Download or read book Mechanisms of sigma 54 Bacterial Transcription Activation written by Alexander Rigel Siegel and published by . This book was released on 2016 with total page 135 pages. Available in PDF, EPUB and Kindle. Book excerpt: This dissertation addresses the mechanism of [sigma]54 activation by the AAA+ ATPase transcriptional activators. The first chapter provides a general introduction to [sigma]54-mediated bacterial transcription initiation by outlining the existing structural and biochemical data on [sigma]54 and its activators. The majority of our structural information comes from high resolution structures of individual [sigma]54 and transcriptional activator domains, with the rest coming from low resolution structures that determine relative positions of the domains. The structural and biochemical properties of these domains, viewed in the context of the mechanisms of related motor proteins, led to our hypothesis of [sigma]54 activation. In this dissertation, I propose that the transcriptional activator's hexameric ATPase domain uses conserved loops, known to contact [sigma]54, to pull on and thread the [sigma]54 N-terminal activator interacting domain through its central pore. In this model, through processive rounds of ATP hydrolysis, the transcriptional activator applies enough force to generate a conformational change in the [sigma]54-RNA polymerase holoenzyme that allows it to melt DNA thus initiating transcription. The primary goal of my work has been the study of the activation mechanism using a variety of techniques, including traditional NMR-based structure determination, in vivo and in vitro biochemistry, and single molecule optical tweezers experiments. The second chapter outlines the central work of this dissertation, the structural characterization of the region of [sigma]54 responsible for contacting the activator and necessary for initiating transcription. We show that the activator interacting domain (AID) is intrinsically disordered, but becomes ordered when bound to the transcriptional activator, NtrC1, in its ATP state. In particular, we show that two predicted helices in the sequence are sufficient for activator binding with native-like affinity, and that the first helix in particular represents the primary region of contact. We applied TROSY-based NMR techniques to the structure determination of this high molecular weight complex, but most signals were broad due to dynamics or disorder, preventing a high resolution structure determination of the AID bound to the activator. This indicates that the AID does not bind the activator in a single conformation, but rather in multiple conformations each experiencing a different chemical environment. This may reflect an activation mechanism involving dynamic changes to the [sigma]54-activator interaction site. The third chapter takes an in vivo biochemical approach to study the [sigma]54 activation mechanism by characterizing the functionality of [sigma]54 with insertions and deletions near the activator interacting domain. These insertions distinguish between two competing mechanisms: whether the [sigma]54 AID only binds the surface of the activator or, as we propose, is threaded through its central pore. We find that a flexible linker region between the sites of activator and RNA polymerase binding is essential for fully functional [sigma]54. While the length of the linker does not matter, the insertion of a small, stably folded domain between these two interaction sites is detrimental to [sigma]54 activity in vivo. This is consistent with the threading of the AID and linker by the transcriptional activator, which would not be inhibited by the addition of extra unstructured residues but would be stalled by the addition of a folded domain in the linker. The fourth chapter outlines single molecule optical tweezers experiments to characterize the effect of force on a domain of [sigma]54. In particular, we examine the possibility that the [sigma]54 core binding domain (CBD), responsible for contacting core RNA polymerase, acts as a conformational fracture point that undergoes rearrangements when force is applied. The NMR structure of the CBD revealed two folded subdomains with a hydrophobic interface that could plausibly be disrupted by the force of the activator threading the N-terminus. By applying force with optical tweezers to either end of the CBD alone, we observed a separate unfolding event likely corresponding to unfolding of its seventh helix, but there was no evidence that the less stable of the two CBD subdomains unfolds before the other. Future experiments to conclusively test the force-dependent activation of [sigma]54 may require reconstituting and pulling on the full RNA polymerase holoenzyme complex, including core RNAP, promoter DNA, and full length [sigma]54. The fifth chapter steps back from the study of the [sigma]54 activation by the transcriptional activators to examine the regulation of the transcriptional activators themselves. Existing evidence shows that phosphorylation of the regulatory receiver domain of the transcriptional activator NtrC changes the population of its active and inactive states, with most states resembling the active conformation after phosphorylation. The activated receiver domain promotes the oligomerization of the ATPase domain, which in turn can activate [sigma]54. In this chapter, I studied an NtrC receiver domain from the piezophilic bacteria, Shewanella violacea, which turns on [sigma]54-dependent gene expression in response to high pressure. We hypothesized that pressure alone might drive the conformational change normally associated with phosphorylation, thereby activating S.v. NtrC independent of its normal, two-component signaling pathway. Using high pressure NMR spectroscopy, we showed that increased pressure alone does not increase the population of the S.v. NtrC receiver domain's active state. Future work must consider the pressure sensing behavior of the other components in the NtrC signaling pathway.
