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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Sasatani M, Xi Y, Daino K, Ishikawa A, Masuda Y, Kajimura J, Piao J, Zaharieva EK, Honda H, Zhou G, Hamasaki K, Kusunoki Y, Shimura T, Kakinuma S, Shimada Y, Doi K, Ishikawa-Fujiwara T, Sotomaru Y, Kamiya K. Rev1 overexpression accelerates N-methyl-N-nitrosourea (MNU)-induced thymic lymphoma by increasing mutagenesis. Cancer Sci 2024. [PMID: 38572512 DOI: 10.1111/cas.16159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/28/2024] [Accepted: 03/10/2024] [Indexed: 04/05/2024] Open
Abstract
Rev1 has two important functions in the translesion synthesis pathway, including dCMP transferase activity, and acts as a scaffolding protein for other polymerases involved in translesion synthesis. However, the role of Rev1 in mutagenesis and tumorigenesis in vivo remains unclear. We previously generated Rev1-overexpressing (Rev1-Tg) mice and reported that they exhibited a significantly increased incidence of intestinal adenoma and thymic lymphoma (TL) after N-methyl-N-nitrosourea (MNU) treatment. In this study, we investigated mutagenesis of MNU-induced TL tumorigenesis in wild-type (WT) and Rev1-Tg mice using diverse approaches, including whole-exome sequencing (WES). In Rev1-Tg TLs, the mutation frequency was higher than that in WT TL in most cases. However, no difference in the number of nonsynonymous mutations in the Catalogue of Somatic Mutations in Cancer (COSMIC) genes was observed, and mutations involved in Notch1 and MAPK signaling were similarly detected in both TLs. Mutational signature analysis of WT and Rev1-Tg TLs revealed cosine similarity with COSMIC mutational SBS5 (aging-related) and SBS11 (alkylation-related). Interestingly, the total number of mutations, but not the genotypes of WT and Rev1-Tg, was positively correlated with the relative contribution of SBS5 in individual TLs, suggesting that genetic instability could be accelerated in Rev1-Tg TLs. Finally, we demonstrated that preleukemic cells could be detected earlier in Rev1-Tg mice than in WT mice, following MNU treatment. In conclusion, Rev1 overexpression accelerates mutagenesis and increases the incidence of MNU-induced TL by shortening the latency period, which may be associated with more frequent DNA damage-induced genetic instability.
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Affiliation(s)
- Megumi Sasatani
- Department of Experimental Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Yang Xi
- Department of Experimental Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
- Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo, China
| | - Kazuhiro Daino
- Department of Radiation Effects Research, Institute for Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Atsuko Ishikawa
- Department of Radiation Effects Research, Institute for Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Yuji Masuda
- Department of Experimental Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
- Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
- Department of Molecular Pharmaco-Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Junko Kajimura
- Department of Experimental Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
- Biosample Research Center, Radiation Effects Research Foundation, Hiroshima, Japan
| | - Jinlian Piao
- Department of Experimental Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
- Gastroenterological and Transplant Surgery, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Elena Karamfilova Zaharieva
- Department of Experimental Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Hiroaki Honda
- Institute of Laboratory Animals, Tokyo Women's Medical University, Tokyo, Japan
| | - Guanyu Zhou
- Department of Experimental Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Kanya Hamasaki
- Department of Molecular Biosciences, Radiation Effects Research Foundation, Hiroshima, Japan
| | - Yoichiro Kusunoki
- Department of Molecular Biosciences, Radiation Effects Research Foundation, Hiroshima, Japan
| | - Tsutomu Shimura
- Department of Environmental Health, National Institute of Public Health, Saitama, Japan
| | - Shizuko Kakinuma
- Department of Radiation Effects Research, Institute for Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | | | - Kazutaka Doi
- Department of Radiation Regulatory Science Research, Institute for Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | | | - Yusuke Sotomaru
- Natural Science Center for Basic Research and Development, Hiroshima University, Hiroshima, Japan
| | - Kenji Kamiya
- Department of Experimental Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
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Ong DST, Hu B, Ho YW, Sauvé CG, Bristow CA, Wang Q, Multani AS, Chen P, Nezi L, Jiang S, Gorman CE, Monasterio MM, Koul D, Marchesini M, Colla S, Jin EJ, Sulman EP, Spring DJ, Yung WA, Verhaak RGW, Chin L, Wang YA, DePinho RA. PAF promotes stemness and radioresistance of glioma stem cells. Proc Natl Acad Sci U S A 2017; 114:E9086-95. [PMID: 29073105 DOI: 10.1073/pnas.1708122114] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
An integrated genomic and functional analysis to elucidate DNA damage signaling factors promoting self-renewal of glioma stem cells (GSCs) identified proliferating cell nuclear antigen (PCNA)-associated factor (PAF) up-regulation in glioblastoma. PAF is preferentially overexpressed in GSCs. Its depletion impairs maintenance of self-renewal without promoting differentiation and reduces tumor-initiating cell frequency. Combined transcriptomic and metabolomic analyses revealed that PAF supports GSC maintenance, in part, by influencing DNA replication and pyrimidine metabolism pathways. PAF interacts with PCNA and regulates PCNA-associated DNA translesion synthesis (TLS); consequently, PAF depletion in combination with radiation generated fewer tumorspheres compared with radiation alone. Correspondingly, pharmacological impairment of DNA replication and TLS phenocopied the effect of PAF depletion in compromising GSC self-renewal and radioresistance, providing preclinical proof of principle that combined TLS inhibition and radiation therapy may be a viable therapeutic option in the treatment of glioblastoma multiforme (GBM).
