151
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Sun J, Yuan Z, Bai L, Li H. Cryo-EM of dynamic protein complexes in eukaryotic DNA replication. Protein Sci 2017; 26:40-51. [PMID: 27589669 PMCID: PMC5192969 DOI: 10.1002/pro.3033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 08/27/2016] [Accepted: 08/29/2016] [Indexed: 12/21/2022]
Abstract
DNA replication in Eukaryotes is a highly dynamic process that involves several dozens of proteins. Some of these proteins form stable complexes that are amenable to high-resolution structure determination by cryo-EM, thanks to the recent advent of the direct electron detector and powerful image analysis algorithm. But many of these proteins associate only transiently and flexibly, precluding traditional biochemical purification. We found that direct mixing of the component proteins followed by 2D and 3D image sorting can capture some very weakly interacting complexes. Even at 2D average level and at low resolution, EM images of these flexible complexes can provide important biological insights. It is often necessary to positively identify the feature-of-interest in a low resolution EM structure. We found that systematically fusing or inserting maltose binding protein (MBP) to selected proteins is highly effective in these situations. In this chapter, we describe the EM studies of several protein complexes involved in the eukaryotic DNA replication over the past decade or so. We suggest that some of the approaches used in these studies may be applicable to structural analysis of other biological systems.
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Affiliation(s)
- Jingchuan Sun
- Cryo‐EM Structural Biology LaboratoryVan Andel Research InstituteGrand RapidsMichigan49503
| | - Zuanning Yuan
- Cryo‐EM Structural Biology LaboratoryVan Andel Research InstituteGrand RapidsMichigan49503
- The Biochemistry and Structural Biology ProgramStony Brook UniversityStony BrookNew York11794
| | - Lin Bai
- Cryo‐EM Structural Biology LaboratoryVan Andel Research InstituteGrand RapidsMichigan49503
| | - Huilin Li
- Cryo‐EM Structural Biology LaboratoryVan Andel Research InstituteGrand RapidsMichigan49503
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152
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Bai L, Yuan Z, Sun J, Georgescu R, O'Donnell ME, Li H. Architecture of the Saccharomyces cerevisiae Replisome. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1042:207-228. [PMID: 29357060 DOI: 10.1007/978-981-10-6955-0_10] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Eukaryotic replication proteins are highly conserved, and thus study of Saccharomyces cerevisiae replication can inform about this central process in higher eukaryotes including humans. The S. cerevisiae replisome is a large and dynamic assembly comprised of ~50 proteins. The core of the replisome is composed of 31 different proteins including the 11-subunit CMG helicase; RFC clamp loader pentamer; PCNA clamp; the heteroligomeric DNA polymerases ε, δ, and α-primase; and the RPA heterotrimeric single strand binding protein. Many additional protein factors either travel with or transiently associate with these replisome proteins at particular times during replication. In this chapter, we summarize several recent structural studies on the S. cerevisiae replisome and its subassemblies using single particle electron microscopy and X-ray crystallography. These recent structural studies have outlined the overall architecture of a core replisome subassembly and shed new light on the mechanism of eukaryotic replication.
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Affiliation(s)
- Lin Bai
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Zuanning Yuan
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, MI, USA
- Biochemistry and Structural Biology Graduate Program, Stony Brook University, Stony Brook, NY, USA
| | - Jingchuan Sun
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Roxana Georgescu
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Michael E O'Donnell
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
| | - Huilin Li
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, MI, USA.
- Biochemistry and Structural Biology Graduate Program, Stony Brook University, Stony Brook, NY, USA.
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153
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Duncker BP. Mechanisms Governing DDK Regulation of the Initiation of DNA Replication. Genes (Basel) 2016; 8:genes8010003. [PMID: 28025497 PMCID: PMC5294998 DOI: 10.3390/genes8010003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 12/13/2016] [Accepted: 12/16/2016] [Indexed: 12/14/2022] Open
Abstract
The budding yeast Dbf4-dependent kinase (DDK) complex—comprised of cell division cycle (Cdc7) kinase and its regulatory subunit dumbbell former 4 (Dbf4)—is required to trigger the initiation of DNA replication through the phosphorylation of multiple minichromosome maintenance complex subunits 2-7 (Mcm2-7). DDK is also a target of the radiation sensitive 53 (Rad53) checkpoint kinase in response to replication stress. Numerous investigations have determined mechanistic details, including the regions of Mcm2, Mcm4, and Mcm6 phosphorylated by DDK, and a number of DDK docking sites. Similarly, the way in which the Rad53 forkhead-associated 1 (FHA1) domain binds to DDK—involving both canonical and non-canonical interactions—has been elucidated. Recent work has revealed mutual promotion of DDK and synthetic lethal with dpb11-1 3 (Sld3) roles. While DDK phosphorylation of Mcm2-7 subunits facilitates their interaction with Sld3 at origins, Sld3 in turn stimulates DDK phosphorylation of Mcm2. Details of a mutually antagonistic relationship between DDK and Rap1-interacting factor 1 (Rif1) have also recently come to light. While Rif1 is able to reverse DDK-mediated Mcm2-7 complex phosphorylation by targeting the protein phosphatase glycogen 7 (Glc7) to origins, there is evidence to suggest that DDK can counteract this activity by binding to and phosphorylating Rif1.
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Affiliation(s)
- Bernard P Duncker
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L3G1, Canada.
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154
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Pozo PN, Cook JG. Regulation and Function of Cdt1; A Key Factor in Cell Proliferation and Genome Stability. Genes (Basel) 2016; 8:genes8010002. [PMID: 28025526 PMCID: PMC5294997 DOI: 10.3390/genes8010002] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 12/13/2016] [Accepted: 12/14/2016] [Indexed: 12/30/2022] Open
Abstract
Successful cell proliferation requires efficient and precise genome duplication followed by accurate chromosome segregation. The Cdc10-dependent transcript 1 protein (Cdt1) is required for the first step in DNA replication, and in human cells Cdt1 is also required during mitosis. Tight cell cycle controls over Cdt1 abundance and activity are critical to normal development and genome stability. We review here recent advances in elucidating Cdt1 molecular functions in both origin licensing and kinetochore–microtubule attachment, and we describe the current understanding of human Cdt1 regulation.
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Affiliation(s)
- Pedro N Pozo
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Jeanette Gowen Cook
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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155
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Abstract
The machinery at the eukaryotic replication fork has seen many new structural advances using electron microscopy and crystallography. Recent structures of eukaryotic replisome components include the Mcm2-7 complex, the CMG helicase, DNA polymerases, a Ctf4 trimer hub and the first look at a core replisome of 20 different proteins containing the helicase, primase, leading polymerase and a lagging strand polymerase. The eukaryotic core replisome shows an unanticipated architecture, with one polymerase sitting above the helicase and the other below. Additionally, structures of Mcm2 bound to an H3/H4 tetramer suggest a direct role of the replisome in handling nucleosomes, which are important to DNA organization and gene regulation. This review provides a summary of some of the many recent advances in the structure of the eukaryotic replisome.
