1
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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]
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2
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Jiang Z, Lai Y, Beaver JM, Tsegay PS, Zhao ML, Horton JK, Zamora M, Rein HL, Miralles F, Shaver M, Hutcheson JD, Agoulnik I, Wilson SH, Liu Y. Oxidative DNA Damage Modulates DNA Methylation Pattern in Human Breast Cancer 1 (BRCA1) Gene via the Crosstalk between DNA Polymerase β and a de novo DNA Methyltransferase. Cells 2020; 9:E225. [PMID: 31963223 PMCID: PMC7016758 DOI: 10.3390/cells9010225] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/15/2019] [Accepted: 01/13/2020] [Indexed: 12/13/2022] Open
Abstract
DNA damage and base excision repair (BER) are actively involved in the modulation of DNA methylation and demethylation. However, the underlying molecular mechanisms remain unclear. In this study, we seek to understand the mechanisms by exploring the effects of oxidative DNA damage on the DNA methylation pattern of the tumor suppressor breast cancer 1 (BRCA1) gene in the human embryonic kidney (HEK) HEK293H cells. We found that oxidative DNA damage simultaneously induced DNA demethylation and generation of new methylation sites at the CpGs located at the promoter and transcribed regions of the gene ranging from -189 to +27 in human cells. We demonstrated that DNA damage-induced demethylation was mediated by nucleotide misincorporation by DNA polymerase β (pol β). Surprisingly, we found that the generation of new DNA methylation sites was mediated by coordination between pol β and the de novo DNA methyltransferase, DNA methyltransferase 3b (DNMT3b), through the interaction between the two enzymes in the promoter and encoding regions of the BRCA1 gene. Our study provides the first evidence that oxidative DNA damage can cause dynamic changes in DNA methylation in the BRCA1 gene through the crosstalk between BER and de novo DNA methylation.
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Affiliation(s)
- Zhongliang Jiang
- Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA; (Z.J.); (J.M.B.); (P.S.T.)
| | - Yanhao Lai
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (Y.L.); (M.Z.); (H.L.R.); (F.M.)
| | - Jill M. Beaver
- Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA; (Z.J.); (J.M.B.); (P.S.T.)
| | - Pawlos S. Tsegay
- Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA; (Z.J.); (J.M.B.); (P.S.T.)
| | - Ming-Lang Zhao
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA; (M.-L.Z.); (J.K.H.); (S.H.W.)
| | - Julie K. Horton
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA; (M.-L.Z.); (J.K.H.); (S.H.W.)
| | - Marco Zamora
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (Y.L.); (M.Z.); (H.L.R.); (F.M.)
| | - Hayley L. Rein
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (Y.L.); (M.Z.); (H.L.R.); (F.M.)
| | - Frank Miralles
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (Y.L.); (M.Z.); (H.L.R.); (F.M.)
| | - Mohammad Shaver
- Department of Biomedical Engineering, Florida International University, Miami, FL 33199, USA; (M.S.); (J.D.H.)
| | - Joshua D. Hutcheson
- Department of Biomedical Engineering, Florida International University, Miami, FL 33199, USA; (M.S.); (J.D.H.)
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA;
| | - Irina Agoulnik
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA;
- Department of Human and Molecular Genetics, Florida International University, Miami, FL 33199, USA
| | - Samuel H. Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA; (M.-L.Z.); (J.K.H.); (S.H.W.)
| | - Yuan Liu
- Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA; (Z.J.); (J.M.B.); (P.S.T.)
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (Y.L.); (M.Z.); (H.L.R.); (F.M.)
