Valeria Simonelli ◽  
Alessio Cardinale ◽  
...  
Keyword(s):  
Dna Damage ◽  
Genome Stability ◽  
Oxidative Dna Damage ◽  
Excision Repair ◽  
Strand Breaks ◽  
Single Strand Breaks ◽  
Age Related ◽  
Neurological Alterations ◽  
Base Excision ◽  
And Function

There is a growing body of evidence indicating that the mechanisms that control genome stability are of key importance in the development and function of the nervous system. The major threat for neurons is oxidative DNA damage, which is repaired by the base excision repair (BER) pathway. Functional mutations of enzymes that are involved in the processing of single-strand breaks (SSB) that are generated during BER have been causally associated with syndromes that present important neurological alterations and cognitive decline. In this review, the plasticity of BER during neurogenesis and the importance of an efficient BER for correct brain function will be specifically addressed paying particular attention to the brain region and neuron-selectivity in SSB repair-associated neurological syndromes and age-related neurodegenerative diseases.

scholarly journals DNA damage response and repair in perspective: Aedes aegypti, Drosophila melanogaster and Homo sapiens

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Maria Beatriz S. Mota ◽  
Marcelo Alex Carvalho ◽  
Alvaro N. A. Monteiro ◽  
Rafael D. Mesquita
Keyword(s):  
Dna Damage ◽  
Aedes Aegypti ◽  
Dna Damage Response ◽  
Genetic Manipulation ◽  
Homo Sapiens ◽  
Excision Repair ◽  
Lesion Detection ◽  
Strand Breaks ◽  
Damage Response ◽  
Base Excision

Abstract Background The maintenance of genomic integrity is the responsibility of a complex network, denominated the DNA damage response (DDR), which controls the lesion detection and DNA repair. The main repair pathways are base excision repair (BER), nucleotide excision repair (NER), mismatch repair (MMR), homologous recombination repair (HR) and non-homologous end joining repair (NHEJ). They correct double-strand breaks (DSB), single-strand breaks, mismatches and others, or when the damage is quite extensive and repair insufficient, apoptosis is activated. Methods In this study we used the BLAST reciprocal best-hit methodology to search for DDR orthologs proteins in Aedes aegypti. We also provided a comparison between Ae. aegypti, D. melanogaster and human DDR network. Results Our analysis revealed the presence of ATR and ATM signaling, including the H2AX ortholog, in Ae. aegypti. Key DDR proteins (orthologs to RAD51, Ku and MRN complexes, XP-components, MutS and MutL) were also identified in this insect. Other proteins were not identified in both Ae. aegypti and D. melanogaster, including BRCA1 and its partners from BRCA1-A complex, TP53BP1, PALB2, POLk, CSA, CSB and POLβ. In humans, their absence affects DSB signaling, HR and sub-pathways of NER and BER. Seven orthologs not known in D. melanogaster were found in Ae. aegypti (RNF168, RIF1, WRN, RAD54B, RMI1, DNAPKcs, ARTEMIS). Conclusions The presence of key DDR proteins in Ae. aegypti suggests that the main DDR pathways are functional in this insect, and the identification of proteins not known in D. melanogaster can help fill gaps in the DDR network. The mapping of the DDR network in Ae. aegypti can support mosquito biology studies and inform genetic manipulation approaches applied to this vector.

Graphene oxide nanosheets induce DNA damage and activate the base excision repair (BER) signaling pathway both in vitro and in vivo

Chemosphere ◽  
2017 ◽  
Vol 184 ◽  
pp. 795-805 ◽  
Author(s):  
Chun-Jiao Lu ◽  
Xue-Feng Jiang ◽  
Muhammad Junaid ◽  
Yan-Bo Ma ◽  
Pan-Pan Jia ◽  
...  
Keyword(s):  
Dna Damage ◽  
Graphene Oxide ◽  
Signaling Pathway ◽  
Base Excision Repair ◽  
Excision Repair ◽  
Graphene Oxide Nanosheets ◽  
Base Excision

scholarly journals Characterization of FFPE-induced bacterial DNA damage and development of a repair method

2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Yensi Flores Bueso ◽  
Sidney P Walker ◽  
Mark Tangney
Keyword(s):  
Dna Damage ◽  
Oxidative Dna Damage ◽  
Excision Repair ◽  
Human Microbiome ◽  
Bacterial Dna ◽  
Microbiome Research ◽  
Formalin Fixed Paraffin Embedded ◽  
Sequencing Quality ◽  
Base Excision

Abstract Formalin-fixed, paraffin-embedded (FFPE) specimens have huge potential as source material in the field of human microbiome research. However, the effects of FFPE processing on bacterial DNA remain uncharacterized. Any effects are relevant for microbiome studies, where DNA template is often minimal and sequences studied are not limited to one genome. As such, we aimed to both characterize this FFPE-induced bacterial DNA damage and develop strategies to reduce and repair this damage. Our analyses indicate that bacterial FFPE DNA is highly fragmented, a poor template for PCR, crosslinked and bears sequence artefacts derived predominantly from oxidative DNA damage. Two strategies to reduce this damage were devised – an optimized decrosslinking procedure reducing sequence artefacts generated by high-temperature incubation, and secondly, an in vitro reconstitution of the base excision repair pathway. As evidenced by whole genome sequencing, treatment with these strategies significantly increased fragment length, reduced the appearance of sequence artefacts and improved the sequencing readability of bacterial and mammalian FFPE DNA. This study provides a new understanding of the condition of bacterial DNA in FFPE specimens and how this impacts downstream analyses, in addition to a strategy to improve the sequencing quality of bacterial and possibly mammalian FFPE DNA.

scholarly journals Nickel Carcinogenesis Mechanism: DNA Damage

2019 ◽  
Vol 20 (19) ◽  
pp. 4690 ◽  
Author(s):  
Hongrui Guo ◽  
Huan Liu ◽  
Hongbin Wu ◽  
Hengmin Cui ◽  
Jing Fang ◽  
...  
Keyword(s):  
Dna Damage ◽  
Dna Repair ◽  
Molecular Mechanisms ◽  
Excision Repair ◽  
Nonhomologous End Joining ◽  
End Joining ◽  
Damage Repair ◽  
Occupational And Environmental Exposure ◽  
Base Excision

Nickel (Ni) is known to be a major carcinogenic heavy metal. Occupational and environmental exposure to Ni has been implicated in human lung and nasal cancers. Currently, the molecular mechanisms of Ni carcinogenicity remain unclear, but studies have shown that Ni-caused DNA damage is an important carcinogenic mechanism. Therefore, we conducted a literature search of DNA damage associated with Ni exposure and summarized known Ni-caused DNA damage effects. In vitro and vivo studies demonstrated that Ni can induce DNA damage through direct DNA binding and reactive oxygen species (ROS) stimulation. Ni can also repress the DNA damage repair systems, including direct reversal, nucleotide repair (NER), base excision repair (BER), mismatch repair (MMR), homologous-recombination repair (HR), and nonhomologous end-joining (NHEJ) repair pathways. The repression of DNA repair is through direct enzyme inhibition and the downregulation of DNA repair molecule expression. Up to now, the exact mechanisms of DNA damage caused by Ni and Ni compounds remain unclear. Revealing the mechanisms of DNA damage from Ni exposure may contribute to the development of preventive strategies in Ni carcinogenicity.

Sign in / Sign up

Export Citation Format

Share Document