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DNA REPLICATION - CURRENT ADVANCES

DNA REPLICATION
Edited by Hervé Seligmann .
708 pages .

This book includes a selection of authoritative reviews and contributions in the general 
field of DNA replication. One of the characteristics of this collection is that it touches a 
number of diverse domains, fromthe stereochemistry of DNA (chapters by Ostrovskii 
and Kadyshevich, Xu, Ho and Carter, Wang et al.), its physicochemical properties as 
determining the dynamics of mutations (chapters by Guo and Ning, Seligmann), the 
epidemiology of some replication-associated diseases (chapters by Kurg, Urata et al., 
Zekan et al., Gouveris et al.), and interactions with various protein complexes 
responsible for its replication and regulation of that process (most other chapters).
Nevertheless, some subjects can be felt as missing or relatively neglected. For example, 
the functional protein family of DNA polymerases, given its central role in DNA 
replication, is fairly little mentioned, and only the famous DNA polymerase is given 
some attention (chapter by Apostolova and Esplugues). An analysis of fidelities of 
DNA polymerases would have been an adequate chapter subject in the scope of this 
book, especially if integrated with other, non-enzymatic processes leading to 
mutations, but current interests of the contributors did not focus on this. Similarly, 
viral DNA replication is relatively underrepresented in this volume, as compared to
and despite its crucial contribution to the study of DNA replication in general 
(Wussow et al.). The book’s contents therefore reflect mainly current trends on the 
subject of DNA replication.
Some chapters describe very surprising analyses, in the sense that they touch 
fundamental properties of DNA. One could have believed that basic DNA 
fundamentals are assessed and do not include major undiscovered or unresolved 
points after more than half a century of intensive study and exploration by the 
scientific community. Especially because this community currently happens to be the 
largest of its kind human history has ever known, and that the study of DNA involves 
major discoveries in terms of technical importance, outcompeted in importance only 
by discoveries such as that of fire, the number zero, the conceptualization of causeeffect 
relations or metallurgy .
Among these “new” DNA properties, for example, Wang et al. show in their chapter 
that the phosphate DNA backbone sometimes includes sulphur atoms, instead of 
oxygen, which is probably frequently used as a processing signal. Another major, 
perhaps controversial, issue is that of the orientation of the DNA’s double helix 
(chapter by Xu) in which the author suggests that the double helix might be 
occasionally left-handed. The issue of left-handed DNA as a way of reducing physical 
tension in DNA molecules is in a way predicted by a number of other known 
phenomena, such as the inverse association between replication rates and distances 
between replication forks mentioned in the chapter by Guzmán et al. As amply 
explained in the chapter by Xu, this potential discovery, though contradicting 
commonly accepted concepts on DNA structure, does not revolutionize our 
understanding of DNA. It rather is a useful amendment to the model of DNA
structure and function. Despite this, its publication necessitated a major, 
multidecennial effort on behalf of the author. This reflects more the theologicalaristotelian 
origins of the modern scientific process of expansion of human knowledge 
through authority and sometimes censorship by a few rather than the current, ideally 
transparent, open (=published) evaluation and discussion of evidence and its 
interpretation, available to and by each one interested. The fact that some other
chapters report no less or even more revolutionary findings on DNA, underlines the 
need to keep an open mind attitude, even towards commonly “accepted truths” on 
presumably well-known subjects. The deep conviction that no human knowledge is 
perfect, but only perfectible, should function as a fair safeguard in this respect. It is, in 
my opinion, a simple but effective way to prevent as much as possible the unavoidable 
psychological barriers that impede on the advancement of our understanding of 
natural phenomena through open discussion.
But perhaps the most astonishing and challenging novelty in this book is the approach 
of DNA structure and chemical dynamics by focusing on its interactions with its 
natural solvent, the water molecules, and the changes in water concentrations through 
the cell’s life cycle (chapter by Ostrovskii and Kadyshevich). This most interesting 
hypothesis develops a concept that escapes conceptions established through the force 
of habit, which frequently result in dominant, yet unproven intuitive truths. This 
hypothesis will doubtlessly produce new, deep insights into every level of DNAassociated 
processes, and probably also general cell physiology, if given the deserved 
consideration and further developed. The approach in that chapter integrates 
processes associated with DNA and its structure with more basic physical properties 
at a lower scale of natural phenomena, namely the multimolecular dynamical 
structure of water. DNA properties can also be integrated with higher-scale 
phenomena: Seligmann suggests how whole-organism characteristics associate with 
details of DNA replication. Both chapters touch the issue of regulation of DNA 
replication and transcription, DNA versus RNA synthesis, the two main processes 
involving DNA molecules. The issue of integrating DNA and RNA synthesis is at least
mentioned if not extensively explored by a large number of chapters (i.e Chisamore- 
Rob et al., Huang and Zhang). This suggests that the matter of coregulating DNA and 
RNA syntheses is very likely to be developed further by future activities in various 
subdisciplines dealing with DNA replication.
I chose to relatively neglect in this preface the mentioning of studies of the more 
complex organisation of eukaryotic chromosomes and their complex replication 
because this is the topic of the larger portion of this book’s chapters (Matsuura and 
Matsui, Schmidt, Maya et al., McFarlane et al., Sørensen et al., Loyer and Corlu, Kon et 
al., Enserink). Several chapters deal with detection and regulation of eukaryotic 
replication origins (Grutzner and Wright, Kusic-Tisma and Stefanovic, Dalgaard et al., 
Ligasová and Koberna, Thiriet et al.), a matter not well established even in presumably 
simpler genomes (Guzman et al.), without forgetting the matter of DNA-associated 
DNA repair (i.e. Wang, Shen and Zhu). As shown by several chapters in this book, I 
do not think that it is an overstatement to assume that the study of DNA will continue 
for a while to be a leading front of scientific activities.

