1
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Chee CW, Mohd Hashim N, Abdullah I, Nor Rashid N. RNA Sequencing and Bioinformatics Analysis Reveals the Downregulation of DNA Replication Genes by Morindone in Colorectal Cancer Cells. Appl Biochem Biotechnol 2024; 196:3216-3233. [PMID: 37642925 DOI: 10.1007/s12010-023-04690-9] [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] [Accepted: 08/16/2023] [Indexed: 08/31/2023]
Abstract
Morindone, a natural anthraquinone compound, has been reported to have significant pharmacological properties in different cancers. However, its anticancer effects in colorectal cancer (CRC) and the underlying molecular mechanisms remain obscure. In this study, RNA sequencing was used to assess the differentially expressed genes (DEGs) following morindone treatment in two CRC cell lines, HCT116 and HT29 cells. Functional enrichment analysis of overlapping DEGs revealed that negative regulation of cell development from biological processes and the MAPK signalling pathway were the most significant Gene Ontology terms and Kyoto Encyclopaedia of Genes and Genome pathway, respectively. Seven hub genes were identified among the overlapping genes, including MCM5, MCM6, MCM10, GINS2, POLE2, PRIM1, and WDHD1. All hub genes were found downregulated and involved in DNA replication fork. Among these, GINS2 was identified as the most cancer-dependent gene in both cells with better survival outcomes. Validation was performed on seven hub genes with rt-qPCR, and the results were consistent with the RNA sequencing findings. Collectively, this study provides corroboration of the potential therapeutic benefits and suitable pharmacological targets of morindone in the treatment of CRC.
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Affiliation(s)
- Cheok Wui Chee
- Department of Molecular Medicine, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Najihah Mohd Hashim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
- Centre for Natural Products Research and Drug Discovery, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
- Drug Design and Development Research Group, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Iskandar Abdullah
- Drug Design and Development Research Group, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
- Department of Chemistry, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Nurshamimi Nor Rashid
- Department of Molecular Medicine, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
- Centre for Natural Products Research and Drug Discovery, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
- Drug Design and Development Research Group, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
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2
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Boldinova EO, Baranovskiy AG, Filina YV, Miftakhova RR, Shamsutdinova YF, Tahirov TH, Makarova AV. PrimPol Variant V102A with Altered Primase and Polymerase Activities. J Mol Biol 2024; 436:168542. [PMID: 38492718 DOI: 10.1016/j.jmb.2024.168542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/10/2024] [Accepted: 03/12/2024] [Indexed: 03/18/2024]
Abstract
PrimPol is a human DNA primase-polymerase which restarts DNA synthesis beyond DNA lesions and non-B DNA structures blocking replication. Disfunction of PrimPol in cells leads to slowing of DNA replication rates in mitochondria and nucleus, accumulation of chromosome aberrations, cell cycle delay, and elevated sensitivity to DNA-damaging agents. A defective PrimPol has been suggested to be associated with the development of ophthalmic diseases, elevated mitochondrial toxicity of antiviral drugs and increased cell resistance to chemotherapy. Here, we describe a rare missense PrimPol variant V102A with altered biochemical properties identified in patients suffering from ovarian and cervical cancer. The Val102 to Ala substitution dramatically reduced both the primase and DNA polymerase activities of PrimPol as well as specifically decreased its ability to incorporate ribonucleotides. Structural analysis indicates that the V102A substitution can destabilize the hydrophobic pocket adjacent to the active site, affecting dNTP binding and catalysis.
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Affiliation(s)
- Elizaveta O Boldinova
- National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia; Institute of Gene Biology, Russian Academy of Sciences, Vavilova 34 / 5, 119334 Moscow, Russia
| | - Andrey G Baranovskiy
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Yulia V Filina
- "Translational Oncology" Research Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kremlevskaya 18, 420008 Kazan, Russia
| | - Regina R Miftakhova
- "Translational Oncology" Research Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kremlevskaya 18, 420008 Kazan, Russia
| | - Yana F Shamsutdinova
- Chemotherapy Department №1, Republican Clinical Oncology Dispensary of the Ministry of Health of the Republic of Tatarstan Named After Prof. M.Z. Sigal, Sibirskiy trakt 29, 420029 Kazan, Russia
| | - Tahir H Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Alena V Makarova
- National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia; Institute of Gene Biology, Russian Academy of Sciences, Vavilova 34 / 5, 119334 Moscow, Russia.
