1
|
Rechkunova NI, Zhdanova PV, Lebedeva NA, Maltseva EA, Koval VV, Lavrik OI. Structural features of DNA polymerases β and λ in complex with benzo[a]pyrene-adducted DNA cause a difference in lesion tolerance. DNA Repair (Amst) 2022; 116:103353. [DOI: 10.1016/j.dnarep.2022.103353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 05/31/2022] [Indexed: 11/28/2022]
|
2
|
Starostenko LV, Maltseva EA, Lebedeva NA, Pestryakov PE, Lavrik OI, Rechkunova NI. Interaction of Nucleotide Excision Repair Protein XPC-RAD23B with DNA Containing Benzo[a]pyrene-Derived Adduct and Apurinic/Apyrimidinic Site within a Cluster. BIOCHEMISTRY (MOSCOW) 2017; 81:233-41. [PMID: 27262192 DOI: 10.1134/s0006297916030056] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
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.
Collapse
Affiliation(s)
- L V Starostenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| | | | | | | | | | | |
Collapse
|
3
|
Processing of the abasic sites clustered with the benzo[a]pyrene adducts by the base excision repair enzymes. DNA Repair (Amst) 2016; 50:43-53. [PMID: 28065385 DOI: 10.1016/j.dnarep.2016.12.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 11/02/2016] [Accepted: 12/12/2016] [Indexed: 11/23/2022]
Abstract
The major enzyme in eukaryotic cells that catalyzes the cleavage of apurinic/apyrimidinic (AP or abasic) sites is AP endonuclease 1 (APE1) that cleaves the phosphodiester bond on the 5'-side of AP sites. We found that the efficiency of AP site cleavage by APE1 was affected by the benzo[a]pyrenyl-DNA adduct (BPDE-dG) in the opposite strand. AP sites directly opposite of the modified dG or shifted toward the 5' direction were hydrolyzed by APE1 with an efficiency moderately lower than the AP site in the control DNA duplex, whereas AP sites shifted toward the 3' direction were hydrolyzed significantly less efficiently. For all DNA structures except DNA with the AP site shifted by 3 nucleotides in the 3' direction (AP+3-BP-DNA), hydrolysis was more efficient in the case of (+)-trans-BPDE-dG. Using molecular dynamic simulation, we have shown that in the complex of APE1 with the AP+3-BP-DNA, the BP residue is located within the DNA bend induced by APE1 and contacts the amino acids in the enzyme catalytic center and the catalytic metal ion. The geometry of the APE1 active site is perturbed more significantly by the trans-isomer of BPDE-dG that intercalates into the APE1-DNA complex near the cleaved phosphodiester bond. The ability of DNA polymerases β (Polβ), λ and ι to catalyze gap-filling synthesis in cooperation with APE1 was also analyzed. Polβ was shown to inhibit the 3'→5' exonuclease activity of APE1 when both enzymes were added simultaneously and to insert the correct nucleotide into the gap arising after AP site hydrolysis. Therefore, further evidence for the functional cooperation of APE1 and Polβ in base excision repair was obtained.
Collapse
|
4
|
Xiao M, Xiao S, Straaten TVD, Xue P, Zhang G, Zheng X, Zhang Q, Cai Y, Jin C, Yang J, Wu S, Zhu G, Lu X. Genetic polymorphisms in 19q13.3 genes associated with alteration of repair capacity to BPDE-DNA adducts in primary cultured lymphocytes. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2016; 812:39-47. [PMID: 27908386 DOI: 10.1016/j.mrgentox.2016.10.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 10/18/2016] [Accepted: 10/25/2016] [Indexed: 12/27/2022]
Abstract
Benzo[a]pyrene(B[a]P), and its ultimate metabolite Benzo[a]pyrene 7,8-diol 9,10-epoxide (BPDE), are classic DNA damaging carcinogens. DNA damage in cells caused by BPDE is normally repaired by Nucleotide Excision Repair (NER) and Base Excision Repair (BER). Genetic variations in NER and BER can change individual DNA repair capacity to DNA damage induced by BPDE. In the present study we determined the number of in vitro induced BPDE-DNA adducts in lymphocytes, to reflect individual susceptibility to Polycyclic aromatic hydrocarbons (PAHs)-induced carcinogenesis. The BPDE-DNA adduct level in lymphocytes were assessed by high performance liquid chromatography (HPLC) in 281 randomly selected participants. We genotyped for 9 single nucleotide polymorphisms (SNPs) in genes involved in NER (XPB rs4150441, XPC rs2228001, rs2279017 and XPF rs4781560), BER (XRCC1 rs25487, rs25489 and rs1799782) and genes located on chromosome 19q13.2-3 (PPP1R13L rs1005165 and CAST rs967591). We found that 3 polymorphisms in chromosome 19q13.2-3 were associated with lower levels of BPDE-DNA adducts (MinorT allele in XRCC1 rs1799782, minor T allele in PPP1R13L rs1005165 and minor A allele in CAST rs967571). In addition, a modified comet assay was performed to further confirm the above conclusions. We found both minor T allele in PPP1R13L rs1005165 and minor A allele in CAST rs967571 were associated with the lower levels of BPDE-adducts. Our data suggested that the variant genotypes of genes in chromosome 19q13.2-3 are associated with the alteration of repair efficiency to DNA damage caused by Benzo[a]pyrene, and may contribute to enhance predictive value for individual's DNA repair capacity in response to environmental carcinogens.