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA;
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3
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Luo H, Wang L, Bao D, Wang L, Zhao H, Lian Y, Yan M, Mohan C, Li QZ. Novel Autoantibodies Related to Cell Death and DNA Repair Pathways in Systemic Lupus Erythematosus. GENOMICS PROTEOMICS & BIOINFORMATICS 2019; 17:248-259. [PMID: 31494269 PMCID: PMC6818352 DOI: 10.1016/j.gpb.2018.11.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 10/16/2018] [Accepted: 12/25/2018] [Indexed: 12/12/2022]
Abstract
Systemic lupus erythematosus (SLE) is a complex autoimmune syndrome characterized by various co-existing autoantibodies (autoAbs) in patients’ blood. However, the full spectrum of autoAbs in SLE has not been comprehensively elucidated. In this study, a commercial platform bearing 9400 antigens (ProtoArray) was used to identify autoAbs that were significantly elevated in the sera of SLE patients. By comparing the autoAb profiles of SLE patients with those of healthy controls, we identified 437 IgG and 1213 IgM autoAbs that the expression levels were significantly increased in SLE (P < 0.05). Use of the ProtoArray platform uncovered over 300 novel autoAbs targeting a broad range of nuclear, cytoplasmic, and membrane antigens. Molecular interaction network analysis revealed that the antigens targeted by the autoAbs were most significantly enriched in cell death, cell cycle, and DNA repair pathways. A group of autoAbs associated with cell apoptosis and DNA repair function, including those targeting APEX1, AURKA, POLB, AGO1, HMGB1, IFIT5, MAPKAPK3, PADI4, RGS3, SRP19, UBE2S, and VRK1, were further validated by ELISA and Western blot in a larger cohort. In addition, the levels of autoAbs against APEX1, HMGB1, VRK1, AURKA, PADI4, and SRP19 were positively correlated with the level of anti-dsDNA in SLE patients. Comprehensive autoAb screening has identified novel autoAbs, which may shed light on potential pathogenic pathways leading to lupus.
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Affiliation(s)
- Hui Luo
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha 410008, China; Department of Immunology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ling Wang
- Department of Immunology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Nephrology, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, China
| | - Ding Bao
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - Li Wang
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha 410008, China; Department of Immunology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hongjun Zhao
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha 410008, China; Department of Immunology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yun Lian
- Department of Immunology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mei Yan
- Department of Immunology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chandra Mohan
- Department of Biomedical Engineering, University of Houston, Houston, TX 77004, USA
| | - Quan-Zhen Li
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha 410008, China; Department of Immunology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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4
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Gowda ASP, Lee M, Spratt TE. N 2
-Substituted 2′-Deoxyguanosine Triphosphate Derivatives as Selective Substrates for Human DNA Polymerase κ. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611607] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- A. S. Prakasha Gowda
- Department of Biochemistry and Molecular Biology; Pennsylvania State University; 500 University Dr. Hershey PA 17033 USA
| | - Marietta Lee
- Department of Biochemistry and Molecular Biology; New York Medical College; Valhalla NY 10595 USA
| | - Thomas E. Spratt
- Department of Biochemistry and Molecular Biology; Pennsylvania State University; 500 University Dr. Hershey PA 17033 USA
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5
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Gowda ASP, Lee M, Spratt TE. N 2 -Substituted 2'-Deoxyguanosine Triphosphate Derivatives as Selective Substrates for Human DNA Polymerase κ. Angew Chem Int Ed Engl 2017; 56:2628-2631. [PMID: 28140505 DOI: 10.1002/anie.201611607] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/12/2017] [Indexed: 11/09/2022]
Abstract
N2 -Alkyl-2'-deoxyguanosine triphosphate (N2 -alkyl-dGTP) derivatives with methyl, butyl, benzyl, or 4-ethynylbenzyl substituents were prepared and tested as substrates for human DNA polymerases. N2 -Benzyl-dGTP was equal to dGTP as a substrate for DNA polymerase κ (pol κ), but was a poor substrate for pols β, δ, η, ι, or ν. In vivo reactivity was evaluated through incubation of N2 -4-ethynylbenzyl-dG with wild-type and pol κ deficient mouse embryonic fibroblasts. CuAAC reaction with 5(6)-FAM-azide demonstrated that only cells containing pol κ were able to incorporate N2 -4-ethynylbenzyl-dG into the nucleus. This is the first instance of a Y-family-polymerase-specific dNTP, and this method could be used to probe the activity of pol κ in vivo.
