Download or read book A Molecular Mechanism Allowing Transposon Tn7 to Target Active DNA Replication written by Zaoping Li and published by . This book was released on 2012 with total page 498 pages. Available in PDF, EPUB and Kindle. Book excerpt: Transposons are jumping genes that are ubiquitous and abundant in all domains of life. They can move between locations that lack homology within a genome. Transposons drive the evolution of genomes through gene inactivation, expression modulation, and genome rearrangement. The bacterial transposon Tn7 and its relatives are widespread in diverse bacteria, likely due to their ability to control the frequency and targeting of transposition. My work presented here focuses on understanding the molecular mechanism of the TnsABC+E pathway of Tn7 transposition that preferentially targets actively transferring mobile DNA. I was able to establish a sensitive in vitro system for this transposition reaction with purified proteins and gapped DNA substrates preloaded with the [beta]-clamp. The transposition profile recapitulates that observed in vivo, indicating that the minimal features recognized by TnsE to target DNA replication are 3' recessed ends found in target DNA and the [beta]-clamp processivity factor (DnaN). I further show that the TnsE-[beta] interaction is largely conserved among Tn7-like elements; however, this interaction is also species specific. In a heterologous expression study, I found that TnsE homologs from Idiomarina loihiensis and Shewanella baltica only promoted transposition when DnaN from the same host was used in the cell. I propose that TnsE may have evolved to interact with the more variable portion of the clamp to avoid interfering with the normal traffic on the clamp. In an effort to screen for host proteins that may affect TnsE-mediated transposition, I found and confirmed an interaction between TnsE and SeqA, a protein involved in replication initiation control and organizing newly replicated chromosome DNA. Results from genetic studies support a model where TnsE interacts with SeqA to disrupt the SeqA superstructure that tracks with the replication fork. I also show that in wild type background, TnsE is able to direct transposition into the origin region and DNA undergoing leading-strand replication, consistent with the emerging picture that both the leading-strand and lagging-strand DNA replication are essentially discontinuous. These data point to a perspective of using Tn7 as a genetic tool in understanding the replication and repair processes in the cell.
Download or read book Tn7 Transposes Into Replicating DNA Using an Interaction with the Processivity Factor Facilitating Genome Evolution written by Adam Robert Parks and published by . This book was released on 2008 with total page 225 pages. Available in PDF, EPUB and Kindle. Book excerpt: Transposons are mobile genetic elements that can move between locations in DNA that lack homology. Transposons play an important role in the evolution of genomes in every domain of life through activities such as horizontal gene transfer, gene disruption, gene expression modulation, and recombination. The bacterial transposon Tn7 maintains two distinct lifestyles, one in horizontally transferred DNA and the other in bacterial chromosomes. Access to these two DNA pools is mediated by two separate target selection pathways. The proteins involved in these pathways have evolved to specifically recognize their cognate target-sites using entirely different mechanisms but the same core transposition machinery. In this work, analyze over 50 Tn7-like transposons and discuss how the molecular mechanisms of these genetic elements contribute to the success of both transposon and host. I focus particularly on the TnsE-pathway of transposition that is credited with optimizing transposition into DNA that is transported between bacterial hosts, and likely explains the presence of this transposon in phylogenetically diverse bacteria occupying a broad range of ecological niches. I show that the TnsE protein physically and functionally interacts with the processivity factor of the DNA replication machinery. I propose that this interaction allows Tn7 to identify insertion sites and to orient in one direction with active DNA replication by a process that is ubiquitous in bacteria. The TnsE interaction with an essential and conserved component of the replication machinery reveals a new mechanism by which Tn7, and possibly other elements, select target-sites associated with DNA replication. These results provide insight into various processes in eukaryotic and prokaryotic organisms involving processivity factors. I also analyze specific genetic pathways that affect the frequency of TnsE-mediated transposition, and correlate these genetic effects with protein-DNA complexes that may be recognized by TnsE and could be expected to be commonly found in these genetic backgrounds. The data presented here reveals ways in which Tn7 has directed the evolution of host genomes, and points to ways in which Tn7 might be used as a tool for understanding genetic phenomena.
