1
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Dukaj L, Rhind N. The capacity of origins to load MCM establishes replication timing patterns. PLoS Genet 2021; 17:e1009467. [PMID: 33764973 PMCID: PMC8023499 DOI: 10.1371/journal.pgen.1009467] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/06/2021] [Accepted: 03/04/2021] [Indexed: 11/24/2022] Open
Abstract
Loading of the MCM replicative helicase at origins of replication is a highly regulated process that precedes DNA replication in all eukaryotes. The stoichiometry of MCM loaded at origins has been proposed to be a key determinant of when those origins initiate replication during S phase. Nevertheless, the genome-wide regulation of MCM loading stoichiometry and its direct effect on replication timing remain unclear. In order to investigate why some origins load more MCM than others, we perturbed MCM levels in budding yeast cells and, for the first time, directly measured MCM levels and replication timing in the same experiment. Reduction of MCM levels through degradation of Mcm4, one of the six obligate components of the MCM complex, slowed progression through S phase and increased sensitivity to replication stress. Reduction of MCM levels also led to differential loading at origins during G1, revealing origins that are sensitive to reductions in MCM and others that are not. Sensitive origins loaded less MCM under normal conditions and correlated with a weak ability to recruit the origin recognition complex (ORC). Moreover, reduction of MCM loading at specific origins of replication led to a delay in their replication during S phase. In contrast, overexpression of MCM had no effects on cell cycle progression, relative MCM levels at origins, or replication timing, suggesting that, under optimal growth conditions, cellular MCM levels are not limiting for MCM loading. Our results support a model in which the loading capacity of origins is the primary determinant of MCM stoichiometry in wild-type cells, but that stoichiometry is controlled by origins' ability to recruit ORC and compete for MCM when MCM becomes limiting.
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Affiliation(s)
- Livio Dukaj
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School Worcester, Massachusetts, United States of America
| | - Nicholas Rhind
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School Worcester, Massachusetts, United States of America
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2
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Hsu RYC, Lin YC, Redon C, Sun Q, Singh DK, Wang Y, Aggarwal V, Mitra J, Matur A, Moriarity B, Ha T, Aladjem MI, Prasanth KV, Prasanth SG. ORCA/LRWD1 Regulates Homologous Recombination at ALT-Telomeres by Modulating Heterochromatin Organization. iScience 2020; 23:101038. [PMID: 32344376 PMCID: PMC7186530 DOI: 10.1016/j.isci.2020.101038] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 03/26/2020] [Accepted: 04/01/2020] [Indexed: 12/23/2022] Open
Abstract
Telomeres are maintained by telomerase or in a subset of cancer cells by a homologous recombination (HR)-based mechanism, Alternative Lengthening of Telomeres (ALT). The mechanisms regulating telomere-homeostasis in ALT cells remain unclear. We report that a replication initiator protein, Origin Recognition Complex-Associated (ORCA/LRWD1), by localizing at the ALT-telomeres, modulates HR activity. ORCA's localization to the ALT-telomeres is facilitated by its interaction to SUMOylated shelterin components. The loss of ORCA in ALT-positive cells elevates the levels of two mediators of HR, RPA and RAD51, and consistent with this, we observe increased ALT-associated promyelocytic leukemia body formation and telomere sister chromatid exchange. ORCA binds to RPA and modulates the association of RPA to telomeres. Finally, the loss of ORCA causes global chromatin decondensation, including at the telomeres. Our results demonstrate that ORCA acts as an inhibitor of HR by modulating RPA binding to ssDNA and inducing chromatin compaction.
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Affiliation(s)
- Rosaline Y C Hsu
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Yo-Chuen Lin
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Christophe Redon
- Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda MD 20892, USA
| | - Qinyu Sun
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Deepak K Singh
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Yating Wang
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Vasudha Aggarwal
- Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jaba Mitra
- Materials Engineering Department, UIUC, Urbana, IL 61801, USA
| | - Abhijith Matur
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | | | - Taekjip Ha
- Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda MD 20892, USA
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA; Cancer Center at Illinois, UIUC, Urbana, IL 61801, USA
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA; Cancer Center at Illinois, UIUC, Urbana, IL 61801, USA.
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3
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Knockdown of MCM10 Gene Impairs Glioblastoma Cell Proliferation, Migration and Invasion and the Implications for the Regulation of Tumorigenesis. J Mol Neurosci 2020; 70:759-768. [PMID: 32030558 DOI: 10.1007/s12031-020-01486-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 01/17/2020] [Indexed: 10/24/2022]
Abstract
Minichromosome maintenance 10 (MCM10) plays an important role in DNA replication and is expressed in a variety of tumors, including glioma. However, its role and mechanism in glioma remain elusive. The purpose of this study was to examine the molecular function of MCM10 in glioblastoma cell lines in vitro and to further investigate the molecular mechanisms in the network mediated by MCM10. Cell proliferation, invasion, and migration were investigated in the absence of MCM10 mediated by RNA interference (RNAi) in U87 and U251 cell lines. Microarray data were obtained from U87 cells infected with a lentivirus expressing a small interfering RNA (siRNA) targeting MCM10, and ingenuity pathway analysis (IPA) was performed. Molecular signaling pathways, gene functions, and upstream and downstream regulatory genes and networks were analyzed. MCM10 was positively stained in human glioblastoma multiforme (GBM) samples according to immunohistochemistry. Silencing MCM10 in U87 and U251 cells significantly reduced cell proliferation, migration, and invasion. In U87 cells transfected with MCM10, 274 genes were significantly upregulated, while 313 genes were downregulated. IPA revealed that MCM10 is involved in the IGF-1 signaling pathway, and calcitriol appears to be a significant upstream regulator of MCM10. Other factors, such as TWIST1 and Stat3, also interact within the MCM10-mediated network. Our data indicate that MCM10 is involved in the regulation of GBM in vitro and may provide more evidence for understanding the molecular mechanisms of this fatal disease.
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4
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McDaniel SL, Hollatz AJ, Branstad AM, Gaskill MM, Fox CA, Harrison MM. Tissue-Specific DNA Replication Defects in Drosophila melanogaster Caused by a Meier-Gorlin Syndrome Mutation in Orc4. Genetics 2020; 214:355-367. [PMID: 31818869 PMCID: PMC7017028 DOI: 10.1534/genetics.119.302938] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023] Open
Abstract
Meier-Gorlin syndrome is a rare recessive disorder characterized by a number of distinct tissue-specific developmental defects. Genes encoding members of the origin recognition complex (ORC) and additional proteins essential for DNA replication (CDC6, CDT1, GMNN, CDC45, MCM5, and DONSON) are mutated in individuals diagnosed with MGS. The essential role of ORC is to license origins during the G1 phase of the cell cycle, but ORC has also been implicated in several nonreplicative functions. Because of its essential role in DNA replication, ORC is required for every cell division during development. Thus, it is unclear how the Meier-Gorlin syndrome mutations in genes encoding ORC lead to the tissue-specific defects associated with the disease. To begin to address these issues, we used Cas9-mediated genome engineering to generate a Drosophila melanogaster model of individuals carrying a specific Meier-Gorlin syndrome mutation in ORC4 along with control strains. Together these strains provide the first metazoan model for an MGS mutation in which the mutation was engineered at the endogenous locus along with precisely defined control strains. Flies homozygous for the engineered MGS allele reach adulthood, but with several tissue-specific defects. Genetic analysis revealed that this Orc4 allele was a hypomorph. Mutant females were sterile, and phenotypic analyses suggested that defects in DNA replication was an underlying cause. By leveraging the well-studied Drosophila system, we provide evidence that a disease-causing mutation in Orc4 disrupts DNA replication, and we propose that in individuals with MGS defects arise preferentially in tissues with a high-replication demand.
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Affiliation(s)
- Stephen L McDaniel
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706
| | - Allison J Hollatz
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706
| | - Anna M Branstad
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706
| | - Marissa M Gaskill
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706
| | - Catherine A Fox
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706
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5
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Meagher M, Epling LB, Enemark EJ. DNA translocation mechanism of the MCM complex and implications for replication initiation. Nat Commun 2019; 10:3117. [PMID: 31308367 PMCID: PMC6629641 DOI: 10.1038/s41467-019-11074-3] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 06/18/2019] [Indexed: 12/12/2022] Open
Abstract
The DNA translocation activity of the minichromosome maintenance (MCM) complex powers DNA strand separation of the replication forks of eukaryotes and archaea. Here we illustrate an atomic level mechanism for this activity with a crystal structure of an archaeal MCM hexamer bound to single-stranded DNA and nucleotide cofactors. Sequence conservation indicates this rotary mechanism is fully possible for all eukaryotes and archaea. The structure definitively demonstrates the ring orients during translocation with the N-terminal domain leading, indicating that the translocation activity could also provide the physical basis of replication initiation where a double-hexamer idly encircling double-stranded DNA transforms to single-hexamers that encircle only one strand. In this mechanism, each strand binds to the N-terminal tier of one hexamer and the AAA+ tier of the other hexamer such that one ring pulls on the other, aligning equivalent interfaces to enable each hexamer to pull its translocation strand outside of the opposing hexamer.
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Affiliation(s)
- Martin Meagher
- Department of Structural Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 311, Memphis, TN, 38105, USA
| | - Leslie B Epling
- Department of Structural Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 311, Memphis, TN, 38105, USA.,Incyte Research Institute, 1801 Augustine Cut-off, Wilmington, DE, 19803, 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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Abstract
The maintenance of genome stability in eukaryotic cells relies on accurate and efficient replication along each chromosome following every cell division. The terminal position, repetitive sequence, and structural complexities of the telomeric DNA make the telomere an inherently difficult region to replicate within the genome. Thus, despite functioning to protect genome stability mammalian telomeres are also a source of replication stress and have been recognized as common fragile sites within the genome. Telomere fragility is exacerbated at telomeres that rely on the Alternative Lengthening of Telomeres (ALT) pathway. Like common fragile sites, ALT telomeres are prone to chromosome breaks and are frequent sites of recombination suggesting that ALT telomeres are subjected to chronic replication stress. Here, we will review the features of telomeric DNA that challenge the replication machinery and also how the cell overcomes these challenges to maintain telomere stability and ensure the faithful duplication of the human genome.
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Affiliation(s)
- Emily Mason-Osann
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
- Department of Medicine, Cancer Center, Boston University School of Medicine, Boston, MA, USA
| | - Himabindu Gali
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
- Department of Medicine, Cancer Center, Boston University School of Medicine, Boston, MA, USA
| | - Rachel Litman Flynn
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA.
- Department of Medicine, Cancer Center, Boston University School of Medicine, Boston, MA, USA.
