1
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Yuan Z, Georgescu R, Yao NY, Yurieva O, O’Donnell ME, Li H. Mechanism of PCNA loading by Ctf18-RFC for leading-strand DNA synthesis. Science 2024; 385:eadk5901. [PMID: 39088616 PMCID: PMC11349045 DOI: 10.1126/science.adk5901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 02/10/2024] [Accepted: 05/31/2024] [Indexed: 08/03/2024]
Abstract
The proliferating cell nuclear antigen (PCNA) clamp encircles DNA to hold DNA polymerases (Pols) to DNA for processivity. The Ctf18-RFC PCNA loader, a replication factor C (RFC) variant, is specific to the leading-strand Pol (Polε). We reveal here the underlying mechanism of Ctf18-RFC specificity to Polε using cryo-electron microscopy and biochemical studies. We found that both Ctf18-RFC and Polε contain specific structural features that direct PCNA loading onto DNA. Unlike other clamp loaders, Ctf18-RFC has a disordered ATPase associated with a diverse cellular activities (AAA+) motor that requires Polε to bind and stabilize it for efficient PCNA loading. In addition, Ctf18-RFC can pry prebound Polε off of DNA, then load PCNA onto DNA and transfer the PCNA-DNA back to Polε. These elements in both Ctf18-RFC and Polε provide specificity in loading PCNA onto DNA for Polε.
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Affiliation(s)
- Zuanning Yuan
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Roxana Georgescu
- DNA Replication Laboratory, The Rockefeller University, New York, New York, USA
- Howard Hughes Medical Institute, New York, New York, USA
| | - Nina Y. Yao
- DNA Replication Laboratory, The Rockefeller University, New York, New York, USA
| | - Olga Yurieva
- DNA Replication Laboratory, The Rockefeller University, New York, New York, USA
- Howard Hughes Medical Institute, New York, New York, USA
| | - Michael E. O’Donnell
- DNA Replication Laboratory, The Rockefeller University, New York, New York, USA
- Howard Hughes Medical Institute, New York, New York, USA
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA
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2
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Mullins EA, Salay LE, Durie CL, Bradley NP, Jackman JE, Ohi MD, Chazin WJ, Eichman BF. A mechanistic model of primer synthesis from catalytic structures of DNA polymerase α-primase. Nat Struct Mol Biol 2024; 31:777-790. [PMID: 38491139 PMCID: PMC11102853 DOI: 10.1038/s41594-024-01227-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 01/12/2024] [Indexed: 03/18/2024]
Abstract
The mechanism by which polymerase α-primase (polα-primase) synthesizes chimeric RNA-DNA primers of defined length and composition, necessary for replication fidelity and genome stability, is unknown. Here, we report cryo-EM structures of Xenopus laevis polα-primase in complex with primed templates representing various stages of DNA synthesis. Our data show how interaction of the primase regulatory subunit with the primer 5' end facilitates handoff of the primer to polα and increases polα processivity, thereby regulating both RNA and DNA composition. The structures detail how flexibility within the heterotetramer enables synthesis across two active sites and provide evidence that termination of DNA synthesis is facilitated by reduction of polα and primase affinities for the varied conformations along the chimeric primer-template duplex. Together, these findings elucidate a critical catalytic step in replication initiation and provide a comprehensive model for primer synthesis by polα-primase.
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Affiliation(s)
- Elwood A Mullins
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Lauren E Salay
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Clarissa L Durie
- Department of Cell and Developmental Biology, University of Michigan School of Medicine, Ann Arbor, MI, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Noah P Bradley
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Jane E Jackman
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Melanie D Ohi
- Department of Cell and Developmental Biology, University of Michigan School of Medicine, Ann Arbor, MI, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Walter J Chazin
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA.
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
| | - Brandt F Eichman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA.
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA.
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3
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Li N, Gao Y, Zhang Y, Yu D, Lin J, Feng J, Li J, Xu Z, Zhang Y, Dang S, Zhou K, Liu Y, Li XD, Tye BK, Li Q, Gao N, Zhai Y. Parental histone transfer caught at the replication fork. Nature 2024; 627:890-897. [PMID: 38448592 DOI: 10.1038/s41586-024-07152-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 02/01/2024] [Indexed: 03/08/2024]
Abstract
In eukaryotes, DNA compacts into chromatin through nucleosomes1,2. Replication of the eukaryotic genome must be coupled to the transmission of the epigenome encoded in the chromatin3,4. Here we report cryo-electron microscopy structures of yeast (Saccharomyces cerevisiae) replisomes associated with the FACT (facilitates chromatin transactions) complex (comprising Spt16 and Pob3) and an evicted histone hexamer. In these structures, FACT is positioned at the front end of the replisome by engaging with the parental DNA duplex to capture the histones through the middle domain and the acidic carboxyl-terminal domain of Spt16. The H2A-H2B dimer chaperoned by the carboxyl-terminal domain of Spt16 is stably tethered to the H3-H4 tetramer, while the vacant H2A-H2B site is occupied by the histone-binding domain of Mcm2. The Mcm2 histone-binding domain wraps around the DNA-binding surface of one H3-H4 dimer and extends across the tetramerization interface of the H3-H4 tetramer to the binding site of Spt16 middle domain before becoming disordered. This arrangement leaves the remaining DNA-binding surface of the other H3-H4 dimer exposed to additional interactions for further processing. The Mcm2 histone-binding domain and its downstream linker region are nested on top of Tof1, relocating the parental histones to the replisome front for transfer to the newly synthesized lagging-strand DNA. Our findings offer crucial structural insights into the mechanism of replication-coupled histone recycling for maintaining epigenetic inheritance.
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Affiliation(s)
- Ningning Li
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Yuan Gao
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Yujie Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Daqi Yu
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Jianwei Lin
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Jianxun Feng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Jian Li
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Zhichun Xu
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Yingyi Zhang
- Biological Cryo-EM Center, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Shangyu Dang
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Keda Zhou
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Yang Liu
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Bik Kwoon Tye
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA.
| | - Qing Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
| | - Ning Gao
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China.
| | - Yuanliang Zhai
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China.
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4
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Cordoba JJ, Mullins EA, Salay LE, Eichman BF, Chazin WJ. Flexibility and Distributive Synthesis Regulate RNA Priming and Handoff in Human DNA Polymerase α-Primase. J Mol Biol 2023; 435:168330. [PMID: 37884206 PMCID: PMC10872500 DOI: 10.1016/j.jmb.2023.168330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/22/2023] [Accepted: 10/18/2023] [Indexed: 10/28/2023]
Abstract
DNA replication in eukaryotes relies on the synthesis of a ∼30-nucleotide RNA/DNA primer strand through the dual action of the heterotetrameric polymerase α-primase (pol-prim) enzyme. Synthesis of the 7-10-nucleotide RNA primer is regulated by the C-terminal domain of the primase regulatory subunit (PRIM2C) and is followed by intramolecular handoff of the primer to pol α for extension by ∼20 nucleotides of DNA. Here, we provide evidence that RNA primer synthesis is governed by a combination of the high affinity and flexible linkage of the PRIM2C domain and the surprisingly low affinity of the primase catalytic domain (PRIM1) for substrate. Using a combination of small angle X-ray scattering and electron microscopy, we found significant variability in the organization of PRIM2C and PRIM1 in the absence and presence of substrate, and that the population of structures with both PRIM2C and PRIM1 in a configuration aligned for synthesis is low. Crosslinking was used to visualize the orientation of PRIM2C and PRIM1 when engaged by substrate as observed by electron microscopy. Microscale thermophoresis was used to measure substrate affinities for a series of pol-prim constructs, which showed that the PRIM1 catalytic domain does not bind the template or emergent RNA-primed templates with appreciable affinity. Together, these findings support a model of RNA primer synthesis in which generation of the nascent RNA strand and handoff of the RNA-primed template from primase to polymerase α is mediated by the high degree of inter-domain flexibility of pol-prim, the ready dissociation of PRIM1 from its substrate, and the much higher affinity of the POLA1cat domain of polymerase α for full-length RNA-primed templates.
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Affiliation(s)
- John J Cordoba
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Elwood A Mullins
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA; Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Lauren E Salay
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
| | - Brandt F Eichman
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA; Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
| | - Walter J Chazin
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA; Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
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5
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Lewis JS, van Oijen AM, Spenkelink LM. Embracing Heterogeneity: Challenging the Paradigm of Replisomes as Deterministic Machines. Chem Rev 2023; 123:13419-13440. [PMID: 37971892 PMCID: PMC10790245 DOI: 10.1021/acs.chemrev.3c00436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 10/15/2023] [Accepted: 10/20/2023] [Indexed: 11/19/2023]
Abstract
The paradigm of cellular systems as deterministic machines has long guided our understanding of biology. Advancements in technology and methodology, however, have revealed a world of stochasticity, challenging the notion of determinism. Here, we explore the stochastic behavior of multi-protein complexes, using the DNA replication system (replisome) as a prime example. The faithful and timely copying of DNA depends on the simultaneous action of a large set of enzymes and scaffolding factors. This fundamental cellular process is underpinned by dynamic protein-nucleic acid assemblies that must transition between distinct conformations and compositional states. Traditionally viewed as a well-orchestrated molecular machine, recent experimental evidence has unveiled significant variability and heterogeneity in the replication process. In this review, we discuss recent advances in single-molecule approaches and single-particle cryo-EM, which have provided insights into the dynamic processes of DNA replication. We comment on the new challenges faced by structural biologists and biophysicists as they attempt to describe the dynamic cascade of events leading to replisome assembly, activation, and progression. The fundamental principles uncovered and yet to be discovered through the study of DNA replication will inform on similar operating principles for other multi-protein complexes.
