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Velázquez-Ruiz C, Blanco L, Martínez-Jiménez MI. 3'dNTP Binding Is Modulated during Primer Synthesis and Translesion by Human PrimPol. Int J Mol Sci 2023; 25:51. [PMID: 38203225 PMCID: PMC10778844 DOI: 10.3390/ijms25010051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/15/2023] [Accepted: 12/17/2023] [Indexed: 01/12/2024] Open
Abstract
PrimPol is a DNA primase/polymerase from the Archaeo-Eukaryotic Primase (AEP) superfamily that enables the progression of stalled replication forks by synthesizing DNA primers ahead of blocking lesions or abnormal structures in the ssDNA template. PrimPol's active site is formed by three AEP-conserved motifs: A, B and C. Motifs A and C of human PrimPol (HsPrimPol) harbor the catalytic residues (Asp114, Glu116, Asp280) acting as metal ligands, whereas motif B includes highly conserved residues (Lys165, Ser167 and His169), which are postulated to stabilize 3' incoming deoxynucleotides (dNTPs). Additionally, other putative nucleotide ligands are situated close to motif C: Lys297, almost invariant in the whole AEP superfamily, and Lys300, specifically conserved in eukaryotic PrimPols. Here, we demonstrate that His169 is absolutely essential for 3'dNTP binding and, hence, for both primase and polymerase activities of HsPrimPol, whereas Ser167 and Lys297 are crucial for the dimer synthesis initiation step during priming, but dispensable for subsequent dNTP incorporation on growing primers. Conversely, the elimination of Lys165 does not affect the overall primase function; however, it is required for damage avoidance via primer-template realignments. Finally, Lys300 is identified as an extra anchor residue to stabilize the 3' incoming dNTP. Collectively, these results demonstrate that individual ligands modulate the stabilization of 3' incoming dNTPs to optimize DNA primer synthesis efficiency during initiation and primer maturation.
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Affiliation(s)
| | - Luis Blanco
- Centro de Biología Molecular Severo Ochoa, (CSIC-UAM), c/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain;
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2
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Papini C, Wang Z, Kudalkar SN, Schrank TP, Tang S, Sasaki T, Wu C, Tejada B, Ziegler SJ, Xiong Y, Issaeva N, Yarbrough WG, Anderson KS. Exploring ABOBEC3A and APOBEC3B substrate specificity and their role in HPV positive head and neck cancer. iScience 2022; 25:105077. [PMID: 36164654 PMCID: PMC9508485 DOI: 10.1016/j.isci.2022.105077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 08/05/2022] [Accepted: 08/31/2022] [Indexed: 12/03/2022] Open
Abstract
APOBEC3 family members are cytidine deaminases catalyzing conversion of cytidine to uracil. Many studies have established a link between APOBEC3 expression and cancer development and progression, especially APOBEC3A (A3A) and APOBEC3B (A3B). Preclinical studies with human papillomavirus positive (HPV+) head and neck squamous cell carcinoma (HNSCC) and clinical trial specimens revealed induction of A3B, but not A3A expression after demethylation. We examined the kinetic features of the cytidine deaminase activity for full length A3B and found that longer substrates and a purine at −2 position favored by A3B, whereas A3A prefers shorter substrates and an adenine or thymine at −2 position. The importance and biological significance of A3B catalytic activity rather than A3A and a preference for purine at the −2 position was also established in HPV+ HNSCCs. Our study explored factors influencing formation of A3A and A3B-related cancer mutations that are essential for understanding APOBEC3-related carcinogenesis and facilitating drug discovery. A3B is upregulated after 5-AzaC treatment and related to 5-AzaC sensitivity in HPV+ HNSCC Full-length A3B prefers longer substrates and a purine at −2 site biochemically A3B also prefers a purine at −2 site in both HPV+ and HPV− HNSCC cells A3B signature at -2 site linked to poor patient survival in HPV+ HNSCC low smokers
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Affiliation(s)
- Christina Papini
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar St., New Haven, CT 06520, USA
| | - Zechen Wang
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar St., New Haven, CT 06520, USA
| | - Shalley N Kudalkar
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar St., New Haven, CT 06520, USA
| | - Travis Parke Schrank
- Department of Otolaryngology/Head and Neck Surgery, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Su Tang
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar St., New Haven, CT 06520, USA
| | - Tomoaki Sasaki
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar St., New Haven, CT 06520, USA
| | - Cory Wu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Brandon Tejada
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Samantha J Ziegler
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Natalia Issaeva
- Department of Otolaryngology/Head and Neck Surgery, University of North Carolina, Chapel Hill, NC 27599, USA.,Department of Pathology and Lab Medicine, Lineberger Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Wendell G Yarbrough
- Department of Otolaryngology/Head and Neck Surgery, University of North Carolina, Chapel Hill, NC 27599, USA.,Department of Pathology and Lab Medicine, Lineberger Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Karen S Anderson
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar St., New Haven, CT 06520, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