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7
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Strand-Specific Analysis of DNA Synthesis and Proteins Association with DNA Replication Forks in Budding Yeast. Methods Mol Biol 2018; 1672:227-238. [PMID: 29043628 DOI: 10.1007/978-1-4939-7306-4_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
DNA replication initiates at DNA replication origins after unwinding of double-strand DNA(dsDNA) by replicative helicase to generate single-stranded DNA (ssDNA) templates for the continuous synthesis of leading-strand and the discontinuous synthesis of lagging-strand. Therefore, methods capable of detecting strand-specific information will likely yield insight into the association of proteins at leading and lagging strand of DNA replication forks and the regulation of leading and lagging strand synthesis during DNA replication. The enrichment and Sequencing of Protein-Associated Nascent DNA (eSPAN), which measure the relative amounts of proteins at nascent leading and lagging strands of DNA replication forks, is a step-wise procedure involving the chromatin immunoprecipitation (ChIP) of a protein of interest followed by the enrichment of protein-associated nascent DNA through BrdU immunoprecipitation. The isolated ssDNA is then subjected to strand-specific sequencing. This method can detect whether a protein is enriched at leading or lagging strand of DNA replication forks. In addition to eSPAN, two other strand-specific methods, (ChIP-ssSeq), which detects potential protein-ssDNA binding and BrdU-IP-ssSeq, which can measure synthesis of both leading and lagging strand, were developed along the way. These methods can provide strand-specific and complementary information about the association of the target protein with DNA replication forks as well as synthesis of leading and lagging strands genome wide. Below, we describe the detailed eSPAN, ChIP-ssSeq, and BrdU-IP-ssSeq protocols.
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Luo H, Quan CL, Peng C, Gao F. Recent development of Ori-Finder system and DoriC database for microbial replication origins. Brief Bioinform 2018; 20:1114-1124. [DOI: 10.1093/bib/bbx174] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/04/2017] [Indexed: 01/28/2023] Open
Abstract
Abstract
DNA replication begins at replication origins in all three domains of life. Identification and characterization of replication origins are important not only in providing insights into the structure and function of the replication origins but also in understanding the regulatory mechanisms of the initiation step in DNA replication. The Z-curve method has been used in the identification of replication origins in archaeal genomes successfully since 2002. Furthermore, the Web servers of Ori-Finder and Ori-Finder 2 have been developed to predict replication origins in both bacterial and archaeal genomes based on the Z-curve method, and the replication origins with manual curation have been collected into an online database, DoriC. Ori-Finder system and DoriC database are currently used in the research field of DNA replication origins in prokaryotes, including: (i) identification of oriC regions in bacterial and archaeal genomes; (ii) discovery and analysis of the conserved sequences within oriC regions; and (iii) strand-biased analysis of bacterial genomes.
Up to now, more and more predicted results by Ori-Finder system were supported by subsequent experiments, and Ori-Finder system has been used to identify the replication origins in > 100 newly sequenced prokaryotes in their genome reports. In addition, the data in DoriC database have been widely used in the large-scale analyses of replication origins and strand bias in prokaryotic genomes. Here, we review the development of Ori-Finder system and DoriC database as well as their applications. Some future directions and aspects for extending the application of Ori-Finder and DoriC are also presented.
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Riera A, Barbon M, Noguchi Y, Reuter LM, Schneider S, Speck C. From structure to mechanism-understanding initiation of DNA replication. Genes Dev 2017; 31:1073-1088. [PMID: 28717046 PMCID: PMC5538431 DOI: 10.1101/gad.298232.117] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In this Review, Riera et al. review recent structural and biochemical insights that start to explain how specific proteins recognize DNA replication origins, load the replicative helicase on DNA, unwind DNA, synthesize new DNA strands, and reassemble chromatin. DNA replication results in the doubling of the genome prior to cell division. This process requires the assembly of 50 or more protein factors into a replication fork. Here, we review recent structural and biochemical insights that start to explain how specific proteins recognize DNA replication origins, load the replicative helicase on DNA, unwind DNA, synthesize new DNA strands, and reassemble chromatin. We focus on the minichromosome maintenance (MCM2–7) proteins, which form the core of the eukaryotic replication fork, as this complex undergoes major structural rearrangements in order to engage with DNA, regulate its DNA-unwinding activity, and maintain genome stability.
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Affiliation(s)
- Alberto Riera
- DNA Replication Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Marta Barbon
- DNA Replication Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,Medical Research Council (MRC) London Institute of Medical Sciences (LMS), London W12 0NN, United Kingdom
| | - Yasunori Noguchi
- DNA Replication Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - L Maximilian Reuter
- DNA Replication Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Sarah Schneider
- DNA Replication Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Christian Speck
- DNA Replication Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,Medical Research Council (MRC) London Institute of Medical Sciences (LMS), London W12 0NN, United Kingdom
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10
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Cryo-EM structure of Mcm2-7 double hexamer on DNA suggests a lagging-strand DNA extrusion model. Proc Natl Acad Sci U S A 2017; 114:E9529-E9538. [PMID: 29078375 PMCID: PMC5692578 DOI: 10.1073/pnas.1712537114] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During replication initiation, the core component of the helicase-the Mcm2-7 hexamer-is loaded on origin DNA as a double hexamer (DH). The two ring-shaped hexamers are staggered, leading to a kinked axial channel. How the origin DNA interacts with the axial channel is not understood, but the interaction could provide key insights into Mcm2-7 function and regulation. Here, we report the cryo-EM structure of the Mcm2-7 DH on dsDNA and show that the DNA is zigzagged inside the central channel. Several of the Mcm subunit DNA-binding loops, such as the oligosaccharide-oligonucleotide loops, helix 2 insertion loops, and presensor 1 (PS1) loops, are well defined, and many of them interact extensively with the DNA. The PS1 loops of Mcm 3, 4, 6, and 7, but not 2 and 5, engage the lagging strand with an approximate step size of one base per subunit. Staggered coupling of the two opposing hexamers positions the DNA right in front of the two Mcm2-Mcm5 gates, with each strand being pressed against one gate. The architecture suggests that lagging-strand extrusion initiates in the middle of the DH that is composed of the zinc finger domains of both hexamers. To convert the Mcm2-7 DH structure into the Mcm2-7 hexamer structure found in the active helicase, the N-tier ring of the Mcm2-7 hexamer in the DH-dsDNA needs to tilt and shift laterally. We suggest that these N-tier ring movements cause the DNA strand separation and lagging-strand extrusion.
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11
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Sanchez JC, Kwan EX, Pohl TJ, Amemiya HM, Raghuraman MK, Brewer BJ. Defective replication initiation results in locus specific chromosome breakage and a ribosomal RNA deficiency in yeast. PLoS Genet 2017; 13:e1007041. [PMID: 29036220 PMCID: PMC5658192 DOI: 10.1371/journal.pgen.1007041] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 10/26/2017] [Accepted: 09/21/2017] [Indexed: 01/23/2023] Open
Abstract
A form of dwarfism known as Meier-Gorlin syndrome (MGS) is caused by recessive mutations in one of six different genes (ORC1, ORC4, ORC6, CDC6, CDT1, and MCM5). These genes encode components of the pre-replication complex, which assembles at origins of replication prior to S phase. Also, variants in two additional replication initiation genes have joined the list of causative mutations for MGS (Geminin and CDC45). The identity of the causative MGS genetic variants strongly suggests that some aspect of replication is amiss in MGS patients; however, little evidence has been obtained regarding what aspect of chromosome replication is faulty. Since the site of one of the missense mutations in the human ORC4 alleles is conserved between humans and yeast, we sought to determine in what way this single amino acid change affects the process of chromosome replication, by introducing the comparable mutation into yeast (orc4Y232C). We find that yeast cells with the orc4Y232C allele have a prolonged S-phase, due to compromised replication initiation at the ribosomal DNA (rDNA) locus located on chromosome XII. The inability to initiate replication at the rDNA locus results in chromosome breakage and a severely reduced rDNA copy number in the survivors, presumably helping to ensure complete replication of chromosome XII. Although reducing rDNA copy number may help ensure complete chromosome replication, orc4Y232C cells struggle to meet the high demand for ribosomal RNA synthesis. This finding provides additional evidence linking two essential cellular pathways-DNA replication and ribosome biogenesis.
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Affiliation(s)
- Joseph C. Sanchez
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, United States of America
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - Elizabeth X. Kwan
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - Thomas J. Pohl
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, United States of America
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - Haley M. Amemiya
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - M. K. Raghuraman
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - Bonita J. Brewer
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, United States of America
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
- * E-mail:
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12
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Ingalls B, Duncker B, Kim D, McConkey B. Systems Level Modeling of the Cell Cycle Using Budding Yeast. Cancer Inform 2017. [DOI: 10.1177/117693510700300020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Proteins involved in the regulation of the cell cycle are highly conserved across all eukaryotes, and so a relatively simple eukaryote such as yeast can provide insight into a variety of cell cycle perturbations including those that occur in human cancer. To date, the budding yeast Saccharomyces cerevisiae has provided the largest amount of experimental and modeling data on the progression of the cell cycle, making it a logical choice for in-depth studies of this process. Moreover, the advent of methods for collection of high-throughput genome, transcriptome, and proteome data has provided a means to collect and precisely quantify simultaneous cell cycle gene transcript and protein levels, permitting modeling of the cell cycle on the systems level. With the appropriate mathematical framework and sufficient and accurate data on cell cycle components, it should be possible to create a model of the cell cycle that not only effectively describes its operation, but can also predict responses to perturbations such as variation in protein levels and responses to external stimuli including targeted inhibition by drugs. In this review, we summarize existing data on the yeast cell cycle, proteomics technologies for quantifying cell cycle proteins, and the mathematical frameworks that can integrate this data into representative and effective models. Systems level modeling of the cell cycle will require the integration of high-quality data with the appropriate mathematical framework, which can currently be attained through the combination of dynamic modeling based on proteomics data and using yeast as a model organism.
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Affiliation(s)
- B.P. Ingalls
- Department of Applied Mathematics, University of Waterloo
| | | | - D.R. Kim
- Department of Biology, University of Waterloo
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13
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Yuan Z, Riera A, Bai L, Sun J, Nandi S, Spanos C, Chen ZA, Barbon M, Rappsilber J, Stillman B, Speck C, Li H. Structural basis of Mcm2-7 replicative helicase loading by ORC-Cdc6 and Cdt1. Nat Struct Mol Biol 2017; 24:316-324. [PMID: 28191893 PMCID: PMC5503505 DOI: 10.1038/nsmb.3372] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 01/09/2017] [Indexed: 12/19/2022]
Abstract
To start DNA replication, the Origin Recognition Complex (ORC) and Cdc6 load a Mcm2-7 double hexamer onto DNA. Without ATP hydrolysis, ORC-Cdc6 recruits one Cdt1-bound Mcm2-7 hexamer, forming an ORC-Cdc6-Cdt1-Mcm2-7 (OCCM) helicase loading intermediate. Here we report a 3.9Å structure of the OCCM on DNA. Flexible Mcm2-7 winged-helix domains (WHD) engage ORC-Cdc6. A three-domain Cdt1 configuration embraces Mcm2, Mcm4, and Mcm6, nearly half of the hexamer. The Cdt1 C-terminal domain extends to the Mcm6 WHD, which binds Orc4 WHD. DNA passes through the ORC-Cdc6 and Mcm2-7 rings. Origin DNA interaction is mediated by an α-helix in Orc4 and positively charged loops in Orc2 and Cdc6. The Mcm2-7 C-tier AAA+ ring is topologically closed by a Mcm5 loop that embraces Mcm2, but the N-tier ring Mcm2-Mcm5 interface remains open. This structure suggests loading mechanics of the first Cdt1-bound Mcm2-7 hexamer by ORC-Cdc6.