Download or read book Structures and Mechanisms of Bacterial O Sigma 54 dependent Transcription Initiation written by Michaeleen Callahan Doucleff and published by . This book was released on 2007 with total page 278 pages. Available in PDF, EPUB and Kindle. Book excerpt: In bacteria, the sigma subunit of RNA polymerase (RNAP) regulates gene expression by directing RNAP to specific promoters and catalyzing the opening of the double-stranded DNA. Two families of sigma factors have been identified: sigma 70 and sigma54. Unlike sigma70-RNAP, C54-RNAP requires interaction with an upstream activator protein to initiate transcription. sigma54 activators respond to environmental or cellular signals by oligomerzing to a state capable of binding sigma 54 and remodeling it to a form that permits transcription initiation.
Download or read book Cryo EM Part A Sample Preparation and Data Collection written by and published by Academic Press. This book was released on 2010-09-30 with total page 466 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cryo-EM Part A: Sample Preparation and Data Collection is dedicated to a description of the instruments, samples, protocols, and analyses that belong to cryo-EM. It emphasizes the relatedness of the ideas, instrumentation, and methods underlying all cryo-EM approaches, which allow practitioners to easily move between them. Within each section, the articles are ordered according to the most common symmetry of the sample to which their methods are applied. - Includes time-tested core methods and new innovations applicable to any researcher - Methods included are useful to both established researchers and newcomers to the field - Relevant background and reference information given for procedures can be used as a guide
Download or read book Diagnostic Molecular Biology written by Chang-Hui Shen and published by Elsevier. This book was released on 2023-06-29 with total page 590 pages. Available in PDF, EPUB and Kindle. Book excerpt: Diagnostic Molecular Biology, Second Edition describes the fundamentals of molecular biology in a clear, concise manner with each technique explained within its conceptual framework and current applications of clinical laboratory techniques comprehensively covered. This targeted approach covers the principles of molecular biology, including basic knowledge of nucleic acids, proteins and chromosomes; the basic techniques and instrumentations commonly used in the field of molecular biology, including detailed procedures and explanations; and the applications of the principles and techniques currently employed in the clinical laboratory. Topics such as whole exome sequencing, whole genome sequencing, RNA-seq, and ChIP-seq round out the discussion. Fully updated, this new edition adds recent advances in the detection of respiratory virus infections in humans, like influenza, RSV, hAdV, hRV but also corona. This book expands the discussion on NGS application and its role in future precision medicine. - Provides explanations on how techniques are used to diagnosis at the molecular level - Explains how to use information technology to communicate and assess results in the lab - Enhances our understanding of fundamental molecular biology and places techniques in context - Places protocols into context with practical applications - Includes extra chapters on respiratory viruses (Corona)
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 Regulation of Gene Expression by Small RNAs written by Rajesh K. Gaur and published by CRC Press. This book was released on 2009-04-27 with total page 440 pages. Available in PDF, EPUB and Kindle. Book excerpt: New Findings Revolutionize Concepts of Gene FunctionEndogenous small RNAs have been found in various organisms, including humans, mice, flies, worms, fungi, and bacteria. Furthermore, it's been shown that microRNAs acting as cellular rheostats have the ability to modulate gene expression. In higher eukaryotes, microRNAs may regulate as much as 50 p
Download or read book Bacteriophage T4 written by Christopher K. Mathews and published by . This book was released on 1983 with total page 432 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Regulation of Bacterial Virulence written by Michael L. Vasil and published by American Society for Microbiology Press. This book was released on 2012-12-05 with total page 1189 pages. Available in PDF, EPUB and Kindle. Book excerpt: A comprehensive compendium of scholarly contributions relating to bacterial virulence gene regulation. • Provides insights into global control and the switch between distinct infectious states (e.g., acute vs. chronic). • Considers key issues about the mechanisms of gene regulation relating to: surface factors, exported toxins and export mechanisms. • Reflects on how the regulation of intracellular lifestyles and the response to stress can ultimately have an impact on the outcome of an infection. • Highlights and examines some emerging regulatory mechanisms of special significance. • Serves as an ideal compendium of valuable topics for students, researchers and faculty with interests in how the mechanisms of gene regulation ultimately affect the outcome of an array of bacterial infectious diseases.
Download or read book Prokaryotic Metabolism and Physiology written by Byung Hong Kim and published by Cambridge University Press. This book was released on 2019-05-16 with total page 509 pages. Available in PDF, EPUB and Kindle. Book excerpt: Extensive and up-to-date review of key metabolic processes in bacteria and archaea and how metabolism is regulated under various conditions.
