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Utkalaja BG, Patel SK, Sahu SR, Dutta A, Acharya N. Critical roles of Dpb3-Dpb4 sub-complex of DNA polymerase epsilon in DNA replication, genome stability, and pathogenesis of Candida albicans. mBio 2024:e0122724. [PMID: 39207097 DOI: 10.1128/mbio.01227-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024] Open
Abstract
DNA polymerase ε (Polε) is an essential replicative polymerase consisting of Pol2, Dpb2, Dpb3, and Dpb4 subunits and has not been explored in the pathogenic yeast Candida albicans. C. albicans is accountable for >40% of deaths due to systemic candidiasis per year worldwide. Genome plasticity is one of the adaptive mechanisms associated with virulence, and as it is associated with DNA polymerase function, this study explored the role of Polε in genome stability and pathogenesis of C. albicans. POL2 and DPB2 are haploinsufficient, but DPB3 and DPB4 are dispensable for cell survival in diploid C. albicans. However, unlike in Saccharomyces cerevisiae, loss of any or both of the nonessential subunits or defective interaction between the two resulted in slow growth and temperature-sensitive phenotypes. Knockout strains of C. albicans (dpb3ΔΔ and dpb4ΔΔ and dpb3ΔΔdpb4ΔΔ) also exhibited sensitivity to genotoxic agents and delayed cell cycle progression. Reduced processive DNA synthesis and increased rate of mutagenesis were observed in dpb3 and dpb4 null strains. Whole-genome sequencing further confirmed the accumulation of indels and SNPs majorly in the intergenic repeat regions of the chromosomes of dpb3ΔΔdpb4ΔΔ. Polε-defective strains were constitutively filamentous and non-pathogenic in mice models of systemic candidiasis. Altogether, this study showed that the function of the Dpb3-Dpb4 subcomplex is critical for fungal morphogenesis and virulence besides its role as a structural component of Polε in DNA replication and genome stability; thus, their interacting interface may be targeted to develop antifungal drugs. IMPORTANCE This study explored the role of DNA polymerase epsilon, especially its non-essential structural subunits in Candida albicans biology. Apart from their role in DNA replication and genome stability, the Dpb3-Dpb4 subcomplex regulates morphological switching and virulence. Since the defective strain is locked in filamentous form and is avirulent, the complex may be targeted for anti-fungal drug development.
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Affiliation(s)
- Bhabasha Gyanadeep Utkalaja
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
- Regional Center of Biotechnology, Faridabad, India
| | - Shraddheya Kumar Patel
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
- Regional Center of Biotechnology, Faridabad, India
| | - Satya Ranjan Sahu
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
- Regional Center of Biotechnology, Faridabad, India
| | - Abinash Dutta
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Narottam Acharya
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
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2
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Duan WY, Zhu XM, Zhang SB, Lv YY, Zhai HC, Wei S, Ma PA, Hu YS. Antifungal effects of carvacrol, the main volatile compound in Origanum vulgare L. essential oil, against Aspergillus flavus in postharvest wheat. Int J Food Microbiol 2024; 410:110514. [PMID: 38070224 DOI: 10.1016/j.ijfoodmicro.2023.110514] [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: 09/05/2023] [Revised: 11/28/2023] [Accepted: 12/03/2023] [Indexed: 12/29/2023]
Abstract
Plant volatile organic compounds (VOCs) with antimicrobial activity could potentially be extremely useful fumigants to prevent and control the fungal decay of agricultural products postharvest. In this study, antifungal effects of volatile compounds in essential oils extracted from Origanum vulgare L. against Aspergillus flavus growth were investigated using transcriptomic and biochemical analyses. Carvacrol was identified as the major volatile constituent of the Origanum vulgare L. essential oil, accounting for 66.01 % of the total content. The minimum inhibitory concentrations of carvacrol were 0.071 and 0.18 μL/mL in gas-phase fumigation and liquid contact, respectively. Fumigation with 0.60 μL/mL of carvacrol could completely inhibit A. flavus proliferation in wheat grains with 20 % moisture, showing its potential as a biofumigant. Scanning electron microscopy revealed that carvacrol treatment caused morphological deformation of A. flavus mycelia, and the resulting increased electrolyte leakage indicates damage to the plasma membrane. Confocal laser scanning microscopy confirmed that the carvacrol treatment caused a decrease in mitochondrial membrane potential, reactive oxygen species accumulation, and DNA damage. Transcriptome analysis revealed that differentially expressed genes were mainly associated with fatty acid degradation, autophagy, peroxisomes, the tricarboxylic acid cycle, oxidative phosphorylation, and DNA replication in A. flavus mycelia exposed to carvacrol. Biochemical analyses of hydrogen peroxide and superoxide anion content, and catalase, superoxide dismutase, and glutathione S-transferase activities showed that carvacrol induced oxidative stress in A. flavus, which agreed with the transcriptome results. In summary, this study provides an experimental basis for the use of carvacrol as a promising biofumigant for the prevention of A. flavus contamination during postharvest grain storage.
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Affiliation(s)
- Wen-Yan Duan
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, People's Republic of China
| | - Xi-Man Zhu
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, People's Republic of China
| | - Shuai-Bing Zhang
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, People's Republic of China.
| | - Yang-Yong Lv
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, People's Republic of China
| | - Huan-Chen Zhai
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, People's Republic of China
| | - Shan Wei
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, People's Republic of China
| | - Ping-An Ma
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, People's Republic of China
| | - Yuan-Sen Hu
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, People's Republic of China
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3
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Xu Z, Feng J, Yu D, Huo Y, Ma X, Lam WH, Liu Z, Li XD, Ishibashi T, Dang S, Zhai Y. Synergism between CMG helicase and leading strand DNA polymerase at replication fork. Nat Commun 2023; 14:5849. [PMID: 37730685 PMCID: PMC10511561 DOI: 10.1038/s41467-023-41506-0] [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: 12/21/2021] [Accepted: 09/07/2023] [Indexed: 09/22/2023] Open
Abstract
The replisome that replicates the eukaryotic genome consists of at least three engines: the Cdc45-MCM-GINS (CMG) helicase that separates duplex DNA at the replication fork and two DNA polymerases, one on each strand, that replicate the unwound DNA. Here, we determined a series of cryo-electron microscopy structures of a yeast replisome comprising CMG, leading-strand polymerase Polε and three accessory factors on a forked DNA. In these structures, Polε engages or disengages with the motor domains of the CMG by occupying two alternative positions, which closely correlate with the rotational movement of the single-stranded DNA around the MCM pore. During this process, the polymerase remains stably coupled to the helicase using Psf1 as a hinge. This synergism is modulated by a concerted rearrangement of ATPase sites to drive DNA translocation. The Polε-MCM coupling is not only required for CMG formation to initiate DNA replication but also facilitates the leading-strand DNA synthesis mediated by Polε. Our study elucidates a mechanism intrinsic to the replisome that coordinates the activities of CMG and Polε to negotiate any roadblocks, DNA damage, and epigenetic marks encountered during translocation along replication forks.
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Affiliation(s)
- Zhichun Xu
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Jianrong Feng
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Daqi Yu
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Yunjing Huo
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Xiaohui Ma
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Wai Hei Lam
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Zheng Liu
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Toyotaka Ishibashi
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Shangyu Dang
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.
- HKUST-Shenzhen Research Institute, 518057, Nanshan, Shenzhen, China.
| | - Yuanliang Zhai
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China.
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4
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Strauss JD, Pursell ZF. Replication DNA polymerases, genome instability and cancer therapies. NAR Cancer 2023; 5:zcad033. [PMID: 37388540 PMCID: PMC10304742 DOI: 10.1093/narcan/zcad033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/24/2023] [Accepted: 06/25/2023] [Indexed: 07/01/2023] Open
Abstract
It has been over a decade since the initial identification of exonuclease domain mutations in the genes encoding the catalytic subunits of replication DNA polymerases ϵ and δ (POLE and POLD1) in tumors from highly mutated endometrial and colorectal cancers. Interest in studying POLE and POLD1 has increased significantly since then. Prior to those landmark cancer genome sequencing studies, it was well documented that mutations in replication DNA polymerases that reduced their DNA synthesis accuracy, their exonuclease activity or their interactions with other factors could lead to increased mutagenesis, DNA damage and even tumorigenesis in mice. There are several recent, well-written reviews of replication DNA polymerases. The aim of this review is to gather and review in some detail recent studies of DNA polymerases ϵ and δ as they pertain to genome instability, cancer and potential therapeutic treatments. The focus here is primarily on recent informative studies on the significance of mutations in genes encoding their catalytic subunits (POLE and POLD1), mutational signatures, mutations in associated genes, model organisms, and the utility of chemotherapy and immune checkpoint inhibition in polymerase mutant tumors.
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Affiliation(s)
- Juliet D Strauss
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, 70118 LA, USA
| | - Zachary F Pursell
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, 70118 LA, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, 70118 LA, USA
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5
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Johnson RE, Prakash L, Prakash S. DNA polymerase ε leading strand signature mutations result from defects in its proofreading activity. J Biol Chem 2023; 299:104913. [PMID: 37307920 PMCID: PMC10371845 DOI: 10.1016/j.jbc.2023.104913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/14/2023] Open
Abstract
The evidence that purified pol2-M644G DNA polymerase (Pol)ε exhibits a highly elevated bias for forming T:dTTP mispairs over A:dATP mispairs and that yeast cells harboring this Polε mutation accumulate A > T signature mutations in the leading strand have been used to assign a role for Polε in replicating the leading strand. Here, we determine whether A > T signature mutations result from defects in Polε proofreading activity by analyzing their rate in Polε proofreading defective pol2-4 and pol2-M644G cells. Since purified pol2-4 Polε exhibits no bias for T:dTTP mispair formation, A > T mutations are expected to occur at a much lower rate in pol2-4 than in pol2-M644G cells if Polε replicated the leading strand. Instead, we find that the rate of A > T signature mutations are as highly elevated in pol2-4 cells as in pol2-M644G cells; furthermore, the highly elevated rate of A > T signature mutations is severely curtailed in the absence of PCNA ubiquitination or Polζ in both the pol2-M644G and pol2-4 strains. Altogether, our evidence supports the conclusion that the leading strand A > T signature mutations derive from defects in Polε proofreading activity and not from the role of Polε as a leading strand replicase, and it conforms with the genetic evidence for a major role of Polδ in replication of both the DNA strands.
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Affiliation(s)
- Robert E Johnson
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | - Louise Prakash
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | - Satya Prakash
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA.
