Download or read book Mechanism for Oxygen Regulation Escherichia Coli Transcription Factor FNR written by Beth A. Lazazzera and published by . This book was released on 1995 with total page 380 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Molecular Engineering of the Escherichia Coli Global Transcription Factor Fnr to Improve Its Stability to Oxygen written by 单越 and published by . This book was released on 2017-01-26 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: This dissertation, "Molecular Engineering of the Escherichia Coli Global Transcription Factor FNR to Improve Its Stability to Oxygen" by 单越, Yue, Shan, was obtained from The University of Hong Kong (Pokfulam, Hong Kong) and is being sold pursuant to Creative Commons: Attribution 3.0 Hong Kong License. The content of this dissertation has not been altered in any way. We have altered the formatting in order to facilitate the ease of printing and reading of the dissertation. All rights not granted by the above license are retained by the author. Abstract: The ability to sense and rapidly respond to oxygen availability is crucial to the survival and physiology of facultative anaerobes. In many gram negative bacteria such as Escherichia coli, this process is primarily controlled by the dimeric, [4Fe〖-4S]〗 DEGREES(2+) containing global transcription factor FNR, which regulates transcription of genes necessary for the anaerobic metabolism. Activity of FNR is directly regulated by the presence of oxygen, which inactivates FNR by oxidizing the [4Fe〖-4S]〗 DEGREES(2+) cluster and causing the dissociation of the FNR dimer. Although the biological function of FNR has been well established, structural and biochemical characterization of the FNR dimer has been limited due to its extreme lability to oxygen. In the current study, I conduct molecular engineering on FNR protein and obtain oxygen stable variants that are suitable for in vitro biochemical studies. By combining several approaches including covalently linking two FNR monomers using a flexible peptide linker, amino acid substitutions to promote dimerization, and removal of protease recognition sites to prevent proteolysis, a series of FNR variants which are potentially active in the presence of oxygen are constructed. Various in vivo and in vitro assays led to the identification of the construct (FNRD154A)2 which covalently links two copies of FNRD154A, an FNR variant that has greater dimerization capability, in tandem displays significantly improved transcription regulation and DNA binding to various FNR regulated promoters in the presence of O2. Circular Dichroism analysis showed that this variant maintains a similar secondary structure as that of native FNRD154A and in vivo transcription assay demonstrated that this protein retains other properties of the native FNR dimer including [4Fe〖-4S]〗 DEGREES(2+) cluster binding, oxygen sensing, and capability to support the anaerobic growth of E. coli. All these together led the conclusion that an FNR variant that retains structural and functional properties of native FNR has been constructed, but with significantly improved O2 stability. Thus, it has the potential to be widely used in various biochemical and structural studies of FNR in the presence of oxygen. In addition to the major project of molecular engineering of FNR protein, in this thesis, I also initiated the study of using metabolomics approaches to identify the cellular substrates of the multidrug efflux pump MdtEF. MdtEF is an important efflux pump in E. coli and its expression has been shown to be induced under a number of stressed conditions. It is thus proposed to have a general detoxification function in E. coli, but the cellular substrates it expels have not been identified. In this study we established and applied metabolite profiling on the wild type and ΔmdtEF E. coli strains and confirmed that indole red, a metabolic by-product formed during anaerobic respiration of nitrate, is one of the cellular substrates of MdtEF under anaerobic conditions. This study provides a general methodology to identify endogenous substrates of efflux pumps and contributes to the understanding of the physiological roles of multidrug efflux pumps in bacteria. DOI: 10.5353/th_b4961737 Subjects: Escherichia coli - Molecular aspects Transcription factors