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3
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Abstract
Significance: The small, multicopy mitochondrial genome (mitochondrial DNA [mtDNA]) is essential for efficient energy production, as alterations in its coding information or a decrease in its copy number disrupt mitochondrial ATP synthesis. However, the mitochondrial replication machinery encounters numerous challenges that may limit its ability to duplicate this important genome and that jeopardize mtDNA stability, including various lesions in the DNA template, topological stress, and an insufficient nucleotide supply. Recent Advances: An ever-growing array of DNA repair or maintenance factors are being reported to localize to the mitochondria. We review current knowledge regarding the mitochondrial factors that may contribute to the tolerance or repair of various types of changes in the mitochondrial genome, such as base damage, incorporated ribonucleotides, and strand breaks. We also discuss the newly discovered link between mtDNA instability and activation of the innate immune response. Critical Issues: By which mechanisms do mitochondria respond to challenges that threaten mtDNA maintenance? What types of mtDNA damage are repaired, and when are the affected molecules degraded instead? And, finally, which forms of mtDNA instability trigger an immune response, and how? Future Directions: Further work is required to understand the contribution of the DNA repair and damage-tolerance factors present in the mitochondrial compartment, as well as the balance between mtDNA repair and degradation. Finally, efforts to understand the events underlying mtDNA release into the cytosol are warranted. Pursuing these and many related avenues can improve our understanding of what goes wrong in mitochondrial disease. Antioxid. Redox Signal. 36, 885-905.
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Affiliation(s)
- Gustavo Carvalho
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Bruno Marçal Repolês
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Isabela Mendes
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Paulina H Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
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4
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PrimPol: A Breakthrough among DNA Replication Enzymes and a Potential New Target for Cancer Therapy. Biomolecules 2022; 12:biom12020248. [PMID: 35204749 PMCID: PMC8961649 DOI: 10.3390/biom12020248] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/29/2022] [Accepted: 02/02/2022] [Indexed: 02/01/2023] Open
Abstract
DNA replication can encounter blocking obstacles, leading to replication stress and genome instability. There are several mechanisms for evading this blockade. One mechanism consists of repriming ahead of the obstacles, creating a new starting point; in humans, PrimPol is responsible for carrying out this task. PrimPol is a primase that operates in both the nucleus and mitochondria. In contrast with conventional primases, PrimPol is a DNA primase able to initiate DNA synthesis de novo using deoxynucleotides, discriminating against ribonucleotides. In vitro, PrimPol can act as a DNA primase, elongating primers that PrimPol itself sythesizes, or as translesion synthesis (TLS) DNA polymerase, elongating pre-existing primers across lesions. However, the lack of evidence for PrimPol polymerase activity in vivo suggests that PrimPol only acts as a DNA primase. Here, we provide a comprehensive review of human PrimPol covering its biochemical properties and structure, in vivo function and regulation, and the processes that take place to fill the gap-containing lesion that PrimPol leaves behind. Finally, we explore the available data on human PrimPol expression in different tissues in physiological conditions and its role in cancer.
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5
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Human PrimPol Discrimination against Dideoxynucleotides during Primer Synthesis. Genes (Basel) 2021; 12:genes12101487. [PMID: 34680882 PMCID: PMC8535229 DOI: 10.3390/genes12101487] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/17/2021] [Accepted: 09/22/2021] [Indexed: 12/02/2022] Open
Abstract
PrimPol is required to re-prime DNA replication at both nucleus and mitochondria, thus facilitating fork progression during replicative stress. ddC is a chain-terminating nucleotide that has been widely used to block mitochondrial DNA replication because it is efficiently incorporated by the replicative polymerase Polγ. Here, we show that human PrimPol discriminates against dideoxynucleotides (ddNTP) when elongating a primer across 8oxoG lesions in the template, but also when starting de novo synthesis of DNA primers, and especially when selecting the 3′nucleotide of the initial dimer. PrimPol incorporates ddNTPs with a very low efficiency compared to dNTPs even in the presence of activating manganese ions, and only a 40-fold excess of ddNTP would significantly disturb PrimPol primase activity. This discrimination against ddNTPs prevents premature termination of the primers, warranting their use for elongation. The crystal structure of human PrimPol highlights Arg291 residue as responsible for the strong dNTP/ddNTP selectivity, since it interacts with the 3′-OH group of the incoming deoxynucleotide, absent in ddNTPs. Arg291, shown here to be critical for both primase and polymerase activities of human PrimPol, would contribute to the preferred binding of dNTPs versus ddNTPs at the 3′elongation site, thus avoiding synthesis of abortive primers.