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3
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Bainbridge LJ, Zabrady K, Doherty AJ. Coordination of Primer Initiation Within the Catalytic Domain of Human PrimPol. J Mol Biol 2023; 435:168338. [PMID: 37923120 DOI: 10.1016/j.jmb.2023.168338] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/07/2023]
Abstract
To facilitate the eukaryotic repriming pathway of DNA damage tolerance, PrimPol synthesises de novo oligonucleotide primers downstream of polymerase-stalling obstacles. These primers enable replicative polymerases to resume synthesis and ensure the timely completion of DNA replication. Initiating synthesis de novo requires the coordination of single-stranded DNA, initiating nucleotides, and metal ions within PrimPol's active site to catalyze the formation of the first phosphodiester bond. Here we examine the interactions between human PrimPol's catalytic domain, nucleotides, and DNA template during each of the various catalytic steps to determine the 'choreography' of primer synthesis, where substrates bind in an ordered manner. Our findings show that the ability of PrimPol to conduct de novo primer synthesis is underpinned by a network of stabilising interactions between the enzyme, template, and nucleotides, as we previously observed for related primase CRISPR-Associated Prim-Pol (CAPP). Together, these findings establish a detailed model for the initiation of DNA synthesis by human PrimPol, which appears highly conserved.
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Affiliation(s)
- Lewis J Bainbridge
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK
| | - Katerina Zabrady
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK
| | - Aidan J Doherty
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK.
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4
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Gromova AS, Boldinova EO, Kim DV, Chuprov-Netochin RN, Leonov SV, Pustovalova MV, Zharkov DO, Makarova AV. Response of PRIMPOL-Knockout Human Lung Adenocarcinoma A549 Cells to Genotoxic Stress. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1933-1943. [PMID: 38105210 DOI: 10.1134/s0006297923110214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 08/08/2023] [Accepted: 09/15/2023] [Indexed: 12/19/2023]
Abstract
Human DNA primase/polymerase PrimPol synthesizes DNA primers de novo after replication fork stalling at the sites of DNA damage, thus contributing to the DNA damage tolerance. The role of PrimPol in response to the different types of DNA damage is poorly understood. We knocked out the PRIMPOL gene in the lung carcinoma A549 cell line and characterized the response of the obtained cells to the DNA damage caused by hydrogen peroxide, methyl methanesulfonate (MMS), cisplatin, bleomycin, and ionizing radiation. The PRIMPOL knockout reduced the number of proliferating cells and cells in the G2 phase after treatment with MMS and caused a more pronounced delay of the S phase in the cisplatin-treated cells. Ionizing radiation at a dose of 10 Gy significantly increased the content of apoptotic cells among the PRIMPOL-deficient cells, while the proportion of cells undergoing necroptosis increased in both parental and knockout cells at any radiation dose. The viability of PRIMPOL-deficient cells upon the hydrogen peroxide-induced oxidative stress increased compared to the control cells, as determined by the methyl tetrazolium (MTT) assay. The obtained data indicate the involvement of PRIMPOL in the modulation of adaptive cell response to various types of genotoxic stress.
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Affiliation(s)
- Anastasia S Gromova
- Institute of Molecular Genetics, Kurchatov Institute National Research Center, Moscow, 123182, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Elizaveta O Boldinova
- Institute of Molecular Genetics, Kurchatov Institute National Research Center, Moscow, 123182, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Daria V Kim
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Roman N Chuprov-Netochin
- School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russia
| | - Sergey V Leonov
- School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russia
- Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino, 142290, Russia
| | - Margarita V Pustovalova
- School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russia
| | - Dmitry O Zharkov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Alena V Makarova
- Institute of Molecular Genetics, Kurchatov Institute National Research Center, Moscow, 123182, Russia.
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
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5
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Boldinova EO, Baranovskiy AG, Gagarinskaya DI, Manukyan A, Makarova A, Tahirov T. The role of catalytic and regulatory domains of human PrimPol in DNA binding and synthesis. Nucleic Acids Res 2023; 51:7541-7551. [PMID: 37326028 PMCID: PMC10415149 DOI: 10.1093/nar/gkad507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/28/2023] [Accepted: 05/31/2023] [Indexed: 06/17/2023] Open
Abstract
Human PrimPol possesses DNA primase and DNA polymerase activities and restarts stalled replication forks protecting cells against DNA damage in nuclei and mitochondria. The zinc-binding motif (ZnFn) of the C-terminal domain (CTD) of PrimPol is required for DNA primase activity but the mechanism is not clear. In this work, we biochemically demonstrate that PrimPol initiates de novo DNA synthesis in cis-orientation, when the N-terminal catalytic domain (NTD) and the CTD of the same molecule cooperate for substrates binding and catalysis. The modeling studies revealed that PrimPol uses a similar mode of initiating NTP coordination as the human primase. The ZnFn motif residue Arg417 is required for binding the 5'-triphosphate group that stabilizes the PrimPol complex with a DNA template-primer. We found that the NTD alone is able to initiate DNA synthesis, and the CTD stimulates the primase activity of NTD. The regulatory role of the RPA-binding motif in the modulation of PrimPol binding to DNA is also demonstrated.
