Alternative Excision Repair Pathways

Yasui, Akira

doi:10.1101/cshperspect.a012617

Cited by 50 publications

(37 citation statements)

References 23 publications

(22 reference statements)

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“…The EndoQ pathway is probably another pathway of alternative excision repair (AER), which is initiated by a single nick near the site of a DNA lesion, in some of the organisms in Archaea. 9) EndoQ has higher affinity for dI-containing DNA than EndoV, and cells produce higher amounts of EndoQ, as compared to EndoV. These data support the proposal that EndoQ primarily functions for, at least, dI-containing DNA.…”

supporting

confidence: 75%

A functional endonuclease Q exists in the bacterial domain: identification and characterization of endonuclease Q from Bacillus pumilus

Shiraishi

Ishino

Cann

et al. 2017

Bioscience, Biotechnology, and Biochemistry

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DNA base deamination occurs spontaneously under physiological conditions and is promoted by high temperature. Therefore, hyperthermophiles are expected to have efficient repair systems of the deaminated bases in their genomes. Endonuclease Q (EndoQ) was originally identified from the hyperthermophlic archaeon, Pyrococcus furiosus, as a hypoxanthine-specific endonuclease recently. Further biochemical analyses revealed that EndoQ also recognizes uracil, xanthine, and the AP site in DNA, and is probably involved in a specific repair process for damaged bases. Initial phylogenetic analysis showed that an EndoQ homolog is found only in the Thermococcales and some of the methanogens in Archaea, and is not present in most members of the domains Bacteria and Eukarya. A better understanding of the distribution of the EndoQ-mediated repair system is, therefore, of evolutionary interest. We showed here that an EndoQ-like polypeptide from Bacillus pumilus, belonging to the bacterial domain, is functional and has similar properties with the archaeal EndoQs.

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supporting

confidence: 75%

A functional endonuclease Q exists in the bacterial domain: identification and characterization of endonuclease Q from Bacillus pumilus

Shiraishi

Ishino

Cann

et al. 2017

Bioscience, Biotechnology, and Biochemistry

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“…Endogenous non-bulky DNA base damage is removed via two overlapping pathways: DNA glycosylase-initiated base excision repair (BER) and apurinic/apyrimidinic (AP) endonuclease-mediated nucleotide incision repair (NIR) (23). In BER, a DNA glycosylase excises the modified base, leaving either an AP site or a SSB with 3′-phosphoaldehyde and/or 3′-phosphate groups; all these genotoxic intermediates are then hydrolysed by an AP endonuclease (APE1 in human cells) prior to the gap-filling synthesis step (24,25).…”

Section: Introductionmentioning

confidence: 99%

Poly(ADP-ribose) polymerases covalently modify strand break termini in DNA fragmentsin vitro

Talhaoui¹,

Лебедева²,

Zarkovic³

et al. 2016

Nucleic Acids Res

101

170

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Poly(ADP-ribose) polymerases (PARPs/ARTDs) use nicotinamide adenine dinucleotide (NAD+) to catalyse the synthesis of a long branched poly(ADP-ribose) polymer (PAR) attached to the acceptor amino acid residues of nuclear proteins. PARPs act on single- and double-stranded DNA breaks by recruiting DNA repair factors. Here, in in vitro biochemical experiments, we found that the mammalian PARP1 and PARP2 proteins can directly ADP-ribosylate the termini of DNA oligonucleotides. PARP1 preferentially catalysed covalent attachment of ADP-ribose units to the ends of recessed DNA duplexes containing 3′-cordycepin, 5′- and 3′-phosphate and also to 5′-phosphate of a single-stranded oligonucleotide. PARP2 preferentially ADP-ribosylated the nicked/gapped DNA duplexes containing 5′-phosphate at the double-stranded termini. PAR glycohydrolase (PARG) restored native DNA structure by hydrolysing PAR-DNA adducts generated by PARP1 and PARP2. Biochemical and mass spectrometry analyses of the adducts suggested that PARPs utilise DNA termini as an alternative to 2′-hydroxyl of ADP-ribose and protein acceptor residues to catalyse PAR chain initiation either via the 2′,1″-O-glycosidic ribose-ribose bond or via phosphodiester bond formation between C1′ of ADP-ribose and the phosphate of a terminal deoxyribonucleotide. This new type of post-replicative modification of DNA provides novel insights into the molecular mechanisms underlying biological phenomena of ADP-ribosylation mediated by PARPs.

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“…The gap that remains is then filled using a DNA polymerase. There are three types of excision repair pathways for UVC-induced lesions: base excision repair (BER) (Krokan and Bjoras, 2013), nucleotide excision repair (NER) (Kisker et al, 2013), and alternative excision repair (AER) (Yasui, 2013). Figure 1 illustrates the differences.…”

Section: Processes Known To Protect Against Uvc-induced Lethalitymentioning

confidence: 99%

Radiation Tolerance

Battista

2016

Encyclopedia of Life Sciences

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Life on earth was not exposed to high‐dose ultraviolet (UV) light or ionising radiation (IR) until the last century. Despite this fact, it is possible to isolate species from within the Bacteria and Archaea that display an unusually high resistance to the lethal effects of UV light and/or IR when compared to the rest of the tree of life. Questions concerning what mechanisms mediate this radiation tolerance and why radiotolerance evolved in an environment void of sources of high‐energy radiation define the study of these species. A great deal is known concerning the specific biochemical and physiological processes that counteract the damage caused by electromagnetic radiations, but almost all species express the proteins that mediate these processes. The nature of what distinguishes a radioresistant species from a radiosensitive species remains elusive. Key Concepts A small subset of Bacteria and Archaea express unusually high resistance to the lethal effects of UV and ionising radiations. Beyond experimental evaluation, there are no overt characteristics that predict radiation tolerance; species can be defined as radiation‐tolerant only empirically. UV and ionising radiations kill by altering the DNA structure in a manner that interferes with the irradiated cell's ability to propagate. A number of active and passive mechanisms are known to contribute to a species' radiation tolerance, but a comprehensive explanation for radioresistance in any single species has remained elusive. Endospores tolerate UV and ionising radiations by mechanisms not available to their vegetative forms. The flux of UV and ionising radiations on earth have never been great enough to explain why high‐level resistance to these stresses evolved; a number of hypotheses have been put forward to account for the existence of radioresistant phenotypes.

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Alternative Excision Repair Pathways

Cited by 50 publications

References 23 publications

A functional endonuclease Q exists in the bacterial domain: identification and characterization of endonuclease Q from Bacillus pumilus

A functional endonuclease Q exists in the bacterial domain: identification and characterization of endonuclease Q from Bacillus pumilus

Poly(ADP-ribose) polymerases covalently modify strand break termini in DNA fragmentsin vitro

Radiation Tolerance

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