1
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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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2
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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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3
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Bulock CR, Xing X, Shcherbakova PV. Mismatch repair and DNA polymerase δ proofreading prevent catastrophic accumulation of leading strand errors in cells expressing a cancer-associated DNA polymerase ϵ variant. Nucleic Acids Res 2020; 48:9124-9134. [PMID: 32756902 PMCID: PMC7498342 DOI: 10.1093/nar/gkaa633] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 07/13/2020] [Accepted: 07/27/2020] [Indexed: 12/15/2022] Open
Abstract
Substitutions in the exonuclease domain of DNA polymerase ϵ cause ultramutated human tumors. Yeast and mouse mimics of the most common variant, P286R, produce mutator effects far exceeding the effect of Polϵ exonuclease deficiency. Yeast Polϵ-P301R has increased DNA polymerase activity, which could underlie its high mutagenicity. We aimed to understand the impact of this increased activity on the strand-specific role of Polϵ in DNA replication and the action of extrinsic correction systems that remove Polϵ errors. Using mutagenesis reporters spanning a well-defined replicon, we show that both exonuclease-deficient Polϵ (Polϵ-exo−) and Polϵ-P301R generate mutations in a strictly strand-specific manner, yet Polϵ-P301R is at least ten times more mutagenic than Polϵ-exo− at each location analyzed. Thus, the cancer variant remains a dedicated leading-strand polymerase with markedly low accuracy. We further show that P301R substitution is lethal in strains lacking Polδ proofreading or mismatch repair (MMR). Heterozygosity for pol2-P301R is compatible with either defect but causes strong synergistic increases in the mutation rate, indicating that Polϵ-P301R errors are corrected by Polδ proofreading and MMR. These data reveal the unexpected ease with which polymerase exchange occurs in vivo, allowing Polδ exonuclease to prevent catastrophic accumulation of Polϵ-P301R-generated errors on the leading strand.
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Affiliation(s)
- Chelsea R Bulock
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Xuanxuan Xing
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Polina V Shcherbakova
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
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Estep KN, Butler TJ, Ding J, Brosh RM. G4-Interacting DNA Helicases and Polymerases: Potential Therapeutic Targets. Curr Med Chem 2019; 26:2881-2897. [PMID: 29149833 DOI: 10.2174/0929867324666171116123345] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 10/16/2017] [Accepted: 10/16/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND Guanine-rich DNA can fold into highly stable four-stranded DNA structures called G-quadruplexes (G4). In recent years, the G-quadruplex field has blossomed as new evidence strongly suggests that such alternately folded DNA structures are likely to exist in vivo. G4 DNA presents obstacles for the replication machinery, and both eukaryotic DNA helicases and polymerases have evolved to resolve and copy G4 DNA in vivo. In addition, G4-forming sequences are prevalent in gene promoters, suggesting that G4-resolving helicases act to modulate transcription. METHODS We have searched the PubMed database to compile an up-to-date and comprehensive assessment of the field's current knowledge to provide an overview of the molecular interactions of Gquadruplexes with DNA helicases and polymerases implicated in their resolution. RESULTS Novel computational tools and alternative strategies have emerged to detect G4-forming sequences and assess their biological consequences. Specialized DNA helicases and polymerases catalytically act upon G4-forming sequences to maintain normal replication and genomic stability as well as appropriate gene regulation and cellular homeostasis. G4 helicases also resolve telomeric repeats to maintain chromosomal DNA ends. Bypass of many G4-forming sequences is achieved by the action of translesion DNS polymerases or the PrimPol DNA polymerase. While the collective work has supported a role of G4 in nuclear DNA metabolism, an emerging field centers on G4 abundance in the mitochondrial genome. CONCLUSION Discovery of small molecules that specifically bind and modulate DNA helicases and polymerases or interact with the G4 DNA structure itself may be useful for the development of anticancer regimes.
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Affiliation(s)
- Katrina N Estep
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, 251 Bayview Blvd Baltimore, MD 21224, United States
| | - Thomas J Butler
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, 251 Bayview Blvd Baltimore, MD 21224, United States
| | - Jun Ding
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, 251 Bayview Blvd Baltimore, MD 21224, United States
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, 251 Bayview Blvd Baltimore, MD 21224, United States
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Hedglin M, Benkovic SJ. Eukaryotic Translesion DNA Synthesis on the Leading and Lagging Strands: Unique Detours around the Same Obstacle. Chem Rev 2017; 117:7857-7877. [PMID: 28497687 PMCID: PMC5662946 DOI: 10.1021/acs.chemrev.7b00046] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
During S-phase, minor DNA damage may be overcome by DNA damage tolerance (DDT) pathways that bypass such obstacles, postponing repair of the offending damage to complete the cell cycle and maintain cell survival. In translesion DNA synthesis (TLS), specialized DNA polymerases replicate the damaged DNA, allowing stringent DNA synthesis by a replicative polymerase to resume beyond the offending damage. Dysregulation of this DDT pathway in human cells leads to increased mutation rates that may contribute to the onset of cancer. Furthermore, TLS affords human cancer cells the ability to counteract chemotherapeutic agents that elicit cell death by damaging DNA in actively replicating cells. Currently, it is unclear how this critical pathway unfolds, in particular, where and when TLS occurs on each template strand. Given the semidiscontinuous nature of DNA replication, it is likely that TLS on the leading and lagging strand templates is unique for each strand. Since the discovery of DDT in the late 1960s, most studies on TLS in eukaryotes have focused on DNA lesions resulting from ultraviolet (UV) radiation exposure. In this review, we revisit these and other related studies to dissect the step-by-step intricacies of this complex process, provide our current understanding of TLS on leading and lagging strand templates, and propose testable hypotheses to gain further insights.
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Affiliation(s)
- Mark Hedglin
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Stephen J. Benkovic
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, U.S.A
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Lujan SA, Williams JS, Kunkel TA. Eukaryotic genome instability in light of asymmetric DNA replication. Crit Rev Biochem Mol Biol 2015; 51:43-52. [PMID: 26822554 DOI: 10.3109/10409238.2015.1117055] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The eukaryotic nuclear genome is replicated asymmetrically, with the leading strand replicated continuously and the lagging strand replicated as discontinuous Okazaki fragments that are subsequently joined. Both strands are replicated with high fidelity, but the processes used to achieve high fidelity are likely to differ. Here we review recent studies of similarities and differences in the fidelity with which the three major eukaryotic replicases, DNA polymerases α, δ, and ɛ, replicate the leading and lagging strands with high nucleotide selectivity and efficient proofreading. We then relate the asymmetric fidelity at the replication fork to the efficiency of DNA mismatch repair, ribonucleotide excision repair and topoisomerase 1 activity.
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Affiliation(s)
- Scott A Lujan
- a Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences , Research Triangle Park , NC , USA
| | - Jessica S Williams
- a Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences , Research Triangle Park , NC , USA
| | - Thomas A Kunkel
- a Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences , Research Triangle Park , NC , USA
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7
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Skoneczna A, Kaniak A, Skoneczny M. Genetic instability in budding and fission yeast-sources and mechanisms. FEMS Microbiol Rev 2015; 39:917-67. [PMID: 26109598 PMCID: PMC4608483 DOI: 10.1093/femsre/fuv028] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2015] [Indexed: 12/17/2022] Open
Abstract
Cells are constantly confronted with endogenous and exogenous factors that affect their genomes. Eons of evolution have allowed the cellular mechanisms responsible for preserving the genome to adjust for achieving contradictory objectives: to maintain the genome unchanged and to acquire mutations that allow adaptation to environmental changes. One evolutionary mechanism that has been refined for survival is genetic variation. In this review, we describe the mechanisms responsible for two biological processes: genome maintenance and mutation tolerance involved in generations of genetic variations in mitotic cells of both Saccharomyces cerevisiae and Schizosaccharomyces pombe. These processes encompass mechanisms that ensure the fidelity of replication, DNA lesion sensing and DNA damage response pathways, as well as mechanisms that ensure precision in chromosome segregation during cell division. We discuss various factors that may influence genome stability, such as cellular ploidy, the phase of the cell cycle, transcriptional activity of a particular region of DNA, the proficiency of DNA quality control systems, the metabolic stage of the cell and its respiratory potential, and finally potential exposure to endogenous or environmental stress. The stability of budding and fission yeast genomes is influenced by two contradictory factors: (1) the need to be fully functional, which is ensured through the replication fidelity pathways of nuclear and mitochondrial genomes through sensing and repairing DNA damage, through precise chromosome segregation during cell division; and (2) the need to acquire changes for adaptation to environmental challenges.
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Affiliation(s)
- Adrianna Skoneczna
- Laboratory of Mutagenesis and DNA Repair, Institute of Biochemistry and Biophysics, Polish Academy of Science, 02-106 Warsaw, Poland
| | - Aneta Kaniak
- Laboratory of Mutagenesis and DNA Repair, Institute of Biochemistry and Biophysics, Polish Academy of Science, 02-106 Warsaw, Poland
| | - Marek Skoneczny
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Science, 02-106 Warsaw, Poland
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8
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Replicative DNA polymerase δ but not ε proofreads errors in Cis and in Trans. PLoS Genet 2015; 11:e1005049. [PMID: 25742645 PMCID: PMC4351087 DOI: 10.1371/journal.pgen.1005049] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 02/02/2015] [Indexed: 01/18/2023] Open
Abstract
It is now well established that in yeast, and likely most eukaryotic organisms, initial DNA replication of the leading strand is by DNA polymerase ε and of the lagging strand by DNA polymerase δ. However, the role of Pol δ in replication of the leading strand is uncertain. In this work, we use a reporter system in Saccharomyces cerevisiae to measure mutation rates at specific base pairs in order to determine the effect of heterozygous or homozygous proofreading-defective mutants of either Pol ε or Pol δ in diploid strains. We find that wild-type Pol ε molecules cannot proofread errors created by proofreading-defective Pol ε molecules, whereas Pol δ can not only proofread errors created by proofreading-defective Pol δ molecules, but can also proofread errors created by Pol ε-defective molecules. These results suggest that any interruption in DNA synthesis on the leading strand is likely to result in completion by Pol δ and also explain the higher mutation rates observed in Pol δ-proofreading mutants compared to Pol ε-proofreading defective mutants. For strains reverting via AT→GC, TA→GC, CG→AT, and GC→AT mutations, we find in addition a strong effect of gene orientation on mutation rate in proofreading-defective strains and demonstrate that much of this orientation dependence is due to differential efficiencies of mispair elongation. We also find that a 3′-terminal 8 oxoG, unlike a 3′-terminal G, is efficiently extended opposite an A and is not subject to proofreading. Proofreading mutations have been shown to result in tumor formation in both mice and humans; the results presented here can help explain the properties exhibited by those proofreading mutants. Many DNA polymerases are able to proofread their errors: after incorporation of a wrong base, the resulting mispair invokes an exonuclease activity of the polymerase that removes the mispaired base and allows replication to continue. Elimination of the proofreading activity thus results in much higher mutation rates. We demonstrate that the two major replicative DNA polymerases in yeast, Pol δ and Pol ε, have different proofreading abilities. In diploid cells, Pol ε is not able to proofread errors created by other Pol ε molecules, whereas Pol δ can proofread not only errors created by other Pol δ molecules but also errors created by Pol ε molecules. We also find that mispaired bases not corrected by proofreading have much different likelihoods of being extended, depending on the particular base-base mismatch. In humans, defects in Pol δ or Pol ε proofreading can lead to cancer, and these results help explain the formation of those tumors and the finding that Pol ε mutants seem to be found as frequently, or more so, in human tumors as Pol δ mutants.