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Affiliation(s)
- Jacob S. Lewis
- Macromolecular
Machines Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Antoine M. van Oijen
- Molecular
Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Lisanne M. Spenkelink
- Molecular
Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
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6
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Mullins EA, Salay LE, Durie CL, Bradley NP, Jackman JE, Ohi MD, Chazin WJ, Eichman BF. A mechanistic model of primer synthesis from catalytic structures of DNA polymerase α-primase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.533013. [PMID: 36993335 PMCID: PMC10055150 DOI: 10.1101/2023.03.16.533013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The mechanism by which polymerase α-primase (polα-primase) synthesizes chimeric RNA-DNA primers of defined length and composition, necessary for replication fidelity and genome stability, is unknown. Here, we report cryo-EM structures of polα-primase in complex with primed templates representing various stages of DNA synthesis. Our data show how interaction of the primase regulatory subunit with the primer 5'-end facilitates handoff of the primer to polα and increases polα processivity, thereby regulating both RNA and DNA composition. The structures detail how flexibility within the heterotetramer enables synthesis across two active sites and provide evidence that termination of DNA synthesis is facilitated by reduction of polα and primase affinities for the varied conformations along the chimeric primer/template duplex. Together, these findings elucidate a critical catalytic step in replication initiation and provide a comprehensive model for primer synthesis by polα-primase.
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7
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Dmowski M, Makiela-Dzbenska K, Sharma S, Chabes A, Fijalkowska IJ. Impairment of the non-catalytic subunit Dpb2 of DNA Pol ɛ results in increased involvement of Pol δ on the leading strand. DNA Repair (Amst) 2023; 129:103541. [PMID: 37481989 DOI: 10.1016/j.dnarep.2023.103541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/29/2023] [Accepted: 07/05/2023] [Indexed: 07/25/2023]
Abstract
The generally accepted model assumes that leading strand synthesis is performed by Pol ε, while lagging-strand synthesis is catalyzed by Pol δ. Pol ε has been shown to target the leading strand by interacting with the CMG helicase [Cdc45 Mcm2-7 GINS(Psf1-3, Sld5)]. Proper functioning of the CMG-Pol ɛ, the helicase-polymerase complex is essential for its progression and the fidelity of DNA replication. Dpb2p, the essential non-catalytic subunit of Pol ε plays a key role in maintaining the correct architecture of the replisome by acting as a link between Pol ε and the CMG complex. Using a temperature-sensitive dpb2-100 mutant previously isolated in our laboratory, and a genetic system which takes advantage of a distinct mutational signature of the Pol δ-L612M variant which allows detection of the involvement of Pol δ in the replication of particular DNA strands we show that in yeast cells with an impaired Dpb2 subunit, the contribution of Pol δ to the replication of the leading strand is significantly increased.
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Affiliation(s)
- Michal Dmowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland.
| | - Karolina Makiela-Dzbenska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Sushma Sharma
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
| | - Iwona J Fijalkowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland.
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8
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Pellegrini L. The CMG DNA helicase and the core replisome. Curr Opin Struct Biol 2023; 81:102612. [PMID: 37244171 DOI: 10.1016/j.sbi.2023.102612] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/19/2023] [Accepted: 04/25/2023] [Indexed: 05/29/2023]
Abstract
Eukaryotic DNA replication is performed by the replisome, a large and dynamic multi-protein machine endowed with the required enzymatic components for the synthesis of new DNA. Recent cryo-electron microscopy (cryoEM) analyses have revealed the conserved architecture of the core eukaryotic replisome, comprising the CMG (Cdc45-MCM-GINS) DNA helicase, the leading-strand DNA polymerase epsilon, the Timeless-Tipin heterodimer, the hub protein AND-1 and the checkpoint protein Claspin. These results bid well for arriving soon at an integrated understanding of the structural basis of semi-discontinuous DNA replication. They further set the scene for the characterisation of the mechanisms that interface DNA synthesis with concurrent processes such as DNA repair, propagation of chromatin structure and establishment of sister chromatid cohesion.
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9
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Cordoba JJ, Mullins EA, Salay LE, Eichman BF, Chazin WJ. Flexibility and distributive synthesis regulate RNA priming and handoff in human DNA polymerase α-primase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.01.551538. [PMID: 37577606 PMCID: PMC10418221 DOI: 10.1101/2023.08.01.551538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
DNA replication in eukaryotes relies on the synthesis of a ~30-nucleotide RNA/DNA primer strand through the dual action of the heterotetrameric polymerase α-primase (pol-prim) enzyme. Synthesis of the 7-10-nucleotide RNA primer is regulated by the C-terminal domain of the primase regulatory subunit (PRIM2C) and is followed by intramolecular handoff of the primer to pol α for extension by ~20 nucleotides of DNA. Here we provide evidence that RNA primer synthesis is governed by a combination of the high affinity and flexible linkage of the PRIM2C domain and the low affinity of the primase catalytic domain (PRIM1) for substrate. Using a combination of small angle X-ray scattering and electron microscopy, we found significant variability in the organization of PRIM2C and PRIM1 in the absence and presence of substrate, and that the population of structures with both PRIM2C and PRIM1 in a configuration aligned for synthesis is low. Crosslinking was used to visualize the orientation of PRIM2C and PRIM1 when engaged by substrate as observed by electron microscopy. Microscale thermophoresis was used to measure substrate affinities for a series of pol-prim constructs, which showed that the PRIM1 catalytic domain does not bind the template or emergent RNA-primed templates with appreciable affinity. Together, these findings support a model of RNA primer synthesis in which generation of the nascent RNA strand and handoff of the RNA-primed template from primase to polymerase α is mediated by the high degree of inter-domain flexibility of pol-prim, the ready dissociation of PRIM1 from its substrate, and the much higher affinity of the POLA1cat domain of polymerase α for full-length RNA-primed templates.
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Affiliation(s)
- John J. Cordoba
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee, USA
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Elwood A. Mullins
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Lauren E. Salay
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee, USA
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Brandt F. Eichman
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee, USA
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Walter J. Chazin
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee, USA
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
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10
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Bocanegra R, Ortíz-Rodríguez M, Zumeta L, Plaza-G A I, Faro E, Ibarra B. DNA replication machineries: Structural insights from crystallography and electron microscopy. Enzymes 2023; 54:249-271. [PMID: 37945174 DOI: 10.1016/bs.enz.2023.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Since the discovery of DNA as the genetic material, scientists have been investigating how the information contained in this biological polymer is transmitted from generation to generation. X-ray crystallography, and more recently, cryo-electron microscopy techniques have been instrumental in providing essential information about the structure, functions and interactions of the DNA and the protein machinery (replisome) responsible for its replication. In this chapter, we highlight several works that describe the structure and structure-function relationships of the core components of the prokaryotic and eukaryotic replisomes. We also discuss the most recent studies on the structural organization of full replisomes.
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Affiliation(s)
| | | | - Lyra Zumeta
- IMDEA Nanociencia, Campus Cantoblanco, Madrid, Spain
| | | | - Elías Faro
- IMDEA Nanociencia, Campus Cantoblanco, Madrid, Spain
| | - Borja Ibarra
- IMDEA Nanociencia, Campus Cantoblanco, Madrid, Spain.
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11
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Rouillon C, Eckhardt BV, Kollenstart L, Gruss F, Verkennis AE, Rondeel I, Krijger PHL, Ricci G, Biran A, van Laar T, Delvaux de Fenffe CM, Luppens G, Albanese P, Sato K, Scheltema RA, de Laat W, Knipscheer P, Dekker N, Groth A, Mattiroli F. CAF-1 deposits newly synthesized histones during DNA replication using distinct mechanisms on the leading and lagging strands. Nucleic Acids Res 2023; 51:3770-3792. [PMID: 36942484 PMCID: PMC10164577 DOI: 10.1093/nar/gkad171] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 02/18/2023] [Accepted: 02/23/2023] [Indexed: 03/23/2023] Open
Abstract
During every cell cycle, both the genome and the associated chromatin must be accurately replicated. Chromatin Assembly Factor-1 (CAF-1) is a key regulator of chromatin replication, but how CAF-1 functions in relation to the DNA replication machinery is unknown. Here, we reveal that this crosstalk differs between the leading and lagging strand at replication forks. Using biochemical reconstitutions, we show that DNA and histones promote CAF-1 recruitment to its binding partner PCNA and reveal that two CAF-1 complexes are required for efficient nucleosome assembly under these conditions. Remarkably, in the context of the replisome, CAF-1 competes with the leading strand DNA polymerase epsilon (Polϵ) for PCNA binding. However, CAF-1 does not affect the activity of the lagging strand DNA polymerase Delta (Polδ). Yet, in cells, CAF-1 deposits newly synthesized histones equally on both daughter strands. Thus, on the leading strand, chromatin assembly by CAF-1 cannot occur simultaneously to DNA synthesis, while on the lagging strand these processes may be coupled. We propose that these differences may facilitate distinct parental histone recycling mechanisms and accommodate the inherent asymmetry of DNA replication.
