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 Nuclear Magnetic Resonance of Biological Macromolecules Part A written by Thomas L. James and published by Academic Press. This book was released on 2001 with total page 528 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume and its companion, Volume 339, supplement Volumes 176, 177, 239, and 261. Chapters are written with a "hands-on" perspective. That is, practical applications with critical evaluations of methodologies and experimental considerations needed to design, execute, and interpret NMR experiments pertinent to biological molecules.

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 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 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 Listeria monocytogenes Pathogenesis and Host Response written by Howard Goldfine and published by Springer Science & Business Media. This book was released on 2007-06-24 with total page 292 pages. Available in PDF, EPUB and Kindle. Book excerpt: During the past twenty years Listeria monocytogenes has emerged as one of the most intensely studied bacterial pathogens. New windows are constantly being opened into the complexity of host cell biology and the interplay of the signals connecting the various cells and organs involved in the host response. This volume includes research from studies at the molecular level on the pathogenesis of Listeria monocytogenes and the response of the host to its infections.

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 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 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 Programming Bacterial Gene Expression Using Synthetic CRISPR Cas Transcriptional Regulators written by Chen Dong and published by . This book was released on 2019 with total page 211 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bacteria play a central role in biosynthesis to produce value-added organic chemicals due to its diverse carbon and energy source preferences. Implementing synthetic transcriptional regulation devices can advance our ability to modify gene expression in bacteria for engineering production strains. The CRISPR-Cas activation (CRISPRa) system, a programmable transcriptional activator with wide applications in eukaryotic organisms, has been under-utilized in bacterial due to the lack of efficient transcriptional activation domains. This work describes our contribution to the development and understanding of bacterial CRISPR-Cas-based transcriptional regulation devices. We screened novel bacterial activation domains to be used as CRISPR-Cas activators in E. coli, and optimized our strongest activation domain, SoxS into a programmable CRISPR activator. In addition, we investigated the properties of the well-established CRISPRi repression system and found that partial repression can be achieved by controlling the expression level of the sgRNA. Combining CRISPRa and CRISPRi, we demonstrated inducible simultaneous up- and down-regulation of a dual reporter gene and the CRISPR-mediated regulation of the ethanol bioproduction pathway. Moreover, we also learned important properties of the bacterial CRISPRa system which is much more restrictive than the eukaryotic CRISPRa system. CRISPRa activity is dependent on the sigma factor that the promoter recruits, the baseline strength of the promoter, the sequence composition of the promoter, the presence of nearby transcription factors, and the precise positioning of the scRNA target. We attempted to relieve these restrictions by implementing an engineered Cas protein that can bind to a wider range of targets. Lastly, we describe our efforts to transport the CRISPRa system into other non-E.coli bacteria. CRISPR-SoxS activator proved to be active in Pseudomonas putida, but not in the other organisms we tested. Therefore, we propose to characterize host-specific activation domains for bacteria whose cellular machineries are incompatible with SoxS. Together, this work provided a novel programmable gene activation device in bacteria and sets up the foundation for the development of complex, broad-host-range bacterial cellular devices for biosynthetic applications.

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 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.

Download or read book Transcription Factors in Eukaryotes written by Athanasios Papavassiliou and published by International Thomson Publishing Services. This book was released on 1997 with total page 388 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Systems Evaluation of Regulatory Components in Bacterial Transcription Initiation written by Donghyuk Kim and published by . This book was released on 2014 with total page 138 pages. Available in PDF, EPUB and Kindle. Book excerpt: In bacterial transcription, transcription initiation is arguably the most important regulatory point, because transcribing unnecessary genes into RNA could be a waste of energy, time and resources. There are multiple components which are involved in bacterial transcription initiation: RNA polymerase, [sigma]-factors, transcription factors, and transcription start sites. Each component has been intensively investigated, however in a limited scope and mostly with low-throughput methods. New technologies, such as hybridization on microarray and deep-sequencing, enabled researchers to study each component in a systems level, in a combination of two or more components, and in comparison between different species. In order to facilitate the analysis, integration, and comparison, software, MetaScope, was developed to accommodate multiple genome-scale datasets to visualize, analyze, integrate, and compare. TSS-seq, modified 5'-RACE with deep-sequencing, gave a genome-scale landscape of transcription start sites, and comparison of TSSs of conserved genes between closely-related species, E. coli and K. pneumoniae, showed significantly different usage of promoters, which implies different regulation of orthologous genes. To further investigate properties of promoters which were identified by TSS-seq, ChIP-chip experiments were performed for [sigma]-factors in E. coli to determine [sigma]-factor regulons. From the reconstructed [sigma]-factor network, extensive overlaps between regulons were observed. [sigma]70 and [sigma]38 share the largest set of genes in E. coli, and additional experiments revealed that those [sigma]-factors work in competition and utilize the negative regulation by [sigma]38 . ChIP-exo, which applies exonuclease to present better resolution of DNA-binding, and RNA-seq implemented more detailed identification of Fur regulon in E. coli. Reconstruction of Fur regulon completed the previous knowledge of bacterial response to iron change, and also enabled its role over iron metabolism. In order to understand how bacteria respond to nitrogen limitation, the same methods were used under conditions that were predicted from model-based prediction, and resulted in reconstruction of regulons for major transcription factors, NtrC and Nac. Determination of those regulons expanded the current knowledge of nitrogen metabolism and how it is regulated in bacteria. Thus, systems approaches enabled a genome-scale assessment of regulatory components in multiple levels, and contributed to expansion of the current knowledge of bacterial transcription initiation.

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 Molecular Biology and Pathogenicity of Mycoplasmas written by Shmuel Razin and published by Springer Science & Business Media. This book was released on 2007-05-08 with total page 574 pages. Available in PDF, EPUB and Kindle. Book excerpt: was the result of the efforts of Robert Cleverdon. The rapidly developing discipline of molecular biology and the rapidly expanding knowledge of the PPLO were brought together at this meeting. In addition to the PPLO specialists, the conference invited Julius Marmur to compare PPLO DNA to DNA of other organisms; David Garfinkel, who was one of the first to develop computer models of metabolism; Cyrus Levinthal to talk about coding; and Henry Quastler to discuss information theory constraints on very small cells. The conference was an announcement of the role of PPLO in the fundamental understanding of molecular biology. Looking back 40-some years to the Connecticut meeting, it was a rather bold enterprise. The meeting was international and inter-disciplinary and began a series of important collaborations with influences resonating down to the present. If I may be allowed a personal remark, it was where I first met Shmuel Razin, who has been a leading figure in the emerging mycoplasma research and a good friend. This present volume is in some ways the fulfillment of the promise of that early meeting. It is an example of the collaborative work of scientists in building an understanding of fundamental aspects of biology.