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9
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Garbacz M, Araki H, Flis K, Bebenek A, Zawada AE, Jonczyk P, Makiela-Dzbenska K, Fijalkowska IJ. Fidelity consequences of the impaired interaction between DNA polymerase epsilon and the GINS complex. DNA Repair (Amst) 2015; 29:23-35. [PMID: 25758782 DOI: 10.1016/j.dnarep.2015.02.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 02/03/2015] [Accepted: 02/04/2015] [Indexed: 01/08/2023]
Abstract
DNA polymerase epsilon interacts with the CMG (Cdc45-MCM-GINS) complex by Dpb2p, the non-catalytic subunit of DNA polymerase epsilon. It is postulated that CMG is responsible for targeting of Pol ɛ to the leading strand. We isolated a mutator dpb2-100 allele which encodes the mutant form of Dpb2p. We showed previously that Dpb2-100p has impaired interactions with Pol2p, the catalytic subunit of Pol ɛ. Here, we present that Dpb2-100p has strongly impaired interaction with the Psf1 and Psf3 subunits of the GINS complex. Our in vitro results suggest that while dpb2-100 does not alter Pol ɛ's biochemical properties including catalytic efficiency, processivity or proofreading activity - it moderately decreases the fidelity of DNA synthesis. As the in vitro results did not explain the strong in vivo mutator effect of the dpb2-100 allele we analyzed the mutation spectrum in vivo. The analysis of the mutation rates in the dpb2-100 mutant indicated an increased participation of the error-prone DNA polymerase zeta in replication. However, even in the absence of Pol ζ activity the presence of the dpb2-100 allele was mutagenic, indicating that a significant part of mutagenesis is Pol ζ-independent. A strong synergistic mutator effect observed for transversions in the triple mutant dpb2-100 pol2-4 rev3Δ as compared to pol2-4 rev3Δ and dpb2-100 rev3Δ suggests that in the presence of the dpb2-100 allele the number of replication errors is enhanced. We hypothesize that in the dpb2-100 strain, where the interaction between Pol ɛ and GINS is weakened, the access of Pol δ to the leading strand may be increased. The increased participation of Pol δ on the leading strand in the dpb2-100 mutant may explain the synergistic mutator effect observed in the dpb2-100 pol3-5DV double mutant.
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Affiliation(s)
- Marta Garbacz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Laboratory of Mutagenesis and DNA Repair, Pawinskiego 5A, Warsaw 02-106, Poland
| | - Hiroyuki Araki
- National Institute of Genetics, Division of Microbial Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Krzysztof Flis
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Laboratory of Mutagenesis and DNA Repair, Pawinskiego 5A, Warsaw 02-106, Poland
| | - Anna Bebenek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Department of Molecular Biology, Pawinskiego 5A, Warsaw 02-106, Poland
| | - Anna E Zawada
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Laboratory of Mutagenesis and DNA Repair, Pawinskiego 5A, Warsaw 02-106, Poland
| | - Piotr Jonczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Laboratory of Mutagenesis and DNA Repair, Pawinskiego 5A, Warsaw 02-106, Poland
| | - Karolina Makiela-Dzbenska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Laboratory of Mutagenesis and DNA Repair, Pawinskiego 5A, Warsaw 02-106, Poland.
| | - Iwona J Fijalkowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Laboratory of Mutagenesis and DNA Repair, Pawinskiego 5A, Warsaw 02-106, Poland.
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10
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Henninger EE, Pursell ZF. DNA polymerase ε and its roles in genome stability. IUBMB Life 2014; 66:339-51. [PMID: 24861832 DOI: 10.1002/iub.1276] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 05/02/2014] [Indexed: 12/14/2022]
Abstract
DNA Polymerase Epsilon (Pol ε) is one of three DNA Polymerases (along with Pol δ and Pol α) required for nuclear DNA replication in eukaryotes. Pol ε is comprised of four subunits, the largest of which is encoded by the POLE gene and contains the catalytic polymerase and exonuclease activities. The 3'-5' exonuclease proofreading activity is able to correct DNA synthesis errors and helps protect against genome instability. Recent cancer genome sequencing efforts have shown that 3% of colorectal and 7% of endometrial cancers contain mutations within the exonuclease domain of POLE and are associated with significantly elevated levels of single nucleotide substitutions (15-500 per Mb) and microsatellite stability. POLE mutations have also been found in other tumor types, though at lower frequency, suggesting roles in tumorigenesis more broadly in different tissue types. In addition to its proofreading activity, Pol ε contributes to genome stability through multiple mechanisms that are discussed in this review.
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Affiliation(s)
- Erin E Henninger
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
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11
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Singh J. Role of DNA replication in establishment and propagation of epigenetic states of chromatin. Semin Cell Dev Biol 2014; 30:131-43. [PMID: 24794003 DOI: 10.1016/j.semcdb.2014.04.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 04/03/2014] [Indexed: 10/25/2022]
Abstract
DNA replication is the fundamental process of duplication of the genetic information that is vital for survival of all living cells. The basic mechanistic steps of replication initiation, elongation and termination are conserved among bacteria, lower eukaryotes, like yeast and metazoans. However, the details of the mechanisms are different. Furthermore, there is a close coordination between chromatin assembly pathways and various components of replication machinery whereby DNA replication is coupled to "chromatin replication" during cell cycle. Thereby, various epigenetic modifications associated with different states of gene expression in differentiated cells and the related chromatin structures are faithfully propagated during the cell division through tight coupling with the DNA replication machinery. Several examples are found in lower eukaryotes like budding yeast and fission yeast with close parallels in metazoans.
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Affiliation(s)
- Jagmohan Singh
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India.
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12
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Honma H, Hirai M, Nakamura S, Hakimi H, Kawazu SI, Palacpac NMQ, Hisaeda H, Matsuoka H, Kawai S, Endo H, Yasunaga T, Ohashi J, Mita T, Horii T, Furusawa M, Tanabe K. Generation of rodent malaria parasites with a high mutation rate by destructing proofreading activity of DNA polymerase δ. DNA Res 2014; 21:439-46. [PMID: 24670267 PMCID: PMC4131837 DOI: 10.1093/dnares/dsu009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Plasmodium falciparum malaria imposes a serious public health concern throughout the tropics. Although genetic tools are principally important to fully investigate malaria parasites, currently available forward and reverse tools are fairly limited. It is expected that parasites with a high mutation rate can readily acquire novel phenotypes/traits; however, they remain an untapped tool for malaria biology. Here, we generated a mutator malaria parasite (hereinafter called a ‘malaria mutator’), using site-directed mutagenesis and gene transfection techniques. A mutator Plasmodium berghei line with a defective proofreading 3′ → 5′ exonuclease activity in DNA polymerase δ (referred to as PbMut) and a control P. berghei line with wild-type DNA polymerase δ (referred to as PbCtl) were maintained by weekly passage in ddY mice for 122 weeks. High-throughput genome sequencing analysis revealed that two PbMut lines had 175–178 mutations and a 86- to 90-fold higher mutation rate than that of a PbCtl line. PbMut, PbCtl, and their parent strain, PbWT, showed similar course of infection. Interestingly, PbMut lost the ability to form gametocytes during serial passages. We believe that the malaria mutator system could provide a novel and useful tool to investigate malaria biology.
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Affiliation(s)
- Hajime Honma
- Laboratory of Malariology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan Department of Molecular Protozoology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Makoto Hirai
- Department of Parasitology, Graduate School of Medicine, Gunma University, Maebashi, Gunma 371-8511, Japan
| | - Shota Nakamura
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hassan Hakimi
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada, Obihiro, Hokkaido 080-8555, Japan
| | - Shin-Ichiro Kawazu
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada, Obihiro, Hokkaido 080-8555, Japan
| | - Nirianne M Q Palacpac
- Department of Molecular Protozoology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hajime Hisaeda
- Department of Parasitology, Graduate School of Medicine, Gunma University, Maebashi, Gunma 371-8511, Japan
| | - Hiroyuki Matsuoka
- Division of Medical Zoology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan
| | - Satoru Kawai
- Laboratory of Tropical Medicine and Parasitology, Institute of International Education and Research, Dokkyo Medical University, Shimotsuga, Tochigi 321-0293, Japan
| | - Hiroyoshi Endo
- Department of International Affairs and Tropical Medicine, Tokyo Women's Medical University School of Medicine, Kawada-cho, Shinjuku, Tokyo 162-8666, Japan
| | - Teruo Yasunaga
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Jun Ohashi
- Faculty of Medicine, University of Tsukuba, Ibaragi 305-8575, Japan
| | - Toshihiro Mita
- Department of International Affairs and Tropical Medicine, Tokyo Women's Medical University School of Medicine, Kawada-cho, Shinjuku, Tokyo 162-8666, Japan Department of Molecular and Cellular Parasitology, Juntendo University School of Medicine, Hongo, Bunkyo, Tokyo 113-8421, Japan
| | - Toshihiro Horii
- Department of Molecular Protozoology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Mitsuru Furusawa
- Neo-Morgan Laboratory, Inc., Nogawa, Miyamae, Kawasaki, Kanagawa 216-0001, Japan
| | - Kazuyuki Tanabe
- Laboratory of Malariology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan Department of Molecular Protozoology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
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13
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Heitzer E, Tomlinson I. Replicative DNA polymerase mutations in cancer. Curr Opin Genet Dev 2014; 24:107-13. [PMID: 24583393 PMCID: PMC4003352 DOI: 10.1016/j.gde.2013.12.005] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 12/20/2013] [Indexed: 12/18/2022]
Abstract
Three DNA polymerases - Pol α, Pol δ and Pol ɛ - are essential for DNA replication. After initiation of DNA synthesis by Pol α, Pol δ or Pol ɛ take over on the lagging and leading strand respectively. Pol δ and Pol ɛ perform the bulk of replication with very high fidelity, which is ensured by Watson-Crick base pairing and 3'exonuclease (proofreading) activity. Yeast models have shown that mutations in the exonuclease domain of Pol δ and Pol ɛ homologues can cause a mutator phenotype. Recently, we identified germline exonuclease domain mutations (EDMs) in human POLD1 and POLE that predispose to 'polymerase proofreading associated polyposis' (PPAP), a disease characterised by multiple colorectal adenomas and carcinoma, with high penetrance and dominant inheritance. Moreover, somatic EDMs in POLE have also been found in sporadic colorectal and endometrial cancers. Tumors with EDMs are microsatellite stable and show an 'ultramutator' phenotype, with a dramatic increase in base substitutions.