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6
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Boldinova EO, Manukyan АА, Makarova АV. The DNA ligands Arg47 and Arg76 are crucial for catalysis by human PrimPol. DNA Repair (Amst) 2021; 100:103048. [PMID: 33571927 DOI: 10.1016/j.dnarep.2021.103048] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/08/2020] [Accepted: 01/09/2021] [Indexed: 01/22/2023]
Abstract
Human primase and DNA polymerase PrimPol re-starts stalled replication forks by repriming downstream DNA lesions and protects cells against DNA damage. Structure of the catalytic core of PrimPol with DNA primer, template and incoming dATP was solved but the mechanisms of DNA polymerase and primase activities of PrimPol are not fully understood. In this work, using site-directed mutagenesis we biochemically analyzed the role of active site residues Arg47 and Arg76 contacting DNA template in DNA polymerase and primase activities of PrimPol. The substitution R47A diminished the DNA polymerase and primase activities of PrimPol whereas the single amino acid substitution R76A caused almost complete loss of catalytic activities. Both amino acid substitutions affected the spectrum of dNMPs incorporation on undamaged DNA templates and opposite 8-oxoguanine. Finally, substitutions of the Arg47 and Arg76 residues attenuated the formation of the stable PrimPol:DNA complex in the presence of ATP/dNTPs. Together, these findings suggest a key role of the Arg47 and Arg76 in DNA synthesis by PrimPol.
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Affiliation(s)
- Elizaveta O Boldinova
- National Research Center «Kurchatov Institute» - Institute of Molecular Genetics, Moscow, 123182, Russia
| | - Аnna А Manukyan
- National Research Center «Kurchatov Institute» - Institute of Molecular Genetics, Moscow, 123182, Russia; D. Mendeleev University of Chemical Technology of Russia (D. Mendeleyev University, MUCTR), Moscow, 125047, Russia
| | - Аlena V Makarova
- National Research Center «Kurchatov Institute» - Institute of Molecular Genetics, Moscow, 123182, Russia.
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7
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Boldinova EO, Belousova EA, Gagarinskaya DI, Maltseva EA, Khodyreva SN, Lavrik OI, Makarova AV. Strand Displacement Activity of PrimPol. Int J Mol Sci 2020; 21:ijms21239027. [PMID: 33261049 PMCID: PMC7729601 DOI: 10.3390/ijms21239027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/18/2020] [Accepted: 11/23/2020] [Indexed: 02/08/2023] Open
Abstract
Human PrimPol is a unique enzyme possessing DNA/RNA primase and DNA polymerase activities. In this work, we demonstrated that PrimPol efficiently fills a 5-nt gap and possesses the conditional strand displacement activity stimulated by Mn2+ ions and accessory replicative proteins RPA and PolDIP2. The DNA displacement activity of PrimPol was found to be more efficient than the RNA displacement activity and FEN1 processed the 5′-DNA flaps generated by PrimPol in vitro.
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Affiliation(s)
- Elizaveta O. Boldinova
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Kurchatov sq. 2, 123182 Moscow, Russia; (E.O.B.); (D.I.G.)
| | - Ekaterina A. Belousova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentiev Avenue, 630090 Novosibirsk, Russia; (E.A.B.); (E.A.M.); (S.N.K.); (O.I.L.)
| | - Diana I. Gagarinskaya
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Kurchatov sq. 2, 123182 Moscow, Russia; (E.O.B.); (D.I.G.)
| | - Ekaterina A. Maltseva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentiev Avenue, 630090 Novosibirsk, Russia; (E.A.B.); (E.A.M.); (S.N.K.); (O.I.L.)
| | - Svetlana N. Khodyreva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentiev Avenue, 630090 Novosibirsk, Russia; (E.A.B.); (E.A.M.); (S.N.K.); (O.I.L.)
| | - Olga I. Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentiev Avenue, 630090 Novosibirsk, Russia; (E.A.B.); (E.A.M.); (S.N.K.); (O.I.L.)
| | - Alena V. Makarova
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Kurchatov sq. 2, 123182 Moscow, Russia; (E.O.B.); (D.I.G.)
- Correspondence:
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8
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Conti BA, Smogorzewska A. Mechanisms of direct replication restart at stressed replisomes. DNA Repair (Amst) 2020; 95:102947. [PMID: 32853827 PMCID: PMC7669714 DOI: 10.1016/j.dnarep.2020.102947] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/02/2020] [Accepted: 08/04/2020] [Indexed: 02/09/2023]
Affiliation(s)
- Brooke A Conti
- Laboratory of Genome Maintenance, The Rockefeller University, New York 10065, USA
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York 10065, USA.