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Affiliation(s)
- Mike O'Donnell
- DNA Replication Lab, The Rockefeller University, 1230 York Avenue, New York, New York, USA; Howard Hughes Medical Institute.
| | - Huilin Li
- Department of Biochemistry & Cell Biology, Stony Brook University, Stony Brook, New York, USA; Biology Department, Brookhaven National Laboratory, Upton, New York, USA.
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156
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Swuec P, Renault L, Borg A, Shah F, Murphy VJ, van Twest S, Snijders AP, Deans AJ, Costa A. The FA Core Complex Contains a Homo-dimeric Catalytic Module for the Symmetric Mono-ubiquitination of FANCI-FANCD2. Cell Rep 2016; 18:611-623. [PMID: 27986592 PMCID: PMC5266791 DOI: 10.1016/j.celrep.2016.11.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/22/2016] [Accepted: 10/31/2016] [Indexed: 12/20/2022] Open
Abstract
Activation of the main DNA interstrand crosslink repair pathway in higher eukaryotes requires mono-ubiquitination of FANCI and FANCD2 by FANCL, the E3 ligase subunit of the Fanconi anemia core complex. FANCI and FANCD2 form a stable complex; however, the molecular basis of their ubiquitination is ill defined. FANCD2 mono-ubiquitination by FANCL is stimulated by the presence of the FANCB and FAAP100 core complex components, through an unknown mechanism. How FANCI mono-ubiquitination is achieved remains unclear. Here, we use structural electron microscopy, combined with crosslink-coupled mass spectrometry, to find that FANCB, FANCL, and FAAP100 form a dimer of trimers, containing two FANCL molecules that are ideally poised to target both FANCI and FANCD2 for mono-ubiquitination. The FANCC-FANCE-FANCF subunits bridge between FANCB-FANCL-FAAP100 and the FANCI-FANCD2 substrate. A transient interaction with FANCC-FANCE-FANCF alters the FANCI-FANCD2 configuration, stabilizing the dimerization interface. Our data provide a model to explain how equivalent mono-ubiquitination of FANCI and FANCD2 occurs. FANCB, FANCL, and FAAP100 form a symmetric dimer of trimers FANCL is ideally poised for the symmetric mono-ubiquitination of FANCI-FANCD2 Two separate FANCC-FANCE-FANCF complexes bind to the opposing poles of FANCB-FANCL-FAAP100 FANCC-FANCE-FANCF stabilizes FANCI-FANCD2 for efficient mono-ubiquitination
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Affiliation(s)
- Paolo Swuec
- Macromolecular Machines Laboratory, Clare Hall Laboratory, The Francis Crick Institute, Blanche Lane, South Mimms, EN6 3LD, UK
| | - Ludovic Renault
- Macromolecular Machines Laboratory, Clare Hall Laboratory, The Francis Crick Institute, Blanche Lane, South Mimms, EN6 3LD, UK
| | - Aaron Borg
- Mass Spectrometry Proteomics and Metabolomics, Clare Hall Laboratory, The Francis Crick Institute, Blanche Lane, South Mimms, EN6 3LD, UK
| | - Fenil Shah
- Genome Stability Unit, St. Vincent's Institute of Medical Research, 9 Princes St Fitzroy, Victoria, VIC 3065, Australia
| | - Vincent J Murphy
- Genome Stability Unit, St. Vincent's Institute of Medical Research, 9 Princes St Fitzroy, Victoria, VIC 3065, Australia
| | - Sylvie van Twest
- Genome Stability Unit, St. Vincent's Institute of Medical Research, 9 Princes St Fitzroy, Victoria, VIC 3065, Australia
| | - Ambrosius P Snijders
- Mass Spectrometry Proteomics and Metabolomics, Clare Hall Laboratory, The Francis Crick Institute, Blanche Lane, South Mimms, EN6 3LD, UK
| | - Andrew J Deans
- Genome Stability Unit, St. Vincent's Institute of Medical Research, 9 Princes St Fitzroy, Victoria, VIC 3065, Australia
| | - Alessandro Costa
- Macromolecular Machines Laboratory, Clare Hall Laboratory, The Francis Crick Institute, Blanche Lane, South Mimms, EN6 3LD, UK.
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157
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Swuec P, Costa A. DNA replication and inter-strand crosslink repair: Symmetric activation of dimeric nanomachines? Biophys Chem 2016; 225:15-19. [PMID: 27989548 DOI: 10.1016/j.bpc.2016.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 10/28/2016] [Accepted: 11/01/2016] [Indexed: 10/20/2022]
Abstract
Eukaryotic DNA replication initiation and the Fanconi anemia pathway of interstrand crosslink repair both revolve around the recruitment of a set of DNA-processing factors onto a dimeric protein complex, which functions as a loading platform (MCM and FANCI-FANCD2 respectively). Here we compare and contrast the two systems, identifying a set of unresolved mechanistic questions. How is the dimeric loading platform assembled on the DNA? How can equivalent covalent modification of both factors in a dimer be achieved? Are multicomponent DNA-interacting machines built symmetrically around their dimeric loading platform? Recent biochemical reconstitution studies are starting to shed light on these issues.
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Affiliation(s)
- Paolo Swuec
- Macromolecular Machines Laboratory, Clare Hall Laboratory, The Francis Crick Institute, Blanche Lane, South Mimms, EN6 3LD, UK
| | - Alessandro Costa
- Macromolecular Machines Laboratory, Clare Hall Laboratory, The Francis Crick Institute, Blanche Lane, South Mimms, EN6 3LD, UK.
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158
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Yu J, Wang R, Wu J, Dang Z, Zhang Q, Li B. Knockdown of minichromosome maintenance proteins inhibits foci forming of mediator of DNA-damage checkpoint 1 in response to DNA damage in human esophageal squamous cell carcinoma TE-1 cells. BIOCHEMISTRY (MOSCOW) 2016; 81:1221-1228. [DOI: 10.1134/s0006297916100205] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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159
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Unravelling biological macromolecules with cryo-electron microscopy. Nature 2016; 537:339-46. [PMID: 27629640 DOI: 10.1038/nature19948] [Citation(s) in RCA: 262] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 07/15/2016] [Indexed: 12/11/2022]
Abstract
Knowledge of the three-dimensional structures of proteins and other biological macromolecules often aids understanding of how they perform complicated tasks in the cell. Because many such tasks involve the cleavage or formation of chemical bonds, structural characterization at the atomic level is most useful. Developments in the electron microscopy of frozen hydrated samples (cryo-electron microscopy) are providing unprecedented opportunities for the structural characterization of biological macromolecules. This is resulting in a wave of information about processes in the cell that were impossible to characterize with existing techniques in structural biology.
