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Mohammed Khalid AA, Parisse P, Medagli B, Onesti S, Casalis L. Atomic Force Microscopy Investigation of the Interactions between the MCM Helicase and DNA. MATERIALS 2021; 14:ma14030687. [PMID: 33540751 PMCID: PMC7867263 DOI: 10.3390/ma14030687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/21/2021] [Accepted: 01/26/2021] [Indexed: 11/16/2022]
Abstract
The MCM (minichromosome maintenance) protein complex forms an hexameric ring and has a key role in the replication machinery of Eukaryotes and Archaea, where it functions as the replicative helicase opening up the DNA double helix ahead of the polymerases. Here, we present a study of the interaction between DNA and the archaeal MCM complex from Methanothermobacter thermautotrophicus by means of atomic force microscopy (AFM) single molecule imaging. We first optimized the protocol (surface treatment and buffer conditions) to obtain AFM images of surface-equilibrated DNA molecules before and after the interaction with the protein complex. We discriminated between two modes of interaction, one in which the protein induces a sharp bend in the DNA, and one where there is no bending. We found that the presence of the MCM complex also affects the DNA contour length. A possible interpretation of the observed behavior is that in one case the hexameric ring encircles the dsDNA, while in the other the nucleic acid wraps on the outside of the ring, undergoing a change of direction. We confirmed this topographical assignment by testing two mutants, one affecting the N-terminal β-hairpins projecting towards the central channel, and thus preventing DNA loading, the other lacking an external subdomain and thus preventing wrapping. The statistical analysis of the distribution of the protein complexes between the two modes, together with the dissection of the changes of DNA contour length and binding angle upon interaction, for the wild type and the two mutants, is consistent with the hypothesis. We discuss the results in view of the various modes of nucleic acid interactions that have been proposed for both archaeal and eukaryotic MCM complexes.
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Affiliation(s)
- Amna Abdalla Mohammed Khalid
- Elettra-Sincrotrone Trieste, 34149 Trieste, Italy; (A.A.M.K.); (B.M.)
- Department of Physics, PhD School in Nanotechnology, University of Trieste, 34127 Trieste, Italy
| | - Pietro Parisse
- Elettra-Sincrotrone Trieste, 34149 Trieste, Italy; (A.A.M.K.); (B.M.)
- Istituto Officina dei Materiali, Consiglio Nazionale delle Ricerche (IOM-CNR), 34149 Trieste, Italy
- Correspondence: (P.P.); (S.O.); (L.C.)
| | - Barbara Medagli
- Elettra-Sincrotrone Trieste, 34149 Trieste, Italy; (A.A.M.K.); (B.M.)
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, 34127 Trieste, Italy
| | - Silvia Onesti
- Elettra-Sincrotrone Trieste, 34149 Trieste, Italy; (A.A.M.K.); (B.M.)
- Correspondence: (P.P.); (S.O.); (L.C.)
| | - Loredana Casalis
- Elettra-Sincrotrone Trieste, 34149 Trieste, Italy; (A.A.M.K.); (B.M.)
- Correspondence: (P.P.); (S.O.); (L.C.)
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Abstract
It is now well recognized that the information processing machineries of archaea are far more closely related to those of eukaryotes than to those of their prokaryotic cousins, the bacteria. Extensive studies have been performed on the structure and function of the archaeal DNA replication origins, the proteins that define them, and the macromolecular assemblies that drive DNA unwinding and nascent strand synthesis. The results from various archaeal organisms across the archaeal domain of life show surprising levels of diversity at many levels-ranging from cell cycle organization to chromosome ploidy to replication mode and nature of the replicative polymerases. In the following, we describe recent advances in the field, highlighting conserved features and lineage-specific innovations.
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Affiliation(s)
- Mark D Greci
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA;
| | - Stephen D Bell
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA; .,Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA
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3
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Graham BW, Bougoulias ME, Dodge KL, Thaxton CT, Olaso D, Tao Y, Young NL, Marshall AG, Trakselis MA. Control of Hexamerization, Assembly, and Excluded Strand Specificity for the Sulfolobus solfataricus MCM Helicase. Biochemistry 2018; 57:5672-5682. [DOI: 10.1021/acs.biochem.8b00766] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Brian W. Graham
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Michael E. Bougoulias
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Katie L. Dodge
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Carly T. Thaxton
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Danae Olaso
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Yeqing Tao
- Department of Chemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Nicolas L. Young
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030-3411, United States
| | - Alan G. Marshall
- Department of Chemistry, Florida State University, Tallahassee, Florida 32306, United States
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Michael A. Trakselis
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
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4
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Neves H, Kwok HF. In sickness and in health: The many roles of the minichromosome maintenance proteins. Biochim Biophys Acta Rev Cancer 2017; 1868:295-308. [DOI: 10.1016/j.bbcan.2017.06.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 05/29/2017] [Accepted: 06/01/2017] [Indexed: 01/09/2023]
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5
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Sysoeva TA. Assessing heterogeneity in oligomeric AAA+ machines. Cell Mol Life Sci 2017; 74:1001-1018. [PMID: 27669691 PMCID: PMC11107579 DOI: 10.1007/s00018-016-2374-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 09/13/2016] [Accepted: 09/19/2016] [Indexed: 10/20/2022]
Abstract
ATPases Associated with various cellular Activities (AAA+ ATPases) are molecular motors that use the energy of ATP binding and hydrolysis to remodel their target macromolecules. The majority of these ATPases form ring-shaped hexamers in which the active sites are located at the interfaces between neighboring subunits. Structural changes initiate in an active site and propagate to distant motor parts that interface and reshape the target macromolecules, thereby performing mechanical work. During the functioning cycle, the AAA+ motor transits through multiple distinct states. Ring architecture and placement of the catalytic sites at the intersubunit interfaces allow for a unique level of coordination among subunits of the motor. This in turn results in conformational differences among subunits and overall asymmetry of the motor ring as it functions. To date, a large amount of structural information has been gathered for different AAA+ motors, but even for the most characterized of them only a few structural states are known and the full mechanistic cycle cannot be yet reconstructed. Therefore, the first part of this work will provide a broad overview of what arrangements of AAA+ subunits have been structurally observed focusing on diversity of ATPase oligomeric ensembles and heterogeneity within the ensembles. The second part of this review will concentrate on methods that assess structural and functional heterogeneity among subunits of AAA+ motors, thus bringing us closer to understanding the mechanism of these fascinating molecular motors.
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Affiliation(s)
- Tatyana A Sysoeva
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA.
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6
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Abstract
Cellular DNA replication factories depend on ring-shaped hexameric helicases to aid DNA synthesis by processively unzipping the parental DNA helix. Replicative helicases are loaded onto DNA by dedicated initiator, loader, and accessory proteins during the initiation of DNA replication in a tightly regulated, multistep process. We discuss here the molecular choreography of DNA replication initiation across the three domains of life, highlighting similarities and differences in the strategies used to deposit replicative helicases onto DNA and to melt the DNA helix in preparation for replisome assembly. Although initiators and loaders are phylogenetically related, the mechanisms they use for accomplishing similar tasks have diverged considerably and in an unpredictable manner.
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Affiliation(s)
- Franziska Bleichert
- 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.
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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7
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Cannone G, Visentin S, Palud A, Henneke G, Spagnolo L. Structure of an octameric form of the minichromosome maintenance protein from the archaeon Pyrococcus abyssi. Sci Rep 2017; 7:42019. [PMID: 28176822 PMCID: PMC5296750 DOI: 10.1038/srep42019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 01/05/2017] [Indexed: 12/12/2022] Open
Abstract
Cell division is a complex process that requires precise duplication of genetic material. Duplication is concerted by replisomes. The Minichromosome Maintenance (MCM) replicative helicase is a crucial component of replisomes. Eukaryotic and archaeal MCM proteins are highly conserved. In fact, archaeal MCMs are powerful tools for elucidating essential features of MCM function. However, while eukaryotic MCM2-7 is a heterocomplex made of different polypeptide chains, the MCM complexes of many Archaea form homohexamers from a single gene product. Moreover, some archaeal MCMs are polymorphic, and both hexameric and heptameric architectures have been reported for the same polypeptide. Here, we present the structure of the archaeal MCM helicase from Pyrococcus abyssi in its single octameric ring assembly. To our knowledge, this is the first report of a full-length octameric MCM helicase.