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Affiliation(s)
- Ellen Heitzer
- Institute of Human Genetics, Medical University of Graz, Harrachgasse 21/8, A-8010 Graz, Austria.
| | - Ian Tomlinson
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK; Oxford NIHR Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
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14
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Kunz BA. Mutational specificity analysis: assay for mutations in the yeast SUP4-o gene. Methods Mol Biol 2014; 1163:201-212. [PMID: 24841309 DOI: 10.1007/978-1-4939-0799-1_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Mutational specificity analysis can yield valuable insights into processes that generate genetic change or maintain genetic stability. Powerful diagnostic tools for such analysis have been created by combining genetic assays for mutation with DNA sequencing. Here, steps for isolating spontaneous mutations in the yeast (Saccharomyces cerevisiae) suppressor tRNA gene SUP4-o as a prelude to sequence characterization are described (modifications of this protocol can be used to study induction of mutations by various physical or chemical agents). Mutations in SUP4-o are selected on drug-containing medium by virtue of their inactivation of suppressor activity. The small size, detailed knowledge of detectably mutable sites, and other features of the target gene facilitate subsequent analysis of these mutations.
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Affiliation(s)
- Bernard A Kunz
- Life and Environmental Sciences, Deakin University, 75 Pigdons Road, Waurn Ponds, VIC, 3216, Australia,
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15
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Smith EC, Blanc H, Vignuzzi M, Denison MR. Coronaviruses lacking exoribonuclease activity are susceptible to lethal mutagenesis: evidence for proofreading and potential therapeutics. PLoS Pathog 2013; 9:e1003565. [PMID: 23966862 PMCID: PMC3744431 DOI: 10.1371/journal.ppat.1003565] [Citation(s) in RCA: 324] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 07/03/2013] [Indexed: 12/14/2022] Open
Abstract
No therapeutics or vaccines currently exist for human coronaviruses (HCoVs). The Severe Acute Respiratory Syndrome-associated coronavirus (SARS-CoV) epidemic in 2002–2003, and the recent emergence of Middle East Respiratory Syndrome coronavirus (MERS-CoV) in April 2012, emphasize the high probability of future zoonotic HCoV emergence causing severe and lethal human disease. Additionally, the resistance of SARS-CoV to ribavirin (RBV) demonstrates the need to define new targets for inhibition of CoV replication. CoVs express a 3′-to-5′ exoribonuclease in nonstructural protein 14 (nsp14-ExoN) that is required for high-fidelity replication and is conserved across the CoV family. All genetic and biochemical data support the hypothesis that nsp14-ExoN has an RNA proofreading function. Thus, we hypothesized that ExoN is responsible for CoV resistance to RNA mutagens. We demonstrate that while wild-type (ExoN+) CoVs were resistant to RBV and 5-fluorouracil (5-FU), CoVs lacking ExoN activity (ExoN−) were up to 300-fold more sensitive. While the primary antiviral activity of RBV against CoVs was not mutagenesis, ExoN− CoVs treated with 5-FU demonstrated both enhanced sensitivity during multi-cycle replication, as well as decreased specific infectivity, consistent with 5-FU functioning as a mutagen. Comparison of full-genome next-generation sequencing of 5-FU treated SARS-CoV populations revealed a 16-fold increase in the number of mutations within the ExoN− population as compared to ExoN+. Ninety percent of these mutations represented A:G and U:C transitions, consistent with 5-FU incorporation during RNA synthesis. Together our results constitute direct evidence that CoV ExoN activity provides a critical proofreading function during virus replication. Furthermore, these studies identify ExoN as the first viral protein distinct from the RdRp that determines the sensitivity of RNA viruses to mutagens. Finally, our results show the importance of ExoN as a target for inhibition, and suggest that small-molecule inhibitors of ExoN activity could be potential pan-CoV therapeutics in combination with RBV or RNA mutagens. RNA viruses have high mutation rates (10−3 to 10−5 mutations/nucleotide/round of replication), allowing for rapid viral adaptation in response to selective pressure. While RNA viruses have long been considered unable to correct mistakes during replication, CoVs such as SARS-CoV and the recently emerged MERS-CoV are important exceptions to this paradigm. All CoVs encode an exoribonuclease activity in nonstructural protein 14 (nsp14-ExoN) that is proposed to prevent and/or remove misincorporated nucleotides. Because of the demonstrated resistance of SARS-CoV to the antiviral drug ribavirin (RBV), we hypothesized that ExoN is responsible for CoV resistance to RNA mutagens. Using RBV and the RNA mutagen 5-fluorouracil (5-FU), we show that CoVs lacking ExoN activity (ExoN−) are highly susceptible to RBV and 5-FU, in contrast to wild-type (ExoN+) CoVs. The inhibitory activity of 5-FU against ExoN− viruses resulted specifically from 5-FU incorporation during viral RNA synthesis that lead to extensive mutagenesis within the viral population, and was associated with a profound decrease in virus specific infectivity. These results demonstrate the proofreading activity of ExoN during virus replication and suggest that inhibitors of ExoN activity could be broadly useful inhibitors of CoV replication in combination with RBV or RNA mutagens.
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Affiliation(s)
- Everett Clinton Smith
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- The Elizabeth B. Lamb Center for Pediatric Research, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Hervé Blanc
- Institut Pasteur, Centre National de la Recherche Scientifique Unité de Recherche Associée 3015, Paris, France
| | - Marco Vignuzzi
- Institut Pasteur, Centre National de la Recherche Scientifique Unité de Recherche Associée 3015, Paris, France
| | - Mark R. Denison
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- The Elizabeth B. Lamb Center for Pediatric Research, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- * E-mail:
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16
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Emergence of DNA polymerase ε antimutators that escape error-induced extinction in yeast. Genetics 2013; 193:751-70. [PMID: 23307893 DOI: 10.1534/genetics.112.146910] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA polymerases (Pols) ε and δ perform the bulk of yeast leading- and lagging-strand DNA synthesis. Both Pols possess intrinsic proofreading exonucleases that edit errors during polymerization. Rare errors that elude proofreading are extended into duplex DNA and excised by the mismatch repair (MMR) system. Strains that lack Pol proofreading or MMR exhibit a 10- to 100-fold increase in spontaneous mutation rate (mutator phenotype), and inactivation of both Pol δ proofreading (pol3-01) and MMR is lethal due to replication error-induced extinction (EEX). It is unclear whether a similar synthetic lethal relationship exists between defects in Pol ε proofreading (pol2-4) and MMR. Using a plasmid-shuffling strategy in haploid Saccharomyces cerevisiae, we observed synthetic lethality of pol2-4 with alleles that completely abrogate MMR (msh2Δ, mlh1Δ, msh3Δ msh6Δ, or pms1Δ mlh3Δ) but not with partial MMR loss (msh3Δ, msh6Δ, pms1Δ, or mlh3Δ), indicating that high levels of unrepaired Pol ε errors drive extinction. However, variants that escape this error-induced extinction (eex mutants) frequently emerged. Five percent of pol2-4 msh2Δ eex mutants encoded second-site changes in Pol ε that reduced the pol2-4 mutator phenotype between 3- and 23-fold. The remaining eex alleles were extragenic to pol2-4. The locations of antimutator amino-acid changes in Pol ε and their effects on mutation spectra suggest multiple mechanisms of mutator suppression. Our data indicate that unrepaired leading- and lagging-strand polymerase errors drive extinction within a few cell divisions and suggest that there are polymerase-specific pathways of mutator suppression. The prevalence of suppressors extragenic to the Pol ε gene suggests that factors in addition to proofreading and MMR influence leading-strand DNA replication fidelity.
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17
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Waisertreiger ISR, Liston VG, Menezes MR, Kim HM, Lobachev KS, Stepchenkova EI, Tahirov TH, Rogozin IB, Pavlov YI. Modulation of mutagenesis in eukaryotes by DNA replication fork dynamics and quality of nucleotide pools. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2012; 53:699-724. [PMID: 23055184 PMCID: PMC3893020 DOI: 10.1002/em.21735] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 08/13/2012] [Accepted: 08/15/2012] [Indexed: 06/01/2023]
Abstract
The rate of mutations in eukaryotes depends on a plethora of factors and is not immediately derived from the fidelity of DNA polymerases (Pols). Replication of chromosomes containing the anti-parallel strands of duplex DNA occurs through the copying of leading and lagging strand templates by a trio of Pols α, δ and ϵ, with the assistance of Pol ζ and Y-family Pols at difficult DNA template structures or sites of DNA damage. The parameters of the synthesis at a given location are dictated by the quality and quantity of nucleotides in the pools, replication fork architecture, transcription status, regulation of Pol switches, and structure of chromatin. The result of these transactions is a subject of survey and editing by DNA repair.
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Affiliation(s)
- Irina S.-R. Waisertreiger
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
| | - Victoria G. Liston
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
| | - Miriam R. Menezes
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
| | - Hyun-Min Kim
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, U.S.A
| | - Kirill S. Lobachev
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, U.S.A
| | - Elena I. Stepchenkova
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
- Saint Petersburg Branch of Vavilov Institute of General Genetics, Universitetskaya emb. 7/9, St Petersburg, 199034, Russia
- Department of Genetics, Saint Petersburg University, Universitetskaya emb. 7/9, St Petersburg, 199034, Russia
| | - Tahir H. Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
| | - Igor B. Rogozin
- National Center for Biotechnology Information NLM, National Institutes of Health, Bethesda, MD 20894, U.S.A
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia
| | - Youri. I. Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
- Department of Genetics, Saint Petersburg University, Universitetskaya emb. 7/9, St Petersburg, 199034, Russia
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18
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Abstract
DNA polymerase ε (Pol ε) is one of three replicative DNA polymerases in eukaryotic cells. Pol ε is a multi-subunit DNA polymerase with many functions. For example, recent studies in yeast have suggested that Pol ε is essential during the initiation of DNA replication and also participates during leading strand synthesis. In this chapter, we will discuss the structure of Pol ε, the individual subunits and their function.