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Affiliation(s)
- A S Prakasha Gowda
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, 500 University Dr., Hershey, PA, 17033, USA
| | - Marietta Lee
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY, 10595, USA
| | - Thomas E Spratt
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, 500 University Dr., Hershey, PA, 17033, USA
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6
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Jiang Z, Xu M, Lai Y, Laverde EE, Terzidis MA, Masi A, Chatgilialoglu C, Liu Y. Bypass of a 5',8-cyclopurine-2'-deoxynucleoside by DNA polymerase β during DNA replication and base excision repair leads to nucleotide misinsertions and DNA strand breaks. DNA Repair (Amst) 2015; 33:24-34. [PMID: 26123757 DOI: 10.1016/j.dnarep.2015.06.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 04/23/2015] [Accepted: 06/09/2015] [Indexed: 12/18/2022]
Abstract
5',8-Cyclopurine-2'-deoxynucleosides including 5',8-cyclo-dA (cdA) and 5',8-cyclo-dG (cdG) are induced by hydroxyl radicals resulting from oxidative stress such as ionizing radiation. 5',8-cyclopurine-2'-deoxynucleoside lesions are repaired by nucleotide excision repair with low efficiency, thereby leading to their accumulation in the human genome and lesion bypass by DNA polymerases during DNA replication and base excision repair (BER). In this study, for the first time, we discovered that DNA polymerase β (pol β) efficiently bypassed a 5'R-cdA, but inefficiently bypassed a 5'S-cdA during DNA replication and BER. We found that cell extracts from pol β wild-type mouse embryonic fibroblasts exhibited significant DNA synthesis activity in bypassing a cdA lesion located in replication and BER intermediates. However, pol β knock-out cell extracts exhibited little DNA synthesis to bypass the lesion. This indicates that pol β plays an important role in bypassing a cdA lesion during DNA replication and BER. Furthermore, we demonstrated that pol β inserted both a correct and incorrect nucleotide to bypass a cdA at a low concentration. Nucleotide misinsertion was significantly stimulated by a high concentration of pol β, indicating a mutagenic effect induced by pol β lesion bypass synthesis of a 5',8-cyclopurine-2'-deoxynucleoside. Moreover, we found that bypass of a 5'S-cdA by pol β generated an intermediate that failed to be extended by pol β, resulting in accumulation of single-strand DNA breaks. Our study provides the first evidence that pol β plays an important role in bypassing a 5',8-cyclo-dA during DNA replication and repair, as well as new insight into mutagenic effects and genome instability resulting from pol β bypassing of a cdA lesion.
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Affiliation(s)
- Zhongliang Jiang
- Department of Chemistry and Biochemistry, USA; Biochemistry Ph.D. Program, USA
| | - Meng Xu
- Department of Chemistry and Biochemistry, USA
| | - Yanhao Lai
- Department of Chemistry and Biochemistry, USA
| | | | - Michael A Terzidis
- ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy
| | - Annalisa Masi
- ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy
| | - Chryssostomos Chatgilialoglu
- ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy; Institute of Nanoscience and Nanotechnology, N.C.S.R. "Demokritos", 15341, Agia Paraskevi, Athens, Greece
| | - Yuan Liu
- Department of Chemistry and Biochemistry, USA; Biochemistry Ph.D. Program, USA; Biomolecular Sciences Institute, School of Integrated Sciences and Humanities, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA.
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7
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Abstract
Scaffold proteins play a central role in DNA repair by recruiting and organizing sets of enzymes required to perform multi-step repair processes. X-ray cross complementing group 1 protein (XRCC1) forms enzyme complexes optimized for single-strand break repair, but participates in other repair pathways as well. Available structural data for XRCC1 interactions is summarized and evaluated in terms of its proposed roles in DNA repair. Mutational approaches related to the abrogation of specific XRCC1 interactions are also discussed. Although substantial progress has been made in elucidating the structural basis for XRCC1 function, the molecular mechanisms of XRCC1 recruitment related to several proposed roles of the XRCC1 DNA repair complex remain undetermined.