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Affiliation(s)
- Clément Rouillon
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bruna V Eckhardt
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht, The Netherlands
| | - Leonie Kollenstart
- Novo Nordisk Foundation Center for Protein Research (CPR), University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Center, University of Copenhagen, Copenhagen, Denmark
| | - Fabian Gruss
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Inge Rondeel
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht, The Netherlands
| | - Peter H L Krijger
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Giulia Ricci
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht, The Netherlands
| | - Alva Biran
- Novo Nordisk Foundation Center for Protein Research (CPR), University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Center, University of Copenhagen, Copenhagen, Denmark
| | - Theo van Laar
- Kavli Institute of Nanoscience Delft, TU Delft, The Netherlands
| | | | - Georgiana Luppens
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht, The Netherlands
| | - Pascal Albanese
- Utrecht Institute for Pharmaceutical Sciences, Utrecht University, the Netherlands
| | - Koichi Sato
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Richard A Scheltema
- Utrecht Institute for Pharmaceutical Sciences, Utrecht University, the Netherlands
| | - Wouter de Laat
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Puck Knipscheer
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Nynke H Dekker
- Kavli Institute of Nanoscience Delft, TU Delft, The Netherlands
| | - Anja Groth
- Novo Nordisk Foundation Center for Protein Research (CPR), University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Center, University of Copenhagen, Copenhagen, Denmark
| | - Francesca Mattiroli
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht, The Netherlands
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12
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Li Z, Kaur P, Lo CY, Chopra N, Smith J, Wang H, Gao Y. Structural and dynamic basis of DNA capture and translocation by mitochondrial Twinkle helicase. Nucleic Acids Res 2022; 50:11965-11978. [PMID: 36400570 PMCID: PMC9723800 DOI: 10.1093/nar/gkac1089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/21/2022] [Accepted: 10/26/2022] [Indexed: 11/21/2022] Open
Abstract
Twinkle is a mitochondrial replicative helicase which can self-load onto and unwind mitochondrial DNA. Nearly 60 mutations on Twinkle have been linked to human mitochondrial diseases. Using cryo-electron microscopy (cryo-EM) and high-speed atomic force microscopy (HS-AFM), we obtained the atomic-resolution structure of a vertebrate Twinkle homolog with DNA and captured in real-time how Twinkle is self-loaded onto DNA. Our data highlight the important role of the non-catalytic N-terminal domain of Twinkle. The N-terminal domain directly contacts the C-terminal helicase domain, and the contact interface is a hotspot for disease-related mutations. Mutations at the interface destabilize Twinkle hexamer and reduce helicase activity. With HS-AFM, we observed that a highly dynamic Twinkle domain, which is likely to be the N-terminal domain, can protrude ∼5 nm to transiently capture nearby DNA and initialize Twinkle loading onto DNA. Moreover, structural analysis and subunit doping experiments suggest that Twinkle hydrolyzes ATP stochastically, which is distinct from related helicases from bacteriophages.
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Affiliation(s)
- Zhuo Li
- BioSciences Department, Rice University, Houston, TX 77005, USA
| | - Parminder Kaur
- Physics Department, North Carolina State University, Raleigh, NC 27695, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695, USA
| | - Chen-Yu Lo
- BioSciences Department, Rice University, Houston, TX 77005, USA
| | - Neil Chopra
- BioSciences Department, Rice University, Houston, TX 77005, USA
| | - Jamie Smith
- BioSciences Department, Rice University, Houston, TX 77005, USA
| | - Hong Wang
- Physics Department, North Carolina State University, Raleigh, NC 27695, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695, USA
- Toxicology Program, North Carolina State University, Raleigh, NC 27695, USA
| | - Yang Gao
- BioSciences Department, Rice University, Houston, TX 77005, USA
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13
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Pradhan B, Barth R, Kim E, Davidson IF, Bauer B, van Laar T, Yang W, Ryu JK, van der Torre J, Peters JM, Dekker C. SMC complexes can traverse physical roadblocks bigger than their ring size. Cell Rep 2022; 41:111491. [PMID: 36261017 DOI: 10.1101/2021.07.15.452501] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 05/19/2022] [Accepted: 09/21/2022] [Indexed: 05/17/2023] Open
Abstract
Ring-shaped structural maintenance of chromosomes (SMC) complexes like condensin and cohesin extrude loops of DNA. It remains, however, unclear how they can extrude DNA loops in chromatin that is bound with proteins. Here, we use in vitro single-molecule visualization to show that nucleosomes, RNA polymerase, and dCas9 pose virtually no barrier to loop extrusion by yeast condensin. We find that even DNA-bound nanoparticles as large as 200 nm, much bigger than the SMC ring size, also translocate into DNA loops during extrusion by condensin and cohesin. This even occurs for a single-chain version of cohesin in which the ring-forming subunits are covalently linked and cannot open to entrap DNA. The data show that SMC-driven loop extrusion has surprisingly little difficulty in accommodating large roadblocks into the loop. The findings also show that the extruded DNA does not pass through the SMC ring (pseudo)topologically, hence pointing to a nontopological mechanism for DNA loop extrusion.
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Affiliation(s)
- Biswajit Pradhan
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Roman Barth
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Eugene Kim
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Iain F Davidson
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Benedikt Bauer
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Theo van Laar
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands; Nynke Dekker Lab, Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Wayne Yang
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Je-Kyung Ryu
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Jaco van der Torre
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands.
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14
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SMC complexes can traverse physical roadblocks bigger than their ring size. Cell Rep 2022; 41:111491. [DOI: 10.1016/j.celrep.2022.111491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 05/19/2022] [Accepted: 09/21/2022] [Indexed: 11/24/2022] Open
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15
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Wilkinson EM, Spenkelink LM, van Oijen AM. Observing protein dynamics during DNA-lesion bypass by the replisome. Front Mol Biosci 2022; 9:968424. [PMID: 36213113 PMCID: PMC9534484 DOI: 10.3389/fmolb.2022.968424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
Faithful DNA replication is essential for all life. A multi-protein complex called the replisome contains all the enzymatic activities required to facilitate DNA replication, including unwinding parental DNA and synthesizing two identical daughter molecules. Faithful DNA replication can be challenged by both intrinsic and extrinsic factors, which can result in roadblocks to replication, causing incomplete replication, genomic instability, and an increased mutational load. This increased mutational load can ultimately lead to a number of diseases, a notable example being cancer. A key example of a roadblock to replication is chemical modifications in the DNA caused by exposure to ultraviolet light. Protein dynamics are thought to play a crucial role to the molecular pathways that occur in the presence of such DNA lesions, including potential damage bypass. Therefore, many assays have been developed to study these dynamics. In this review, we discuss three methods that can be used to study protein dynamics during replisome–lesion encounters in replication reactions reconstituted from purified proteins. Specifically, we focus on ensemble biochemical assays, single-molecule fluorescence, and cryo-electron microscopy. We discuss two key model DNA replication systems, derived from Escherichia coli and Saccharomyces cerevisiae. The main methods of choice to study replication over the last decades have involved biochemical assays that rely on ensemble averaging. While these assays do not provide a direct readout of protein dynamics, they can often be inferred. More recently, single-molecule techniques including single-molecule fluorescence microscopy have been used to visualize replisomes encountering lesions in real time. In these experiments, individual proteins can be fluorescently labeled in order to observe the dynamics of specific proteins during DNA replication. Finally, cryo-electron microscopy can provide detailed structures of individual replisome components, which allows functional data to be interpreted in a structural context. While classic cryo-electron microscopy approaches provide static information, recent developments such as time-resolved cryo-electron microscopy help to bridge the gap between static structures and dynamic single-molecule techniques by visualizing sequential steps in biochemical pathways. In combination, these techniques will be capable of visualizing DNA replication and lesion encounter dynamics in real time, whilst observing the structural changes that facilitate these dynamics.
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Affiliation(s)
- Elise M. Wilkinson
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Lisanne M. Spenkelink
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- *Correspondence: Lisanne M. Spenkelink, ; Antoine M. van Oijen,
| | - Antoine M. van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- *Correspondence: Lisanne M. Spenkelink, ; Antoine M. van Oijen,
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16
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MCM6 Promotes Hepatocellular Carcinoma Progression via the Notch Pathway: Clinical, Functional, and Genomic Insights. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:3116303. [PMID: 35720029 PMCID: PMC9203181 DOI: 10.1155/2022/3116303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/21/2022] [Accepted: 04/30/2022] [Indexed: 11/17/2022]
Abstract
Objective To evaluate the expression profile of MCM6 in HCC and the relationship between MCM6 level and clinicopathological parameters through bioinformatics analysis of several databases. Methods MCM expression level, clinical parameters, survival data, and gene set enrichment analysis were analyzed by bioinformatics database, including Oncomine™, UALCAN, HCCDB, TCGA, cBioPortal, and LinkedOmics. Real-time PCR, western blotting, and IHC staining were conducted to identify the expression of MCM6 in HCC compared to normal liver tissues. Results Bioinformatics analysis indicated that the mRNA of MCM6 was obviously increased in multiple cancer types, especially in HCC. MCM6 level was positively associated with multiple clinical parameters (stage 3 and grades 3 and 4) and negatively associated with patient outcomes (overall survival). Moreover, enrichment of functions and signaling pathways analysis of MCM6 suggested that MCM6 might mediate DNA replication and cellular metabolism to promote the development and progression of HCC. Furthermore, IHC staining and western blotting indicated that the MCM6 was enhanced in HCC tissue, and MCM6 could promote HCC proliferation in activating Notch pathway via WB and bioinformatic analysis. Conclusion This study actually revealed the expression and related functions of MCM6 in HCC. Furthermore, MCM6 is a carcinogenic role in activating Notch pathway to promote HCC cell proliferation, which may be a new prognostic biomarker and therapeutic target for HCC patients.