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9
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Narendran S, Pereira F, Yerramothu P, Apicella I, Wang SB, Varshney A, Baker KL, Marion KM, Ambati M, Ambati VL, Ambati K, Sadda SR, Gelfand BD, Ambati J. A Clinical Metabolite of Azidothymidine Inhibits Experimental Choroidal Neovascularization and Retinal Pigmented Epithelium Degeneration. Invest Ophthalmol Vis Sci 2020; 61:4. [PMID: 32749462 PMCID: PMC7441363 DOI: 10.1167/iovs.61.10.4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/12/2020] [Indexed: 12/14/2022] Open
Abstract
Purpose Azidothymidine (AZT), a nucleoside reverse transcriptase inhibitor, possesses anti-inflammatory and anti-angiogenic activity independent of its ability to inhibit reverse transcriptase. The aim of this study was to evaluate the efficacy of 5'-glucuronyl azidothymidine (GAZT), an antiretrovirally inert hepatic clinical metabolite of AZT, in mouse models of retinal pigment epithelium (RPE) degeneration and choroidal neovascularization (CNV), hallmark features of dry and wet age-related macular degeneration (AMD), respectively. Methods RPE degeneration was induced in wild-type (WT) C57BL/6J mice by subretinal injection of Alu RNA. RPE degeneration was assessed by fundus photography and confocal microscopy of zonula occludens-1-stained RPE flat mounts. Choroidal neovascularization was induced by laser injury in WT mice, and CNV volume was measured by confocal microscopy. AZT and GAZT were delivered by intravitreous injections. Inflammasome activation was monitored by western blotting for caspase-1 and by ELISA for IL-1β in Alu RNA-treated bone marrow-derived macrophages (BMDMs). Results GAZT inhibited Alu RNA-induced RPE degeneration and laser-induced CNV. GAZT also reduced Alu RNA-induced caspase-1 activation and IL-1β release in BMDMs. Conclusions GAZT possesses dual anti-inflammatory and anti-angiogenic properties and could be a viable treatment option for both forms of AMD.
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Affiliation(s)
- Siddharth Narendran
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, Virginia, United States
| | - Felipe Pereira
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, Virginia, United States
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, Virginia, United States
| | - Praveen Yerramothu
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, Virginia, United States
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, Virginia, United States
| | - Ivana Apicella
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, Virginia, United States
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, Virginia, United States
| | - Shao-bin Wang
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, Virginia, United States
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, Virginia, United States
| | - Akhil Varshney
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, Virginia, United States
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, Virginia, United States
| | - Kirstie L. Baker
- Doheny Eye Institute, Los Angeles, Los Angeles, California, United States
| | - Kenneth M. Marion
- Doheny Eye Institute, Los Angeles, Los Angeles, California, United States
| | - Meenakshi Ambati
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, Virginia, United States
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, Virginia, United States
- Center for Digital Image Evaluation, Charlottesville, Virginia, United States
| | - Vidya L. Ambati
- Center for Digital Image Evaluation, Charlottesville, Virginia, United States
| | - Kameshwari Ambati
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, Virginia, United States
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, Virginia, United States
| | - Srinivas R. Sadda
- Doheny Eye Institute, Los Angeles, Los Angeles, California, United States
- Department of Ophthalmology, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, California, United States
| | - Bradley D. Gelfand
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, Virginia, United States
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, Virginia, United States
- Department of Biomedical Engineering, University of Virginia School of Medicine, Charlottesville, Virginia, United States
| | - Jayakrishna Ambati
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, Virginia, United States
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, Virginia, United States
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, Virginia, United States
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10
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Identifying the role of PrimPol in TDF-induced toxicity and implications of its loss of function mutation in an HIV+ patient. Sci Rep 2020; 10:9343. [PMID: 32518272 PMCID: PMC7283272 DOI: 10.1038/s41598-020-66153-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 05/14/2020] [Indexed: 12/25/2022] Open
Abstract
A key component of antiretroviral therapy (ART) for HIV patients is the nucleoside reverse transcriptase inhibitor (NRTI) is tenofovir. Recent reports of tenofovir toxicity in patients taking ART for HIV cannot be explained solely on the basis of off-target inhibition of mitochondrial DNA polymerase gamma (Polγ). PrimPol was discovered as a primase-polymerase localized to the mitochondria with repriming and translesion synthesis capabilities and, therefore, a potential contributor to mitochondrial toxicity. We established a possible role of PrimPol in tenofovir-induced toxicity in vitro and show that tenofovir-diphosphate incorporation by PrimPol is dependent on the n-1 nucleotide. We identified and characterized a PrimPol mutation, D114N, in an HIV+ patient on tenofovir-based ART with mitochondrial toxicity. This mutant form of PrimPol, targeting a catalytic metal ligand, was unable to synthesize primers, likely due to protein instability and weakened DNA binding. We performed cellular respiration and toxicity assays using PrimPol overexpression and shRNA knockdown strains in renal proximal tubular epithelial cells. The PrimPol-knockdown strain was hypersensitive to tenofovir treatment, indicating that PrimPol protects against tenofovir-induced mitochondrial toxicity. We show that a major cellular role of PrimPol is protecting against toxicity caused by ART and individuals with inactivating mutations may be predisposed to these effects.
