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Mullins EA, Salay LE, Durie CL, Bradley NP, Jackman JE, Ohi MD, Chazin WJ, Eichman BF. A mechanistic model of primer synthesis from catalytic structures of DNA polymerase α-primase. Nat Struct Mol Biol 2024; 31:777-790. [PMID: 38491139 PMCID: PMC11102853 DOI: 10.1038/s41594-024-01227-4] [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: 02/25/2023] [Accepted: 01/12/2024] [Indexed: 03/18/2024]
Abstract
The mechanism by which polymerase α-primase (polα-primase) synthesizes chimeric RNA-DNA primers of defined length and composition, necessary for replication fidelity and genome stability, is unknown. Here, we report cryo-EM structures of Xenopus laevis polα-primase in complex with primed templates representing various stages of DNA synthesis. Our data show how interaction of the primase regulatory subunit with the primer 5' end facilitates handoff of the primer to polα and increases polα processivity, thereby regulating both RNA and DNA composition. The structures detail how flexibility within the heterotetramer enables synthesis across two active sites and provide evidence that termination of DNA synthesis is facilitated by reduction of polα and primase affinities for the varied conformations along the chimeric primer-template duplex. Together, these findings elucidate a critical catalytic step in replication initiation and provide a comprehensive model for primer synthesis by polα-primase.
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Affiliation(s)
- Elwood A Mullins
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Lauren E Salay
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Clarissa L Durie
- Department of Cell and Developmental Biology, University of Michigan School of Medicine, Ann Arbor, MI, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Noah P Bradley
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Jane E Jackman
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Melanie D Ohi
- Department of Cell and Developmental Biology, University of Michigan School of Medicine, Ann Arbor, MI, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Walter J Chazin
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA.
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
| | - Brandt F Eichman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA.
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA.
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Mullins EA, Salay LE, Durie CL, Bradley NP, Jackman JE, Ohi MD, Chazin WJ, Eichman BF. A mechanistic model of primer synthesis from catalytic structures of DNA polymerase α-primase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.533013. [PMID: 36993335 PMCID: PMC10055150 DOI: 10.1101/2023.03.16.533013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The mechanism by which polymerase α-primase (polα-primase) synthesizes chimeric RNA-DNA primers of defined length and composition, necessary for replication fidelity and genome stability, is unknown. Here, we report cryo-EM structures of polα-primase in complex with primed templates representing various stages of DNA synthesis. Our data show how interaction of the primase regulatory subunit with the primer 5'-end facilitates handoff of the primer to polα and increases polα processivity, thereby regulating both RNA and DNA composition. The structures detail how flexibility within the heterotetramer enables synthesis across two active sites and provide evidence that termination of DNA synthesis is facilitated by reduction of polα and primase affinities for the varied conformations along the chimeric primer/template duplex. Together, these findings elucidate a critical catalytic step in replication initiation and provide a comprehensive model for primer synthesis by polα-primase.
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Gao S, Song Q, Liu J, Zhang X, Ji X, Wang P. E2F1 mediates the downregulation of POLD1 in replicative senescence. Cell Mol Life Sci 2019; 76:2833-2850. [PMID: 30895337 PMCID: PMC6588650 DOI: 10.1007/s00018-019-03070-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 03/10/2019] [Accepted: 03/13/2019] [Indexed: 12/21/2022]
Abstract
POLD1, the catalytic subunit of DNA Pol δ, plays an important role in DNA synthesis and DNA damage repair, and POLD1 is downregulated in replicative senescence and mediates cell aging. However, the mechanisms of age-related downregulation of POLD1 expression have not been elucidated. In this study, four potential CpG islands in the POLD1 promoter were found, and the methylation levels of the POLD1 promoter were increased in aging 2BS cells, WI-38 cells and peripheral blood lymphocytes, especially at a single site, CpG 36, in CpG island 3. Then, the transcription factor E2F1 was observed to bind to these sites. The binding affinity of E2F1 for the POLD1 promoter was found to show age-related attenuation and was confirmed to be positively regulated by the E2F1 level and negatively regulated by POLD1 promoter methylation. Moreover, cell senescence characteristics were observed in the cells transfected with shRNA-E2F1 and could contribute to the downregulation of POLD1 induced by the E2F1 decline. Collectively, these results indicated that the attenuation of the binding affinity of E2F1 for the POLD1 promoter, mediated by an age-related decline in E2F1 and increased methylation of CpG island 3, downregulates POLD1 expression in aging.