Download or read book Snyder and Champness Molecular Genetics of Bacteria written by Tina M. Henkin and published by John Wiley & Sons. This book was released on 2020-10-27 with total page 642 pages. Available in PDF, EPUB and Kindle. Book excerpt: The single most comprehensive and authoritative textbook on bacterial molecular genetics Snyder & Champness Molecular Genetics of Bacteria is a new edition of a classic text, updated to address the massive advances in the field of bacterial molecular genetics and retitled as homage to the founding authors. In an era experiencing an avalanche of new genetic sequence information, this updated edition presents important experiments and advanced material relevant to current applications of molecular genetics, including conclusions from and applications of genomics; the relationships among recombination, replication, and repair and the importance of organizing sequences in DNA; the mechanisms of regulation of gene expression; the newest advances in bacterial cell biology; and the coordination of cellular processes during the bacterial cell cycle. The topics are integrated throughout with biochemical, genomic, and structural information, allowing readers to gain a deeper understanding of modern bacterial molecular genetics and its relationship to other fields of modern biology. Although the text is centered on the most-studied bacteria, Escherichia coli and Bacillus subtilis, many examples are drawn from other bacteria of experimental, medical, ecological, and biotechnological importance. The book's many useful features include Text boxes to help students make connections to relevant topics related to other organisms, including humans A summary of main points at the end of each chapter Questions for discussion and independent thought A list of suggested readings for background and further investigation in each chapter Fully illustrated with detailed diagrams and photos in full color A glossary of terms highlighted in the text While intended as an undergraduate or beginning graduate textbook, Molecular Genetics of Bacteria is an invaluable reference for anyone working in the fields of microbiology, genetics, biochemistry, bioengineering, medicine, molecular biology, and biotechnology. "This is a marvelous textbook that is completely up-to-date and comprehensive, but not overwhelming. The clear prose and excellent figures make it ideal for use in teaching bacterial molecular genetics." —Caroline Harwood, University of Washington
Download or read book Mobile DNA III written by Michael Chandler and published by John Wiley & Sons. This book was released on 2020-07-24 with total page 1321 pages. Available in PDF, EPUB and Kindle. Book excerpt: An exploration of the raw power of genetic material to refashion itself to any purpose... Virtually all organisms contain multiple mobile DNAs that can move from place to place, and in some organisms, mobile DNA elements make up a significant portion of the genome. Mobile DNA III provides a comprehensive review of recent research, including findings suggesting the important role that mobile elements play in genome evolution and stability. Editor-in-Chief Nancy L. Craig assembled a team of multidisciplinary experts to develop this cutting-edge resource that covers the specific molecular mechanisms involved in recombination, including a detailed structural analysis of the enzymes responsible presents a detailed account of the many different recombination systems that can rearrange genomes examines the tremendous impact of mobile DNA in virtually all organisms Mobile DNA III is valuable as an in-depth supplemental reading for upper level life sciences students and as a reference for investigators exploring new biological systems. Biomedical researchers will find documentation of recent advances in understanding immune-antigen conflict between host and pathogen. It introduces biotechnicians to amazing tools for in vivo control of designer DNAs. It allows specialists to pick and choose advanced reviews of specific elements and to be drawn in by unexpected parallels and contrasts among the elements in diverse organisms. Mobile DNA III provides the most lucid reviews of these complex topics available anywhere.
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 Mobile DNA written by Douglas E. Berg and published by Amer Society for Microbiology. This book was released on 1989-01 with total page 972 pages. Available in PDF, EPUB and Kindle. Book excerpt: Documents the remarkable mobility of DNA in procaryotic and eucaryotic genomes: the ability of various DNA segments to move to new sites, to invert, and to undergo deletion or amplification, generally without the extensive DNA sequence homology needed for classical recombination. Seventy contributors explore the mechanisms of these rearrangements, how they are regulated, their biological consequences, and their potential use as research tools. For students and researchers of molecular genetics. Annotation copyrighted by Book News, Inc., Portland, OR
Download or read book Toxicoepigenetics written by Shaun D. McCullough and published by Academic Press. This book was released on 2018-11-02 with total page 430 pages. Available in PDF, EPUB and Kindle. Book excerpt: Toxicoepigenetics: Core Principles and Applications examines the core aspects of epigenetics, including chromatin biology, DNA methylation, and non-coding RNA, as well as fundamental techniques and considerations for studying each of these mechanisms of epigenetic regulation. Although its integration into the field of toxicology is in its infancy, epigenetics have taken center stage in the study of diseases such as cancer, diabetes, and neurodegeneration. Increasing the presence of epigenetics in toxicological research allows for a more in-depth understanding of important aspects of toxicology such as the role of the environment and lifestyle influencing the individual susceptibility to these effects and the trans-generational transmission of these health effects and susceptibilities. Methods chapters are included to help improve efficacy and efficiency of protocols in both the laboratory and the classroom. Toxicoepigenetics: Core Principles and Applications is an essential book for researchers and academics using epigenetics in toxicology research and study. - Introduces the fundamental principles and practices for understanding the role of the epigenome in toxicology - Presents the foundation of epigenetics for toxicologists with a broad range of backgrounds - Discusses the incorporation of epigenetics and epigenomics into current toxicological studies and interpretation of epigenetic data in toxicological applications
Download or read book HIV 1 Integrase written by Nouri Neamati and published by John Wiley & Sons. This book was released on 2011-08-10 with total page 710 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book comprehensively covers the mechanisms of action and inhibitor design for HIV-1 integrase. It serves as a resource for scientists facing challenging drug design issues and researchers in antiviral drug discovery. Despite numerous review articles and isolated book chapters dealing with HIV-1 integrase, there has not been a single source for those working to devise anti-AIDS drugs against this promising target. But this book fills that gap and offers a valuable introduction to the field for the interdisciplinary scientists who will need to work together to design drugs that target HIV-1 integrase.