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Affiliation(s)
- Giuseppe Cannone
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, University Avenue, Glasgow G12 8QQ, UK
- School of Biological Sciences and Max Born Crescent, Edinburgh EH9 3JR, UK
- Centre for Science at extreme conditions, University of Edinburgh, Max Born Crescent, Edinburgh EH9 3JR, UK
| | - Silvia Visentin
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, University Avenue, Glasgow G12 8QQ, UK
- School of Biological Sciences and Max Born Crescent, Edinburgh EH9 3JR, UK
- ISIS neutron source, Science and Technologies Research Council, Rutherford Appleton Laboratories, Harwell, OX11 0QX United Kingdom
| | - Adeline Palud
- IFREMER, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197, ZI de la pointe du diable CS 10070 29280 Plouzané, France
- Université de Bretagne Occidentale, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, rue Dumont d’Urville 29280 Plouzané, France
- CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, rue Dumont d’Urville 29280 Plouzané, France
| | - Ghislaine Henneke
- IFREMER, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197, ZI de la pointe du diable CS 10070 29280 Plouzané, France
- Université de Bretagne Occidentale, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, rue Dumont d’Urville 29280 Plouzané, France
- CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, rue Dumont d’Urville 29280 Plouzané, France
| | - Laura Spagnolo
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, University Avenue, Glasgow G12 8QQ, UK
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Parker MW, Botchan MR, Berger JM. Mechanisms and regulation of DNA replication initiation in eukaryotes. Crit Rev Biochem Mol Biol 2017; 52:107-144. [PMID: 28094588 DOI: 10.1080/10409238.2016.1274717] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cellular DNA replication is initiated through the action of multiprotein complexes that recognize replication start sites in the chromosome (termed origins) and facilitate duplex DNA melting within these regions. In a typical cell cycle, initiation occurs only once per origin and each round of replication is tightly coupled to cell division. To avoid aberrant origin firing and re-replication, eukaryotes tightly regulate two events in the initiation process: loading of the replicative helicase, MCM2-7, onto chromatin by the origin recognition complex (ORC), and subsequent activation of the helicase by its incorporation into a complex known as the CMG. Recent work has begun to reveal the details of an orchestrated and sequential exchange of initiation factors on DNA that give rise to a replication-competent complex, the replisome. Here, we review the molecular mechanisms that underpin eukaryotic DNA replication initiation - from selecting replication start sites to replicative helicase loading and activation - and describe how these events are often distinctly regulated across different eukaryotic model organisms.
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Affiliation(s)
- Matthew W Parker
- a Department of Biophysics and Biophysical Chemistry , Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - Michael R Botchan
- b Department of Molecular and Cell Biology , University of California Berkeley , Berkeley , CA , USA
| | - James M Berger
- a Department of Biophysics and Biophysical Chemistry , Johns Hopkins University School of Medicine , Baltimore , MD , USA
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9
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Abstract
Hexameric helicases control both the initiation and the elongation phase of DNA replication. The toroidal structure of these enzymes provides an inherent challenge in the opening and loading onto DNA at origins, as well as the conformational changes required to exclude one strand from the central channel and activate DNA unwinding. Recently, high-resolution structures have not only revealed the architecture of various hexameric helicases but also detailed the interactions of DNA within the central channel, as well as conformational changes that occur during loading. This structural information coupled with advanced biochemical reconstitutions and biophysical methods have transformed our understanding of the dynamics of both the helicase structure and the DNA interactions required for efficient unwinding at the replisome.
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Affiliation(s)
- Michael A Trakselis
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, 76798, USA
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10
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Archaeal DNA Replication Origins and Recruitment of the MCM Replicative Helicase. DNA REPLICATION ACROSS TAXA 2016; 39:169-90. [DOI: 10.1016/bs.enz.2016.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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11
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Samson RY, Abeyrathne PD, Bell SD. Mechanism of Archaeal MCM Helicase Recruitment to DNA Replication Origins. Mol Cell 2015; 61:287-96. [PMID: 26725007 DOI: 10.1016/j.molcel.2015.12.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 10/13/2015] [Accepted: 11/18/2015] [Indexed: 11/25/2022]
Abstract
Cellular DNA replication origins direct the recruitment of replicative helicases via the action of initiator proteins belonging to the AAA+ superfamily of ATPases. Archaea have a simplified subset of the eukaryotic DNA replication machinery proteins and possess initiators that appear ancestral to both eukaryotic Orc1 and Cdc6. We have reconstituted origin-dependent recruitment of the homohexameric archaeal MCM in vitro with purified recombinant proteins. Using this system, we reveal that archaeal Orc1-1 fulfills both Orc1 and Cdc6 functions by binding to a replication origin and directly recruiting MCM helicase. We identify the interaction interface between these proteins and reveal how ATP binding by Orc1-1 modulates recruitment of MCM. Additionally, we provide evidence that an open-ring form of the archaeal MCM homohexamer is loaded at origins.
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Affiliation(s)
- Rachel Y Samson
- Department of Molecular and Cellular Biochemistry, Indiana University, Simon Hall MSB, 212 S Hawthorne Drive, Bloomington, IN 47405, USA
| | | | - Stephen D Bell
- Department of Molecular and Cellular Biochemistry, Indiana University, Simon Hall MSB, 212 S Hawthorne Drive, Bloomington, IN 47405, USA; Department of Biology, Indiana University, Simon Hall MSB, 212 S Hawthorne Drive, Bloomington, IN 47405, USA.
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12
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Archaeal MCM Proteins as an Analog for the Eukaryotic Mcm2-7 Helicase to Reveal Essential Features of Structure and Function. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2015; 2015:305497. [PMID: 26539061 PMCID: PMC4619765 DOI: 10.1155/2015/305497] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 04/05/2015] [Indexed: 11/18/2022]
Abstract
In eukaryotes, the replicative helicase is the large multisubunit CMG complex consisting of the Mcm2–7 hexameric ring, Cdc45, and the tetrameric GINS complex. The Mcm2–7 ring assembles from six different, related proteins and forms the core of this complex. In archaea, a homologous MCM hexameric ring functions as the replicative helicase at the replication fork. Archaeal MCM proteins form thermostable homohexamers, facilitating their use as models of the eukaryotic Mcm2–7 helicase. Here we review archaeal MCM helicase structure and function and how the archaeal findings relate to the eukaryotic Mcm2–7 ring.
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Froelich CA, Nourse A, Enemark EJ. MCM ring hexamerization is a prerequisite for DNA-binding. Nucleic Acids Res 2015; 43:9553-63. [PMID: 26365238 PMCID: PMC4627082 DOI: 10.1093/nar/gkv914] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 09/01/2015] [Indexed: 11/22/2022] Open
Abstract
The hexameric Minichromosome Maintenance (MCM) protein complex forms a ring that unwinds DNA at the replication fork in eukaryotes and archaea. Our recent crystal structure of an archaeal MCM N-terminal domain bound to single-stranded DNA (ssDNA) revealed ssDNA associating across tight subunit interfaces but not at the loose interfaces, indicating that DNA-binding is governed not only by the DNA-binding residues of the subunits (MCM ssDNA-binding motif, MSSB) but also by the relative orientation of the subunits. We now extend these findings by showing that DNA-binding by the MCM N-terminal domain of the archaeal organism Pyrococcus furiosus occurs specifically in the hexameric oligomeric form. We show that mutants defective for hexamerization are defective in binding ssDNA despite retaining all the residues observed to interact with ssDNA in the crystal structure. One mutation that exhibits severely defective hexamerization and ssDNA-binding is at a conserved phenylalanine that aligns with the mouse Mcm4(Chaos3) mutation associated with chromosomal instability, cancer, and decreased intersubunit association.
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Affiliation(s)
- Clifford A Froelich
- Department of Structural Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 311, Memphis, TN 38105, USA
| | - Amanda Nourse
- Molecular Interaction Analysis Shared Resource, St Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 311, Memphis, TN 38105, USA
| | - Eric J Enemark
- Department of Structural Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 311, Memphis, TN 38105, USA
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14
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Characterization of the MCM homohexamer from the thermoacidophilic euryarchaeon Picrophilus torridus. Sci Rep 2015; 5:9057. [PMID: 25762096 PMCID: PMC4356968 DOI: 10.1038/srep09057] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 02/05/2015] [Indexed: 01/04/2023] Open
Abstract
The typical archaeal MCM exhibits helicase activity independently invitro. This study characterizes MCM from the euryarchaeon Picrophilus torridus. While PtMCM hydrolyzes ATP in DNA-independent manner, it displays very poor ability to unwind DNA independently, and then too only under acidic conditions. The protein exists stably in complex with PtGINS in whole cell lysates, interacting directly with PtGINS under neutral and acidic conditions. GINS strongly activates MCM helicase activity, but only at low pH. In consonance with this, PtGINS activates PtMCM-mediated ATP hydrolysis only at low pH, with the amount of ATP hydrolyzed during the helicase reaction increasing more than fifty-fold in the presence of GINS. While the stimulation of MCM-mediated helicase activity by GINS has been reported in MCMs from P.furiosus, T.kodakarensis, and very recently, T.acidophilum, to the best of our knowledge, this is the first report of an MCM helicase demonstrating DNA unwinding activity only at such acidic pH, across all archaea and eukaryotes. PtGINS may induce/stabilize a conducive conformation of PtMCM under acidic conditions, favouring PtMCM-mediated DNA unwinding coupled to ATP hydrolysis. Our findings underscore the existence of divergent modes of replication regulation among archaea and the importance of investigating replication events in more archaeal organisms.