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6
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Shrestha S, Minamino M, Chen ZA, Bouchoux C, Rappsilber J, Uhlmann F. Replisome-cohesin interactions provided by the Tof1-Csm3 and Mrc1 cohesion establishment factors. Chromosoma 2023; 132:117-135. [PMID: 37166686 PMCID: PMC10247859 DOI: 10.1007/s00412-023-00797-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/12/2023]
Abstract
The chromosomal cohesin complex establishes sister chromatid cohesion during S phase, which forms the basis for faithful segregation of DNA replication products during cell divisions. Cohesion establishment is defective in the absence of either of three non-essential Saccharomyces cerevisiae replication fork components Tof1-Csm3 and Mrc1. Here, we investigate how these conserved factors contribute to cohesion establishment. Tof1-Csm3 and Mrc1 serve known roles during DNA replication, including replication checkpoint signaling, securing replication fork speed, as well as recruiting topoisomerase I and the histone chaperone FACT. By modulating each of these functions independently, we rule out that one of these known replication roles explains the contribution of Tof1-Csm3 and Mrc1 to cohesion establishment. Instead, using purified components, we reveal direct and multipronged protein interactions of Tof1-Csm3 and Mrc1 with the cohesin complex. Our findings open the possibility that a series of physical interactions between replication fork components and cohesin facilitate successful establishment of sister chromatid cohesion during DNA replication.
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Affiliation(s)
- Sudikchya Shrestha
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Masashi Minamino
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Zhuo A Chen
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, 13355, Berlin, Germany
| | - Céline Bouchoux
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Juri Rappsilber
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, 13355, Berlin, Germany
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
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7
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Nasheuer HP, Onwubiko NO. Lagging Strand Initiation Processes in DNA Replication of Eukaryotes-Strings of Highly Coordinated Reactions Governed by Multiprotein Complexes. Genes (Basel) 2023; 14:genes14051012. [PMID: 37239371 DOI: 10.3390/genes14051012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
In their influential reviews, Hanahan and Weinberg coined the term 'Hallmarks of Cancer' and described genome instability as a property of cells enabling cancer development. Accurate DNA replication of genomes is central to diminishing genome instability. Here, the understanding of the initiation of DNA synthesis in origins of DNA replication to start leading strand synthesis and the initiation of Okazaki fragment on the lagging strand are crucial to control genome instability. Recent findings have provided new insights into the mechanism of the remodelling of the prime initiation enzyme, DNA polymerase α-primase (Pol-prim), during primer synthesis, how the enzyme complex achieves lagging strand synthesis, and how it is linked to replication forks to achieve optimal initiation of Okazaki fragments. Moreover, the central roles of RNA primer synthesis by Pol-prim in multiple genome stability pathways such as replication fork restart and protection of DNA against degradation by exonucleases during double-strand break repair are discussed.
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Affiliation(s)
- Heinz Peter Nasheuer
- Centre for Chromosome Biology, Arts & Science Building, Main Concourse, School of Biological and Chemical Sciences, Biochemistry, University of Galway, Distillery Road, H91 TK33 Galway, Ireland
| | - Nichodemus O Onwubiko
- Centre for Chromosome Biology, Arts & Science Building, Main Concourse, School of Biological and Chemical Sciences, Biochemistry, University of Galway, Distillery Road, H91 TK33 Galway, Ireland
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8
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Klassen R, Gangavarapu V, Johnson RE, Prakash L, Prakash S. Mismatch repair operates at the replication fork in direct competition with mismatch extension by DNA polymerase δ. J Biol Chem 2023; 299:104598. [PMID: 36898578 PMCID: PMC10124943 DOI: 10.1016/j.jbc.2023.104598] [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: 02/07/2023] [Revised: 03/05/2023] [Accepted: 03/06/2023] [Indexed: 03/12/2023] Open
Abstract
DNA mismatch repair (MMR) in eukaryotes is believed to occur post-replicatively, wherein nicks or gaps in the nascent DNA strand are suggested to serve as strand discrimination signals. However, how such signals are generated in the nascent leading strand has remained unclear. Here we examine the alternative possibility that MMR occurs in conjunction with the replication fork. To this end, we utilize mutations in the PCNA interacting peptide (PIP) domain of the Pol3 or Pol32 subunit of DNA polymerase δ (Polδ) and show that these pip mutations suppress the greatly elevated mutagenesis in yeast strains harboring the pol3-01 mutation defective in Polδ proofreading activity. And strikingly, they suppress the synthetic lethality of pol3-01 pol2-4 double mutant strains, which arises from the vastly enhanced mutability due to defects in the proofreading functions of both Polδ and Polε. Our finding that suppression of elevated mutagenesis in pol3-01 by the Polδ pip mutations requires intact MMR supports the conclusion that MMR operates at the replication fork in direct competition with other mismatch removal processes and with extension of synthesis from the mispair by Polδ. Furthermore, the evidence that Polδ pip mutations eliminate almost all the mutability of pol2-4 msh2Δ or pol3-01 pol2-4 adds strong support for a major role of Polδ in replication of both the leading and lagging DNA strands.
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Affiliation(s)
- Roland Klassen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Venkat Gangavarapu
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Robert E Johnson
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Louise Prakash
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Satya Prakash
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA.
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9
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Vipat S, Gupta D, Jonchhe S, Anderspuk H, Rothenberg E, Moiseeva TN. The non-catalytic role of DNA polymerase epsilon in replication initiation in human cells. Nat Commun 2022; 13:7099. [PMID: 36402816 PMCID: PMC9675812 DOI: 10.1038/s41467-022-34911-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 11/10/2022] [Indexed: 11/21/2022] Open
Abstract
DNA polymerase epsilon (PolE) in an enzyme essential for DNA replication. Deficiencies and mutations in PolE cause severe developmental abnormalities and cancers. Paradoxically, the catalytic domain of yeast PolE catalytic subunit is dispensable for survival, and its non-catalytic essential function is linked with replicative helicase (CMG) assembly. Less is known about the PolE role in replication initiation in human cells. Here we use an auxin-inducible degron system to study the effect of POLE1 depletion on replication initiation in U2OS cells. POLE1-depleted cells were able to assemble CMG helicase and initiate DNA synthesis that failed shortly after. Expression of POLE1 non-catalytic domain rescued this defect resulting in slow, but continuous DNA synthesis. We propose a model where in human U2OS cells POLE1/POLE2 are dispensable for CMG assembly, but essential during later steps of replication initiation. Our study provides some insights into the role of PolE in replication initiation in human cells.
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Affiliation(s)
- Sameera Vipat
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, 12618, Estonia
| | - Dipika Gupta
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Sagun Jonchhe
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Hele Anderspuk
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, 12618, Estonia
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Tatiana N Moiseeva
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, 12618, Estonia.
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10
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Li JJX, Ip PPC. Endometrial Cancer: An Update on Prognostic Pathologic Features and Clinically Relevant Biomarkers. Surg Pathol Clin 2022; 15:277-299. [PMID: 35715162 DOI: 10.1016/j.path.2022.02.006] [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] [Indexed: 06/15/2023]
Abstract
The prognosis of endometrial cancers has historically been determined by the evaluation of histologic typing, grading, and staging. Recently, molecular classification, pioneered by the 4 prognostic categories from The Cancer Genome Atlas Research Network, has been shown to independently predict the outcome, correlate with biomarker expression, and predict response to adjuvant chemotherapy. In modern-day pathology practice, it has become necessary to integrate the time-honored prognostic pathologic features with molecular classification to optimize patient management. In this review, the significance of the molecular classification of endometrioid carcinomas, the application of practical diagnostic surrogate algorithms, and interpretation of test results will be addressed. Histologic features and theragnostic biomarkers will also be discussed in relation to the molecular subtypes of endometrial cancers.
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Affiliation(s)
- Joshua J X Li
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR
| | - Philip P C Ip
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, 102 Pok Fu Lam Road, Hong Kong SAR.
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11
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Global genomic instability caused by reduced expression of DNA polymerase ε in yeast. Proc Natl Acad Sci U S A 2022; 119:e2119588119. [PMID: 35290114 PMCID: PMC8944251 DOI: 10.1073/pnas.2119588119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceAlthough most studies of the genetic regulation of genome stability involve an analysis of mutations within the coding sequences of genes required for DNA replication or DNA repair, recent studies in yeast show that reduced levels of wild-type enzymes can also produce a mutator phenotype. By whole-genome sequencing and other methods, we find that reduced levels of the wild-type DNA polymerase ε in yeast greatly increase the rates of mitotic recombination, aneuploidy, and single-base mutations. The observed pattern of genome instability is different from those observed in yeast strains with reduced levels of the other replicative DNA polymerases, Pol α and Pol δ. These observations are relevant to our understanding of cancer and other diseases associated with genetic instability.
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12
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Abstract
DNA replication in eukaryotic cells initiates from large numbers of sites called replication origins. Initiation of replication from these origins must be tightly controlled to ensure the entire genome is precisely duplicated in each cell cycle. This is accomplished through the regulation of the first two steps in replication: loading and activation of the replicative DNA helicase. Here we describe what is known about the mechanism and regulation of these two reactions from a genetic, biochemical, and structural perspective, focusing on recent progress using proteins from budding yeast. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Alessandro Costa
- Macromolecular Machines Laboratory, The Francis Crick Institute, London, UK;
| | - John F X Diffley
- Chromosome Replication Laboratory, The Francis Crick Institute, London, UK;
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13
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Kiktev DA, Dominska M, Zhang T, Dahl J, Stepchenkova EI, Mieczkowski P, Burgers PM, Lujan S, Burkholder A, Kunkel TA, Petes TD. The fidelity of DNA replication, particularly on GC-rich templates, is reduced by defects of the Fe-S cluster in DNA polymerase δ. Nucleic Acids Res 2021; 49:5623-5636. [PMID: 34019669 PMCID: PMC8191807 DOI: 10.1093/nar/gkab371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/22/2021] [Accepted: 05/16/2021] [Indexed: 11/12/2022] Open
Abstract
Iron-sulfur clusters (4Fe–4S) exist in many enzymes concerned with DNA replication and repair. The contribution of these clusters to enzymatic activity is not fully understood. We identified the MET18 (MMS19) gene of Saccharomyces cerevisiae as a strong mutator on GC-rich genes. Met18p is required for the efficient insertion of iron-sulfur clusters into various proteins. met18 mutants have an elevated rate of deletions between short flanking repeats, consistent with increased DNA polymerase slippage. This phenotype is very similar to that observed in mutants of POL3 (encoding the catalytic subunit of Pol δ) that weaken binding of the iron-sulfur cluster. Comparable mutants of POL2 (Pol ϵ) do not elevate deletions. Further support for the conclusion that met18 strains result in impaired DNA synthesis by Pol δ are the observations that Pol δ isolated from met18 strains has less bound iron and is less processive in vitro than the wild-type holoenzyme.