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11
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Xu W, Zhao W, Morehouse N, Tree MO, Zhao L. Divalent Cations Alter the Rate-Limiting Step of PrimPol-Catalyzed DNA Elongation. J Mol Biol 2019; 431:673-686. [PMID: 30633872 DOI: 10.1016/j.jmb.2019.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 12/20/2018] [Accepted: 01/02/2019] [Indexed: 11/28/2022]
Abstract
PrimPol is the most recently discovered human DNA polymerase/primase and plays an emerging role in nuclear and mitochondrial genomic maintenance. As a member of archaeo-eukaryotic primase superfamily enzymes, PrimPol possesses DNA polymerase and primase activities that are important for replication fork progression in vitro and in cellulo. The enzymatic activities of PrimPol are critically dependent on the nucleotidyl-transfer reaction to incorporate deoxyribonucleotides successively; however, our knowledge concerning the kinetic mechanism of the reaction remains incomplete. Using enzyme kinetic analyses and computer simulations, we dissected the mechanism by which PrimPol transfers a nucleotide to a primer-template DNA, which comprises DNA binding, conformational transition, nucleotide binding, phosphoester bond formation, and dissociation steps. We obtained the rate constants of the steps by steady-state and pre-steady-state kinetic analyses and simulations. Our data demonstrate that the rate-limiting step of PrimPol-catalyzed DNA elongation depends on the metal cofactor involved. In the presence of Mn2+, a conformational transition step from non-productive to productive PrimPol:DNA complexes limits the enzymatic turnover, whereas in the presence of Mg2+, the chemical step becomes rate limiting. As evidenced from our kinetic and simulation data, PrimPol maintains the same kinetic mechanism under either millimolar or physiological micromolar Mn2+ concentration. Our study revealed the underlying mechanism by which PrimPol catalyzes nucleotide incorporation with two common metal cofactors and provides a kinetic basis for further understanding the regulatory mechanism of this functionally diverse primase-polymerase.
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Affiliation(s)
- Wenyan Xu
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI 48859, USA
| | - Wenxin Zhao
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI 48859, USA
| | - Nana Morehouse
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI 48859, USA
| | - Maya O Tree
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI 48859, USA
| | - Linlin Zhao
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI 48859, USA; Biochemistry, Cellular and Molecular Biology Graduate Program, Central Michigan University, Mount Pleasant, MI 48859, USA.
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12
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Dengue drug discovery: Progress, challenges and outlook. Antiviral Res 2018; 163:156-178. [PMID: 30597183 DOI: 10.1016/j.antiviral.2018.12.016] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 12/22/2018] [Accepted: 12/25/2018] [Indexed: 12/14/2022]
Abstract
In the context of the only available vaccine (DENGVAXIA) that was marketed in several countries, but poses higher risks to unexposed individuals, the development of antivirals for dengue virus (DENV), whilst challenging, would bring significant benefits to public health. Here recent progress in the field of DENV drug discovery made in academic laboratories and industry is reviewed. Characteristics of an ideal DENV antiviral molecule, given the specific immunopathology provoked by this acute viral infection, are described. New chemical classes identified from biochemical, biophysical and phenotypic screens that target viral (especially NS4B) and host proteins, offer promising opportunities for further development. In particular, new methodologies ("omics") can accelerate the discovery of much awaited flavivirus specific inhibitors. Challenges and opportunities in lead identification activities as well as the path to clinical development of dengue drugs are discussed. To galvanize DENV drug discovery, collaborative public-public partnerships and open-access resources will greatly benefit both the DENV research community and DENV patients.
