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O.i. Lavrik - One of the best experts on this subject based on the ideXlab platform.
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apurinic Apyrimidinic endonuclease 1 and tyrosyl dna phosphodiesterase 1 prevent suicidal covalent dna protein crosslink at apurinic Apyrimidinic Site
Frontiers in Cell and Developmental Biology, 2021Co-Authors: N A Lebedeva, Nadejda I Rechkunova, Anton V Endutkin, O.i. LavrikAbstract:Bifunctional 8-oxoguanine-DNA glycosylase (OGG1), a crucial DNA-repair enzyme, removes from DNA 8-oxo-7,8-dihydroguanine (8-oxoG) with following cleavage of the arising apurinic/Apyrimidinic (AP) Site. The major enzyme in eukaryotic cells that catalyzes the cleavage of AP Sites is AP endonuclease 1 (APE1). Alternatively, AP Sites can be cleaved by tyrosyl-DNA phosphodiesterase 1 (TDP1) to initiate APE1-independent repair, thus expanding the ability of the base excision repair (BER) process. Poly(ADP-ribose) polymerase 1 (PARP1) is a regulatory protein of DNA repair. PARP2 is also activated in response to DNA damage and can be regarded as the BER participant. Here we analyze PARP1 and PARP2 interactions with DNA intermediates of the initial stages of the BER process (8-oxoG and AP-Site containing DNA) and their interplay with the proteins recognizing and processing these DNA structures focusing on OGG1. OGG1 as well as PARP1 and PARP2 form covalent complex with AP Site-containing DNA without borohydride reduction. AP Site incision by APE1 or TDP1 removal of protein adducts but not proteins' PARylation prevent DNA-protein crosslinks.
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interaction of nucleotide excision repair protein xpc rad23b with dna containing benzo a pyrene derived adduct and apurinic Apyrimidinic Site within a cluster
Biochemistry, 2016Co-Authors: L V Starostenko, O.i. Lavrik, N A Lebedeva, N I Rechkunova, E A Maltseva, P E PestryakovAbstract:The combined action of reactive metabolites of benzo[a]pyrene (B[a]P) and oxidative stress can lead to cluster-type DNA damage that includes both a bulky lesion and an apurinic/Apyrimidinic (AP) Site, which are repaired by the nucleotide and base excision repair mechanisms - NER and BER, respectively. Interaction of NER protein XPC-RAD23B providing primary damage recognition with DNA duplexes containing a B[a]P-derived residue linked to the exocyclic amino group of a guanine (BPDE-N(2)-dG) in the central position of one strand and AP Site in different positions of the other strand was analyzed. It was found that XPC-RAD23B crosslinks to DNA containing (+)-trans-BPDE-N(2)-dG more effectively than to DNA containing cis-isomer, independently of the AP Site position in the oppoSite strand; protein affinity to DNA containing one of the BPDE-N(2)-dG isomers depends on the AP Site position in the oppoSite strand. The influence of XPC-RAD23B on hydrolysis of an AP Site clustered with BPDE-N(2)-dG catalyzed by the apurinic/Apyrimidinic endonuclease 1 (APE1) was examined. XPC-RAD23B was shown to stimulate the endonuclease and inhibit the 3'-5' exonuclease activity of APE1. These data demonstrate the possibility of cooperation of two proteins belonging to different DNA repair systems in the repair of cluster-type DNA damage.