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Affiliation(s)
- Denis A Kiktev
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Margaret Dominska
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Tony Zhang
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Joseph Dahl
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Elena I Stepchenkova
- Department of Genetics and Biotechnology, Saint-Petersburg State University, St. Petersburg, Russia.,Vavilov Institute of General Genetics, Saint-Petersburg Branch, Russian Academy of Sciences, St. Petersburg, Russia
| | - Piotr Mieczkowski
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7264, USA
| | - Peter M Burgers
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Scott Lujan
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Adam Burkholder
- Office of Environmental Science Cyberinfrastructure, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Thomas A Kunkel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Thomas D Petes
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
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14
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Zach R, Carr AM. Increased expression of Polδ does not alter the canonical replication program in vivo. Wellcome Open Res 2021; 6:44. [PMID: 33796794 PMCID: PMC7974630 DOI: 10.12688/wellcomeopenres.16600.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2021] [Indexed: 01/08/2023] Open
Abstract
Background: In vitro experiments utilising the reconstituted Saccharomyces cerevisiae eukaryotic replisome indicated that the efficiency of the leading strand replication is impaired by a moderate increase in Polδ concentration. It was hypothesised that the slower rate of the leading strand synthesis characteristic for reactions containing two-fold and four-fold increased concentration of Polδ represented a consequence of a relatively rare event, during which Polδ stochastically outcompeted Polε and, in an inefficient manner, temporarily facilitated extension of the leading strand. Inspired by this observation, we aimed to determine whether similarly increased Polδ levels influence replication dynamics in vivo using the fission yeast Schizosaccharomyces pombe as a model system. Methods: To generate S. pombe strains over-expressing Polδ, we utilised Cre-Lox mediated cassette exchange and integrated one or three extra genomic copies of all four Polδ genes. To estimate expression of respective Polδ genes in Polδ-overexpressing mutants, we measured relative transcript levels of cdc1 + , cdc6 + (or cdc6 L591G ), cdc27 + and cdm1 + by reverse transcription followed by quantitative PCR (RT-qPCR). To assess the impact of Polδ over-expression on cell physiology and replication dynamics, we used standard cell biology techniques and polymerase usage sequencing. Results: We provide an evidence that two-fold and four-fold over-production of Polδ does not significantly alter growth rate, cellular morphology and S-phase duration. Polymerase usage sequencing analysis further indicates that increased Polδ expression does not change activities of Polδ, Polε and Polα at replication initiation sites and across replication termination zones. Additionally, we show that mutants over-expressing Polδ preserve WT-like distribution of replication origin efficiencies. Conclusions: Our experiments do not disprove the existence of opportunistic polymerase switches; however, the data indicate that, if stochastic replacement of Polε for Polδ does occur i n vivo, it represents a rare phenomenon that does not significantly influence canonical replication program.
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Affiliation(s)
- Róbert Zach
- Genome Damage and Stability Centre, School of Life Sciences, Science Park Road, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - Antony M. Carr
- Genome Damage and Stability Centre, School of Life Sciences, Science Park Road, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
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15
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Chanet R, Baïlle D, Golinelli-Cohen MP, Riquier S, Guittet O, Lepoivre M, Huang ME, Vernis L. Fe-S coordination defects in the replicative DNA polymerase delta cause deleterious DNA replication in vivo and subsequent DNA damage in the yeast Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2021; 11:6261760. [PMID: 34009341 PMCID: PMC8495945 DOI: 10.1093/g3journal/jkab124] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/06/2021] [Indexed: 11/12/2022]
Abstract
B-type eukaryotic polymerases contain a [4Fe-4S] cluster in their C-terminus domain, whose role is not fully understood yet. Among them, DNA polymerase delta (Polδ) plays an essential role in chromosomal DNA replication, mostly during lagging strand synthesis. Previous in vitro work suggested that the Fe-S cluster in Polδ is required for efficient binding of the Pol31 subunit, ensuring stability of the Polδ complex. Here we analyzed the in vivo consequences resulting from an impaired coordination of the Fe-S cluster in Polδ. We show that a single substitution of the very last cysteine coordinating the cluster by a serine is responsible for the generation of massive DNA damage during S phase, leading to checkpoint activation, requirement of homologous recombination for repair, and ultimately to cell death when the repair capacities of the cells are overwhelmed. These data indicate that impaired Fe-S cluster coordination in Polδ is responsible for aberrant replication. More generally, Fe-S in Polδ may be compromised by various stress including anti-cancer drugs. Possible in vivo Polδ Fe-S cluster oxidation and collapse may thus occur, and we speculate this could contribute to induced genomic instability and cell death, comparable to that observed in pol3-13 cells.
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Affiliation(s)
- Roland Chanet
- Institut Curie, PSL Research University, CNRS UMR3348, Université Paris-Sud, Université Paris-Saclay, 91400 Orsay, France
| | - Dorothée Baïlle
- Institut Curie, PSL Research University, CNRS UMR3348, Université Paris-Sud, Université Paris-Saclay, 91400 Orsay, France
| | - Marie-Pierre Golinelli-Cohen
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198 Gif-sur-Yvette, France
| | - Sylvie Riquier
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198 Gif-sur-Yvette, France
| | - Olivier Guittet
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198 Gif-sur-Yvette, France
| | - Michel Lepoivre
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198 Gif-sur-Yvette, France
| | - Meng-Er Huang
- Institut Curie, PSL Research University, CNRS UMR3348, Université Paris-Sud, Université Paris-Saclay, 91400 Orsay, France.,Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198 Gif-sur-Yvette, France
| | - Laurence Vernis
- Institut Curie, PSL Research University, CNRS UMR3348, Université Paris-Sud, Université Paris-Saclay, 91400 Orsay, France.,Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198 Gif-sur-Yvette, France
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16
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Stepchenkova EI, Zhuk AS, Cui J, Tarakhovskaya ER, Barbari SR, Shcherbakova PV, Polev DE, Fedorov R, Poliakov E, Rogozin IB, Lada AG, Pavlov YI. Compensation for the absence of the catalytically active half of DNA polymerase ε in yeast by positively selected mutations in CDC28. Genetics 2021; 218:6222163. [PMID: 33844024 DOI: 10.1093/genetics/iyab060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 04/02/2021] [Indexed: 11/14/2022] Open
Abstract
Current eukaryotic replication models postulate that leading and lagging DNA strands are replicated predominantly by dedicated DNA polymerases. The catalytic subunit of the leading strand DNA polymerase ε, Pol2, consists of two halves made of two different ancestral B-family DNA polymerases. Counterintuitively, the catalytically active N-terminal half is dispensable, while the inactive C-terminal part is required for viability. Despite extensive studies of yeast Saccharomyces cerevisiae strains lacking the active N-terminal half, it is still unclear how these strains survive and recover. We designed a robust method for constructing mutants with only the C-terminal part of Pol2. Strains without the active polymerase part show severe growth defects, sensitivity to replication inhibitors, chromosomal instability, and elevated spontaneous mutagenesis. Intriguingly, the slow-growing mutant strains rapidly accumulate fast-growing clones. Analysis of genomic DNA sequences of these clones revealed that the adaptation to the loss of the catalytic N-terminal part of Pol2 occurs by a positive selection of mutants with improved growth. Elevated mutation rates help generate sufficient numbers of these variants. Single nucleotide changes in the cell cycle-dependent kinase gene, CDC28, improve the growth of strains lacking the N-terminal part of Pol2, and rescue their sensitivity to replication inhibitors and, in parallel, lower mutation rates. Our study predicts that changes in mammalian homologs of cyclin-dependent kinases may contribute to cellular responses to the leading strand polymerase defects.
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Affiliation(s)
- Elena I Stepchenkova
- Laboratory of Mutagenesis and Genetic Toxicology, Vavilov Institute of General Genetics, Saint-Petersburg Branch, Russian Academy of Sciences, Saint-Petersburg 199034, Russia.,Department of Genetics and Biotechnology, Saint-Petersburg State University, Saint-Petersburg 199034, Russia.,Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Anna S Zhuk
- ITMO University, Saint-Petersburg 191002, Russia
| | - Jian Cui
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Elena R Tarakhovskaya
- Laboratory of Mutagenesis and Genetic Toxicology, Vavilov Institute of General Genetics, Saint-Petersburg Branch, Russian Academy of Sciences, Saint-Petersburg 199034, Russia.,Department of Plant Physiology and Biochemistry, Saint-Petersburg State University, Saint-Petersburg 199034, Russia
| | - Stephanie R Barbari
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Polina V Shcherbakova
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Dmitrii E Polev
- Research Resource Center "Biobank," Research Park, Saint-Petersburg State University, Saint-Petersburg 198504, Russia
| | - Roman Fedorov
- Department of Mathematics, University of Pittsburgh, PA 15213, USA
| | - Eugenia Poliakov
- Laboratory of Retinal Cell and Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Artem G Lada
- Department of Microbiology and Molecular Genetics, University of California Davis, Davis, CA 92697, USA
| | - Youri I Pavlov
- Department of Genetics and Biotechnology, Saint-Petersburg State University, Saint-Petersburg 199034, Russia.,Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA.,Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA.,Department of Microbiology and Pathology, University of Nebraska Medical Center, Omaha, NE 68198, USA.,Department of Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
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17
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Abstract
The faithful and timely copying of DNA by molecular machines known as replisomes depends on a disparate suite of enzymes and scaffolding factors working together in a highly orchestrated manner. Large, dynamic protein-nucleic acid assemblies that selectively morph between distinct conformations and compositional states underpin this critical cellular process. In this article, we discuss recent progress outlining the physical basis of replisome construction and progression in eukaryotes.
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Affiliation(s)
- Ilan Attali
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA;
| | - Michael R Botchan
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA;
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18
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Zach R, Carr AM. Increased expression of Polδ does not alter the canonical replication program in vivo. Wellcome Open Res 2021; 6:44. [PMID: 33796794 PMCID: PMC7974630 DOI: 10.12688/wellcomeopenres.16600.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2021] [Indexed: 11/20/2022] Open
Abstract
Background: In vitro experiments utilising the reconstituted Saccharomyces cerevisiae eukaryotic replisome indicated that the efficiency of the leading strand replication is impaired by a moderate increase in Polδ concentration. It was hypothesised that the slower rate of the leading strand synthesis characteristic for reactions containing two-fold and four-fold increased concentration of Polδ represented a consequence of a relatively rare event, during which Polδ stochastically outcompeted Polε and, in an inefficient manner, temporarily facilitated extension of the leading strand. Inspired by this observation, we aimed to determine whether similarly increased Polδ levels influence replication dynamics in vivo using the fission yeast Schizosaccharomyces pombe as a model system. Methods: To generate S. pombe strains over-expressing Polδ, we utilised Cre-Lox mediated cassette exchange and integrated one or three extra genomic copies of all four Polδ genes. To estimate expression of respective Polδ genes in Polδ-overexpressing mutants, we measured relative transcript levels of cdc1 + , cdc6 + (or cdc6 L591G ), cdc27 + and cdm1 + by reverse transcription followed by quantitative PCR (RT-qPCR). To assess the impact of Polδ over-expression on cell physiology and replication dynamics, we used standard cell biology techniques and polymerase usage sequencing. Results: We provide an evidence that two-fold and four-fold over-production of Polδ does not significantly alter growth rate, cellular morphology and S-phase duration. Polymerase usage sequencing analysis further indicates that increased Polδ expression does not change activities of Polδ, Polε and Polα at replication initiation sites and across replication termination zones. Additionally, we show that mutants over-expressing Polδ preserve WT-like distribution of replication origin efficiencies. Conclusions: Our experiments do not disprove the existence of opportunistic polymerase switches; however, the data indicate that, if stochastic replacement of Polε for Polδ does occur i n vivo, it represents a rare phenomenon that does not significantly influence canonical replication program.