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15
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Wiedemann C, Szambowska A, Häfner S, Ohlenschläger O, Gührs KH, Görlach M. Structure and regulatory role of the C-terminal winged helix domain of the archaeal minichromosome maintenance complex. Nucleic Acids Res 2015; 43:2958-67. [PMID: 25712103 PMCID: PMC4357721 DOI: 10.1093/nar/gkv120] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The minichromosome maintenance complex (MCM) represents the replicative DNA helicase both in eukaryotes and archaea. Here, we describe the solution structure of the C-terminal domains of the archaeal MCMs of Sulfolobus solfataricus (Sso) and Methanothermobacter thermautotrophicus (Mth). Those domains consist of a structurally conserved truncated winged helix (WH) domain lacking the two typical ‘wings’ of canonical WH domains. A less conserved N-terminal extension links this WH module to the MCM AAA+ domain forming the ATPase center. In the Sso MCM this linker contains a short α-helical element. Using Sso MCM mutants, including chimeric constructs containing Mth C-terminal domain elements, we show that the ATPase and helicase activity of the Sso MCM is significantly modulated by the short α-helical linker element and by N-terminal residues of the first α-helix of the truncated WH module. Finally, based on our structural and functional data, we present a docking-derived model of the Sso MCM, which implies an allosteric control of the ATPase center by the C-terminal domain.
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Affiliation(s)
- Christoph Wiedemann
- Research Group Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research-Fritz Lipmann Institute (FLI), Beutenbergstr. 11, D-07745 Jena, Germany
| | - Anna Szambowska
- Research Group Biochemistry, Leibniz Institute for Age Research-Fritz Lipmann Institute (FLI), Beutenbergstr. 11, D-07745 Jena, Germany Laboratory of Molecular Biology IBB PAS, affiliated with University of Gdansk, Wita Stwosza 59, Gdansk, Poland
| | - Sabine Häfner
- Research Group Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research-Fritz Lipmann Institute (FLI), Beutenbergstr. 11, D-07745 Jena, Germany
| | - Oliver Ohlenschläger
- Research Group Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research-Fritz Lipmann Institute (FLI), Beutenbergstr. 11, D-07745 Jena, Germany
| | - Karl-Heinz Gührs
- Protein laboratory, Leibniz Institute for Age Research-Fritz Lipmann Institute (FLI), Beutenbergstr. 11, D-07745 Jena, Germany
| | - Matthias Görlach
- Research Group Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research-Fritz Lipmann Institute (FLI), Beutenbergstr. 11, D-07745 Jena, Germany
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16
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Yu XJ, Greenleaf WB, Shi YS, Chen XS. Mechanism of subunit coordination of an AAA+ hexameric molecular nanomachine. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2014; 11:531-41. [PMID: 25555349 DOI: 10.1016/j.nano.2014.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 10/15/2014] [Accepted: 11/11/2014] [Indexed: 12/18/2022]
Abstract
Simian virus 40 large tumor antigen (LT) is both a potent oncogenic protein and an efficient hexameric nanomachine that harnesses the energy from ATP binding/hydrolysis to melt origin DNA and unwind replication forks. However, how the six subunits of the helicase motor coordinate during ATP hydrolysis and DNA unwinding/translocation is unresolved. Here we investigated the subunit coordination mechanisms "binomial distribution mutant doping" experiments in the presence of various DNA substrates. For ATP hydrolysis, we observed multiple coordination modes, ranging from random and semi-random, and semi-coordinated modes, depending on which type of DNA is present. For DNA unwinding, however, the results indicated a fully-coordinated mode for the natural origin-containing duplex DNA, but a semi-coordinated mode for a pre-existing fork-DNA, providing direct evidence for LT to use potentially different mechanisms to unwind the two types of substrates. The results of this study provide insights into DNA translocation and unwinding mechanisms for LT hexameric biomotor. From the clinical editor: The study describes the subunit coordination of simian virus 40 large tumor antigen (LT) showing that multiple mechanisms exist that handle the specific needs of different stages of DNA replication.
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Affiliation(s)
- Xian Jessica Yu
- Molecular and Computational Biology Program, Department of Biology, University of Southern California, Los Angeles, CA, USA
| | - William B Greenleaf
- Molecular and Computational Biology Program, Department of Biology, University of Southern California, Los Angeles, CA, USA
| | - Yemin Stanley Shi
- Molecular and Computational Biology Program, Department of Biology, University of Southern California, Los Angeles, CA, USA
| | - Xiaojiang S Chen
- Molecular and Computational Biology Program, Department of Biology, University of Southern California, Los Angeles, CA, USA; Department of Chemistry, University of Southern California, Los Angeles, CA, USA; Norris Cancer Center, University of Southern California, Los Angeles, CA, USA.
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17
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Miller JM, Arachea BT, Epling LB, Enemark EJ. Analysis of the crystal structure of an active MCM hexamer. eLife 2014; 3:e03433. [PMID: 25262915 PMCID: PMC4359371 DOI: 10.7554/elife.03433] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 08/28/2014] [Indexed: 12/26/2022] Open
Abstract
In a previous Research article (Froelich et al., 2014), we suggested an MCM helicase activation mechanism, but were limited in discussing the ATPase domain because it was absent from the crystal structure. Here we present the crystal structure of a nearly full-length MCM hexamer that is helicase-active and thus has all features essential for unwinding DNA. The structure is a chimera of Sulfolobus solfataricus N-terminal domain and Pyrococcus furiosus ATPase domain. We discuss three major findings: 1) a novel conformation for the A-subdomain that could play a role in MCM regulation; 2) interaction of a universally conserved glutamine in the N-terminal Allosteric Communication Loop with the AAA+ domain helix-2-insert (h2i); and 3) a recessed binding pocket for the MCM ssDNA-binding motif influenced by the h2i. We suggest that during helicase activation, the h2i clamps down on the leading strand to facilitate strand retention and regulate ATP hydrolysis. DOI:http://dx.doi.org/10.7554/eLife.03433.001
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Affiliation(s)
- Justin M Miller
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, United States
| | - Buenafe T Arachea
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, United States
| | - Leslie B Epling
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, United States
| | - Eric J Enemark
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, United States
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Froelich CA, Kang S, Epling LB, Bell SP, Enemark EJ. A conserved MCM single-stranded DNA binding element is essential for replication initiation. eLife 2014; 3:e01993. [PMID: 24692448 PMCID: PMC3970758 DOI: 10.7554/elife.01993] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The ring-shaped MCM helicase is essential to all phases of DNA replication. The complex loads at replication origins as an inactive double-hexamer encircling duplex DNA. Helicase activation converts this species to two active single hexamers that encircle single-stranded DNA (ssDNA). The molecular details of MCM DNA interactions during these events are unknown. We determined the crystal structure of the Pyrococcus furiosus MCM N-terminal domain hexamer bound to ssDNA and define a conserved MCM-ssDNA binding motif (MSSB). Intriguingly, ssDNA binds the MCM ring interior perpendicular to the central channel with defined polarity. In eukaryotes, the MSSB is conserved in several Mcm2-7 subunits, and MSSB mutant combinations in S. cerevisiae Mcm2-7 are not viable. Mutant Mcm2-7 complexes assemble and are recruited to replication origins, but are defective in helicase loading and activation. Our findings identify an important MCM-ssDNA interaction and suggest it functions during helicase activation to select the strand for translocation. DOI:http://dx.doi.org/10.7554/eLife.01993.001 When DNA was first recognised to be a double helix, it was clear that this structure could easily explain how DNA could be replicated. Each strand was made of bases—represented by the letters ‘A’, ‘C’, ‘G’ and ‘T’—and the two strands were held together by bonds between pairs of bases, one from each strand. Moreover, ‘A’ always paired with ‘T’, and ‘C’ always paired with ‘G’. Therefore, if the two strands were separated, each could be used as a template to guide the synthesis of a new complementary strand and thus create two copies of the original double-stranded molecule. One of the first steps in this replication process involves a ring-shaped complex of six proteins, called an MCM helicase, separating the two strands. To prepare for DNA replication, two MCM helicase rings wrap around the double-stranded DNA. Then, after the helicase has been activated, the bonds between the DNA base pairs break, and the two rings separate with one ring encircling each DNA strand. However, the details of the interactions between the helicase and the DNA during these events are not fully understood. Now Froelich, Kang et al. have solved the three-dimensional structure of an MCM helicase ring—taken from a microbe originally found at deep ocean vents—on its own and also when bound to a short piece of single-stranded DNA. The helicase ring becomes more oval when the DNA binds to it. Moreover, rather than passing straight through the ring, the DNA wraps part of the way around the inside of the ring. Specific amino acids—the building blocks of proteins—on the inside of the ring interact with the single-stranded DNA, and these amino acids are also found in MCM proteins in many other organisms. Furthermore, swapping these amino acids for different amino acids significantly reduced the ability of the ring to bind to single-stranded DNA, but its ability to bind to double-stranded DNA was only slightly affected. Engineering similar changes into the ring complexes of yeast cells was lethal, and the mutant complexes were less able to be loaded onto the DNA, or to be activated and separate the two strands ready for replication. These insights into how helicases are loaded onto double-stranded DNA, and select one DNA strand to encircle, have improved our understanding of how DNA replication is initiated: a process that is vital for living things. DOI:http://dx.doi.org/10.7554/eLife.01993.002
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Affiliation(s)
- Clifford A Froelich
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, United States
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Fu Y, Slaymaker IM, Wang J, Wang G, Chen XS. The 1.8-Å crystal structure of the N-terminal domain of an archaeal MCM as a right-handed filament. J Mol Biol 2013; 426:1512-23. [PMID: 24378617 DOI: 10.1016/j.jmb.2013.12.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 12/18/2013] [Accepted: 12/19/2013] [Indexed: 11/16/2022]
Abstract
Mini-chromosome maintenance (MCM) proteins are the replicative helicase necessary for DNA replication in both eukarya and archaea. Most of archaea only have one MCM gene. Here, we report a 1.8-Å crystal structure of the N-terminal MCM from the archaeon Thermoplasma acidophilum (tapMCM). In the structure, the MCM N-terminus forms a right-handed filament that contains six subunits in each turn, with a diameter of 25Å of the central channel opening. The inner surface is highly positively charged, indicating DNA binding. This filament structure with six subunits per turn may also suggests a potential role for an open-ring structure for hexameric MCM and dynamic conformational changes in initiation and elongation stages of DNA replication.