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Affiliation(s)
- Elizaveta O Boldinova
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov 34/5, 119334 Moscow, Russia
| | - Andrey G Baranovskiy
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Diana I Gagarinskaya
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Anna A Manukyan
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov 34/5, 119334 Moscow, Russia
| | - Alena V Makarova
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov 34/5, 119334 Moscow, Russia
| | - Tahir H Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
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6
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Boldinova EO, Makarova AV. Regulation of Human DNA Primase-Polymerase PrimPol. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1139-1155. [PMID: 37758313 DOI: 10.1134/s0006297923080084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 10/03/2023]
Abstract
Transmission of genetic information depends on successful completion of DNA replication. Genomic DNA is subjected to damage on a daily basis. DNA lesions create obstacles for DNA polymerases and can lead to the replication blockage, formation of DNA breaks, cell cycle arrest, and apoptosis. Cells have evolutionary adapted to DNA damage by developing mechanisms allowing elimination of lesions prior to DNA replication (DNA repair) and helping to bypass lesions during DNA synthesis (DNA damage tolerance). The second group of mechanisms includes the restart of DNA synthesis at the sites of DNA damage by DNA primase-polymerase PrimPol. Human PrimPol was described in 2013. The properties and functions of this enzyme have been extensively studied in recent years, but very little is known about the regulation of PrimPol and association between the enzyme dysfunction and diseases. In this review, we described the mechanisms of human PrimPol regulation in the context of DNA replication, discussed in detail interactions of PrimPol with other proteins, and proposed possible pathways for the regulation of human PrimPol activity. The article also addresses the association of PrimPol dysfunction with human diseases.
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Affiliation(s)
- Elizaveta O Boldinova
- Kurchatov Institute National Research Centre, Moscow, 123182, Russia.
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Alena V Makarova
- Kurchatov Institute National Research Centre, Moscow, 123182, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
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7
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Bailey LJ, Teague R, Kolesar P, Bainbridge LJ, Lindsay HD, Doherty AJ. PLK1 regulates the PrimPol damage tolerance pathway during the cell cycle. SCIENCE ADVANCES 2021; 7:eabh1004. [PMID: 34860556 PMCID: PMC8641930 DOI: 10.1126/sciadv.abh1004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 10/14/2021] [Indexed: 05/14/2023]
Abstract
Replication stress and DNA damage stall replication forks and impede genome synthesis. During S phase, damage tolerance pathways allow lesion bypass to ensure efficient genome duplication. One such pathway is repriming, mediated by Primase-Polymerase (PrimPol) in human cells. However, the mechanisms by which PrimPol is regulated are poorly understood. Here, we demonstrate that PrimPol is phosphorylated by Polo-like kinase 1 (PLK1) at a conserved residue between PrimPol’s RPA binding motifs. This phosphorylation is differentially modified throughout the cell cycle, which prevents aberrant recruitment of PrimPol to chromatin. Phosphorylation can also be delayed and reversed in response to replication stress. The absence of PLK1-dependent regulation of PrimPol induces phenotypes including chromosome breaks, micronuclei, and decreased survival after treatment with camptothecin, olaparib, and UV-C. Together, these findings establish that deregulated repriming leads to genomic instability, highlighting the importance of regulating this damage tolerance pathway following fork stalling and throughout the cell cycle.
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Affiliation(s)
- Laura J. Bailey
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Rebecca Teague
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Peter Kolesar
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Lewis J. Bainbridge
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Howard D. Lindsay
- Lancaster Medical School, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YQ, UK
| | - Aidan J. Doherty
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK
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8
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García-Medel PL, Peralta-Castro A, Baruch-Torres N, Fuentes-Pascacio A, Pedroza-García JA, Cruz-Ramirez A, Brieba LG. Arabidopsis thaliana PrimPol is a primase and lesion bypass DNA polymerase with the biochemical characteristics to cope with DNA damage in the nucleus, mitochondria, and chloroplast. Sci Rep 2021; 11:20582. [PMID: 34663822 PMCID: PMC8523556 DOI: 10.1038/s41598-021-00151-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/07/2021] [Indexed: 11/09/2022] Open
Abstract
PrimPol is a novel Primase–Polymerase that synthesizes RNA and DNA primers de novo and extents from these primers as a DNA polymerase. Animal PrimPol is involved in nuclear and mitochondrial DNA replication by virtue of its translesion DNA synthesis (TLS) and repriming activities. Here we report that the plant model Arabidopsis thaliana encodes a functional PrimPol (AtPrimPol). AtPrimPol is a low fidelity and a TLS polymerase capable to bypass DNA lesions, like thymine glycol and abasic sites, by incorporating directly across these lesions or by skipping them. AtPrimPol is also an efficient primase that preferentially recognizes the single-stranded 3′-GTCG-5′ DNA sequence, where the 3′-G is cryptic. AtPrimPol is the first DNA polymerase that localizes in three cellular compartments: nucleus, mitochondria, and chloroplast. In vitro, AtPrimPol synthesizes primers that are extended by the plant organellar DNA polymerases and this reaction is regulated by organellar single-stranded binding proteins. Given the constant exposure of plants to endogenous and exogenous DNA-damaging agents and the enzymatic capabilities of lesion bypass and re-priming of AtPrimPol, we postulate a predominant role of this enzyme in avoiding replication fork collapse in all three plant genomes, both as a primase and as a TLS polymerase.