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Affiliation(s)
- Zuanning Yuan
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, Michigan, USA
| | - Alberto Riera
- MRC London Institute of Medical Sciences (LMS), London, UK.,DNA Replication Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Lin Bai
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, Michigan, USA
| | - Jingchuan Sun
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, Michigan, USA
| | - Saikat Nandi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Christos Spanos
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Zhuo Angel Chen
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Marta Barbon
- MRC London Institute of Medical Sciences (LMS), London, UK.,DNA Replication Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.,Chair of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Bruce Stillman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Christian Speck
- MRC London Institute of Medical Sciences (LMS), London, UK.,DNA Replication Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Huilin Li
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, Michigan, USA
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14
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Abstract
In recent years it has become clear that complex regulatory circuits control the initiation step of DNA replication by directing the assembly of a multicomponent molecular machine (the orisome) that separates DNA strands and loads replicative helicase at oriC, the unique chromosomal origin of replication. This chapter discusses recent efforts to understand the regulated protein-DNA interactions that are responsible for properly timed initiation of chromosome replication. It reviews information about newly identified nucleotide sequence features within Escherichia coli oriC and the new structural and biochemical attributes of the bacterial initiator protein DnaA. It also discusses the coordinated mechanisms that prevent improperly timed DNA replication. Identification of the genes that encoded the initiators came from studies on temperature-sensitive, conditional-lethal mutants of E. coli, in which two DNA replication-defective phenotypes, "immediate stop" mutants and "delayed stop" mutants, were identified. The kinetics of the delayed stop mutants suggested that the defective gene products were required specifically for the initiation step of DNA synthesis, and subsequently, two genes, dnaA and dnaC, were identified. The DnaA protein is the bacterial initiator, and in E. coli, the DnaC protein is required to load replicative helicase. Regulation of DnaA accessibility to oriC, the ordered assembly and disassembly of a multi-DnaA complex at oriC, and the means by which DnaA unwinds oriC remain important questions to be answered and the chapter discusses the current state of knowledge on these topics.
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15
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Reubens MC, Biller MD, Bedsole SE, Hopkins LT, Ables ET, Christensen TW. Mcm10 is required for oogenesis and early embryogenesis in Drosophila. Mech Dev 2015; 138 Pt 3:291-9. [PMID: 26369283 DOI: 10.1016/j.mod.2015.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 08/27/2015] [Accepted: 09/08/2015] [Indexed: 01/05/2023]
Abstract
Efficient replication of the genome and the establishment of endogenous chromatin states are processes that are essential to eukaryotic life. It is well documented that Mcm10 is intimately linked to both of these important biological processes; therefore, it is not surprising that Mcm10 is commonly misregulated in many human cancers. Most of the research regarding the biological roles of Mcm10 has been performed in single-cell or cell-free in-vitro systems. Though these systems are informative, they are unable to provide information on the cell-specific function of Mcm10 in the context of the tissue and organ systems that comprise multicellular eukaryotes. We therefore sought to identify the potential biological functions of Mcm10 in the context of a complex multicellular organism by continuing our analysis in Drosophila using three novel hypomorphic alleles. Observation of embryonic nuclear morphology and quantification of embryo hatch rates reveal that maternal loading of Mcm10 is required for embryonic nuclear stability, and suggest a role for Mcm10 post zygotic transition. Contrary to the essential nature of Mcm10 depicted in the literature, it does not appear to be required for adult viability in Drosophila if embryonic requirements are met. Although not required for adult somatic viability, analysis of fecundity and ovarian morphology in mutant females suggest that Mcm10 plays a role in maintenance of the female germline. Taken together, our results demonstrate critical roles for Mcm10 during early embryogenesis, and mark the first data linking Mcm10 to female specific reproduction in multicellular eukaryotes.
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Affiliation(s)
- Michael C Reubens
- Department of Biology, East Carolina University, Greenville, NC 27878, USA.
| | - Megan D Biller
- Department of Biology, East Carolina University, Greenville, NC 27878, USA.
| | - Sidney E Bedsole
- Department of Biology, East Carolina University, Greenville, NC 27878, USA.
| | - Lucas T Hopkins
- Department of Biology, East Carolina University, Greenville, NC 27878, USA.
| | - Elizabeth T Ables
- Department of Biology, East Carolina University, Greenville, NC 27878, USA.
| | - Tim W Christensen
- Department of Biology, East Carolina University, Greenville, NC 27878, USA.
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16
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Chaban Y, Stead JA, Ryzhenkova K, Whelan F, Lamber EP, Antson A, Sanders CM, Orlova EV. Structural basis for DNA strand separation by a hexameric replicative helicase. Nucleic Acids Res 2015; 43:8551-63. [PMID: 26240379 PMCID: PMC4787811 DOI: 10.1093/nar/gkv778] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Accepted: 07/20/2015] [Indexed: 11/12/2022] Open
Abstract
Hexameric helicases are processive DNA unwinding machines but how they engage with a replication fork during unwinding is unknown. Using electron microscopy and single particle analysis we determined structures of the intact hexameric helicase E1 from papillomavirus and two complexes of E1 bound to a DNA replication fork end-labelled with protein tags. By labelling a DNA replication fork with streptavidin (dsDNA end) and Fab (5′ ssDNA) we located the positions of these labels on the helicase surface, showing that at least 10 bp of dsDNA enter the E1 helicase via a side tunnel. In the currently accepted ‘steric exclusion’ model for dsDNA unwinding, the active 3′ ssDNA strand is pulled through a central tunnel of the helicase motor domain as the dsDNA strands are wedged apart outside the protein assembly. Our structural observations together with nuclease footprinting assays indicate otherwise: strand separation is taking place inside E1 in a chamber above the helicase domain and the 5′ passive ssDNA strands exits the assembly through a separate tunnel opposite to the dsDNA entry point. Our data therefore suggest an alternative to the current general model for DNA unwinding by hexameric helicases.
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Affiliation(s)
- Yuriy Chaban
- Department of Biological Sciences, Birkbeck College, Institute of Structural and Molecular Biology, Malet Street, London WC1E 7HX, UK
| | - Jonathan A Stead
- Academic Unit of Molecular Oncology, University of Sheffield Medical School, Beech Hill Road, Sheffield S10 2RX, UK
| | - Ksenia Ryzhenkova
- Department of Biological Sciences, Birkbeck College, Institute of Structural and Molecular Biology, Malet Street, London WC1E 7HX, UK
| | - Fiona Whelan
- Departament of Biolody, University of York, York YO10 5DD, UK
| | - Ekaterina P Lamber
- Department of Biological Sciences, Birkbeck College, Institute of Structural and Molecular Biology, Malet Street, London WC1E 7HX, UK
| | - Alfred Antson
- Departament of Biolody, University of York, York YO10 5DD, UK
| | - Cyril M Sanders
- Academic Unit of Molecular Oncology, University of Sheffield Medical School, Beech Hill Road, Sheffield S10 2RX, UK
| | - Elena V Orlova
- Department of Biological Sciences, Birkbeck College, Institute of Structural and Molecular Biology, Malet Street, London WC1E 7HX, UK
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17
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A global profile of replicative polymerase usage. Nat Struct Mol Biol 2015; 22:192-198. [PMID: 25664722 PMCID: PMC4789492 DOI: 10.1038/nsmb.2962] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 12/23/2014] [Indexed: 12/19/2022]
Abstract
Three eukaryotic DNA polymerases are essential for genome replication. Polymerase (Pol) α-primase initiates each synthesis event and is rapidly replaced by processive DNA polymerases: Polɛ replicates the leading strand, whereas Polδ performs lagging-strand synthesis. However, it is not known whether this division of labor is maintained across the whole genome or how uniform it is within single replicons. Using Schizosaccharomyces pombe, we have developed a polymerase usage sequencing (Pu-seq) strategy to map polymerase usage genome wide. Pu-seq provides direct replication-origin location and efficiency data and indirect estimates of replication timing. We confirm that the division of labor is broadly maintained across an entire genome. However, our data suggest a subtle variability in the usage of the two polymerases within individual replicons. We propose that this results from occasional leading-strand initiation by Polδ followed by exchange for Polɛ.
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18
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Alonso N, Guillen R, Chambers JW, Leng F. A rapid and sensitive high-throughput screening method to identify compounds targeting protein-nucleic acids interactions. Nucleic Acids Res 2015; 43:e52. [PMID: 25653160 PMCID: PMC4417145 DOI: 10.1093/nar/gkv069] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 01/19/2015] [Indexed: 01/09/2023] Open
Abstract
DNA-binding and RNA-binding proteins are usually considered ‘undruggable’ partly due to the lack of an efficient method to identify inhibitors from existing small molecule repositories. Here we report a rapid and sensitive high-throughput screening approach to identify compounds targeting protein–nucleic acids interactions based on protein–DNA or protein–RNA interaction enzyme-linked immunosorbent assays (PDI-ELISA or PRI-ELISA). We validated the PDI-ELISA method using the mammalian high-mobility-group protein AT-hook 2 (HMGA2) as the protein of interest and netropsin as the inhibitor of HMGA2–DNA interactions. With this method we successfully identified several inhibitors and an activator for HMGA2–DNA interactions from a collection of 29 DNA-binding compounds. Guided by this screening excise, we showed that netropsin, the specific inhibitor of HMGA2–DNA interactions, strongly inhibited the differentiation of the mouse pre-adipocyte 3T3-L1 cells into adipocytes, most likely through a mechanism by which the inhibition is through preventing the binding of HMGA2 to the target DNA sequences. This method should be broadly applicable to identify compounds or proteins modulating many DNA-binding or RNA-binding proteins.