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Affiliation(s)
- Róbert Zach
- Genome Damage and Stability Centre, School of Life Sciences, Science Park Road, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - Antony M. Carr
- Genome Damage and Stability Centre, School of Life Sciences, Science Park Road, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
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19
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Koussa NC, Smith DJ. Limiting DNA polymerase delta alters replication dynamics and leads to a dependence on checkpoint activation and recombination-mediated DNA repair. PLoS Genet 2021; 17:e1009322. [PMID: 33493195 PMCID: PMC7861531 DOI: 10.1371/journal.pgen.1009322] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 02/04/2021] [Accepted: 12/23/2020] [Indexed: 12/20/2022] Open
Abstract
DNA polymerase delta (Pol δ) plays several essential roles in eukaryotic DNA replication and repair. At the replication fork, Pol δ is responsible for the synthesis and processing of the lagging-strand. At replication origins, Pol δ has been proposed to initiate leading-strand synthesis by extending the first Okazaki fragment. Destabilizing mutations in human Pol δ subunits cause replication stress and syndromic immunodeficiency. Analogously, reduced levels of Pol δ in Saccharomyces cerevisiae lead to pervasive genome instability. Here, we analyze how the depletion of Pol δ impacts replication origin firing and lagging-strand synthesis during replication elongation in vivo in S. cerevisiae. By analyzing nascent lagging-strand products, we observe a genome-wide change in both the establishment and progression of replication. S-phase progression is slowed in Pol δ depletion, with both globally reduced origin firing and slower replication progression. We find that no polymerase other than Pol δ is capable of synthesizing a substantial amount of lagging-strand DNA, even when Pol δ is severely limiting. We also characterize the impact of impaired lagging-strand synthesis on genome integrity and find increased ssDNA and DNA damage when Pol δ is limiting; these defects lead to a strict dependence on checkpoint signaling and resection-mediated repair pathways for cellular viability.
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Affiliation(s)
- Natasha C. Koussa
- Department of Biology, New York University, New York City, New York, United State of America
| | - Duncan J. Smith
- Department of Biology, New York University, New York City, New York, United State of America
- * E-mail:
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20
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Abstract
In all cell types, a multi-protein machinery is required to accurately duplicate the large duplex DNA genome. This central life process requires five core replisome factors in all cellular life forms studied thus far. Unexpectedly, three of the five core replisome factors have no common ancestor between bacteria and eukaryotes. Accordingly, the replisome machines of bacteria and eukaryotes have important distinctions in the way that they are organized and function. This chapter outlines the major replication proteins that perform DNA duplication at replication forks, with particular attention to differences and similarities in the strategies used by eukaryotes and bacteria.
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Affiliation(s)
- Nina Y Yao
- DNA Replication Laboratory, The Rockefeller University, New York, USA, 10065
| | - Michael E O'Donnell
- DNA Replication Laboratory, The Rockefeller University, New York, USA, 10065. .,Howard Hughes Medical Institute, The Rockefeller University, New York, USA, 10065.
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21
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Denkiewicz-Kruk M, Jedrychowska M, Endo S, Araki H, Jonczyk P, Dmowski M, Fijalkowska IJ. Recombination and Pol ζ Rescue Defective DNA Replication upon Impaired CMG Helicase-Pol ε Interaction. Int J Mol Sci 2020; 21:ijms21249484. [PMID: 33322195 PMCID: PMC7762974 DOI: 10.3390/ijms21249484] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/06/2020] [Accepted: 12/09/2020] [Indexed: 11/22/2022] Open
Abstract
The CMG complex (Cdc45, Mcm2–7, GINS (Psf1, 2, 3, and Sld5)) is crucial for both DNA replication initiation and fork progression. The CMG helicase interaction with the leading strand DNA polymerase epsilon (Pol ε) is essential for the preferential loading of Pol ε onto the leading strand, the stimulation of the polymerase, and the modulation of helicase activity. Here, we analyze the consequences of impaired interaction between Pol ε and GINS in Saccharomyces cerevisiae cells with the psf1-100 mutation. This significantly affects DNA replication activity measured in vitro, while in vivo, the psf1-100 mutation reduces replication fidelity by increasing slippage of Pol ε, which manifests as an elevated number of frameshifts. It also increases the occurrence of single-stranded DNA (ssDNA) gaps and the demand for homologous recombination. The psf1-100 mutant shows elevated recombination rates and synthetic lethality with rad52Δ. Additionally, we observe increased participation of DNA polymerase zeta (Pol ζ) in DNA synthesis. We conclude that the impaired interaction between GINS and Pol ε requires enhanced involvement of error-prone Pol ζ, and increased participation of recombination as a rescue mechanism for recovery of impaired replication forks.
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Affiliation(s)
- Milena Denkiewicz-Kruk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; (M.D.-K.); (M.J.); (P.J.)
| | - Malgorzata Jedrychowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; (M.D.-K.); (M.J.); (P.J.)
| | - Shizuko Endo
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan; (S.E.); (H.A.)
| | - Hiroyuki Araki
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan; (S.E.); (H.A.)
| | - Piotr Jonczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; (M.D.-K.); (M.J.); (P.J.)
| | - Michal Dmowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; (M.D.-K.); (M.J.); (P.J.)
- Correspondence: (M.D.); (I.J.F.); Tel.: +48-22-5921128 (M.D.); +48-22-5921113 (I.J.F.)
| | - Iwona J. Fijalkowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; (M.D.-K.); (M.J.); (P.J.)
- Correspondence: (M.D.); (I.J.F.); Tel.: +48-22-5921128 (M.D.); +48-22-5921113 (I.J.F.)
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22
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Pavlov YI, Zhuk AS, Stepchenkova EI. DNA Polymerases at the Eukaryotic Replication Fork Thirty Years after: Connection to Cancer. Cancers (Basel) 2020; 12:E3489. [PMID: 33255191 PMCID: PMC7760166 DOI: 10.3390/cancers12123489] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/13/2020] [Accepted: 11/13/2020] [Indexed: 12/13/2022] Open
Abstract
Recent studies on tumor genomes revealed that mutations in genes of replicative DNA polymerases cause a predisposition for cancer by increasing genome instability. The past 10 years have uncovered exciting details about the structure and function of replicative DNA polymerases and the replication fork organization. The principal idea of participation of different polymerases in specific transactions at the fork proposed by Morrison and coauthors 30 years ago and later named "division of labor," remains standing, with an amendment of the broader role of polymerase δ in the replication of both the lagging and leading DNA strands. However, cancer-associated mutations predominantly affect the catalytic subunit of polymerase ε that participates in leading strand DNA synthesis. We analyze how new findings in the DNA replication field help elucidate the polymerase variants' effects on cancer.
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Affiliation(s)
- Youri I. Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases and Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Department of Genetics and Biotechnology, Saint-Petersburg State University, 199034 Saint Petersburg, Russia;
| | - Anna S. Zhuk
- International Laboratory of Computer Technologies, ITMO University, 197101 Saint Petersburg, Russia;
| | - Elena I. Stepchenkova
- Department of Genetics and Biotechnology, Saint-Petersburg State University, 199034 Saint Petersburg, Russia;
- Laboratory of Mutagenesis and Genetic Toxicology, Vavilov Institute of General Genetics, Saint-Petersburg Branch, Russian Academy of Sciences, 199034 Saint Petersburg, Russia
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23
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Sviderskiy VO, Blumenberg L, Gorodetsky E, Karakousi TR, Hirsh N, Alvarez SW, Terzi EM, Kaparos E, Whiten GC, Ssebyala S, Tonzi P, Mir H, Neel BG, Huang TT, Adams S, Ruggles KV, Possemato R. Hyperactive CDK2 Activity in Basal-like Breast Cancer Imposes a Genome Integrity Liability that Can Be Exploited by Targeting DNA Polymerase ε. Mol Cell 2020; 80:682-698.e7. [PMID: 33152268 PMCID: PMC7687292 DOI: 10.1016/j.molcel.2020.10.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 08/12/2020] [Accepted: 10/09/2020] [Indexed: 02/06/2023]
Abstract
Knowledge of fundamental differences between breast cancer subtypes has driven therapeutic advances; however, basal-like breast cancer (BLBC) remains clinically intractable. Because BLBC exhibits alterations in DNA repair enzymes and cell-cycle checkpoints, elucidation of factors enabling the genomic instability present in this subtype has the potential to reveal novel anti-cancer strategies. Here, we demonstrate that BLBC is especially sensitive to suppression of iron-sulfur cluster (ISC) biosynthesis and identify DNA polymerase epsilon (POLE) as an ISC-containing protein that underlies this phenotype. In BLBC cells, POLE suppression leads to replication fork stalling, DNA damage, and a senescence-like state or cell death. In contrast, luminal breast cancer and non-transformed mammary cells maintain viability upon POLE suppression but become dependent upon an ATR/CHK1/CDC25A/CDK2 DNA damage response axis. We find that CDK1/2 targets exhibit hyperphosphorylation selectively in BLBC tumors, indicating that CDK2 hyperactivity is a genome integrity vulnerability exploitable by targeting POLE.
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Affiliation(s)
- Vladislav O Sviderskiy
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Lili Blumenberg
- Department of Medicine, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Elizabeth Gorodetsky
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Triantafyllia R Karakousi
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Nicole Hirsh
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Samantha W Alvarez
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Erdem M Terzi
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Efiyenia Kaparos
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Gabrielle C Whiten
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Shakirah Ssebyala
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Peter Tonzi
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Hannan Mir
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Benjamin G Neel
- Department of Medicine, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Tony T Huang
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Sylvia Adams
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Kelly V Ruggles
- Department of Medicine, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Richard Possemato
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA.