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Affiliation(s)
- Matthew Hogg
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, SE-90187, Sweden
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19
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Aksenova A, Volkov K, Maceluch J, Pursell ZF, Rogozin IB, Kunkel TA, Pavlov YI, Johansson E. Mismatch repair-independent increase in spontaneous mutagenesis in yeast lacking non-essential subunits of DNA polymerase ε. PLoS Genet 2010; 6:e1001209. [PMID: 21124948 PMCID: PMC2987839 DOI: 10.1371/journal.pgen.1001209] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Accepted: 10/15/2010] [Indexed: 01/31/2023] Open
Abstract
Yeast DNA polymerase ε (Pol ε) is a highly accurate and processive enzyme that participates in nuclear DNA replication of the leading strand template. In addition to a large subunit (Pol2) harboring the polymerase and proofreading exonuclease active sites, Pol ε also has one essential subunit (Dpb2) and two smaller, non-essential subunits (Dpb3 and Dpb4) whose functions are not fully understood. To probe the functions of Dpb3 and Dpb4, here we investigate the consequences of their absence on the biochemical properties of Pol ε in vitro and on genome stability in vivo. The fidelity of DNA synthesis in vitro by purified Pol2/Dpb2, i.e. lacking Dpb3 and Dpb4, is comparable to the four-subunit Pol ε holoenzyme. Nonetheless, deletion of DPB3 and DPB4 elevates spontaneous frameshift and base substitution rates in vivo, to the same extent as the loss of Pol ε proofreading activity in a pol2-4 strain. In contrast to pol2-4, however, the dpb3Δdpb4Δ does not lead to a synergistic increase of mutation rates with defects in DNA mismatch repair. The increased mutation rate in dpb3Δdpb4Δ strains is partly dependent on REV3, as well as the proofreading capacity of Pol δ. Finally, biochemical studies demonstrate that the absence of Dpb3 and Dpb4 destabilizes the interaction between Pol ε and the template DNA during processive DNA synthesis and during processive 3′ to 5′exonucleolytic degradation of DNA. Collectively, these data suggest a model wherein Dpb3 and Dpb4 do not directly influence replication fidelity per se, but rather contribute to normal replication fork progression. In their absence, a defective replisome may more frequently leave gaps on the leading strand that are eventually filled by Pol ζ or Pol δ, in a post-replication process that generates errors not corrected by the DNA mismatch repair system. The high fidelity of DNA replication is safeguarded by the accuracy of nucleotide selection by DNA polymerases, proofreading activity of the replicative polymerases, and the DNA mismatch repair system. Errors made by replicative polymerases are corrected by mismatch repair, and inactivation of the mismatch repair system results in a multiplicative increase in error rates when combined with a proofreading deficient allele of a replicative polymerase. In this study, we demonstrate that the deletion of two non-essential genes encoding for two subunits of Pol ε give an increased mutation rate due to increased synthesis by the error-prone DNA polymerase ζ. Surprisingly, there was no multiplicative increase in error rates when the mismatch repair system was inactivated. We propose that the deletion of DPB3 and DPB4 gives a defective replisome, which in turn gives increased synthesis, in part, by Pol ζ during an error-prone post-replication process that is not efficiently repaired by the mismatch repair system.
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Affiliation(s)
- Anna Aksenova
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
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20
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Korona DA, Lecompte KG, Pursell ZF. The high fidelity and unique error signature of human DNA polymerase epsilon. Nucleic Acids Res 2010; 39:1763-73. [PMID: 21036870 PMCID: PMC3061053 DOI: 10.1093/nar/gkq1034] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Bulk replicative DNA synthesis in eukaryotes is highly accurate and efficient, primarily because of two DNA polymerases (Pols): Pols δ and ε. The high fidelity of these enzymes is due to their intrinsic base selectivity and proofreading exonuclease activity which, when coupled with post-replication mismatch repair, helps to maintain human mutation rates at less than one mutation per genome duplication. Conditions that reduce polymerase fidelity result in increased mutagenesis and can lead to cancer in mice. Whereas yeast Pol ε has been well characterized, human Pol ε remains poorly understood. Here, we present the first report on the fidelity of human Pol ε. We find that human Pol ε carries out DNA synthesis with high fidelity, even in the absence of its 3′→5′ exonucleolytic proofreading and is significantly more accurate than yeast Pol ε. Though its spectrum of errors is similar to that of yeast Pol ε, there are several notable exceptions. These include a preference of the human enzyme for T→A over A→T transversions. As compared with other replicative DNA polymerases, human Pol ε is particularly accurate when copying homonucleotide runs of 4–5 bases. The base pair substitution specificity and high fidelity for frameshift errors observed for human Pol ε are distinct from the errors made by human Pol δ.
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Affiliation(s)
- Dagmara A Korona
- Department of Biochemistry and Tulane Cancer Center, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
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21
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Preston BD, Albertson TM, Herr AJ. DNA replication fidelity and cancer. Semin Cancer Biol 2010; 20:281-93. [PMID: 20951805 PMCID: PMC2993855 DOI: 10.1016/j.semcancer.2010.10.009] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2010] [Accepted: 10/07/2010] [Indexed: 12/14/2022]
Abstract
Cancer is fueled by mutations and driven by adaptive selection. Normal cells avoid deleterious mutations by replicating their genomes with extraordinary accuracy. Here we review the pathways governing DNA replication fidelity and discuss evidence implicating replication errors (point mutation instability or PIN) in carcinogenesis.
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Affiliation(s)
- Bradley D Preston
- Department of Pathology, University of Washington, Seattle, WA 98195, USA.
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22
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DNA polymerase epsilon and delta proofreading suppress discrete mutator and cancer phenotypes in mice. Proc Natl Acad Sci U S A 2009; 106:17101-4. [PMID: 19805137 DOI: 10.1073/pnas.0907147106] [Citation(s) in RCA: 171] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Organisms require faithful DNA replication to avoid deleterious mutations. In yeast, replicative leading- and lagging-strand DNA polymerases (Pols epsilon and delta, respectively) have intrinsic proofreading exonucleases that cooperate with each other and mismatch repair to limit spontaneous mutation to less than 1 per genome per cell division. The relationship of these pathways in mammals and their functions in vivo are unknown. Here we show that mouse Pol epsilon and delta proofreading suppress discrete mutator and cancer phenotypes. We found that inactivation of Pol epsilon proofreading elevates base-substitution mutations and accelerates a unique spectrum of spontaneous cancers; the types of tumors are entirely different from those triggered by loss of Pol delta proofreading. Intercrosses of Pol epsilon-, Pol delta-, and mismatch repair-mutant mice show that Pol epsilon and delta proofreading act in parallel pathways to prevent spontaneous mutation and cancer. These findings distinguish Pol epsilon and delta functions in vivo and reveal tissue-specific requirements for DNA replication fidelity.
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23
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Pavlov YI, Shcherbakova PV. DNA polymerases at the eukaryotic fork-20 years later. Mutat Res 2009; 685:45-53. [PMID: 19682465 DOI: 10.1016/j.mrfmmm.2009.08.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Accepted: 08/05/2009] [Indexed: 10/20/2022]
Abstract
Function of the eukaryotic genome depends on efficient and accurate replication of anti-parallel DNA strands. Eukaryotic DNA polymerases have different properties adapted to perform a wide spectrum of DNA transactions. Here we focus on major players in the bulk replication, DNA polymerases of the B-family. We review the organization of the replication fork in eukaryotes in a historical perspective, analyze contemporary models and propose a new integrative model of the fork.
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Affiliation(s)
- Youri I Pavlov
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA.
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24
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Kunkel TA, Burgers PM. Dividing the workload at a eukaryotic replication fork. Trends Cell Biol 2008; 18:521-7. [PMID: 18824354 DOI: 10.1016/j.tcb.2008.08.005] [Citation(s) in RCA: 201] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Revised: 08/22/2008] [Accepted: 08/26/2008] [Indexed: 10/21/2022]
Abstract
Efficient and accurate replication of the eukaryotic nuclear genome requires DNA polymerases (Pols) alpha, delta and epsilon. In all current replication fork models, polymerase alpha initiates replication. However, several models have been proposed for the roles of Pol delta and Pol epsilon in subsequent chain elongation and the division of labor between these two polymerases is still unclear. Here, we revisit this issue, considering recent studies with diagnostic mutator polymerases that support a model wherein Pol epsilon is primarily responsible for copying the leading-strand template and Pol delta is primarily responsible for copying the lagging-strand template. We also review earlier studies in light of this model and then consider prospects for future investigations of possible variations on this simple division of labor.
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Affiliation(s)
- Thomas A Kunkel
- Laboratory of Molecular Genetics and Laboratory of Structural Biology, 111 T.W. Alexander Drive, National Institute of Environmental Health Sciences, National Institute of Health, DHHS, Research Triangle Park, NC 27709, USA.
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25
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Pursell ZF, Kunkel TA. DNA polymerase epsilon: a polymerase of unusual size (and complexity). PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2008; 82:101-45. [PMID: 18929140 PMCID: PMC3694787 DOI: 10.1016/s0079-6603(08)00004-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zachary F. Pursell
- Laboratory of Molecular Genetics and Laboratory of Structural Biology National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709
| | - Thomas A. Kunkel
- Laboratory of Molecular Genetics and Laboratory of Structural Biology National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709
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26
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Chilkova O, Stenlund P, Isoz I, Stith CM, Grabowski P, Lundström EB, Burgers PM, Johansson E. The eukaryotic leading and lagging strand DNA polymerases are loaded onto primer-ends via separate mechanisms but have comparable processivity in the presence of PCNA. Nucleic Acids Res 2007; 35:6588-97. [PMID: 17905813 PMCID: PMC2095795 DOI: 10.1093/nar/gkm741] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Saccharomyces cerevisiae DNA polymerase delta (Pol delta) and DNA polymerase epsilon (Pol epsilon) are replicative DNA polymerases at the replication fork. Both enzymes are stimulated by PCNA, although to different levels. To understand why and to explore the interaction with PCNA, we compared Pol delta and Pol epsilon in physical interactions with PCNA and nucleic acids (with or without RPA), and in functional assays measuring activity and processivity. Using surface plasmon resonance technique, we show that Pol epsilon has a high affinity for DNA, but a low affinity for PCNA. In contrast, Pol delta has a low affinity for DNA and a high affinity for PCNA. The true processivity of Pol delta and Pol epsilon was measured for the first time in the presence of RPA, PCNA and RFC on single-stranded DNA. Remarkably, in the presence of PCNA, the processivity of Pol delta and Pol epsilon on RPA-coated DNA is comparable. Finally, more PCNA molecules were found on the template after it was replicated by Pol epsilon when compared to Pol delta. We conclude that Pol epsilon and Pol delta exhibit comparable processivity, but are loaded on the primer-end via different mechanisms.