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Affiliation(s)
- Nicole Alonso
- Biomolecular Sciences Institute, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA Department of Chemistry & Biochemistry, Florida International University, 11200 SW 8th Street, FL 33199, USA
| | - Roboan Guillen
- Biomolecular Sciences Institute, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA Department of Chemistry & Biochemistry, Florida International University, 11200 SW 8th Street, FL 33199, USA
| | - Jeremy W Chambers
- Biomolecular Sciences Institute, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Fenfei Leng
- Biomolecular Sciences Institute, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA Department of Chemistry & Biochemistry, Florida International University, 11200 SW 8th Street, FL 33199, USA
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19
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Cheng HM, Gröger P, Hartmann A, Schlierf M. Bacterial initiators form dynamic filaments on single-stranded DNA monomer by monomer. Nucleic Acids Res 2014; 43:396-405. [PMID: 25477384 PMCID: PMC4288177 DOI: 10.1093/nar/gku1284] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
DNA replication initiation is mediated across all domains of life by initiator proteins oligomerizing at replication origins. Recently, it was shown that initiators can directly bind single-stranded DNA (ssDNA) and thus might enhance origin melting. In this study, we used single-molecule fluorescence assays to probe the ssDNA binding mechanism of the replication initiator DnaA. Our experiments revealed that DnaA forms a dynamic filament on ssDNA in 3′ to 5′ directionality in the presence of ATP and analogs. After nucleation with a three-monomer seed, monomers dynamically assemble and disassemble one monomer at a time at the 5′ end, each monomer binding three nucleotides of ssDNA. The addition of adjacent double-stranded DnaA binding sites stabilized the DnaA filament on ssDNA. Our results extend the current models of origin melting via DnaA ssDNA interaction.
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Affiliation(s)
- Hsin-Mei Cheng
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstraße 18, 01307 Dresden, Germany
| | - Philip Gröger
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstraße 18, 01307 Dresden, Germany
| | - Andreas Hartmann
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstraße 18, 01307 Dresden, Germany
| | - Michael Schlierf
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstraße 18, 01307 Dresden, Germany
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20
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Johansson P, Jeffery J, Al-Ejeh F, Schulz RB, Callen DF, Kumar R, Khanna KK. SCF-FBXO31 E3 ligase targets DNA replication factor Cdt1 for proteolysis in the G2 phase of cell cycle to prevent re-replication. J Biol Chem 2014; 289:18514-25. [PMID: 24828503 DOI: 10.1074/jbc.m114.559930] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
FBXO31 was originally identified as a putative tumor suppressor gene in breast, ovarian, hepatocellular, and prostate cancers. By screening a set of cell cycle-regulated proteins as potential FBXO31 interaction partners, we have now identified Cdt1 as a novel substrate. Cdt1 DNA replication licensing factor is part of the pre-replication complex and essential for the maintenance of genomic integrity. We show that FBXO31 specifically interacts with Cdt1 and regulates its abundance by ubiquitylation leading to subsequent degradation. We also show that Cdt1 regulation by FBXO31 is limited to the G2 phase of the cell cycle and is independent of the pathways previously described for Cdt1 proteolysis in S and G2 phase. FBXO31 targeting of Cdt1 is mediated through the N terminus of Cdt1, a region previously shown to be responsible for its cell cycle regulation. Finally, we show that Cdt1 stabilization due to FBXO31 depletion results in re-replication. Our data present an additional pathway that contributes to the FBXO31 function as a tumor suppressor.
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Affiliation(s)
- Pegah Johansson
- From the Sahlgrenska University Hospital, Department of Clinical Chemistry, Bruna Stråket 16, 41345 Gothenburg, Sweden
| | - Jessie Jeffery
- Signal Transduction Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Fares Al-Ejeh
- Signal Transduction Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Renèe B Schulz
- Centre for Personalised Cancer Medicine and Discipline of Medicine, University of Adelaide, Adelaide, South Australia 5000, Australia
| | - David F Callen
- Centre for Personalised Cancer Medicine and Discipline of Medicine, University of Adelaide, Adelaide, South Australia 5000, Australia
| | - Raman Kumar
- School of Paediatrics and Reproductive Health and Discipline of Medicine, University of Adelaide, Adelaide and Women's and Children's Health Research Institute, North Adelaide, South Australia 5006, Australia, and
| | - Kum Kum Khanna
- Signal Transduction Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
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21
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Abstract
Evolutionary selection for optimal genome preservation, replication, and expression should yield similar chromosome organizations in any type of cells. And yet, the chromosome organization is surprisingly different between eukaryotes and prokaryotes. The nuclear versus cytoplasmic accommodation of genetic material accounts for the distinct eukaryotic and prokaryotic modes of genome evolution, but it falls short of explaining the differences in the chromosome organization. I propose that the two distinct ways to organize chromosomes are driven by the differences between the global-consecutive chromosome cycle of eukaryotes and the local-concurrent chromosome cycle of prokaryotes. Specifically, progressive chromosome segregation in prokaryotes demands a single duplicon per chromosome, while other "precarious" features of the prokaryotic chromosomes can be viewed as compensations for this severe restriction.
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22
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Beck JL, Urathamakul T, Watt SJ, Sheil MM, Schaeffer PM, Dixon NE. Proteomic dissection of DNA polymerization. Expert Rev Proteomics 2014; 3:197-211. [PMID: 16608433 DOI: 10.1586/14789450.3.2.197] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
DNA polymerases replicate the genome by associating with a range of other proteins that enable rapid, high-fidelity copying of DNA. This complex of proteins and nucleic acids is termed the replisome. Proteins of the replisome must interact with other networks of proteins, such as those involved in DNA repair. Many of the proteins involved in DNA polymerization and the accessory proteins are known, but the array of proteins they interact with, and the spatial and temporal arrangement of these interactions, are current research topics. Mass spectrometry is a technique that can be used to identify the sites of these interactions and to determine the precise stoichiometries of binding partners in a functional complex. A complete understanding of the macromolecular interactions involved in DNA replication and repair may lead to discovery of new targets for antibiotics against bacteria and biomarkers for diagnosis of diseases, such as cancer, in humans.
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Affiliation(s)
- Jennifer L Beck
- Department of Chemistry, University of Wollongong, Wollongong, NSW 2522, Australia.
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23
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Evrin C, Fernández-Cid A, Riera A, Zech J, Clarke P, Herrera MC, Tognetti S, Lurz R, Speck C. The ORC/Cdc6/MCM2-7 complex facilitates MCM2-7 dimerization during prereplicative complex formation. Nucleic Acids Res 2013; 42:2257-69. [PMID: 24234446 PMCID: PMC3936773 DOI: 10.1093/nar/gkt1148] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The replicative mini-chromosome-maintenance 2–7 (MCM2-7) helicase is loaded in Saccharomyces cerevisiae and other eukaryotes as a head-to-head double-hexamer around origin DNA. At first, ORC/Cdc6 recruits with the help of Cdt1 a single MCM2-7 hexamer to form an ‘initial’ ORC/Cdc6/Cdt1/MCM2-7 complex. Then, on ATP hydrolysis and Cdt1 release, the ‘initial’ complex is transformed into an ORC/Cdc6/MCM2-7 (OCM) complex. However, it remains unclear how the OCM is subsequently converted into a MCM2-7 double-hexamer. Through analysis of MCM2-7 hexamer-interface mutants we discovered a complex competent for MCM2-7 dimerization. We demonstrate that these MCM2-7 mutants arrest during prereplicative complex (pre-RC) assembly after OCM formation, but before MCM2-7 double-hexamer assembly. Remarkably, only the OCM complex, but not the ‘initial’ ORC/Cdc6/Cdt1/MCM2-7 complex, is competent for MCM2-7 dimerization. The MCM2-7 dimer, in contrast to the MCM2-7 double-hexamer, interacts with ORC/Cdc6 and is salt-sensitive, classifying the arrested complex as a helicase-loading intermediate. Accordingly, we found that overexpression of the mutants cause cell-cycle arrest and dominant lethality. Our work identifies the OCM complex as competent for MCM2-7 dimerization, reveals MCM2-7 dimerization as a limiting step during pre-RC formation and defines critical mechanisms that explain how origins are licensed.
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Affiliation(s)
- Cecile Evrin
- DNA Replication Group, MRC Clinical Sciences Centre, Imperial College, Du Cane Road, London W12 0NN, UK and Microscopy Unit, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
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24
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Li B, Su T, Ferrari R, Li JY, Kurdistani SK. A unique epigenetic signature is associated with active DNA replication loci in human embryonic stem cells. Epigenetics 2013; 9:257-67. [PMID: 24172870 DOI: 10.4161/epi.26870] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The cellular epigenetic landscape changes as pluripotent stem cells differentiate to somatic cells or when differentiated cells transform to a cancerous state. These epigenetic changes are commonly correlated with differences in gene expression. Whether active DNA replication is also associated with distinct chromatin environments in these developmentally and phenotypically diverse cell types has not been known. Here, we used BrdU-seq to map active DNA replication loci in human embryonic stem cells (hESCs), normal primary fibroblasts and a cancer cell line, and correlated these maps to the epigenome. In all cell lines, the majority of BrdU peaks were enriched in euchromatin and at DNA repetitive elements, especially at microsatellite repeats, and coincided with previously determined replication origins. The most prominent BrdU peaks were shared between all cells but a sizable fraction of the peaks were specific to each cell type and associated with cell type-specific genes. Surprisingly, the BrdU peaks that were common to all cell lines were associated with H3K18ac, H3K56ac, and H4K20me1 histone marks only in hESCs but not in normal fibroblasts or cancer cells. Depletion of the histone acetyltransferases for H3K18 and H3K56 dramatically decreased the number and intensity of BrdU peaks in hESCs. Our data reveal a unique epigenetic signature that distinguishes active replication loci in hESCs from normal somatic or malignant cells.
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Affiliation(s)
- Bing Li
- Department of Biological Chemistry; University of California; Los Angeles, CA USA
| | - Trent Su
- Department of Biological Chemistry; University of California; Los Angeles, CA USA; Division of Oral Biology and Medicine; School of Dentistry; University of California; Los Angeles, CA USA
| | - Roberto Ferrari
- Department of Biological Chemistry; University of California; Los Angeles, CA USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research; David Geffen School of Medicine; University of California; Los Angeles, CA USA
| | - Jing-Yu Li
- Department of Biological Chemistry; University of California; Los Angeles, CA USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research; David Geffen School of Medicine; University of California; Los Angeles, CA USA
| | - Siavash K Kurdistani
- Department of Biological Chemistry; University of California; Los Angeles, CA USA; Molecular Biology Institute; University of California; Los Angeles, CA USA; Department of Pathology and Laboratory Medicine; University of California; Los Angeles, CA USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research; David Geffen School of Medicine; University of California; Los Angeles, CA USA
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25
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Abstract
In both eukaryotes and prokaryotes, chromosomal DNA undergoes replication, condensation-decondensation and segregation, sequentially, in some fixed order. Other conditions, like sister-chromatid cohesion (SCC), may span several chromosomal events. One set of these chromosomal transactions within a single cell cycle constitutes the 'chromosome cycle'. For many years it was generally assumed that the prokaryotic chromosome cycle follows major phases of the eukaryotic one: -replication-condensation-segregation-(cell division)-decondensation-, with SCC of unspecified length. Eventually it became evident that, in contrast to the strictly consecutive chromosome cycle of eukaryotes, all stages of the prokaryotic chromosome cycle run concurrently. Thus, prokaryotes practice 'progressive' chromosome segregation separated from replication by a brief SCC, and all three transactions move along the chromosome at the same fast rate. In other words, in addition to replication forks, there are 'segregation forks' in prokaryotic chromosomes. Moreover, the bulk of prokaryotic DNA outside the replication-segregation transition stays compacted. I consider possible origins of this concurrent replication-segregation and outline the 'nucleoid administration' system that organizes the dynamic part of the prokaryotic chromosome cycle.
