THE MECHANISMS OF DNA REPLICATION Edited by David Stuart The Mechanisms of DNA Replication http://dx.doi.org/10.5772/3433 Edited by David Stuart Contributors Andrey Aleksandrovich Grach, Lynne Cox, Penelope Mason, Christophe Thiriet, Angélique Galvani, Agustino Martinez- Antonio, Laura Espindola-Serna, César Quiñones-Valles, Susan Forsburg, Sarah Sabatinos, Radmila Capkova Frydrychova, James Mason, Naoki Sato, Takashi Moriyama, Apolonija Bedina Zavec, Amine Aloui, Herve Seligmann, Yoshizumi Ishino, Takeo Kubota, Maria Vittoria Di Tomaso, Alba Guarne, Lindsay Matthews, David Stuart, Douglas Maya, Mari Cruz Muñoz-Centeno, Macarena Morillo-Huesca, Sebastian Chavez, Lidia Delgado Ramos, Dianne C. 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No responsibility is accepted for the accuracy of information contained in the published chapters. The publisher assumes no responsibility for any damage or injury to persons or property arising out of the use of any materials, instructions, methods or ideas contained in the book. Publishing Process Manager Ana Pantar Technical Editor InTech DTP team Cover InTech Design team First published February, 2013 Printed in Croatia A free online edition of this book is available at www.intechopen.com Additional hard copies can be obtained from orders@intechopen.com The Mechanisms of DNA Replication, Edited by David Stuart p. cm. ISBN 978-953-51-0991-4 free online editions of InTech Books and Journals can be found at www.intechopen.com Contents Preface IX Section 1 Machines that Drive DNA Replication 1 Chapter 1 Pulling the Trigger to Fire Origins of DNA Replication 3 David Stuart Chapter 2 Replicative Helicases as the Central Organizing Motor Proteins in the Molecular Machines of the Elongating Eukaryotic Replication Fork 29 John C. Fisk, Michaelle D. Chojnacki and Thomas Melendy Chapter 3 The MCM and RecQ Helicase Families: Ancient Roles in DNA Replication and Genomic Stability Lead to Distinct Roles in Human Disease 59 Dianne C. Daniel*, Ayuna V. Dagdanova and Edward M. Johnson Chapter 4 DNA Replication in Archaea, the Third Domain of Life 91 Yoshizumi Ishino and Sonoko Ishino Chapter 5 Proposal for a Minimal DNA Auto-Replicative System 127 Agustino Martinez-Antonio, Laura Espindola-Serna and Cesar Quiñones-Valles Chapter 6 Extending the Interaction Repertoire of FHA and BRCT Domains 145 Lindsay A. Matthews and Alba Guarné Chapter 7 Intrinsically Disoredered Proteins in Replication Process 169 Apolonija Bedina Zavec Section 2 Mechanisms that Protect Chromosome Integrity During DNA Replication 191 Chapter 8 Preserving the Replication Fork in Response to Nucleotide Starvation: Evading the Replication Fork Collapse Point 193 Sarah A. Sabatinos and Susan L. Forsburg Chapter 9 The Role of WRN Helicase/Exonuclease in DNA Replication 219 Lynne S. Cox and Penelope A. Mason Section 3 Replication of Organellar Chromosomes 255 Chapter 10 Replicational Mutation Gradients, Dipole Moments, Nearest Neighbour Effects and DNA Polymerase Gamma Fidelity in Human Mitochondrial Genomes 257 Hervé Seligmann Chapter 11 The Plant and Protist Organellar DNA Replication Enzyme POP Showing Up in Place of DNA Polymerase Gamma May Be a Suitable Antiprotozoal Drug Target 287 Takashi Moriyama and Naoki Sato Section 4 Chromatin and Epigenetic Influences on DNA Replication 313 Chapter 12 Roles of Methylation and Sequestration in the Mechanisms of DNA Replication in some Members of the Enterobacteriaceae Family 315 Amine Aloui, Alya El May, Saloua Kouass Sahbani and Ahmed Landoulsi Chapter 13 The Mechanisms of Epigenetic Modifications During DNA Replication 333 Takeo Kubota, Kunio Miyake and Takae Hirasawa Chapter 14 Chromatin Damage Patterns Shift According to Eu/ Heterochromatin Replication 351 María Vittoria Di Tomaso, Pablo Liddle, Laura Lafon-Hughes, Ana Laura Reyes-Ábalos and Gustavo Folle ContentsVI Chapter 15 A Histone Cycle 377 Douglas Maya, Macarena Morillo-Huesca, Lidia Delgado Ramos, Sebastián Chávez and Mari-Cruz Muñoz-Centeno Chapter 16 Replicating – DNA in the Refractory Chromatin Environment 403 Angélique Galvani and Christophe Thiriet Section 5 Telomeres 421 Chapter 17 Telomeres: Their Structure and Maintenance 423 Radmila Capkova Frydrychova and James M. Mason Chapter 18 Telomere Shortening Mechanisms 445 Andrey Grach Contents VII Preface DNA replication is a fundamental part of the life cycle of all organisms. Not surprisingly many aspects of this process display profound conservation across organisms in all domains of life. Successful duplication of the genetic material can decide the life or death of an organ‐ ism. Hence, the integrity of the DNA replication process is paramount and any defects or errors can lead to a myriad of problems ranging from