Download or read book Functions and Physiological Significance of the N And C Terminal Regions of the Escherichia Coli Global Transcription Factor Fnr written by Qing Pan and published by Open Dissertation Press. This book was released on 2017-01-26 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: This dissertation, "Functions and Physiological Significance of the N- and C- Terminal Regions of the Escherichia Coli Global Transcription Factor FNR" by Qing, Pan, 潘庆, 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: A facultative anaerobe such as Escherichia coli is able to switch between the aerobic and anaerobic modes of metabolism in response to O2 availability. This adaptation is primarily controlled by a global transcription regulator called FNR (fumarate nitrate reduction). The key property that allows FNR to act as an O2 responsive transcription factor is its capability to dimerize and being activated upon binding of an O2 labile [4Fe-4S]2+ cluster. Previous functional studies have largely focused on the regions of FNR analogous to CRP (cAMP receptor protein), a prototype CRP/FNR family protein which X-ray crystal structure has been resolved. However, E. coli FNR contains extra N- and C-terminal regions that are conserved among various FNR orthologs but are absent in CRP. The functions of these two regions have not been resolved. In this study, their functions and physiological significance to the O2 sensing capacity of FNR were systematically investigated. A three-alanine (3-Ala) scanning library on amino acid 2-19 and 236-250 of FNR was constructed and selective 3-Ala substitution mutants exhibited variable defects. These defects were found to be due to their impairment of intracellular FNR protein levels which was unique only among FNR mutations in these two regions. Introduction of 3-Ala substitution at the residues 239-244, resulting in LAQ239-241A3 and LAG242-244A3 respectively, caused an especially accelerated degradation and decrease of intracellular FNR proteins. These variants were found to be degraded by the ClpXP protease. Sequence alignment of FNR orthologs revealed a highly conserved "L239XXL242XG244" motif, and my experimental data further revealed that L239 and L242 were important residues and were responsible for the defects of LAQ239-241A3 and LAG242-244A3, respectively. Circular dichroism analysis revealed that introduction of LAQ239-241A3 caused conformational changes with a significant loss of secondary structures in FNR. These studies taken together suggest that the N- and C-terminal regions of FNR play an important role in mediating the intracellular protein level of FNR. My studies also specified the ClpXP signals as the N-terminal RR9-10 and C-terminal VA249-250, and indicated that VA249-250 is a more important site than RR9-10 in targeting FNR to proteolysis. The second topic of the thesis involves exploration of the regulatory mechanism of an anaerobically activated multidrug efflux pump MdtEF in E. coli. MdtEF is an important multidrug efflux pump that causes antibiotic resistance upon overexpression. Previous studies revealed that expression of MdtEF was significantly upregulated under anaerobic conditions, but its regulatory mechanism was unknown. In the current study, systematic analyses on the unusually long promoter region of the gadE-mdtEF operon which drives the expression of MdtEF were performed. It was found that unlike FNR, mdtEF was not regulated at post-translational level by proteolysis, but at transcriptional level through the promoter region of gadE. My study showed that anaerobic activation of mdtEF was mediated by the anaerobic regulator ArcA and nitrate responsive regulators NarL and NarP. Important promoter regions P3 and P1 were also identified. This study provides essential molecular basis for the upregulation of MdtEF in a host and clinically relevant conditions. DOI: 10.5353/th
Download or read book Functions and Physiological Significance of the N and C Terminal Regions of the Escherichia Coli Global Transcription Factor FNR written by 潘庆 and published by . This book was released on 2013 with total page 350 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Functions and Physiological Significance of the N and C Terminal Regions of the Escherichia Coli Global Transcription Factor FNR written by Qing Pan (Ph. D.) and published by . This book was released on 2013 with total page 350 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 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 Integrating Genome wide Analyses to Investigate the Regulatory Role of FNR and IscR in Response to Anaerobiosis in Escherichia Coli written by and published by . This book was released on 2013 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Escherichia coli contains multiple O2-sensing transcription factors, including FNR and IscR. FNR is predominantly active under anaerobic conditions, where it ligates an O20́3labile [4Fe0́34S] cluster for dimerization and DNA binding. Ligation of a [2Fe0́32S] cluster by IscR broadens its DNA binding specificity from binding only a Type 2 site to binding both Type 1 and Type 2 sites. Fe0́3S occupancy of IscR is regulated by O2 availability and a complex pattern of gene expression results under aerobic and anaerobic conditions. We studied the FNR and IscR regulons on a genome0́3scale and found little overlap between the two regulons. FNR occupancy at many sites was strongly influenced by nucleoid0́3associated proteins (NAPs). While only a subset of predicted FNR binding sites were bound in vivo, many sites appeared to be masked by the NAPs H0́3NS, IHF, and Fis. Cells lacking H0́3NS and its paralog StpA showed increased FNR occupancy at sites normally bound by H0́3NS, indicating that the genome is not readily accessible for FNR binding. Correlation of FNR ChIP0́3seq peaks with transcriptomic data showed that less than half of the FNR regulated operons could be attributed to direct FNR binding. FNR bound some promoters without regulating expression, presumably requiring additional condition specific transcription factors. ChIP0́3chip analysis of IscR binding revealed that IscR primarily binds Type 2 sites under aerobic and anaerobic conditions. Correlation of IscR binding regions containing a Type 1 or Type 2 site with the transcriptomic data revealed 33 operons directly regulated by IscR under aerobic or anaerobic conditions. The four previously reported promoters containing Type 1 sites and both known and novel promoters containing Type 2 sites were identified. The previous finding that promoters with Type 2 sites are also regulated by IscR primarily under aerobic conditions extended to newly identified operons. Further analyses suggested that multiple mechanisms prevent IscR regulation of Type 2 sites under anaerobic conditions including action of other global transcription factors FNR, ArcA, and Fur. In summary, this work expands our knowledge of the FNR and IscR regulons and the role of combinatorial regulation in the E. coli response to changes in O2 concentration.