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Affiliation(s)
- Yang Fu
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Ian M Slaymaker
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Junfeng Wang
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Ganggang Wang
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Xiaojiang S Chen
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA; Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA; Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, CA 90089, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA.
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20
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Structure and evolutionary origins of the CMG complex. Chromosoma 2013; 122:47-53. [PMID: 23412083 DOI: 10.1007/s00412-013-0397-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 01/24/2013] [Accepted: 01/25/2013] [Indexed: 01/20/2023]
Abstract
The CMG (Cdc45-MCM-GINS) complex is the eukaryotic replicative helicase, the enzyme that unwinds double-stranded DNA at replication forks. All three components of the CMG complex are essential for its function, but only in the case of MCM, the molecular motor that harnesses the energy of ATP hydrolysis to catalyse strand separation, is that function clear. Here, we review current knowledge of the three-dimensional structure of the CMG complex and its components and highlight recent advances in our understanding of its evolutionary origins.
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21
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Slaymaker IM, Fu Y, Toso DB, Ranatunga N, Brewster A, Forsburg SL, Zhou ZH, Chen XS. Mini-chromosome maintenance complexes form a filament to remodel DNA structure and topology. Nucleic Acids Res 2013; 41:3446-56. [PMID: 23361460 PMCID: PMC3597688 DOI: 10.1093/nar/gkt022] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Deregulation of mini-chromosome maintenance (MCM) proteins is associated with genomic instability and cancer. MCM complexes are recruited to replication origins for genome duplication. Paradoxically, MCM proteins are in excess than the number of origins and are associated with chromatin regions away from the origins during G1 and S phases. Here, we report an unusually wide left-handed filament structure for an archaeal MCM, as determined by X-ray and electron microscopy. The crystal structure reveals that an α-helix bundle formed between two neighboring subunits plays a critical role in filament formation. The filament has a remarkably strong electro-positive surface spiraling along the inner filament channel for DNA binding. We show that this MCM filament binding to DNA causes dramatic DNA topology change. This newly identified function of MCM to change DNA topology may imply a wider functional role for MCM in DNA metabolisms beyond helicase function. Finally, using yeast genetics, we show that the inter-subunit interactions, important for MCM filament formation, play a role for cell growth and survival.
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Affiliation(s)
- Ian M Slaymaker
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
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22
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Medagli B, Onesti S. Structure and mechanism of hexameric helicases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 767:75-95. [PMID: 23161007 DOI: 10.1007/978-1-4614-5037-5_4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Hexameric helicases are responsible for many biological processes, ranging from DNA replication in various life domains to DNA repair, transcriptional regulation and RNA metabolism, and encompass superfamilies 3-6 (SF3-6).To harness the chemical energy from ATP hydrolysis for mechanical work, hexameric helicases have a conserved core engine, called ASCE, that belongs to a subdivision of the P-loop NTPases. Some of the ring helicases (SF4 and SF5) use a variant of ASCE known as RecA-like, while some (SF3 and SF6) use another variant known as AAA+ fold. The NTP-binding sites are located at the interface between monomers and include amino-acid residues coming from neighbouring subunits, providing a mean for small structural changes within the ATP-binding site to be amplified into large inter-subunit movement.The ring structure has a central channel which encircles the nucleic acid. The topological link between the protein and the nucleic acid substrate increases the stability and processivity of the enzyme. This is probably the reason why within cellular systems the critical step of unwinding dsDNA ahead of the replication fork seems to be almost invariably carried out by a toroidal helicase, whether in bacteria, archaea or eukaryotes, as well as in some viruses.Over the last few years, a large number of biochemical, biophysical and structural data have thrown new light onto the architecture and function of these remarkable machines. Although the evidence is still limited to a couple of systems, biochemical and structural results suggest that motors based on RecA and AAA+ folds have converged on similar mechanisms to couple ATP-driven conformational changes to movement along nucleic acids.
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Affiliation(s)
- Barbara Medagli
- Structural Biology, Sincrotrone Trieste (Elettra), Area Science Pk, Basovizza, Trieste, Italy,
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23
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Liu C, Wu R, Zhou B, Wang J, Wei Z, Tye BK, Liang C, Zhu G. Structural insights into the Cdt1-mediated MCM2-7 chromatin loading. Nucleic Acids Res 2012; 40:3208-17. [PMID: 22140117 PMCID: PMC3326298 DOI: 10.1093/nar/gkr1118] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2011] [Revised: 10/31/2011] [Accepted: 11/07/2011] [Indexed: 12/23/2022] Open
Abstract
Initiation of DNA replication in eukaryotes is exquisitely regulated to ensure that DNA replication occurs exactly once in each cell division. A conserved and essential step for the initiation of eukaryotic DNA replication is the loading of the mini-chromosome maintenance 2-7 (MCM2-7) helicase onto chromatin at replication origins by Cdt1. To elucidate the molecular mechanism of this event, we determined the structure of the human Cdt1-Mcm6 binding domains, the Cdt1(410-440)/MCM6(708-821) complex by NMR. Our structural and site-directed mutagenesis studies showed that charge complementarity is a key determinant for the specific interaction between Cdt1 and Mcm2-7. When this interaction was interrupted by alanine substitutions of the conserved interacting residues, the corresponding yeast Cdt1 and Mcm6 mutants were defective in DNA replication and the chromatin loading of Mcm2, resulting in cell death. Having shown that Cdt1 and Mcm6 interact through their C-termini, and knowing that Cdt1 is tethered to Orc6 during the loading of MCM2-7, our results suggest that the MCM2-7 hexamer is loaded with its C terminal end facing the ORC complex. These results provide a structural basis for the Cdt1-mediated MCM2-7 chromatin loading.
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Affiliation(s)
- Changdong Liu
- Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China and Department of Molecular Biology & Genetics, Cornell University, USA
| | - Rentian Wu
- Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China and Department of Molecular Biology & Genetics, Cornell University, USA
| | - Bo Zhou
- Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China and Department of Molecular Biology & Genetics, Cornell University, USA
| | - Jiafeng Wang
- Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China and Department of Molecular Biology & Genetics, Cornell University, USA
| | - Zhun Wei
- Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China and Department of Molecular Biology & Genetics, Cornell University, USA
| | - Bik K. Tye
- Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China and Department of Molecular Biology & Genetics, Cornell University, USA
| | - Chun Liang
- Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China and Department of Molecular Biology & Genetics, Cornell University, USA
| | - Guang Zhu
- Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China and Department of Molecular Biology & Genetics, Cornell University, USA
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Stelter M, Gutsche I, Kapp U, Bazin A, Bajic G, Goret G, Jamin M, Timmins J, Terradot L. Architecture of a Dodecameric Bacterial Replicative Helicase. Structure 2012; 20:554-64. [DOI: 10.1016/j.str.2012.01.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2011] [Revised: 01/17/2012] [Accepted: 01/22/2012] [Indexed: 10/28/2022]
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25
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Abstract
Minichromosome maintenance (MCM) complexes have been identified as the primary replicative helicases responsible for unwinding DNA for genome replication. The focus of this chapter is to discuss the current structural and functional understanding of MCMs and their role at origins of replication, which are based mostly on the studies of MCM proteins and MCM complexes from archaeal genomes.
