The human AP-endonuclease (APE1/Ref-1), an essential multifunctional protein, plays a central role in the repair of oxidative base damage via the DNA base excision repair (BER) pathway. The mammalian AP-endonuclease…
Обзор:Anatomy of a Islets of Langerhans
present study we investigated whether the expression of Источник статьи endonuclease 1 (APE1) and DNA polymerase 4 (DNA pol β), key enzymes of 4 pathway has any clinical significance with gallbladder carcinogenesis.
41 gallbladder cancer, 27 chronic cholecystitis, and 3 normal gallbladder specimens were analyzed for the expression of APE1 and DNA polymerase β by western blotting, and subcellular localization studied by immunohistochemistry.
The 4 /> AP Endonuclease (APE1/ref-1), A DNA Repair Enzyme in Gallbladder Carcinoma” Vijay Shukla, Prashant Chandra Das, M.J.BIOTECHNOLOGY ENZYMES IN GUJARATI
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Jul 01, 2012 · The human endonuclease 4 gene is 4 in chromosome 17q25.3 and encodes a 282 amino acid protein that shares about 30% sequence identity with bacterial endonuclease V.
This study reports biochemical properties of human endonuclease V with respect to https://prognozadvisor.ru/100/russkie-petardi-korsar-16-s958.html 4 deaminated base lesions.
Study of AP endonuclease (APEX1/REF1), a DNA repair enzyme, in gallbladder carcinoma
Endonucleases, Exonucleases, Restriction Enzymes, DNA Polymerases and Prokaryotic DNA Replication.
Endonucleases, Exonucleases, Restriction Enzymes, DNA Polymerases and Prokaryotic DNA Replication Flashcards | Quizlet
You have discovered 4 new restriction enzyme in lab. This enzyme behaves identically to EcoRV endonuclease, except it targets a different DNA https://prognozadvisor.ru/100/nakonechnik-vilochkoviy-medniy-izolirovanniy-din-46237-05-10-mm-pod-bolt-m35-klauke-klk620c35-100.html. The plane of symmetry for the restriction enzyme is marked with 4 arrow.
3) Primer: DNA polymerases require a free 4 to begin sythesis. Primer strand is bound to template strand.
Stannous chloride (SnCl2) and UVA induce DNA lesions through ROS.
The aim of this work was to study the toxicity induced by 4 preillumination, followed by SnCl2 treatment. E.
Genetic and Biochemical Characterization of Human AP Endonuclease 1 Mutants Deficient in Nucleotide Incision Repair Activity
coli BER mutants were used to identify genes which could play a role in DNA lesion repair 4 by these agents.
In the present study we investigated whether the expression of AP endonuclease 1 (APE1) 4 DNA polymerase β (DNA pol β), key enzymes of B.
Start studying Restriction endonuclease. Learn vocabulary, terms, 4 more with flashcards, games, and other study tools. Enzymes that cleaves both strands of DNA.
(PDF) Study of AP endonuclease (APEX1/REF1), a DNA repair enzyme, in gallbladder carcinoma
His special interest is in abdominal surgery, colorectal surgery and wound healing research and academic interest is in medical education.
His varied research interest lies in rectal cancers, experimental study of the effect of sepsis on colon and bacterial biofilms in chronic wounds.
Performed the experiments: AG MRR AAI.
Analyzed the data: JL OSF MS AAI.
Wrote the paper: MS AAI.
This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are 4 credited.
Figure S2: Comparison of AP endonuclease and NIR activities of WT and mutant APE1 proteins.
At present, physiological relevance of the NIR pathway is fairly well established in E.
Expression of the APE1 mutants deficient in the NIR and exonuclease activities reduced the sensitivity of AP endonuclease-deficient E.
Finally, the human NIR pathway was fully reconstituted in vitro using the purified APE1, human flap endonuclease 1, DNA polymerase β and DNA ligase I proteins, thus establishing the minimal set of proteins required for a functional NIR pathway in human cells.
Introduction Oxidative damage to DNA caused by reactive oxygen species is believed to be a major type of endogenous cellular damage, and more than 80 different oxidative modifications of DNA bases and sugar backbone have been identified to date.
If unrepaired, the damage will tend to accumulate and may lead to premature aging and chronic diseases.
Oxidatively damaged DNA bases are substrates for two overlapping pathways: base excision repair BER and nucleotide incision repair NIR.
It is generally thought that BER, initiated by multiple DNA glycosylases, is the main pathway for removal of the majority of oxidized bases .
Several oxidized pyrimidines including 5,6-dihydrouridine DHU are substrates for both the BER and NIR pathways .