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24
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Kazlauskas D, Krupovic M, Guglielmini J, Forterre P, Venclovas Č. Diversity and evolution of B-family DNA polymerases. Nucleic Acids Res 2020; 48:10142-10156. [PMID: 32976577 PMCID: PMC7544198 DOI: 10.1093/nar/gkaa760] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/27/2020] [Accepted: 09/02/2020] [Indexed: 12/20/2022] Open
Abstract
B-family DNA polymerases (PolBs) represent the most common replicases. PolB enzymes that require RNA (or DNA) primed templates for DNA synthesis are found in all domains of life and many DNA viruses. Despite extensive research on PolBs, their origins and evolution remain enigmatic. Massive accumulation of new genomic and metagenomic data from diverse habitats as well as availability of new structural information prompted us to conduct a comprehensive analysis of the PolB sequences, structures, domain organizations, taxonomic distribution and co-occurrence in genomes. Based on phylogenetic analysis, we identified a new, widespread group of bacterial PolBs that are more closely related to the catalytically active N-terminal half of the eukaryotic PolEpsilon (PolEpsilonN) than to Escherichia coli Pol II. In Archaea, we characterized six new groups of PolBs. Two of them show close relationships with eukaryotic PolBs, the first one with PolEpsilonN, and the second one with PolAlpha, PolDelta and PolZeta. In addition, structure comparisons suggested common origin of the catalytically inactive C-terminal half of PolEpsilon (PolEpsilonC) and PolAlpha. Finally, in certain archaeal PolBs we discovered C-terminal Zn-binding domains closely related to those of PolAlpha and PolEpsilonC. Collectively, the obtained results allowed us to propose a scenario for the evolution of eukaryotic PolBs.
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Affiliation(s)
- Darius Kazlauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania
| | - Mart Krupovic
- Archaeal Virology Unit, Department of Microbiology, Institut Pasteur, 25 rue du Docteur Roux, Paris 75015, France
| | - Julien Guglielmini
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Patrick Forterre
- Archaeal Virology Unit, Department of Microbiology, Institut Pasteur, 25 rue du Docteur Roux, Paris 75015, France
| | - Česlovas Venclovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania
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25
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Guilliam TA, Yeeles JTP. An updated perspective on the polymerase division of labor during eukaryotic DNA replication. Crit Rev Biochem Mol Biol 2020; 55:469-481. [PMID: 32883112 DOI: 10.1080/10409238.2020.1811630] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In eukaryotes three DNA polymerases (Pols), α, δ, and ε, are tasked with bulk DNA synthesis of nascent strands during genome duplication. Most evidence supports a model where Pol α initiates DNA synthesis before Pol ε and Pol δ replicate the leading and lagging strands, respectively. However, a number of recent reports, enabled by advances in biochemical and genetic techniques, have highlighted emerging roles for Pol δ in all stages of leading-strand synthesis; initiation, elongation, and termination, as well as fork restart. By focusing on these studies, this review provides an updated perspective on the division of labor between the replicative polymerases during DNA replication.
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Affiliation(s)
- Thomas A Guilliam
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Joseph T P Yeeles
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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26
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Structure of the polymerase ε holoenzyme and atomic model of the leading strand replisome. Nat Commun 2020; 11:3156. [PMID: 32572031 PMCID: PMC7308368 DOI: 10.1038/s41467-020-16910-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/02/2020] [Indexed: 01/01/2023] Open
Abstract
The eukaryotic leading strand DNA polymerase (Pol) ε contains 4 subunits, Pol2, Dpb2, Dpb3 and Dpb4. Pol2 is a fusion of two B-family Pols; the N-terminal Pol module is catalytic and the C-terminal Pol module is non-catalytic. Despite extensive efforts, there is no atomic structure for Pol ε holoenzyme, critical to understanding how DNA synthesis is coordinated with unwinding and the DNA path through the CMG helicase-Pol ε-PCNA clamp. We show here a 3.5-Å cryo-EM structure of yeast Pol ε revealing that the Dpb3–Dpb4 subunits bridge the two DNA Pol modules of Pol2, holding them rigid. This information enabled an atomic model of the leading strand replisome. Interestingly, the model suggests that an OB fold in Dbp2 directs leading ssDNA from CMG to the Pol ε active site. These results complete the DNA path from entry of parental DNA into CMG to exit of daughter DNA from PCNA. DNA polymerase epsilon (Pol ε) is responsible for leading strand synthesis during DNA replication. Here the authors use Cryo-EM to describe the architecture of the Pol ε holoenzyme and to provide an atomic model for the leading strand replisome.
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27
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Ivanova T, Maier M, Missarova A, Ziegler-Birling C, Dam M, Gomar-Alba M, Carey LB, Mendoza M. Budding yeast complete DNA synthesis after chromosome segregation begins. Nat Commun 2020; 11:2267. [PMID: 32385287 PMCID: PMC7210879 DOI: 10.1038/s41467-020-16100-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 04/14/2020] [Indexed: 01/22/2023] Open
Abstract
To faithfully transmit genetic information, cells must replicate their entire genome before division. This is thought to be ensured by the temporal separation of replication and chromosome segregation. Here we show that in 20–40% of unperturbed yeast cells, DNA synthesis continues during anaphase, late in mitosis. High cyclin-Cdk activity inhibits DNA synthesis in metaphase, and the decrease in cyclin-Cdk activity during mitotic exit allows DNA synthesis to finish at subtelomeric and some difficult-to-replicate regions. DNA synthesis during late mitosis correlates with elevated mutation rates at subtelomeric regions, including copy number variation. Thus, yeast cells temporally overlap DNA synthesis and chromosome segregation during normal growth, possibly allowing cells to maximize population-level growth rate while simultaneously exploring greater genetic space. In the S phase of the cell cycle, the full genome needs to be replicated before cell division occurs. Here, authors show that in budding yeast DNA synthesis is completed after chromosome segregation begins.
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Affiliation(s)
- Tsvetomira Ivanova
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Michael Maier
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | | | | | - Monica Dam
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Mercè Gomar-Alba
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Lucas B Carey
- Universitat Pompeu Fabra (UPF), Barcelona, Spain. .,Center for Quantitative Biology and Peking-Tsinghua Center for the Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
| | - Manuel Mendoza
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain. .,Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France. .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France. .,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France. .,Université de Strasbourg, Strasbourg, France.
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28
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Miller JC, Delzell SB, Concepción-Acevedo J, Boucher MJ, Klingbeil MM. A DNA polymerization-independent role for mitochondrial DNA polymerase I-like protein C in African trypanosomes. J Cell Sci 2020; 133:jcs.233072. [PMID: 32079654 DOI: 10.1242/jcs.233072] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 02/10/2020] [Indexed: 01/01/2023] Open
Abstract
Mitochondrial DNA of Trypanosoma brucei and related parasites is a catenated network containing thousands of minicircles and tens of maxicircles, called kinetoplast DNA (kDNA). Replication of a single nucleoid requires at least three DNA polymerase I-like proteins (i.e. POLIB, POLIC and POLID), each showing discrete localizations near the kDNA during S phase. POLIB and POLID have roles in minicircle replication but the specific role of POLIC in kDNA maintenance is less clear. Here, we use an RNA interference (RNAi)-complementation system to dissect the functions of two distinct POLIC regions, i.e. the conserved family A DNA polymerase (POLA) domain and the uncharacterized N-terminal region (UCR). While RNAi complementation with wild-type POLIC restored kDNA content and cell cycle localization of kDNA, active site point mutations in the POLA domain impaired minicircle replication similar to that of POLIB and POLID depletions. Complementation with POLA domain alone abolished the formation of POLIC foci and partially rescued the RNAi phenotype. Furthermore, we provide evidence that the UCR is crucial in cell cycle-dependent protein localization and facilitates proper distribution of progeny networks. This is the first report of a DNA polymerase that impacts on mitochondrial nucleoid distribution.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Jonathan C Miller
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Stephanie B Delzell
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Jeniffer Concepción-Acevedo
- Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Infectious Diseases, 1600 Clifton Road, Atlanta, GA 30329, USA
| | - Michael J Boucher
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Michele M Klingbeil
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA .,Division of Foodborne,Waterborne, and Environmental Diseases, The Institute of Applied Life Sciences, University of Massachusetts, Amherst, MA 01003, USA
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29
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Sui Y, Qi L, Zhang K, Saini N, Klimczak LJ, Sakofsky CJ, Gordenin DA, Petes TD, Zheng DQ. Analysis of APOBEC-induced mutations in yeast strains with low levels of replicative DNA polymerases. Proc Natl Acad Sci U S A 2020; 117:9440-9450. [PMID: 32277034 PMCID: PMC7196835 DOI: 10.1073/pnas.1922472117] [Citation(s) in RCA: 16] [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] [Indexed: 01/06/2023] Open
Abstract
Yeast strains with low levels of the replicative DNA polymerases (alpha, delta, and epsilon) have high levels of chromosome deletions, duplications, and translocations. By examining the patterns of mutations induced in strains with low levels of DNA polymerase by the human protein APOBEC3B (a protein that deaminates cytosine in single-stranded DNA), we show dramatically elevated amounts of single-stranded DNA relative to a wild-type strain. During DNA replication, one strand (defined as the leading strand) is replicated processively by DNA polymerase epsilon and the other (the lagging strand) is replicated as short fragments initiated by DNA polymerase alpha and extended by DNA polymerase delta. In the low DNA polymerase alpha and delta strains, the APOBEC-induced mutations are concentrated on the lagging-strand template, whereas in the low DNA polymerase epsilon strain, mutations occur on the leading- and lagging-strand templates with similar frequencies. In addition, for most genes, the transcribed strand is mutagenized more frequently than the nontranscribed strand. Lastly, some of the APOBEC-induced clusters in strains with low levels of DNA polymerase alpha or delta are greater than 10 kb in length.
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Affiliation(s)
- Yang Sui
- Ocean College, Zhejiang University, 316021 Zhoushan, China
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710
| | - Lei Qi
- Ocean College, Zhejiang University, 316021 Zhoushan, China
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710
| | - Ke Zhang
- Ocean College, Zhejiang University, 316021 Zhoushan, China
| | - Natalie Saini
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709
| | - Leszek J Klimczak
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709
| | - Cynthia J Sakofsky
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709
| | - Dmitry A Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709
| | - Thomas D Petes
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710;
| | - Dao-Qiong Zheng
- Ocean College, Zhejiang University, 316021 Zhoushan, China;
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710
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30
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Rad53 limits CMG helicase uncoupling from DNA synthesis at replication forks. Nat Struct Mol Biol 2020; 27:461-471. [PMID: 32341532 PMCID: PMC7225081 DOI: 10.1038/s41594-020-0407-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 03/06/2020] [Indexed: 12/13/2022]
Abstract
The coordination of DNA unwinding and synthesis at replication forks promotes efficient and faithful replication of chromosomal DNA. Disruption of the balance between helicase and polymerase activities during replication stress leads to fork progression defects and activation of the Rad53 checkpoint kinase, which is essential for the functional maintenance of stalled replication forks. The mechanism of Rad53-dependent fork stabilization is not known. Using reconstituted budding yeast replisomes, we show that mutational inactivation of the leading strand DNA polymerase, Pol ε, dNTP depletion, and chemical inhibition of DNA polymerases cause excessive DNA unwinding by the replicative DNA helicase, CMG, demonstrating that budding yeast replisomes lack intrinsic mechanisms that control helicase-polymerase coupling at the fork. Importantly, we find that the Rad53 kinase restricts excessive DNA unwinding at replication forks by limiting CMG helicase activity, suggesting a mechanism for fork stabilization by the replication checkpoint.
