Download or read book Helicase SSB Interactions In Recombination Dependent DNA Repair and Replication written by Christian S. Jordan and published by . This book was released on 2014 with total page 466 pages. Available in PDF, EPUB and Kindle. Book excerpt: Dda, one of three helicases encoded by bacteriophage T4, has been well- characterized biochemically but its biological role remains unclear. It is thought to be involved in origin-dependent replication, recombination-dependent replication, anti- recombination, recombination repair, as well as in replication fork progression past template-bound nucleosomes and RNA polymerase. One of the proteins that most strongly interacts with Dda, Gp32, is the only single-stranded DNA binding protein (SSB) encoded by T4, is essential for DNA replication, recombination, and repair. Previous studies have shown that Gp32 is essential for Dda stimulation of replication fork progression. Our studies show that interactions between Dda and Gp32 play a critical role in regulating replication fork restart during recombination repair. When the leading strand polymerase stalls at a site of ssDNA damage and the lagging strand machinery continues, Gp32 binds the resulting ssDNA gap ahead of the stalled leading strand polymerase. We found that a Gp32 cluster on leading strand ssDNA blocks Dda loading on the lagging strand ssDNA, blocks stimulation of fork progression by Dda, and stimulates Dda to displace the stalled polymerase and the 3' end of the daughter strand. This unwinding generates conditions necessary for polymerase template switching in order to regress the DNA damage-stalled replication fork. Helicase trafficking by Gp32 could play a role in preventing premature fork progression until the events required for error-free translesion DNA synthesis have taken place. Interestingly, we found that Dda helicase activity is strongly stimulated by the N-terminal deletion mutant Gp32-B, suggesting the N-terminal truncation to generate Gp32-B reveals a cryptic helicase stimulatory activity of Gp32 that may be revealed in the context of a moving polymerase, or through direct interactions of Gp32 with other replisome components. Additionally, our findings support a role for Dda-Gp32 interactions in double strand break (DSB) repair by homology-directed repair (HDR), which relies on homologous recombination and the formation of a displacement loop (D-loop) that can initiate DNA synthesis. We examined the D-loop unwinding activity of Dda, Gp41, and UvsW, the D-loop strand extension activity of Gp43 polymerase, and the effect of the helicases and their modulators on D-loop extension. Dda and UvsW, but not Gp41, catalyze D-loop invading strand by DNA unwinding. The relationship between Dda and Gp43 was modulated by the presence of Gp32. Dda D-loop unwinding competes with D- loop extension by Gp43 only in the presence of Gp32, resulting in a decreased frequency of invading strand extension when all three proteins are present. These data suggest Dda functions as an antirecombinase and negatively regulates the replicative extension of D- loops. Invading strand extension is observed in the presence of Dda, indicating that invading strand extension and unwinding can occur in a coordinated manner. The result is a translocating D-loop, called bubble migration synthesis, a hallmark of break-induced repair (BIR) and synthesis dependent strand annealing (SDSA). Gp41 did not unwind D- loops studied and may serve as a secondary helicase loaded subsequent to D-loop processing by Dda. Dda is proposed to be a mixed function helicase that can work both as an antirecombinase and to promote recombination-dependent DNA synthesis, consistent with the notion that Dda stimulates branch migration. These results have implications on the repair of ssDNA damage, DSB repair, and replication fork regulation, which are highly conserved processes sustained in all organisms.
Download or read book Links Between Recombination and Replication written by Proceedings of the National Academy of Sciences and published by National Academies Press. This book was released on 2002-09-18 with total page 303 pages. Available in PDF, EPUB and Kindle. Book excerpt: There has been a sea change in how we view genetic recombination. When germ cells are produced in higher organisms, genetic recombination assures the proper segregation of like chromosomes. In the course of that process, called meiosis, recombination not only assures segregation of one chromosome of each type to progeny germ cells, but also further shuffles the genetic deck, contributing to the unique inheritance of individuals. In a nutshell, that is the classical view of recombination. We have also known for many years that in bacteria recombination plays a role in horizontal gene transfer and in replication itself, the latter by establishing some of the replication forks that are the structural scaffolds for copying DNA. In recent years, however, we have become increasingly aware that replication, which normally starts without any help from recombination, is a vulnerable process that frequently leads to broken DNA. The enzymes of recombination play a vital role in the repair of those breaks. The recombination enzymes can function via several different pathways that mediate the repair of breaks, as well as restoration of replication forks that are stalled by other kinds of damage to DNA. Thus, to the classical view of recombination as an engine of inheritance we must add the view of recombination as a vital housekeeping function that repairs breaks suffered in the course of replication. We have also known for many years that genomic instability--including mutations, chromosomal rearrangements, and aneuploidy--is a hallmark of cancer cells. Although genomic instability has many contributing causes, including faulty replication, there are many indications that recombination, faulty or not, contributes to genome instability and cancer as well. The (Nas colloquium) Links Between Recombination and Replication: Vital Roles of Recombination was convened to broaden awareness of this evolving area of research. Papers generated by this colloquium are published here. To encourage the desired interactions of specialists, we invited some contributions that deal only with recombination or replication in addition to contributions on the central thesis of functional links between recombination and replication. To aid the nonspecialist and specialist alike, we open the set of papers with a historical overview by Michael Cox and we close the set with a commentary on the meeting and the field by Andrei Kuzminov.