Download or read book Mechanisms of Transcription Regulation by the Escherichia Coli Transcription Factor FNR written by Stephen Michael Williams and published by . This book was released on 1998 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book FNR dependent Transcriptional Regulation in Escherichia Coli written by Eva Christine Ziegelhoffer and published by . This book was released on 1996 with total page 430 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book FNR and Oxygen regulated Gene Expression in Escherichia Coli written by Wenmao Meng and published by . This book was released on 1997 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Molecular Engineering of the Escherichia Coli Global Transcription Factor FNR to Improve Its Stability to Oxygen written by Yue Shan and published by . This book was released on 2012 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Oxygen Sensing in Escherichia Coli and the Role of Cyclic Regulation written by Dean Alexander Tolla and published by . This book was released on 2010 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: This work examines the role of a cyclic genetic regulatory circuit acting as an environmental sensor. As a representative of this class of systems, we focus on the FNR regulatory circuit of Escherichia coli for which a large body of experimental evidence describing its molecular components and their individual interactions exists. However, until recently this information had never been integrated into a coherent model of the intact system. The FNR protein is an oxygen sensor that acts as a global transcription factor and when active modifies gene expression to adapt the cell to anaerobic growth. Our study provides strong support for an integrated model of FNR regulation that demonstrates self-consistency of a large body of experimental work, makes predictions of additional mutant behavior that are validated by experimental data, predicts the dynamics of the aerobic-to-anaerobic transition, provides estimates of active FNR in vivo, and makes it possible to predict in situ the dimerization rate of the transcription factor. We provide an original definition of what is meant by phenotype at the molecular level that is based on the concept of a "system design space". This definition allows us to rigorously characterize the regulatory phenotypes exhibited by the master transcription factor FNR. We identify 15 qualitatively-distinct phenotypes, analyze the alternatives, and compare their relative fitness. Our analysis reveals desirable and undesirable phenotypes as well as an optimal band of operation corresponding to the transition between aerobic and anaerobic environments. We analyze specific mutations and predict their associated phenotypic changes. By identifying the phenotypic repertoire our design space analysis provides a means to evaluate the evolutionary pressures that have shaped this system. Our application of the design space approach to the FNR network provides a detailed framework for characterizing other environmental sensing regulatory networks, and this approach is sufficiently general that it can be used to analyze the distinct behaviors presented by essentially any biochemical network. By examining a family of FNR models each with different cycling speeds but mathematically constrained to be otherwise equivalent, we are able to elucidate the relationship between the cycling rate and response time of the FNR circuit. We identify an optimum cycling rate for the FNR system. Our analysis of a currently uncharacterized double mutant argues in favor of these predicted results and provides a means to test our predictions in the laboratory. We examine the phenotype of increasing the number of fnr gene copies and show that the copy-number mutant exaggerates the predicted dynamics of active FNR induction. We provide an experimental method capable of capturing the dynamics of active FNR induction and repression, and predict its results for the wild-type, double mutant, and copy-number mutant.
Download or read book Molecular Engineering of the Escherichia Coli Global Transcription Factor FNR to Improve Its Stability to Oxygen written by Yue Shan and published by . This book was released on 2012 with total page 268 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Regulation of Gene Expression in Escherichia coli written by E. C. C. Lin and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 1010 pages. Available in PDF, EPUB and Kindle. Book excerpt: This up-to-date guide focuses on the understanding of key regulatory mechanisms governing gene expression in Escherichia coli. Studies of E. coli not only provide the first models of gene regulation, but research continues to yield different control mechanisms.