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31
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Acharya N, Khandagale P, Thakur S, Sahu JK, Utkalaja BG. Quaternary structural diversity in eukaryotic DNA polymerases: monomeric to multimeric form. Curr Genet 2020; 66:635-655. [PMID: 32236653 DOI: 10.1007/s00294-020-01071-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/13/2020] [Accepted: 03/24/2020] [Indexed: 12/14/2022]
Abstract
Sixteen eukaryotic DNA polymerases have been identified and studied so far. Based on the sequence similarity of the catalytic subunits of DNA polymerases, these have been classified into four A, B, X and Y families except PrimPol, which belongs to the AEP family. The quaternary structure of these polymerases also varies depending upon whether they are composed of one or more subunits. Therefore, in this review, we used a quaternary structure-based classification approach to group DNA polymerases as either monomeric or multimeric and highlighted functional significance of their accessory subunits. Additionally, we have briefly summarized various DNA polymerase discoveries from a historical perspective, emphasized unique catalytic mechanism of each DNA polymerase and highlighted recent advances in understanding their cellular functions.
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Affiliation(s)
- Narottam Acharya
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India.
| | - Prashant Khandagale
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India
| | - Shweta Thakur
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India
| | - Jugal Kishor Sahu
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India
| | - Bhabasha Gyanadeep Utkalaja
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India
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32
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Hoitsma NM, Whitaker AM, Schaich MA, Smith MR, Fairlamb MS, Freudenthal BD. Structure and function relationships in mammalian DNA polymerases. Cell Mol Life Sci 2020; 77:35-59. [PMID: 31722068 PMCID: PMC7050493 DOI: 10.1007/s00018-019-03368-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/11/2019] [Accepted: 10/31/2019] [Indexed: 12/19/2022]
Abstract
DNA polymerases are vital for the synthesis of new DNA strands. Since the discovery of DNA polymerase I in Escherichia coli, a diverse library of mammalian DNA polymerases involved in DNA replication, DNA repair, antibody generation, and cell checkpoint signaling has emerged. While the unique functions of these DNA polymerases are differentiated by their association with accessory factors and/or the presence of distinctive catalytic domains, atomic resolution structures of DNA polymerases in complex with their DNA substrates have revealed mechanistic subtleties that contribute to their specialization. In this review, the structure and function of all 15 mammalian DNA polymerases from families B, Y, X, and A will be reviewed and discussed with special emphasis on the insights gleaned from recently published atomic resolution structures.
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Affiliation(s)
- Nicole M Hoitsma
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Amy M Whitaker
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Matthew A Schaich
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Mallory R Smith
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Max S Fairlamb
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
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33
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Garbacz MA, Cox PB, Sharma S, Lujan SA, Chabes A, Kunkel TA. The absence of the catalytic domains of Saccharomyces cerevisiae DNA polymerase ϵ strongly reduces DNA replication fidelity. Nucleic Acids Res 2019; 47:3986-3995. [PMID: 30698744 DOI: 10.1093/nar/gkz048] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/15/2019] [Accepted: 01/23/2019] [Indexed: 11/13/2022] Open
Abstract
The four B-family DNA polymerases α, δ, ϵ and ζ cooperate to accurately replicate the eukaryotic nuclear genome. Here, we report that a Saccharomyces cerevisiae strain encoding the pol2-16 mutation that lacks Pol ϵ's polymerase and exonuclease activities has increased dNTP concentrations and an increased mutation rate at the CAN1 locus compared to wild type yeast. About half of this mutagenesis disappears upon deleting the REV3 gene encoding the catalytic subunit of Pol ζ. The remaining, still strong, mutator phenotype is synergistically elevated in an msh6Δ strain and has a mutation spectrum characteristic of mistakes made by Pol δ. The results support a model wherein slow-moving replication forks caused by the lack of Pol ϵ's catalytic domains result in greater involvement of mutagenic DNA synthesis by Pol ζ as well as diminished proofreading by Pol δ during replication.
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Affiliation(s)
- Marta A Garbacz
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA
| | - Phillip B Cox
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA
| | - Sushma Sharma
- Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
| | - Scott A Lujan
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA
| | - Andrei Chabes
- Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
| | - Thomas A Kunkel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA
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34
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Chojnacki M, Melendy T. The human papillomavirus DNA helicase E1 binds, stimulates, and confers processivity to cellular DNA polymerase epsilon. Nucleic Acids Res 2019; 46:229-241. [PMID: 29155954 PMCID: PMC5758917 DOI: 10.1093/nar/gkx1103] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/24/2017] [Indexed: 12/31/2022] Open
Abstract
The papillomavirus (PV) helicase protein E1 recruits components of the cellular DNA replication machinery to the PV replication fork, such as Replication Protein A (RPA), DNA polymerase α-primase (pol α) and topoisomerase I (topo I). Here we show that E1 binds to DNA polymerase ϵ (pol ϵ) and dramatically stimulates the DNA synthesis activity of pol ϵ. This stimulation of pol ϵ by E1 is highly specific and occurs even in the absence of the known pol ϵ cofactors Replication Factor C (RFC), Proliferating Cell Nuclear Antigen (PCNA) and RPA. This stimulation is due to an increase in the processivity of pol ϵ and occurs independently of pol ϵ’s replication cofactors. This increase in processivity is dependent on the ability of the E1 helicase to hydrolyze ATP, suggesting it is dependent on E1’s helicase action. In addition, RPA, thought to be vital for processive DNA synthesis by both pol ϵ and pol δ, was found to be dispensable for processive synthesis by pol ϵ in the presence of E1. Overall, E1 appears to be conferring processivity to pol ϵ by directly tethering pol ϵ to the DNA parental strand and towing ϵ behind the E1 helicase as the replication fork progresses; and thereby apparently obviating the need for RPA for leading strand synthesis. Thus far only pol α and pol δ have been implicated in the DNA replication of mammalian viruses; this is the first reported example of a virus recruiting pol ϵ. Furthermore, this demonstrates a unique capacity of a viral helicase having evolved to stimulate a cellular replicative DNA polymerase.
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Affiliation(s)
- Michaelle Chojnacki
- Departments of Microbiology & Immunology and Biochemistry, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, Buffalo, NY 14214, USA
| | - Thomas Melendy
- Departments of Microbiology & Immunology and Biochemistry, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, Buffalo, NY 14214, USA
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35
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Hizume K, Araki H. Replication fork pausing at protein barriers on chromosomes. FEBS Lett 2019; 593:1449-1458. [PMID: 31199500 DOI: 10.1002/1873-3468.13481] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 06/07/2019] [Accepted: 06/10/2019] [Indexed: 12/16/2022]
Abstract
When a cell divides prior to completion of DNA replication, serious DNA damage may occur. Thus, in addition to accuracy, the processivity of the replication forks is important. DNA synthesis at replication forks should be completed in time, and forks overcome aberrant structures on the template DNA, including damaged sites, using trans-lesion synthesis, occasionally introducing mutations. By contrast, the protein barrier built on the DNA is known to block the progression of replication forks at specific chromosomal loci. Such protein barriers avert any collision of replication and transcription machineries, or control the recombination of specific loci. The components and the mechanisms of action of protein barriers have been revealed mainly using genetic and biochemical techniques. In addition to proteins involved in replication fork pausing, the interaction of the replicative helicase and DNA polymerase is also essential for replication fork pausing. Here, we provide an overview of replication fork pausing at protein barriers.
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Affiliation(s)
- Kohji Hizume
- Division of RI Laboratory, Biomedical Research Center, Saitama Medical University, Japan
| | - Hiroyuki Araki
- Microbial Genetics Laboratory, National Institute of Genetics, Mishima, Japan.,Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
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36
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Park VS, Pursell ZF. POLE proofreading defects: Contributions to mutagenesis and cancer. DNA Repair (Amst) 2019; 76:50-59. [PMID: 30818169 PMCID: PMC6467506 DOI: 10.1016/j.dnarep.2019.02.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 12/14/2022]
Abstract
DNA polymerases are uniquely poised to contribute to the elevated mutation burdens seen in many human tumors. These mutations can arise through a number of different polymerase-dependent mechanisms, including intrinsic errors made using template DNA and precursor dNTPs free from chemical modifications, misinsertion events opposite chemically damaged template DNA or insertion events using modified nucleotides. While specific DNA repair polymerases have been known to contribute to tumorigenesis, the role of replication polymerases in mutagenesis in human disease has come into sharp focus over the last decade. This review describes how mutations in these replication DNA polymerases help to drive mutagenesis and tumor development, with particular attention to DNA polymerase epsilon. Recent studies using cancer genome sequencing, mutational signature analyses, yeast and mouse models, and the influence of mismatch repair on tumors with DNA polymerase mutations are discussed.
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Affiliation(s)
- Vivian S Park
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Zachary F Pursell
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA; Tulane Cancer Center, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA, USA.
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37
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Villa-Hernández S, Bermejo R. Replisome-Cohesin Interfacing: A Molecular Perspective. Bioessays 2018; 40:e1800109. [PMID: 30106480 DOI: 10.1002/bies.201800109] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/23/2018] [Indexed: 12/27/2022]
Abstract
Cohesion is established in S-phase through the action of key replisome factors as replication forks engage cohesin molecules. By holding sister chromatids together, cohesion critically assists both an equal segregation of the duplicated genetic material and an efficient repair of DNA breaks. Nonetheless, the molecular events leading the entrapment of nascent chromatids by cohesin during replication are only beginning to be understood. The authors describe here the essential structural features of the cohesin complex in connection to its ability to associate DNA molecules and review the current knowledge on the architectural-functional organization of the eukaryotic replisome, significantly advanced by recent biochemical and structural studies. In light of this novel insight, the authors discuss the mechanisms proposed to assist interfacing of replisomes with chromatin-bound cohesin complexes and elaborate on models for nascent chromatids entrapment by cohesin in the environment of the replication fork.