Collapse
Affiliation(s)
- Mingyang Xiao
- Dept. of Toxicology, School of Public Health, China Medical University, Shenyang, PR China
| | - Sha Xiao
- Dept. of Toxicology, School of Public Health, China Medical University, Shenyang, PR China
| | - Tahar van der Straaten
- Dept. Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ping Xue
- Dept. of Toxicology, School of Public Health, China Medical University, Shenyang, PR China
| | - Guopei Zhang
- Dept. of Toxicology, School of Public Health, China Medical University, Shenyang, PR China
| | - Xiao Zheng
- Dept. of Toxicology, School of Public Health, China Medical University, Shenyang, PR China
| | - Qianye Zhang
- Dept. of Toxicology, School of Public Health, China Medical University, Shenyang, PR China
| | - Yuan Cai
- Dept. of Toxicology, School of Public Health, China Medical University, Shenyang, PR China
| | - Cuihong Jin
- Dept. of Toxicology, School of Public Health, China Medical University, Shenyang, PR China
| | - Jinghua Yang
- Dept. of Toxicology, School of Public Health, China Medical University, Shenyang, PR China
| | - Shengwen Wu
- Dept. of Toxicology, School of Public Health, China Medical University, Shenyang, PR China
| | - Guolian Zhu
- Dept. of Toxicology, School of Public Health, China Medical University, Shenyang, PR China
| | - Xiaobo Lu
- Dept. of Toxicology, School of Public Health, China Medical University, Shenyang, PR China.
| |
Collapse
|
5
|
Liu Z, Ding S, Kropachev K, Lei J, Amin S, Broyde S, Geacintov NE. Resistance to Nucleotide Excision Repair of Bulky Guanine Adducts Opposite Abasic Sites in DNA Duplexes and Relationships between Structure and Function. PLoS One 2015; 10:e0137124. [PMID: 26340000 PMCID: PMC4560436 DOI: 10.1371/journal.pone.0137124] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 08/12/2015] [Indexed: 01/06/2023] Open
Abstract
The nucleotide excision repair of certain bulky DNA lesions is abrogated in some specific non-canonical DNA base sequence contexts, while the removal of the same lesions by the nucleotide excision repair mechanism is efficient in duplexes in which all base pairs are complementary. Here we show that the nucleotide excision repair activity in human cell extracts is moderate-to-high in the case of two stereoisomeric DNA lesions derived from the pro-carcinogen benzo[a]pyrene (cis- and trans-B[a]P-N2-dG adducts) in a normal DNA duplex. By contrast, the nucleotide excision repair activity is completely abrogated when the canonical cytosine base opposite the B[a]P-dG adducts is replaced by an abasic site in duplex DNA. However, base excision repair of the abasic site persists. In order to understand the structural origins of these striking phenomena, we used NMR and molecular spectroscopy techniques to evaluate the conformational features of 11mer DNA duplexes containing these B[a]P-dG lesions opposite abasic sites. Our results show that in these duplexes containing the clustered lesions, both B[a]P-dG adducts adopt base-displaced intercalated conformations, with the B[a]P aromatic rings intercalated into the DNA helix. To explain the persistence of base excision repair in the face of the opposed bulky B[a]P ring system, molecular modeling results suggest how the APE1 base excision repair endonuclease, that excises abasic lesions, can bind productively even with the trans-B[a]P-dG positioned opposite the abasic site. We hypothesize that the nucleotide excision repair resistance is fostered by local B[a]P residue-DNA base stacking interactions at the abasic sites, that are facilitated by the absence of the cytosine partner base in the complementary strand. More broadly, this study sets the stage for elucidating the interplay between base excision and nucleotide excision repair in processing different types of clustered DNA lesions that are substrates of nucleotide excision repair or base excision repair mechanisms.
Collapse
Affiliation(s)
- Zhi Liu
- Department of Chemistry, New York University, New York, New York, United States of America
| | - Shuang Ding
- Department of Biology, New York University, New York, New York, United States of America
| | - Konstantin Kropachev
- Department of Chemistry, New York University, New York, New York, United States of America
| | - Jia Lei
- Department of Biology, New York University, New York, New York, United States of America
| | - Shantu Amin
- Department of Pharmacology, Pennsylvania State University, Hershey, Pennsylvania, United States of America
| | - Suse Broyde
- Department of Biology, New York University, New York, New York, United States of America
| | - Nicholas E. Geacintov
- Department of Chemistry, New York University, New York, New York, United States of America
| |
Collapse
|