Download or read book Cellular Contexts and Biochemical Mechanisms of Dna Replication Restart in Escherichia Coli written by Aidan Mair McKenzie and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Before cells can divide, they must first duplicate their genome through DNA replication. DNA replication is facilitated by the coordinated activities of multiprotein complexes (replisomes). While the speed and abilities of replisomes are mystifying, they are frequently met with challenges to their progression. During active replication, Escherichia coli replisomes are estimated to physically dissociate from the genome at least once per cell cycle after colliding with DNA damage or tightly associated proteins. To sustain cellular viability, DNA replication needs to be reinitiated at these abandoned replication forks through the process of DNA replication restart. Here, I present a genetic, biochemical, and structural investigation of DNA replication restart in E. coli to better define its cellular role and mechanistic details. In Chapter 1, I outline the original discovery of replication restart proteins (RRPs) and the evidence used to propose a three-pathway model for DNA replication restart in E. coli (consisting of the PriA/PriB, PriA/PriC, and PriC/Rep pathways). To facilitate replication restart, each pathway recognizes an abandoned replication fork, remodels the fork, recruits additional RRPs, and ultimately reloads the replicative helicase (DnaB) onto the DNA with the help of its helicase loader (DnaC). Chapter 2 describes a genetic study that systematically defined the roles of specific replication restart pathways in a variety of cellular environments. My results helped integrate DNA replication restart within other cellular processes by revealing a tight link between the repair of double-strand breaks and the PriA/PriB restart pathway. In Chapter 3, I exploited a streamlined DnaB reloading system afforded by PriC to structurally define its manner of binding to the replicative helicase/loader (DnaB6/DnaC6) complex. The cryoEM structure identified dramatic conformational changes required to satisfy the binding interface between PriC and DnaB, and subsequent biochemical investigation identified a hydrophobic packing interface as important for sustained binding. A summary of the findings in Chapters 2 and 3, as well as future directions, are provided in Chapter 4. This work probed mechanistic details of DNA replication restart in E. coli by revealing the cellular processes (and missteps) that necessitate replication restart and helped define the biochemical mechanism of PriC-mediated replicative helicase loading.
Download or read book DNA Replication Control in Microbial Cell Factories written by Monika Glinkowska and published by Springer. This book was released on 2014-09-23 with total page 56 pages. Available in PDF, EPUB and Kindle. Book excerpt: This work describes the current knowledge of biochemical mechanisms regulating initiation of DNA replication in Escherichia coli, which focuses on the control of activity of the DnaA protein. Examples of direct linkages between DNA replication and other cellular processes are provided. In addition, similarities of the mechanisms of regulation of DNA replication operating in prokaryotic and eukaryotic cells are identified, and implications for understanding more complex processes, like carcinogenesis are suggested. Studies of recent years provided evidence that regulation of DNA replication in bacteria is more complex than previously anticipated. Multiple layers of control seem to ensure coordination of this process with the increase of cellular mass and the division cycle. Metabolic processes and membrane composition may serve as points where integration of genome replication with growth conditions occurs. It is also likely that coupling of DNA synthesis with cellular metabolism may involve interactions of replication proteins with other macromolecular complexes, responsible for various cellular processes. Thus, the exact set of factors participating in triggering the replication initiation may differ depending on growth conditions. Therefore, understanding the regulation of DNA duplication requires placing this process in the context of the current knowledge on bacterial metabolism, as well as cellular and chromosomal structure. Moreover, in both Escherichia coli and eukaryotic cells, replication initiator proteins were shown to play other roles in addition to driving the assembly of replication complexes, which constitutes another, yet not sufficiently understood, layer of coordinating DNA replication with the cell cycle.