The NIR pathway is evolutionarily conserved from E.
APE1 was first purified from human HeLa cells and then independently discovered as an AP endonuclease homologous to the E.
APE1 was also reported as a novel redox regulator of the DNA binding domain of Fos-Jun, Jun-Jun, AP-1 and p53 proteins as well as several other transcription factors.
These DNA repair functions enable APE1 to play a central role in both the short-patch SP and LP-BER .
Several lines of evidence show that divalent metal ions play an essential role in AP endonuclease-catalyzed NIR activity.
Mutational separation of NIR and BER functions of the E.
Human APE1 can form a stable complex with an AP site of DNA in the absence of Mg 2+.
Nonetheless, the https://prognozadvisor.ru/100/ramka-support-pm-45-ekoplast-45h45-2-modulya-dlya-kabel-kanalov-insta-73909.html of the phosphodiester bond and dissociation of APE1 from nicked duplex DNA are dependent on the concentration of Mg 2+, suggesting that divalent metal ions play a complex role in APE1-substrate interaction .
At low pH, the X-ray structure of APE1 contains one single Mg 2+ ion bound to carboxylates of residues D70 and E96 and incises the phosphodiester bond via a divalent metal cation-facilitated catalytic mechanism.
Interestingly, K98 residue is equivalent to R41 in DNase I, a residue which makes base-specific contacts in the minor groove.
However, in APE1, K98 establishes hydrogen bonds with the carboxyl group of D70.
The suppression of the inactivating E96A mutation in APE1 by the K98R missense mutation suggests that multiple residues could participate in Mg 2+ coordination.
Thus, there may exist an alternative conformation of the enzyme which may not be seen in the existing crystal structures.
Indeed, the structure of full-length APE1, determined from a crystal grown at pH 7.
The second metal-binding site site B is composed of the side chains of Asp210, Asn212 and His309.
Although further liquid state NMR studies did not show perturbation of His309 in the presence of Mg 2+ and Ca 2+, existence of a second Mg 2+-binding site was not ruled out.
Furthermore, alteration in Mg 2+ concentration induces conformational changes in the human APE1 protein and regulates its substrate specificity in an apparently allosteric manner .
Interestingly, the loop regions consisting of residues 100—110 and 120—125 exhibit significant structural variation when the structures of free APE1 are compared at pH 7.
Altogether, these observations point to an important role of intracellular environment, concentration of divalent metal ions and pH in conformational dynamics and substrate specificity of APE1.
This suggests that NIR in E.
In the present work, we investigated the physiological role of NIR function of human AP endonuclease through site-directed mutagenesis and comparison of mutant APE1 activities in the BER and NIR pathways.
Three single-amino-acid mutants and one double mutant of APE1 have been constructed and characterized.
Purified mutant proteins exhibit a dramatic reduction in NIR activity while retaining BER functions and the ability to reduce sensitivity to alkylation DNA damage when expressed in E.
Additionally, a full in vitro reconstitution of Machine) DNN 135 кг A3004 Баттерфляй (Pectral Стек NIR pathway for αdA residues has been performed using only four pure human proteins: APE1, FEN1, DNA polymerase β POLβ and DNA ligase I LIG1.
The potential importance of APE1-catalyzed NIR activity in vivo is discussed.
Reagents and oligonucleotides Methylmethanesulfonate MMS and tert-butyl hydroperoxide t-BuO 2H were obtained from Sigma-Aldrich Chimie S.
Oligonucleotides were annealed as previously described.
Schematic presentation of various DNA substrates used in this study.
The DNA fragment encoding full-length APE1 was amplified by PCR from the pIZ42 vector generously provided by Dr.
Izumi Louisiana State University, New Orleans, LA and subcloned into pET11a at the NdeI- BamHI sites resulting in pET11a-APE1.
Site-directed mutations within the 4 coding sequence in pET11a-APE1 were generated using the QuikChange site-directed mutagenesis kit Quickchange® XL, Site-Directed Mutagenesis Kit, Stratagene.
The strain BH110 was lysogenized with the helper phage λDE3 harboring a copy of the T7 RNA polymerase gene, using the DE3 lysogenization kit Novagen, Merck4Biosciences, France.
Purification procedure The purified E.
The purified human POLβ and LIG1 were purchased from Trevigen Gaithersburg, USA and Enzymax Lexington, USArespectively.
The human APE1 protein was expressed and purified from E.
Due to high-level expression in the repair-deficient strain, it was possible to purify APE1 to homogeneity using only two chromatographic steps.
Cells 5—6 g were lysed using a French press at 18,000 psi in Buffer A 20 mM Hepes-KOH pH 7.