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design of a new fluorescent oligonucleotide based assay for a highly specific real time detection of apurinic Apyrimidinic Site cleavage by tyrosyl dna phosphodiesterase 1
Bioconjugate Chemistry, 2015Co-Authors: N A Lebedeva, Nadejda I Rechkunova, Rashid O Anarbaev, Maxim S Kupryushkin, D V Pyshnyi, Dmitry A Stetsenko, O.i. LavrikAbstract:Tyrosyl-DNA phosphodiesterase 1 (Tdp1) promotes catalytic scission of a phosphodiester bond between the 3'-end of DNA and the hydroxyl group of a tyrosine residue, as well as cleaving off a variety of other 3'-terminal phosphate-linked DNA substituents. We have shown recently that Tdp1 can initiate an apurinic/Apyrimidinic (AP) Site repair pathway that is independent from the one mediated by AP endonuclease 1 (APE1). Until recently, there was no method available of tracking the AP-Site cleaving activity of Tdp1 by real-time fluorescence assay. In the present study we demonstrate a highly specific real-time detection of the AP-Site cleaving activity of Tdp1 which allows one to distinguish it from the activity of APE1 by using a short hairpin oligonucleotide with a 1,12-dodecanediol loop, a 5'-fluorophore, and a 3'-quencher. Specific phosphodiesterase activity of Tdp1, which is usually able to remove quencher from the 3'-end of DNA, was suppressed in our approach by introducing a noncleavable phosphate group mimic between the 3'-end and the quencher. As a nondigestible 3'-phosphate analogue, we have used a new uncharged tetramethyl phosphoryl guanidine (Tmg) group, which is resistant to 3'-phosphodiesterase cleavage.
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clustered dna lesions containing 5 formyluracil and ap Site repair via the ber system
PLOS ONE, 2013Co-Authors: Elena A. Belousova, Inna A Vasileva, Nina Moor, Timofei S. Zatsepin, Tatiana S. Oretskaya, O.i. LavrikAbstract:Lesions in the DNA arise under ionizing irradiation conditions or various chemical oxidants as a single damage or as part of a multiply damaged Site within 1–2 helical turns (clustered lesion). Here, we explored the repair opportunity of the apurinic/Apyrimidinic Site (AP Site) composed of the clustered lesion with 5-formyluracil (5-foU) by the base excision repair (BER) proteins. We found, that if the AP Site is shifted relative to the 5-foU of the oppoSite strand, it could be repaired primarily via the short-patch BER pathway. In this case, the cleavage efficiency of the AP Site-containing DNA strand catalyzed by human apurinic/Apyrimidinic endonuclease 1 (hAPE1) decreased under AP Site excursion to the 3'-side relative to the lesion in the other DNA strand. DNA synthesis catalyzed by DNA polymerase lambda was more accurate in comparison to the one catalyzed by DNA polymerase beta. If the AP Site was located exactly oppoSite 5-foU it was expected to switch the repair to the long-patch BER pathway. In this situation, human processivity factor hPCNA stimulates the process.
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interaction of nucleotide excision repair proteins with dna containing bulky lesion and apurinic Apyrimidinic Site
Biochemistry, 2012Co-Authors: L V Skosareva, N A Lebedeva, N I Rechkunova, E A Maltseva, P E Pestryakov, O.i. LavrikAbstract:The interaction of nucleotide excision repair (NER) proteins (XPC-HR23b, RPA, and XPA) with 48-mer DNA duplexes containing the bulky lesion-mimicking fluorescein-substituted derivative of dUMP (5-{3-[6-(carboxyamidofluo-resceinyl)amidocapromoyl]allyl}-2′-deoxyuridine-5′-monophosphate) in a cluster with a lesion of another type (apurinic/Apyrimidinic (AP) Site) has been studied. It is shown that XPC-HR23b is modified to a greater extent by the DNA duplex containing an AP Site oppoSite nucleotide adjacent to the fluorescein residue than by DNA containing an AP Site shifted to the 3′-or 5′-end of the DNA strand. The efficiency of XPA modification by DNA duplexes containing both AP Site and fluorescein residue is higher than that by DNA lacking the bulky lesion; the modification pattern in this case depends on the AP Site position. In accordance with its major function, RPA interacts more efficiently with single-stranded DNA than with DNA duplexes, including those bearing bulky lesions. The observed interaction between the proteins involved in nucleotide excision repair and DNA structures containing a bulky lesion processed by NER and the AP Site repaired via base excision repair may be significant for both these repair pathways in cells and requires the specific sequence of repair of clustered DNA lesions.