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Affiliation(s)
- Andrei Kuzminov
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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26
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Herrup K. Post-mitotic role of the cell cycle machinery. Curr Opin Cell Biol 2013; 25:711-6. [PMID: 24055434 DOI: 10.1016/j.ceb.2013.08.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 08/08/2013] [Indexed: 12/27/2022]
Abstract
The process of cell division is highly complex. The DNA of the genome must be accurately replicated and segregated into two precisely equal portions; the cytoskeleton must be actively rearranged; and the cellular motor forces that allow the separation of the replicated chromosomes and the splitting of the mother cell into two daughters must be kept under strict spatial and temporal regulation. Not surprisingly for a process of this complexity, there is a wide range of proteins whose location and activity must be accurately controlled to ensure both efficiency and precision. Although the demands placed on these cell cycle proteins are high, once cells such as neurons differentiate they enter a long non-mitotic phase where evolution has conspired to repurpose many of these proteins, leading them to assume new and often unrelated cellular tasks. In neurons there is a wide range of non-cycling functions for these 'cell cycle' proteins and this review covers some of the best-known examples. There is little apparent logic to the second use, but the sheer number of examples suggests that there must be a significant evolutionary advantage to this repurposing strategy.
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Affiliation(s)
- Karl Herrup
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; Dept. of Cell Biology and Neuroscience, Rutgers University, 604 Allison Road, Piscataway, NJ 08854, United States.
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27
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Hoggard T, Shor E, Müller CA, Nieduszynski CA, Fox CA. A Link between ORC-origin binding mechanisms and origin activation time revealed in budding yeast. PLoS Genet 2013; 9:e1003798. [PMID: 24068963 PMCID: PMC3772097 DOI: 10.1371/journal.pgen.1003798] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 07/30/2013] [Indexed: 01/19/2023] Open
Abstract
Eukaryotic DNA replication origins are selected in G1-phase when the origin recognition complex (ORC) binds chromosomal positions and triggers molecular events culminating in the initiation of DNA replication (a.k.a. origin firing) during S-phase. Each chromosome uses multiple origins for its duplication, and each origin fires at a characteristic time during S-phase, creating a cell-type specific genome replication pattern relevant to differentiation and genome stability. It is unclear whether ORC-origin interactions are relevant to origin activation time. We applied a novel genome-wide strategy to classify origins in the model eukaryote Saccharomyces cerevisiae based on the types of molecular interactions used for ORC-origin binding. Specifically, origins were classified as DNA-dependent when the strength of ORC-origin binding in vivo could be explained by the affinity of ORC for origin DNA in vitro, and, conversely, as ‘chromatin-dependent’ when the ORC-DNA interaction in vitro was insufficient to explain the strength of ORC-origin binding in vivo. These two origin classes differed in terms of nucleosome architecture and dependence on origin-flanking sequences in plasmid replication assays, consistent with local features of chromatin promoting ORC binding at ‘chromatin-dependent’ origins. Finally, the ‘chromatin-dependent’ class was enriched for origins that fire early in S-phase, while the DNA-dependent class was enriched for later firing origins. Conversely, the latest firing origins showed a positive association with the ORC-origin DNA paradigm for normal levels of ORC binding, whereas the earliest firing origins did not. These data reveal a novel association between ORC-origin binding mechanisms and the regulation of origin activation time. Cell division requires the duplication of chromosomes, protein-DNA complexes harboring genetic information. Specific chromosomal positions, origins, initiate this duplication. Multiple origins are required for accurate, efficient duplication—an insufficient number leads to mistakes in the genetic material and pathologies such as cancer. Origins are chosen when the origin recognition complex (ORC) binds to them. The molecular interactions controlling this binding remain unclear. Understanding these interactions will lead to new ways to control cell division, which could aid in treatments of disease. Experiments were performed in the eukaryotic microbe budding yeast to define the types of molecular interactions ORC uses to bind origins. Yeasts are useful for these studies because chromosome duplication and structure are well conserved from yeast to humans. While ORC-DNA interactions were important, interactions between ORC and chromosomal proteins played a role. In addition, different origins relied on different types of molecular interactions with ORC. Finally, ORC-protein interactions but not ORC-DNA interactions were associated with enhanced origin function during chromosome-duplication, revealing an unanticipated link between the types of molecular interactions ORC uses to select an origin and the ultimate function of that origin. These results have implications for interfering with ORC-origin interactions to control cell division.
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Affiliation(s)
- Timothy Hoggard
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Program in Cellular and Molecular Biology, College of Agriculture and Life Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Erika Shor
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Carolin A. Müller
- Centre for Genetics and Genomics, University of Nottingham Queen's Medical Centre, Nottingham, United Kingdom
| | - Conrad A. Nieduszynski
- Centre for Genetics and Genomics, University of Nottingham Queen's Medical Centre, Nottingham, United Kingdom
- * E-mail: (CAN); (CAF)
| | - Catherine A. Fox
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Program in Cellular and Molecular Biology, College of Agriculture and Life Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail: (CAN); (CAF)
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28
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Sun J, Evrin C, Samel SA, Fernández-Cid A, Riera A, Kawakami H, Stillman B, Speck C, Li H. Cryo-EM structure of a helicase loading intermediate containing ORC-Cdc6-Cdt1-MCM2-7 bound to DNA. Nat Struct Mol Biol 2013; 20:944-51. [PMID: 23851460 PMCID: PMC3735830 DOI: 10.1038/nsmb.2629] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 05/29/2013] [Indexed: 01/08/2023]
Abstract
In eukaryotes, the Cdt1-bound replicative helicase core MCM2-7 is loaded onto DNA by the ORC-Cdc6 ATPase to form a prereplicative complex (pre-RC) with an MCM2-7 double hexamer encircling DNA. Using purified components in the presence of ATP-γS, we have captured in vitro an intermediate in pre-RC assembly that contains a complex between the ORC-Cdc6 and Cdt1-MCM2-7 heteroheptamers called the OCCM. Cryo-EM studies of this 14-subunit complex reveal that the two separate heptameric complexes are engaged extensively, with the ORC-Cdc6 N-terminal AAA+ domains latching onto the C-terminal AAA+ motor domains of the MCM2-7 hexamer. The conformation of ORC-Cdc6 undergoes a concerted change into a right-handed spiral with helical symmetry that is identical to that of the DNA double helix. The resulting ORC-Cdc6 helicase loader shows a notable structural similarity to the replication factor C clamp loader, suggesting a conserved mechanism of action.
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Affiliation(s)
- Jingchuan Sun
- Biosciences Department, Brookhaven National Laboratory, Upton, New York, USA
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29
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O'Donnell M, Langston L, Stillman B. Principles and concepts of DNA replication in bacteria, archaea, and eukarya. Cold Spring Harb Perspect Biol 2013; 5:5/7/a010108. [PMID: 23818497 DOI: 10.1101/cshperspect.a010108] [Citation(s) in RCA: 214] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The accurate copying of genetic information in the double helix of DNA is essential for inheritance of traits that define the phenotype of cells and the organism. The core machineries that copy DNA are conserved in all three domains of life: bacteria, archaea, and eukaryotes. This article outlines the general nature of the DNA replication machinery, but also points out important and key differences. The most complex organisms, eukaryotes, have to coordinate the initiation of DNA replication from many origins in each genome and impose regulation that maintains genomic integrity, not only for the sake of each cell, but for the organism as a whole. In addition, DNA replication in eukaryotes needs to be coordinated with inheritance of chromatin, developmental patterning of tissues, and cell division to ensure that the genome replicates once per cell division cycle.
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Affiliation(s)
- Michael O'Donnell
- The Rockefeller University and Howard Hughes Medical Institute, New York, New York 10065, USA
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30
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Duderstadt KE, Berger JM. A structural framework for replication origin opening by AAA+ initiation factors. Curr Opin Struct Biol 2012; 23:144-53. [PMID: 23266000 DOI: 10.1016/j.sbi.2012.11.012] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 11/26/2012] [Accepted: 11/29/2012] [Indexed: 10/27/2022]
Abstract
ATP-dependent initiation factors help process replication origins and coordinate replisome assembly to control the onset of DNA synthesis. Although the specific properties and regulatory mechanisms of initiator proteins can vary greatly between different organisms, certain nucleotide-binding elements and assembly patterns appear preserved not only within the three domains of cellular life (bacteria, archaea, and eukaryotes), but also with certain classes of double-stranded DNA viruses. Structural studies of replication initiation proteins, both as higher-order oligomers and in complex with cognate DNA substrates, are revealing how an evolutionarily related ATPase fold can support different modes of macromolecular assembly and function. Comparative studies between initiation systems in turn provide clues as to how duplex origin regions may be melted during initiation events.
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Affiliation(s)
- Karl E Duderstadt
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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31
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Chisamore-Robert P, Peeters S, Shostak K, Yankulov K. Directional telomeric silencing and lack of canonical B1 elements in two silencer Autonomously Replicating Sequences in S. cerevisiae. BMC Mol Biol 2012; 13:34. [PMID: 23157664 PMCID: PMC3545912 DOI: 10.1186/1471-2199-13-34] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 11/15/2012] [Indexed: 12/29/2022] Open
Abstract
Background Autonomously Replicating Sequences (ARS) in S. cerevisiae serve as origins of DNA replication or as components of cis-acting silencers, which impose positional repression at the mating type loci and at the telomeres. Both types of ARS can act as replicators or silencers, however it is not clear how these quite diverse functions are executed. It is believed that all ARS contain a core module of an essential ARS Consensus Sequence (ACS) and a non-essential B1 element. Results We have tested how the B1 elements contribute to the silencer and replicator function of ARS. We report that the ACS-B1 orientation of ARS has a profound effect on the levels of gene silencing at telomeres. We also report that the destruction of the canonical B1 elements in two silencer ARS (ARS317 and ARS319) has no effect on their silencer and replicator activity. Conclusions The observed orientation effects on gene silencing suggest that ARSs can act as both proto-silencers and as insulator elements. In addition, the lack of B1 suggests that the ACS-B1 module could be different in silencer and replicator ARS.