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17
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Abstract
Gene regulation arises out of dynamic competition between nucleosomes, transcription factors, and other chromatin proteins for the opportunity to bind genomic DNA. The timescales of nucleosome assembly and binding of factors to DNA determine the outcomes of this competition at any given locus. Here, we review how these properties of chromatin proteins and the interplay between the dynamics of different factors are critical for gene regulation. We discuss how molecular structures of large chromatin-associated complexes, kinetic measurements, and high resolution mapping of protein-DNA complexes in vivo set the boundary conditions for chromatin dynamics, leading to models of how the steady state behaviors of regulatory elements arise.
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Affiliation(s)
- Kami Ahmad
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA;
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA;
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Srinivas Ramachandran
- Department of Biochemistry and Molecular Genetics and RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado, USA
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18
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López-Jiménez E, González-Aguilera C. Role of Chromatin Replication in Transcriptional Plasticity, Cell Differentiation and Disease. Genes (Basel) 2022; 13:genes13061002. [PMID: 35741764 PMCID: PMC9222293 DOI: 10.3390/genes13061002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 11/16/2022] Open
Abstract
Chromatin organization is essential to maintain a correct regulation of gene expression and establish cell identity. However, during cell division, the replication of the genetic material produces a global disorganization of chromatin structure. In this paper, we describe the new scientific breakthroughs that have revealed the nature of the post-replicative chromatin and the mechanisms that facilitate its restoration. Moreover, we highlight the implications of these chromatin alterations in gene expression control and their impact on key biological processes, such as cell differentiation, cell reprogramming or human diseases linked to cell proliferation, such as cancer.
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Affiliation(s)
- Elena López-Jiménez
- Faculty of Medicine, National Heart and Lung Institute, Margaret Turner Warwick Centre for Fibrosing Lung Disease, Royal Brompton Campus, Imperial College London, London SW3 6LY, UK;
| | - Cristina González-Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
- Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain
- Correspondence:
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19
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Zaffar E, Ferreira P, Sanchez-Pulido L, Boos D. The Role of MTBP as a Replication Origin Firing Factor. BIOLOGY 2022; 11:biology11060827. [PMID: 35741348 PMCID: PMC9219753 DOI: 10.3390/biology11060827] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/20/2022] [Accepted: 05/22/2022] [Indexed: 12/12/2022]
Abstract
The initiation step of replication at replication origins determines when and where in the genome replication machines, replisomes, are generated. Tight control of replication initiation helps facilitate the two main tasks of genome replication, to duplicate the genome accurately and exactly once each cell division cycle. The regulation of replication initiation must ensure that initiation occurs during the S phase specifically, that no origin fires more than once per cell cycle, that enough origins fire to avoid non-replicated gaps, and that the right origins fire at the right time but only in favorable circumstances. Despite its importance for genetic homeostasis only the main molecular processes of eukaryotic replication initiation and its cellular regulation are understood. The MTBP protein (Mdm2-binding protein) is so far the last core replication initiation factor identified in metazoan cells. MTBP is the orthologue of yeast Sld7. It is essential for origin firing, the maturation of pre-replicative complexes (pre-RCs) into replisomes, and is emerging as a regulation focus targeted by kinases and by regulated degradation. We present recent insight into the structure and cellular function of the MTBP protein in light of recent structural and biochemical studies revealing critical molecular details of the eukaryotic origin firing reaction. How the roles of MTBP in replication and other cellular processes are mutually connected and are related to MTBP's contribution to tumorigenesis remains largely unclear.
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Affiliation(s)
- Eman Zaffar
- Molecular Genetics II, Centre for Medical Biotechnology, University of Duisburg-Essen, 45141 Essen, Germany; (E.Z.); (P.F.)
| | - Pedro Ferreira
- Molecular Genetics II, Centre for Medical Biotechnology, University of Duisburg-Essen, 45141 Essen, Germany; (E.Z.); (P.F.)
| | - Luis Sanchez-Pulido
- Medical Research Council Human Genetics Unit, IGC, University of Edinburgh, Edinburgh EH9 3JR, UK;
| | - Dominik Boos
- Molecular Genetics II, Centre for Medical Biotechnology, University of Duisburg-Essen, 45141 Essen, Germany; (E.Z.); (P.F.)
- Correspondence: ; Tel.: +49-201-183-4132
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20
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Mak CH. Nucleic acid folding simulations using a physics-based atomistic free energy model. J Chem Phys 2022; 156:174114. [PMID: 35525642 DOI: 10.1063/5.0086304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Performing full-resolution atomistic simulations of nucleic acid folding has remained a challenge for biomolecular modeling. Understanding how nucleic acids fold and how they transition between different folded structures as they unfold and refold has important implications for biology. This paper reports a theoretical model and computer simulation of the ab initio folding of DNA inverted repeat sequences. The formulation is based on an all-atom conformational model of the sugar-phosphate backbone via chain closure, and it incorporates three major molecular-level driving forces-base stacking, counterion-induced backbone self-interactions, and base pairing-via separate analytical theories designed to capture and reproduce the effects of the solvent without requiring explicit water and ions in the simulation. To accelerate computational throughput, a mixed numerical/analytical algorithm for the calculation of the backbone conformational volume is incorporated into the Monte Carlo simulation, and special stochastic sampling techniques were employed to achieve the computational efficiency needed to fold nucleic acids from scratch. This paper describes implementation details, benchmark results, and the advantages and technical challenges with this approach.
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Affiliation(s)
- Chi H Mak
- Departments of Chemistry and Quantitative and Computational Biology, and Center of Applied Mathematical Sciences, University of Southern California, Los Angeles, California 90089, USA
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21
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Multiple roles of Pol epsilon in eukaryotic chromosome replication. Biochem Soc Trans 2022; 50:309-320. [PMID: 35129614 PMCID: PMC9022971 DOI: 10.1042/bst20210082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/23/2021] [Accepted: 01/06/2022] [Indexed: 11/17/2022]
Abstract
Pol epsilon is a tetrameric assembly that plays distinct roles during eukaryotic chromosome replication. It catalyses leading strand DNA synthesis; yet this function is dispensable for viability. Its non-catalytic domains instead play an essential role in the assembly of the active replicative helicase and origin activation, while non-essential histone-fold subunits serve a critical function in parental histone redeposition onto newly synthesised DNA. Furthermore, Pol epsilon plays a structural role in linking the RFC–Ctf18 clamp loader to the replisome, supporting processive DNA synthesis, DNA damage response signalling as well as sister chromatid cohesion. In this minireview, we discuss recent biochemical and structural work that begins to explain various aspects of eukaryotic chromosome replication, with a focus on the multiple roles of Pol epsilon in this process.
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22
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Increased contribution of DNA polymerase delta to the leading strand replication in yeast with an impaired CMG helicase complex. DNA Repair (Amst) 2022; 110:103272. [DOI: 10.1016/j.dnarep.2022.103272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/24/2021] [Accepted: 01/04/2022] [Indexed: 11/19/2022]
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23
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DNA Polymerase-Parental DNA Interaction Is Essential for Helicase-Polymerase Coupling during Bacteriophage T7 DNA Replication. Int J Mol Sci 2022; 23:ijms23031342. [PMID: 35163266 PMCID: PMC8835902 DOI: 10.3390/ijms23031342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/19/2022] [Accepted: 01/22/2022] [Indexed: 11/17/2022] Open
Abstract
DNA helicase and polymerase work cooperatively at the replication fork to perform leading-strand DNA synthesis. It was believed that the helicase migrates to the forefront of the replication fork where it unwinds the duplex to provide templates for DNA polymerases. However, the molecular basis of the helicase-polymerase coupling is not fully understood. The recently elucidated T7 replisome structure suggests that the helicase and polymerase sandwich parental DNA and each enzyme pulls a daughter strand in opposite directions. Interestingly, the T7 polymerase, but not the helicase, carries the parental DNA with a positively charged cleft and stacks at the fork opening using a β-hairpin loop. Here, we created and characterized T7 polymerases each with a perturbed β-hairpin loop and positively charged cleft. Mutations on both structural elements significantly reduced the strand-displacement synthesis by T7 polymerase but had only a minor effect on DNA synthesis performed against a linear DNA substrate. Moreover, the aforementioned mutations eliminated synergistic helicase-polymerase binding and unwinding at the DNA fork and processive fork progressions. Thus, our data suggested that T7 polymerase plays a dominant role in helicase-polymerase coupling and replisome progression.