N A Lebedeva - One of the best experts on this subject based on the ideXlab platform.
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apurinic Apyrimidinic endonuclease 1 and tyrosyl dna phosphodiesterase 1 prevent suicidal covalent dna protein crosslink at apurinic Apyrimidinic Site
Frontiers in Cell and Developmental Biology, 2021Co-Authors: N A Lebedeva, Nadejda I Rechkunova, Anton V Endutkin, O.i. LavrikAbstract:Bifunctional 8-oxoguanine-DNA glycosylase (OGG1), a crucial DNA-repair enzyme, removes from DNA 8-oxo-7,8-dihydroguanine (8-oxoG) with following cleavage of the arising apurinic/Apyrimidinic (AP) Site. The major enzyme in eukaryotic cells that catalyzes the cleavage of AP Sites is AP endonuclease 1 (APE1). Alternatively, AP Sites can be cleaved by tyrosyl-DNA phosphodiesterase 1 (TDP1) to initiate APE1-independent repair, thus expanding the ability of the base excision repair (BER) process. Poly(ADP-ribose) polymerase 1 (PARP1) is a regulatory protein of DNA repair. PARP2 is also activated in response to DNA damage and can be regarded as the BER participant. Here we analyze PARP1 and PARP2 interactions with DNA intermediates of the initial stages of the BER process (8-oxoG and AP-Site containing DNA) and their interplay with the proteins recognizing and processing these DNA structures focusing on OGG1. OGG1 as well as PARP1 and PARP2 form covalent complex with AP Site-containing DNA without borohydride reduction. AP Site incision by APE1 or TDP1 removal of protein adducts but not proteins' PARylation prevent DNA-protein crosslinks.
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interaction of nucleotide excision repair protein xpc rad23b with dna containing benzo a pyrene derived adduct and apurinic Apyrimidinic Site within a cluster
Biochemistry, 2016Co-Authors: L V Starostenko, O.i. Lavrik, N A Lebedeva, N I Rechkunova, E A Maltseva, P E PestryakovAbstract:The combined action of reactive metabolites of benzo[a]pyrene (B[a]P) and oxidative stress can lead to cluster-type DNA damage that includes both a bulky lesion and an apurinic/Apyrimidinic (AP) Site, which are repaired by the nucleotide and base excision repair mechanisms - NER and BER, respectively. Interaction of NER protein XPC-RAD23B providing primary damage recognition with DNA duplexes containing a B[a]P-derived residue linked to the exocyclic amino group of a guanine (BPDE-N(2)-dG) in the central position of one strand and AP Site in different positions of the other strand was analyzed. It was found that XPC-RAD23B crosslinks to DNA containing (+)-trans-BPDE-N(2)-dG more effectively than to DNA containing cis-isomer, independently of the AP Site position in the oppoSite strand; protein affinity to DNA containing one of the BPDE-N(2)-dG isomers depends on the AP Site position in the oppoSite strand. The influence of XPC-RAD23B on hydrolysis of an AP Site clustered with BPDE-N(2)-dG catalyzed by the apurinic/Apyrimidinic endonuclease 1 (APE1) was examined. XPC-RAD23B was shown to stimulate the endonuclease and inhibit the 3'-5' exonuclease activity of APE1. These data demonstrate the possibility of cooperation of two proteins belonging to different DNA repair systems in the repair of cluster-type DNA damage.