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Affiliation(s)
- Robert E London
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, United States.
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8
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Starostenko LV, Rechkunova NI, Lebedeva NA, Kolbanovskiy A, Geacintov NE, Lavrik OI. Human DNA polymerases catalyze lesion bypass across benzo[ a ]pyrene-derived DNA adduct clustered with an abasic site. DNA Repair (Amst) 2014; 24:1-9. [DOI: 10.1016/j.dnarep.2014.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 09/10/2014] [Accepted: 10/03/2014] [Indexed: 01/30/2023]
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9
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Xu M, Lai Y, Jiang Z, Terzidis MA, Masi A, Chatgilialoglu C, Liu Y. A 5', 8-cyclo-2'-deoxypurine lesion induces trinucleotide repeat deletion via a unique lesion bypass by DNA polymerase β. Nucleic Acids Res 2014; 42:13749-63. [PMID: 25428354 PMCID: PMC4267656 DOI: 10.1093/nar/gku1239] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
5',8-cyclo-2'-deoxypurines (cdPus) are common forms of oxidized DNA lesions resulting from endogenous and environmental oxidative stress such as ionizing radiation. The lesions can only be repaired by nucleotide excision repair with a low efficiency. This results in their accumulation in the genome that leads to stalling of the replication DNA polymerases and poor lesion bypass by translesion DNA polymerases. Trinucleotide repeats (TNRs) consist of tandem repeats of Gs and As and therefore are hotspots of cdPus. In this study, we provided the first evidence that both (5'R)- and (5'S)-5',8-cyclo-2'-deoxyadenosine (cdA) in a CAG repeat tract caused CTG repeat deletion exclusively during DNA lagging strand maturation and base excision repair. We found that a cdA induced the formation of a CAG loop in the template strand, which was skipped over by DNA polymerase β (pol β) lesion bypass synthesis. This subsequently resulted in the formation of a long flap that was efficiently cleaved by flap endonuclease 1, thereby leading to repeat deletion. Our study indicates that accumulation of cdPus in the human genome can lead to TNR instability via a unique lesion bypass by pol β.
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Affiliation(s)
- Meng Xu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW, 8th Street, Miami, FL 33199, USA
| | - Yanhao Lai
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW, 8th Street, Miami, FL 33199, USA
| | - Zhongliang Jiang
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW, 8th Street, Miami, FL 33199, USA
| | - Michael A Terzidis
- ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy
| | - Annalisa Masi
- ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy
| | - Chryssostomos Chatgilialoglu
- ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy Institute of Nanoscience and Nanotechnology, N.C.S.R. 'Demokritos', 15341 Agia, Paraskevi, Athens, Greece
| | - Yuan Liu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW, 8th Street, Miami, FL 33199, USA Biomolecular Sciences Institute, School of Integrated Sciences and Humanities, Florida International University, 11200 SW, 8th Street, Miami, FL 33199, USA
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10
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Xu L, Vaidyanathan VG, Cho BP. Real-time surface plasmon resonance study of biomolecular interactions between polymerase and bulky mutagenic DNA lesions. Chem Res Toxicol 2014; 27:1796-807. [PMID: 25195494 PMCID: PMC4203393 DOI: 10.1021/tx500252z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
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Surface plasmon resonance (SPR) was
used to measure polymerase-binding
interactions of the bulky mutagenic DNA lesions N-(2′-deoxyguanosin-8-yl)-4′-fluoro-4-aminobiphenyl
(FABP) or N-(2′-deoxyguanosin-8-yl)-7-fluoro-2-acetylaminofluorene
(FAAF) in the context of two unique 5′-flanking bases (CG*A and TG*A). The enzymes used
were exo-nuclease-deficient Klenow fragment (Kf-exo–) or polymerase β (pol β). Specific binary and ternary
DNA binding affinities of the enzymes were characterized at subnanomolar
concentrations. The SPR results showed that Kf-exo– binds strongly to a double strand/single strand template/primer
junction, whereas pol β binds preferentially to double-stranded
DNA having a one-nucleotide gap. Both enzymes exhibited tight binding
to native DNA, with high nucleotide selectivity, where the KD values for each base pair increased in the
order dCTP ≪ dTTP ∼ dATP ≪ dGTP. In contrast
to that for pol β, Kf-exo– binds tightly to
lesion-modified templates; however, both polymerases exhibited minimal
nucleotide selectivity toward adducted DNA. Primer steady-state kinetics
and 19F NMR results support the SPR data. The relative
insertion efficiency fins of dCTP opposite
FABP was significantly higher in the TG*A sequence
compared to that in CG*A. Although Kf-exo– was not sensitive to the presence of a DNA lesion,
FAAF-induced conformational heterogeneity perturbed the active site
of pol β, weakening the enzyme’s ability to bind to FAAF
adducts compared to FABP adducts. The present study demonstrates the
effectiveness of SPR for elucidating how lesion-induced conformational
heterogeneity affects the binding capability of polymerases and ultimately
the nucleotide insertion efficiency.