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24
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Optimizing CMG helicase and CMG-dependent replication assays by designing DNA fork substrates and choosing nucleotide analogues for helicase preloading. Methods Enzymol 2022; 672:173-202. [DOI: 10.1016/bs.mie.2022.02.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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25
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van Schie JJM, de Lange J. The Interplay of Cohesin and the Replisome at Processive and Stressed DNA Replication Forks. Cells 2021; 10:3455. [PMID: 34943967 PMCID: PMC8700348 DOI: 10.3390/cells10123455] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 12/12/2022] Open
Abstract
The cohesin complex facilitates faithful chromosome segregation by pairing the sister chromatids after DNA replication until mitosis. In addition, cohesin contributes to proficient and error-free DNA replication. Replisome progression and establishment of sister chromatid cohesion are intimately intertwined processes. Here, we review how the key factors in DNA replication and cohesion establishment cooperate in unperturbed conditions and during DNA replication stress. We discuss the detailed molecular mechanisms of cohesin recruitment and the entrapment of replicated sister chromatids at the replisome, the subsequent stabilization of sister chromatid cohesion via SMC3 acetylation, as well as the role and regulation of cohesin in the response to DNA replication stress.
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Affiliation(s)
- Janne J. M. van Schie
- Cancer Center Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
| | - Job de Lange
- Cancer Center Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
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26
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Jones ML, Baris Y, Taylor MRG, Yeeles JTP. Structure of a human replisome shows the organisation and interactions of a DNA replication machine. EMBO J 2021; 40:e108819. [PMID: 34694004 PMCID: PMC8634136 DOI: 10.15252/embj.2021108819] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/28/2021] [Accepted: 09/30/2021] [Indexed: 02/01/2023] Open
Abstract
The human replisome is an elaborate arrangement of molecular machines responsible for accurate chromosome replication. At its heart is the CDC45-MCM-GINS (CMG) helicase, which, in addition to unwinding the parental DNA duplex, arranges many proteins including the leading-strand polymerase Pol ε, together with TIMELESS-TIPIN, CLASPIN and AND-1 that have key and varied roles in maintaining smooth replisome progression. How these proteins are coordinated in the human replisome is poorly understood. We have determined a 3.2 Å cryo-EM structure of a human replisome comprising CMG, Pol ε, TIMELESS-TIPIN, CLASPIN and AND-1 bound to replication fork DNA. The structure permits a detailed understanding of how AND-1, TIMELESS-TIPIN and Pol ε engage CMG, reveals how CLASPIN binds to multiple replisome components and identifies the position of the Pol ε catalytic domain. Furthermore, the intricate network of contacts contributed by MCM subunits and TIMELESS-TIPIN with replication fork DNA suggests a mechanism for strand separation.
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27
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Abstract
Ring-shaped hexameric helicases are essential motor proteins that separate duplex nucleic acid strands for DNA replication, recombination, and transcriptional regulation. Two evolutionarily distinct lineages of these enzymes, predicated on RecA and AAA+ ATPase folds, have been identified and characterized to date. Hexameric helicases couple NTP hydrolysis with conformational changes that move nucleic acid substrates through a central pore in the enzyme. How hexameric helicases productively engage client DNA or RNA segments and use successive rounds of NTPase activity to power translocation and unwinding have been longstanding questions in the field. Recent structural and biophysical findings are beginning to reveal commonalities in NTP hydrolysis and substrate translocation by diverse hexameric helicase families. Here, we review these molecular mechanisms and highlight aspects of their function that are yet to be understood.
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28
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Jenkyn-Bedford M, Jones ML, Baris Y, Labib KPM, Cannone G, Yeeles JTP, Deegan TD. A conserved mechanism for regulating replisome disassembly in eukaryotes. Nature 2021; 600:743-747. [PMID: 34700328 PMCID: PMC8695382 DOI: 10.1038/s41586-021-04145-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/14/2021] [Indexed: 11/28/2022]
Abstract
Replisome disassembly is the final step of eukaryotic DNA replication and is triggered by ubiquitylation of the CDC45-MCM-GINS (CMG) replicative helicase1-3. Despite being driven by evolutionarily diverse E3 ubiquitin ligases in different eukaryotes (SCFDia2 in budding yeast1, CUL2LRR1 in metazoa4-7), replisome disassembly is governed by a common regulatory principle, in which ubiquitylation of CMG is suppressed before replication termination, to prevent replication fork collapse. Recent evidence suggests that this suppression is mediated by replication fork DNA8-10. However, it is unknown how SCFDia2 and CUL2LRR1 discriminate terminated from elongating replisomes, to selectively ubiquitylate CMG only after termination. Here we used cryo-electron microscopy to solve high-resolution structures of budding yeast and human replisome-E3 ligase assemblies. Our structures show that the leucine-rich repeat domains of Dia2 and LRR1 are structurally distinct, but bind to a common site on CMG, including the MCM3 and MCM5 zinc-finger domains. The LRR-MCM interaction is essential for replisome disassembly and, crucially, is occluded by the excluded DNA strand at replication forks, establishing the structural basis for the suppression of CMG ubiquitylation before termination. Our results elucidate a conserved mechanism for the regulation of replisome disassembly in eukaryotes, and reveal a previously unanticipated role for DNA in preserving replisome integrity.
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Affiliation(s)
| | | | | | - Karim P M Labib
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, UK
| | | | | | - Tom D Deegan
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, UK.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK.
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29
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Determining translocation orientations of nucleic acid helicases. Methods 2021; 204:160-171. [PMID: 34758393 PMCID: PMC9076756 DOI: 10.1016/j.ymeth.2021.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 11/20/2022] Open
Abstract
Helicase enzymes translocate along an RNA or DNA template with a defined polarity to unwind, separate, or remodel duplex strands for a variety of genome maintenance processes. Helicase mutations are commonly associated with a variety of diseases including aging, cancer, and neurodegeneration. Biochemical characterization of these enzymes has provided a wealth of information on the kinetics of unwinding and substrate preferences, and several high-resolution structures of helicases alone and bound to oligonucleotides have been solved. Together, they provide mechanistic insights into the structural translocation and unwinding orientations of helicases. However, these insights rely on structural inferences derived from static snapshots. Instead, continued efforts should be made to combine structure and kinetics to better define active translocation orientations of helicases. This review explores many of the biochemical and biophysical methods utilized to map helicase binding orientation to DNA or RNA substrates and includes several time-dependent methods to unequivocally map the active translocation orientation of these enzymes to better define the active leading and trailing faces.
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Oki K, Nagata M, Yamagami T, Numata T, Ishino S, Oyama T, Ishino Y. Family D DNA polymerase interacts with GINS to promote CMG-helicase in the archaeal replisome. Nucleic Acids Res 2021; 50:3601-3615. [PMID: 34568951 PMCID: PMC9023282 DOI: 10.1093/nar/gkab799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/29/2021] [Accepted: 09/06/2021] [Indexed: 11/12/2022] Open
Abstract
Genomic DNA replication requires replisome assembly. We show here the molecular mechanism by which CMG (GAN-MCM-GINS)-like helicase cooperates with the family D DNA polymerase (PolD) in Thermococcus kodakarensis. The archaeal GINS contains two Gins51 subunits, the C-terminal domain of which (Gins51C) interacts with GAN. We discovered that Gins51C also interacts with the N-terminal domain of PolD's DP1 subunit (DP1N) to connect two PolDs in GINS. The two replicases in the replisome should be responsible for leading- and lagging-strand synthesis, respectively. Crystal structure analysis of the DP1N-Gins51C-GAN ternary complex was provided to understand the structural basis of the connection between the helicase and DNA polymerase. Site-directed mutagenesis analysis supported the interaction mode obtained from the crystal structure. Furthermore, the assembly of helicase and replicase identified in this study is also conserved in Eukarya. PolD enhances the parental strand unwinding via stimulation of ATPase activity of the CMG-complex. This is the first evidence of the functional connection between replicase and helicase in Archaea. These results suggest that the direct interaction of PolD with CMG-helicase is critical for synchronizing strand unwinding and nascent strand synthesis and possibly provide a functional machinery for the effective progression of the replication fork.
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Affiliation(s)
- Keisuke Oki
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Mariko Nagata
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Takeshi Yamagami
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Tomoyuki Numata
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Sonoko Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Takuji Oyama
- Faculty of Life and Environmental Sciences, University of Yamanashi, Kofu, Yamanashi 400-8510, Japan
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
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31
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Guilliam TA. Mechanisms for Maintaining Eukaryotic Replisome Progression in the Presence of DNA Damage. Front Mol Biosci 2021; 8:712971. [PMID: 34295925 PMCID: PMC8290200 DOI: 10.3389/fmolb.2021.712971] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 06/25/2021] [Indexed: 12/04/2022] Open
Abstract
The eukaryotic replisome coordinates template unwinding and nascent-strand synthesis to drive DNA replication fork progression and complete efficient genome duplication. During its advancement along the parental template, each replisome may encounter an array of obstacles including damaged and structured DNA that impede its progression and threaten genome stability. A number of mechanisms exist to permit replisomes to overcome such obstacles, maintain their progression, and prevent fork collapse. A combination of recent advances in structural, biochemical, and single-molecule approaches have illuminated the architecture of the replisome during unperturbed replication, rationalised the impact of impediments to fork progression, and enhanced our understanding of DNA damage tolerance mechanisms and their regulation. This review focusses on these studies to provide an updated overview of the mechanisms that support replisomes to maintain their progression on an imperfect template.