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32
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Ozaki S, Noguchi Y, Hayashi Y, Miyazaki E, Katayama T. Differentiation of the DnaA-oriC subcomplex for DNA unwinding in a replication initiation complex. J Biol Chem 2012; 287:37458-71. [PMID: 22942281 DOI: 10.1074/jbc.m112.372052] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In Escherichia coli, ATP-DnaA multimers formed on the replication origin oriC promote duplex unwinding, which leads to helicase loading. Based on a detailed functional analysis of the oriC sequence motifs, we previously proposed that the left half of oriC forms an ATP-DnaA subcomplex competent for oriC unwinding, whereas the right half of oriC forms a distinct ATP-DnaA subcomplex that facilitates helicase loading. However, the molecular basis for the functional difference between these ATP-DnaA subcomplexes remains unclear. By analyzing a series of novel DnaA mutants, we found that structurally distinct DnaA multimers form on each half of oriC. DnaA AAA+ domain residues Arg-227 and Leu-290 are specifically required for oriC unwinding. Notably, these residues are required for the ATP-DnaA-specific structure of DnaA multimers in complex with the left half of oriC but not for that with the right half. These results support the idea that the ATP-DnaA multimers formed on oriC are not uniform and that they can adopt different conformations. Based on a structural model, we propose that Arg-227 and Leu-290 play a crucial role in inter-ATP-DnaA interaction and are a prerequisite for the formation of unwinding-competent DnaA subcomplexes on the left half of oriC. These residues are not required for the interaction with DnaB, nucleotide binding, or regulatory DnaA-ATP hydrolysis, which further supports their important role in inter-DnaA interaction. The corresponding residues are evolutionarily conserved and are required for unwinding in the initial complexes of Thermotoga maritima, an ancient hyperthermophile. Therefore, our findings suggest a novel and common mechanism for ATP-DnaA-dependent activation of initial complexes.
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Affiliation(s)
- Shogo Ozaki
- Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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Hossain M, Stillman B. Meier-Gorlin syndrome mutations disrupt an Orc1 CDK inhibitory domain and cause centrosome reduplication. Genes Dev 2012; 26:1797-810. [PMID: 22855792 DOI: 10.1101/gad.197178.112] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Like DNA replication, centrosomes are licensed to duplicate once per cell division cycle to ensure genetic stability. In addition to regulating DNA replication, the Orc1 subunit of the human origin recognition complex controls centriole and centrosome copy number. Here we report that Orc1 harbors a PACT centrosome-targeting domain and a separate domain that differentially inhibits the protein kinase activities of Cyclin E-CDK2 and Cyclin A-CDK2. A cyclin-binding motif (Cy motif) is required for Orc1 to bind Cyclin A and inhibit Cyclin A-CDK2 kinase activity but has no effect on Cyclin E-CDK2 kinase activity. In contrast, Orc1 inhibition of Cyclin E-CDK2 kinase activity occurs by a different mechanism that is affected by Orc1 mutations identified in Meier-Gorlin syndrome patients. The cyclin/CDK2 kinase inhibitory domain of Orc1, when tethered to the PACT domain, localizes to centrosomes and blocks centrosome reduplication. Meier-Gorlin syndrome mutations that disrupt Cyclin E-CDK2 kinase inhibition also allow centrosome reduplication. Thus, Orc1 contains distinct domains that control centrosome copy number and DNA replication. We suggest that the Orc1 mutations present in some Meier-Gorlin syndrome patients contribute to the pronounced microcephaly and dwarfism observed in these individuals by altering centrosome duplication in addition to DNA replication defects.
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Affiliation(s)
- Manzar Hossain
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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34
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Sun J, Kawakami H, Zech J, Speck C, Stillman B, Li H. Cdc6-induced conformational changes in ORC bound to origin DNA revealed by cryo-electron microscopy. Structure 2012; 20:534-44. [PMID: 22405012 DOI: 10.1016/j.str.2012.01.011] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 01/16/2012] [Accepted: 01/17/2012] [Indexed: 01/21/2023]
Abstract
The eukaryotic origin recognition complex (ORC) interacts with and remodels origins of DNA replication prior to initiation in S phase. Here, we report a single-particle cryo-EM-derived structure of the supramolecular assembly comprising Saccharomyces cerevisiae ORC, the replication initiation factor Cdc6, and double-stranded ARS1 origin DNA in the presence of ATPγS. The six subunits of ORC are arranged as Orc1:Orc4:Orc5:Orc2:Orc3, with Orc6 binding to Orc2. Cdc6 binding changes the conformation of ORC, in particular reorienting the Orc1 N-terminal BAH domain. Segmentation of the 3D map of ORC-Cdc6 on DNA and docking with the crystal structure of the homologous archaeal Orc1/Cdc6 protein suggest an origin DNA binding model in which the DNA tracks along the interior surface of the crescent-like ORC. Thus, ORC bends and wraps the DNA. This model is consistent with the observation that binding of a single Cdc6 extends the ORC footprint on origin DNA from both ends.
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Affiliation(s)
- Jingchuan Sun
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
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35
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Blitzblau HG, Chan CS, Hochwagen A, Bell SP. Separation of DNA replication from the assembly of break-competent meiotic chromosomes. PLoS Genet 2012; 8:e1002643. [PMID: 22615576 PMCID: PMC3355065 DOI: 10.1371/journal.pgen.1002643] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 02/17/2012] [Indexed: 01/10/2023] Open
Abstract
The meiotic cell division reduces the chromosome number from diploid to haploid to form gametes for sexual reproduction. Although much progress has been made in understanding meiotic recombination and the two meiotic divisions, the processes leading up to recombination, including the prolonged pre-meiotic S phase (meiS) and the assembly of meiotic chromosome axes, remain poorly defined. We have used genome-wide approaches in Saccharomyces cerevisiae to measure the kinetics of pre-meiotic DNA replication and to investigate the interdependencies between replication and axis formation. We found that replication initiation was delayed for a large number of origins in meiS compared to mitosis and that meiotic cells were far more sensitive to replication inhibition, most likely due to the starvation conditions required for meiotic induction. Moreover, replication initiation was delayed even in the absence of chromosome axes, indicating replication timing is independent of the process of axis assembly. Finally, we found that cells were able to install axis components and initiate recombination on unreplicated DNA. Thus, although pre-meiotic DNA replication and meiotic chromosome axis formation occur concurrently, they are not strictly coupled. The functional separation of these processes reveals a modular method of building meiotic chromosomes and predicts that any crosstalk between these modules must occur through superimposed regulatory mechanisms.
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Affiliation(s)
- Hannah G. Blitzblau
- Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts, United States of America
| | - Clara S. Chan
- Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Andreas Hochwagen
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts, United States of America
- Department of Biology, New York University, New York, New York, United States of America
| | - Stephen P. Bell
- Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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36
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Calderano SG, de Melo Godoy PD, Motta MCM, Mortara RA, Schenkman S, Elias MC. Trypanosoma cruzi DNA replication includes the sequential recruitment of pre-replication and replication machineries close to nuclear periphery. Nucleus 2012; 2:136-45. [PMID: 21738836 DOI: 10.4161/nucl.2.2.15134] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 02/03/2011] [Accepted: 02/11/2011] [Indexed: 11/19/2022] Open
Abstract
In eukaryotes, many nuclear processes are spatially compartmentalized. Previously, we have shown that in Trypanosoma cruzi, an early-divergent eukaryote, DNA replication occurs at the nuclear periphery where chromosomes remain constrained during the S phase of the cell cycle. We followed Orc1/Cdc6, a pre-replication machinery component and the proliferating cell nuclear antigen (PCNA), a component of replication machinery, during the cell cycle of this protozoon. We found that, at the G(1) stage, TcOrc1/Cdc6 and TcPCNA are dispersed throughout the nuclear space. During the G(1)/S transition, TcOrc1/Cdc6 migrates to a region close to nuclear periphery. At the onset of S phase, TcPCNA is loaded onto the DNA and remains constrained close to nuclear periphery. Finally, in G(2), mitosis and cytokinesis, TcOrc1/Cdc6 and TcPCNA are dispersed throughout the nuclear space. Based on these findings, we propose that DNA replication in T. cruzi is accomplished by the organization of functional machineries in a spatial-temporal manner.
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Affiliation(s)
- Simone Guedes Calderano
- Laboratório de Parasitologia, Instituto Butantan, Universidade Federal de São Paulo, São Paulo, Brazil
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37
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Abstract
One of the mechanisms controlling the initiation of DNA replication is the dynamic interaction between Cdt1, which promotes assembly of the pre-replication license complex, and Geminin, which inhibits it. Specifically, Cdt1 cooperates with the cell cycle protein Cdc6 to promote loading of the minichromosome maintenance helicases (MCM) onto the chromatin-bound origin recognition complex (ORC), by directly interacting with the MCM complex, and by modulating histone acetylation and inducing chromatin unfolding. Geminin, on the other hand, prevents the loading of the MCM onto the ORC both by directly binding to Cdt1, and by modulating Cdt1 stability and activity. Protein levels of Geminin and Cdt1 are tightly regulated through the cell cycle, and the Cdt1-Geminin complex likely acts as a molecular switch that can enable or disable the firing of each origin of replication. In this review we summarize structural studies of Cdt1 and Geminin and subsequent insights into how this molecular switch may function to ensure DNA is faithfully replicated only once during S phase of each cell cycle.
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Affiliation(s)
- Christophe Caillat
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
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38
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Schuck S, Stenlund A. Mechanistic analysis of local ori melting and helicase assembly by the papillomavirus E1 protein. Mol Cell 2011; 43:776-87. [PMID: 21884978 DOI: 10.1016/j.molcel.2011.06.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 05/22/2011] [Accepted: 06/28/2011] [Indexed: 11/16/2022]
Abstract
Preparation of DNA templates for replication requires opening of the duplex to expose single-stranded (ss) DNA. The locally melted DNA is required for replicative DNA helicases to initiate unwinding. How local melting is generated in eukaryotic replicons is unknown, but initiator proteins from a handful of eukaryotic viruses can perform this function. Here we dissect the local melting process carried out by the papillomavirus E1 protein. We characterize the melting process kinetically and identify mutations in the E1 helicase and in the ori that arrest the local melting process. We show that a subset of these mutants have specific defects for melting of the center of the ori containing the binding sites for E1 and demonstrate that these mutants fail to untwist the ori DNA. This understanding of how E1 generates local melting suggests possible mechanisms for local melting in other replicons.