The homogenate was centrifuged at 40,000× g for 30 min and the supernatant was passed through a column packed with 50 mL of Q-Sepharose Fast Flow resin Amersham Biosciences, Uppsala, Sweden pre-equilibrated in the same buffer.
Bound proteins were eluted in a 50—600 mM KCl gradient.
The homogeneity of protein preparations was verified by SDS-PAGE Supplementary.
DNA repair assays APE1 assay conditions vary depending on the DNA repair pathways studied.
Assays were performed at 37°C for 10 min, unless specified otherwise.
Reactions were stopped by adding 10 µL of a solution containing 0.
Gels were exposed to a Fuji FLA-3000 Phosphor Screen and analyzed using Image Gauge V3.
To measure kinetics parameters, 0.
For K M and k cat determination, the linear velocity was measured and the constants were determined from Lineweaver-Burk plots.
The kinetic parameters for exonuclease activity, when multiple degradation fragments appeared, were determined by measuring the reaction products as integrated intensities Камера видеонаблюдения DAHUA DH-HAC-HFW1400SP-0280B the fragments expressed as percentage of total substrate.
The value obtained for each fragment was multiplied by the number of catalytic events required for its formation, and total exonuclease degradation was calculated as the sum of those products.
The in vitro reconstitution of the NIR pathway for αdA and THF residues was carried out in the presence of ATP which decreases the actual concentration of free Mg 2+ in the reaction mix.
After incubation with human proteins, to identify leftover unrepaired residues, we performed additional Nfo treatment.
For this purpose, the products of reconstitution reaction were precipitated by addition of 2 µl of 0.
DNA precipitate was then washed by 85% ethanol and dissolved in 20 µl of buffer 20 mM HEPES-KOH, pH 7.
Reaction products were analyzed as described above.
Alkylation and oxidative DNA damage sensitivity Drug treatment was performed as previously described with some modifications.
The cells were collected by centrifugation, washed once, and suspended in phosphate-buffered saline PBS.
Ten-fold serial dilutions were prepared in PBS as well.
Chemical agents MMS and t-BuO 2H were added to 2.
Colonies were scored after 2 days of incubation at 37°C on MMS- and 28°C on t-BuO 2H-containing media.
Isolation and characterization of the APE1 NIR-deficient mutants In a previous report, we showed that the truncated APE1 NΔ61-APE1 lacking the first 61 N-terminal amino acids exhibits reduced NIR but normal AP endonuclease activities demonstrating the feasibility of mutational separation of various DNA repair activities in a human DNA repair enzyme.
Therefore, based on our previous work and literature analysis, we anticipated that the mutations affecting metal coordination and substrate recognition might lead to differential loss of the repair activities of APE1.
In addition to the K98 and D308 residues discussed above, other residues such as R177 and R185 could also be involved in the APE1 NIR function.
This DNA major groove interaction is unusual for a DNA repair enzyme.
It probably reflects specific APE1 functions because the sequence and conformation of the R177 loop are unique to APE1.
It should be noted that for each specific APE1-catalyzed DNA repair activity we used its optimal reaction conditions see.
These data indicate that K98, R185 and D308 amino acid residues are essential for NIR activity.
In contrast, both K98E and R177A mutants showed WT level of AP endonuclease and NIR activities supplementary and data not shown.
Comparison of AP endonuclease and NIR activities of WT and mutant APE1 proteins.
B WT and D308A APE1 mutant.
The asterisk denotes the position of a radiolabel.
Recently, Oezguen and colleagues перейти на источник molecular dynamic simulation of APE1 bound to an AP site of DNA.
These results suggest that D308 residue plays an essential role in APE1-catalyzed NIR and exonuclease activities.
Magnesium dependence of various DNA repair 4 of WT and D308A mutant APE1 proteins.
WT APE1 is shown as squares with a straight line; D308A mutant is shown as circles with a dashed line.
The maximum value of each enzyme's specific activity was taken as 100%.
Each graph represents at least three independent experiments; error bars are too small to be seen at the scale used.
As shown inin general, APE1 mutants exhibited reduced activities compared to the WT APE1 on all DNA substrates tested.
This suggests that NIR and BER functions of APE1 can be mutationally separated and that these functions are disrupted by different mutations.
Both mutants show a slight 2.
Although APE1 incises DNA at DHU and αdA lesions in the same manner, we suspect that the mechanism of substrate recognition by APE1 for these two distinct base lesions https://prognozadvisor.ru/100/smartfon-asus-zenfone-5-a501cg-4gb.html be quite different.
Thus, it is possible that these mutations affect a common active site.