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Affiliation(s)
- Olga Chilkova
- Department of Medical Biochemistry and Biophysics, Department of Biochemistry, Umeå University, 901 87 Umeå, Sweden and Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Peter Stenlund
- Department of Medical Biochemistry and Biophysics, Department of Biochemistry, Umeå University, 901 87 Umeå, Sweden and Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Isabelle Isoz
- Department of Medical Biochemistry and Biophysics, Department of Biochemistry, Umeå University, 901 87 Umeå, Sweden and Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Carrie M. Stith
- Department of Medical Biochemistry and Biophysics, Department of Biochemistry, Umeå University, 901 87 Umeå, Sweden and Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Pawel Grabowski
- Department of Medical Biochemistry and Biophysics, Department of Biochemistry, Umeå University, 901 87 Umeå, Sweden and Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Else-Britt Lundström
- Department of Medical Biochemistry and Biophysics, Department of Biochemistry, Umeå University, 901 87 Umeå, Sweden and Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Peter M. Burgers
- Department of Medical Biochemistry and Biophysics, Department of Biochemistry, Umeå University, 901 87 Umeå, Sweden and Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Erik Johansson
- Department of Medical Biochemistry and Biophysics, Department of Biochemistry, Umeå University, 901 87 Umeå, Sweden and Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO 63110, USA
- *To whom correspondence should be addressed. +46 90 786 6638+46 90 786 9795
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27
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Titok M, Suski C, Dalmais B, Ehrlich SD, Jannière L. The replicative polymerases PolC and DnaE are required for theta replication of the Bacillus subtilis plasmid pBS72. MICROBIOLOGY-SGM 2006; 152:1471-1478. [PMID: 16622063 DOI: 10.1099/mic.0.28693-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Plasmids are the tools of choice for studying bacterial functions involved in DNA maintenance. Here a genetic study on the replication of a novel, low-copy-number, Bacillus subtilis plasmid, pBS72, is reported. The results show that two plasmid elements, the initiator protein RepA and an iteron-containing origin, and at least nine host-encoded replication proteins, the primosomal proteins DnaB, DnaC, DnaD, DnaG and DnaI, the DNA polymerases DnaE and PolC, and the polymerase cofactors DnaN and DnaX, are required for pBS72 replication. On the contrary, the cellular initiators DnaA and PriA, the helicase PcrA and DNA polymerase I are dispensable. From this, it is inferred that pBS72 replication is of the theta type and is initiated by an original mechanism. Indirect evidence suggests that during this process the DnaC helicase might be delivered to the plasmid origin by the weakly active DnaD pathway stimulated by a predicted interaction between DnaC and a domain of RepA homologous to the major DnaC-binding domain of the cellular initiator DnaA. The plasmid pBS72 replication fork appears to require the same functions as the bacterial chromosome and the unrelated plasmid pAMbeta1. Most importantly, this replication machinery contains the two type C polymerases, PolC and DnaE. As the mechanism of initiation of the three genomes is substantially different, this suggests that both type C polymerases might be required in any Cairns replication in B. subtilis and presumably in other bacteria encoding PolC and DnaE.
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Affiliation(s)
- Marina Titok
- Belarussian State University, Biological Faculty, Department of Genetics and Biotechnology, Minsk 220050, 4 Scorina Avenue, Belarus
| | | | - Bérengère Dalmais
- Laboratoire de Génétique Microbienne, Bâtiment des Biotechnologies, INRA, 78352 Jouy en Josas, France
| | - S Dusko Ehrlich
- Laboratoire de Génétique Microbienne, Bâtiment des Biotechnologies, INRA, 78352 Jouy en Josas, France
| | - Laurent Jannière
- Laboratoire de Génétique Microbienne, Bâtiment des Biotechnologies, INRA, 78352 Jouy en Josas, France
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Abstract
Almost forty years after the key contributions to the field by Okazaki and coworkers that gave rise to the concept of leading and the lagging strand, we are still at the state of uncertainty about the proteins that replicate each strand. Perhaps, one main conclusion that should be drawn from the data currently available is that the protein architecture at the fork is more plastic than originally thought.
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Affiliation(s)
- Akio Sugino
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.
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Shikata K, Sasa-Masuda T, Okuno Y, Waga S, Sugino A. The DNA polymerase activity of Pol epsilon holoenzyme is required for rapid and efficient chromosomal DNA replication in Xenopus egg extracts. BMC BIOCHEMISTRY 2006; 7:21. [PMID: 16925818 PMCID: PMC1560149 DOI: 10.1186/1471-2091-7-21] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2006] [Accepted: 08/22/2006] [Indexed: 12/31/2022]
Abstract
BACKGROUND DNA polymerase epsilon (Pol epsilon) is involved in DNA replication, repair, and cell-cycle checkpoint control in eukaryotic cells. Although the roles of replicative Pol alpha and Pol delta in chromosomal DNA replication are relatively well understood and well documented, the precise role of Pol epsilon in chromosomal DNA replication is not well understood. RESULTS This study uses a Xenopus egg extract DNA replication system to further elucidate the replicative role(s) played by Pol epsilon. Previous studies show that the initiation timing and elongation of chromosomal DNA replication are markedly impaired in Pol epsilon-depleted Xenopus egg extracts, with reduced accumulation of replicative intermediates and products. This study shows that normal replication is restored by addition of Pol epsilon holoenzyme to Pol epsilon-depleted extracts, but not by addition of polymerase-deficient forms of Pol epsilon, including polymerase point or deletion mutants or incomplete enzyme complexes. Evidence is also provided that Pol epsilon holoenzyme interacts directly with GINS, Cdc45p and Cut5p, each of which plays an important role in initiation of chromosomal DNA replication in eukaryotic cells. CONCLUSION These results indicate that the DNA polymerase activity of Pol epsilon holoenzyme plays an essential role in normal chromosomal DNA replication in Xenopus egg extracts. These are the first biochemical data to show the DNA polymerase activity of Pol epsilon holoenzyme is essential for chromosomal DNA replication in higher eukaryotes, unlike in yeasts.
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Affiliation(s)
- Koh Shikata
- Laboratories for Biomolecular Networks, Graduate School of Frontier Biosciences, Osaka University, 1–3 Yamada-oka, Suita, Osaka 565-0871, Japan
- Research Institute, Thermostable Enzyme Laboratory Co., Ltd, 1-8-31 Midoriga-oka, Ikeda, Osaka 563-8577, Japan
| | - Taro Sasa-Masuda
- Laboratories for Biomolecular Networks, Graduate School of Frontier Biosciences, Osaka University, 1–3 Yamada-oka, Suita, Osaka 565-0871, Japan
- Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
- Braun Laboratories 147-75, California Institute of Technology, Pasadena, California 91125, USA
| | - Yukiko Okuno
- Laboratories for Biomolecular Networks, Graduate School of Frontier Biosciences, Osaka University, 1–3 Yamada-oka, Suita, Osaka 565-0871, Japan
- Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Shou Waga
- Laboratories for Biomolecular Networks, Graduate School of Frontier Biosciences, Osaka University, 1–3 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Akio Sugino
- Laboratories for Biomolecular Networks, Graduate School of Frontier Biosciences, Osaka University, 1–3 Yamada-oka, Suita, Osaka 565-0871, Japan
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30
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Seki T, Akita M, Kamimura Y, Muramatsu S, Araki H, Sugino A. GINS Is a DNA Polymerase ϵ Accessory Factor during Chromosomal DNA Replication in Budding Yeast. J Biol Chem 2006; 281:21422-21432. [PMID: 16714283 DOI: 10.1074/jbc.m603482200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
GINS is a protein complex found in eukaryotic cells that is composed of Sld5p, Psf1p, Psf2p, and Psf3p. GINS polypeptides are highly conserved in eukaryotes, and the GINS complex is required for chromosomal DNA replication in yeasts and Xenopus egg. This study reports purification and biochemical characterization of GINS from Saccharomyces cerevisiae. The results presented here demonstrate that GINS forms a 1:1 complex with DNA polymerase epsilon (Pol epsilon) holoenzyme and greatly stimulates its catalytic activity in vitro. In the presence of GINS, Pol epsilon is more processive and dissociates more readily from replicated DNA, while under identical conditions, proliferating cell nuclear antigen slightly stimulates Pol epsilon in vitro. These results strongly suggest that GINS is a Pol epsilon accessory protein during chromosomal DNA replication in budding yeast. Based on these results, we propose a model for molecular dynamics at eukaryotic chromosomal replication fork.
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Affiliation(s)
- Takashi Seki
- Laboratories for Biomolecular Networks, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamada-oka, Suita, Osaka 565-0871; Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602
| | - Masaki Akita
- Laboratories for Biomolecular Networks, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamada-oka, Suita, Osaka 565-0871
| | - Yoichiro Kamimura
- Division of Microbial Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Sachiko Muramatsu
- Division of Microbial Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Hiroyuki Araki
- Division of Microbial Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Akio Sugino
- Laboratories for Biomolecular Networks, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamada-oka, Suita, Osaka 565-0871; Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602.
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31
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Rytkönen AK, Vaara M, Nethanel T, Kaufmann G, Sormunen R, Läärä E, Nasheuer HP, Rahmeh A, Lee MYWT, Syväoja JE, Pospiech H. Distinctive activities of DNA polymerases during human DNA replication. FEBS J 2006; 273:2984-3001. [PMID: 16762037 DOI: 10.1111/j.1742-4658.2006.05310.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The contributions of human DNA polymerases (pols) alpha, delta and epsilon during S-phase progression were studied in order to elaborate how these enzymes co-ordinate their functions during nuclear DNA replication. Pol delta was three to four times more intensely UV cross-linked to nascent DNA in late compared with early S phase, whereas the cross-linking of pols alpha and epsilon remained nearly constant throughout the S phase. Consistently, the chromatin-bound fraction of pol delta, unlike pols alpha and epsilon, increased in the late S phase. Moreover, pol delta neutralizing antibodies inhibited replicative DNA synthesis most efficiently in late S-phase nuclei, whereas antibodies against pol epsilon were most potent in early S phase. Ultrastructural localization of the pols by immuno-electron microscopy revealed pol epsilon to localize predominantly to ring-shaped clusters at electron-dense regions of the nucleus, whereas pol delta was mainly dispersed on fibrous structures. Pol alpha and proliferating cell nuclear antigen displayed partial colocalization with pol delta and epsilon, despite the very limited colocalization of the latter two pols. These data are consistent with models where pols delta and epsilon pursue their functions at least partly independently during DNA replication.