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Affiliation(s)
- Sara Villa-Hernández
- Centro de Investigaciones Biológicas (CIB-CSIC), Calle Ramiro de Maeztu 928040 Madrid, Spain
| | - Rodrigo Bermejo
- Centro de Investigaciones Biológicas (CIB-CSIC), Calle Ramiro de Maeztu 928040 Madrid, Spain
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38
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Ohashi E, Tsurimoto T. Functions of Multiple Clamp and Clamp-Loader Complexes in Eukaryotic DNA Replication. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1042:135-162. [PMID: 29357057 DOI: 10.1007/978-981-10-6955-0_7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Proliferating cell nuclear antigen (PCNA) and replication factor C (RFC) were identified in the late 1980s as essential factors for replication of simian virus 40 DNA in human cells, by reconstitution of the reaction in vitro. Initially, they were only thought to be involved in the elongation stage of DNA replication. Subsequent studies have demonstrated that PCNA functions as more than a replication factor, through its involvement in multiple protein-protein interactions. PCNA appears as a functional hub on replicating and replicated chromosomal DNA and has an essential role in the maintenance genome integrity in proliferating cells.Eukaryotes have multiple paralogues of sliding clamp, PCNA and its loader, RFC. The PCNA paralogues, RAD9, HUS1, and RAD1 form the heterotrimeric 9-1-1 ring that is similar to the PCNA homotrimeric ring, and the 9-1-1 clamp complex is loaded onto sites of DNA damage by its specific loader RAD17-RFC. This alternative clamp-loader system transmits DNA-damage signals in genomic DNA to the checkpoint-activation network and the DNA-repair apparatus.Another two alternative loader complexes, CTF18-RFC and ELG1-RFC, have roles that are distinguishable from the role of the canonical loader, RFC. CTF18-RFC interacts with one of the replicative DNA polymerases, Polε, and loads PCNA onto leading-strand DNA, and ELG1-RFC unloads PCNA after ligation of lagging-strand DNA. In the progression of S phase, these alternative PCNA loaders maintain appropriate amounts of PCNA on the replicating sister DNAs to ensure that specific enzymes are tethered at specific chromosomal locations.
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Affiliation(s)
- Eiji Ohashi
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Toshiki Tsurimoto
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan.
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39
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Garbacz MA, Lujan SA, Burkholder AB, Cox PB, Wu Q, Zhou ZX, Haber JE, Kunkel TA. Evidence that DNA polymerase δ contributes to initiating leading strand DNA replication in Saccharomyces cerevisiae. Nat Commun 2018; 9:858. [PMID: 29487291 PMCID: PMC5829166 DOI: 10.1038/s41467-018-03270-4] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 02/01/2018] [Indexed: 01/01/2023] Open
Abstract
To investigate nuclear DNA replication enzymology in vivo, we have studied Saccharomyces cerevisiae strains containing a pol2-16 mutation that inactivates the catalytic activities of DNA polymerase ε (Pol ε). Although pol2-16 mutants survive, they present very tiny spore colonies, increased doubling time, larger than normal cells, aberrant nuclei, and rapid acquisition of suppressor mutations. These phenotypes reveal a severe growth defect that is distinct from that of strains that lack only Pol ε proofreading (pol2-4), consistent with the idea that Pol ε is the major leading-strand polymerase used for unstressed DNA replication. Ribonucleotides are incorporated into the pol2-16 genome in patterns consistent with leading-strand replication by Pol δ when Pol ε is absent. More importantly, ribonucleotide distributions at replication origins suggest that in strains encoding all three replicases, Pol δ contributes to initiation of leading-strand replication. We describe two possible models. DNA polymerases δ and ε (Pols δ and ε) are thought to be responsible for lagging and leading strand synthesis, respectively. Here the authors present evidence that Pol δ contributes to the initiation of leading strand replication in budding yeast by synthesizing DNA of both strands at replication origins.
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Affiliation(s)
- Marta A Garbacz
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, Durham, NC, 27709, USA
| | - Scott A Lujan
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, Durham, NC, 27709, USA
| | - Adam B Burkholder
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, Durham, NC, 27709, USA
| | - Phillip B Cox
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, Durham, NC, 27709, USA
| | - Qiuqin Wu
- Department of Biology, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, 02454, USA
| | - Zhi-Xiong Zhou
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, Durham, NC, 27709, USA
| | - James E Haber
- Department of Biology, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, 02454, USA
| | - Thomas A Kunkel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, Durham, NC, 27709, USA.
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40
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Scherr MJ, Safaric B, Duderstadt KE. Noise in the Machine: Alternative Pathway Sampling is the Rule During DNA Replication. Bioessays 2017; 40. [PMID: 29282758 DOI: 10.1002/bies.201700159] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 12/01/2017] [Indexed: 11/07/2022]
Abstract
The astonishing efficiency and accuracy of DNA replication has long suggested that refined rules enforce a single highly reproducible sequence of molecular events during the process. This view was solidified by early demonstrations that DNA unwinding and synthesis are coupled within a stable molecular factory, known as the replisome, which consists of conserved components that each play unique and complementary roles. However, recent single-molecule observations of replisome dynamics have begun to challenge this view, revealing that replication may not be defined by a uniform sequence of events. Instead, multiple exchange pathways, pauses, and DNA loop types appear to dominate replisome function. These observations suggest we must rethink our fundamental assumptions and acknowledge that each replication cycle may involve sampling of alternative, sometimes parallel, pathways. Here, we review our current mechanistic understanding of DNA replication while highlighting findings that exemplify multi-pathway aspects of replisome function and considering the broader implications.
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Affiliation(s)
- Matthias J Scherr
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Barbara Safaric
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Karl E Duderstadt
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany.,Physik Department, Technische Universität München, Garching, Germany
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41
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Miyazawa-Onami M, Araki H, Tanaka S. Pre-initiation complex assembly functions as a molecular switch that splits the Mcm2-7 double hexamer. EMBO Rep 2017; 18:1752-1761. [PMID: 28818838 DOI: 10.15252/embr.201744206] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 07/19/2017] [Accepted: 07/21/2017] [Indexed: 11/09/2022] Open
Abstract
Initiation of chromosomal DNA replication in eukaryotes involves two steps: licensing and firing. In licensing, a core component of the replicative helicase, the Mcm2-7 complex, is loaded onto replication origins as an inactive double hexamer, which is activated in the firing step by firing factors. A reaction intermediate called the pre-initiation complex (pre-IC) has been proposed to assemble transiently during firing, but the existence of the pre-IC has not yet been confirmed. Here, we show, by systematic chromatin immunoprecipitation, that a distinct intermediate that fits the definition of the pre-IC assembles during firing in the budding yeast Saccharomyces cerevisiae Pre-IC assembly is observed in the absence of Mcm10, one of the firing factors, and is mutually dependent on all the firing factors whose association to replication origins is triggered by cyclin-dependent kinase. In the pre-IC, the Mcm2-7 double hexamer is separated into single hexamers, as in the active helicase. Our data indicate that pre-IC assembly functions as an all-or-nothing molecular switch that splits the Mcm2-7 double hexamer.
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Affiliation(s)
- Mayumi Miyazawa-Onami
- Division of Microbial Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Hiroyuki Araki
- Division of Microbial Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan.,Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan
| | - Seiji Tanaka
- Division of Microbial Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan .,Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan.,School of Environmental Science and Engineering, Kochi University of Technology, Kami, Kochi, Japan
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42
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Abstract
The instability of microsatellite DNA repeats is responsible for at least 40 neurodegenerative diseases. Recently, Mirkin and co-workers presented a novel mechanism for microsatellite expansions based on break-induced replication (BIR) at sites of microsatellite-induced replication stalling and fork collapse. The BIR model aims to explain single-step, large expansions of CAG/CTG trinucleotide repeats in dividing cells. BIR has been characterized extensively in Saccharomyces cerevisiae as a mechanism to repair broken DNA replication forks (single-ended DSBs) and degraded telomeric DNA. However, the structural footprints of BIR-like DSB repair have been recognized in human genomic instability and tied to the etiology of diverse developmental diseases; thus, the implications of the paper by Kim et al. (Kim JC, Harris ST, Dinter T, Shah KA, et al., Nat Struct Mol Biol 24: 55-60) extend beyond trinucleotide repeat expansion in yeast and microsatellite instability in human neurological disorders. Significantly, insight into BIR-like repair can explain certain pathways of complex genome rearrangements (CGRs) initiated at non-B form microsatellite DNA in human cancers.
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Affiliation(s)
- Michael Leffak
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH, USA
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43
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Abstract
The accurate and complete replication of genomic DNA is essential for all life. In eukaryotic cells, the assembly of the multi-enzyme replisomes that perform replication is divided into stages that occur at distinct phases of the cell cycle. Replicative DNA helicases are loaded around origins of DNA replication exclusively during G1 phase. The loaded helicases are then activated during S phase and associate with the replicative DNA polymerases and other accessory proteins. The function of the resulting replisomes is monitored by checkpoint proteins that protect arrested replisomes and inhibit new initiation when replication is inhibited. The replisome also coordinates nucleosome disassembly, assembly, and the establishment of sister chromatid cohesion. Finally, when two replisomes converge they are disassembled. Studies in Saccharomyces cerevisiae have led the way in our understanding of these processes. Here, we review our increasingly molecular understanding of these events and their regulation.
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44
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Yurieva O, O'Donnell M. Reconstitution of a eukaryotic replisome reveals the mechanism of asymmetric distribution of DNA polymerases. Nucleus 2017; 7:360-8. [PMID: 27416113 PMCID: PMC5039002 DOI: 10.1080/19491034.2016.1205774] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Eukaryotes require 3 DNA polymerases for normal replisome operations, DNA polymerases (Pol) α, delta and epsilon. Recent biochemical and structural studies support the asymmetric use of these polymerases on the leading and lagging strands. Pol epsilon interacts with the 11-subunit CMG helicase, forming a 15-protein leading strand complex that acts processively in leading strand synthesis in vitro, but Pol epsilon is inactive on the lagging strand. The opposite results are observed for Pol delta with CMG. Pol delta is highly active on the lagging strand in vitro, but has only feeble activity with CMG on the leading strand. Pol α also functions with CMG to prime both strands, and is even capable of extending both strands with CMG present. However, extensive DNA synthesis by Pol α is sharply curtailed by the presence of either Pol epsilon or Pol delta, which limits the role of the low fidelity Pol α to the initial priming of synthesis.
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Affiliation(s)
- Olga Yurieva
- a Howard Hughes Medical Institute and DNA Replication Laboratory, The Rockefeller University , New York , NY , USA
| | - Mike O'Donnell
- a Howard Hughes Medical Institute and DNA Replication Laboratory, The Rockefeller University , New York , NY , USA
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45
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Sun J, Yuan Z, Georgescu R, Li H, O'Donnell M. The eukaryotic CMG helicase pumpjack and integration into the replisome. Nucleus 2017; 7:146-54. [PMID: 27310307 PMCID: PMC4916876 DOI: 10.1080/19491034.2016.1174800] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The eukaryotic replisome is α multiprotein machine that contains DNA polymerases, sliding clamps, helicase, and primase along with several factors that participate in cell cycle and checkpoint control. The detailed structure of the 11-subunit CMG helicase (Cdc45/Mcm2-7/GINS) has been solved recently by cryoEM single-particle 3D reconstruction and reveals pumpjack motions that imply an unexpected mechanism of DNA translocation. CMG is also the organizing center of the replisome. Recent in vitro reconstitution of leading and lagging strand DNA synthesis has enabled structural analysis of the replisome. By building the replisome in stages from pure proteins, single-particle EM studies have identified the overall architecture of the eukaryotic replisome. Suprisingly leading and lagging strand polymerases bind to opposite faces of the CMG helicase, unlike the long-held view that DNA polymerases are located in back of the helicase to act on the unwound strands.