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Affiliation(s)
- Lifang Xu
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States
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11
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Villani G, Shevelev I, Orlando E, Pospiech H, Syvaoja JE, Markkanen E, Hubscher U, Le Gac NT. Gap-directed translesion DNA synthesis of an abasic site on circular DNA templates by a human replication complex. PLoS One 2014; 9:e93908. [PMID: 24710081 PMCID: PMC3977967 DOI: 10.1371/journal.pone.0093908] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 03/08/2014] [Indexed: 12/02/2022] Open
Abstract
DNA polymerase ε (pol ε) is believed to be the leading strand replicase in eukaryotes whereas pols λ and β are thought to be mainly involved in re-synthesis steps of DNA repair. DNA elongation by the human pol ε is halted by an abasic site (apurinic/apyrimidinic (AP) site). We have previously reported that human pols λ, β and η can perform translesion synthesis (TLS) of an AP site in the presence of pol ε. In the case of pol λ and β, this TLS requires the presence of a gap downstream from the product synthetized by the ε replicase. However, since these studies were conducted exclusively with a linear DNA template, we decided to test whether the structure of the template could influence the capacity of the pols ε, λ, β and η to perform TLS of an AP site. Therefore, we have investigated the replication of damaged “minicircle” DNA templates. In addition, replication of circular DNA requires, beyond DNA pols, the processivity clamp PCNA, the clamp loader replication factor C (RFC), and the accessory proteins replication protein A (RPA). Finally we have compared the capacity of unmodified versus monoubiquitinated PCNA in sustaining TLS by pols λ and η on a circular template. Our results indicate that in vitro gap-directed TLS synthesis by pols λ and β in the presence of pol ε, RPA and PCNA is unaffected by the structure of the DNA template. Moreover, monoubiquitination of PCNA does not affect TLS by pol λ while it appears to slightly stimulate TLS by pol η.