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160
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Staphylococcal SCCmec elements encode an active MCM-like helicase and thus may be replicative. Nat Struct Mol Biol 2016; 23:891-898. [PMID: 27571176 PMCID: PMC5052118 DOI: 10.1038/nsmb.3286] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Accepted: 08/05/2016] [Indexed: 01/07/2023]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a public-health threat worldwide. Although the mobile genomic island responsible for this phenotype, staphylococcal cassette chromosome (SCC), has been thought to be nonreplicative, we predicted DNA-replication-related functions for some of the conserved proteins encoded by SCC. We show that one of these, Cch, is homologous to the self-loading initiator helicases of an unrelated family of genomic islands, that it is an active 3'-to-5' helicase and that the adjacent ORF encodes a single-stranded DNA-binding protein. Our 2.9-Å crystal structure of intact Cch shows that it forms a hexameric ring. Cch, like the archaeal and eukaryotic MCM-family replicative helicases, belongs to the pre-sensor II insert clade of AAA+ ATPases. Additionally, we found that SCC elements are part of a broader family of mobile elements, all of which encode a replication initiator upstream of their recombinases. Replication after excision would enhance the efficiency of horizontal gene transfer.
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161
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Schaffitzel C. MCM2-7 conformational changes in the presence of DNA. Cell Cycle 2016; 15:2391-2. [PMID: 27485286 DOI: 10.1080/15384101.2016.1214046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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162
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Fundamental Characteristics of AAA+ Protein Family Structure and Function. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2016; 2016:9294307. [PMID: 27703410 PMCID: PMC5039278 DOI: 10.1155/2016/9294307] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 07/21/2016] [Indexed: 12/22/2022]
Abstract
Many complex cellular events depend on multiprotein complexes known as molecular machines to efficiently couple the energy derived from adenosine triphosphate hydrolysis to the generation of mechanical force. Members of the AAA+ ATPase superfamily (ATPases Associated with various cellular Activities) are critical components of many molecular machines. AAA+ proteins are defined by conserved modules that precisely position the active site elements of two adjacent subunits to catalyze ATP hydrolysis. In many cases, AAA+ proteins form a ring structure that translocates a polymeric substrate through the central channel using specialized loops that project into the central channel. We discuss the major features of AAA+ protein structure and function with an emphasis on pivotal aspects elucidated with archaeal proteins.
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163
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Oyama T, Ishino S, Shirai T, Yamagami T, Nagata M, Ogino H, Kusunoki M, Ishino Y. Atomic structure of an archaeal GAN suggests its dual roles as an exonuclease in DNA repair and a CMG component in DNA replication. Nucleic Acids Res 2016; 44:9505-9517. [PMID: 27599844 PMCID: PMC5100581 DOI: 10.1093/nar/gkw789] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 08/29/2016] [Indexed: 12/29/2022] Open
Abstract
In eukaryotic DNA replication initiation, hexameric MCM (mini-chromosome maintenance) unwinds the template double-stranded DNA to form the replication fork. MCM is activated by two proteins, Cdc45 and GINS, which constitute the ‘CMG’ unwindosome complex together with the MCM core. The archaeal DNA replication system is quite similar to that of eukaryotes, but only limited knowledge about the DNA unwinding mechanism is available, from a structural point of view. Here, we describe the crystal structure of an archaeal GAN (GINS-associated nuclease) from Thermococcus kodakaraensis, the homolog of eukaryotic Cdc45, in both the free form and the complex with the C-terminal domain of the cognate Gins51 subunit (Gins51C). This first archaeal GAN structure exhibits a unique, ‘hybrid’ structure between the bacterial RecJ and the eukaryotic Cdc45. GAN possesses the conserved DHH and DHH1 domains responsible for the exonuclease activity, and an inserted CID (CMG interacting domain)-like domain structurally comparable to that in Cdc45, suggesting its dual roles as an exonuclease in DNA repair and a CMG component in DNA replication. A structural comparison of the GAN–Gins51C complex with the GINS tetramer suggests that GINS uses the mobile Gins51C as a hook to bind GAN for CMG formation.
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Affiliation(s)
- Takuji Oyama
- Faculty of Life and Environmental Sciences, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan
| | - Sonoko Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Fukuoka 812-8581, Japan
| | - Tsuyoshi Shirai
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan
| | - Takeshi Yamagami
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Fukuoka 812-8581, Japan
| | - Mariko Nagata
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Fukuoka 812-8581, Japan
| | - Hiromi Ogino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Fukuoka 812-8581, Japan
| | - Masami Kusunoki
- Faculty of Life and Environmental Sciences, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Fukuoka 812-8581, Japan
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164
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Abstract
DNA replication origins strikingly differ between eukaryotic species and cell types. Origins are localized and can be highly efficient in budding yeast, are randomly located in early fly and frog embryos, which do not transcribe their genomes, and are clustered in broad (10-100 kb) non-transcribed zones, frequently abutting transcribed genes, in mammalian cells. Nonetheless, in all cases, origins are established during the G1-phase of the cell cycle by the loading of double hexamers of the Mcm 2-7 proteins (MCM DHs), the core of the replicative helicase. MCM DH activation in S-phase leads to origin unwinding, polymerase recruitment, and initiation of bidirectional DNA synthesis. Although MCM DHs are initially loaded at sites defined by the binding of the origin recognition complex (ORC), they ultimately bind chromatin in much greater numbers than ORC and only a fraction are activated in any one S-phase. Data suggest that the multiplicity and functional redundancy of MCM DHs provide robustness to the replication process and affect replication time and that MCM DHs can slide along the DNA and spread over large distances around the ORC. Recent studies further show that MCM DHs are displaced along the DNA by collision with transcription complexes but remain functional for initiation after displacement. Therefore, eukaryotic DNA replication relies on intrinsically mobile and flexible origins, a strategy fundamentally different from bacteria but conserved from yeast to human. These properties of MCM DHs likely contribute to the establishment of broad, intergenic replication initiation zones in higher eukaryotes.
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Affiliation(s)
- Olivier Hyrien
- Institut de Biologie de l'Ecole Normale Superieure (IBENS), Ecole Normale Superieure, PSL Research University, Paris, France
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165
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Pellegrini L, Costa A. New Insights into the Mechanism of DNA Duplication by the Eukaryotic Replisome. Trends Biochem Sci 2016; 41:859-871. [PMID: 27555051 DOI: 10.1016/j.tibs.2016.07.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 07/20/2016] [Accepted: 07/22/2016] [Indexed: 11/26/2022]
Abstract
The DNA replication machinery, or replisome, is a macromolecular complex that combines DNA unwinding, priming and synthesis activities. In eukaryotic cells, the helicase and polymerases are multi-subunit, highly-dynamic assemblies whose structural characterization requires an integrated approach. Recent studies have combined single-particle electron cryo-microscopy and protein crystallography to gain insights into the mechanism of DNA duplication by the eukaryotic replisome. We review current understanding of how replication fork unwinding by the CMG helicase is coupled to leading-strand synthesis by polymerase (Pol) ɛ and lagging-strand priming by Pol α/primase, and discuss emerging principles of replisome organization.