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 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 Advances in Microbial Physiology written by and published by Academic Press. This book was released on 2019-05-22 with total page 530 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in Microbial Physiology, Volume 74, the latest release in this ongoing series, continues the long tradition of topical, important, cutting-edge reviews in microbiology. The book contains updates in the field, with comprehensive chapters covering The electrifying physiology of Geobacter bacteria 30 years on, Adaptive morphogenesis in bacteria, Bacterial energetics and respiratory metabolism, Bacteria respiration during infection, Regulation of Organohalide Respiration, Bioenergetics of Campylobacter jejuni, Formate Hydrogenlyases, Bioenergetical Aspects of the Bacterial and Archaeal Hydrogen Metabolism, and more. Contains contributions from leading authorities in microbial physiology Informs and updates on all the latest developments in the field of microbial physiology
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 Cumulated Index Medicus written by and published by . This book was released on 1996 with total page 1340 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Molybdenum Enzymes written by Thomas G. Spiro and published by Wiley-Interscience. This book was released on 1985-11-14 with total page 632 pages. Available in PDF, EPUB and Kindle. Book excerpt: Volume 7 in the Metal Ions in Biology Series, divided into two parts, covers the nitrogenase enzyme complex and the molybdenum redox enzymes. Part one covers the chemistry of Mo-Fe-S clusters and their relationship to nitrogenase, cofactor chemistry and biochemistry of nitrogenase, spectroscopic and electrochemical studies of the Fe-Mo cofactor and Fe-S clusters, and more. Part Two surveys oxo-molybdenum chemistry, discusses the nature of the molybdo-pterin complex, and describes the characteristics of several of the Mo redox enzymes.
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 Metal Transporters written by Jose M. Arguello and published by Academic Press. This book was released on 2012-10-25 with total page 478 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume of Current Topics in Membranes focuses on metal transmembrane transporters and pumps, a recently discovered family of membrane proteins with many important roles in the physiology of living organisms. The book summarizes the most recent advances in the field of metal ion transport and provides a broad overview of the major classes of transporters involved in homeostasis of heavy metals. Various families of the transporters and metal specificities are discussed with the focus on the structural and mechanistic aspects of their function and regulation. The reader will access information obtained through a variety of approaches ranging from X-ray crystallography to cell biology and bioinformatics, which have been applied to transporters identified in diverse biological systems, such as pathogenic bacteria, plants, humans and others. Field is cutting-edge and a lot of the information is new to research community Wide breadth of topic coverage Contributors of high renown and expertise
Download or read book The Biological Chemistry of Nickel written by Deborah Zamble and published by Royal Society of Chemistry. This book was released on 2017-03-24 with total page 396 pages. Available in PDF, EPUB and Kindle. Book excerpt: Metal ions play key roles in biology. Many are essential for catalysis, for electron transfer and for the fixation, sensing, and metabolism of gases. Others compete with those essential metal ions or have toxic or pharmacological effects. This book is structured around the periodic table and focuses on the control of metal ions in cells. It addresses the molecular aspects of binding, transport and storage that ensure balanced levels of the essential elements. Organisms have also developed mechanisms to deal with the non-essential metal ions. However, through new uses and manufacturing processes, organisms are increasingly exposed to changing levels of both essential and non-essential ions in new chemical forms. They may not have developed defenses against some of these forms (such as nanoparticles). Many diseases such as cancer, diabetes and neurodegeneration are associated with metal ion imbalance. There may be a deficiency of the essential metals, overload of either essential or non-essential metals or perturbation of the overall natural balance. This book is the first to comprehensively survey the molecular nature of the overall natural balance of metal ions in nutrition, toxicology and pharmacology. It is written as an introduction to research for students and researchers in academia and industry and begins with a chapter by Professor R J P Williams FRS.
Download or read book Index Medicus written by and published by . This book was released on 2004 with total page 2036 pages. Available in PDF, EPUB and Kindle. Book excerpt: Vols. for 1963- include as pt. 2 of the Jan. issue: Medical subject headings.
Download or read book The Physiology of Microalgae written by Michael A. Borowitzka and published by Springer. This book was released on 2016-03-21 with total page 673 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers the state-of-the-art of microalgae physiology and biochemistry (and the several –omics). It serves as a key reference work for those working with microalgae, whether in the lab, the field, or for commercial applications. It is aimed at new entrants into the field (i.e. PhD students) as well as experienced practitioners. It has been over 40 years since the publication of a book on algal physiology. Apart from reviews and chapters no other comprehensive book on this topic has been published. Research on microalgae has expanded enormously since then, as has the commercial exploitation of microalgae. This volume thoroughly deals with the most critical physiological and biochemical processes governing algal growth and production.
