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Hürtgen D, Mascarenhas J, Heymann M, Murray SM, Schwille P, Sourjik V. Reconstitution and Coupling of DNA Replication and Segregation in a Biomimetic System. Chembiochem 2019; 20:2633-2642. [PMID: 31344304 PMCID: PMC6899551 DOI: 10.1002/cbic.201900299] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/20/2019] [Indexed: 12/30/2022]
Abstract
A biomimetic system capable of replication and segregation of genetic material constitutes an essential component for the future design of a minimal synthetic cell. Here we have used the simple T7 bacteriophage system and the plasmid-derived ParMRC system to establish in vitro DNA replication and DNA segregation, respectively. These processes were incorporated into biomimetic compartments providing an enclosed reaction space. The functional lifetime of the encapsulated segregation system could be prolonged by equipping it with ATP-regenerating and oxygen-scavenging systems. Finally, we showed that DNA replication and segregation processes could be coupled in vitro by using condensed DNA nanoparticles resulting from DNA replication. ParM spindles extended over tens of micrometers and could thus be used for segregation in compartments that are significantly longer than bacterial cell size. Overall, this work demonstrates the successful bottom-up assembly and coupling of molecular machines that mediate replication and segregation, thus providing an important step towards the development of a fully functional minimal cell.
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Affiliation(s)
- Daniel Hürtgen
- Max Planck Institute for Terrestrial Microbiology &LOEWE Center for Synthetic Microbiology (Synmikro)Karl-von-Frisch Strasse 1635043MarburgGermany
| | - Judita Mascarenhas
- Max Planck Institute for Terrestrial Microbiology &LOEWE Center for Synthetic Microbiology (Synmikro)Karl-von-Frisch Strasse 1635043MarburgGermany
| | - Michael Heymann
- Max Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Seán M. Murray
- Max Planck Institute for Terrestrial Microbiology &LOEWE Center for Synthetic Microbiology (Synmikro)Karl-von-Frisch Strasse 1635043MarburgGermany
| | - Petra Schwille
- Max Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology &LOEWE Center for Synthetic Microbiology (Synmikro)Karl-von-Frisch Strasse 1635043MarburgGermany
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Xing X, Kane DP, Bulock CR, Moore EA, Sharma S, Chabes A, Shcherbakova PV. A recurrent cancer-associated substitution in DNA polymerase ε produces a hyperactive enzyme. Nat Commun 2019; 10:374. [PMID: 30670691 PMCID: PMC6343027 DOI: 10.1038/s41467-018-08145-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 12/12/2018] [Indexed: 11/17/2022] Open
Abstract
Alterations in the exonuclease domain of DNA polymerase ε (Polε) cause ultramutated tumors. Severe mutator effects of the most common variant, Polε-P286R, modeled in yeast suggested that its pathogenicity involves yet unknown mechanisms beyond simple proofreading deficiency. We show that, despite producing a catastrophic amount of replication errors in vivo, the yeast Polε-P286R analog retains partial exonuclease activity and is more accurate than exonuclease-dead Polε. The major consequence of the arginine substitution is a dramatically increased DNA polymerase activity. This is manifested as a superior ability to copy synthetic and natural templates, extend mismatched primer termini, and bypass secondary DNA structures. We discuss a model wherein the cancer-associated substitution limits access of the 3’-terminus to the exonuclease site and promotes binding at the polymerase site, thus stimulating polymerization. We propose that the ultramutator effect results from increased polymerase activity amplifying the contribution of Polε errors to the genomic mutation rate. Somatic alterations in the exonuclease domain of DNA polymerase ɛ have been linked to the development of highly mutated cancers. Here, the authors report that a major consequence of the most common cancer-associated Polɛ variant is a dramatically increased DNA polymerase activity.