Hervé Seligmann,
Herpetological Collection National Natural History Collections (NNHC),
The Hebrew University of Jerusalem,
Israel

Center for Ecological and Evolutionary Synthesis,
University of Oslo,
Norway

Department of Life Sciences,
Ben Gurion University,
Israel

CONTENTS :

Part 1 DNA Structure 1


Chapter 1 DNA Structure: Alphabet Soup for the Cellular Soul 3
P. Shing Ho and Megan Carter

Chapter 2 Replication Demands an Amendment 
of the Double Helix 29
You Cheng Xu

Chapter 3 Phosphorothioation: An Unusual Post-Replicative 
Modification on the DNA Backbone 57
Lianrong Wang, Shi Chen and Zixin Deng

Chapter 4 Mitosis and DNA Replication 
and Life Origination Hydrate Hypotheses: Common Physical and Chemical Grounds 75
Ostrovskii Victor E. and Kadyshevich Elena A.

Part 2 Mutations 115


Chapter 5 Strand-specific Composition Bias 
in Bacterial Genomes 117
Feng-Biao Guo and Lu-Wen Ning

Chapter 6 Mutation Patterns Due to Converging Mitochondrial Replication and Transcription Increase Lifespan, and Cause Growth Rate-Longevity Tradeoffs 137
Hervé Seligmann

Chapter 7 Mitochondrial DNA Replication in Health and Disease 167
Nadezda Apostolova and Juan V. Esplugues

Chapter 8 Damage and Replication Stress Responses 183
Haiying Wang, Ping Shen and Wei-Guo Zhu

Part 3 Replication Origins, Forks, Chromatine Organization 201


Chapter 9 Relationship between Fork Progression 
and Initiation of Chromosome Replication in E. coli 203
Elena C. Guzmán, Israel Salguero, Carmen Mata Martín, Elena López Acedo, Estrella Guarino, Mª Antonia Sánchez-Romero, Vic Norris and Alfonso Jiménez-Sánchez

Chapter 10 Replication Origin Selection 
and Pre-Replication Complex Assembly 221
Kusic-Tisma Jelena and Stefanovic Dragana