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Affiliation(s)
- Jingchuan Sun
- a Biology Department , Brookhaven National Laboratory , Upton , NY , USA
| | - Zuanning Yuan
- b Department of Biochemistry & Cell Biology , Stony Brook University , Stony Brook , NY , USA
| | - Roxanna Georgescu
- c Howard Hughes Medical Institute and the DNA Replication Laboratory , The Rockefeller University , New York , NY , USA
| | - Huilin Li
- a Biology Department , Brookhaven National Laboratory , Upton , NY , USA.,b Department of Biochemistry & Cell Biology , Stony Brook University , Stony Brook , NY , USA
| | - Mike O'Donnell
- c Howard Hughes Medical Institute and the DNA Replication Laboratory , The Rockefeller University , New York , NY , USA
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46
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Daigaku Y, Etheridge TJ, Nakazawa Y, Nakayama M, Watson AT, Miyabe I, Ogi T, Osborne MA, Carr AM. PCNA ubiquitylation ensures timely completion of unperturbed DNA replication in fission yeast. PLoS Genet 2017; 13:e1006789. [PMID: 28481910 PMCID: PMC5440044 DOI: 10.1371/journal.pgen.1006789] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 05/22/2017] [Accepted: 05/01/2017] [Indexed: 11/18/2022] Open
Abstract
PCNA ubiquitylation on lysine 164 is required for DNA damage tolerance. In many organisms PCNA is also ubiquitylated in unchallenged S phase but the significance of this has not been established. Using Schizosaccharomyces pombe, we demonstrate that lysine 164 ubiquitylation of PCNA contributes to efficient DNA replication in the absence of DNA damage. Loss of PCNA ubiquitylation manifests most strongly at late replicating regions and increases the frequency of replication gaps. We show that PCNA ubiquitylation increases the proportion of chromatin associated PCNA and the co-immunoprecipitation of Polymerase δ with PCNA during unperturbed replication and propose that ubiquitylation acts to prolong the chromatin association of these replication proteins to allow the efficient completion of Okazaki fragment synthesis by mediating gap filling. PCNA is a homotrimeric complex that clamps around the DNA to provide a sliding platform for DNA polymerases and other replication and repair enzymes. The covalent modification of PCNA by ubiquitin on lysine reside 164 has been extensively studied in the context of DNA repair: it is required to mediate the bypass of damaged template bases during DNA replication. Previous work has shown that PCNA is modified by ubiquitin during normal S phase in the absence of DNA damage, but the significance of this modification has not been explored. Here we show that, in addition to regulating bypass of damaged bases, lysine 164 ubiquitylation plays a role in ensuring the completion of unperturbed DNA replication.
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Affiliation(s)
- Yasukazu Daigaku
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, United Kingdom
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
- * E-mail: (AMC); (YD)
| | - Thomas J. Etheridge
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, United Kingdom
| | - Yuka Nakazawa
- Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Mayumi Nakayama
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, Japan
| | - Adam T. Watson
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, United Kingdom
| | - Izumi Miyabe
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, United Kingdom
| | - Tomoo Ogi
- Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
- Department of Genome Repair, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Mark A. Osborne
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, United Kingdom
| | - Antony M. Carr
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, United Kingdom
- * E-mail: (AMC); (YD)
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47
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McVey M, Khodaverdian VY, Meyer D, Cerqueira PG, Heyer WD. Eukaryotic DNA Polymerases in Homologous Recombination. Annu Rev Genet 2017; 50:393-421. [PMID: 27893960 DOI: 10.1146/annurev-genet-120215-035243] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Homologous recombination (HR) is a central process to ensure genomic stability in somatic cells and during meiosis. HR-associated DNA synthesis determines in large part the fidelity of the process. A number of recent studies have demonstrated that DNA synthesis during HR is conservative, less processive, and more mutagenic than replicative DNA synthesis. In this review, we describe mechanistic features of DNA synthesis during different types of HR-mediated DNA repair, including synthesis-dependent strand annealing, break-induced replication, and meiotic recombination. We highlight recent findings from diverse eukaryotic organisms, including humans, that suggest both replicative and translesion DNA polymerases are involved in HR-associated DNA synthesis. Our focus is to integrate the emerging literature about DNA polymerase involvement during HR with the unique aspects of these repair mechanisms, including mutagenesis and template switching.
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Affiliation(s)
- Mitch McVey
- Department of Biology, Tufts University, Medford, Massachusetts 02155;
| | | | - Damon Meyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, California 95616; .,College of Health Sciences, California Northstate University, Rancho Cordova, California 95670
| | - Paula Gonçalves Cerqueira
- Department of Microbiology and Molecular Genetics, University of California, Davis, California 95616;
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, California 95616; .,Department of Molecular and Cellular Biology, University of California, Davis, California 95616
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48
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Zhou JC, Janska A, Goswami P, Renault L, Abid Ali F, Kotecha A, Diffley JFX, Costa A. CMG-Pol epsilon dynamics suggests a mechanism for the establishment of leading-strand synthesis in the eukaryotic replisome. Proc Natl Acad Sci U S A 2017; 114:4141-4146. [PMID: 28373564 PMCID: PMC5402455 DOI: 10.1073/pnas.1700530114] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The replisome unwinds and synthesizes DNA for genome duplication. In eukaryotes, the Cdc45-MCM-GINS (CMG) helicase and the leading-strand polymerase, Pol epsilon, form a stable assembly. The mechanism for coupling DNA unwinding with synthesis is starting to be elucidated, however the architecture and dynamics of the replication fork remain only partially understood, preventing a molecular understanding of chromosome replication. To address this issue, we conducted a systematic single-particle EM study on multiple permutations of the reconstituted CMG-Pol epsilon assembly. Pol epsilon contains two flexibly tethered lobes. The noncatalytic lobe is anchored to the motor of the helicase, whereas the polymerization domain extends toward the side of the helicase. We observe two alternate configurations of the DNA synthesis domain in the CMG-bound Pol epsilon. We propose that this conformational switch might control DNA template engagement and release, modulating replisome progression.
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Affiliation(s)
- Jin Chuan Zhou
- Macromolecular Machines Laboratory, The Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Agnieszka Janska
- Chromosome Replication Laboratory, The Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Panchali Goswami
- Macromolecular Machines Laboratory, The Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Ludovic Renault
- Macromolecular Machines Laboratory, The Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Ferdos Abid Ali
- Macromolecular Machines Laboratory, The Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Abhay Kotecha
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - John F X Diffley
- Chromosome Replication Laboratory, The Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Alessandro Costa
- Macromolecular Machines Laboratory, The Francis Crick Institute, London, NW1 1AT, United Kingdom;
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49
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Abstract
This review focuses on the biogenesis and composition of the eukaryotic DNA replication fork, with an emphasis on the enzymes that synthesize DNA and repair discontinuities on the lagging strand of the replication fork. Physical and genetic methodologies aimed at understanding these processes are discussed. The preponderance of evidence supports a model in which DNA polymerase ε (Pol ε) carries out the bulk of leading strand DNA synthesis at an undisturbed replication fork. DNA polymerases α and δ carry out the initiation of Okazaki fragment synthesis and its elongation and maturation, respectively. This review also discusses alternative proposals, including cellular processes during which alternative forks may be utilized, and new biochemical studies with purified proteins that are aimed at reconstituting leading and lagging strand DNA synthesis separately and as an integrated replication fork.
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Affiliation(s)
- Peter M J Burgers
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110;
| | - Thomas A Kunkel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709;
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50
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Dmowski M, Rudzka J, Campbell JL, Jonczyk P, Fijałkowska IJ. Mutations in the Non-Catalytic Subunit Dpb2 of DNA Polymerase Epsilon Affect the Nrm1 Branch of the DNA Replication Checkpoint. PLoS Genet 2017; 13:e1006572. [PMID: 28107343 PMCID: PMC5291541 DOI: 10.1371/journal.pgen.1006572] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 02/03/2017] [Accepted: 01/05/2017] [Indexed: 12/14/2022] Open
Abstract
To preserve genome integrity, the S-phase checkpoint senses damaged DNA or nucleotide depletion and when necessary, arrests replication progression and delays cell division. Previous studies, based on two pol2 mutants have suggested the involvement of DNA polymerase epsilon (Pol ε) in sensing DNA replication accuracy in Saccharomyces cerevisiae. Here we have studied the involvement of Pol ε in sensing proper progression of DNA replication, using a mutant in DPB2, the gene coding for a non-catalytic subunit of Pol ε. Under genotoxic conditions, the dpb2-103 cells progress through S phase faster than wild-type cells. Moreover, the Nrm1-dependent branch of the checkpoint, which regulates the expression of many replication checkpoint genes, is impaired in dpb2-103 cells. Finally, deletion of DDC1 in the dpb2-103 mutant is lethal supporting a model of strand-specific activation of the replication checkpoint. This lethality is suppressed by NRM1 deletion. We postulate that improper activation of the Nrm1-branch may explain inefficient replication checkpoint activation in Pol ε mutants. The viability of living organisms depends on the integrity of their genomes. Each cell has to constantly monitor DNA replication and coordinate it with cell division to avoid genomic instability. This is achieved through pathways known as cell cycle checkpoints. Therefore, upon replication perturbation, DNA synthesis slows down and cell division is delayed. For that, a specific signal is induced and propagated through a mechanism that have already been identified but still need investigations. We have isolated a mutated form of Dpb2, the essential subunit of DNA polymerase epsilon (Pol ε) holoenzyme. This mutated form of Pol ε impairs proper activation of the cellular response to replication stress. We show that yeast cells with mutations in the DPB2 gene fail to activate the Nrm1-regulated branch of the checkpoint, which controls numerous genes expressed in response to replication stress. Moreover, our results support the model of parallel activation of replication checkpoint from the leading and lagging DNA strands. This strongly suggests that Pol ε, the leading strand replicase, is involved in replication checkpoint activation from this strand. Our results contribute to the understanding of mechanisms of cellular response to replication stress, which are necessary to preserve genome stability.
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Affiliation(s)
- Michał Dmowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences Pawińskiego 5a, Warsaw, POLAND
- * E-mail:
| | - Justyna Rudzka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences Pawińskiego 5a, Warsaw, POLAND
| | - Judith L. Campbell
- Braun Laboratories, California Institute of Technology, Pasadena, CA, United States of America
| | - Piotr Jonczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences Pawińskiego 5a, Warsaw, POLAND
| | - Iwona J. Fijałkowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences Pawińskiego 5a, Warsaw, POLAND
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