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design of a new fluorescent oligonucleotide based assay for a highly specific real time detection of apurinic Apyrimidinic Site cleavage by tyrosyl dna phosphodiesterase 1
Bioconjugate Chemistry, 2015Co-Authors: N A Lebedeva, Nadejda I Rechkunova, Rashid O Anarbaev, Maxim S Kupryushkin, D V Pyshnyi, Dmitry A Stetsenko, O.i. LavrikAbstract:Tyrosyl-DNA phosphodiesterase 1 (Tdp1) promotes catalytic scission of a phosphodiester bond between the 3'-end of DNA and the hydroxyl group of a tyrosine residue, as well as cleaving off a variety of other 3'-terminal phosphate-linked DNA substituents. We have shown recently that Tdp1 can initiate an apurinic/Apyrimidinic (AP) Site repair pathway that is independent from the one mediated by AP endonuclease 1 (APE1). Until recently, there was no method available of tracking the AP-Site cleaving activity of Tdp1 by real-time fluorescence assay. In the present study we demonstrate a highly specific real-time detection of the AP-Site cleaving activity of Tdp1 which allows one to distinguish it from the activity of APE1 by using a short hairpin oligonucleotide with a 1,12-dodecanediol loop, a 5'-fluorophore, and a 3'-quencher. Specific phosphodiesterase activity of Tdp1, which is usually able to remove quencher from the 3'-end of DNA, was suppressed in our approach by introducing a noncleavable phosphate group mimic between the 3'-end and the quencher. As a nondigestible 3'-phosphate analogue, we have used a new uncharged tetramethyl phosphoryl guanidine (Tmg) group, which is resistant to 3'-phosphodiesterase cleavage.
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interaction of nucleotide excision repair proteins with dna containing bulky lesion and apurinic Apyrimidinic Site
Biochemistry, 2012Co-Authors: L V Skosareva, N A Lebedeva, N I Rechkunova, E A Maltseva, P E Pestryakov, O.i. LavrikAbstract:The interaction of nucleotide excision repair (NER) proteins (XPC-HR23b, RPA, and XPA) with 48-mer DNA duplexes containing the bulky lesion-mimicking fluorescein-substituted derivative of dUMP (5-{3-[6-(carboxyamidofluo-resceinyl)amidocapromoyl]allyl}-2′-deoxyuridine-5′-monophosphate) in a cluster with a lesion of another type (apurinic/Apyrimidinic (AP) Site) has been studied. It is shown that XPC-HR23b is modified to a greater extent by the DNA duplex containing an AP Site oppoSite nucleotide adjacent to the fluorescein residue than by DNA containing an AP Site shifted to the 3′-or 5′-end of the DNA strand. The efficiency of XPA modification by DNA duplexes containing both AP Site and fluorescein residue is higher than that by DNA lacking the bulky lesion; the modification pattern in this case depends on the AP Site position. In accordance with its major function, RPA interacts more efficiently with single-stranded DNA than with DNA duplexes, including those bearing bulky lesions. The observed interaction between the proteins involved in nucleotide excision repair and DNA structures containing a bulky lesion processed by NER and the AP Site repaired via base excision repair may be significant for both these repair pathways in cells and requires the specific sequence of repair of clustered DNA lesions.
Xiang Xiao - One of the best experts on this subject based on the ideXlab platform.
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thermococcus eurythermalis endonuclease iv can cleave various apurinic Apyrimidinic Site analogues in ssdna and dsdna
International Journal of Molecular Sciences, 2018Co-Authors: Weiwei Wang, Gangshun Yi, Fengping Wang, Jianhua He, Huan Zhou, Xiang XiaoAbstract:Endonuclease IV (EndoIV) is a DNA damage-specific endonuclease that mainly hydrolyzes the phosphodiester bond located at 5′ of an apurinic/Apyrimidinic (AP) Site in DNA. EndoIV also possesses 3′-exonuclease activity for removing 3′-blocking groups and normal nucleotides. Here, we report that Thermococcus eurythermalis EndoIV (TeuendoIV) shows AP endonuclease and 3′-exonuclease activities. The effect of AP Site structures, positions and clustered patterns on the activity was characterized. The AP endonuclease activity of TeuendoIV can incise DNA 5′ to various AP Site analogues, including the alkane chain Spacer and polyethylene glycol Spacer. However, the short Spacer C2 strongly inhibits the AP endonuclease activity. The kinetic parameters also support its preference to various AP Site analogues. In addition, the efficient cleavage at AP Sites requires ≥2 normal nucleotides existing at the 5′-terminus. The 3′-exonuclease activity of TeuendoIV can remove one or more consecutive AP Sites at the 3′-terminus. Mutations on the residues for substrate recognition show that binding AP Site-containing or complementary strand plays a key role for the hydrolysis of phosphodiester bonds. Our results provide a comprehensive biochemical characterization of the cleavage/removal of AP Site analogues and some insight for repairing AP Sites in hyperthermophile cells.