Download or read book Structural and Biochemical Mechanisms of Replicative Helicase Loading in E Coli written by Sarah Diane McMillan and published by . This book was released on 2024 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA replication is an essential process in all organisms and begins with loading of the replicative helicase, DnaB. This process requires a loading factor, DnaC, which helps to crack open the hexameric helicase to facilitate loading onto DNA. At the origin of replication, an initiator protein recruits the DnaB/DnaC complex to initiate replication in a sequence-dependent manner. However, once replication is initiated, the replication machinery (replisome) can encounter barriers that lead to the replisome dissociating from DNA. When this happens, the DnaB/DnaC complex must be recruited back to the DNA in a structure specific manner with the help of Replication Restart Proteins (RRPs). In this thesis, I characterize the DnaB loading process and examine how a RRP, PriC, mechanistically loads the DnaB/DnaC complex. First, in Chapter 2, I characterize a panel of DnaC variants that alter the type of substrate that DnaB is loaded onto. This work has increased our understanding of how replicative helicase loading is regulated. I next characterize PriC-mediated DnaB loading through a cryo-EM structure that shows that PriC binds to the DnaB/DnaC complex in the "crack" that is exposed when DnaC binds to the helicase (Chapter 3). Finally, I characterize a panel of RRP variants that decrease loading of DnaB by disrupting a protein-protein interface between two RRPs (Chapter 4). Overall, my results increase our understand of DnaB loading, both generally and in the context of replication restart.
Download or read book Crystallographic Studies of the E Coli DNA Replication Restart Primosome written by Aude Izaac and published by . This book was released on 2005 with total page 366 pages. Available in PDF, EPUB and Kindle. Book excerpt: Understanding the mechanisms of DNA replication has been one of the main research topics in biochemistry for decades, due to the tremendous potential applications involved, such as medical treatments and better knowledge of the biological evolution of organisms. In this perspective, macromolecular X ray crystallography provides a very powerful tool. By solving the 3 dimensional structure of the proteins involved in replication mechanisms, one can get a good insight at complicated biological systems at the atomic level. It is also important to study the protein-protein and protein-substrate interactions when they form biological complexes. This work focused on studying several proteins which are associated with the assembly of the replication restart primosome in Escherichia coli, during the repair of damaged DNA. The crystallization of PriA, the most important of the restart primosome proteins, was investigated. Two truncations of PriA (the PriA N and PriA NI domains) were expressed, purified and characterized to be prepared for crystallization. Three additional replication restart proteins: PriB, PriC and DnaT, were expressed and purified. The solubility of each protein was optimized by identifying the best solution conditions. The proteins were characterized, alone and in complexes, using several biophysical techniques. DnaT was successfully crystallized and screened for X-ray diffraction. Finally, using ten standard test proteins, the correlation between the optimization of protein solubility (and solution conditions) and the success of crystal screening was studied.
Download or read book DNA Replication and the Cell Cycle written by Gesellschaft für Biologische Chemie. Colloquium and published by Springer. This book was released on 1993 with total page 288 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Recombinational Repair of DNA Damage written by Andrei Kuzminov and published by Landes Bioscience. This book was released on 1996 with total page 234 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Molecular Biology of the Cell written by and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book DNA Repair and Mutagenesis written by Errol C. Friedberg and published by American Society for Microbiology Press. This book was released on 2005-11-22 with total page 2587 pages. Available in PDF, EPUB and Kindle. Book excerpt: An essential resource for all scientists researching cellular responses to DNA damage. • Introduces important new material reflective of the major changes and developments that have occurred in the field over the last decade. • Discussed the field within a strong historical framework, and all aspects of biological responses to DNA damage are detailed. • Provides information on covering sources and consequences of DNA damage; correcting altered bases in DNA: DNA repair; DNA damage tolerance and mutagenesis; regulatory responses to DNA damage in eukaryotes; and disease states associated with defective biological responses to DNA damage.
Download or read book DNA Repair Mechanisms written by ICN Pharmaceuticals, inc and published by . This book was released on 1978 with total page 840 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA Repair Mechanisms is an account of the proceedings at a major international conference on DNA Repair Mechanisms held at Keystone, Colorado on February 1978. The conference discusses through plenary sessions the overall standpoint of DNA repair. The papers presented and other important documents, such as short summaries by the workshop session conveners, comprise this book. The compilation describes the opposing views, those that agree and dispute about certain topic areas. This book, divided into 15 parts, is arranged according to the proceedings in the conference. The plenary sessions are ...