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Affiliation(s)
- Paola L García-Medel
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, CP 36821, Irapuato, Guanajuato, Mexico
| | - Antolín Peralta-Castro
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, CP 36821, Irapuato, Guanajuato, Mexico
| | - Noe Baruch-Torres
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, CP 36821, Irapuato, Guanajuato, Mexico.,Department of Pharmacology and Toxicology, The University of Texas Medical Branch at Galveston, Galveston, TX, 77555, USA
| | - Alma Fuentes-Pascacio
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, CP 36821, Irapuato, Guanajuato, Mexico
| | - José A Pedroza-García
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Apartado Postal 510-3, 62250, Cuernavaca, Morelos, Mexico
| | - Alfredo Cruz-Ramirez
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, CP 36821, Irapuato, Guanajuato, Mexico
| | - Luis G Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, CP 36821, Irapuato, Guanajuato, Mexico.
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9
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Kang Z, Fu P, Alcivar AL, Fu H, Redon C, Foo TK, Zuo Y, Ye C, Baxley R, Madireddy A, Buisson R, Bielinsky AK, Zou L, Shen Z, Aladjem MI, Xia B. BRCA2 associates with MCM10 to suppress PRIMPOL-mediated repriming and single-stranded gap formation after DNA damage. Nat Commun 2021; 12:5966. [PMID: 34645815 PMCID: PMC8514439 DOI: 10.1038/s41467-021-26227-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 09/23/2021] [Indexed: 11/28/2022] Open
Abstract
The BRCA2 tumor suppressor protects genome integrity by promoting homologous recombination-based repair of DNA breaks, stability of stalled DNA replication forks and DNA damage-induced cell cycle checkpoints. BRCA2 deficient cells display the radio-resistant DNA synthesis (RDS) phenotype, however the mechanism has remained elusive. Here we show that cells without BRCA2 are unable to sufficiently restrain DNA replication fork progression after DNA damage, and the underrestrained fork progression is due primarily to Primase-Polymerase (PRIMPOL)-mediated repriming of DNA synthesis downstream of lesions, leaving behind single-stranded DNA gaps. Moreover, we find that BRCA2 associates with the essential DNA replication factor MCM10 and this association suppresses PRIMPOL-mediated repriming and ssDNA gap formation, while having no impact on the stability of stalled replication forks. Our findings establish an important function for BRCA2, provide insights into replication fork control during the DNA damage response, and may have implications in tumor suppression and therapy response. Tumor suppressor BRCA2 is known to stabilize and restart stalled DNA replication forks. Here the authors show that BRCA2 is recruited to the replication fork through its interaction with MCM10 and inhibits Primase-Polymerase-mediated repriming, lesion bypass and single strand DNA gap formation after DNA damage.
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Affiliation(s)
- Zhihua Kang
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Pan Fu
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.,Department of Clinical Microbiology Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Allen L Alcivar
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.,Bristol-Myers Squibb Company, Bloomsbury, NJ, 08804, USA
| | - Haiqing Fu
- Developmental Therapeutics Group, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Christophe Redon
- Developmental Therapeutics Group, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Tzeh Keong Foo
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Yamei Zuo
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Caiyong Ye
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.,School of Radiation Medicine and Protection, Soochow University, Suzhou, China
| | - Ryan Baxley
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Advaitha Madireddy
- Department of Pediatric Hematology/Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Remi Buisson
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA.,Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - Zhiyuan Shen
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Group, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Bing Xia
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.
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10
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Guilliam TA. Mechanisms for Maintaining Eukaryotic Replisome Progression in the Presence of DNA Damage. Front Mol Biosci 2021; 8:712971. [PMID: 34295925 PMCID: PMC8290200 DOI: 10.3389/fmolb.2021.712971] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 06/25/2021] [Indexed: 12/04/2022] Open
Abstract
The eukaryotic replisome coordinates template unwinding and nascent-strand synthesis to drive DNA replication fork progression and complete efficient genome duplication. During its advancement along the parental template, each replisome may encounter an array of obstacles including damaged and structured DNA that impede its progression and threaten genome stability. A number of mechanisms exist to permit replisomes to overcome such obstacles, maintain their progression, and prevent fork collapse. A combination of recent advances in structural, biochemical, and single-molecule approaches have illuminated the architecture of the replisome during unperturbed replication, rationalised the impact of impediments to fork progression, and enhanced our understanding of DNA damage tolerance mechanisms and their regulation. This review focusses on these studies to provide an updated overview of the mechanisms that support replisomes to maintain their progression on an imperfect template.