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thermococcus eurythermalis endonuclease iv can cleave various apurinic Apyrimidinic Site analogues in ssdna and dsdna
International Journal of Molecular Sciences, 2018Co-Authors: Weiwei Wang, Gangshun Yi, Fengping Wang, Jianhua He, Huan Zhou, Xiang XiaoAbstract:Endonuclease IV (EndoIV) is a DNA damage-specific endonuclease that mainly hydrolyzes the phosphodiester bond located at 5′ of an apurinic/Apyrimidinic (AP) Site in DNA. EndoIV also possesses 3′-exonuclease activity for removing 3′-blocking groups and normal nucleotides. Here, we report that Thermococcus eurythermalis EndoIV (TeuendoIV) shows AP endonuclease and 3′-exonuclease activities. The effect of AP Site structures, positions and clustered patterns on the activity was characterized. The AP endonuclease activity of TeuendoIV can incise DNA 5′ to various AP Site analogues, including the alkane chain Spacer and polyethylene glycol Spacer. However, the short Spacer C2 strongly inhibits the AP endonuclease activity. The kinetic parameters also support its preference to various AP Site analogues. In addition, the efficient cleavage at AP Sites requires ≥2 normal nucleotides existing at the 5′-terminus. The 3′-exonuclease activity of TeuendoIV can remove one or more consecutive AP Sites at the 3′-terminus. Mutations on the residues for substrate recognition show that binding AP Site-containing or complementary strand plays a key role for the hydrolysis of phosphodiester bonds. Our results provide a comprehensive biochemical characterization of the cleavage/removal of AP Site analogues and some insight for repairing AP Sites in hyperthermophile cells.
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Thermococcus Eurythermalis Endonuclease IV Can Cleave Various Apurinic/Apyrimidinic Site Analogues in ssDNA and dsDNA
MDPI AG, 2018Co-Authors: Weiwei Wang, Fengping Wang, Huan Zhou, Xiang Xiao, Juan-juan Xie, Xi-peng LiuAbstract:Endonuclease IV (EndoIV) is a DNA damage-specific endonuclease that mainly hydrolyzes the phosphodiester bond located at 5′ of an apurinic/Apyrimidinic (AP) Site in DNA. EndoIV also possesses 3′-exonuclease activity for removing 3′-blocking groups and normal nucleotides. Here, we report that Thermococcus eurythermalis EndoIV (TeuendoIV) shows AP endonuclease and 3′-exonuclease activities. The effect of AP Site structures, positions and clustered patterns on the activity was characterized. The AP endonuclease activity of TeuendoIV can incise DNA 5′ to various AP Site analogues, including the alkane chain Spacer and polyethylene glycol Spacer. However, the short Spacer C2 strongly inhibits the AP endonuclease activity. The kinetic parameters also support its preference to various AP Site analogues. In addition, the efficient cleavage at AP Sites requires ≥2 normal nucleotides existing at the 5′-terminus. The 3′-exonuclease activity of TeuendoIV can remove one or more consecutive AP Sites at the 3′-terminus. Mutations on the residues for substrate recognition show that binding AP Site-containing or complementary strand plays a key role for the hydrolysis of phosphodiester bonds. Our results provide a comprehensive biochemical characterization of the cleavage/removal of AP Site analogues and some insight for repairing AP Sites in hyperthermophile cells
Olga S Fedorova - One of the best experts on this subject based on the ideXlab platform.