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Affiliation(s)
- Ian M Slaymaker
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
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26
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Sanchez-Berrondo J, Mesa P, Ibarra A, Martínez-Jiménez MI, Blanco L, Méndez J, Boskovic J, Montoya G. Molecular architecture of a multifunctional MCM complex. Nucleic Acids Res 2011; 40:1366-80. [PMID: 21984415 PMCID: PMC3273815 DOI: 10.1093/nar/gkr831] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
DNA replication is strictly regulated through a sequence of steps that involve many macromolecular protein complexes. One of them is the replicative helicase, which is required for initiation and elongation phases. A MCM helicase found as a prophage in the genome of Bacillus cereus is fused with a primase domain constituting an integrative arrangement of two essential activities for replication. We have isolated this helicase–primase complex (BcMCM) showing that it can bind DNA and displays not only helicase and primase but also DNA polymerase activity. Using single-particle electron microscopy and 3D reconstruction, we obtained structures of BcMCM using ATPγS or ADP in the absence and presence of DNA. The complex depicts the typical hexameric ring shape. The dissection of the unwinding mechanism using site-directed mutagenesis in the Walker A, Walker B, arginine finger and the helicase channels, suggests that the BcMCM complex unwinds DNA following the extrusion model similarly to the E1 helicase from papillomavirus.
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Affiliation(s)
- June Sanchez-Berrondo
- Structural Biology and Biocomputing Programme, Macromolecular Crystallography Group, Spanish National Cancer Research Center (CNIO), c/Melchor Fdez. Almagro 3, 28029-Madrid, Spain
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27
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Graham BW, Schauer GD, Leuba SH, Trakselis MA. Steric exclusion and wrapping of the excluded DNA strand occurs along discrete external binding paths during MCM helicase unwinding. Nucleic Acids Res 2011; 39:6585-95. [PMID: 21576224 PMCID: PMC3159478 DOI: 10.1093/nar/gkr345] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Revised: 04/25/2011] [Accepted: 04/26/2011] [Indexed: 11/17/2022] Open
Abstract
The minichromosome maintenance (MCM) helicase complex is essential for the initiation and elongation of DNA replication in both the eukaryotic and archaeal domains. The archaeal homohexameric MCM helicase from Sulfolobus solfataricus serves as a model for understanding mechanisms of DNA unwinding. In this report, the displaced 5'-tail is shown to provide stability to the MCM complex on DNA and contribute to unwinding. Mutations in a positively charged patch on the exterior surface of the MCM hexamer destabilize this interaction, alter the path of the displaced 5'-tail DNA and reduce unwinding. DNA footprinting and single-molecule fluorescence experiments support a previously unrecognized wrapping of the 5'-tail. This mode of hexameric helicase DNA unwinding is termed the steric exclusion and wrapping (SEW) model, where the 3'-tail is encircled by the helicase while the displaced 5'-tail wraps around defined paths on the exterior of the helicase. The novel wrapping mechanism stabilizes the MCM complex in a positive unwinding mode, protects the displaced single-stranded DNA tail and prevents reannealing.
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Affiliation(s)
- Brian W. Graham
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260 and Department of Cell Biology and Physiology, Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Grant D. Schauer
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260 and Department of Cell Biology and Physiology, Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Sanford H. Leuba
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260 and Department of Cell Biology and Physiology, Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Michael A. Trakselis
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260 and Department of Cell Biology and Physiology, Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
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Ogino H, Ishino S, Mayanagi K, Haugland GT, Birkeland NK, Yamagishi A, Ishino Y. The GINS complex from the thermophilic archaeon, Thermoplasma acidophilum may function as a homotetramer in DNA replication. Extremophiles 2011; 15:529-39. [PMID: 21656171 DOI: 10.1007/s00792-011-0383-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 05/20/2011] [Indexed: 11/30/2022]
Abstract
The eukaryotic GINS heterotetramer, consisting of Sld5, Psf1, Psf2, and Psf3, participates in "CMG complex" formation with mini-chromosome maintenance (MCM) and Cdc45 as a key component of a replicative helicase. There are only two homologs of the GINS proteins in Archaea, and these proteins, Gins51 and Gins23, form a heterotetrameric GINS with a 2:2 molar ratio. The Pyrococcus furiosus GINS stimulates the ATPase and helicase activities of its cognate MCM, whereas the Sulfolobus solfataricus GINS does not affect those activities of its cognate MCM, although the proteins bind each other. Intriguingly, Thermoplasma acidophilum, as well as many euryarchaea, have only one gene encoding the sequence homologous to that of archaeal Gins protein (Gins51) on the genome. In this study, we investigated the biochemical properties of the gene product (TaGins51). A gel filtration and electron microscopy revealed that TaGins51 forms a homotetramer. A physical interaction between TaGins51 and TaMcm was detected by a surface plasmon resonance analysis. Unexpectedly, TaGins51 inhibited the ATPase activity, but did not affect the helicase activity of its cognate MCM. These results suggest that another factor is required to form a stable helicase complex with MCM and GINS at the replication fork in T. acidophilum cells.
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Affiliation(s)
- Hiromi Ogino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Hakozaki, Higashi-ku, Fukuoka, Japan
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Costa A, Ilves I, Tamberg N, Petojevic T, Nogales E, Botchan MR, Berger JM. The structural basis for MCM2-7 helicase activation by GINS and Cdc45. Nat Struct Mol Biol 2011; 18:471-7. [PMID: 21378962 PMCID: PMC4184033 DOI: 10.1038/nsmb.2004] [Citation(s) in RCA: 268] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Accepted: 12/09/2010] [Indexed: 11/09/2022]
Abstract
Two central steps for initiating eukaryotic DNA replication involve loading of the Mcm2-7 helicase onto double-stranded DNA and its activation by GINS-Cdc45. To better understand these events, we determined the structures of Mcm2-7 and the CMG complex by using single-particle electron microscopy. Mcm2-7 adopts two conformations--a lock-washer-shaped spiral state and a planar, gapped-ring form--in which Mcm2 and Mcm5 flank a breach in the helicase perimeter. GINS and Cdc45 bridge this gap, forming a topologically closed assembly with a large interior channel; nucleotide binding further seals off the discontinuity between Mcm2 and Mcm5, partitioning the channel into two smaller pores. Together, our data help explain how GINS and Cdc45 activate Mcm2-7, indicate that Mcm2-7 loading may be assisted by a natural predisposition of the hexamer to form open rings, and suggest a mechanism by which the CMG complex assists DNA strand separation.
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Affiliation(s)
- Alessandro Costa
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
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30
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Yang SCH, Rhind N, Bechhoefer J. Modeling genome-wide replication kinetics reveals a mechanism for regulation of replication timing. Mol Syst Biol 2011; 6:404. [PMID: 20739926 PMCID: PMC2950085 DOI: 10.1038/msb.2010.61] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Accepted: 07/16/2010] [Indexed: 11/09/2022] Open
Abstract
We developed analytical models of DNA replication that include probabilistic initiation of origins, fork progression, passive replication, and asynchrony. We fit the model to budding yeast genome-wide microarray data probing the replication fraction and found that initiation times correlate with the precision of timing. We extracted intrinsic origin properties, such as potential origin efficiency and firing-time distribution, which cannot be done using phenomenological approaches. We propose that origin timing is controlled by stochastically activated initiators bound to origin sites rather than explicit time-measuring mechanisms.