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Affiliation(s)
- Luca Pellegrini
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.
| | - Alessandro Costa
- Macromolecular Machines Laboratory, Clare Hall Laboratory, The Francis Crick Institute, Blanche Lane, South Mimms EN6 3LD, UK.
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166
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Fenwick AL, Kliszczak M, Cooper F, Murray J, Sanchez-Pulido L, Twigg SRF, Goriely A, McGowan SJ, Miller KA, Taylor IB, Logan C, Bozdogan S, Danda S, Dixon J, Elsayed SM, Elsobky E, Gardham A, Hoffer MJV, Koopmans M, McDonald-McGinn DM, Santen GWE, Savarirayan R, de Silva D, Vanakker O, Wall SA, Wilson LC, Yuregir OO, Zackai EH, Ponting CP, Jackson AP, Wilkie AOM, Niedzwiedz W, Bicknell LS. Mutations in CDC45, Encoding an Essential Component of the Pre-initiation Complex, Cause Meier-Gorlin Syndrome and Craniosynostosis. Am J Hum Genet 2016; 99:125-38. [PMID: 27374770 PMCID: PMC5005452 DOI: 10.1016/j.ajhg.2016.05.019] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 05/09/2016] [Indexed: 11/19/2022] Open
Abstract
DNA replication precisely duplicates the genome to ensure stable inheritance of genetic information. Impaired licensing of origins of replication during the G1 phase of the cell cycle has been implicated in Meier-Gorlin syndrome (MGS), a disorder defined by the triad of short stature, microtia, and a/hypoplastic patellae. Biallelic partial loss-of-function mutations in multiple components of the pre-replication complex (preRC; ORC1, ORC4, ORC6, CDT1, or CDC6) as well as de novo stabilizing mutations in the licensing inhibitor, GMNN, cause MGS. Here we report the identification of mutations in CDC45 in 15 affected individuals from 12 families with MGS and/or craniosynostosis. CDC45 encodes a component of both the pre-initiation (preIC) and CMG helicase complexes, required for initiation of DNA replication origin firing and ongoing DNA synthesis during S-phase itself, respectively, and hence is functionally distinct from previously identified MGS-associated genes. The phenotypes of affected individuals range from syndromic coronal craniosynostosis to severe growth restriction, fulfilling diagnostic criteria for Meier-Gorlin syndrome. All mutations identified were biallelic and included synonymous mutations altering splicing of physiological CDC45 transcripts, as well as amino acid substitutions expected to result in partial loss of function. Functionally, mutations reduce levels of full-length transcripts and protein in subject cells, consistent with partial loss of CDC45 function and a predicted limited rate of DNA replication and cell proliferation. Our findings therefore implicate the preIC as an additional protein complex involved in the etiology of MGS and connect the core cellular machinery of genome replication with growth, chondrogenesis, and cranial suture homeostasis.
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Affiliation(s)
- Aimee L Fenwick
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Maciej Kliszczak
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Fay Cooper
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Jennie Murray
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Luis Sanchez-Pulido
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Stephen R F Twigg
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Anne Goriely
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Simon J McGowan
- Computational Biology Research Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Kerry A Miller
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Indira B Taylor
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Clare Logan
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Sevcan Bozdogan
- Department of Medical Genetics, Mersin University, Mersin, 33343 Cukurova, Turkey
| | - Sumita Danda
- Department of Clinical Genetics, Christian Medical College and Hospital, Vellore, Tamil Nadu 632004, India
| | - Joanne Dixon
- Genetic Health Service NZ-South Island Hub, Christchurch Hospital, Christchurch, Canterbury 8140, New Zealand
| | - Solaf M Elsayed
- Children's Hospital, Ain Shams University, Cairo 11566, Egypt
| | - Ezzat Elsobky
- Children's Hospital, Ain Shams University, Cairo 11566, Egypt
| | - Alice Gardham
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Mariette J V Hoffer
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Marije Koopmans
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Donna M McDonald-McGinn
- Clinical Genetics, The Children's Hospital of Philadelphia, 34th & Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Ravi Savarirayan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Deepthi de Silva
- Department of Physiology, Faculty of Medicine, University of Kelaniya, Ragama, Gampaha GQ 11010, Sri Lanka
| | - Olivier Vanakker
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
| | - Steven A Wall
- Craniofacial Unit, Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Louise C Wilson
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Ozge Ozalp Yuregir
- Genetic Diagnosis Center, Adana Numune Training and Research Hospital, Cukurova, Adana, 01170, Turkey
| | - Elaine H Zackai
- Clinical Genetics, The Children's Hospital of Philadelphia, 34th & Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Chris P Ponting
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Andrew P Jackson
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Andrew O M Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Craniofacial Unit, Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Wojciech Niedzwiedz
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Louise S Bicknell
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh EH4 2XU, UK; Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, Otago 9016, New Zealand.
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167
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Meagher M, Enemark EJ. Structure of a double hexamer of the Pyrococcus furiosus minichromosome maintenance protein N-terminal domain. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2016; 72:545-51. [PMID: 27380371 DOI: 10.1107/s2053230x1600858x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 05/27/2016] [Indexed: 11/11/2022]
Abstract
The crystal structure of the N-terminal domain of the Pyrococcus furiosus minichromosome maintenance (MCM) protein as a double hexamer is described. The MCM complex is a ring-shaped helicase that unwinds DNA at the replication fork of eukaryotes and archaea. Prior to replication initiation, the MCM complex assembles as an inactive double hexamer at specific sites of DNA. The presented structure is highly consistent with previous MCM double-hexamer structures and shows two MCM hexamers with a head-to-head interaction mediated by the N-terminal domain. Minor differences include a diminished head-to-head interaction and a slightly reduced inter-hexamer rotation.
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Affiliation(s)
- Martin Meagher
- Department of Structural Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Eric J Enemark
- Department of Structural Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
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168
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Boskovic J, Bragado-Nilsson E, Saligram Prabhakar B, Yefimenko I, Martínez-Gago J, Muñoz S, Méndez J, Montoya G. Molecular architecture of the recombinant human MCM2-7 helicase in complex with nucleotides and DNA. Cell Cycle 2016; 15:2431-40. [PMID: 27249176 DOI: 10.1080/15384101.2016.1191712] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
DNA replication is a key biological process that involves different protein complexes whose assembly is rigorously regulated in a successive order. One of these complexes is a replicative hexameric helicase, the MCM complex, which is essential for the initiation and elongation phases of replication. After the assembly of a double heterohexameric MCM2-7 complex at replication origins in G1, the 2 heterohexamers separate from each other and associate with Cdc45 and GINS proteins in a CMG complex that is capable of unwinding dsDNA during S phase. Here, we have reconstituted and characterized the purified human MCM2-7 (hMCM2-7) hexameric complex by co-expression of its 6 different subunits in insect cells. The conformational variability of the complex has been analyzed by single particle electron microscopy in the presence of different nucleotide analogs and DNA. The interaction with nucleotide stabilizes the complex while DNA introduces conformational changes in the hexamer inducing a cylindrical shape. Our studies suggest that the assembly of GINS and Cdc45 to the hMCM2-7 hexamer would favor conformational changes on the hexamer bound to ssDNA shifting the cylindrical shape of the complex into a right-handed spiral conformation as observed in the CMG complex bound to DNA.