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13
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Baranovskiy AG, Duong VN, Babayeva ND, Zhang Y, Pavlov YI, Anderson KS, Tahirov TH. Activity and fidelity of human DNA polymerase α depend on primer structure. J Biol Chem 2018; 293:6824-6843. [PMID: 29555682 DOI: 10.1074/jbc.ra117.001074] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 03/09/2018] [Indexed: 12/13/2022] Open
Abstract
DNA polymerase α (Polα) plays an important role in genome replication. In a complex with primase, Polα synthesizes chimeric RNA-DNA primers necessary for replication of both chromosomal DNA strands. During RNA primer extension with deoxyribonucleotides, Polα needs to use double-stranded helical substrates having different structures. Here, we provide a detailed structure-function analysis of human Polα's interaction with dNTPs and DNA templates primed with RNA, chimeric RNA-DNA, or DNA. We report the crystal structures of two ternary complexes of the Polα catalytic domain containing dCTP, a DNA template, and either a DNA or an RNA primer. Unexpectedly, in the ternary complex with a DNA:DNA duplex and dCTP, the "fingers" subdomain of Polα is in the open conformation. Polα induces conformational changes in the DNA and hybrid duplexes to produce the universal double helix form. Pre-steady-state kinetic studies indicated for both duplex types that chemical catalysis rather than product release is the rate-limiting step. Moreover, human Polα extended DNA primers with higher efficiency but lower processivity than it did with RNA and chimeric primers. Polα has a substantial propensity to make errors during DNA synthesis, and we observed that its fidelity depends on the type of sugar at the primer 3'-end. A detailed structural comparison of Polα with other replicative DNA polymerases disclosed common features and some differences, which may reflect the specialization of each polymerase in genome replication.
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Affiliation(s)
- Andrey G Baranovskiy
- From the Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, and
| | - Vincent N Duong
- the Departments of Pharmacology and Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06510
| | - Nigar D Babayeva
- From the Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, and
| | - Yinbo Zhang
- From the Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, and
| | - Youri I Pavlov
- From the Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, and.,the Departments of Biochemistry and Molecular Biology, Pathology and Microbiology, and Genetics and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska 68198 and
| | - Karen S Anderson
- the Departments of Pharmacology and Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06510
| | - Tahir H Tahirov
- From the Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, and
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14
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Young MJ. Off-Target Effects of Drugs that Disrupt Human Mitochondrial DNA Maintenance. Front Mol Biosci 2017; 4:74. [PMID: 29214156 PMCID: PMC5702650 DOI: 10.3389/fmolb.2017.00074] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 10/31/2017] [Indexed: 12/17/2022] Open
Abstract
Nucleoside reverse transcriptase inhibitors (NRTIs) were the first drugs used to treat human immunodeficiency virus (HIV) the cause of acquired immunodeficiency syndrome. Development of severe mitochondrial toxicity has been well documented in patients infected with HIV and administered NRTIs. In vitro biochemical experiments have demonstrated that the replicative mitochondrial DNA (mtDNA) polymerase gamma, Polg, is a sensitive target for inhibition by metabolically active forms of NRTIs, nucleotide reverse transcriptase inhibitors (NtRTIs). Once incorporated into newly synthesized daughter strands NtRTIs block further DNA polymerization reactions. Human cell culture and animal studies have demonstrated that cell lines and mice exposed to NRTIs display mtDNA depletion. Further complicating NRTI off-target effects on mtDNA maintenance, two additional DNA polymerases, Pol beta and PrimPol, were recently reported to localize to mitochondria as well as the nucleus. Similar to Polg, in vitro work has demonstrated both Pol beta and PrimPol incorporate NtRTIs into nascent DNA. Cell culture and biochemical experiments have also demonstrated that antiviral ribonucleoside drugs developed to treat hepatitis C infection act as off-target substrates for POLRMT, the mitochondrial RNA polymerase and primase. Accompanying the above-mentioned topics, this review examines: (1) mtDNA maintenance in human health and disease, (2) reports of DNA polymerases theta and zeta (Rev3) localizing to mitochondria, and (3) additional drugs with off-target effects on mitochondrial function. Lastly, mtDNA damage may induce cell death; therefore, the possibility of utilizing compounds that disrupt mtDNA maintenance to kill cancer cells is discussed.