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Affiliation(s)
- Thomas A. Guilliam
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
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11
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Bainbridge LJ, Teague R, Doherty AJ. Repriming DNA synthesis: an intrinsic restart pathway that maintains efficient genome replication. Nucleic Acids Res 2021; 49:4831-4847. [PMID: 33744934 PMCID: PMC8136793 DOI: 10.1093/nar/gkab176] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/01/2021] [Accepted: 03/05/2021] [Indexed: 12/25/2022] Open
Abstract
To bypass a diverse range of fork stalling impediments encountered during genome replication, cells possess a variety of DNA damage tolerance (DDT) mechanisms including translesion synthesis, template switching, and fork reversal. These pathways function to bypass obstacles and allow efficient DNA synthesis to be maintained. In addition, lagging strand obstacles can also be circumvented by downstream priming during Okazaki fragment generation, leaving gaps to be filled post-replication. Whether repriming occurs on the leading strand has been intensely debated over the past half-century. Early studies indicated that both DNA strands were synthesised discontinuously. Although later studies suggested that leading strand synthesis was continuous, leading to the preferred semi-discontinuous replication model. However, more recently it has been established that replicative primases can perform leading strand repriming in prokaryotes. An analogous fork restart mechanism has also been identified in most eukaryotes, which possess a specialist primase called PrimPol that conducts repriming downstream of stalling lesions and structures. PrimPol also plays a more general role in maintaining efficient fork progression. Here, we review and discuss the historical evidence and recent discoveries that substantiate repriming as an intrinsic replication restart pathway for maintaining efficient genome duplication across all domains of life.
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Affiliation(s)
- Lewis J Bainbridge
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, BN1 9RQ, UK
| | - Rebecca Teague
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, BN1 9RQ, UK
| | - Aidan J Doherty
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, BN1 9RQ, UK
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12
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Yan Y, Xu Z, Huang J, Guo G, Gao M, Kim W, Zeng X, Kloeber JA, Zhu Q, Zhao F, Luo K, Lou Z. The deubiquitinase USP36 Regulates DNA replication stress and confers therapeutic resistance through PrimPol stabilization. Nucleic Acids Res 2021; 48:12711-12726. [PMID: 33237263 PMCID: PMC7736794 DOI: 10.1093/nar/gkaa1090] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/21/2020] [Accepted: 10/29/2020] [Indexed: 02/07/2023] Open
Abstract
PrimPol has been recently identified as a DNA damage tolerant polymerase that plays an important role in replication stress response. However, the regulatory mechanisms of PrimPol are not well defined. In this study, we identify that the deubiquitinase USP36 interferes with degradation of PrimPol to regulate the replication stress response. Mechanistically, USP36 is deubiquitinated following DNA replication stress, which in turn facilitates its upregulation and interaction with PrimPol. USP36 deubiquitinates K29-linked polyubiquitination of PrimPol and increases its protein stability. Depletion of USP36 results in replication stress-related defects and elevates cell sensitivity to DNA-damage agents, such as cisplatin and olaparib. Moreover, USP36 expression positively correlates with the level of PrimPol protein and poor prognosis in patient samples. These findings indicate that the regulation of PrimPol K29-linked ubiquitination by USP36 plays a critical role in DNA replication stress and chemotherapy response.
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Affiliation(s)
- Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhijie Xu
- Department of Pathology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Jinzhou Huang
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Guijie Guo
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Ming Gao
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Wootae Kim
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Xiangyu Zeng
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jake A Kloeber
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA.,Mayo Clinic Medical Scientist Training Program, Mayo Clinic, Rochester, MN 55905, USA.,Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Qian Zhu
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Fei Zhao
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Kuntian Luo
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
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13
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Bailey LJ, Bianchi J, Doherty AJ. PrimPol is required for the maintenance of efficient nuclear and mitochondrial DNA replication in human cells. Nucleic Acids Res 2019; 47:4026-4038. [PMID: 30715459 PMCID: PMC6486543 DOI: 10.1093/nar/gkz056] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 01/14/2019] [Accepted: 01/28/2019] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic Primase-Polymerase (PrimPol) is an enzyme that maintains efficient DNA duplication by repriming replication restart downstream of replicase stalling lesions and structures. To elucidate the cellular requirements for PrimPol in human cells, we generated PrimPol-deleted cell lines and show that it plays key roles in maintaining active replication in both the nucleus and mitochondrion, even in the absence of exogenous damage. Human cells lacking PrimPol exhibit delayed recovery after UV-C damage and increased mutation frequency, micronuclei and sister chromatin exchanges but are not sensitive to genotoxins. PrimPol is also required during mitochondrial replication, with PrimPol-deficient cells having increased mtDNA copy number but displaying a significant decrease in replication. Deletion of PrimPol in XPV cells, lacking functional polymerase Eta, causes an increase in DNA damage sensitivity and pronounced fork stalling after UV-C treatment. We show that, unlike canonical TLS polymerases, PrimPol is important for allowing active replication to proceed, even in the absence of exogenous damage, thus preventing the accumulation of excessive fork stalling and genetic mutations. Together, these findings highlight the importance of PrimPol for maintaining efficient DNA replication in unperturbed cells and its complementary roles, with Pol Eta, in damage tolerance in human cells.