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Affiliation(s)
- Jasminka Boskovic
- a Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Macromolecular Crystallography Group , c/Melchor Fdez. Almagro 3, Madrid , Spain
| | - Elisabeth Bragado-Nilsson
- b Protein Structure & Function Programme, Novo Nordisk Foundation Centre for Protein Research, Faculty of Heath and Medical Sciences, University of Copenhagen , Denmark
| | - Bhargrav Saligram Prabhakar
- b Protein Structure & Function Programme, Novo Nordisk Foundation Centre for Protein Research, Faculty of Heath and Medical Sciences, University of Copenhagen , Denmark
| | - Igor Yefimenko
- a Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Macromolecular Crystallography Group , c/Melchor Fdez. Almagro 3, Madrid , Spain
| | - Jaime Martínez-Gago
- a Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Macromolecular Crystallography Group , c/Melchor Fdez. Almagro 3, Madrid , Spain
| | - Sergio Muñoz
- c DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO) , Madrid , Spain
| | - Juan Méndez
- c DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO) , Madrid , Spain
| | - Guillermo Montoya
- b Protein Structure & Function Programme, Novo Nordisk Foundation Centre for Protein Research, Faculty of Heath and Medical Sciences, University of Copenhagen , Denmark
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169
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Simon AC, Sannino V, Costanzo V, Pellegrini L. Structure of human Cdc45 and implications for CMG helicase function. Nat Commun 2016; 7:11638. [PMID: 27189187 PMCID: PMC4873980 DOI: 10.1038/ncomms11638] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 04/14/2016] [Indexed: 01/05/2023] Open
Abstract
Cell division cycle protein 45 (Cdc45) is required for DNA synthesis during genome duplication, as a component of the Cdc45-MCM-GINS (CMG) helicase. Despite its essential biological function, its biochemical role in DNA replication has remained elusive. Here we report the 2.1-Å crystal structure of human Cdc45, which confirms its evolutionary link with the bacterial RecJ nuclease and reveals several unexpected features that underpin its function in eukaryotic DNA replication. These include a long-range interaction between N- and C-terminal DHH domains, blocking access to the DNA-binding groove of its RecJ-like fold, and a helical insertion in its N-terminal DHH domain, which appears poised for replisome interactions. In combination with available electron microscopy data, we validate by mutational analysis the mechanism of Cdc45 association with the MCM ring and GINS co-activator, critical for CMG assembly. These findings provide an indispensable molecular basis to rationalize the essential role of Cdc45 in genomic duplication. The cell cycle division protein Cdc45 is required for genome duplication in eukaryotes. Here, the authors determine the crystal structure of human Cdc45 and combine it with functional data to improve our understanding of its role in DNA replication.
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Affiliation(s)
- Aline C Simon
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Vincenzo Sannino
- DNA Metabolism Laboratory, FIRC Institute of Molecular Oncology Foundation, 20139 Milan, Italy
| | - Vincenzo Costanzo
- DNA Metabolism Laboratory, FIRC Institute of Molecular Oncology Foundation, 20139 Milan, Italy
| | - Luca Pellegrini
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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170
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Abstract
Recent work suggests that DNA replication origins are regulated by the number of multiple mini-chromosome maintenance (MCM) complexes loaded. Origins are defined by the loading of MCM - the replicative helicase which initiates DNA replication and replication kinetics determined by origin's location and firing times. However, activation of MCM is heterogeneous; different origins firing at different times in different cells. Also, more MCMs are loaded in G1 than are used in S phase. These aspects of MCM biology are explained by the observation that multiple MCMs are loaded at origins. Having more MCMs at early origins makes them more likely to fire, effecting differences in origin efficiency that define replication timing. Nonetheless, multiple MCM loading raises new questions, such as how they are loaded, where these MCMs reside at origins, and how their presence affects replication timing. In this review, we address these questions and discuss future avenues of research.
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Affiliation(s)
- Shankar P Das
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Nicholas Rhind
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
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171
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Abid Ali F, Costa A. The MCM Helicase Motor of the Eukaryotic Replisome. J Mol Biol 2016; 428:1822-32. [PMID: 26829220 DOI: 10.1016/j.jmb.2016.01.024] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 01/23/2016] [Indexed: 10/22/2022]
Abstract
The MCM motor of the CMG helicase powers ahead of the eukaryotic replication machinery to unwind DNA, in a process that requires ATP hydrolysis. The reconstitution of DNA replication in vitro has established the succession of events that lead to replication origin activation by the MCM and recent studies have started to elucidate the structural basis of duplex DNA unwinding. Despite the exciting progress, how the MCM translocates on DNA remains a matter of debate.
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Affiliation(s)
- Ferdos Abid Ali
- Architecture and Dynamics of Macromolecular Machines, Clare Hall Laboratory, The Francis Crick Institute, Blanche Lane, South Mimms EN6 3LD, United Kingdom
| | - Alessandro Costa
- Architecture and Dynamics of Macromolecular Machines, Clare Hall Laboratory, The Francis Crick Institute, Blanche Lane, South Mimms EN6 3LD, United Kingdom.
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172
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Protein-protein interaction analysis for functional characterization of helicases. Methods 2016; 108:56-64. [PMID: 27090004 DOI: 10.1016/j.ymeth.2016.04.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 04/11/2016] [Accepted: 04/13/2016] [Indexed: 11/22/2022] Open
Abstract
Helicases are enzymes involved in nucleic acid metabolism, playing major roles in replication, transcription, and repair. Defining helicases oligomerization state and transient and persistent protein interactions is essential for understanding of their function. In this article we review current methods for the protein-protein interaction analysis, and discuss examples of its application to the study of helicases: Pif1 and DDX3. Proteomics methods are our main focus - affinity pull-downs and chemical cross-linking followed by mass spectrometry. We review advantages and limitations of these methods and provide general guidelines for their implementation in the functional analysis of helicases.