Download or read book DNA helicases expression functions and clinical implications written by Fumiaki Uchiumi and published by Frontiers Media SA. This book was released on 2015-06-26 with total page 80 pages. Available in PDF, EPUB and Kindle. Book excerpt: Helicases are the proteins that bind to double- or single-stranded DNA and/or RNA chains to unwind higher order structures, usually consuming energy from the hydrolysis of ATP molecules. The biological roles of helicases are associated with a variety of DNA and/or RNA metabolisms, including DNA-replication, -repair, -recombination, RNA processing, and transcription. Dysfunctions of helicases cause various diseases, such as xeroderma pigmentosum (XP), premature aging syndrome, cancer and immunodeficiency, in humans. Moreover, recent genetic analyses revealed that mutations in helicase-encoding genes are frequently found in patients of specific diseases. Some helicases regulate cellular senescence by controlling integrity of genomes, and others play a role in neuromuscular functions presumably by modulating processing of mRNAs. However, the molecular mechanisms of how helicases are regulated in order to maintain our health are not yet fully understood. In this research topic, we will focus on the expression and functions of helicases and their encoding genes, reviewing recent research progresses that provide new insights into development of clinical and pharmaceutical treatments targeting helicases.
Download or read book Zinc Finger Proteins written by Shiro Iuchi and published by Springer Science & Business Media. This book was released on 2007-03-06 with total page 291 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the early 1980s, a few scientists started working on a Xenopus transcription factor, TFIIIA. They soon discovered a novel domain associated with zinc, and named this domain "zinc finger. " Th e number of proteins with similar zinc fingers grew quickly and these proteins are now called C2H2, Cys2His2 or classical zinc finger proteins. To date, about 24,000 C2H2 zinc finger proteins have been recognized. Approximately 700 human genes, or more than 2% of the genome, have been estimated to encode C2H2 finger proteins. From the beginning these proteins were thought to be numerous, but no one could have predicted such a huge number. Perhaps thousands of scientists are now working on C2H2 zinc finger proteins fi-om variou s viewpoints. This field is a good example of how a new science begins with the insight of a few scientists and how it develops by efforts of numerous independent scientists, in contrast to a policy-driven scientific project, such as the Human Genome Project, with goals clearly set at its inception and with work performed by a huge collaboration throughout the world. As more zinc finger proteins were discovered, several subfamilies, such as C2C2, CCHC, CCCH, LIM, RING, TAZ, and FYVE emerged, increasing our understanding of zinc fingers. The knowledge was overwhelming. Moreover, scientists began defining the term "zinc finger" differently and using various names for identical zinc fingers. These complications may explain why no single comprehensive resource of zinc finger proteins was available before this publication.
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 The DNA Replication Repair Interface written by and published by Academic Press. This book was released on 2021-11-12 with total page 454 pages. Available in PDF, EPUB and Kindle. Book excerpt: Replication-Coupled Repair, Volume 661 in the Methods in Enzymology series, highlights new advances in the field, with this new volume presenting interesting chapters on a variety of timely topics, including the Repair of replication-born DNA breaks by sister chromatid recombination, High resolution and high throughput DNA cyclization measurements to interrogate DNA bendability, A programmable detection method for genomic signatures: from disease diagnosis to genome editing, Characterization of the telomerase modulating activities of yeast DNA helicases, Eukaryotic DNA replication with purified budding yeast proteins, Single molecule studies of yeast Rad51 paralogs, Light activation and deactivation of Cas9 for DNA repair studies, and more. Other chapters explore MIDAS: Direct sequencing to map mitotic DNA synthesis and common fragile sites at high precision, Studying the DNA damage response in embryonic systems, GLASS-ChIP to map Mre11 cleavage sites in the human genome, New chemical biology approaches to trap reaction intermediates in living cells, Single-molecule imaging approaches for monitoring replication fork conflicts at genomic DNA G4 structures and R-loops in human cells, Monitoring the replication of structured DNA through heritable epigenetic change, Visualizing replication fork encounters with DNA interstrand crosslinks, and much more. - Provides the authority and expertise of leading contributors from an international board of authors - Presents the latest release in Methods in Enzymology series - Includes the latest information on replication-coupled repair
Download or read book Human DNA Helicase B in Replication Fork Surveillance and Replication Stress Recovery written by Gülfem Dilek Güler and published by . This book was released on 2012 with total page 117 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 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 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 Helicases from All Domains of Life written by Renu Tuteja and published by Academic Press. This book was released on 2018-10-15 with total page 200 pages. Available in PDF, EPUB and Kindle. Book excerpt: Helicases are ubiquitous enzymes found throughout evolution. Research in the helicase field has been going on for a long time now but in recent past with the completion of so many genomes, these enzymes have been discovered in a number of organisms. But the available literature is scattered. The huge number of identified DNA and RNA helicases, along with the structural and functional differences among them, make difficult for the interested scholar to grasp a comprehensive view of the field. Helicases from all Domains of Life is the first book to compile information about helicases from many different organisms in one place. Knowledge of the functions and features of helicases across the different kingdoms of life are a valuable source of novel ideas and information The book begins with a chapter on the evolutionary history of helicases followed by three "overview" chapters: one for bacteria/archaea (which are not mentioned), one for plants/algae and one for human helicases The overview chapters are followed by specific chapters on selected helicases of great importance from a biological/applicative point of view