cell death and developmental failure to increased propensity for cancer. The importance of accurately regulating the initiation and progression of DNA synthesis is reflected in the complexity involved in assembling the molecular machines that carry out chromosomal DNA synthesis. Chapters by Ishino & Ishino and Martinez-Antonio et al. dis‐ cuss the process of DNA replication in bacteria and archaea and reveal aspects of the proc‐ ess that are conserved, and aspects that are unique when compared to eukaryotes. The large size of eukaryotic chromosomes presents challenges to accomplishing accurate and timely DNA replication required for cell proliferation. The molecular machines that drive DNA unwinding and chromosomal DNA synthesis are assembled in a multi-step process that allows for many layers of potential regulation to ensure that DNA replication is initiated accurately and only when appropriate. Many of these mechanisms serve double duty to ensure that DNA replication is initiated only once in any given cell cycle. This is essential to ensure that all portions of the genome are replicated but that none are over-re‐ plicated which could lead to the formation of structures at risk for breakage or inappropriate recombination. The assembly and activity of the DNA helicases and“replisome” that unwinds chromosomal DNA and drives DNA replication are reviewed and discussed in chapters by Stuart, Fisk et al., and Daniel, et al. The assembly of these fantastic DNA replication machines depends upon highly specific and exquisitely regulated protein-protein interactions achieved by spe‐ cific interaction domains and a subset of these important interaction domains and mecha‐ nisms are reviewed in chapters by Matthews & Guarne and Zavec. The Integrity of chromosomal DNA replication is a high priority for cells and there are many mechanisms devoted to ensuring that damage to chromosomes is limited during the duplication processes. The intra S-phase checkpoint and mechanisms that retain integrity of the replication forks in the face of conditions that lead to pausing or stalling of the replica‐ tion process is discussed by Sabatinos & Forsburg who also present a model for the conse‐ quences of replication fork collapse during conditions when fork stalling or pausing occurs globally during the replication process. Cox & Mason describe the current state of under‐ standing of the WRN helicase that functions in mammalian cells with emphasis on the effect of loss of function mutations in WRN that lead to Werners Syndrome, a disorder that reca‐ pitulates cellular aging. Cellular DNA is not “naked” but is wrapped and folded into complex three-dimensional structures through its interaction with histone and other chromosomal proteins that com‐ prise chromatin. The histone proteins are subject to an array of post-translational modifica‐ tions that include acetylation, methylation, ubiquitination, and phosphorylation. The DNA- protein complex that is chromatin can exist in a range of structures varying in the degree of condensation and modification state of the proteins. Not surprisingly the state of the chro‐ matin has significant effects on the replication of the DNA, influencing the selection of start sites for DNA replication, the rate of fork progression and extent of fork pausing, as well as having effects on DNA repair and recombination. Chapters by Kubota et al., Aloui et al, Di Tomaso et al., Maya et al., and Galvani & Thiriet review aspects of the relationship of DNA replication to chromatin structure and epigenetic regulation. Not all segments of chromosomal DNA are the same even within the same cell. Some re‐ gions of the chromosomes have unique characteristics required to carry out a particular function. The ends or telomeres of eukaryotic chromosomes are particularly interesting as they present a problem of how to fully replicate both strands without a loss of genetic information. The end replication problem and mechanisms that solve the problem are de‐ scribed in chapters by Grach and by Frydrychova and Mason. This volume outlines and reviews the current state of knowledge on several key aspects of the DNA replication process. This is a critical process in both normal growth and develop‐ ment and in relation to a broad variety of pathological conditions including cancer. Under‐ standing and defining the molecular mechanisms that drive and regulate DNA replication will offer insight into the fundamental process that allows cellular life and proliferation. Ad‐ ditionally, these insights will ultimately offer the hope of controlling diseases like cancer that deregulate DAN replication and cell proliferation. David Stuart Associate Professor Department of Biochemistry University of Alberta Edmonton, Alberta Canada Preface X [...]