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173
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Abstract
The cellular replicating machine, or "replisome," is composed of numerous different proteins. The core replication proteins in all cell types include a helicase, primase, DNA polymerases, sliding clamp, clamp loader, and single-strand binding (SSB) protein. The core eukaryotic replisome proteins evolved independently from those of bacteria and thus have distinct architectures and mechanisms of action. The core replisome proteins of the eukaryote include: an 11-subunit CMG helicase, DNA polymerase alpha-primase, leading strand DNA polymerase epsilon, lagging strand DNA polymerase delta, PCNA clamp, RFC clamp loader, and the RPA SSB protein. There are numerous other proteins that travel with eukaryotic replication forks, some of which are known to be involved in checkpoint regulation or nucleosome handling, but most have unknown functions and no bacterial analogue. Recent studies have revealed many structural and functional insights into replisome action. Also, the first structure of a replisome from any cell type has been elucidated for a eukaryote, consisting of 20 distinct proteins, with quite unexpected results. This review summarizes the current state of knowledge of the eukaryotic core replisome proteins, their structure, individual functions, and how they are organized at the replication fork as a machine.
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Affiliation(s)
- D Zhang
- The Rockefeller University, New York, NY, United States
| | - M O'Donnell
- The Rockefeller University, New York, NY, United States; Howard Hughes Medical Institute, The Rockefeller University, New York, NY, United States.
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174
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Graham BW, Tao Y, Dodge KL, Thaxton CT, Olaso D, Young NL, Marshall AG, Trakselis MA. DNA Interactions Probed by Hydrogen-Deuterium Exchange (HDX) Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Confirm External Binding Sites on the Minichromosomal Maintenance (MCM) Helicase. J Biol Chem 2016; 291:12467-12480. [PMID: 27044751 DOI: 10.1074/jbc.m116.719591] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Indexed: 11/06/2022] Open
Abstract
The archaeal minichromosomal maintenance (MCM) helicase from Sulfolobus solfataricus (SsoMCM) is a model for understanding structural and mechanistic aspects of DNA unwinding. Although interactions of the encircled DNA strand within the central channel provide an accepted mode for translocation, interactions with the excluded strand on the exterior surface have mostly been ignored with regard to DNA unwinding. We have previously proposed an extension of the traditional steric exclusion model of unwinding to also include significant contributions with the excluded strand during unwinding, termed steric exclusion and wrapping (SEW). The SEW model hypothesizes that the displaced single strand tracks along paths on the exterior surface of hexameric helicases to protect single-stranded DNA (ssDNA) and stabilize the complex in a forward unwinding mode. Using hydrogen/deuterium exchange monitored by Fourier transform ion cyclotron resonance MS, we have probed the binding sites for ssDNA, using multiple substrates targeting both the encircled and excluded strand interactions. In each experiment, we have obtained >98.7% sequence coverage of SsoMCM from >650 peptides (5-30 residues in length) and are able to identify interacting residues on both the interior and exterior of SsoMCM. Based on identified contacts, positively charged residues within the external waist region were mutated and shown to generally lower DNA unwinding without negatively affecting the ATP hydrolysis. The combined data globally identify binding sites for ssDNA during SsoMCM unwinding as well as validating the importance of the SEW model for hexameric helicase unwinding.
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Affiliation(s)
- Brian W Graham
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Yeqing Tao
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306
| | - Katie L Dodge
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798
| | - Carly T Thaxton
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798
| | - Danae Olaso
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798
| | - Nicolas L Young
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310
| | - Alan G Marshall
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306; National High Magnetic Field Laboratory, Tallahassee, Florida 32310
| | - Michael A Trakselis
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798.
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175
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Deegan TD, Diffley JFX. MCM: one ring to rule them all. Curr Opin Struct Biol 2016; 37:145-51. [PMID: 26866665 DOI: 10.1016/j.sbi.2016.01.014] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 01/26/2016] [Accepted: 01/26/2016] [Indexed: 11/25/2022]
Abstract
Precise replication of the eukaryotic genome is achieved primarily through strict regulation of the enzyme responsible for DNA unwinding, the replicative helicase. The motor of this helicase is a hexameric AAA+ ATPase called MCM. The loading of MCM onto DNA and its subsequent activation and disassembly are each restricted to separate cell cycle phases; this ensures that a functional replisome is only built once at any replication origin. In recent years, biochemical and structural studies have shown that distinct conformational changes in MCM, each requiring post-translational modifications and/or the activity of other replication proteins, define the various stages of the chromosome replication cycle. Here, we review recent progress in this area.
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Affiliation(s)
- Tom D Deegan
- The Francis Crick Institute, Clare Hall Laboratory, South Mimms, Herts EN6 3LD, United Kingdom
| | - John F X Diffley
- The Francis Crick Institute, Clare Hall Laboratory, South Mimms, Herts EN6 3LD, United Kingdom.
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176
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Douglas ME, Diffley JFX. Recruitment of Mcm10 to Sites of Replication Initiation Requires Direct Binding to the Minichromosome Maintenance (MCM) Complex. J Biol Chem 2016; 291:5879-5888. [PMID: 26719337 PMCID: PMC4786722 DOI: 10.1074/jbc.m115.707802] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 12/28/2015] [Indexed: 01/11/2023] Open
Abstract
Mcm10 is required for the initiation of eukaryotic DNA replication and contributes in some unknown way to the activation of the Cdc45-MCM-GINS (CMG) helicase. How Mcm10 is localized to sites of replication initiation is unclear, as current models indicate that direct binding to minichromosome maintenance (MCM) plays a role, but the details and functional importance of this interaction have not been determined. Here, we show that purified Mcm10 can bind both DNA-bound double hexamers and soluble single hexamers of MCM. The binding of Mcm10 to MCM requires the Mcm10 C terminus. Moreover, the binding site for Mcm10 on MCM includes the Mcm2 and Mcm6 subunits and overlaps that for the loading factor Cdt1. Whether Mcm10 recruitment to replication origins depends on CMG helicase assembly has been unclear. We show that Mcm10 recruitment occurs via two modes: low affinity recruitment in the absence of CMG assembly ("G1-like") and high affinity recruitment when CMG assembly takes place ("S-phase-like"). Mcm10 that cannot bind directly to MCM is defective in both modes of recruitment and is unable to support DNA replication. These findings indicate that Mcm10 is localized to replication initiation sites by directly binding MCM through the Mcm10 C terminus.
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Affiliation(s)
- Max E Douglas
- From The Francis Crick Institute, Clare Hall Laboratory, South Mimms, Hertfordshire EN6 3LD, United Kingdom
| | - John F X Diffley
- From The Francis Crick Institute, Clare Hall Laboratory, South Mimms, Hertfordshire EN6 3LD, United Kingdom.