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Affiliation(s)
- Thomas A. Guilliam
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
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32
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Bainbridge LJ, Teague R, Doherty AJ. Repriming DNA synthesis: an intrinsic restart pathway that maintains efficient genome replication. Nucleic Acids Res 2021; 49:4831-4847. [PMID: 33744934 PMCID: PMC8136793 DOI: 10.1093/nar/gkab176] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/01/2021] [Accepted: 03/05/2021] [Indexed: 12/25/2022] Open
Abstract
To bypass a diverse range of fork stalling impediments encountered during genome replication, cells possess a variety of DNA damage tolerance (DDT) mechanisms including translesion synthesis, template switching, and fork reversal. These pathways function to bypass obstacles and allow efficient DNA synthesis to be maintained. In addition, lagging strand obstacles can also be circumvented by downstream priming during Okazaki fragment generation, leaving gaps to be filled post-replication. Whether repriming occurs on the leading strand has been intensely debated over the past half-century. Early studies indicated that both DNA strands were synthesised discontinuously. Although later studies suggested that leading strand synthesis was continuous, leading to the preferred semi-discontinuous replication model. However, more recently it has been established that replicative primases can perform leading strand repriming in prokaryotes. An analogous fork restart mechanism has also been identified in most eukaryotes, which possess a specialist primase called PrimPol that conducts repriming downstream of stalling lesions and structures. PrimPol also plays a more general role in maintaining efficient fork progression. Here, we review and discuss the historical evidence and recent discoveries that substantiate repriming as an intrinsic replication restart pathway for maintaining efficient genome duplication across all domains of life.
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Affiliation(s)
- Lewis J Bainbridge
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, BN1 9RQ, UK
| | - Rebecca Teague
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, BN1 9RQ, UK
| | - Aidan J Doherty
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, BN1 9RQ, UK
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33
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Willhoft O, Costa A. A structural framework for DNA replication and transcription through chromatin. Curr Opin Struct Biol 2021; 71:51-58. [PMID: 34218162 DOI: 10.1016/j.sbi.2021.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 05/13/2021] [Indexed: 10/21/2022]
Abstract
In eukaryotic cells, DNA replication and transcription machineries uncoil nucleosomes along the double helix, to achieve the exposure of the single-stranded DNA template for nucleic acid synthesis. The replisome and RNA polymerases then redeposit histones onto DNA behind the advancing molecular motor, in a process that is crucial for epigenetic inheritance and homeostasis, respectively. Here, we compare and contrast the mechanisms by which these molecular machines advance through nucleosome arrays and discuss how chromatin remodellers can facilitate DNA replication and transcription.
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Affiliation(s)
- Oliver Willhoft
- Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Alessandro Costa
- Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
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34
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Henrikus SS, Costa A. Towards a Structural Mechanism for Sister Chromatid Cohesion Establishment at the Eukaryotic Replication Fork. BIOLOGY 2021; 10:466. [PMID: 34073213 PMCID: PMC8229022 DOI: 10.3390/biology10060466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 12/23/2022]
Abstract
Cohesion between replicated chromosomes is essential for chromatin dynamics and equal segregation of duplicated genetic material. In the G1 phase, the ring-shaped cohesin complex is loaded onto duplex DNA, enriching at replication start sites, or "origins". During the same phase of the cell cycle, and also at the origin sites, two MCM helicases are loaded as symmetric double hexamers around duplex DNA. During the S phase, and through the action of replication factors, cohesin switches from encircling one parental duplex DNA to topologically enclosing the two duplicated DNA filaments, which are known as sister chromatids. Despite its vital importance, the structural mechanism leading to sister chromatid cohesion establishment at the replication fork is mostly elusive. Here we review the current understanding of the molecular interactions between the replication machinery and cohesin, which support sister chromatid cohesion establishment and cohesin function. In particular, we discuss how cryo-EM is shedding light on the mechanisms of DNA replication and cohesin loading processes. We further expound how frontier cryo-EM approaches, combined with biochemistry and single-molecule fluorescence assays, can lead to understanding the molecular basis of sister chromatid cohesion establishment at the replication fork.
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Affiliation(s)
| | - Alessandro Costa
- Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK;
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35
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Abstract
The faithful and timely copying of DNA by molecular machines known as replisomes depends on a disparate suite of enzymes and scaffolding factors working together in a highly orchestrated manner. Large, dynamic protein-nucleic acid assemblies that selectively morph between distinct conformations and compositional states underpin this critical cellular process. In this article, we discuss recent progress outlining the physical basis of replisome construction and progression in eukaryotes.
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Affiliation(s)
- Ilan Attali
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA;
| | - Michael R Botchan
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA;
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36
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Caught in the act: structural dynamics of replication origin activation and fork progression. Biochem Soc Trans 2021; 48:1057-1066. [PMID: 32369549 PMCID: PMC7329347 DOI: 10.1042/bst20190998] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 04/09/2020] [Accepted: 04/14/2020] [Indexed: 01/03/2023]
Abstract
This review discusses recent advances in single-particle cryo-EM and single-molecule approaches used to visualise eukaryotic DNA replication reactions reconstituted in vitro. We comment on the new challenges facing structural biologists, as they turn to describing the dynamic cascade of events that lead to replication origin activation and fork progression.
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37
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Guilliam TA, Yeeles JT. The eukaryotic replisome tolerates leading-strand base damage by replicase switching. EMBO J 2021; 40:e107037. [PMID: 33555053 PMCID: PMC7917549 DOI: 10.15252/embj.2020107037] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/09/2020] [Accepted: 01/07/2021] [Indexed: 01/15/2023] Open
Abstract
The high‐fidelity replicative DNA polymerases, Pol ε and Pol δ, are generally thought to be poorly equipped to replicate damaged DNA. Direct and complete replication of a damaged template therefore typically requires the activity of low‐fidelity translesion synthesis (TLS) polymerases. Here we show that a yeast replisome, reconstituted with purified proteins, is inherently tolerant of the common oxidative lesion thymine glycol (Tg). Surprisingly, leading‐strand Tg was bypassed efficiently in the presence and absence of the TLS machinery. Our data reveal that following helicase–polymerase uncoupling a switch from Pol ε, the canonical leading‐strand replicase, to the lagging‐strand replicase Pol δ, facilitates rapid, efficient and error‐free lesion bypass at physiological nucleotide levels. This replicase switch mechanism also promotes bypass of the unrelated oxidative lesion, 8‐oxoguanine. We propose that replicase switching may promote continued leading‐strand synthesis whenever the replisome encounters leading‐strand damage that is bypassed more efficiently by Pol δ than by Pol ε.
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Affiliation(s)
- Thomas A Guilliam
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Joseph Tp Yeeles
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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38
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Abstract
In all cell types, a multi-protein machinery is required to accurately duplicate the large duplex DNA genome. This central life process requires five core replisome factors in all cellular life forms studied thus far. Unexpectedly, three of the five core replisome factors have no common ancestor between bacteria and eukaryotes. Accordingly, the replisome machines of bacteria and eukaryotes have important distinctions in the way that they are organized and function. This chapter outlines the major replication proteins that perform DNA duplication at replication forks, with particular attention to differences and similarities in the strategies used by eukaryotes and bacteria.
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Affiliation(s)
- Nina Y Yao
- DNA Replication Laboratory, The Rockefeller University, New York, USA, 10065
| | - Michael E O'Donnell
- DNA Replication Laboratory, The Rockefeller University, New York, USA, 10065. .,Howard Hughes Medical Institute, The Rockefeller University, New York, USA, 10065.
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39
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Anatomy of a twin DNA replication factory. Biochem Soc Trans 2020; 48:2769-2778. [PMID: 33300972 PMCID: PMC7752080 DOI: 10.1042/bst20200640] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 11/30/2022]
Abstract
The replication of DNA in chromosomes is initiated at sequences called origins at which two replisome machines are assembled at replication forks that move in opposite directions. Interestingly, in vivo studies observe that the two replication forks remain fastened together, often referred to as a replication factory. Replication factories containing two replisomes are well documented in cellular studies of bacteria (Escherichia coli and Bacillus subtilis) and the eukaryote, Saccharomyces cerevisiae. This basic twin replisome factory architecture may also be preserved in higher eukaryotes. Despite many years of documenting the existence of replication factories, the molecular details of how the two replisome machines are tethered together has been completely unknown in any organism. Recent structural studies shed new light on the architecture of a eukaryote replisome factory, which brings with it a new twist on how a replication factory may function.
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40
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Denkiewicz-Kruk M, Jedrychowska M, Endo S, Araki H, Jonczyk P, Dmowski M, Fijalkowska IJ. Recombination and Pol ζ Rescue Defective DNA Replication upon Impaired CMG Helicase-Pol ε Interaction. Int J Mol Sci 2020; 21:ijms21249484. [PMID: 33322195 PMCID: PMC7762974 DOI: 10.3390/ijms21249484] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/06/2020] [Accepted: 12/09/2020] [Indexed: 11/22/2022] Open
Abstract
The CMG complex (Cdc45, Mcm2–7, GINS (Psf1, 2, 3, and Sld5)) is crucial for both DNA replication initiation and fork progression. The CMG helicase interaction with the leading strand DNA polymerase epsilon (Pol ε) is essential for the preferential loading of Pol ε onto the leading strand, the stimulation of the polymerase, and the modulation of helicase activity. Here, we analyze the consequences of impaired interaction between Pol ε and GINS in Saccharomyces cerevisiae cells with the psf1-100 mutation. This significantly affects DNA replication activity measured in vitro, while in vivo, the psf1-100 mutation reduces replication fidelity by increasing slippage of Pol ε, which manifests as an elevated number of frameshifts. It also increases the occurrence of single-stranded DNA (ssDNA) gaps and the demand for homologous recombination. The psf1-100 mutant shows elevated recombination rates and synthetic lethality with rad52Δ. Additionally, we observe increased participation of DNA polymerase zeta (Pol ζ) in DNA synthesis. We conclude that the impaired interaction between GINS and Pol ε requires enhanced involvement of error-prone Pol ζ, and increased participation of recombination as a rescue mechanism for recovery of impaired replication forks.