... to the external surface of the complex Pulling the Trigger to Fire Origins of DNA Replication http://dx.doi.org/10.5772/55319 7 The business end: Polymerases at the origin The final critical steps of origin firing are the recruitment of the replicative polymerases, unwinding of the dsDNA and initiation of DNA synthesis While all cells encode multiple different DNA polymerases the enzymes with the. .. to cancer [3] The integrity of the DNA replication process is ensured partly by DNA repair mechanisms and checkpoint controls However, the primary mechanism that safeguards the DNA replication process is the complex and multi-step process that leads to the assembly and activation of an active replication complex at chromosomal origins of DNA replication The assembly and activation of DNA replication. .. strand while displacing the other strand [65, 159] Achieving this end requires that the dsDNA initially bound be melted and locally unwound allowing release of one strand to the outside surface of the complex and retaining the other within the central channel of the hexamer Although the molecular details 13 14 The Mechanisms of DNA Replication of this process remain unclear some of the current models to... G1-phase prior to the initiation of DNA replication in S-phase The base of the pre-RC is the chromatin bound Orc1-6, which acts as a landing pad for the assembly of a series of other protein factors required to assembly a replication fork and initiate bidirectional DNA synthesis A key requirement for processive DNA synthesis is a dsDNA helicase that can unwind the chromosomal DNA The Orc1-6 itself... orientation, with the dsDNA running through a central channel in the complex [67, 76] The double hexamers can slide on the duplex DNA 7 8 The Mechanisms of DNA Replication creating the potential to load multimers of double hexamer structures at a single ORI This may explain why the number of double hexamers loaded on to the DNA can greatly exceed the number of origins that are activated in the subsequent... by the Anaphase Promoting Complex (APC) in G2-phase [44-48] As Orc1-6 is required for DNA replication initiated at ORIs, the regulated binding of Orc in metazoans provides an additional layer of regulation that may be used to control the initiation of DNA replication 5 6 The Mechanisms of DNA Replication The Orc1-6 proteins act as a marker of chromosomal ORI sites and a platform for the assembly of replication. .. that they simply recognize and bind to the protein -DNA structure formed by the initial unwinding of the ORI DNA Owing to its ssDNA binding capability RPA associates with the RC once unwinding of the ORI DNA is underway; here it assists in stabilizing the nascent replication bubble and provides access for the replicative DNA polymerases [157] All three subunits of DNA Polδ make contact with PCNA and these... activation of the Mcm2-7 complex and unwinding of the DNA depends upon the further ordered addition of the protein factors Sld3, Cdc45, Sld2, Dpb11, the GINS complex (composed of Psf1, Psf2, Psf3, and Sld5], Mcm10, the replicative DNA polymerases Polε, Polδ, and Polα-primase, along with numerous accessory factors The addition of these factors to the ORI bound Orc1-6 – Mcm2-7 is dependent upon the activity of. .. strand DNA synthesis [158] These factors influence the processivity and integrity of DNA synthesis Unwinding the ORI DNA to provide ssDNA as template for the DNA polymerases and to construct bidirectional replication forks is accomplished by the activated Mcm2-7 hexamer in concert with associated proteins Cdc45, GINS, Mcm10 and the replicative DNA polymerases In vitro the Mcm2-7 hexamer unwinds DNA by... topisomerase The helicase activity of the Mcm2-7 hexamers then drives bidirectional dsDNA unwinding and replication fork movement along the chromosome allowing the synthesis of new DNA Initiating DNA replication is a serious event for a cell The chromosomal DNA is rarely more at risk of damage than when it is being unwound and copied During this processes single stranded DNA is revealed and the fork structures . varying in the degree of condensation and modification state of the proteins. Not surprisingly the state of the chro‐ matin has significant effects on the replication of the DNA, influencing the selection. recruitment of the replicative helicase to origins of DNA replication. The replicative helicase in S. cerevisiae is the minichromosome maintenance The Mechanisms of DNA Replication 6 complex (Mcm2-7). The. G1-phase prior to the initiation of DNA replication in S-phase. The base of the pre-RC is the chromatin bound Orc1-6, which acts as a landing pad for the assembly of a series of other protein factors