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177
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Abid Ali F, Renault L, Gannon J, Gahlon HL, Kotecha A, Zhou JC, Rueda D, Costa A. Cryo-EM structures of the eukaryotic replicative helicase bound to a translocation substrate. Nat Commun 2016; 7:10708. [PMID: 26888060 PMCID: PMC4759635 DOI: 10.1038/ncomms10708] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 01/12/2016] [Indexed: 02/06/2023] Open
Abstract
The Cdc45-MCM-GINS (CMG) helicase unwinds DNA during the elongation step of eukaryotic genome duplication and this process depends on the MCM ATPase function. Whether CMG translocation occurs on single- or double-stranded DNA and how ATP hydrolysis drives DNA unwinding remain open questions. Here we use cryo-electron microscopy to describe two subnanometre resolution structures of the CMG helicase trapped on a DNA fork. In the predominant state, the ring-shaped C-terminal ATPase of MCM is compact and contacts single-stranded DNA, via a set of pre-sensor 1 hairpins that spiral around the translocation substrate. In the second state, the ATPase module is relaxed and apparently substrate free, while DNA intimately contacts the downstream amino-terminal tier of the MCM motor ring. These results, supported by single-molecule FRET measurements, lead us to suggest a replication fork unwinding mechanism whereby the N-terminal and AAA+ tiers of the MCM work in concert to translocate on single-stranded DNA.
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Affiliation(s)
- Ferdos Abid Ali
- Macromolecular Machines, Clare Hall Laboratory, The Francis Crick Institute, Blanche Lane, South Mimms EN6 3LD, UK
| | - Ludovic Renault
- Macromolecular Machines, Clare Hall Laboratory, The Francis Crick Institute, Blanche Lane, South Mimms EN6 3LD, UK
- National Institute for Biological Standards and Control, Microscopy and Imaging, Blanche Lane, South Mimms EN6 3QG, UK
| | - Julian Gannon
- Macromolecular Machines, Clare Hall Laboratory, The Francis Crick Institute, Blanche Lane, South Mimms EN6 3LD, UK
| | - Hailey L. Gahlon
- Section of Virology and Single Molecule Imaging Group, Department of Medicine, MRC Clinical Centre, Imperial College London, London W12 0NN, UK
| | - Abhay Kotecha
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Jin Chuan Zhou
- Macromolecular Machines, Clare Hall Laboratory, The Francis Crick Institute, Blanche Lane, South Mimms EN6 3LD, UK
| | - David Rueda
- Section of Virology and Single Molecule Imaging Group, Department of Medicine, MRC Clinical Centre, Imperial College London, London W12 0NN, UK
| | - Alessandro Costa
- Macromolecular Machines, Clare Hall Laboratory, The Francis Crick Institute, Blanche Lane, South Mimms EN6 3LD, UK
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178
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Yuan Z, Bai L, Sun J, Georgescu R, Liu J, O'Donnell ME, Li H. Structure of the eukaryotic replicative CMG helicase suggests a pumpjack motion for translocation. Nat Struct Mol Biol 2016; 23:217-24. [PMID: 26854665 PMCID: PMC4812828 DOI: 10.1038/nsmb.3170] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 01/06/2016] [Indexed: 01/06/2023]
Abstract
The CMG helicase is composed of Cdc45, Mcm2-7 and GINS. Here we report the structure of the Saccharomyces cerevisiae CMG, determined by cryo-EM at a resolution of 3.7-4.8 Å. The structure reveals that GINS and Cdc45 scaffold the N tier of the helicase while enabling motion of the AAA+ C tier. CMG exists in two alternating conformations, compact and extended, thus suggesting that the helicase moves like an inchworm. The N-terminal regions of Mcm2-7, braced by Cdc45-GINS, form a rigid platform upon which the AAA+ C domains make longitudinal motions, nodding up and down like an oil-rig pumpjack attached to a stable platform. The Mcm ring is remodeled in CMG relative to the inactive Mcm2-7 double hexamer. The Mcm5 winged-helix domain is inserted into the central channel, thus blocking entry of double-stranded DNA and supporting a steric-exclusion DNA-unwinding model.
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Affiliation(s)
- Zuanning Yuan
- Department of Biochemistry &Cell Biology, Stony Brook University, Stony Brook, New York, USA.,Biology Department, Brookhaven National Laboratory, Upton, New York, USA
| | - Lin Bai
- Biology Department, Brookhaven National Laboratory, Upton, New York, USA
| | - Jingchuan Sun
- Biology Department, Brookhaven National Laboratory, Upton, New York, USA
| | - Roxana Georgescu
- DNA Replication Laboratory, Rockefeller University, New York, New York, USA.,Howard Hughes Medical Institute, Rockefeller University, New York, New York, USA
| | - Jun Liu
- Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston, Houston, Texas, USA
| | - Michael E O'Donnell
- DNA Replication Laboratory, Rockefeller University, New York, New York, USA.,Howard Hughes Medical Institute, Rockefeller University, New York, New York, USA
| | - Huilin Li
- Department of Biochemistry &Cell Biology, Stony Brook University, Stony Brook, New York, USA.,Biology Department, Brookhaven National Laboratory, Upton, New York, USA
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179
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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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180
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Muñoz S, Méndez J. DNA replication stress: from molecular mechanisms to human disease. Chromosoma 2016; 126:1-15. [PMID: 26797216 DOI: 10.1007/s00412-016-0573-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 01/04/2016] [Accepted: 01/05/2016] [Indexed: 12/29/2022]
Abstract
The genome of proliferating cells must be precisely duplicated in each cell division cycle. Chromosomal replication entails risks such as the possibility of introducing breaks and/or mutations in the genome. Hence, DNA replication requires the coordinated action of multiple proteins and regulatory factors, whose deregulation causes severe developmental diseases and predisposes to cancer. In recent years, the concept of "replicative stress" (RS) has attracted much attention as it impinges directly on genomic stability and offers a promising new avenue to design anticancer therapies. In this review, we summarize recent progress in three areas: (1) endogenous and exogenous factors that contribute to RS, (2) molecular mechanisms that mediate the cellular responses to RS, and (3) the large list of diseases that are directly or indirectly linked to RS.
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Affiliation(s)
- Sergio Muñoz
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, E-28029, Madrid, Spain
| | - Juan Méndez
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, E-28029, Madrid, Spain.
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181
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Silva-Martin N, Daudén MI, Glatt S, Hoffmann NA, Kastritis P, Bork P, Beck M, Müller CW. The Combination of X-Ray Crystallography and Cryo-Electron Microscopy Provides Insight into the Overall Architecture of the Dodecameric Rvb1/Rvb2 Complex. PLoS One 2016; 11:e0146457. [PMID: 26745716 PMCID: PMC4706439 DOI: 10.1371/journal.pone.0146457] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 12/17/2015] [Indexed: 01/08/2023] Open
Abstract
The Rvb1/Rvb2 complex is an essential component of many cellular pathways. The Rvb1/Rvb2 complex forms a dodecameric assembly where six copies of each subunit form two heterohexameric rings. However, due to conformational variability, the way the two rings pack together is still not fully understood. Here, we present the crystal structure and two cryo-electron microscopy reconstructions of the dodecameric, full-length Rvb1/Rvb2 complex, all showing that the interaction between the two heterohexameric rings is mediated through the Rvb1/Rvb2-specific domain II. Two conformations of the Rvb1/Rvb2 dodecamer are present in solution: a stretched conformation also present in the crystal, and a compact conformation. Novel asymmetric features observed in the reconstruction of the compact conformation provide additional insight into the plasticity of the Rvb1/Rvb2 complex.