Download or read book DNA Replication Recombination and Repair written by Fumio Hanaoka and published by Springer. This book was released on 2016-01-22 with total page 548 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is a comprehensive review of the detailed molecular mechanisms of and functional crosstalk among the replication, recombination, and repair of DNA (collectively called the "3Rs") and the related processes, with special consciousness of their biological and clinical consequences. The 3Rs are fundamental molecular mechanisms for organisms to maintain and sometimes intentionally alter genetic information. DNA replication, recombination, and repair, individually, have been important subjects of molecular biology since its emergence, but we have recently become aware that the 3Rs are actually much more intimately related to one another than we used to realize. Furthermore, the 3R research fields have been growing even more interdisciplinary, with better understanding of molecular mechanisms underlying other important processes, such as chromosome structures and functions, cell cycle and checkpoints, transcriptional and epigenetic regulation, and so on. This book comprises 7 parts and 21 chapters: Part 1 (Chapters 1–3), DNA Replication; Part 2 (Chapters 4–6), DNA Recombination; Part 3 (Chapters 7–9), DNA Repair; Part 4 (Chapters 10–13), Genome Instability and Mutagenesis; Part 5 (Chapters 14–15), Chromosome Dynamics and Functions; Part 6 (Chapters 16–18), Cell Cycle and Checkpoints; Part 7 (Chapters 19–21), Interplay with Transcription and Epigenetic Regulation. This volume should attract the great interest of graduate students, postdoctoral fellows, and senior scientists in broad research fields of basic molecular biology, not only the core 3Rs, but also the various related fields (chromosome, cell cycle, transcription, epigenetics, and similar areas). Additionally, researchers in neurological sciences, developmental biology, immunology, evolutionary biology, and many other fields will find this book valuable.
Download or read book Physical Biology of the Cell written by Rob Phillips and published by Garland Science. This book was released on 2012-10-29 with total page 1089 pages. Available in PDF, EPUB and Kindle. Book excerpt: Physical Biology of the Cell is a textbook for a first course in physical biology or biophysics for undergraduate or graduate students. It maps the huge and complex landscape of cell and molecular biology from the distinct perspective of physical biology. As a key organizing principle, the proximity of topics is based on the physical concepts that
Download or read book Bacterial Physiology written by Walid El-Sharoud and published by Springer Science & Business Media. This book was released on 2007-12-07 with total page 377 pages. Available in PDF, EPUB and Kindle. Book excerpt: The application of new molecular methodologies in the study of bacterial behavior and cell architecture has enabled new revolutionary insights and discoveries in these areas. This new text presents recent developments in bacterial physiology that are highly relevant to a wide range of readership including those interested in basic and applied knowledge. Its chapters are written by international scientific authorities at the forefront of the subject. The value of this recent knowledge in bacterial physiology is not only restricted to fundamental biology. It also extends to biotechnology and drug-discovery disciplines.
Download or read book Human Dna Polymerases Biology Medicine And Biotechnology written by Giovanni Maga and published by World Scientific. This book was released on 2017-11-10 with total page 398 pages. Available in PDF, EPUB and Kindle. Book excerpt: Maintenance of the information embedded in the genomic DNA sequence is essential for life. DNA polymerases play pivotal roles in the complex processes that maintain genetic integrity. Besides their tasks in vivo, DNA polymerases are the workhorses in numerous biotechnology applications such as the polymerase chain reaction (PCR), cDNA cloning, next generation sequencing, nucleic acids based diagnostics and in techniques to analyze ancient and otherwise damaged DNA (e.g. for forensic applications). Moreover, some diseases are related to DNA polymerase defects and chemotherapy through inhibition of DNA polymerases is used to fight HIV, Herpes and Hepatitis B and C infections. This book focuses on (i) biology of DNA polymerases, (ii) medical aspects of DNA polymerases and (iii) biotechnological applications of DNA polymerases. It is intended for a wide audience from basic scientists, to diagnostic laboratories, to companies and to clinicians, who seek a better understanding and the practical use of these fascinating enzymes.