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Affiliation(s)
- Laura J Bailey
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Julie Bianchi
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Aidan J Doherty
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
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14
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Brieba LG. Structure-Function Analysis Reveals the Singularity of Plant Mitochondrial DNA Replication Components: A Mosaic and Redundant System. PLANTS 2019; 8:plants8120533. [PMID: 31766564 PMCID: PMC6963530 DOI: 10.3390/plants8120533] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 02/06/2023]
Abstract
Plants are sessile organisms, and their DNA is particularly exposed to damaging agents. The integrity of plant mitochondrial and plastid genomes is necessary for cell survival. During evolution, plants have evolved mechanisms to replicate their mitochondrial genomes while minimizing the effects of DNA damaging agents. The recombinogenic character of plant mitochondrial DNA, absence of defined origins of replication, and its linear structure suggest that mitochondrial DNA replication is achieved by a recombination-dependent replication mechanism. Here, I review the mitochondrial proteins possibly involved in mitochondrial DNA replication from a structural point of view. A revision of these proteins supports the idea that mitochondrial DNA replication could be replicated by several processes. The analysis indicates that DNA replication in plant mitochondria could be achieved by a recombination-dependent replication mechanism, but also by a replisome in which primers are synthesized by three different enzymes: Mitochondrial RNA polymerase, Primase-Helicase, and Primase-Polymerase. The recombination-dependent replication model and primers synthesized by the Primase-Polymerase may be responsible for the presence of genomic rearrangements in plant mitochondria.
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Affiliation(s)
- Luis Gabriel Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato, Guanajuato C.P. 36821, Mexico
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15
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Estep KN, Butler TJ, Ding J, Brosh RM. G4-Interacting DNA Helicases and Polymerases: Potential Therapeutic Targets. Curr Med Chem 2019; 26:2881-2897. [PMID: 29149833 DOI: 10.2174/0929867324666171116123345] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 10/16/2017] [Accepted: 10/16/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND Guanine-rich DNA can fold into highly stable four-stranded DNA structures called G-quadruplexes (G4). In recent years, the G-quadruplex field has blossomed as new evidence strongly suggests that such alternately folded DNA structures are likely to exist in vivo. G4 DNA presents obstacles for the replication machinery, and both eukaryotic DNA helicases and polymerases have evolved to resolve and copy G4 DNA in vivo. In addition, G4-forming sequences are prevalent in gene promoters, suggesting that G4-resolving helicases act to modulate transcription. METHODS We have searched the PubMed database to compile an up-to-date and comprehensive assessment of the field's current knowledge to provide an overview of the molecular interactions of Gquadruplexes with DNA helicases and polymerases implicated in their resolution. RESULTS Novel computational tools and alternative strategies have emerged to detect G4-forming sequences and assess their biological consequences. Specialized DNA helicases and polymerases catalytically act upon G4-forming sequences to maintain normal replication and genomic stability as well as appropriate gene regulation and cellular homeostasis. G4 helicases also resolve telomeric repeats to maintain chromosomal DNA ends. Bypass of many G4-forming sequences is achieved by the action of translesion DNS polymerases or the PrimPol DNA polymerase. While the collective work has supported a role of G4 in nuclear DNA metabolism, an emerging field centers on G4 abundance in the mitochondrial genome. CONCLUSION Discovery of small molecules that specifically bind and modulate DNA helicases and polymerases or interact with the G4 DNA structure itself may be useful for the development of anticancer regimes.