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Affiliation(s)
- Noella Silva-Martin
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - María I. Daudén
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Sebastian Glatt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Niklas A. Hoffmann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Panagiotis Kastritis
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Christoph W. Müller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- * E-mail:
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182
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Zhang L, Jiang H, Sheong F, Pardo-Avila F, Cheung PH, Huang X. Constructing Kinetic Network Models to Elucidate Mechanisms of Functional Conformational Changes of Enzymes and Their Recognition with Ligands. Methods Enzymol 2016; 578:343-71. [DOI: 10.1016/bs.mie.2016.05.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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183
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Abstract
The machines that decode and regulate genetic information require the translation, transcription and replication pathways essential to all living cells. Thus, it might be expected that all cells share the same basic machinery for these pathways that were inherited from the primordial ancestor cell from which they evolved. A clear example of this is found in the translation machinery that converts RNA sequence to protein. The translation process requires numerous structural and catalytic RNAs and proteins, the central factors of which are homologous in all three domains of life, bacteria, archaea and eukarya. Likewise, the central actor in transcription, RNA polymerase, shows homology among the catalytic subunits in bacteria, archaea and eukarya. In contrast, while some "gears" of the genome replication machinery are homologous in all domains of life, most components of the replication machine appear to be unrelated between bacteria and those of archaea and eukarya. This review will compare and contrast the central proteins of the "replisome" machines that duplicate DNA in bacteria, archaea and eukarya, with an eye to understanding the issues surrounding the evolution of the DNA replication apparatus.
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Affiliation(s)
- Nina Y Yao
- a DNA Replication Laboratory, The Rockefeller University , New York , NY , USA and
| | - Mike E O'Donnell
- a DNA Replication Laboratory, The Rockefeller University , New York , NY , USA and.,b Howard Hughes Medical Institute, The Rockefeller University , New York , NY , USA
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184
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Quan Y, Xia Y, Liu L, Cui J, Li Z, Cao Q, Chen XS, Campbell JL, Lou H. Cell-Cycle-Regulated Interaction between Mcm10 and Double Hexameric Mcm2-7 Is Required for Helicase Splitting and Activation during S Phase. Cell Rep 2015; 13:2576-2586. [PMID: 26686640 DOI: 10.1016/j.celrep.2015.11.018] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 09/22/2015] [Accepted: 11/03/2015] [Indexed: 10/22/2022] Open
Abstract
Mcm2-7 helicase is loaded onto double-stranded origin DNA as an inactive double hexamer (DH) in G1 phase. The mechanisms of Mcm2-7 remodeling that trigger helicase activation in S phase remain unknown. Here, we develop an approach to detect and purify the endogenous DHs directly. Through cellular fractionation, we provide in vivo evidence that DHs are assembled on chromatin in G1 phase and separated during S phase. Interestingly, Mcm10, a robust MCM interactor, co-purifies exclusively with the DHs in the context of chromatin. Deletion of the main interaction domain, Mcm10 C terminus, causes growth and S phase defects, which can be suppressed through Mcm10-MCM fusions. By monitoring the dynamics of MCM DHs, we show a significant delay in DH dissolution during S phase in the Mcm10-MCM interaction-deficient mutants. Therefore, we propose an essential role for Mcm10 in Mcm2-7 remodeling through formation of a cell-cycle-regulated supercomplex with DHs.
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Affiliation(s)
- Yun Quan
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, 2 Yuan-Ming-Yuan West Road, Beijing 100193, China
| | - Yisui Xia
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, 2 Yuan-Ming-Yuan West Road, Beijing 100193, China
| | - Lu Liu
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, 2 Yuan-Ming-Yuan West Road, Beijing 100193, China
| | - Jiamin Cui
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, 2 Yuan-Ming-Yuan West Road, Beijing 100193, China
| | - Zhen Li
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, 2 Yuan-Ming-Yuan West Road, Beijing 100193, China
| | - Qinhong Cao
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, 2 Yuan-Ming-Yuan West Road, Beijing 100193, China
| | - Xiaojiang S Chen
- Molecular and Computational Biology, USC Norris Cancer Center, and Chemistry Department, University of Southern California, Los Angeles, CA 90089, USA
| | - Judith L Campbell
- Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| | - Huiqiang Lou
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, 2 Yuan-Ming-Yuan West Road, Beijing 100193, China.
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185
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Sun J, Shi Y, Georgescu RE, Yuan Z, Chait BT, Li H, O'Donnell ME. The architecture of a eukaryotic replisome. Nat Struct Mol Biol 2015; 22:976-82. [PMID: 26524492 DOI: 10.1038/nsmb.3113] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 09/21/2015] [Indexed: 12/14/2022]
Abstract
At the eukaryotic DNA replication fork, it is widely believed that the Cdc45-Mcm2-7-GINS (CMG) helicase is positioned in front to unwind DNA and that DNA polymerases trail behind the helicase. Here we used single-particle EM to directly image a Saccharomyces cerevisiae replisome. Contrary to expectations, the leading strand Pol ɛ is positioned ahead of CMG helicase, whereas Ctf4 and the lagging-strand polymerase (Pol) α-primase are behind the helicase. This unexpected architecture indicates that the leading-strand DNA travels a long distance before reaching Pol ɛ, first threading through the Mcm2-7 ring and then making a U-turn at the bottom and reaching Pol ɛ at the top of CMG. Our work reveals an unexpected configuration of the eukaryotic replisome, suggests possible reasons for this architecture and provides a basis for further structural and biochemical replisome studies.
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Affiliation(s)
- Jingchuan Sun
- Biosciences Department, Brookhaven National Laboratory, Upton, New York, USA.,Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
| | - Yi Shi
- DNA Replication Laboratory, Rockefeller University, New York, New York, USA
| | - Roxana E Georgescu
- DNA Replication Laboratory, Rockefeller University, New York, New York, USA.,Howard Hughes Medical Institute, Rockefeller University, New York, New York, USA
| | - Zuanning Yuan
- Biosciences Department, Brookhaven National Laboratory, Upton, New York, USA.,Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
| | - Brian T Chait
- DNA Replication Laboratory, Rockefeller University, New York, New York, USA
| | - Huilin Li
- Biosciences Department, Brookhaven National Laboratory, Upton, New York, USA.,Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
| | - Michael E O'Donnell
- DNA Replication Laboratory, Rockefeller University, New York, New York, USA.,Howard Hughes Medical Institute, Rockefeller University, New York, New York, USA
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186
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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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187
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