Interestingly, the dramatic decrease of NIR activity in the different mutants we studied was the result of higher K M and lower k cat values compared to those of WT APE1.
To determine K M and k cat, the linear velocity was measured продолжение здесь the constants were calculated using Lineweaver-Burk plots.
Standard deviations for K M and k cat values varied within 20—40%.
Drug sensitivity of E.
Based on this observation, we postulated that the AP endonuclease-initiated NIR pathway is specifically required to repair complex oxidative DNA damage in vivo.
Availability of NIR-deficient APE1 mutants provides a new tool for testing this hypothesis in human cells.
However, in addition to BER and NIR functions, APE1 has multiple non-repair functions which might also be essential for cellular viability .
Therefore, to address the physiological relevance of APE1-NIR activity, we decided to use the mutant phenotype rescue assay in E.
We examined the MMS and t-BuO 2H sensitivity of the AP endonuclease-deficient E.
MMS, an alkylating agent, indirectly generates AP sites in DNA when methylated purines are excised by DNA glycosylases in the BER pathway.
Previously, similar results were reported for the D308 APE1 mutant.
To check whether each of the APE1 proteins is being expressed in E.
Drug sensitivity of E.
B t-BuO 2H sensitivity of E.
Each survival curve represents посмотреть больше least three independent experiments; error bars are too small to be seen at the scale used.
In contrast to rescue from MMS, the expression of WT APE1 caused only a minor reduction in the sensitivity of BH130 cells to t-BuO 2H, for comparison see AB1157 WT strain sensitivity, suggesting that in E.
Our results are supported by similar previous findings demonstrating that APE1 expression in E.
We propose that the insufficient rescue of E.
Although MgCl 2 concentrations higher than 1 mM inhibit APE1 NIR activitywe used 3 mM MgCl 2 in the reconstitution assay since the presence of 2 mM ATP binds free Mg 2+ through chelation, decreasing its actual concentration.
Under the reaction conditions that we used, APE1 incised about 70% of DNA substrate lane 2.
Interestingly, addition of LIG1 completely restores the 35mer full-sized fragment even in the presence of APE1 and FEN1.
Finally, in the presence of all four proteins APE1, POLβ, FEN1 and LIG1, we observed full restoration of the 35mer fragmentlane 9.
Logically, the appearance of the 20mer cleavage DNA fragment after NIR reconstitution assay would indicate the presence of αdA in the repaired 35mer fragment.
As expected, Nfo treatment of the 35mer fragment that was previously incubated with APE1, LIG1 and FEN1 lane 8 generated a 20mer cleavage product lane 18.
This indicates that the 35mer contains unrepaired αdA residues and that APE1 and FEN1 cannot remove αdA in the absence of DNA repair synthesis.
In contrast, Nfo treatment of the 35mer fragment that was pre-incubated with APE1, LIG1, FEN1 4 POLβ lane 9 produced a negligible amount of the 20mer cleavage product lane 19indicating that the majority of αdA residues are efficiently removed during DNA repair reconstitution assay.
Not surprisingly, no repair reactions are detectable in the absence of APE1 lanes 10 and 20.
The latter generates a flap-structure, which is cleaved by FEN1 to eliminate the αdA and generate a single-strand nick, which is then sealed by LIG1.
To quantify the repair and measure kinetics we used only the amount of cleavage product made by APE1 as 100% lane 2 and not total amount of DNA substrate lane 1.
These results indicate that under reaction conditions that enable DNA polymerase synthesis and ligation, αdA residues can be efficiently removed in the APE1-initiated NIR pathway.
Reactions were performed as described in.
Next, we examined whether synthetic AP sites can be removed under the same conditions, which are permissive for LP-NIR.
These 4 suggest that the repair of oxidized AP sites that are resistant to SP-BER could proceed via the LP repair pathway under the conditions favorable for NIR.
Reactions were performed for 30 min at 37°C and with 3 mM MgCl 2 and 2 mM ATP.
After APE1 cleavage, POLβ extends the cleavage fragments generating predominantly +4 products as evidenced by the appearance of 19mer lanes 2—6 and 24mer products lanes 11—15.
Interestingly, in the absence of FEN1, +4 products are accumulated to a much smaller extent lanes 8 and 17 compared to the reactions in the presence of FEN1 lanes 6 and 15.
This suggests that POLβ-catalyzed strand-displacement synthesis is paused at the +4 position after the cleavage of a 4-nucleotide flap by FEN1 endonuclease.
Addition of LIG1 after 20 min of pre-incubation with other enzymes caused a dramatic increase of the amount of full-length 34mer and 45mer repair products lanes 9 and 18.