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Affiliation(s)
- Katrina N Estep
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, 251 Bayview Blvd Baltimore, MD 21224, United States
| | - Thomas J Butler
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, 251 Bayview Blvd Baltimore, MD 21224, United States
| | - Jun Ding
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, 251 Bayview Blvd Baltimore, MD 21224, United States
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, 251 Bayview Blvd Baltimore, MD 21224, United States
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16
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Comparative genomics sheds light on the predatory lifestyle of accipitrids and owls. Sci Rep 2019; 9:2249. [PMID: 30783131 PMCID: PMC6381159 DOI: 10.1038/s41598-019-38680-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 12/31/2018] [Indexed: 02/08/2023] Open
Abstract
Raptors are carnivorous birds including accipitrids (Accipitridae, Accipitriformes) and owls (Strigiformes), which are diurnal and nocturnal, respectively. To examine the evolutionary basis of adaptations to different light cycles and hunting behavior between accipitrids and owls, we de novo assembled besra (Accipiter virgatus, Accipitridae, Accipitriformes) and oriental scops owl (Otus sunia, Strigidae, Strigiformes) draft genomes. Comparative genomics demonstrated four PSGs (positively selected genes) (XRCC5, PRIMPOL, MDM2, and SIRT1) related to the response to ultraviolet (UV) radiation in accipitrids, and one PSG (ALCAM) associated with retina development in owls, which was consistent with their respective diurnal/nocturnal predatory lifestyles. We identified five accipitrid-specific and two owl-specific missense mutations and most of which were predicted to affect the protein function by PolyPhen-2. Genome comparison showed the diversification of raptor olfactory receptor repertoires, which may reflect an important role of olfaction in their predatory lifestyle. Comparison of TAS2R gene (i.e. linked to tasting bitterness) number in birds with different dietary lifestyles suggested that dietary toxins were a major selective force shaping the diversity of TAS2R repertoires. Fewer TAS2R genes in raptors reflected their carnivorous diet, since animal tissues are less likely to contain toxins than plant material. Our data and findings provide valuable genomic resources for studying the genetic mechanisms of raptors’ environmental adaptation, particularly olfaction, nocturnality and response to UV radiation.
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17
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Lee WH, Chen LC, Lee CJ, Huang CC, Ho YS, Yang PS, Ho CT, Chang HL, Lin IH, Chang HW, Liu YR, Wu CH, Tu SH. DNA primase polypeptide 1 (PRIM1) involves in estrogen-induced breast cancer formation through activation of the G2/M cell cycle checkpoint. Int J Cancer 2018; 144:615-630. [PMID: 30097999 DOI: 10.1002/ijc.31788] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 07/24/2018] [Indexed: 12/22/2022]
Abstract
The DNA primase polypeptide 1 (PRIM1) is responsible for synthesizing small RNA primers for Okazaki fragments generated during discontinuous DNA replication. PRIM1 mRNA expression levels in breast tumor samples were detected by real-time PCR analysis. Xenografted tumor model was established to study the carcinogenic role of PRIM1 and its potential therapeutic applications. The average PRIM1 mRNA (copy number × 103 /μg) expression was 4.7-fold higher in tumors than in normal tissue (*p = 0.005, n = 254). PRIM1 was detected preferentially at a higher level (>40-fold) in poorly differentiated tumor tissues (n = 46) compared with more highly differentiated tumors tissues (n = 10) (*p = 0.005). Poor overall survival rate was correlated to the estrogen receptor positive (ER+, n = 20) patients with higher PRIM1 expression when compare to the ER- (n = 10) patients (Chi Square test, p = 0.03). Stable expression of PRIM1-siRNA in the ER+ BT-474 cells-xenograft tumors significantly reduced tumor volume in SCID mice (*p = 0.005). The anti-tumoral effects of inotilone isolated from Phellinus linteus was tested and had significant effects on the inhibition of PRIM1 protein expression in ER+ breast cancer cells. In vivo study was performed by administering inotilone (10 mg/kg, twice a week for 6 weeks), which resulted in significantly reduced BT-474-xenografted tumor growth volume compared with control (n =5 per group, *p < 0.05). This study provides evidences for the prognostic effects of PRIM1 with poor overall survival rate in the ER+ patients and will be valuable to test for therapeutic purpose.
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Affiliation(s)
- Wei-Hwa Lee
- Department of Pathology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Pathology, Taipei Medical University-Shuang Ho Hospital, New Taipei City, Taiwan
| | - Li-Ching Chen
- Breast Medical Center, Taipei Medical University Hospital, Taipei, Taiwan.,Taipei Cancer Center, Taipei Medical University, Taipei, Taiwan.,TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chia-Jung Lee
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chi-Cheng Huang
- Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,School of Medicine, College of Medicine, Fu-Jen Catholic University, New Taipei City, Taiwan.,Department of Surgery, Fu-Jen Catholic University Hospital, New Taipei City, Taiwan
| | - Yuan-Soon Ho
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan.,Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei, Taiwan.,School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Po-Sheng Yang
- Department of Surgery, Mackay Memorial Hospital, Taipei, Taiwan.,Department of Medicine, Mackay Medical College, New Taipei City, Taiwan
| | - Chi-Tang Ho
- Department of Food Science, Rutgers University, New Brunswick, NJ, USA
| | - Hang-Lung Chang
- Department of General Surgery, En Chu Kong Hospital, New Taipei City, Taiwan
| | - I-Hsuan Lin
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan
| | - Hui-Wen Chang
- Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei, Taiwan
| | - Yun-Ru Liu
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan.,Joint Biobank, Office of Human Research, Taipei Medical University, Taipei, Taiwan
| | - Chih-Hsiung Wu
- Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Department of General Surgery, En Chu Kong Hospital, New Taipei City, Taiwan
| | - Shih-Hsin Tu
- Breast Medical Center, Taipei Medical University Hospital, Taipei, Taiwan.,Taipei Cancer Center, Taipei Medical University, Taipei, Taiwan.,Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
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18
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Abstract
Eukaryotic PrimPol is a recently discovered DNA-dependent DNA primase and translesion synthesis DNA polymerase found in the nucleus and mitochondria. Although PrimPol has been shown to be required for repriming of stalled replication forks in the nucleus, its role in mitochondria has remained unresolved. Here we demonstrate in vivo and in vitro that PrimPol can reinitiate stalled mtDNA replication and can prime mtDNA replication from nonconventional origins. Our results not only help in the understanding of how mitochondria cope with replicative stress but can also explain some controversial features of the lagging-strand replication.