The kinetics of DNA replication must be controlled for cells to develop properly. Although the biochemical mechanisms of origin initiations are increasingly well understood, the organization of initiation timing as a genome-wide program is still a mystery. With the advance of technology, researchers have been able to generate large amounts of data revealing aspects of replication kinetics. In particular, the use of microarrays to probe the replication fraction of budding yeast genome wide has been a successful first step towards unraveling the details of the replication program (Raghuraman et al, 2001; Alvino et al, 2007; McCune et al, 2008). On the surface, the microarray data shows apparent patterns of early and late replicating regions and seems to support the prevailing picture of eukaryotic replication—origins are positioned at defined sites and initiated at defined, preprogrammed times (Donaldson, 2005). Molecular combing, a single-molecule technique, however, showed that the initiation of origins is stochastic (Czajkowsky et al, 2008). Motivated by these conflicting viewpoints, we developed a model that is flexible enough to describe both deterministic and stochastic initiation. We modeled origin initiation as probabilistic events. We first propose a model where each origin is allowed to have its distinct ‘firing-time distribution.' Origins that have well-determined initiation times have narrow distributions, whereas more stochastic origins have wider distributions. Similar models based on simulations have previously been proposed (Lygeros et al, 2008; Blow and Ge, 2009; de Moura et al, 2010); however, our model is novel in that it is analytic. It is much faster than simulations and allowed us, for the first time, to fit genome-wide microarray data and extract parameters that describe the replication program in unprecedented detail (Figure 2). Our main result is this: origins that fire early, on average, have precisely defined initiation times, whereas origins that fire late, on average, do not have a well-defined initiation time and initiate throughout S phase. What kind of global controlling mechanism can account for this trend? We propose a second model where an origin is composed of multiple initiators, each of which fires independently and identically. A good candidate for the initiator is the minichromosome maintenance (MCM) complex, as it is found to be associated with origin firing and loaded in abundance (Hyrien et al, 2003). We show that the aforementioned relationship can be explained quantitatively if the earlier-firing origins have more MCM complexes. This model offers a new view of replication: controlled origin timing can emerge from stochastic firing and does not need an explicit time-measuring mechanism, a ‘clock.' This model provides a new, detailed, plausible, and testable mechanism for replication timing control. Our models also capture the effects of passive replication, which is often neglected in phenomenological approaches (Eshaghi et al, 2007). There are two ways an origin site can be replicated. The site can be replicated by the origin binding to it but can also be passively replicated by neighboring origins. This complication makes it difficult to extract the intrinsic properties of origins. By modeling passive replication, we can separate the contribution from each origin and extract the potential efficiency of origins, i.e., the efficiency of the origin given that there is no passive replication. We found that while most origins are potentially highly efficient, their observed efficiency varies greatly. This implies that many origins, though capable of initiating, are often passively replicated and appear dormant. Such a design makes the replication process robust against replication stress such as fork stalling (Blow and Ge, 2009). If two approaching forks stall, normally dormant origins in the region, not being passively replicated, will initiate to replicate the gap. With the advance of the microarray and molecular-combing technology, experiments have been done to probe many different types of cells, and large amounts of replication fraction data have been generated. Our model can be applied to spatiotemporally resolved replication fraction data for any organism, as the model is flexible enough to capture a wide range of replication kinetics. The analytical model is also much faster than simulation-based models. For these reasons, we believe that the model is a powerful tool for analyzing these large datasets. This work opens the possibility for understanding the replication program across species in more rigor and detail (Goldar et al, 2009). Microarrays are powerful tools to probe genome-wide replication kinetics. The rich data sets that result contain more information than has been extracted by current methods of analysis. In this paper, we present an analytical model that incorporates probabilistic initiation of origins and passive replication. Using the model, we performed least-squares fits to a set of recently published time course microarray data on Saccharomyces cerevisiae. We extracted the distribution of firing times for each origin and found that the later an origin fires on average, the greater the variation in firing times. To explain this trend, we propose a model where earlier-firing origins have more initiator complexes loaded and a more accessible chromatin environment. The model demonstrates how initiation can be stochastic and yet occur at defined times during S phase, without an explicit timing program. Furthermore, we hypothesize that the initiators in this model correspond to loaded minichromosome maintenance complexes. This model is the first to suggest a detailed, testable, biochemically plausible mechanism for the regulation of replication timing in eukaryotes.
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31
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Gai D, Chang YP, Chen XS. Origin DNA melting and unwinding in DNA replication. Curr Opin Struct Biol 2010; 20:756-62. [PMID: 20870402 DOI: 10.1016/j.sbi.2010.08.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Revised: 08/25/2010] [Accepted: 08/31/2010] [Indexed: 02/04/2023]
Abstract
Genomic DNA replication is a necessary step in the life cycles of all organisms. To initiate DNA replication, the double-stranded DNA (dsDNA) at the origin of replication must be separated or melted; this melted region is propagated and a mature replication fork is formed. To accomplish origin recognition, initial DNA melting, and the eventual formation of a replication fork, coordinated activity of initiators, helicases, and other cellular factors are required. In this review, we focus on recent advances in the structural and biochemical studies of the initiators and the replicative helicases in multiple replication systems, with emphasis on the systems in archaeal and eukaryotic cells. These studies have yielded insights into the plausible mechanisms of the early stages of DNA replication.
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Affiliation(s)
- Dahai Gai
- Molecular and Computational Biology, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, USA
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Brewster AS, Chen XS. Insights into the MCM functional mechanism: lessons learned from the archaeal MCM complex. Crit Rev Biochem Mol Biol 2010; 45:243-56. [PMID: 20441442 DOI: 10.3109/10409238.2010.484836] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The helicase function of the minichromosome maintenance protein (MCM) is essential for genomic DNA replication in archaea and eukaryotes. There has been rapid progress in studies of the structure and function of MCM proteins from different organisms, leading to better understanding of the MCM helicase mechanism. Because there are a number of excellent reviews on this topic, we will use this review to summarize some of the recent progress, with particular focus on the structural aspects of MCM and their implications for helicase function. Given the hexameric and double hexameric architecture observed by X-ray crystallography and electron microscopy of MCMs from archaeal and eukaryotic cells, we summarize and discuss possible unwinding modes by either a hexameric or a double hexameric helicase. Additionally, our recent crystal structure of a full length archaeal MCM has provided structural information on an intact, multi-domain MCM protein, which includes the salient features of four unusual beta-hairpins from each monomer, and the side channels of a hexamer/double hexamer. These new structural data enable a closer examination of the structural basis of the unwinding mechanisms by MCM.
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Affiliation(s)
- Aaron S Brewster
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
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33
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Abstract
Replication fork helicases unwind DNA at a replication fork, providing polymerases with single-stranded DNA templates for replication. In bacteria, DnaB unwinds DNA at a replication fork, while in archaeal and eukaryotic organisms the Mcm proteins catalyze replication fork unwinding. Unwinding in archaea is catalyzed by a single Mcm protein that forms multimeric rings, whereas eukaryotic helicase activity is catalyzed by the heterohexameric Mcm2-7 complex acting in concert with Cdc45 and the GINS complex. A subcomplex of eukaryotic Mcm proteins, the Mcm4,6,7 complex, unwinds DNA in vitro, and studies of this assembly reveal insight into the mechanism of the eukaryotic Mcm helicase. Detailed methods for the investigation of replication fork helicase mechanism are described in this chapter. Described herein are methods for the design of DNA substrates for unwinding and branch migration studies, annealing DNA, purifying replication fork helicase proteins, and analyzing DNA unwinding activity.
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34
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Cuesta I, Núñez-Ramírez R, Scheres SHW, Gai D, Chen XS, Fanning E, Carazo JM. Conformational rearrangements of SV40 large T antigen during early replication events. J Mol Biol 2010; 397:1276-86. [PMID: 20219473 DOI: 10.1016/j.jmb.2010.02.042] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Revised: 02/20/2010] [Accepted: 02/23/2010] [Indexed: 11/25/2022]
Abstract
The Simian virus 40 (SV40) large tumor antigen (LTag) functions as the replicative helicase and initiator for viral DNA replication. For SV40 replication, the first essential step is the assembly of an LTag double hexamer at the origin DNA that will subsequently melt the origin DNA to initiate fork unwinding. In this study, we used three-dimensional cryo-electron microscopy to visualize early events in the activation of DNA replication in the SV40 model system. We obtained structures of wild-type double-hexamer complexes of LTag bound to SV40 origin DNA, to which atomic structures have been fitted. Wild-type LTag was observed in two distinct conformations: In one conformation, the central module containing the J-domains and the origin binding domains of both hexamers is a compact closed ring. In the other conformation, the central module is an open ring with a gap formed by rearrangement of the N-terminal regions of the two hexamers, potentially allowing for the passage of single-stranded DNA generated from the melted origin DNA. Double-hexamer complexes containing mutant LTag that lacks the N-terminal J-domain show the central module predominantly in the closed-ring state. Analyses of the LTag C-terminal regions reveal that the LTag hexamers bound to the A/T-rich tract origin of replication and early palindrome origin of replication elements are structurally distinct. Lastly, visualization of DNA density protruding from the LTag C-terminal domains suggests that oligomerization of the LTag complex takes place on double-stranded DNA.
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Affiliation(s)
- Isabel Cuesta
- Unidad de Biocomputación, Centro Nacional de Biotecnología-CSIC, C/Darwin 3, 28049 Madrid, Spain
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35
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Abstract
The Mcm2-7 complex serves as the eukaryotic replicative helicase, the molecular motor that both unwinds duplex DNA and powers fork progression during DNA replication. Consistent with its central role in this process, much prior work has illustrated that Mcm2-7 loading and activation are landmark events in the regulation of DNA replication. Unlike any other hexameric helicase, Mcm2-7 is composed of six unique and essential subunits. Although the unusual oligomeric nature of this complex has long hampered biochemical investigations, recent advances with both the eukaryotic as well as the simpler archaeal Mcm complexes provide mechanistic insight into their function. In contrast to better-studied homohexameric helicases, evidence suggests that the six Mcm2-7 complex ATPase active sites are functionally distinct and are likely specialized to accommodate the regulatory constraints of the eukaryotic process.