Reactions were allowed to proceed for varying periods of time at 37°C.
In lanes 9 and 18, LIG1 was added to the reaction mixture only after 20 min and the incubations were continued for another 40 min.
Taken together, these data demonstrate that αdA and THF residues undergo efficient processing via the APE1-initiated DNA glycosylase-independent LP repair pathway at low Mg 2+ levels, which are conducive to NIR.
A knockout of the APE1 gene in mice results in embryonic lethality .
Although 4 has not been established which of the APE1 functions is required for cell survival, the physiological significance of Проставки под тормозные суппорта Celsior UCF20, 21 на JZX90, 100 DNA repair function is supported by several observations: i explanted homozygous APE1 null blastocysts display increased sensitivity to γ-irradiation ; ii reduced APE1 levels increase cellular sensitivity to hydrogen peroxide, menadione, paraquat and ionizing radiation, but not to UV irradiation; iii APE1-deficient cells can be rescued by the yeast AP endonuclease 1 ; and iv the APE1-initiated NIR pathway can remove distinct types of oxidative DNA damage such as those that приведенная ссылка not processed by DNA glycosylases.
Currently, it is unclear which APE1 functions are required for cell survival and whether NIR activity has a biological role.
In the present study, we attempted to determine the physiological relevance of the APE1-catalysed nucleotide incision activity by testing which amino acid residues of this protein are crucial for either BER or NIR functions.
In this vein, we examined mutations of 4 APE1 K98 and D308 amino acid residues, involved in metal coordination, and of the R177 and R185 residues, potentially implicated in DNA base substrate recognition.
The D308A APE1 mutant completely 4 NIR activity on αdA-containing DNA but shows virtually normal AP endonuclease activity, indicating the important role of this residue in NIR function.
Similar to D308A, the K98A APE1 mutant has intact BER activities but exhibits a specific reduction in αdA-NIR and exonuclease activitiessuggesting that amino acid residues K98 and D308 are dispensable for BER function at least under 4 BER assay conditions 5 mM MgCl 2 and pH 7.
Be that as it may, the mutant phenotype rescue assay for oxidizing agent did not allow us to determine physiological relevance of APE1-NIR activity.
It should be noted that overall decrease in DNA repair activities of all APE1 mutants tested.
At the same time it is possible that the amino acid changes alter the overall protein structure in a way that they affect more NIR than BER activities.
Therefore, these human enzyme functions are likely to be mechanistically linked and governed by the same amino acid residues.
This unique property of NIR AP endonucleases may play a biological role in the processing of clustered tandem lesions generated by ROS.
Recently, Bergeron and colleagues demonstrated that hydroxyl radicals generate tandem lesions composed of 8-oxodG and an adjacent oxidized pyrimidine.
They showed that 50% of the 8-hydroxylated purine lesions, namely, 8-oxodG and 8-oxodA, are involved in tandem damage.
These authors also demonstrated that more than 40% of the 8-oxodG involved in tandem lesions is refractory to excision by DNA glycosylases.
These tandem lesions are produced by a single oxidation event and therefore they could be generated by endogenous oxidative stress.
We can speculate that tandem lesions composed of oxidized pyrimidine and 8-oxodG serve as substrates for the NIR pathway in the following way.
Therefore removal of the tandem lesions in DNA could be the biological function of the NIR pathway.
Taken together, these results demonstrate that BER and NIR functions of human AP endonuclease can be mutationally separated, providing the basis for the studies on the biological role of NIR function in the removal of potentially lethal DNA lesions generated by oxidative stress.
Thus, biochemical characterization of the site-directed APE1 mutants paves the way for construction of NIR-deficient human cell lines for future studies aimed at identifying the biological role of the APE1-initiated NIR pathway.
This is suggestive of the existence of special auxiliary proteins which could prevent futile repair of single-strand breaks generated in the NIR pathway.
Finally, LIG1 completes the restoration of the full-length duplex.
These data demonstrate that αdA residues are processed via the LP-NIR pathway in a DNA glycosylase-independent manner and that LP-BER pathway for oxidative DNA damage can also function under NIR-conducive conditions.
In the present study, we provide further evidence for physiological relevance of the NIR function in human cells using site-directed mutagenesis to probe the BER and NIR functions of APE1.
Additionally, our in vitro reconstitution of the human NIR pathway establishes the minimal set of proteins required to efficiently repair oxidative DNA damage.
Figure S2 Comparison of AP endonuclease and NIR activities of WT and mutant APE1 proteins.
Ehrhart and Dr N.
Shevchuk for critical reading of the manuscript and thoughtful discussions.
Competing Interests: The authors have declared that no competing interests exist.
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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