Download or read book The Maize Genome written by Jeffrey Bennetzen and published by Springer. This book was released on 2018-11-24 with total page 390 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book discusses advances in our understanding of the structure and function of the maize genome since publication of the original B73 reference genome in 2009, and the progress in translating this knowledge into basic biology and trait improvement. Maize is an extremely important crop, providing a large proportion of the world’s human caloric intake and animal feed, and serving as a model species for basic and applied research. The exceptionally high level of genetic diversity within maize presents opportunities and challenges in all aspects of maize genetics, from sequencing and genotyping to linking genotypes to phenotypes. Topics covered in this timely book range from (i) genome sequencing and genotyping techniques, (ii) genome features such as centromeres and epigenetic regulation, (iii) tools and resources available for trait genomics, to (iv) applications of allele mining and genomics-assisted breeding. This book is a valuable resource for researchers and students interested in maize genetics and genomics.
Download or read book CRISPR Cas Systems written by Rodolphe Barrangou and published by Springer Science & Business Media. This book was released on 2012-12-13 with total page 300 pages. Available in PDF, EPUB and Kindle. Book excerpt: CRISPR/Cas is a recently described defense system that protects bacteria and archaea against invasion by mobile genetic elements such as viruses and plasmids. A wide spectrum of distinct CRISPR/Cas systems has been identified in at least half of the available prokaryotic genomes. On-going structural and functional analyses have resulted in a far greater insight into the functions and possible applications of these systems, although many secrets remain to be discovered. In this book, experts summarize the state of the art in this exciting field.
Download or read book A Short Course in Bacterial Genetics written by Jeffrey H. Miller and published by CSHL Press. This book was released on 1992 with total page 484 pages. Available in PDF, EPUB and Kindle. Book excerpt: University of California, Los Angeles. Introduction to bacterial genetics, including laboratory methods, for advanced students and beginning researchers. Handbook with plastic spiral-bound laboratory manual.
Download or read book Experiments in Molecular Genetics written by Jeffrey H. Miller and published by . This book was released on 1974 with total page 466 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Evolution written by James Alan Shapiro and published by Pearson Education. This book was released on 2011 with total page 273 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book proposes an important new paradigm for understanding biological evolution. Shapiro demonstrates why traditional views of evolution are inadequate to explain the latest evidence, and presents an alternative. His information- and systems-based approach integrates advances in symbiogenesis, epigenetics, and saltationism, and points toward an emerging synthesis of physical, information, and biological sciences.
Download or read book Restriction Endonucleases written by Alfred Pingoud and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 462 pages. Available in PDF, EPUB and Kindle. Book excerpt: Restriction enzymes are highly specific nucleases which occur ubiquitously among prokaryotic organisms, where they serve to protect bacterial cells against foreign DNA. Many different types of restriction enzymes are known, among them multi-subunit enzymes which depend on ATP or GTP hydrolysis for target site location. The best known representatives, the orthodox type II restriction endonucleases, are homodimers which recognize palindromic sequences, 4 to 8 base pairs in length, and cleave the DNA within or immediately adjacent to the recognition site. In addition to their important biological role (up to 10 % of the genomes of prokaryotic organisms code for restriction/modification systems!), they are among the most important enzymes used for the analysis and recombination of DNA. In addition, they are model systems for the study of protein-nucleic acids interactions and, because of their ubiquitous occurence, also for the understanding of the mechanisms of evolution.
Download or read book Molecular Genetics of Bacteria written by Larry Snyder and published by . This book was released on 2007 with total page 768 pages. Available in PDF, EPUB and Kindle. Book excerpt: Providing the single most comprehensive and authoritative textbook on bacterial molecular genetics, this updated edition provides descriptive background information, detailed experimental methods, examples of genetic analyses, and advanced material relevant to current applications of molecular genetics.
Download or read book Bacterial Integrative Mobile Genetic Elements written by Adam P. Roberts and published by CRC Press. This book was released on 2022-03-07 with total page 456 pages. Available in PDF, EPUB and Kindle. Book excerpt: As our understanding of mobile genetic elements continues to grow we are gaining a deeper appreciation of their importance in shaping the bacterial genome and in the properties they confer to their bacterial hosts. These include, but are by no means limited to, resistance to antibiotics, and heavy metals, toxin production and increased virulence, production of antibiotics and the ability to utilize a diverse range of metabolic substrates. We are also gaining an understanding of diversity of these elements and their interactions with each other; a property which continually complicates any attempt to classify them. We are learning more about the molecular mechanisms by which they translocate to new genomic sites both within genomes and between different bacteria. This book provides a timely, state of the art update on the properties of an important selection of different bacterial integrative mobile genetic elements and the myriad of different ways in which they move and influence the biology of the host bacterium. The chapters are all written by authors who have undertaken pioneering work in their respective fields, making this book vital reading for all who are interested in the biology of bacteria and the mobile elements they carry.