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Affiliation(s)
- Shichao Gao
- Clinical Laboratory of Xuanwu Hospital, Capital Medical University, Beijing, 100053, People's Republic of China
| | - Qiao Song
- Clinical Laboratory of Xuanwu Hospital, Capital Medical University, Beijing, 100053, People's Republic of China
| | - Jing Liu
- Clinical Laboratory of Xuanwu Hospital, Capital Medical University, Beijing, 100053, People's Republic of China
| | - Xiaomin Zhang
- Clinical Laboratory of Xuanwu Hospital, Capital Medical University, Beijing, 100053, People's Republic of China
| | - Xunming Ji
- Beijing Institute of Brain Disorders, Capital Medical University, Beijing, 100053, People's Republic of China
| | - Peichang Wang
- Clinical Laboratory of Xuanwu Hospital, Capital Medical University, Beijing, 100053, People's Republic of China.
- Beijing Institute of Brain Disorders, Capital Medical University, Beijing, 100053, People's Republic of China.
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Song J, Hong P, Liu C, Zhang Y, Wang J, Wang P. Human POLD1 modulates cell cycle progression and DNA damage repair. BMC BIOCHEMISTRY 2015; 16:14. [PMID: 26087769 PMCID: PMC4471906 DOI: 10.1186/s12858-015-0044-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 06/05/2015] [Indexed: 11/22/2022]
Abstract
Background The activity of eukaryotic DNA polymerase delta (Pol δ) plays an essential role in genome stability through its effects on DNA replication and repair. The p125 catalytic subunit of Pol δ is encoded by POLD1 gene in human cells. To clarify biological functions of POLD1, we investigated the effects of POLD1 overexpression or downregulation on cell proliferation, cell cycle progression, DNA synthesis and oxidative DNA damage induced by H2O2. Methods HEK293 cells were transfected with POLD1 expression plasmid or shRNA, cell proliferation, cell cycle progression, and DNA synthesis in HEK293 cells were analyzed. Results HEK293 cells were transfected with POLD1 expression plasmid or shRNA. POLD1 downregulation by shRNA suppressed cell proliferation, cell cycle progression, and DNA synthesis in HEK293 cells. However, POLD1 overexpression had no significant effects on these processes. Finally, comet assay showed that POLD1 downregulation led to increased DNA damage. Conclusions Our results suggest that human POLD1 plays important role in the regulation of cell cycle progression and DNA damage repair.
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Affiliation(s)
- Jing Song
- Department of Clinical Laboratory, Xuanwu Hospital Capital Medical University, No.45 Changchun Street, Xicheng District, Beijing, 100053, China.
| | - Ping Hong
- Department of Clinical Laboratory, Xuanwu Hospital Capital Medical University, No.45 Changchun Street, Xicheng District, Beijing, 100053, China.
| | - Chengeng Liu
- Department of Clinical Laboratory, Xuanwu Hospital Capital Medical University, No.45 Changchun Street, Xicheng District, Beijing, 100053, China.
| | - Yueqi Zhang
- Department of Clinical Laboratory, Xuanwu Hospital Capital Medical University, No.45 Changchun Street, Xicheng District, Beijing, 100053, China.
| | - Jinling Wang
- Department of Clinical Laboratory, Xuanwu Hospital Capital Medical University, No.45 Changchun Street, Xicheng District, Beijing, 100053, China.
| | - Peichang Wang
- Department of Clinical Laboratory, Xuanwu Hospital Capital Medical University, No.45 Changchun Street, Xicheng District, Beijing, 100053, China.
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Beck JL, Urathamakul T, Watt SJ, Sheil MM, Schaeffer PM, Dixon NE. Proteomic dissection of DNA polymerization. Expert Rev Proteomics 2014; 3:197-211. [PMID: 16608433 DOI: 10.1586/14789450.3.2.197] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
DNA polymerases replicate the genome by associating with a range of other proteins that enable rapid, high-fidelity copying of DNA. This complex of proteins and nucleic acids is termed the replisome. Proteins of the replisome must interact with other networks of proteins, such as those involved in DNA repair. Many of the proteins involved in DNA polymerization and the accessory proteins are known, but the array of proteins they interact with, and the spatial and temporal arrangement of these interactions, are current research topics. Mass spectrometry is a technique that can be used to identify the sites of these interactions and to determine the precise stoichiometries of binding partners in a functional complex. A complete understanding of the macromolecular interactions involved in DNA replication and repair may lead to discovery of new targets for antibiotics against bacteria and biomarkers for diagnosis of diseases, such as cancer, in humans.