Download or read book The FNR Protein and Oxygen regulated Gene Expression in Escherichia Coli written by Stephen Spiro and published by . This book was released on 1987 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book The Role of FNR in Transcriptional Regulation in Escherichia Coli written by Karl Derek Weber and published by . This book was released on 2004 with total page 176 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Oxygen Control of Respiratory Gene Expression in Escherichia Coli written by Jeffrey Allan Albrecht and published by . This book was released on 1996 with total page 470 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Stress and Environmental Regulation of Gene Expression and Adaptation in Bacteria written by Frans J. de Bruijn and published by John Wiley & Sons. This book was released on 2016-07-13 with total page 1472 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bacteria in various habitats are subject to continuously changing environmental conditions, such as nutrient deprivation, heat and cold stress, UV radiation, oxidative stress, dessication, acid stress, nitrosative stress, cell envelope stress, heavy metal exposure, osmotic stress, and others. In order to survive, they have to respond to these conditions by adapting their physiology through sometimes drastic changes in gene expression. In addition they may adapt by changing their morphology, forming biofilms, fruiting bodies or spores, filaments, Viable But Not Culturable (VBNC) cells or moving away from stress compounds via chemotaxis. Changes in gene expression constitute the main component of the bacterial response to stress and environmental changes, and involve a myriad of different mechanisms, including (alternative) sigma factors, bi- or tri-component regulatory systems, small non-coding RNA’s, chaperones, CHRIS-Cas systems, DNA repair, toxin-antitoxin systems, the stringent response, efflux pumps, alarmones, and modulation of the cell envelope or membranes, to name a few. Many regulatory elements are conserved in different bacteria; however there are endless variations on the theme and novel elements of gene regulation in bacteria inhabiting particular environments are constantly being discovered. Especially in (pathogenic) bacteria colonizing the human body a plethora of bacterial responses to innate stresses such as pH, reactive nitrogen and oxygen species and antibiotic stress are being described. An attempt is made to not only cover model systems but give a broad overview of the stress-responsive regulatory systems in a variety of bacteria, including medically important bacteria, where elucidation of certain aspects of these systems could lead to treatment strategies of the pathogens. Many of the regulatory systems being uncovered are specific, but there is also considerable “cross-talk” between different circuits. Stress and Environmental Regulation of Gene Expression and Adaptation in Bacteria is a comprehensive two-volume work bringing together both review and original research articles on key topics in stress and environmental control of gene expression in bacteria. Volume One contains key overview chapters, as well as content on one/two/three component regulatory systems and stress responses, sigma factors and stress responses, small non-coding RNAs and stress responses, toxin-antitoxin systems and stress responses, stringent response to stress, responses to UV irradiation, SOS and double stranded systems repair systems and stress, adaptation to both oxidative and osmotic stress, and desiccation tolerance and drought stress. Volume Two covers heat shock responses, chaperonins and stress, cold shock responses, adaptation to acid stress, nitrosative stress, and envelope stress, as well as iron homeostasis, metal resistance, quorum sensing, chemotaxis and biofilm formation, and viable but not culturable (VBNC) cells. Covering the full breadth of current stress and environmental control of gene expression studies and expanding it towards future advances in the field, these two volumes are a one-stop reference for (non) medical molecular geneticists interested in gene regulation under stress.
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 Signaling written by Reinhard Krämer and published by John Wiley & Sons. This book was released on 2009-12-09 with total page 513 pages. Available in PDF, EPUB and Kindle. Book excerpt: Providing a comprehensive insight into cellular signaling processes in bacteria with a special focus on biotechnological implications, this is the first book to cover intercellular as well as intracellular signaling and its relevance for biofilm formation, host pathogen interactions, symbiotic relationships, and photo- and chemotaxis. In addition, it deals in detail with principal bacterial signaling mechanisms -- making this a valuable resource for all advanced students in microbiology. Dr. Krämer is a world-renowned expert in intracellular signaling and its implications for biotechnology processes, while Dr. Jung is an expert on intercellular signaling and its relevance for biomedicine and agriculture.
Download or read book Iron sulfur Proteins written by and published by . This book was released on with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Characterization Properties and Applications written by Tracey Rouault and published by Walter de Gruyter GmbH & Co KG. This book was released on 2017-08-21 with total page 466 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume on iron-sulfur proteins includes chapters that describe the initial discovery of iron-sulfur proteins in the 1960s to elucidation of the roles of iron sulfur clusters as prosthetic groups of enzymes, such as the citric acid cycle enzyme, aconitase, and numerous other proteins, ranging from nitrogenase to DNA repair proteins. The capacity of iron sulfur clusters to accept and delocalize single electrons is explained by basic chemical principles, which illustrate why iron sulfur proteins are uniquely suitable for electron transport and other activities. Techniques used for detection and stabilization of iron-sulfur clusters, including EPR and Mossbauer spectroscopies, are discussed because they are important for characterizing unrecognized and elusive iron sulfur proteins. Recent insights into how nitrogenase works have arisen from multiple advances, described here, including studies of high-resolution crystal structures.