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19
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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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20
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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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21
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Guilliam TA, Doherty AJ. PrimPol-Prime Time to Reprime. Genes (Basel) 2017; 8:genes8010020. [PMID: 28067825 PMCID: PMC5295015 DOI: 10.3390/genes8010020] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 12/09/2016] [Accepted: 12/16/2016] [Indexed: 01/16/2023] Open
Abstract
The complex molecular machines responsible for genome replication encounter many obstacles during their progression along DNA. Tolerance of these obstructions is critical for efficient and timely genome duplication. In recent years, primase-polymerase (PrimPol) has emerged as a new player involved in maintaining eukaryotic replication fork progression. This versatile replicative enzyme, a member of the archaeo-eukaryotic primase (AEP) superfamily, has the capacity to perform a range of template-dependent and independent synthesis activities. Here, we discuss the emerging roles of PrimPol as a leading strand repriming enzyme and describe the mechanisms responsible for recruiting and regulating the enzyme during this process. This review provides an overview and update of the current PrimPol literature, as well as highlighting unanswered questions and potential future avenues of investigation.
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Affiliation(s)
- Thomas A Guilliam
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK.
| | - Aidan J Doherty
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK.
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22
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Kobayashi K, Guilliam TA, Tsuda M, Yamamoto J, Bailey LJ, Iwai S, Takeda S, Doherty AJ, Hirota K. Repriming by PrimPol is critical for DNA replication restart downstream of lesions and chain-terminating nucleosides. Cell Cycle 2016; 15:1997-2008. [PMID: 27230014 PMCID: PMC4968974 DOI: 10.1080/15384101.2016.1191711] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 05/12/2016] [Accepted: 05/14/2016] [Indexed: 01/28/2023] Open
Abstract
PrimPol is a DNA damage tolerance enzyme possessing both translesion synthesis (TLS) and primase activities. To uncover its potential role in TLS-mediated IgVλ hypermutation and define its interplay with other TLS polymerases, PrimPol(-/-) and PrimPol(-/-)/Polη(-/-)/Polζ (-/-) gene knockouts were generated in avian cells. Loss of PrimPol had no significant impact on the rate of hypermutation or the mutation spectrum of IgVλ. However, PrimPol(-/-) cells were sensitive to methylmethane sulfonate, suggesting that it may bypass abasic sites at the IgVλ segment by repriming DNA synthesis downstream of these sites. PrimPol(-/-) cells were also sensitive to cisplatin and hydroxyurea, indicating that it assists in maintaining / restarting replication at a variety of lesions. To accurately measure the relative contribution of the TLS and primase activities, we examined DNA damage sensitivity in PrimPol(-/-) cells complemented with polymerase or primase-deficient PrimPol. Polymerase-defective, but not primase-deficient, PrimPol suppresses the hypersensitivity of PrimPol(-/-) cells. This indicates that its primase, rather than TLS activity, is pivotal for DNA damage tolerance. Loss of TLS polymerases, Polη and Polζ has an additive effect on the sensitivity of PrimPol(-/-) cells. Moreover, we found that PrimPol and Polη-Polζ redundantly prevented cell death and facilitated unperturbed cell cycle progression. PrimPol(-/-) cells also exhibited increased sensitivity to a wide variety of chain-terminating nucleoside analogs (CTNAs). PrimPol could perform close-coupled repriming downstream of CTNAs and oxidative damage in vitro. Together, these results indicate that PrimPol's repriming activity plays a central role in reinitiating replication downstream from CTNAs and other specific DNA lesions.
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Affiliation(s)
- Kaori Kobayashi
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji-shi, Tokyo, Japan
| | - Thomas A. Guilliam
- Genome Damage and Stability Center, School of Life Sciences, University of Sussex, Brighton, UK
| | - Masataka Tsuda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto, Japan
| | - Junpei Yamamoto
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, Japan
| | - Laura J. Bailey
- Genome Damage and Stability Center, School of Life Sciences, University of Sussex, Brighton, UK
| | - Shigenori Iwai
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, Japan
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto, Japan
| | - Aidan J. Doherty
- Genome Damage and Stability Center, School of Life Sciences, University of Sussex, Brighton, UK
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji-shi, Tokyo, Japan
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