Download or read book Human Herpesviruses written by Ann Arvin and published by Cambridge University Press. This book was released on 2007-08-16 with total page 1325 pages. Available in PDF, EPUB and Kindle. Book excerpt: This comprehensive account of the human herpesviruses provides an encyclopedic overview of their basic virology and clinical manifestations. This group of viruses includes human simplex type 1 and 2, Epstein–Barr virus, Kaposi's Sarcoma-associated herpesvirus, cytomegalovirus, HHV6A, 6B and 7, and varicella-zoster virus. The viral diseases and cancers they cause are significant and often recurrent. Their prevalence in the developed world accounts for a major burden of disease, and as a result there is a great deal of research into the pathophysiology of infection and immunobiology. Another important area covered within this volume concerns antiviral therapy and the development of vaccines. All these aspects are covered in depth, both scientifically and in terms of clinical guidelines for patient care. The text is illustrated generously throughout and is fully referenced to the latest research and developments.
Download or read book Mechanisms of DNA Replication and Recombination written by Nicholas R. Cozzarelli and published by . This book was released on 1983 with total page 912 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proceedings of a UCLA Symposium held in Keystone, Colorado, April, 3-9, 1983.
Download or read book Single Molecule Enzymology Fluorescence Based and High Throughput Methods written by and published by Academic Press. This book was released on 2016-10-28 with total page 618 pages. Available in PDF, EPUB and Kindle. Book excerpt: Single-Molecule Enzymology, Part A, the latest volume in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers research methods in single-molecule enzymology, and includes sections on such topics as force-based and hybrid approaches, fluorescence, high-throughput sm enzymology, nanopores, and tethered particle motion. - Continues the legacy of this premier serial with quality chapters authored by leaders in the field - Covers research methods in single-molecule enzymology - Contains sections on such topics as force-based and hybrid approaches, fluorescence, high-throughput sm enzymology, nanopores, and tethered particle motion
Download or read book Molecular Life Sciences written by Robert D. Wells and published by Springer. This book was released on 2018-01-12 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular Life Sciences: An Encyclopedic Reference will focus on understanding biological phenomena at the level of molecules and their interactions that govern life processes. The work will include articles on genes and genomes, protein structure and function, systems biology using genomics and proteomics as the focus, molecular aspects of cell structure and function, unifying concepts and theories from biology, chemistry, mathematics and physics that are essential for understanding the molecular life sciences (including teaching perspectives and assessment tools), and basic aspects of the various experimental approaches that are used in the Molecular Life Sciences.
Download or read book Molecular Biology written by Stephen H Howell and published by Springer. This book was released on 2014-10-01 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this book, plant biology is considered from the perspective of plants and their surrounding environment, including both biotic and abiotic interactions. The intended audience is undergraduate students in the middle or final phases of their programs of study. Topics are developed to provide a rudimentary understanding of how plant-environment interactions span multiple spatiotemporal scales, and how this rudimentary knowledge can be applied to understand the causes of ecosystem vulnerabilities in the face of global climate change and expansion of natural resource use by human societies. In all chapters connections are made from smaller to larger scales of ecological organization, providing a foundation for understanding plant ecology. Where relevant, environmental threats to ecological systems are identified and future research needs are discussed. As future generations take on the responsibility for managing ecosystem goods and services, one of the most effective resources that can be passed on is accumulated knowledge of how organisms, populations, species, communities and ecosystems function and interact across scales of organization. Molecular Biology is intended to provide some of that knowledge, and hopefully provide those generations with the ability to avoid some of the catastrophic environmental mistakes that prior generations have made.
Download or read book Live Cell Imaging written by Robert D. Goldman and published by CSHL Press. This book was released on 2005 with total page 658 pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent advances in imaging technology reveal, in real time and great detail, critical changes in living cells and organisms. This manual is a compendium of emerging techniques, organized into two parts: specific methods such as fluorescent labeling, and delivery and detection of labeled molecules in cells; and experimental approaches ranging from the detection of single molecules to the study of dynamic processes in organelles, organs, and whole animals. Although presented primarily as a laboratory manual, the book includes introductory and background material and could be used as a textbook in advanced courses. It also includes a DVD containing movies of living cells in action, created by investigators using the imaging techniques discussed in the book. The editors, David Spector and Robert Goldman, whose previous book was Cells: A Laboratory Manual,are highly respected investigators who have taught microscopy courses at Cold Spring Harbor Laboratory, the Marine Biology Laboratory at Woods Hole, and Northwestern University.