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Affiliation(s)
- 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.,Comprehensive Cancer Center, Ohio State University, Columbus, OH, 43210, USA
| | - Daniel P Kane
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA.,Department of Biological and Environmental Sciences, Le Moyne College, Syracuse, NY, 13214, USA
| | - 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
| | - Elizabeth A Moore
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Sushma Sharma
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87, Umeå, Sweden
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87, Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden, Umeå University, 901 87, Umeå, Sweden
| | - 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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Kunkel TA, Burgers PMJ. Arranging eukaryotic nuclear DNA polymerases for replication: Specific interactions with accessory proteins arrange Pols α, δ, and ϵ in the replisome for leading-strand and lagging-strand DNA replication. Bioessays 2017; 39:10.1002/bies.201700070. [PMID: 28749073 PMCID: PMC5579836 DOI: 10.1002/bies.201700070] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Biochemical and cryo-electron microscopy studies have just been published revealing interactions among proteins of the yeast replisome that are important for highly coordinated synthesis of the two DNA strands of the nuclear genome. These studies reveal key interactions important for arranging DNA polymerases α, δ, and ϵ for leading and lagging strand replication. The CMG (Mcm2-7, Cdc45, GINS) helicase is central to this interaction network. These are but the latest examples of elegant studies performed in the recent past that lead to a much better understanding of how the eukaryotic replication fork achieves efficient DNA replication that is accurate enough to prevent diseases yet allows evolution.
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Affiliation(s)
- Thomas A. Kunkel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC, USA
| | - Peter M. J. Burgers
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
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Lee MYWT, Wang X, Zhang S, Zhang Z, Lee EYC. Regulation and Modulation of Human DNA Polymerase δ Activity and Function. Genes (Basel) 2017; 8:genes8070190. [PMID: 28737709 PMCID: PMC5541323 DOI: 10.3390/genes8070190] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 07/07/2017] [Accepted: 07/11/2017] [Indexed: 12/28/2022] Open
Abstract
This review focuses on the regulation and modulation of human DNA polymerase δ (Pol δ). The emphasis is on the mechanisms that regulate the activity and properties of Pol δ in DNA repair and replication. The areas covered are the degradation of the p12 subunit of Pol δ, which converts it from a heterotetramer (Pol δ4) to a heterotrimer (Pol δ3), in response to DNA damage and also during the cell cycle. The biochemical mechanisms that lead to degradation of p12 are reviewed, as well as the properties of Pol δ4 and Pol δ3 that provide insights into their functions in DNA replication and repair. The second focus of the review involves the functions of two Pol δ binding proteins, polymerase delta interaction protein 46 (PDIP46) and polymerase delta interaction protein 38 (PDIP38), both of which are multi-functional proteins. PDIP46 is a novel activator of Pol δ4, and the impact of this function is discussed in relation to its potential roles in DNA replication. Several new models for the roles of Pol δ3 and Pol δ4 in leading and lagging strand DNA synthesis that integrate a role for PDIP46 are presented. PDIP38 has multiple cellular localizations including the mitochondria, the spliceosomes and the nucleus. It has been implicated in a number of cellular functions, including the regulation of specialized DNA polymerases, mitosis, the DNA damage response, mouse double minute 2 homolog (Mdm2) alternative splicing and the regulation of the NADPH oxidase 4 (Nox4).
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Affiliation(s)
- Marietta Y W T Lee
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
| | - Xiaoxiao Wang
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
| | - Sufang Zhang
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
| | - Zhongtao Zhang
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
| | - Ernest Y C Lee
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
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Zhao L, Washington MT. Translesion Synthesis: Insights into the Selection and Switching of DNA Polymerases. Genes (Basel) 2017; 8:genes8010024. [PMID: 28075396 PMCID: PMC5295019 DOI: 10.3390/genes8010024] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/04/2017] [Accepted: 01/04/2017] [Indexed: 01/05/2023] Open
Abstract
DNA replication is constantly challenged by DNA lesions, noncanonical DNA structures and difficult-to-replicate DNA sequences. Two major strategies to rescue a stalled replication fork and to ensure continuous DNA synthesis are: (1) template switching and recombination-dependent DNA synthesis; and (2) translesion synthesis (TLS) using specialized DNA polymerases to perform nucleotide incorporation opposite DNA lesions. The former pathway is mainly error-free, and the latter is error-prone and a major source of mutagenesis. An accepted model of translesion synthesis involves DNA polymerase switching steps between a replicative DNA polymerase and one or more TLS DNA polymerases. The mechanisms that govern the selection and exchange of specialized DNA polymerases for a given DNA lesion are not well understood. In this review, recent studies concerning the mechanisms of selection and switching of DNA polymerases in eukaryotic systems are summarized.
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Affiliation(s)
- Linlin Zhao
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI 48859, USA.
- Science of Advanced Materials Program, Central Michigan University, Mount Pleasant, MI 48859, USA.
| | - M Todd Washington
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
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