Download or read book DNA Recombination and Repair written by Paul James Smith and published by Oxford University Press, USA. This book was released on 1999 with total page 260 pages. Available in PDF, EPUB and Kindle. Book excerpt: The processes of DNA recombination and repair are vital to cell integrity - an error can lead to disease such as cancer. It is therefore a large and exciting area of research and is also taught on postgraduate and undergraduate courses. This book is not a comprehensive view of the field, but a selection of the issues currently at the forefront of knowledge.
Download or read book DNA Helicases and DNA Motor Proteins written by Maria Spies and published by Springer Science & Business Media. This book was released on 2012-11-19 with total page 308 pages. Available in PDF, EPUB and Kindle. Book excerpt: In recent years, a number of groundbreaking structural and mechanistic studies deepened our understanding of helicase mechanisms and established new approaches for their analyses. Many fundamental mechanistic questions ranging from the mechanism of force generation, mechanochemical coupling to distinct mechanisms by which the same enzyme translocates on DNA removing obstacles, unwinds DNA and/or remodels nucleoprotein complexes, however, remain to be answered. It is even less understood how the helicase motors are incorporated into a wide range of genome maintenance and repair machines. The field has reached a stage when the studies of molecular mechanisms and basic biology of helicases can and shall be integrated with the studies of development, cancer and longevity. The objective of this book is to provide the first systematic overview of structure, function and regulation of DNA helicases and related molecular motors. By integrating the knowledge obtained through the diverse technical approaches ranging from single-molecule biophysics to cellular and molecular biological studies the editors aim to provide a unified view on how helicases function in the cell, are regulated in response to different cellular stresses and are integrated into large macromolecular assemblies to form a complex and adaptive living system.
Download or read book Modern Microbial Genetics written by Uldis N. Streips and published by John Wiley & Sons. This book was released on 2004-03-24 with total page 673 pages. Available in PDF, EPUB and Kindle. Book excerpt: In accordance with its predecessor, the completely revised and expanded Second Edition of Modern Microbial Genetics focuses on how bacteria and bacteriophage arrange and rearrange their genetic material through mutation, evolution, and genetic exchange to take optimal advantage of their environment. The text is divided into three sections: DNA Metabolism, Genetic Response, and Genetic Exchange. The first addresses how DNA replicates, repairs itself, and recombines, as well as how it may be manipulated. The second section is devoted to how microorganisms interact with their environment, including chapters on sporulation and stress shock, and the final section contains the latest information on classic exchange mechanisms such as transformation and conjugation. Chapters include: * Gene Expression and Its Regulation * Single-Stranded DNA Phages * Genetic Tools for Dissecting Motility and Development of Myxococcus xanthus * Molecular Mechanism of Quorum Sensing * Transduction in Gram-Negative Bacteria * Genetic Approaches in Bacteria with No Natural Genetic Systems The editors also cultivate an attention to global regulatory systems throughout the book, elucidating how certain genes and operons in bacteria, defined as regulons, network and cooperate to suit the needs of the bacterial cell. With clear appreciation for the impact of molecular genomics, this completely revised and updated edition proves that Modern Microbial Genetics remains the benchmark text in its field.
Download or read book Bacterial Physiology written by C. H. Werkman and published by Elsevier. This book was released on 2013-10-22 with total page 724 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bacterial Physiology focuses on the physiology and chemistry of microorganisms and the value of bacterial physiology in the other fields of biology. The selection first underscores the chemistry and structure of bacterial cells, including the chemical composition of cells, direct and indirect methods of cytology, vegetative multiplication, spores of bacteria, and cell structure. The text then elaborates on inheritance, variation, and adaptation and growth of bacteria. The publication reviews the physical and chemical factors affecting growth and death. Topics include hydrogen ion concentration and osmotic pressure; surface and other forces determining the distribution of bacteria in their environment; dynamics of disinfection and bacteriostasis; bacterial resistance; and types of antibacterial agents. The text also ponders on the anaerobic dissimilation of carbohydrates, bacterial oxidations, and autotrophic assimilation of carbon dioxide. The selection is a dependable reference for readers interested in bacterial physiology.