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Affiliation(s)
- Anna K Rytkönen
- Biocenter Oulu and Department of Biochemistry, University of Oulu, Finland
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32
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Abdulovic A, Kim N, Jinks-Robertson S. Mutagenesis and the three R's in yeast. DNA Repair (Amst) 2006; 5:409-21. [PMID: 16412705 DOI: 10.1016/j.dnarep.2005.11.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2005] [Revised: 11/17/2005] [Accepted: 11/17/2005] [Indexed: 11/19/2022]
Abstract
Mutagenesis is a prerequisite for evolution and also is an important contributor to human diseases. Most mutations in actively dividing cells originate during DNA replication as errors introduced when copying an undamaged DNA template or during the bypass of DNA lesions. In addition, mutations can be introduced during the repair of DNA double-strand breaks by either homologous recombination or non-homologous end-joining pathways. Finally, although generally considered to be a very high-fidelity process, the excision repair of DNA damage may be an important contributor to mutagenesis in non-dividing cells. In this review, we will discuss the well-known contributions of DNA replication to mutagenesis in Saccharomyces cerevisiae, as well as the less-appreciated contributions of recombination and repair to mutagenesis in this organism.
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Affiliation(s)
- Amy Abdulovic
- Biochemistry, Cell and Developmental Biology Program of the Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA 30322, USA
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33
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Pavlov YI, Shcherbakova PV, Rogozin IB. Roles of DNA Polymerases in Replication, Repair, and Recombination in Eukaryotes. INTERNATIONAL REVIEW OF CYTOLOGY 2006; 255:41-132. [PMID: 17178465 DOI: 10.1016/s0074-7696(06)55002-8] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The functioning of the eukaryotic genome depends on efficient and accurate DNA replication and repair. The process of replication is complicated by the ongoing decomposition of DNA and damage of the genome by endogenous and exogenous factors. DNA damage can alter base coding potential resulting in mutations, or block DNA replication, which can lead to double-strand breaks (DSB) and to subsequent chromosome loss. Replication is coordinated with DNA repair systems that operate in cells to remove or tolerate DNA lesions. DNA polymerases can serve as sensors in the cell cycle checkpoint pathways that delay cell division until damaged DNA is repaired and replication is completed. Eukaryotic DNA template-dependent DNA polymerases have different properties adapted to perform an amazingly wide spectrum of DNA transactions. In this review, we discuss the structure, the mechanism, and the evolutionary relationships of DNA polymerases and their possible functions in the replication of intact and damaged chromosomes, DNA damage repair, and recombination.
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Affiliation(s)
- Youri I Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, Departments of Biochemistry and Molecular Biology, and Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198-6805, USA
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34
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Asturias FJ, Cheung IK, Sabouri N, Chilkova O, Wepplo D, Johansson E. Structure of Saccharomyces cerevisiae DNA polymerase epsilon by cryo-electron microscopy. Nat Struct Mol Biol 2005; 13:35-43. [PMID: 16369485 DOI: 10.1038/nsmb1040] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2005] [Accepted: 11/17/2005] [Indexed: 11/08/2022]
Abstract
The structure of the multisubunit yeast DNA polymerase epsilon (Pol epsilon) was determined to 20-A resolution using cryo-EM and single-particle image analysis. A globular domain comprising the catalytic Pol2 subunit is flexibly connected to an extended structure formed by subunits Dpb2, Dpb3 and Dpb4. Consistent with the reported involvement of the latter in interaction with nucleic acids, the Dpb portion of the structure directly faces a single cleft in the Pol2 subunit that seems wide enough to accommodate double-stranded DNA. Primer-extension experiments reveal that Pol epsilon processivity requires a minimum length of primer-template duplex that corresponds to the dimensions of the extended Dpb structure. Together, these observations suggest a mechanism for interaction of Pol epsilon with DNA that might explain how the structure of the enzyme contributes to its intrinsic processivity.
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Affiliation(s)
- Francisco J Asturias
- Department of Structural Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
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35
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Abstract
Three DNA polymerases are thought to function at the eukaryotic DNA replication fork. Currently, a coherent model has been derived for the composition and activities of the lagging strand machinery. RNA-DNA primers are initiated by DNA polymerase ot-primase. Loading of the proliferating cell nuclear antigen, PCNA, dissociates DNA polymerase ca and recruits DNA polymerase S and the flap endonuclease FEN1 for elongation and in preparation for its requirement during maturation, respectively. Nick translation by the strand displacement action of DNA polymerase 8, coupled with the nuclease action of FEN1, results in processive RNA degradation until a proper DNA nick is reached for closure by DNA ligase I. In the event of excessive strand displacement synthesis, other factors, such as the Dna2 nuclease/helicase, are required to trim excess flaps. Paradoxically, the composition and activity of the much simpler leading strand machinery has not been clearly established. The burden of evidence suggests that DNA polymerase E normally replicates this strand,but under conditions of dysfunction, DNA polymerase 8 may substitute.
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Affiliation(s)
- Parie Garg
- Washington University School of Medicine, St. Louis, MO 63110, USA
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36
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Abstract
Initiation and completion of DNA replication defines the beginning and ending of S phase of the cell cycle. Successful progression through S phase requires that replication be properly regulated and monitored to ensure that the entire genome is duplicated exactly once, without errors, in a timely fashion. Given the immense size and complexity of eukaryotic genomes, this presents a significant challenge for the cell. As a result, DNA replication has evolved into a tightly regulated process involving the coordinated action of numerous factors that function in all phases of the cell cycle. We will review our current understanding of these processes from the formation of prereplicative complexes in preparation for S phase to the series of events that culminate in the loading of DNA polymerases during S phase. We will incorporate structural data from archaeal and bacterial replication proteins and discuss their implications for understanding the mechanism of action of their corresponding eukaryotic homologues. We will also describe the concept of replication licensing which protects against genomic instability by limiting initiation events to once per cell cycle. Lastly, we will review our knowledge of checkpoint pathways that maintain the integrity of stalled forks and relay defects in replication to the rest of the cell cycle.
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Affiliation(s)
- David Y Takeda
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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37
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Hiraga SI, Hagihara-Hayashi A, Ohya T, Sugino A. DNA polymerases α, δ, and ɛ localize and function together at replication forks in Saccharomyces cerevisiae. Genes Cells 2005; 10:297-309. [PMID: 15773893 DOI: 10.1111/j.1365-2443.2005.00843.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Early in eukaryotic cell cycle, a pre-RC is assembled at each replication origin with ORC, Cdc6, Cdt1 and Mcm2-7 proteins to license the origin for use in the subsequent S phase. Licensed origin must then be activated by S-Cdk and Ddk. At the onset of S phase, RPA is loaded on to the ARS in a reaction stimulated by S-Cdk and Ddk, followed by Cdc45-dependent loading of pol alpha, -delta, and -epsilon. This study examines cell cycle-dependent localization of pol alpha, -delta and -epsilon in Saccharomyces cerevisiae using immuno-histochemical and chromatin immuno-precipitation methods. The results show that pol alpha, -delta, or -epsilon localizes on chromatin as punctate foci at all stages of the cell cycle. However, some foci overlap with or are adjacent to foci pulse-labeled with bromodeoxyuridine during S phase, indicating these are replicating foci. DNA microarray analysis localized pol alpha, -delta, and -epsilon to early firing ARSs on yeast chromosome III and VI at the beginning of S phase. These data collectively suggest that bidirectional replication occurs at specific foci in yeast chromosomes and that pol alpha, -delta, and -epsilon localize and function together at multiple replication forks during S phase.
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Affiliation(s)
- Shin-Ichiro Hiraga
- Laboratories for Biomolecular Networks, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamada-oka, Suita, Osaka 565-0871, Japan
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38
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Dell'Era P, Nicoli S, Peri G, Nieddu M, Ennas MG, Presta M. FGF2-induced upregulation of DNA polymerase-δ p12 subunit in endothelial cells. Oncogene 2004; 24:1117-21. [PMID: 15608665 DOI: 10.1038/sj.onc.1208359] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
p12 represents the smallest, so far poorly characterized subunit of the mammalian DNA polymerase delta (pol delta) heterotetramer. Previously, to gain a molecular understanding of endothelial cell activation by fibroblast growth factor-2 (FGF2), we identified an upregulated transcript in FGF2-overexpressing murine aortic endothelial cells (FGF2-T-MAE cells) showing 89% identity with human p12. Here, we cloned the open reading frame of the murine p12 cDNA and confirmed the capacity of overexpressed or exogenously added FGF2 to upregulate p12 mRNA and protein in endothelial and NIH3T3 cells with no effect on the other pol delta subunits. p12 expression was instead unaffected by serum and different mitogens. Also, anti-p12 antibodies decorated FGF2-T-MAE cell nuclei and their chromosome outline during metaphase. Small interfering RNA-mediated knockdown of p12 caused a significant decrease in FGF2-driven proliferation rate of FGF2-T-MAE cells, in keeping with a modulatory role of p12 in pol delta activity. Immunoistochemistry of FGF2-embedded Matrigel plugs and FGF2-overexpressing tumor xenografts demonstrated a nuclear p12 staining of angiogenic CD31(+) endothelium. p12 immunoreactivity was also observed in the CD45(+)/CD11b(+) inflammatory infiltrate. Thus, FGF2 upregulates p12 expression in endothelial cells in vitro and in vivo. p12 expression in infiltrating inflammatory cells may suggest additional, cell proliferation-unrelated functions for this pol delta subunit.