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36
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Abstract
The eukaryotic MCM2-7 complex is recruited onto origins of replication during the G1 phase of the cell cycle and acts as the main helicase at the replication fork during the S phase. Over the last few years a number of structural reports on MCM proteins using both electron microscopy and protein crystallography have been published. The crystal structures of two (almost) full-length archaeal homologs provide the first atomic pictures of a MCM helicase. However one of the structures is at low resolution and the other is of an inactive MCM. Moreover, both proteins are monomeric in the crystal, whereas the activity of the complex is critically dependent on oligomerization. Lower resolution structures derived from electron microscopy studies are therefore crucial to complement the crystallographic analysis and to assemble the multimeric complex that is active in the cell. A critical analysis of all the structural results elucidates the potential conformational changes and dynamic behavior of MCM helicase to provide a first insight into the gamut of molecular configurations adopted during the processes of DNA melting and unwinding.
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37
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Scheres SHW, Carazo JM. Introducing robustness to maximum-likelihood refinement of electron-microscopy data. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:672-8. [PMID: 19564687 PMCID: PMC2703573 DOI: 10.1107/s0907444909012049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Accepted: 03/31/2009] [Indexed: 11/21/2022]
Abstract
An expectation-maximization algorithm for maximum-likelihood refinement of electron-microscopy images is presented that is based on fitting mixtures of multivariate t-distributions. The novel algorithm has intrinsic characteristics for providing robustness against atypical observations in the data, which is illustrated using an experimental test set with artificially generated outliers. Tests on experimental data revealed only minor differences in two-dimensional classifications, while three-dimensional classification with the new algorithm gave stronger elongation factor G density in the corresponding class of a structurally heterogeneous ribosome data set than the conventional algorithm for Gaussian mixtures.
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Affiliation(s)
- Sjors H W Scheres
- Centro Nacional de Biotecnología-CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
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38
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Adams P, Kandiah E, Effantin G, Steven AC, Ehrenfeld E. Poliovirus 2C protein forms homo-oligomeric structures required for ATPase activity. J Biol Chem 2009; 284:22012-22021. [PMID: 19520852 DOI: 10.1074/jbc.m109.031807] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The poliovirus protein 2C plays an essential role in viral RNA replication, although its precise biochemical activities or structural requirements have not been elucidated. The protein has several distinctive properties, including ATPase activity and membrane and RNA binding, that are conserved among orthologs of many positive-strand RNA viruses. Sequence alignments have placed these proteins in the SF3 helicase family, a subset of the AAA+ ATPase superfamily. A feature common to AAA+ proteins is the formation of oligomeric rings that are essential for their catalytic functions. Here we show that a recombinant protein, MBP-2C, in which maltose-binding protein was fused to 2C, formed soluble oligomers and that ATPase activity was restricted to oligomer-containing fractions from gel-filtration chromatography. The active fraction was visualized by negative-staining electron microscopy as ring-like particles composed of 5-8 protomers. This conclusion was confirmed by mass measurements obtained by scanning transmission electron microscopy. Mutation of amino acid residues in the 2C nucleotide-binding domain demonstrated that loss of the ability to bind or hydrolyze ATP did not affect oligomerization. Co-expression of active MBP-2C and inactive mutant proteins generated mixed oligomers that exhibited little ATPase activity, suggesting that incorporation of inactive subunits eliminates the function of the entire particle. Finally, deletion of the N-terminal 38 amino acids blocked oligomerization of the fusion protein and eliminated ATPase activity, despite retention of an unaltered nucleotide-binding domain.
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Affiliation(s)
| | | | - Grégory Effantin
- NIAMS, National Institutes of Health, Bethesda, Maryland 20892-8011
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39
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Sakakibara N, Kelman LM, Kelman Z. Unwinding the structure and function of the archaeal MCM helicase. Mol Microbiol 2009; 72:286-96. [DOI: 10.1111/j.1365-2958.2009.06663.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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40
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Jenkinson ER, Costa A, Leech AP, Patwardhan A, Onesti S, Chong JPJ. Mutations in subdomain B of the minichromosome maintenance (MCM) helicase affect DNA binding and modulate conformational transitions. J Biol Chem 2009; 284:5654-61. [PMID: 19116205 PMCID: PMC2683335 DOI: 10.1074/jbc.m806973200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Minichromosome maintenance (MCM) proteins are believed to provide the replicative helicase activity in eukaryotes and archaea. The single MCM orthologue from Methanothermobacter thermautotrophicus (MthMCM) has been extensively characterized as a model of the eukaryotic heterohexameric MCM complex. MthMCM forms high molecular weight complexes in solution consistent with a dodecamer. Visualization of this complex by electron microscopy suggests that single and double heptameric or hexameric rings can form. We have mutated two arginine residues (Arg-137, Arg-160) in the N-terminal subdomain B of MthMCM based on their apparent potential to form inter-ring hydrogen bonds. Both the single R137A and the double R137A,R160A mutants were characterized by a combination of biophysical, biochemical, and electron microscopy techniques. Biophysical analysis coupled with electron microscopy studies shows that the R137A mutant forms a double heptameric ring, whereas the R137A,R160A protein assembles as a single heptamer. They both show a defect in DNA binding and a concomitant conformational change in subdomain A, with the double mutant displaying significant defects in helicase activity as well. We propose a model in which MCM loading and the subsequent activation of the helicase activity involve a conformational transition that is connected to a DNA binding event.
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Affiliation(s)
- Elizabeth R Jenkinson
- Department of Biology and Technology Facility, University of York, York YO10 5YW, United Kingdom
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41
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How is the archaeal MCM helicase assembled at the origin? Possible mechanisms. Biochem Soc Trans 2009; 37:7-11. [PMID: 19143593 DOI: 10.1042/bst0370007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In order for any organism to replicate its DNA, a helicase must unwind the duplex DNA in front of the replication fork. In archaea, the replicative helicase is the MCM (minichromosome maintenance) helicase. Although much is known about the biochemical properties of the MCM helicase, the mechanism of assembly at the origin of replication is unknown. In the present paper, several possible mechanisms for the loading process are described.
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42
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Bae B, Chen YH, Costa A, Onesti S, Brunzelle JS, Lin Y, Cann IK, Nair SK. Insights into the Architecture of the Replicative Helicase from the Structure of an Archaeal MCM Homolog. Structure 2009; 17:211-22. [DOI: 10.1016/j.str.2008.11.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Revised: 11/13/2008] [Accepted: 11/13/2008] [Indexed: 10/21/2022]
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43
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Fanning E, Zhao K. SV40 DNA replication: from the A gene to a nanomachine. Virology 2008; 384:352-9. [PMID: 19101707 DOI: 10.1016/j.virol.2008.11.038] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2008] [Accepted: 11/18/2008] [Indexed: 12/23/2022]
Abstract
Duplication of the simian virus 40 (SV40) genome is the best understood eukaryotic DNA replication process to date. Like most prokaryotic genomes, the SV40 genome is a circular duplex DNA organized in a single replicon. This small viral genome, its association with host histones in nucleosomes, and its dependence on the host cell milieu for replication factors and precursors led to its adoption as a simple and powerful model. The steps in replication, the viral initiator, the host proteins, and their mechanisms of action were initially defined using a cell-free SV40 replication reaction. Although our understanding of the vastly more complex host replication fork is advancing, no eukaryotic replisome has yet been reconstituted and the SV40 paradigm remains a point of reference. This article reviews some of the milestones in the development of this paradigm and speculates on its potential utility to address unsolved questions in eukaryotic genome maintenance.
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Affiliation(s)
- Ellen Fanning
- Department of Biological Sciences, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN 37235-1634, USA.
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44
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Crystal structure of a near-full-length archaeal MCM: functional insights for an AAA+ hexameric helicase. Proc Natl Acad Sci U S A 2008; 105:20191-6. [PMID: 19073923 DOI: 10.1073/pnas.0808037105] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The minichromosome maintenance protein (MCM) complex is an essential replicative helicase for DNA replication in Archaea and Eukaryotes. Whereas the eukaryotic complex consists of 6 homologous proteins (MCM2-7), the archaeon Sulfolobus solfataricus has only 1 MCM protein (ssoMCM), 6 subunits of which form a homohexamer. Here, we report a 4.35-A crystal structure of the near-full-length ssoMCM. The structure shows an elongated fold, with 5 subdomains that are organized into 2 large N- and C-terminal domains. A near-full-length ssoMCM hexamer generated based on the 6-fold symmetry of the N-terminal Methanothermobacter thermautotrophicus (mtMCM) hexamer shows intersubunit distances suitable for bonding contacts, including the interface around the ATP pocket. Four unusual beta-hairpins of each subunit are located inside the central channel or around the side channels in the hexamer. Additionally, the hexamer fits well into the double-hexamer EM map of mtMCM. Our mutational analysis of residues at the intersubunit interfaces and around the side channels demonstrates their critical roles for hexamerization and helicase function. These structural and biochemical results provide a basis for future study of the helicase mechanisms of the archaeal and eukaryotic MCM complexes in DNA replication.