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Affiliation(s)
- Milena Denkiewicz-Kruk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; (M.D.-K.); (M.J.); (P.J.)
| | - Malgorzata Jedrychowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; (M.D.-K.); (M.J.); (P.J.)
| | - Shizuko Endo
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan; (S.E.); (H.A.)
| | - Hiroyuki Araki
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan; (S.E.); (H.A.)
| | - Piotr Jonczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; (M.D.-K.); (M.J.); (P.J.)
| | - Michal Dmowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; (M.D.-K.); (M.J.); (P.J.)
- Correspondence: (M.D.); (I.J.F.); Tel.: +48-22-5921128 (M.D.); +48-22-5921113 (I.J.F.)
| | - Iwona J. Fijalkowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; (M.D.-K.); (M.J.); (P.J.)
- Correspondence: (M.D.); (I.J.F.); Tel.: +48-22-5921128 (M.D.); +48-22-5921113 (I.J.F.)
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41
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Mognato M, Burdak-Rothkamm S, Rothkamm K. Interplay between DNA replication stress, chromatin dynamics and DNA-damage response for the maintenance of genome stability. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2020; 787:108346. [PMID: 34083038 DOI: 10.1016/j.mrrev.2020.108346] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/02/2020] [Accepted: 11/09/2020] [Indexed: 12/17/2022]
Abstract
DNA replication stress is a major source of DNA damage, including double-stranded breaks that promote DNA damage response (DDR) signaling. Inefficient repair of such lesions can affect genome integrity. During DNA replication different factors act on chromatin remodeling in a coordinated way. While recent studies have highlighted individual molecular mechanisms of interaction, less is known about the orchestration of chromatin changes under replication stress. In this review we attempt to explore the complex relationship between DNA replication stress, DDR and genome integrity in mammalian cells, taking into account the role of chromatin disposition as an important modulator of DNA repair. Recent data on chromatin restoration and epigenetic re-establishment after DNA replication stress are reviewed.
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Affiliation(s)
| | - Susanne Burdak-Rothkamm
- University Medical Center Hamburg-Eppendorf, Department of Radiotherapy, Laboratory of Radiobiology & Experimental Radiation Oncology, Germany.
| | - Kai Rothkamm
- University Medical Center Hamburg-Eppendorf, Department of Radiotherapy, Laboratory of Radiobiology & Experimental Radiation Oncology, Germany.
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42
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Yuan Z, Li H. Molecular mechanisms of eukaryotic origin initiation, replication fork progression, and chromatin maintenance. Biochem J 2020; 477:3499-3525. [PMID: 32970141 PMCID: PMC7574821 DOI: 10.1042/bcj20200065] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/29/2020] [Accepted: 09/04/2020] [Indexed: 12/13/2022]
Abstract
Eukaryotic DNA replication is a highly dynamic and tightly regulated process. Replication involves several dozens of replication proteins, including the initiators ORC and Cdc6, replicative CMG helicase, DNA polymerase α-primase, leading-strand DNA polymerase ε, and lagging-strand DNA polymerase δ. These proteins work together in a spatially and temporally controlled manner to synthesize new DNA from the parental DNA templates. During DNA replication, epigenetic information imprinted on DNA and histone proteins is also copied to the daughter DNA to maintain the chromatin status. DNA methyltransferase 1 is primarily responsible for copying the parental DNA methylation pattern into the nascent DNA. Epigenetic information encoded in histones is transferred via a more complex and less well-understood process termed replication-couple nucleosome assembly. Here, we summarize the most recent structural and biochemical insights into DNA replication initiation, replication fork elongation, chromatin assembly and maintenance, and related regulatory mechanisms.
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Affiliation(s)
- Zuanning Yuan
- Structural Biology Program, Van Andel Institute, Grand Rapids, Michigan, U.S.A
| | - Huilin Li
- Structural Biology Program, Van Andel Institute, Grand Rapids, Michigan, U.S.A
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43
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Eickhoff P, Kose HB, Martino F, Petojevic T, Abid Ali F, Locke J, Tamberg N, Nans A, Berger JM, Botchan MR, Yardimci H, Costa A. Molecular Basis for ATP-Hydrolysis-Driven DNA Translocation by the CMG Helicase of the Eukaryotic Replisome. Cell Rep 2020; 28:2673-2688.e8. [PMID: 31484077 PMCID: PMC6737378 DOI: 10.1016/j.celrep.2019.07.104] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/15/2019] [Accepted: 07/26/2019] [Indexed: 01/12/2023] Open
Abstract
In the eukaryotic replisome, DNA unwinding by the Cdc45-MCM-Go-Ichi-Ni-San (GINS) (CMG) helicase requires a hexameric ring-shaped ATPase named minichromosome maintenance (MCM), which spools single-stranded DNA through its central channel. Not all six ATPase sites are required for unwinding; however, the helicase mechanism is unknown. We imaged ATP-hydrolysis-driven translocation of the CMG using cryo-electron microscopy (cryo-EM) and found that the six MCM subunits engage DNA using four neighboring protomers at a time, with ATP binding promoting DNA engagement. Morphing between different helicase states leads us to suggest a non-symmetric hand-over-hand rotary mechanism, explaining the asymmetric requirements of ATPase function around the MCM ring of the CMG. By imaging of a higher-order replisome assembly, we find that the Mrc1-Csm3-Tof1 fork-stabilization complex strengthens the interaction between parental duplex DNA and the CMG at the fork, which might support the coupling between DNA translocation and fork unwinding. Vertical DNA movement through the MCM ring requires rotation inside the pore Structural asymmetries in MCM-DNA are captured during ATPase-powered translocation Asymmetric rotation explains selective ATPase site requirements for translocation The fork-stabilization complex strengthens parental-DNA engagement by the MCM
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Affiliation(s)
- Patrik Eickhoff
- Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Hazal B Kose
- Single Molecule Imaging of Genome Duplication and Maintenance Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Fabrizio Martino
- Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Tatjana Petojevic
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ferdos Abid Ali
- Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Julia Locke
- Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Nele Tamberg
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - Andrea Nans
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Michael R Botchan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hasan Yardimci
- Single Molecule Imaging of Genome Duplication and Maintenance Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
| | - Alessandro Costa
- Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
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44
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Guilliam TA, Yeeles JTP. An updated perspective on the polymerase division of labor during eukaryotic DNA replication. Crit Rev Biochem Mol Biol 2020; 55:469-481. [PMID: 32883112 DOI: 10.1080/10409238.2020.1811630] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In eukaryotes three DNA polymerases (Pols), α, δ, and ε, are tasked with bulk DNA synthesis of nascent strands during genome duplication. Most evidence supports a model where Pol α initiates DNA synthesis before Pol ε and Pol δ replicate the leading and lagging strands, respectively. However, a number of recent reports, enabled by advances in biochemical and genetic techniques, have highlighted emerging roles for Pol δ in all stages of leading-strand synthesis; initiation, elongation, and termination, as well as fork restart. By focusing on these studies, this review provides an updated perspective on the division of labor between the replicative polymerases during DNA replication.
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Affiliation(s)
- Thomas A Guilliam
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Joseph T P Yeeles
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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45
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Liu L, Zhang Y, Zhang J, Wang JH, Cao Q, Li Z, Campbell JL, Dong MQ, Lou H. Characterization of the dimeric CMG/pre-initiation complex and its transition into DNA replication forks. Cell Mol Life Sci 2020; 77:3041-3058. [PMID: 31728581 PMCID: PMC11104849 DOI: 10.1007/s00018-019-03333-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 09/17/2019] [Accepted: 10/07/2019] [Indexed: 02/07/2023]
Abstract
The pre-initiation complex (pre-IC) has been proposed for two decades as an intermediate right before the maturation of the eukaryotic DNA replication fork. However, its existence and biochemical nature remain enigmatic. Here, through combining several enrichment strategies, we are able to isolate an endogenous dimeric CMG-containing complex (designated as d-CMG) distinct from traditional single CMG (s-CMG) and in vitro reconstituted dimeric CMG. D-CMG is assembled upon entry into the S phase and shortly matures into s-CMG/replisome, leading to the fact that only ~ 5% of the total CMG-containing complexes can be detected as d-CMG in vivo. Mass spectra reveal that RPA and DNA Pol α/primase co-purify with s-CMG, but not with d-CMG. Consistently, the former fraction is able to catalyze DNA unwinding and de novo synthesis, while the latter catalyzes neither. The two CMGs in d-CMG display flexibly orientated conformations under an electronic microscope. When DNA Pol α-primase is inactivated, d-CMG % rose up to 29%, indicating an incomplete pre-IC/fork transition. These findings reveal biochemical properties of the d-CMG/pre-IC and provide in vivo evidence to support the pre-IC/fork transition as a bona fide step in replication initiation.