Download or read book Bacterial Enhancer dependent Transcription Regulation by the Interaction of Sigma Factor and Core Promoter written by Lei Wang and published by . This book was released on 2000 with total page 262 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Molecular Mechanisms of Microbial Evolution written by Pabulo H. Rampelotto and published by Springer. This book was released on 2018-10-12 with total page 452 pages. Available in PDF, EPUB and Kindle. Book excerpt: One of the most profound paradigms that have transformed our understanding about life over the last decades was the acknowledgement that microorganisms play a central role in shaping the past and present environments on Earth and the nature of all life forms. Each organism is the product of its history and all extant life traces back to common ancestors, which were microorganisms. Nowadays, microorganisms represent the vast majority of biodiversity on Earth and have survived nearly 4 billion years of evolutionary change. Microbial evolution occurred and continues to take place in a great variety of environmental conditions. However, we still know little about the processes of evolution as applied to microorganisms and microbial populations. In addition, the molecular mechanisms by which microorganisms communicate/interact with each other and with multicellular organisms remains poorly understood. Such patterns of microbe-host interaction are essential to understand the evolution of microbial symbiosis and pathogenesis.Recent advances in DNA sequencing, high-throughput technologies, and genetic manipulation systems have enabled studies that directly characterize the molecular and genomic bases of evolution, producing data that are making us change our view of the microbial world. The notion that mutations in the coding regions of genomes are, in combination with selective forces, the main contributors to biodiversity needs to be re-examined as evidence accumulates, indicating that many non-coding regions that contain regulatory signals show a high rate of variation even among closely related organisms. Comparative analyses of an increasing number of closely related microbial genomes have yielded exciting insight into the sources of microbial genome variability with respect to gene content, gene order and evolution of genes with unknown functions. Furthermore, laboratory studies (i.e. experimental microbial evolution) are providing fundamental biological insight through direct observation of the evolution process. They not only enable testing evolutionary theory and principles, but also have applications to metabolic engineering and human health. Overall, these studies ranging from viruses to Bacteria to microbial Eukaryotes are illuminating the mechanisms of evolution at a resolution that Darwin, Delbruck and Dobzhansky could barely have imagined. Consequently, it is timely to review and highlight the progress so far as well as discuss what remains unknown and requires future research. This book explores the current state of knowledge on the molecular mechanisms of microbial evolution with a collection of papers written by authors who are leading experts in the field.
Download or read book Principles of Bacterial Pathogenesis written by Eduardo A. Groisman and published by Academic Press. This book was released on 2001-01-09 with total page 863 pages. Available in PDF, EPUB and Kindle. Book excerpt: Principles of Bacterial Pathogenesis presents a molecular perspective on a select group of bacterial pathogens by having the leaders of the field present their perspective in a clear and authoritative manner. Each chapter contains a comprehensive review devoted to a single pathogen. Several chapters include work from authors outside the pathogenesis field, providing general perspectives on the evolution, regulation, and secretion of virulence and determinants. - Explains the basic principles of bacterial pathogenesis - Covers diverse aspects integrating regulation, cellular microbiology and evolution of microbial disease of humans - Discusses current strategies for the identification of virulence determinants and the methods used by microbes to deliver virulence factors - Presents authoritative treatises of the major disease microorganisms
Download or read book Nucleic Acid Polymerases written by Katsuhiko S. Murakami and published by Springer Science & Business Media. This book was released on 2013-10-22 with total page 342 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a review of the multitude of nucleic acid polymerases, including DNA and RNA polymerases from Archea, Bacteria and Eukaryota, mitochondrial and viral polymerases, and other specialized polymerases such as telomerase, template-independent terminal nucleotidyl transferase and RNA self-replication ribozyme. Although many books cover several different types of polymerases, no book so far has attempted to catalog all nucleic acid polymerases. The goal of this book is to be the top reference work for postgraduate students, postdocs, and principle investigators who study polymerases of all varieties. In other words, this book is for polymerase fans by polymerase fans. Nucleic acid polymerases play a fundamental role in genome replication, maintenance, gene expression and regulation. Throughout evolution these enzymes have been pivotal in transforming life towards RNA self-replicating systems as well as into more stable DNA genomes. These enzymes are generally extremely efficient and accurate in RNA transcription and DNA replication and share common kinetic and structural features. How catalysis can be so amazingly fast without loss of specificity is a question that has intrigued researchers for over 60 years. Certain specialized polymerases that play a critical role in cellular metabolism are used for diverse biotechnological applications and are therefore an essential tool for research.