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Affiliation(s)
- Stephen Schuck
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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39
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Verma SC, Lu J, Cai Q, Kosiyatrakul S, McDowell ME, Schildkraut CL, Robertson ES. Single molecule analysis of replicated DNA reveals the usage of multiple KSHV genome regions for latent replication. PLoS Pathog 2011; 7:e1002365. [PMID: 22072974 PMCID: PMC3207954 DOI: 10.1371/journal.ppat.1002365] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Accepted: 09/22/2011] [Indexed: 12/17/2022] Open
Abstract
Kaposi's sarcoma associated herpesvirus (KSHV), an etiologic agent of Kaposi's sarcoma, Body Cavity Based Lymphoma and Multicentric Castleman's Disease, establishes lifelong latency in infected cells. The KSHV genome tethers to the host chromosome with the help of a latency associated nuclear antigen (LANA). Additionally, LANA supports replication of the latent origins within the terminal repeats by recruiting cellular factors. Our previous studies identified and characterized another latent origin, which supported the replication of plasmids ex-vivo without LANA expression in trans. Therefore identification of an additional origin site prompted us to analyze the entire KSHV genome for replication initiation sites using single molecule analysis of replicated DNA (SMARD). Our results showed that replication of DNA can initiate throughout the KSHV genome and the usage of these regions is not conserved in two different KSHV strains investigated. SMARD also showed that the utilization of multiple replication initiation sites occurs across large regions of the genome rather than a specified sequence. The replication origin of the terminal repeats showed only a slight preference for their usage indicating that LANA dependent origin at the terminal repeats (TR) plays only a limited role in genome duplication. Furthermore, we performed chromatin immunoprecipitation for ORC2 and MCM3, which are part of the pre-replication initiation complex to determine the genomic sites where these proteins accumulate, to provide further characterization of potential replication initiation sites on the KSHV genome. The ChIP data confirmed accumulation of these pre-RC proteins at multiple genomic sites in a cell cycle dependent manner. Our data also show that both the frequency and the sites of replication initiation vary within the two KSHV genomes studied here, suggesting that initiation of replication is likely to be affected by the genomic context rather than the DNA sequences.
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Affiliation(s)
- Subhash C. Verma
- Department of Microbiology & Immunology, University of Nevada, Reno, School of Medicine, Center for Molecular Medicine, Reno, Nevada, United States of America
| | - Jie Lu
- Department of Microbiology and Tumor Virology Program of the Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Qiliang Cai
- Department of Microbiology and Tumor Virology Program of the Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Settapong Kosiyatrakul
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Maria E. McDowell
- Department of Microbiology & Immunology, University of Nevada, Reno, School of Medicine, Center for Molecular Medicine, Reno, Nevada, United States of America
| | - Carl L. Schildkraut
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Erle S. Robertson
- Department of Microbiology and Tumor Virology Program of the Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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40
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Duderstadt KE, Chuang K, Berger JM. DNA stretching by bacterial initiators promotes replication origin opening. Nature 2011; 478:209-13. [PMID: 21964332 PMCID: PMC3192921 DOI: 10.1038/nature10455] [Citation(s) in RCA: 151] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Accepted: 08/12/2011] [Indexed: 11/10/2022]
Abstract
Many replication initiators form higher-order oligomers that process host replication origins to promote replisome formation. In addition to dedicated duplex-DNA-binding domains, cellular initiators possess AAA+ (ATPases associated with various cellular activities) elements that drive functions ranging from protein assembly to origin recognition. In bacteria, the AAA+ domain of the initiator DnaA has been proposed to assist in single-stranded DNA formation during origin melting. Here we show crystallographically and in solution that the ATP-dependent assembly of Aquifex aeolicus DnaA into a spiral oligomer creates a continuous surface that allows successive AAA+ domains to bind and extend single-stranded DNA segments. The mechanism of binding is unexpectedly similar to that of RecA, a homologous recombination factor, but it differs in that DnaA promotes a nucleic acid conformation that prevents pairing of a complementary strand. These findings, combined with strand-displacement assays, indicate that DnaA opens replication origins by a direct ATP-dependent stretching mechanism. Comparative studies reveal notable commonalities between the approach used by DnaA to engage DNA substrates and other, nucleic-acid-dependent, AAA+ systems.
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Affiliation(s)
- Karl E. Duderstadt
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kevin Chuang
- Department of Molecular and Cell Biology, California Institute for Quantitative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - James M. Berger
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, California Institute for Quantitative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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41
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Taylor JA, Ouimet MC, Wargachuk R, Marczynski GT. The Caulobacter crescentus chromosome replication origin evolved two classes of weak DnaA binding sites. Mol Microbiol 2011; 82:312-26. [PMID: 21843309 DOI: 10.1111/j.1365-2958.2011.07785.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The Caulobacter crescentus replication initiator DnaA and essential response regulator CtrA compete to control chromosome replication. The C. crescentus replication origin (Cori) contains five strong CtrA binding sites but only two apparent DnaA boxes, termed G-boxes (with a conserved second position G, TGATCCACA). Since clusters of DnaA boxes typify bacterial replication origins, this discrepancy suggested that C. crescentus DnaA recognizes different DNA sequences or compensates with novel DNA-binding proteins. We searched for novel DNA sites by scanning mutagenesis of the most conserved Cori DNA. Autonomous replication assays showed that G-boxes and novel W-boxes (TCCCCA) are essential for replication. Further analyses showed that C. crescentus DnaA binds G-boxes with moderate and W-boxes with very weak affinities significantly below DnaA's capacity for high-affinity Escherichia coli-boxes (TTATCCACA). Cori has five conserved W-boxes. Increasing W-box affinities increases or decreases autonomous replication depending on their strategic positions between the G-boxes. In vitro, CtrA binding displaces DnaA from proximal G-boxes and from distal W-boxes implying CtrA-DnaA competition and DnaA-DnaA cooperation between G-boxes and W-boxes. Similarly, during cell cycle progression, CtrA proteolysis coincides with DnaA binding to Cori. We also observe highly conserved W-boxes in other replication origins lacking E. coli-boxes. Therefore, strategically weak DnaA binding can be a general means of replication control.
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Affiliation(s)
- James A Taylor
- Dept. Microbiology and Immunology, McGill University, 3775 University Street, Montreal, QC, Canada.
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42
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Calderano SG, de Melo Godoy PD, da Cunha JPC, Elias MC. Trypanosome prereplication machinery: a potential new target for an old problem. Enzyme Res 2011; 2011:518258. [PMID: 21755041 PMCID: PMC3112515 DOI: 10.4061/2011/518258] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 03/16/2011] [Accepted: 03/30/2011] [Indexed: 12/17/2022] Open
Abstract
Approximately ten million people suffer from Chagas disease worldwide, caused by Trypanosoma cruzi, with the disease burden predominately focused in Latin America. Sleeping sickness is another serious health problem, caused by Trypanosoma brucei, especially in sub-Saharan countries. Unfortunately, the drugs currently available to treat these diseases have toxic effects and are not effective against all disease phases or parasite strains. Therefore, there is a clear need for the development of novel drugs and drug targets to treat these diseases. We propose the trypanosome prereplication machinery component, Orc1/Cdc6, as a potential target for drug development. In trypanosomes, Orc1/Cdc6 is involved in nuclear DNA replication, and, despite its involvement in such a conserved process, Orc1/Cdc6 is distinct from mammalian Orc1 and Cdc6 proteins. Moreover, RNAi-mediated silencing of trypanosome Orc1/Cdc6 expression in T. brucei decreased cell survival, indicating that Orc1/Cdc6 is critical for trypanosome survival.
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Affiliation(s)
- Simone Guedes Calderano
- Laboratório Especial de Toxinologia Aplicada (LETA) Center for Applied Toxinology (CAT/CEPID), Instituto Butantan, Avenida Vital Brasil 1500, 05503-000 São Paulo, SP, Brazil
| | - Patricia Diogo de Melo Godoy
- Laboratório Especial de Toxinologia Aplicada (LETA) Center for Applied Toxinology (CAT/CEPID), Instituto Butantan, Avenida Vital Brasil 1500, 05503-000 São Paulo, SP, Brazil
| | - Julia Pinheiro Chagas da Cunha
- Laboratório Especial de Toxinologia Aplicada (LETA) Center for Applied Toxinology (CAT/CEPID), Instituto Butantan, Avenida Vital Brasil 1500, 05503-000 São Paulo, SP, Brazil
| | - Maria Carolina Elias
- Laboratório Especial de Toxinologia Aplicada (LETA) Center for Applied Toxinology (CAT/CEPID), Instituto Butantan, Avenida Vital Brasil 1500, 05503-000 São Paulo, SP, Brazil
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43
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Guernsey DL, Matsuoka M, Jiang H, Evans S, Macgillivray C, Nightingale M, Perry S, Ferguson M, LeBlanc M, Paquette J, Patry L, Rideout AL, Thomas A, Orr A, McMaster CR, Michaud JL, Deal C, Langlois S, Superneau DW, Parkash S, Ludman M, Skidmore DL, Samuels ME. Mutations in origin recognition complex gene ORC4 cause Meier-Gorlin syndrome. Nat Genet 2011; 43:360-4. [PMID: 21358631 DOI: 10.1038/ng.777] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Accepted: 01/14/2011] [Indexed: 12/17/2022]
Abstract
Meier-Gorlin syndrome is a rare autosomal recessive genetic condition whose primary clinical hallmarks include small stature, small external ears and small or absent patellae. Using marker-assisted mapping in multiple families from a founder population and traditional coding exon sequencing of positional candidate genes, we identified three different mutations in the gene encoding ORC4, a component of the eukaryotic origin recognition complex, in five individuals with Meier-Gorlin syndrome. In two such individuals that were negative for mutations in ORC4, we found potential mutations in ORC1 and CDT1, two other genes involved in origin recognition. ORC4 is well conserved in eukaryotes, and the yeast equivalent of the human ORC4 missense mutation was shown to be pathogenic in functional assays of cell growth. This is the first report, to our knowledge, of a germline mutation in any gene of the origin recognition complex in a vertebrate organism.
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Affiliation(s)
- Duane L Guernsey
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
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44
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Rangasamy D. An S/MAR-based L1 retrotransposition cassette mediates sustained levels of insertional mutagenesis without suffering from epigenetic silencing of DNA methylation. Epigenetics 2010; 5:601-11. [PMID: 20595816 DOI: 10.4161/epi.5.7.12647] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
L1 is an insertional mutagen that is capable of mediating permanent gene disruption in mammalian genomes. However, currently available L1 retrotransposition vectors exhibit low or unstable transgene expression when expressed in somatic cells and tissues. This restriction limits their potential utility in long-term screening procedures or somatic mutagenesis applications. In this study, we addressed this problem by developing a minicircle, nonviral L1 retrotransposition vector using a scaffold/matrix attachment region (S/MAR) in the vector backbone and evaluated its utility in human cell lines. The S/MAR-based L1 retrotransposition vector provides stable, elevated levels of L1 expression compared to the currently used EBNA1-based L1 vector. In addition, the S/MAR elements effectively mediate sustained levels of L1 retrotransposition in prolonged cell culturing without suffering from epigenetic silencing by DNA methylation or from vector integration problems even in the absence of selection pressure. These findings indicate that the simple inclusion of S/MAR in the vector backbone increased levels of L1 expression and retrotransposition that can be used as an effective tool to generate insertional mutagenesis in large-scale somatic mutagenesis applications in mammalian cells.