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Affiliation(s)
- Matthew J Young
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL, United States
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15
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Boldinova EO, Stojkovič G, Khairullin R, Wanrooij S, Makarova AV. Optimization of the expression, purification and polymerase activity reaction conditions of recombinant human PrimPol. PLoS One 2017; 12:e0184489. [PMID: 28902865 PMCID: PMC5597260 DOI: 10.1371/journal.pone.0184489] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 08/24/2017] [Indexed: 12/02/2022] Open
Abstract
Human PrimPol is a DNA primase/polymerase involved in DNA damage tolerance and prevents nuclear genome instability. PrimPol is also localized to the mitochondria, but its precise function in mitochondrial DNA maintenance has remained elusive. PrimPol works both as a translesion (TLS) polymerase and as the primase that restarts DNA replication after a lesion. However, the observed biochemical activities of PrimPol vary considerably between studies as a result of different reaction conditions used. To reveal the effects of reaction composition on PrimPol DNA polymerase activity, we tested the polymerase activity in the presence of various buffer agents, salt concentrations, pH values and metal cofactors. Additionally, the enzyme stability was analyzed under various conditions. We demonstrate that the reaction buffer with pH 6–6.5, low salt concentrations and 3 mM Mg2+ or 0.3–3 mM Mn2+ cofactor ions supports the highest DNA polymerase activity of human PrimPol in vitro. The DNA polymerase activity of PrimPol was found to be stable after multiple freeze-thaw cycles and prolonged protein incubation on ice. However, rapid heat-inactivation of the enzyme was observed at 37ºC. We also for the first time describe the purification of human PrimPol from a human cell line and compare the benefits of this approach to the expression in Escherichia coli and in Saccharomyces cerevisiae cells. Our results show that active PrimPol can be purified from E. coli and human suspension cell line in high quantities and that the activity of the purified enzyme is similar in both expression systems. Conversely, the yield of full-length protein expressed in S. cerevisiae was considerably lower and this system is therefore not recommended for expression of full-length recombinant human PrimPol.
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Affiliation(s)
- Elizaveta O. Boldinova
- Institute of Molecular Genetics of Russian Academy of Sciences, Kurchatov sq. 2, Moscow, Russia
- Moscow State University of Fine Chemical Technologies, Vernadsky Prospect 78, Moscow, Russia
| | - Gorazd Stojkovič
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Rafil Khairullin
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, K.Marx, 18 Kazan, Russia
| | - Sjoerd Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- * E-mail: (AVM); (SW)
| | - Alena V. Makarova
- Institute of Molecular Genetics of Russian Academy of Sciences, Kurchatov sq. 2, Moscow, Russia
- * E-mail: (AVM); (SW)
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16
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Boldinova EO, Wanrooij PH, Shilkin ES, Wanrooij S, Makarova AV. DNA Damage Tolerance by Eukaryotic DNA Polymerase and Primase PrimPol. Int J Mol Sci 2017; 18:E1584. [PMID: 28754021 PMCID: PMC5536071 DOI: 10.3390/ijms18071584] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 07/14/2017] [Accepted: 07/16/2017] [Indexed: 12/31/2022] Open
Abstract
PrimPol is a human deoxyribonucleic acid (DNA) polymerase that also possesses primase activity and is involved in DNA damage tolerance, the prevention of genome instability and mitochondrial DNA maintenance. In this review, we focus on recent advances in biochemical and crystallographic studies of PrimPol, as well as in identification of new protein-protein interaction partners. Furthermore, we discuss the possible functions of PrimPol in both the nucleus and the mitochondria.
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Affiliation(s)
- Elizaveta O Boldinova
- Institute of Molecular Genetics of Russian Academy of Sciences, Kurchatov sq. 2, 123182 Moscow, Russia.
| | - Paulina H Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden.
| | - Evgeniy S Shilkin
- Institute of Molecular Genetics of Russian Academy of Sciences, Kurchatov sq. 2, 123182 Moscow, Russia.
| | - Sjoerd Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden.
| | - Alena V Makarova
- Institute of Molecular Genetics of Russian Academy of Sciences, Kurchatov sq. 2, 123182 Moscow, Russia.
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17
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Mitochondrial DNA replication: a PrimPol perspective. Biochem Soc Trans 2017; 45:513-529. [PMID: 28408491 PMCID: PMC5390496 DOI: 10.1042/bst20160162] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 02/20/2017] [Accepted: 02/21/2017] [Indexed: 12/20/2022]
Abstract
PrimPol, (primase-polymerase), the most recently identified eukaryotic polymerase, has roles in both nuclear and mitochondrial DNA maintenance. PrimPol is capable of acting as a DNA polymerase, with the ability to extend primers and also bypass a variety of oxidative and photolesions. In addition, PrimPol also functions as a primase, catalysing the preferential formation of DNA primers in a zinc finger-dependent manner. Although PrimPol's catalytic activities have been uncovered in vitro, we still know little about how and why it is targeted to the mitochondrion and what its key roles are in the maintenance of this multicopy DNA molecule. Unlike nuclear DNA, the mammalian mitochondrial genome is circular and the organelle has many unique proteins essential for its maintenance, presenting a differing environment within which PrimPol must function. Here, we discuss what is currently known about the mechanisms of DNA replication in the mitochondrion, the proteins that carry out these processes and how PrimPol is likely to be involved in assisting this vital cellular process.