Download or read book Encyclopedia of Biological Chemistry written by and published by Elsevier. This book was released on 2021-08-16 with total page 5350 pages. Available in PDF, EPUB and Kindle. Book excerpt: Encyclopedia of Biological Chemistry has always been characterized by its unique and comprehensive content. Since publication of the 2nd edition, many important discoveries have been made leading to novel concepts in several areas of biochemistry, and new technologies have advanced our understanding of key processes of life. All of these advances are included in the new and expanded third edition. This is the most up-to-date and complete resource on biochemistry and molecular biology, provided through contributions by leading experts in the field. A 'one-stop', comprehensive resource on "the chemistry of life", including a wealth of information and critical summaries to support research and teaching activities Each chapter is written concisely to guide the reader though the topic, using a consistent and unified terminology Clearly organized into seven logical sections, each curated by a world-leader in the field and the Editor in Chief
Download or read book Bacterial Invasion of Host Cells written by Richard J. Lamont and published by Cambridge University Press. This book was released on 2004-03-29 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book concerns the intimate association between bacteria and host cells. Many bacterial pathogens are able to invade and survive within cells at mucosal membranes. Remarkably, the bacteria themselves orchestrate this process through the exploitation of host cellular signal transduction pathways. Intracellular invasion can lead to disruption of host tissue integrity and perturbation of the immune system. An understanding of the molecular basis of bacterial invasion and of host cell adaptation to intracellular bacteria will provide fundamental insights into the pathophysiology of bacteria and the cell biology of the host. The book details specific examples of bacteria that are masters of manipulation of eukaryotic cell signaling and relates these events to the broader context of host-pathogen interaction. Written by experts in the field, this book will be of interest to researchers and graduate students in microbiology, immunology, biochemistry, as well as molecular medicine and dentistry.
Download or read book The Smallest Biomolecules Diatomics and their Interactions with Heme Proteins written by Abhik Ghosh and published by Elsevier. This book was released on 2011-10-13 with total page 627 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is not a book on NO biology, nor about hemoglobin, nor about heme-based sensors per se. Of course, it covers all these topics and more, but above all, it aims at providing a truly multidisciplinary perspective of heme-diatomic interactions. The overarching goal is to build bridges among disciplines, to bring about a meeting of minds. The contributors to this book hail from diverse university departments and disciplines – chemistry, biochemistry, molecular biology, microbiology, zoology, physics, medicine and surgery, bringing with them very different views of heme-diatomic interactions. The hope is that the juxtaposition of this diversity will lead to increased exchanges of ideas, approaches, and techniques across traditional disciplinary boundaries. The authors represent a veritable Who's Who of heme protein research and include John Olson, Tom Spiro, Walter Zumft, F. Ann Walker, Teizo Kitagawa, W. Robert Scheidt, Pat Farmer, Marie-Alda Gilles-Gonzalez, and many other equally distinguished scientists. - Extremely distinguished list of authors - Multidisciplinary character – equally suitable for chemists and biochemists - Covers the hottest topics in heme protein research: sensors, NO biology, new roles of hemoglobin, etc.
Download or read book Foodborne Pathogens written by Joshua B. Gurtler and published by Springer. This book was released on 2017-06-14 with total page 653 pages. Available in PDF, EPUB and Kindle. Book excerpt: Foodborne illnesses continue to be a major public health concern. All members of a particular bacterial genera (e.g., Salmonella, Campylobacter) or species (e.g., Listeria monocytogenes, Cronobacter sakazakii) are often treated by public health and regulatory agencies as being equally pathogenic; however, this is not necessarily true and is an overly conservative approach to ensuring the safety of foods. Even within species, virulence factors vary to the point that some isolates may be highly virulent, whereas others may rarely, if ever, cause disease in humans. Hence, many food safety scientists have concluded that a more appropriate characterization of bacterial isolates for public health purposes could be by virotyping, i.e., typing food-associated bacteria on the basis of their virulence factors. The book is divided into two sections. Section I, “Foodborne Pathogens and Virulence Factors,” hones in on specific virulence factors of foodborne pathogens and the role they play in regulatory requirements, recalls, and foodborne illness. The oft-held paradigm that all pathogenic strains are equally virulent is untrue. Thus, we will examine variability in virulence between strains such as Listeria, Salmonella, Campylobacter, Cronobacter, etc. This section also examines known factors capable of inducing greater virulence in foodborne pathogens. Section II, “Foodborne Pathogens, Host Susceptibility, and Infectious Dose” , covers the ability of a pathogen to invade a human host based on numerous extraneous factors relative to the host and the environment. Some of these factors include host age, immune status, genetic makeup, infectious dose, food composition and probiotics. Readers of this book will come away with a better understanding of foodborne bacterial pathogen virulence factors and pathogenicity, and host factors that predict the severity of disease in humans.