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kinetic mechanism of the interaction of saccharomyces cerevisiae ap endonuclease 1 with dna substrates
Biochemistry, 2012Co-Authors: Elena Dyakonova, Vladimir V Koval, Alexander A Ishchenko, Murat Saparbaev, R Kaptein, Olga S FedorovaAbstract:The apurinic/Apyrimidinic endonuclease from Saccharomyces cerevisiae Apn1 is one of the key enzymes involved in base excision repair of DNA lesions. A major function of the enzyme is to cleave the upstream phosphodiester bond of an apurinic/Apyrimidinic Site (AP-Site), leading to the formation of a single-strand break with 3′-hydroxyl (OH) and 5′-deoxyribose phosphate (dRP) termini. In this study, the pre-steady-state kinetics and conformational dynamics of DNA substrates during their interaction with Apn1 were investigated. A stopped-flow method with detection of the fluorescence intensity of 2-aminopurine and pyrrolocytosine located adjacent or oppoSite to the damage was used. It was found that upon interaction with Apn1, both DNA strands undergo a number of rapid changes. The location of fluorescent analogs of heterocyclic bases in DNA does not influence the catalytic step of the reaction. Comparison of data obtained for yeast Apn1 and reported data (Kanazhevskaya, L. Yu., Koval, V. V., Vorobjev, Yu. N., and Fedorova, O. S. (2012) Biochemistry, 51, 1306–1321) for human Ape1 revealed some differences in their interaction with DNA substrates.
Gianluca Tell - One of the best experts on this subject based on the ideXlab platform.
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unlike the escherichia coli counterpart archaeal rnase hii cannot process ribose monophosphate abasic Sites and oxidized ribonucleotides embedded in dna
Journal of Biological Chemistry, 2019Co-Authors: Matilde Clarissa Malfatti, Ghislaine Henneke, Sathya Balachander, Kyung Duk Koh, Gary P Newnam, Ryo Uehara, Robert J Crouch, Francesca Storici, Gianluca TellAbstract:The presence of ribonucleoside monophosphates (rNMPs) in nuclear DNA decreases genome stability. To ensure survival despite rNMP insertions, cells have evolved a complex network of DNA repair mechanisms, in which the ribonucleotide excision repair pathway, initiated by type 2 RNase H (RNase HII/2), plays a major role. We recently demonstrated that eukaryotic RNase H2 cannot repair damage, that is, ribose monophosphate abasic (both apurinic or Apyrimidinic) Site (rAP) or oxidized rNMP embedded in DNA. Currently, it remains unclear why RNase H2 is unable to repair these modified nucleic acids having either only a sugar moiety or an oxidized base. Here, we compared the endoribonuclease specificity of the RNase HII enzymes from the archaeon Pyrococcus abyssi and the bacterium Escherichia coli, examining their ability to process damaged rNMPs embedded in DNA in vitro. We found that E. coli RNase HII cleaves both rAP and oxidized rNMP Sites. In contrast, like the eukaryotic RNase H2, P. abyssi RNase HII did not display any rAP or oxidized rNMP incision activities, even though it recognized them. Notably, the archaeal enzyme was also inactive on a mismatched rNMP, whereas the E. coli enzyme displayed a strong preference for the mispaired rNMP over the paired rNMP in DNA. On the basis of our biochemical findings and also structural modeling analyses of RNase HII/2 proteins from organisms belonging to all three domains of life, we propose that RNases HII/2's dual roles in ribonucleotide excision repair and RNA/DNA hydrolysis result in limited acceptance of modified rNMPs embedded in DNA.