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Affiliation(s)
- Patrizia Dell'Era
- Unit of General Pathology and Immunology, Department of Biomedical Sciences and Biotechnology, University of Brescia, viale Europa 11, 25123 Brescia, Italy
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39
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Noguchi E, Noguchi C, McDonald WH, Yates JR, Russell P. Swi1 and Swi3 are components of a replication fork protection complex in fission yeast. Mol Cell Biol 2004; 24:8342-55. [PMID: 15367656 PMCID: PMC516732 DOI: 10.1128/mcb.24.19.8342-8355.2004] [Citation(s) in RCA: 163] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Swi1 is required for programmed pausing of replication forks near the mat1 locus in the fission yeast Schizosaccharomyces pombe. This fork pausing is required to initiate a recombination event that switches mating type. Swi1 is also needed for the replication checkpoint that arrests division in response to fork arrest. How Swi1 accomplishes these tasks is unknown. Here we report that Swi1 copurifies with a 181-amino-acid protein encoded by swi3(+). The Swi1-Swi3 complex is required for survival of fork arrest and for activation of the replication checkpoint kinase Cds1. Association of Swi1 and Swi3 with chromatin during DNA replication correlated with movement of the replication fork. swi1Delta and swi3Delta mutants accumulated Rad22 (Rad52 homolog) DNA repair foci during replication. These foci correlated with the Rad22-dependent appearance of Holliday junction (HJ)-like structures in cells lacking Mus81-Eme1 HJ resolvase. Rhp51 and Rhp54 homologous recombination proteins were not required for viability in swi1Delta or swi3Delta cells, indicating that the HJ-like structures arise from single-strand DNA gaps or rearranged forks instead of broken forks. We propose that Swi1 and Swi3 define a fork protection complex that coordinates leading- and lagging-strand synthesis and stabilizes stalled replication forks.
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Affiliation(s)
- Eishi Noguchi
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.
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40
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Garg P, Stith CM, Sabouri N, Johansson E, Burgers PM. Idling by DNA polymerase delta maintains a ligatable nick during lagging-strand DNA replication. Genes Dev 2004; 18:2764-73. [PMID: 15520275 PMCID: PMC528896 DOI: 10.1101/gad.1252304] [Citation(s) in RCA: 172] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
During each yeast cell cycle, approximately 100,000 nicks are generated during lagging-strand DNA replication. Efficient nick processing during Okazaki fragment maturation requires the coordinated action of DNA polymerase delta (Pol delta) and the FLAP endonuclease FEN1. Misregulation of this process leads to the accumulation of double-stranded breaks and cell lethality. Our studies highlight a remarkably efficient mechanism for Okazaki fragment maturation in which Pol delta by default displaces 2-3 nt of any downstream RNA or DNA it encounters. In the presence of FEN1, efficient nick translation ensues, whereby a mixture of mono- and small oligonucleotides are released. If FEN1 is absent or not optimally functional, the ability of Pol delta to back up via its 3'-5'-exonuclease activity, a process called idling, maintains the polymerase at a position that is ideal either for ligation (in case of a DNA-DNA nick) or for subsequent engagement by FEN1 (in case of a DNA-RNA nick). Consistent with the hypothesis that DNA polymerase epsilon is the leading-strand enzyme, we observed no idling by this enzyme and no cooperation with FEN1 for creating a ligatable nick.
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Affiliation(s)
- Parie Garg
- Department of Biochemistry, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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41
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Tsubota T, Maki S, Kubota H, Sugino A, Maki H. Double-stranded DNA binding properties of Saccharomyces cerevisiae DNA polymerase epsilon and of the Dpb3p-Dpb4p subassembly. Genes Cells 2004; 8:873-88. [PMID: 14622139 DOI: 10.1046/j.1365-2443.2003.00683.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND DNA polymerase epsilon (Pol epsilon) of Saccharomyces cerevisiae participates in many aspects of DNA replication, as well as in DNA repair. In order to clarify molecular mechanisms employed in the multiple tasks of Pol epsilon, we have been characterizing the interaction between Pol epsilon and DNA. RESULTS Analysis of the four-subunit Pol epsilon complex by gel mobility shift assay revealed that the complex binds not only to single-stranded (ss) DNA but also equally well to double-stranded (ds) DNA. A truncated polypeptide consisting of the N-terminal domain of Pol2p catalytic subunit binds to ssDNA but not to dsDNA, indicating that the Pol2p C-terminal domain and/or the auxiliary subunits are involved in the dsDNA-binding. The dsDNA-binding by Pol epsilon does not require DNA ends or specific DNA sequences. Further analysis by competition experiments indicated that Pol epsilon contains at least two distinct DNA-binding sites, one of which binds exclusively to ssDNA and the other to dsDNA. The dsDNA-binding site, however, is suggested to also bind ssDNA. The DNA polymerase activity of Pol epsilon is inhibited by ssDNA but not by dsDNA. Furthermore, purification of the Pol epsilon auxiliary subunits Dpb3p and Dpb4p revealed that these proteins form a heterodimer and associate with dsDNA. CONCLUSIONS Pol epsilon has multiple sites at which it interacts with DNA. One of these sites has a strong affinity for dsDNA, a feature that is not generally associated with DNA polymerases. Involvement of the Dpb3p-Dpb4p complex in the dsDNA-binding of Pol epsilon is inferred.
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Affiliation(s)
- Toshiaki Tsubota
- Department of Molecular Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
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42
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Pavlov YI, Maki S, Maki H, Kunkel TA. Evidence for interplay among yeast replicative DNA polymerases alpha, delta and epsilon from studies of exonuclease and polymerase active site mutations. BMC Biol 2004; 2:11. [PMID: 15163346 PMCID: PMC434536 DOI: 10.1186/1741-7007-2-11] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2004] [Accepted: 05/26/2004] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA polymerase epsilon (Pol epsilon) is essential for S-phase replication, DNA damage repair and checkpoint control in yeast. A pol2-Y831A mutation leading to a tyrosine to alanine change in the Pol epsilon active site does not cause growth defects and confers a mutator phenotype that is normally subtle but strong in a mismatch repair-deficient strain. Here we investigate the mechanism responsible for the mutator effect. RESULTS Purified four-subunit Y831A Pol epsilon turns over more deoxynucleoside triphosphates to deoxynucleoside monophosphates than does wild-type Pol epsilon, suggesting altered coordination between the polymerase and exonuclease active sites. The pol2-Y831A mutation suppresses the mutator effect of the pol2-4 mutation in the exonuclease active site that abolishes proofreading by Pol epsilon, as measured in haploid strain with the pol2-Y831A,4 double mutation. Analysis of mutation rates in diploid strains reveals that the pol2-Y831A allele is recessive to pol2-4. In addition, the mutation rates of strains with the pol2-4 mutation in combination with active site mutator mutations in Pol delta and Pol alpha suggest that Pol epsilon may proofread certain errors made by Pol alpha and Pol delta during replication in vivo. CONCLUSIONS Our data suggest that Y831A replacement in Pol epsilon reduces replication fidelity and its participation in chromosomal replication, but without eliminating an additional function that is essential for viability. This suggests that other polymerases can substitute for certain functions of polymerase epsilon.
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Affiliation(s)
- Youri I Pavlov
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institute of Health, DHHS, Research Triangle Park, NC 27709, USA
- Eppley Institute for Research in Cancer and Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Satoko Maki
- Laboratory of Microbial Molecular Genetics, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara 630-01, Japan
| | - Hisaji Maki
- Laboratory of Microbial Molecular Genetics, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara 630-01, Japan
| | - Thomas A Kunkel
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institute of Health, DHHS, Research Triangle Park, NC 27709, USA
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences National Institute of Health, DHHS, Research Triangle Park, NC 27709, USA
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43
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Johansson E, Garg P, Burgers PMJ. The Pol32 Subunit of DNA Polymerase δ Contains Separable Domains for Processive Replication and Proliferating Cell Nuclear Antigen (PCNA) Binding. J Biol Chem 2004; 279:1907-15. [PMID: 14594808 DOI: 10.1074/jbc.m310362200] [Citation(s) in RCA: 146] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have carried out a domain analysis of POL32, the third subunit of Saccharomyces cerevisiae DNA polymerase delta (Pol delta). Interactions with POL31, the second subunit of Pol delta, are specified by the amino-terminal 92 amino acids, whereas interactions with the replication clamp proliferating cell nuclear antigen (PCNA, POL30) reside at the extreme carboxyl-terminal region. Pol32 binding, in vivo and in vitro, to the large subunit of DNA polymerase alpha, POL1, requires the carboxyl-proximal region of Pol32. The amino-terminal region of Pol32 is essential for damage-induced mutagenesis. However, the presence of its carboxyl-terminal PCNA-binding domain enhances the efficiency of mutagenesis, particularly at high loads of DNA damage. In vitro, in the absence of effector DNA, the PCNA-binding domain of Pol32 is essential for PCNA-Pol delta interactions. However, this domain has minimal importance for processive DNA synthesis by the ternary DNA-PCNA-Pol delta complex. Rather, processivity is determined by PCNA-binding domains located in the Pol3 and/or Pol31 subunits. Using diagnostic PCNA mutants, we show that during DNA synthesis the carboxyl-terminal domain of Pol32 interacts with the carboxyl-terminal region of PCNA, whereas interactions of the other subunit(s) of Pol delta localize largely to a hydrophobic pocket at the interdomain connector loop region of PCNA.
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Affiliation(s)
- Erik Johansson
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
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44
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Yang Z, Lau R, Marcadier JL, Chitayat D, Pearson CE. Replication inhibitors modulate instability of an expanded trinucleotide repeat at the myotonic dystrophy type 1 disease locus in human cells. Am J Hum Genet 2003; 73:1092-105. [PMID: 14574643 PMCID: PMC1180489 DOI: 10.1086/379523] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2003] [Accepted: 08/26/2003] [Indexed: 11/03/2022] Open
Abstract
Gene-specific CTG/CAG repeat expansion is associated with at least 14 human diseases, including myotonic dystrophy type 1 (DM1). Most of our understanding of trinucleotide instability is from nonhuman models, which have presented mixed results, supporting replication errors or processes independent of cell division as causes. Nevertheless, the mechanism occurring at the disease loci in patient cells is poorly understood. Using primary fibroblasts derived from a fetus with DM1, we have shown that spontaneous expansion of the diseased (CTG)(216) allele occurred in proliferating cells but not in quiescent cells. Expansions were "synchronous," with mutation frequencies approaching 100%. Furthermore, cells were treated with agents known to alter DNA synthesis but not to directly damage DNA. Inhibiting replication initiation with mimosine had no effect upon instability. Inhibiting both leading- and lagging-strand synthesis with aphidicolin or blocking only lagging strand synthesis with emetine significantly enhanced CTG expansions. It was striking that only the expanded DM1 allele was altered, leaving the normal allele, (CTG)(12), and other repeat loci unaffected. Standard and small-pool polymerase chain reaction revealed that inhibitors enhanced the magnitude of short expansions in most cells threefold, whereas 11%-25% of cells experienced gains of 122-170 repeats, to sizes of (CTG)(338)-(CTG)(386). Similar results were observed for an adult DM1 cell line. Our results support a role for the perturbation of replication fork dynamics in DM1 CTG expansions within patient fibroblasts. This is the first report that repeat-length alterations specific to a disease allele can be modulated by exogenously added compounds.