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18
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Krasich R, Copeland WC. DNA polymerases in the mitochondria: A critical review of the evidence. FRONT BIOSCI-LANDMRK 2017; 22:692-709. [PMID: 27814640 PMCID: PMC5485829 DOI: 10.2741/4510] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Since 1970, the DNA polymerase gamma (PolG) has been known to be the DNA polymerase responsible for replication and repair of mitochondrial DNA, and until recently it was generally accepted that this was the only polymerase present in mitochondria. However, recent data has challenged that opinion, as several polymerases are now proposed to have activity in mitochondria. To date, their exact role of these other DNA polymerases is unclear and the amount of evidence supporting their role in mitochondria varies greatly. Further complicating matters, no universally accepted standards have been set for definitive proof of the mitochondrial localization of a protein. To gain an appreciation of these newly proposed DNA polymerases in the mitochondria, we review the evidence and standards needed to establish the role of a polymerase in the mitochondria. Employing PolG as an example, we established a list of criteria necessary to verify the existence and function of new mitochondrial proteins. We then apply this criteria towards several other putative mitochondrial polymerases. While there is still a lot left to be done in this exciting new direction, it is clear that PolG is not acting alone in mitochondria, opening new doors for potential replication and repair mechanisms.
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Affiliation(s)
- Rachel Krasich
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - William C Copeland
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, 111 T.W. Alexander Dr., Bldg. 101, Rm. E316, Research Triangle Park, NC 27709,
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19
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Tokarsky EJ, Wallenmeyer PC, Phi KK, Suo Z. Significant impact of divalent metal ions on the fidelity, sugar selectivity, and drug incorporation efficiency of human PrimPol. DNA Repair (Amst) 2016; 49:51-59. [PMID: 27989484 DOI: 10.1016/j.dnarep.2016.11.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 11/24/2016] [Accepted: 11/24/2016] [Indexed: 01/17/2023]
Abstract
Human PrimPol is a recently discovered bifunctional enzyme that displays DNA template-directed primase and polymerase activities. PrimPol has been implicated in nuclear and mitochondrial DNA replication fork progression and restart as well as DNA lesion bypass. Published evidence suggests that PrimPol is a Mn2+-dependent enzyme as it shows significantly improved primase and polymerase activities when binding Mn2+, rather than Mg2+, as a divalent metal ion cofactor. Consistently, our fluorescence anisotropy assays determined that PrimPol binds to a primer/template DNA substrate with affinities of 29 and 979nM in the presence of Mn2+ and Mg2+, respectively. Our pre-steady-state kinetic analysis revealed that PrimPol incorporates correct dNTPs with 100-fold higher efficiency with Mn2+ than with Mg2+. Notably, the substitution fidelity of PrimPol in the presence of Mn2+ was determined to be in the range of 3.4×10-2 to 3.8×10-1, indicating that PrimPol is an error-prone polymerase. Furthermore, we kinetically determined the sugar selectivity of PrimPol to be 57-1800 with Mn2+ and 150-4500 with Mg2+, and found that PrimPol was able to incorporate the triphosphates of two anticancer drugs (cytarabine and gemcitabine), but not two antiviral drugs (emtricitabine and lamivudine).
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Affiliation(s)
- E John Tokarsky
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; The Ohio State Biophysics Program, The Ohio State University, Columbus, OH 43210, USA
| | - Petra C Wallenmeyer
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Kenneth K Phi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Zucai Suo
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; The Ohio State Biophysics Program, The Ohio State University, Columbus, OH 43210, USA.
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20
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Oxidative DNA damage stalls the human mitochondrial replisome. Sci Rep 2016; 6:28942. [PMID: 27364318 PMCID: PMC4929447 DOI: 10.1038/srep28942] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 05/31/2016] [Indexed: 12/27/2022] Open
Abstract
Oxidative stress is capable of causing damage to various cellular constituents, including DNA. There is however limited knowledge on how oxidative stress influences mitochondrial DNA and its replication. Here, we have used purified mtDNA replication proteins, i.e. DNA polymerase γ holoenzyme, the mitochondrial single-stranded DNA binding protein mtSSB, the replicative helicase Twinkle and the proposed mitochondrial translesion synthesis polymerase PrimPol to study lesion bypass synthesis on oxidative damage-containing DNA templates. Our studies were carried out at dNTP levels representative of those prevailing either in cycling or in non-dividing cells. At dNTP concentrations that mimic those in cycling cells, the replication machinery showed substantial stalling at sites of damage, and these problems were further exacerbated at the lower dNTP concentrations present in resting cells. PrimPol, the translesion synthesis polymerase identified inside mammalian mitochondria, did not promote mtDNA replication fork bypass of the damage. This argues against a conventional role for PrimPol as a mitochondrial translesion synthesis DNA polymerase for oxidative DNA damage; however, we show that Twinkle, the mtDNA replicative helicase, is able to stimulate PrimPol DNA synthesis in vitro, suggestive of an as yet unidentified role of PrimPol in mtDNA metabolism.
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