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45
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Shin JH, Heo GY, Kelman Z. The Methanothermobacter thermautotrophicus MCM helicase is active as a hexameric ring. J Biol Chem 2008; 284:540-546. [PMID: 19001412 DOI: 10.1074/jbc.m806803200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The minichromosome maintenance (MCM) complex is thought to function as the replicative helicase in archaea and eukarya. The structure of the single MCM protein homologue from the archaeon Methanothermobacter thermautotrophicus is not yet clear, and hexameric, heptameric, octameric, and dodecameric structures, open rings, and filamentous structures have been reported. Using a combination of biochemical and structural analysis, it is shown here that the M. thermautotrophicus MCM helicase is active as a hexamer.
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Affiliation(s)
- Jae-Ho Shin
- Division of Applied Biology and Chemistry, College of Agriculture and Life Sciences, Kyungpook National University, 1370 Sankyuk-Dong, Daegu 702-701, Republic of Korea and the University of Maryland Biotechnology Institute, Center for Advanced Research in Biotechnology, Rockville, Maryland 20850
| | - Gun-Young Heo
- Division of Applied Biology and Chemistry, College of Agriculture and Life Sciences, Kyungpook National University, 1370 Sankyuk-Dong, Daegu 702-701, Republic of Korea and the University of Maryland Biotechnology Institute, Center for Advanced Research in Biotechnology, Rockville, Maryland 20850
| | - Zvi Kelman
- Division of Applied Biology and Chemistry, College of Agriculture and Life Sciences, Kyungpook National University, 1370 Sankyuk-Dong, Daegu 702-701, Republic of Korea and the University of Maryland Biotechnology Institute, Center for Advanced Research in Biotechnology, Rockville, Maryland 20850.
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46
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Frankenstein Z, Sperling J, Sperling R, Eisenstein M. FitEM2EM--tools for low resolution study of macromolecular assembly and dynamics. PLoS One 2008; 3:e3594. [PMID: 18974836 PMCID: PMC2572833 DOI: 10.1371/journal.pone.0003594] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2008] [Accepted: 10/09/2008] [Indexed: 11/19/2022] Open
Abstract
Studies of the structure and dynamics of macromolecular assemblies often involve comparison of low resolution models obtained using different techniques such as electron microscopy or atomic force microscopy. We present new computational tools for comparing (matching) and docking of low resolution structures, based on shape complementarity. The matched or docked objects are represented by three dimensional grids where the value of each grid point depends on its position with regard to the interior, surface or exterior of the object. The grids are correlated using fast Fourier transformations producing either matches of related objects or docking models depending on the details of the grid representations. The procedures incorporate thickening and smoothing of the surfaces of the objects which effectively compensates for differences in the resolution of the matched/docked objects, circumventing the need for resolution modification. The presented matching tool FitEM2EMin successfully fitted electron microscopy structures obtained at different resolutions, different conformers of the same structure and partial structures, ranking correct matches at the top in every case. The differences between the grid representations of the matched objects can be used to study conformation differences or to characterize the size and shape of substructures. The presented low-to-low docking tool FitEM2EMout ranked the expected models at the top.
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Affiliation(s)
- Ziv Frankenstein
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Joseph Sperling
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Ruth Sperling
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Miriam Eisenstein
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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47
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Kanter DM, Bruck I, Kaplan DL. Mcm subunits can assemble into two different active unwinding complexes. J Biol Chem 2008; 283:31172-82. [PMID: 18801730 DOI: 10.1074/jbc.m804686200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The replication fork helicase in eukaryotes is a large complex that is composed of Mcm2-7, Cdc45, and GINS. The Mcm2-7 proteins form a heterohexameric ring that hydrolyzes ATP and provide the motor function for this unwinding complex. A comprehensive study of how individual Mcm subunit biochemical activities relate to unwinding function has not been accomplished. We studied the mechanism of the Mcm4-Mcm6-Mcm7 complex, a useful model system because this complex has helicase activity in vitro. We separately purified each of three Mcm subunits until they were each nuclease-free, and we then examined the biochemical properties of different combinations of Mcm subunits. We found that Mcm4 and Mcm7 form an active unwinding assembly. The addition of Mcm6 to Mcm4/Mcm7 results in the formation of an active Mcm4/Mcm6/Mcm7 helicase assembly. The Mcm4-Mcm7 complex forms a ringed-shaped hexamer that unwinds DNA with 3' to 5' polarity by a steric exclusion mechanism, similar to Mcm4/Mcm6/Mcm7. The Mcm4-Mcm7 complex has a high level of ATPase activity that is further stimulated by DNA. The ability of different Mcm mixtures to form rings or exhibit DNA stimulation of ATPase activity correlates with the ability of these complexes to unwind DNA. The Mcm4/Mcm7 and Mcm4/Mcm6/Mcm7 assemblies can open to load onto circular DNA to initiate unwinding. We conclude that the Mcm subunits are surprisingly flexible and dynamic in their ability to interact with one another to form active unwinding complexes.
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Affiliation(s)
- Diane M Kanter
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235, USA
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48
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Cryo-electron microscopy reveals a novel DNA-binding site on the MCM helicase. EMBO J 2008; 27:2250-8. [PMID: 18650940 DOI: 10.1038/emboj.2008.135] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2008] [Accepted: 06/24/2008] [Indexed: 11/09/2022] Open
Abstract
The eukaryotic MCM2-7 complex is recruited at origins of replication during the G1 phase and acts as the main helicase at the replication fork during the S phase of the cell cycle. To characterize the interplay between the MCM helicase and DNA prior to the melting of the double helix, we determined the structure of an archaeal MCM orthologue bound to a 5.6-kb double-stranded DNA segment, using cryo-electron microscopy. DNA wraps around the N-terminal face of a single hexameric ring. This interaction requires a conformational change within the outer belt of the MCM N-terminal domain, exposing a previously unrecognized helix-turn-helix DNA-binding motif. Our findings provide novel insights into the role of the MCM complex during the initiation step of DNA replication.
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49
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Abstract
Eukaryotic DNA replication is regulated to ensure all chromosomes replicate once and only once per cell cycle. Replication begins at many origins scattered along each chromosome. Except for budding yeast, origins are not defined DNA sequences and probably are inherited by epigenetic mechanisms. Initiation at origins occurs throughout the S phase according to a temporal program that is important in regulating gene expression during development. Most replication proteins are conserved in evolution in eukaryotes and archaea, but not in bacteria. However, the mechanism of initiation is conserved and consists of origin recognition, assembly of prereplication (pre-RC) initiative complexes, helicase activation, and replisome loading. Cell cycle regulation by protein phosphorylation ensures that pre-RC assembly can only occur in G1 phase, whereas helicase activation and loading can only occur in S phase. Checkpoint regulation maintains high fidelity by stabilizing replication forks and preventing cell cycle progression during replication stress or damage.
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Affiliation(s)
- R A Sclafani
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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50
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Liu W, Pucci B, Rossi M, Pisani FM, Ladenstein R. Structural analysis of the Sulfolobus solfataricus MCM protein N-terminal domain. Nucleic Acids Res 2008; 36:3235-43. [PMID: 18417534 PMCID: PMC2425480 DOI: 10.1093/nar/gkn183] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The Mini-Chromosome Maintenance (MCM) proteins are candidates of replicative DNA helicase in eukarya and archaea. Here we report a 2.8 Å crystal structure of the N-terminal domain (residues 1–268) of the Sulfolobus solfataricus MCM (Sso MCM) protein. The structure reveals single-hexameric ring-like architecture, at variance from the protein of Methanothermobacter thermoautotrophicus (Mth). Moreover, the central channel in Sso MCM seems significantly narrower than the Mth counterpart, which appears to more favorably accommodate single-stranded DNA than double-stranded DNA, as supported by DNA-binding assays. Structural analysis also highlights the essential role played by the zinc-binding domain in the interaction with nucleic acids and allows us to speculate that the Sso MCM N-ter domain may function as a molecular clamp to grasp the single-stranded DNA passing through the central channel. On this basis possible DNA unwinding mechanisms are discussed.
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Affiliation(s)
- Wei Liu
- Center of Structural Biochemistry, Karolinska Institutet NOVUM, 141 57 Huddinge, Sweden.
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