Chapter 11 The Coordination between DNA Replication Initiation 
and Other Cell Cycle Events 233
Shijiao Huang and Chuanmao Zhang

Chapter 12 The Organisation of Replisomes 253
Anna Ligasová and Karel Koberna

Chapter 13 Eukaryotic Replication Barriers: 
How, Why and Where Forks Stall 269
Jacob Z. Dalgaard, Emma L. Godfrey and Ramsay J. MacFarlane

Chapter 14 Control of Telomeric DNA Replication: 
Genetics, Molecular Biology, and Physiology 305
Akira Matsuura and Aiko Matsui

Chapter 15 Telomere Maintenance 
in Organisms without Telomerase 323
James M. Mason, Hemakumar M. Reddy and Radmila Capkova Frydrychova

Chapter 16 Eukaryote DNA Replication and Recombination: 
an Intimate Association 347
Ramsay J. McFarlane, Khalid Al-Zeer and Jacob Z. Dalgaard

Part 4 The Cell Cycle and Replication 389


Chapter 17 Cell Cycle Regulation of 
DNA Replication in S. cerevisiae 391
Jorrit M. Enserink

Chapter 18 Free Histones and the Cell Cycle 409
Douglas Maya, Macarena Morillo-Huesca, Sebastián Chávez and Mari-Cruz Muñoz-Centeno

Chapter 19 Involvement of Linker Histones 
in the Regulation of Replication Timing 427
Christophe Thiriet, Gwenola Auda-Boucher and Yvonnick Chéraud

Chapter 20 Replication Timing: Evolution, Nuclear Organization and Relevance for Human Disease 437
Megan Lynne Wright and Frank Grützner

Chapter 21 The Silencing Face of DNA Replication: Gene Repression 
Mediated by DNA Replication Factors 467
Patricia Chisamore-Robert, Daniel Jeffery and Krassimir Yankulov

Part 5 Proteins in Replication 485

Chapter 22 Faithful DNA Replication Requires Regulation 
of CDK Activity by Checkpoint Kinases 487
Claus Storgaard Sørensen, Halfdan Beck, Viola Nähse-Kumpf and Randi G. Syljuåsen

Chapter 23 Regulation of the G1/S Transition in Adult Liver: 
Expression and Activation of the Cyclin Dependent Kinase Cdk1 in Differentiated Hepatocytes is Controlled by Extracellular Signals and is Crucial for Commitment to DNA Replication 511
Loyer Pascal and Corlu Anne

Chapter 24 Binding of Human MCM-BP with MCM2-7 Proteins 549
Ryoko Kon, Shunsuke Kusunoki, Naohito Nozaki and Yukio Ishimi

Chapter 25 DNA Replication in Animal Systems 
Lacking Thioredoxin Reductase I 565
Edward E. Schmidt

Part 6 Replication and Diseases 585


Chapter 26 Prevalence of Reactivation 
of Hepatitis B Virus DNA Replication in Rheumatoid Arthritis Patients 587
Yukitomo Urata, Ryoko Uesato and Dai Tanaka

Chapter 27 Oncogenic Aspects of HPV Infections 
of the Female Genital Tract 595
Josko Zekan, Maja Sirotkovic-Skerlev and Mihael Skerlev

Chapter 28 The Role of E2 Proteins in 
Papillomavirus DNA Replication 613
Reet Kurg
Chapter 29 Topoisomerase I and II Expression in Recurrent Colorectal Cancer Cells: A Dubious Matter 639
Panagiotis Gouveris, Elias Skopelitis and Nicolas Tsavaris

Chapter 30 Bacterial Genetics of Large Mammalian 
DNA Viruses: Bacterial Artificial Chromosomes as a Prerequisite for Efficiently Studying Viral DNA Replication and Functions 669
Felix Wussow, Tanja Spieckermann, Anne Brunnemann, Linda Hüske, Tuna Toptan and Helmut Fickenscher .


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