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Affiliation(s)
- Jennifer L Beck
- Department of Chemistry, University of Wollongong, Wollongong, NSW 2522, Australia.
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Makpol S, Yeoh TW, Ruslam FAC, Arifin KT, Yusof YAM. Comparative effect of Piper betle, Chlorella vulgaris and tocotrienol-rich fraction on antioxidant enzymes activity in cellular ageing of human diploid fibroblasts. BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE 2013; 13:210. [PMID: 23948056 PMCID: PMC3847057 DOI: 10.1186/1472-6882-13-210] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 08/13/2013] [Indexed: 02/14/2023]
Abstract
Background Human diploid fibroblasts (HDFs) undergo a limited number of cellular divisions in culture and progressively reach a state of irreversible growth arrest, a process termed cellular ageing. Even though beneficial effects of Piper betle, Chlorella vulgaris and tocotrienol-rich fraction (TRF) have been reported, ongoing studies in relation to ageing is of interest to determine possible protective effects that may reverse the effect of ageing. The aim of this study was to evaluate the effect of P. betle, C. vulgaris and TRF in preventing cellular ageing of HDFs by determining the activity of antioxidant enzymes viz.; catalase, superoxide dismutase (SOD) and glutathione peroxidase. Methods Different passages of HDFs were treated with P. betle, C. vulgaris and TRF for 24 h prior to enzymes activity determination. Senescence-associated beta-galactosidase (SA β-gal) expression was assayed to validate cellular ageing. Results In cellular ageing of HDFs, catalase and glutathione peroxidase activities were reduced, but SOD activity was heightened during pre-senescence. P. betle exhibited the strongest antioxidant activity by reducing SA β-gal expression, catalase activities in all age groups, and SOD activity. TRF exhibited a strong antioxidant activity by reducing SA β-gal expression, and SOD activity in senescent HDFs. C. vulgaris extract managed to reduce SOD activity in senescent HDFs. Conclusion P. betle, C. vulgaris, and TRF have the potential as anti-ageing entities which compensated the role of antioxidant enzymes in cellular ageing of HDFs.
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Potential chemopreventive role of chrysin against N-nitrosodiethylamine-induced hepatocellular carcinoma in rats. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.bionut.2011.06.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Rattan SIS. Biogerontology: from here to where? The Lord Cohen Medal Lecture-2011. Biogerontology 2011; 13:83-91. [DOI: 10.1007/s10522-011-9354-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Accepted: 08/18/2011] [Indexed: 01/09/2023]
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Abstract
Abstract
Aging at the molecular level is characterized by the progressive accumulation of molecular damage. The sources of damage act randomly through environmental and metabolically generated free radicals, through spontaneous errors in biochemical reactions, and through nutritional components. However, damage to a macromolecule may depend on its structure, localization and interactions with other macromolecules. Damage to the maintenance and repair pathways comprising homeodynamic machinery leads to age-related failure of homeodynamics, increased molecular heterogeneity, altered cellular functioning, reduced stress tolerance, diseases and ultimate death. Novel approaches for testing and developing effective means of intervention, prevention and modulation of aging involve means to minimize the occurrence and accumulation of molecular damage. Mild stress-induced hormesis by physical, biological and nutritional methods, including hormetins, represents a promising strategy for achieving healthy aging and for preventing age-related diseases.
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Abstract
Traditional categorization of theories of aging into programmed and stochastic ones is outdated and obsolete. Biological aging is considered to occur mainly during the period of survival beyond the natural or essential lifespan (ELS) in Darwinian terms. Organisms survive to achieve ELS by virtue of genetically determined longevity assuring maintenance and repair systems (MRS). Aging at the molecular level is characterized by the progressive accumulation of molecular damage caused by environmental and metabolically generated free radicals, by spontaneous errors in biochemical reactions, and by nutritional components. Damages in the MRS and other pathways lead to age-related failure of MRS, molecular heterogeneity, cellular dysfunctioning, reduced stress tolerance, diseases and ultimate death. A unified theory of biological aging in terms of failure of homeodynamics comprising of MRS, and involving genes, milieu and chance, is acquiring a definitive shape and wider acceptance. Such a theory also establishes the basis for testing and developing effective means of intervention, prevention and modulation of aging.
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Affiliation(s)
- Suresh I S Rattan
- Laboratory of Cellular Ageing, Department of Molecular Biology, Danish Centre for Molecular Gerontology, University of Aarhus, Aarhus-C, Denmark.
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