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Affiliation(s)
- Zhi Yang
- Program of Genetics and Genomic Biology, The Hospital for Sick Children, Department of Molecular and Medical Genetics, University of Toronto, and University Health Network, Toronto
| | - Rachel Lau
- Program of Genetics and Genomic Biology, The Hospital for Sick Children, Department of Molecular and Medical Genetics, University of Toronto, and University Health Network, Toronto
| | - Julien L. Marcadier
- Program of Genetics and Genomic Biology, The Hospital for Sick Children, Department of Molecular and Medical Genetics, University of Toronto, and University Health Network, Toronto
| | - David Chitayat
- Program of Genetics and Genomic Biology, The Hospital for Sick Children, Department of Molecular and Medical Genetics, University of Toronto, and University Health Network, Toronto
| | - Christopher E. Pearson
- Program of Genetics and Genomic Biology, The Hospital for Sick Children, Department of Molecular and Medical Genetics, University of Toronto, and University Health Network, Toronto
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45
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Shcherbakova PV, Pavlov YI, Chilkova O, Rogozin IB, Johansson E, Kunkel TA. Unique error signature of the four-subunit yeast DNA polymerase epsilon. J Biol Chem 2003; 278:43770-80. [PMID: 12882968 DOI: 10.1074/jbc.m306893200] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have purified wild type and exonuclease-deficient four-subunit DNA polymerase epsilon (Pol epsilon) complex from Saccharomyces cerevisiae and analyzed the fidelity of DNA synthesis by the two enzymes. Wild type Pol epsilon synthesizes DNA accurately, generating single-base substitutions and deletions at average error rates of </=2 x 10-5 and </=5 x 10-7, respectively. Pol epsilon lacking 3' --> 5' exonuclease activity is less accurate to a degree suggesting that wild type Pol epsilon proofreads at least 92% of base substitution errors and at least 99% of frameshift errors made by the polymerase. Surprisingly the base substitution fidelity of exonuclease-deficient Pol epsilon is severalfold lower than that of proofreading-deficient forms of other replicative polymerases. Moreover the spectrum of errors shows a feature not seen with other A, B, C, or X family polymerases: a high proportion of transversions resulting from T.dTTP, T.dCTP, and C.dTTP mispairs. This unique error specificity and amino acid sequence alignments suggest that the structure of the polymerase active site of Pol epsilon differs from those of other B family members. We observed both similarities and differences between the spectrum of substitutions generated by proofreading-deficient Pol epsilon in vitro and substitutions occurring in vivo in a yeast strain defective in Pol epsilon proofreading and DNA mismatch repair. We discuss the implications of these findings for the role of Pol epsilon polymerase activity in DNA replication.
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Affiliation(s)
- Polina V Shcherbakova
- Laboratory of Molecular Genetics, NIEHS, National Institutes of Health, North Carolina 27709, USA
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46
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Lenzmeier BA, Freudenreich CH. Trinucleotide repeat instability: a hairpin curve at the crossroads of replication, recombination, and repair. Cytogenet Genome Res 2003; 100:7-24. [PMID: 14526162 DOI: 10.1159/000072836] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2002] [Accepted: 01/06/2003] [Indexed: 11/19/2022] Open
Abstract
The trinucleotide repeats that expand to cause human disease form hairpin structures in vitro that are proposed to be the major source of their genetic instability in vivo. If a replication fork is a train speeding along a track of double-stranded DNA, the trinucleotide repeats are a hairpin curve in the track. Experiments have demonstrated that the train can become derailed at the hairpin curve, resulting in significant damage to the track. Repair of the track often results in contractions and expansions of track length. In this review we introduce the in vitro evidence for why CTG/CAG and CCG/CGG repeats are inherently unstable and discuss how experiments in model organisms have implicated the replication, recombination and repair machinery as contributors to trinucleotide repeat instability in vivo.
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Affiliation(s)
- B A Lenzmeier
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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47
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Chanet R, Heude M. Characterization of mutations that are synthetic lethal with pol3-13, a mutated allele of DNA polymerase delta in Saccharomyces cerevisiae. Curr Genet 2003; 43:337-50. [PMID: 12759774 DOI: 10.1007/s00294-003-0407-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2003] [Revised: 04/11/2003] [Accepted: 04/23/2003] [Indexed: 10/26/2022]
Abstract
The pol3-13 mutation is located in the C-terminal end of POL3, the gene encoding the catalytic subunit of polymerase delta, and confers thermosensitivity onto the Saccharomyces cerevisiae mutant strain. To get insight about DNA replication control, we performed a genetic screen to identify genes that are synthetic lethal with pol3-13. Mutations in genes encoding the two other subunits of DNA polymerase delta (HYS2, POL32) were identified. Mutations in two recombination genes (RAD50, RAD51) were also identified, confirming that homologous recombination is necessary for pol3-13 mutant strain survival. Other mutations were identified in genes involved in repair and genome stability (MET18/ MMS19), in the control of origin-firing and/or transcription (ABF1, SRB7), in the S/G2 checkpoint (RAD53), in the Ras-cAMP signal transduction pathway (MKS1), in nuclear pore metabolism (SEH1), in protein degradation (DOC1) and in folding (YDJ1). Finally, mutations in three genes of unknown function were isolated (NBP35, DRE2, TAH18). Synthetic lethality between pol3-13 and each of the three mutants pol32, mms19 and doc1 could be suppressed by a rad18 deletion, suggesting an important role of ubiquitination in DNA replication control. We propose that the pol3-13 mutant generates replicative problems that need both homologous recombination and an intact checkpoint machinery to be overcome.
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Affiliation(s)
- Roland Chanet
- Institut Curie Recherche, CNRS UMR2027/Institut Curie, Bât. 110, Centre Universitaire, 91405 Orsay Cédex, France.
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48
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Chilkova O, Jonsson BH, Johansson E. The quaternary structure of DNA polymerase epsilon from Saccharomyces cerevisiae. J Biol Chem 2003; 278:14082-6. [PMID: 12571237 DOI: 10.1074/jbc.m211818200] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA polymerase epsilon (Pol epsilon) from Saccharomyces cerevisiae consists of four subunits (Pol2, Dpb2, Dpb3, and Dpb4) and is essential for chromosomal DNA replication. Biochemical characterizations of Pol epsilon have been cumbersome due to protease sensitivity and the limited amounts of Pol epsilon in cells. We have developed a protocol for overexpression and purification of Pol epsilon from S. cerevisiae. The native four-subunit complex was purified to homogeneity by conventional chromatography. Pol epsilon was characterized biochemically by sedimentation velocity experiments and gel filtration experiments. The stoichiometry of the four subunits was estimated to be 1:1:1:1 from colloidal Coomassie-stained gels. Based on the sedimentation coefficient (11.9 S) and the Stokes radius (74.5 A), a molecular mass for Pol epsilon of 371 kDa was calculated, in good agreement with the calculated molecular mass of 379 kDa for a heterotetramer. Furthermore, analytical equilibrium ultracentrifugation experiments support the proposed heterotetrameric structure of Pol epsilon. Thus, both DNA polymerase delta and Pol epsilon are purified as monomeric complexes, in agreement with accumulating evidence that Pol delta and Pol epsilon are located on opposite strands of the eukaryotic replication fork.
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Affiliation(s)
- Olga Chilkova
- Department of Medical Biochemistry and Biophysics, Umeå University, Sweden
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49
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Shcherbakova PV, Bebenek K, Kunkel TA. Functions of eukaryotic DNA polymerases. SCIENCE OF AGING KNOWLEDGE ENVIRONMENT : SAGE KE 2003; 2003:RE3. [PMID: 12844548 DOI: 10.1126/sageke.2003.8.re3] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
A major function of DNA polymerases is to accurately replicate the six billion nucleotides that constitute the human genome. This task is complicated by the fact that the genome is constantly challenged by a variety of endogenous and exogenous DNA-damaging agents. DNA damage can block DNA replication or alter base coding potential, resulting in mutations. In addition, the accumulation of damage in nonreplicating DNA can affect gene expression, which leads to the malfunction of many cellular processes. A number of DNA repair systems operate in cells to remove DNA lesions, and several DNA polymerases are known to be the key components of these repair systems. In the past few years, a number of novel DNA polymerases have been discovered that likely function in replicative bypass of DNA damage missed by DNA repair enzymes or in specialized forms of repair. Furthermore, DNA polymerases can act as sensors in cell cycle checkpoint pathways that prevent entry into mitosis until damaged DNA is repaired and replication is completed. The list of DNA template-dependent eukaryotic DNA polymerases now consists of 14 enzymes with amazingly different properties. In this review, we discuss the possible functions of these polymerases in DNA damage repair, the replication of intact and damaged chromosomes, and cell cycle checkpoints.
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Affiliation(s)
- Polina V Shcherbakova
- Laboratory of Molecular Genetics at the National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
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50
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Xie B, Mazloum N, Liu L, Rahmeh A, Li H, Lee MYWT. Reconstitution and characterization of the human DNA polymerase delta four-subunit holoenzyme. Biochemistry 2002; 41:13133-42. [PMID: 12403614 DOI: 10.1021/bi0262707] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mammalian DNA polymerase delta was originally characterized as a tightly associated heterodimer consisting of the catalytic subunit, p125, and the p50 subunit. Recently, two additional subunits, the third (p68) and fourth subunits (p12), have been identified. The heterotetrameric human pol delta complex was reconstituted by overexpression of the four subunits in Sf9 cells, followed by purification to near-homogeneity using FPLC chromatography. The properties of the four-subunit enzyme were shown to be functionally indistinguishable from those of pol delta isolated from calf thymus. The physicochemical properties of both the reconstituted heterotetramer and the heterodimer of the p125 and p50 subunits were examined by gel filtration and glycerol gradient ultracentrifugation. These studies show quite clearly that the heterodimer and heterotetramer complexes do not behave in solution as dimeric structures. This issue is of significance because several studies of the yeast pol delta complexes have indicated that the third subunit is able to bring about the dimerization of the pol delta complex. The heterodimer is only weakly stimulated by PCNA, whereas the heterotetramer is strongly stimulated to a level with a specific activity comparable to that of the calf thymus enzyme. These results resolve earlier, conflicting reports on the response of the heterodimer to PCNA. Nevertheless, the heterodimer does have some ability to interact functionally with PCNA, consistent with evidence that the p125 subunit itself has an ability to interact with PCNA. The functional interaction of PCNA with the pol delta complex may likely involve multiple contacts.
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Affiliation(s)
- Bin Xie
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York 10595, USA
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