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Ignatov A, Bondarenko K, Makarova A. Non-bulky Lesions in Human DNA: the Ways of Formation, Repair, and Replication. Acta Naturae 2017; 9:12-26. [PMID: 29104772 PMCID: PMC5662270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Indexed: 11/06/2022] Open
Abstract
DNA damage is a major cause of replication interruption, mutations, and cell death. DNA damage is removed by several types of repair processes. The involvement of specialized DNA polymerases in replication provides an important mechanism that helps tolerate persistent DNA damage. Specialized DNA polymerases incorporate nucleotides opposite lesions with high efficiency but demonstrate low accuracy of DNA synthesis. In this review, we summarize the types and mechanisms of formation and repair of non-bulky DNA lesions, and we provide an overview of the role of specialized DNA polymerases in translesion DNA synthesis.
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Affiliation(s)
- A.V. Ignatov
- Institute of Molecular Genetics of Russian Academy of Sciences, Kurchatov sq. 2, Moscow, 123182 , Russia
- Department of Molecular Biology, Faculty of Biology, Moscow State University, Leninskie Gory 1, bldg. 12, Moscow, 119991, Russia
| | - K.A. Bondarenko
- Institute of Molecular Genetics of Russian Academy of Sciences, Kurchatov sq. 2, Moscow, 123182 , Russia
| | - A.V. Makarova
- Institute of Molecular Genetics of Russian Academy of Sciences, Kurchatov sq. 2, Moscow, 123182 , Russia
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Jansen JG, Tsaalbi-Shtylik A, de Wind N. Roles of mutagenic translesion synthesis in mammalian genome stability, health and disease. DNA Repair (Amst) 2015; 29:56-64. [PMID: 25655219 DOI: 10.1016/j.dnarep.2015.01.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/22/2014] [Accepted: 01/07/2015] [Indexed: 01/08/2023]
Abstract
Most spontaneous and DNA damage-induced nucleotide substitutions in eukaryotes depend on translesion synthesis polymerases Rev1 and Pol ζ, the latter consisting of the catalytic subunit Rev3 and the accessory protein Rev7. Here we review the regulation, and the biochemical and cellular functions, of Rev1/Pol ζ-dependent translesion synthesis. These are correlated with phenotypes of mouse models with defects in Rev1, Rev3 or Rev7. The data indicate that Rev1/Pol ζ-mediated translesion synthesis is important for adaptive immunity while playing paradoxical roles in oncogenesis. On the other hand, by enabling the replication of endogenously damaged templates, Rev1/Pol ζ -dependent translesion synthesis protects stem cells, thereby preventing features of ageing. In conclusion, Rev1/Pol ζ-dependent translesion synthesis at DNA helix-distorting nucleotide lesions orchestrates pleiotropic responses that determine organismal fitness and disease.
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Affiliation(s)
- Jacob G Jansen
- Department of Human Genetics, Leiden University Medical Center, PO Box 9600, 2300RC Leiden, The Netherlands
| | - Anastasia Tsaalbi-Shtylik
- Department of Human Genetics, Leiden University Medical Center, PO Box 9600, 2300RC Leiden, The Netherlands
| | - Niels de Wind
- Department of Human Genetics, Leiden University Medical Center, PO Box 9600, 2300RC Leiden, The Netherlands.
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Santiago MJ, Alejandre-Durán E, Ruiz-Rubio M. Alternative splicing of two translesion synthesis DNA polymerases from Arabidopsis thaliana. Plant Sci 2009; 176:591-6. [PMID: 26493150 DOI: 10.1016/j.plantsci.2009.01.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2008] [Revised: 01/06/2009] [Accepted: 01/26/2009] [Indexed: 05/23/2023]
Abstract
DNA damages can be removed by different repair processes, but lesions sometimes remain and block DNA replication. Specialized polymerases are needed to overcome this difficulty. In Arabidopsis, AtPOLH and AtREV1 genes code for two polymerases that are involved in replication of damaged DNA. Alternative splicing was detected in both genes. Complementation analysis of the alternative splicing forms in Saccharomycescerevisiae showed that the C-terminal extreme of AtPOLH protein is essential for recovering wild type UV viability in Rad30 deficient strain. None of the alternative AtREV1 forms recovered the yeast wild type phenotype of Rev1 deficient yeast strains after UV light irradiation or methyl methane sulphonate exposition, suggesting that AtREV1 may not be able to interact with other yeast specific proteins needed for DNA translesion synthesis.
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Affiliation(s)
- María Jesús Santiago
- Departamento de Genética, Facultad de Ciencias, Edificio Gregor Mendel, Campus Rabanales, Universidad de Córdoba, Spain
| | - Encarna Alejandre-Durán
- Departamento de Genética, Facultad de Ciencias, Edificio Gregor Mendel, Campus Rabanales, Universidad de Córdoba, Spain
| | - Manuel Ruiz-Rubio
- Departamento de Genética, Facultad de Ciencias, Edificio Gregor Mendel, Campus Rabanales, Universidad de Córdoba, Spain.
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