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Affiliation(s)
- Lu Liu
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences China Agricultural University, Beijing, China
| | - Yue Zhang
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences China Agricultural University, Beijing, China
| | - Jingjing Zhang
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences China Agricultural University, Beijing, China
| | - Jian-Hua Wang
- National Institute of Biological Sciences (NIBS), Beijing, 102206, China
| | - Qinhong Cao
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences China Agricultural University, Beijing, China
| | - Zhen Li
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences China Agricultural University, Beijing, China
| | - Judith L Campbell
- Braun Laboratories, California Institute of Technology, Pasadena, 91125, CA, USA
| | - Meng-Qiu Dong
- National Institute of Biological Sciences (NIBS), Beijing, 102206, China
| | - Huiqiang Lou
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences China Agricultural University, Beijing, China.
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46
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Berti M, Cortez D, Lopes M. The plasticity of DNA replication forks in response to clinically relevant genotoxic stress. Nat Rev Mol Cell Biol 2020; 21:633-651. [PMID: 32612242 DOI: 10.1038/s41580-020-0257-5] [Citation(s) in RCA: 207] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2020] [Indexed: 12/28/2022]
Abstract
Complete and accurate DNA replication requires the progression of replication forks through DNA damage, actively transcribed regions, structured DNA and compact chromatin. Recent studies have revealed a remarkable plasticity of the replication process in dealing with these obstacles, which includes modulation of replication origin firing, of the architecture of replication forks, and of the functional organization of the replication machinery in response to replication stress. However, these specialized mechanisms also expose cells to potentially dangerous transactions while replicating DNA. In this Review, we discuss how replication forks are actively stalled, remodelled, processed, protected and restarted in response to specific types of stress. We also discuss adaptations of the replication machinery and the role of chromatin modifications during these transactions. Finally, we discuss interesting recent data on the relevance of replication fork plasticity to human health, covering its role in tumorigenesis, its crosstalk with innate immunity responses and its potential as an effective cancer therapy target.
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Affiliation(s)
- Matteo Berti
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland.
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47
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Structure of the polymerase ε holoenzyme and atomic model of the leading strand replisome. Nat Commun 2020; 11:3156. [PMID: 32572031 PMCID: PMC7308368 DOI: 10.1038/s41467-020-16910-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/02/2020] [Indexed: 01/01/2023] Open
Abstract
The eukaryotic leading strand DNA polymerase (Pol) ε contains 4 subunits, Pol2, Dpb2, Dpb3 and Dpb4. Pol2 is a fusion of two B-family Pols; the N-terminal Pol module is catalytic and the C-terminal Pol module is non-catalytic. Despite extensive efforts, there is no atomic structure for Pol ε holoenzyme, critical to understanding how DNA synthesis is coordinated with unwinding and the DNA path through the CMG helicase-Pol ε-PCNA clamp. We show here a 3.5-Å cryo-EM structure of yeast Pol ε revealing that the Dpb3–Dpb4 subunits bridge the two DNA Pol modules of Pol2, holding them rigid. This information enabled an atomic model of the leading strand replisome. Interestingly, the model suggests that an OB fold in Dbp2 directs leading ssDNA from CMG to the Pol ε active site. These results complete the DNA path from entry of parental DNA into CMG to exit of daughter DNA from PCNA. DNA polymerase epsilon (Pol ε) is responsible for leading strand synthesis during DNA replication. Here the authors use Cryo-EM to describe the architecture of the Pol ε holoenzyme and to provide an atomic model for the leading strand replisome.
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48
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Varga M, Csályi K, Bertyák I, Menyhárd DK, Poole RJ, Cerveny KL, Kövesdi D, Barátki B, Rouse H, Vad Z, Hawkins TA, Stickney HL, Cavodeassi F, Schwarz Q, Young RM, Wilson SW. Tissue-Specific Requirement for the GINS Complex During Zebrafish Development. Front Cell Dev Biol 2020; 8:373. [PMID: 32548116 PMCID: PMC7270345 DOI: 10.3389/fcell.2020.00373] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/27/2020] [Indexed: 12/13/2022] Open
Abstract
Efficient and accurate DNA replication is particularly critical in stem and progenitor cells for successful proliferation and survival. The replisome, an amalgam of protein complexes, is responsible for binding potential origins of replication, unwinding the double helix, and then synthesizing complimentary strands of DNA. According to current models, the initial steps of DNA unwinding and opening are facilitated by the CMG complex, which is composed of a GINS heterotetramer that connects Cdc45 with the mini-chromosome maintenance (Mcm) helicase. In this work, we provide evidence that in the absence of GINS function DNA replication is cell autonomously impaired, and we also show that gins1 and gins2 mutants exhibit elevated levels of apoptosis restricted to actively proliferating regions of the central nervous system (CNS). Intriguingly, our results also suggest that the rapid cell cycles during early embryonic development in zebrafish may not require the function of the canonical GINS complex as neither zygotic Gins1 nor Gins2 isoforms seem to be present during these stages.
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Affiliation(s)
- Máté Varga
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary.,Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Kitti Csályi
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - István Bertyák
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Dóra K Menyhárd
- HAS-ELTE Protein Modeling Research Group and Laboratory of Structural Chemistry and Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Richard J Poole
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Kara L Cerveny
- Biology Department, Reed College, Portland, OR, United States
| | - Dorottya Kövesdi
- Office of Supported Research Groups of the Hungarian Academy of Sciences, Budapest, Hungary.,Department of Immunology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Balázs Barátki
- Department of Immunology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Hannah Rouse
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Zsuzsa Vad
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Thomas A Hawkins
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Heather L Stickney
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Florencia Cavodeassi
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom.,Institute of Medical and Biomedical Education, St. George's University of London, London, United Kingdom
| | - Quenten Schwarz
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Rodrigo M Young
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Stephen W Wilson
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
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49
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Ma JB, Chen Z, Xu CH, Huang XY, Jia Q, Zou ZY, Mi CY, Ma DF, Lu Y, Zhang HD, Li M. Dynamic structural insights into the molecular mechanism of DNA unwinding by the bacteriophage T7 helicase. Nucleic Acids Res 2020; 48:3156-3164. [PMID: 32009150 PMCID: PMC7102974 DOI: 10.1093/nar/gkaa057] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 01/17/2020] [Accepted: 01/21/2020] [Indexed: 01/31/2023] Open
Abstract
The hexametric T7 helicase (gp4) adopts a spiral lock-washer form and encircles a coil-like DNA (tracking) strand with two nucleotides bound to each subunit. However, the chemo-mechanical coupling mechanism in unwinding has yet to be elucidated. Here, we utilized nanotensioner-enhanced Förster resonance energy transfer with one nucleotide precision to investigate gp4-induced unwinding of DNA that contains an abasic lesion. We observed that the DNA unwinding activity of gp4 is hindered but not completely blocked by abasic lesions. Gp4 moves back and forth repeatedly when it encounters an abasic lesion, whereas it steps back only occasionally when it unwinds normal DNA. We further observed that gp4 translocates on the tracking strand in step sizes of one to four nucleotides. We propose that a hypothetical intermediate conformation of the gp4-DNA complex during DNA unwinding can help explain how gp4 molecules pass lesions, providing insights into the unwinding dynamics of gp4.
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Affiliation(s)
- Jian-Bing Ma
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Ze Chen
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.,Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, China
| | - Chun-Hua Xu
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xing-Yuan Huang
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qi Jia
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen-Yu Zou
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, China
| | - Chen-Yang Mi
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Dong-Fei Ma
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Lu
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui-Dong Zhang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, China.,Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, China
| | - Ming Li
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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50
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DNA replication protein Cdc45 directly interacts with PCNA via its PIP box in Leishmania donovani and the Cdc45 PIP box is essential for cell survival. PLoS Pathog 2020; 16:e1008190. [PMID: 32413071 PMCID: PMC7255605 DOI: 10.1371/journal.ppat.1008190] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 05/28/2020] [Accepted: 04/16/2020] [Indexed: 12/22/2022] Open
Abstract
DNA replication protein Cdc45 is an integral part of the eukaryotic replicative helicase whose other components are the Mcm2-7 core, and GINS. We identified a PIP box motif in Leishmania donovani Cdc45. This motif is typically linked to interaction with the eukaryotic clamp proliferating cell nuclear antigen (PCNA). The homotrimeric PCNA can potentially bind upto three different proteins simultaneously via a loop region present in each monomer. Multiple binding partners have been identified from among the replication machinery in other eukaryotes, and the concerted /sequential binding of these partners are central to the fidelity of the replication process. Though conserved in Cdc45 across Leishmania species and Trypanosoma cruzi, the PIP box is absent in Trypanosoma brucei Cdc45. Here we investigate the possibility of Cdc45-PCNA interaction and the role of such an interaction in the in vivo context. Having confirmed the importance of Cdc45 in Leishmania DNA replication we establish that Cdc45 and PCNA interact stably in whole cell extracts, also interacting with each other directly in vitro. The interaction is mediated via the Cdc45 PIP box. This PIP box is essential for Leishmania survival. The importance of the Cdc45 PIP box is also examined in Schizosaccharomyces pombe, and it is found to be essential for cell survival here as well. Our results implicate a role for the Leishmania Cdc45 PIP box in recruiting or stabilizing PCNA on chromatin. The Cdc45-PCNA interaction might help tether PCNA and associated replicative DNA polymerase to the DNA template, thus facilitating replication fork elongation. Though multiple replication proteins that associate with PCNA have been identified in other eukaryotes, this is the first report demonstrating a direct interaction between Cdc45 and PCNA, and while our analysis suggests the interaction may not occur in human cells, it indicates that it may not be confined to trypanosomatids.
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