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Affiliation(s)
- Giuseppe Villani
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
- Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
| | - Igor Shevelev
- Leibniz Institute for Age Research - Fritz Lipman Institute, Jena, Germany
- Department of Biochemistry, University of Oulu, Oulu, Finland
| | - Eleonora Orlando
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
- Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
| | - Helmut Pospiech
- Leibniz Institute for Age Research - Fritz Lipman Institute, Jena, Germany
- Department of Biochemistry, University of Oulu, Oulu, Finland
| | - Juhani E. Syvaoja
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Enni Markkanen
- Biochemistry Group, Department of Oncology, Gray Institute for Radiation Oncology and Biology, Oxford, United Kingdom
| | - Ulrich Hubscher
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zürich-Irchel, Zürich, Switzerland
| | - Nicolas Tanguy Le Gac
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
- Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
- * E-mail:
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12
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Skosareva LV, Lebedeva NA, Lavrik OI, Rechkunova NI. Repair of bulky DNA lesions deriving from polycyclic aromatic hydrocarbons. Mol Biol 2013. [DOI: 10.1134/s002689331305018x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Vaidyanathan VG, Liang F, Beard WA, Shock DD, Wilson SH, Cho BP. Insights into the conformation of aminofluorene-deoxyguanine adduct in a DNA polymerase active site. J Biol Chem 2013; 288:23573-85. [PMID: 23798703 DOI: 10.1074/jbc.m113.476150] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The active site conformation of the mutagenic fluoroaminofluorene-deoxyguanine adduct (dG-FAF, N-(2'-deoxyguanosin-8-yl)-7-fluoro-2-aminofluorene) has been investigated in the presence of Klenow fragment of Escherichia coli DNA polymerase I (Kfexo(-)) and DNA polymerase β (pol β) using (19)F NMR, insertion assay, and surface plasmon resonance. In a single nucleotide gap, the dG-FAF adduct adopts both a major-groove- oriented and base-displaced stacked conformation, and this heterogeneity is retained upon binding pol β. The addition of a non-hydrolysable 2'-deoxycytosine-5'-[(α,β)-methyleno]triphosphate (dCMPcPP) nucleotide analog to the binary complex results in an increase of the major groove conformation of the adduct at the expense of the stacked conformation. Similar results were obtained with the addition of an incorrect dAMPcPP analog but with formation of the minor groove binding conformer. In contrast, dG-FAF adduct at the replication fork for the Kfexo(-) complex adopts a mix of the major and minor groove conformers with minimal effect upon the addition of non-hydrolysable nucleotides. For pol β, the insertion of dCTP was preferred opposite the dG-FAF adduct in a single nucleotide gap assay consistent with (19)F NMR data. Surface plasmon resonance binding kinetics revealed that pol β binds tightly with DNA in the presence of correct dCTP, but the adduct weakens binding with no nucleotide specificity. These results provide molecular insights into the DNA binding characteristics of FAF in the active site of DNA polymerases and the role of DNA structure and sequence on its coding potential.
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Affiliation(s)
- Vaidyanathan G Vaidyanathan
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, USA
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14
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Zhao W, Wu M, Lai Y, Deng W, Liu Y, Zhang Z. Involvement of DNA polymerase β overexpression in the malignant transformation induced by benzo[a]pyrene. Toxicology 2013; 309:73-80. [PMID: 23652152 DOI: 10.1016/j.tox.2013.04.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 04/27/2013] [Accepted: 04/27/2013] [Indexed: 02/05/2023]
Abstract
OBJECTIVE To explore the relationship between DNA polymerase β (pol β) overexpression and benzo[a]pyrene (BaP) carcinogenesis. METHODS Firstly, mouse embryonic fibroblasts that express wild-type level of DNA polymerase β (pol β cell) and high level of pol β (pol β oe cell) were treated by various concentrations of BaP to determine genetic instability induced by BaP under differential expression levels of pol β. Secondly, malignant transformation of pol β cells by low concentration of BaP (20 μM) was determined by soft agar colony formation assay and transformation focus assay. Thirdly, the mRNA and protein levels of BaP-transformed pol β cells (named pol β-T cells) was measured by reverse transcriptase-polymerase chain reaction (RT-PCR) and western blot, and the genetic instability of these cells were examined by HPRT gene mutation assay and random amplified polymorphic DNA (RAPD) assay. RESULTS Pol β cells were successfully transformed into malignant pol β-T cells by an exposure to low concentration of BaP for 6 months. Pol β-T cells exhibited increased levels of pol β gene expression, HPRT gene mutation frequency and polymorphisms of RAPD products that were comparable to those of pol β oe cells. CONCLUSION Pol β overexpression and its-associated genetic instability may play a key role in BaP carcinogenesis.
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Affiliation(s)
- Wei Zhao
- Department of Environmental Health, West China School of Public Health, Sichuan University, Chengdu, Sichuan, People's Republic of China
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