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Affiliation(s)
- Danny Rangasamy
- The John Curtin School of Medical Research, Australian National University, Canberra, Australia.
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45
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Müller P, Park S, Shor E, Huebert DJ, Warren CL, Ansari AZ, Weinreich M, Eaton ML, MacAlpine DM, Fox CA. The conserved bromo-adjacent homology domain of yeast Orc1 functions in the selection of DNA replication origins within chromatin. Genes Dev 2010; 24:1418-33. [PMID: 20595233 PMCID: PMC2895200 DOI: 10.1101/gad.1906410] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Accepted: 05/11/2010] [Indexed: 12/15/2022]
Abstract
The origin recognition complex (ORC) binds to the specific positions on chromosomes that serve as DNA replication origins. Although ORC is conserved from yeast to humans, the DNA sequence elements that specify ORC binding are not. In particular, metazoan ORC shows no obvious DNA sequence specificity, whereas yeast ORC binds to a specific DNA sequence within all yeast origins. Thus, whereas chromatin must play an important role in metazoan ORC's ability to recognize origins, it is unclear whether chromatin plays a role in yeast ORC's recognition of origins. This study focused on the role of the conserved N-terminal bromo-adjacent homology domain of yeast Orc1 (Orc1BAH). Recent studies indicate that BAH domains are chromatin-binding modules. We show that the Orc1BAH domain was necessary for ORC's stable association with yeast chromosomes, and was physiologically relevant to DNA replication in vivo. This replication role was separable from the Orc1BAH domain's previously defined role in transcriptional silencing. Genome-wide analyses of ORC binding in ORC1 and orc1bahDelta cells revealed that the Orc1BAH domain contributed to ORC's association with most yeast origins, including a class of origins highly dependent on the Orc1BAH domain for ORC association (orc1bahDelta-sensitive origins). Orc1bahDelta-sensitive origins required the Orc1BAH domain for normal activity on chromosomes and plasmids, and were associated with a distinct local nucleosome structure. These data provide molecular insights into how the Orc1BAH domain contributes to ORC's selection of replication origins, as well as new tools for examining conserved mechanisms governing ORC's selection of origins within eukaryotic chromosomes.
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Affiliation(s)
- Philipp Müller
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Sookhee Park
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Erika Shor
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Dana J. Huebert
- Program in Cellular and Molecular Biology, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Christopher L. Warren
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Aseem Z. Ansari
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Michael Weinreich
- Laboratory for Chromosome Replication, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - Matthew L. Eaton
- Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - David M. MacAlpine
- Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Catherine A. Fox
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Program in Cellular and Molecular Biology, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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Duderstadt KE, Mott ML, Crisona NJ, Chuang K, Yang H, Berger JM. Origin remodeling and opening in bacteria rely on distinct assembly states of the DnaA initiator. J Biol Chem 2010; 285:28229-39. [PMID: 20595381 DOI: 10.1074/jbc.m110.147975] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The initiation of DNA replication requires the melting of chromosomal origins to provide a template for replisomal polymerases. In bacteria, the DnaA initiator plays a key role in this process, forming a large nucleoprotein complex that opens DNA through a complex and poorly understood mechanism. Using structure-guided mutagenesis, biochemical, and genetic approaches, we establish an unexpected link between the duplex DNA-binding domain of DnaA and the ability of the protein to both self-assemble and engage single-stranded DNA in an ATP-dependent manner. Intersubunit cross-talk between this domain and the DnaA ATPase region regulates this link and is required for both origin unwinding in vitro and initiator function in vivo. These findings indicate that DnaA utilizes at least two different oligomeric conformations for engaging single- and double-stranded DNA, and that these states play distinct roles in controlling the progression of initiation.
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Affiliation(s)
- Karl E Duderstadt
- Biophysics Graduate Group, California Institute for Quantitative Biology, University of California, Berkeley, California 94720, USA
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de Moura APS, Retkute R, Hawkins M, Nieduszynski CA. Mathematical modelling of whole chromosome replication. Nucleic Acids Res 2010; 38:5623-33. [PMID: 20457753 PMCID: PMC2943597 DOI: 10.1093/nar/gkq343] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
All chromosomes must be completely replicated prior to cell division, a requirement that demands the activation of a sufficient number of appropriately distributed DNA replication origins. Here we investigate how the activity of multiple origins on each chromosome is coordinated to ensure successful replication. We present a stochastic model for whole chromosome replication where the dynamics are based upon the parameters of individual origins. Using this model we demonstrate that mean replication time at any given chromosome position is determined collectively by the parameters of all origins. Combining parameter estimation with extensive simulations we show that there is a range of model parameters consistent with mean replication data, emphasising the need for caution in interpreting such data. In contrast, the replicated-fraction at time points through S phase contains more information than mean replication time data and allowed us to use our model to uniquely estimate many origin parameters. These estimated parameters enable us to make a number of predictions that showed agreement with independent experimental data, confirming that our model has predictive power. In summary, we demonstrate that a stochastic model can recapitulate experimental observations, including those that might be interpreted as deterministic such as ordered origin activation times.
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Affiliation(s)
- Alessandro P S de Moura
- Department of Physics, University of Aberdeen, Aberdeen AB24 3UE and School of Biology, University of Nottingham, Nottingham NG7 2UH, UK
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48
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Spiesser TW, Diener C, Barberis M, Klipp E. What influences DNA replication rate in budding yeast? PLoS One 2010; 5:e10203. [PMID: 20436919 PMCID: PMC2860512 DOI: 10.1371/journal.pone.0010203] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Accepted: 03/12/2010] [Indexed: 11/18/2022] Open
Abstract
Background DNA replication begins at specific locations called replication origins, where helicase and polymerase act in concert to unwind and process the single DNA filaments. The sites of active DNA synthesis are called replication forks. The density of initiation events is low when replication forks travel fast, and is high when forks travel slowly. Despite the potential involvement of epigenetic factors, transcriptional regulation and nucleotide availability, the causes of differences in replication times during DNA synthesis have not been established satisfactorily, yet. Methodology/Principal Findings Here, we aimed at quantifying to which extent sequence properties contribute to the DNA replication time in budding yeast. We interpreted the movement of the replication machinery along the DNA template as a directed random walk, decomposing influences on DNA replication time into sequence-specific and sequence-independent components. We found that for a large part of the genome the elongation time can be well described by a global average replication rate, thus by a single parameter. However, we also showed that there are regions within the genomic landscape of budding yeast with highly specific replication rates, which cannot be explained by global properties of the replication machinery. Conclusion/Significance Computational models of DNA replication in budding yeast that can predict replication dynamics have rarely been developed yet. We show here that even beyond the level of initiation there are effects governing the replication time that can not be explained by the movement of the polymerase along the DNA template alone. This allows us to characterize genomic regions with significantly altered elongation characteristics, independent of initiation times or sequence composition.
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Affiliation(s)
- Thomas W. Spiesser
- Theoretical Biophysics, Institute for Biology, Humboldt University Berlin, Berlin, Germany
| | - Christian Diener
- Theoretical Biophysics, Institute for Biology, Humboldt University Berlin, Berlin, Germany
| | - Matteo Barberis
- Theoretical Biophysics, Institute for Biology, Humboldt University Berlin, Berlin, Germany
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- * E-mail: (MB); (EK)
| | - Edda Klipp
- Theoretical Biophysics, Institute for Biology, Humboldt University Berlin, Berlin, Germany
- * E-mail: (MB); (EK)
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Kawakami H, Katayama T. DnaA, ORC, and Cdc6: similarity beyond the domains of life and diversity. Biochem Cell Biol 2010; 88:49-62. [PMID: 20130679 DOI: 10.1139/o09-154] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
To initiate chromosomal DNA replication, specific proteins bind to the replication origin region and form multimeric and dynamic complexes. Bacterial DnaA, the eukaryotic origin recognition complex (ORC), and Cdc6 proteins, most of which include an AAA+(-like) motif, play crucial roles in replication initiation. The importance of ATP binding and hydrolysis in these proteins has recently become recognized. ATP binding of Escherichia coli DnaA is required for the formation of the activated form of a DnaA multimer on the replication origin. The ATP-DnaA multimer can unwind duplex DNA in an origin-dependent manner, which is supported by various specific functions of several AAA+ motifs. DnaA-ATP hydrolysis is stimulated after initiation, repressing extra initiations, and sustaining once-per-cell cycle replication. ATP binding of ORC and Cdc6 in Saccharomyces cerevisiae is required for heteromultimeric complex formation and specific DNA binding. ATP hydrolysis of these proteins is important for the efficient loading of the minichromosome maintenance protein complex, a component of the putative replicative helicase. In this review, we discuss the roles of DnaA, ORC, and Cdc6 in replication initiation and its regulation. We also summarize the functional features of the AAA+ domains of these proteins, and the functional divergence of ORC in chromosomal dynamics.
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Affiliation(s)
- Hironori Kawakami
- Cold Spring Harbor Laboratory, 1 Bungtown Rd., Cold Spring Harbor, NY 11724, USA.
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50
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Ilves I, Petojevic T, Pesavento JJ, Botchan MR. Activation of the MCM2-7 helicase by association with Cdc45 and GINS proteins. Mol Cell 2010; 37:247-58. [PMID: 20122406 DOI: 10.1016/j.molcel.2009.12.030] [Citation(s) in RCA: 425] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Revised: 12/02/2009] [Accepted: 12/15/2009] [Indexed: 11/27/2022]
Abstract
MCM2-7 proteins provide essential helicase functions in eukaryotes at chromosomal DNA replication forks. During the G1 phase of the cell cycle, they remain loaded on DNA but are inactive. We have used recombinant methods to show that the Drosophila MCM2-7 helicase is activated in complex with Cdc45 and the four GINS proteins (CMG complex). Biochemical activities of the MCM AAA+ motor are altered and enhanced through such associations: ATP hydrolysis rates are elevated by two orders of magnitude, helicase activity is robust on circular templates, and affinity for DNA substrates is improved. The GINS proteins contribute to DNA substrate affinity and bind specifically to the MCM4 subunit. All pairwise associations among GINS, MCMs, and Cdc45 were detected, but tight association takes place only in the CMG. The onset of DNA replication and unwinding may thus occur through allosteric changes in MCM2-7 affected by the association of these ancillary factors.
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Affiliation(s)
- Ivar Ilves
- Department of Molecular and Cell Biology, Division of Biochemistry and Molecular Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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